Microorganisms Having Increased Lipid Productivity

Abstract

The present invention provides mutant microorganism that have higher lipid productivity than the wild type microorganisms from which they are derived while biomass at levels that are within approximately 50% of wild type biomass productivities under nitrogen replete conditions. Particular mutants produce at least twice as much FAME lipid as wild type while producing at least 75% of the biomass produced by wild type cells under nitrogen replete conditions. Also provided are methods of producing lipid using the mutant strains.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application is a continuation application of U.S. application Ser. No. 16/267,940 filed Feb. 5, 2019, now issued as U.S. Pat. No. 10,563,232; which is a divisional application of U.S. application Ser. No. 15/210,845 filed Jul. 14, 2016, now issued as U.S. Pat. No. 10,227,619; which claims the benefit under 35 USC .sctn. 119(e) to U.S. Application Ser. No. 62/318,161 filed Apr. 4, 2016 and to U.S. Application Ser. No. 62/192,510 filed Jul. 14, 2015, both now expired. The disclosure of each of the prior applications is considered part of and is incorporated by reference in the disclosure of this application.

INCORPORATION BY REFERENCE OF SEQUENCE LISTING

[0002] The material in the accompanying sequence listing is hereby incorporated by reference into the application. The accompanying sequence listing text file, named SGI1920-4_ST25, was created on Feb. 7, 2020 and is 229 KB in size. The file can be accessed using Microsoft Word on a computer that uses Window OS.

BACKGROUND OF THE INVENTION

[0003] The invention relates to mutant microorganisms, such as algae and heterokonts, having increased lipid productivity and their use in producing lipids.

[0004] Many microorganisms such as algae, labyrinthulomycetes ("chytrids"), and oleaginous yeast induce lipid biosynthesis in response to nutrient stress, for example nitrogen starvation. Under conditions of nitrogen depletion, such microorganisms redirect compound biosynthesis from protein to storage lipids, typically triacylglyceride lipids ("TAG"). Because nitrogen depletion simultaneously decreases cell growth, optimal lipid biosynthesis is limited to a relatively short window before the cells become too metabolically impaired to maintain high levels of production.

[0005] Microalgal-derived biodiesel has long been considered a viable alternative to conventional petroleum-based fuels. However, despite decades of biological research, depriving strains of essential macronutrients such as nitrogen, phosphorous, or silicon, to obtain high lipid yields--conditions under which growth of the host microorganism is compromised--remains the modus operandi. Little progress has been made in engineering algal strains to accumulate lipid while maintaining growth as there is only nascent understanding of the regulation of metabolism underlying lipid accumulation (Courchesne et al. (2009) J. Biotechnol. 141:31-41; Goncalves et al. (2016) Plant Biotechnol. J. doi: 1111/12523)

[0006] Various attempts to improve lipid productivity by increasing lipid biosynthesis during nutrient replete growth have focused on manipulating genes encoding enzymes for nitrogen assimilation or lipid metabolism as well as genes encoding polypeptides involved in lipid storage. For example, US2014/0162330 discloses a Phaeodactylum tricornutum strain in which the nitrate reductase (NR) gene has been attenuated by RNAi-based knockdown; Trentacoste et al. ((2013) Proc. Natl. Acad. Sci. USA 110: 19748-19753) disclose diatoms transformed with an RNAi construct targeting the Thaps3_264297 gene predicted to be involved in lipid catabolism; and WO2011127118 discloses transformation of Chlamydomonas with genes encoding oleosins (lipid storage protein) as well as with genes encoding diacylglycerol transferase (DGAT) genes. Although in each case increased lipid production was asserted based on microscopy or staining with lipophilic dyes, no quantitation of lipid by the manipulated cells was provided, nor was the relationship between biomass and lipid productivities over time determined.

[0007] WO 2011/097261 and US 2012/0322157 report that a gene denoted "SN03" encoding an arrestin protein has a role in increasing lipid production under nutrient replete conditions when overexpressed in Chlamydomonas. However, overexpression of the SN03 gene was observed to result in the appearance of unidentified polar lipids, which were not quantified, and did not result in an increase in triglycerides (TAG). Another polypeptide identified as potentially regulating stress-induced lipid biosynthesis has been described by Boyle et al. ((2012) J. Biol. Chem. 287:15811-15825). Knockout of the NRR1 gene in Chlamydomonas encoding a "SQUAMOUSA" domain polypeptide resulted in a reduction of lipid biosynthesis with respect to wild type cells under nitrogen depletion; however, no mutants were obtained demonstrating increased lipid production. US 2010/0255550 recommends the overexpression of putative transcription factors ("TF1, TF2, TF3, TF4, and TF5") in algal cells to increase lipid production, but no mutants having enhanced lipid production are disclosed.

[0008] Daboussi et al. 2014 (Nature Comm. 5:3881) report that disruption of the UGPase gene in Phaeodactylum triconornutum, which is believed to provide precursors to laminarin (storage carbohydrate) synthesis, results in increased lipid accumulation. However, no biochemical data was shown to indicate that laminarin content was affected and lipid and biomass productivities were not reported. Similarly, several groups have reported increases in lipid accumulation in Chlamydomonas starchless mutants (Wang et al. 2009 Eukaryotic Cell 8:1856-1868; Li et al. 2010 Metab Eng. 12:387-391) but successive reports that actually measured lipid productivity concluded that these strains were impaired in growth when grown in phototrophic conditions (Siaut et al. 2011 BMC Biotechnol. 11: 7; Davey et al. 2014 Eukaryot Cell 13:392-400). These reports concluded that the highest lipid productivities (measured as TAG per liter per day) were actually achieved by the wild-type parental strain.

SUMMARY OF THE INVENTION

[0009] Algal mutants having elevated levels of constitutive lipid production are provided herein. As demonstrated in the examples, analysis of early transcriptional profiles of Nannochloropsis gaditana to N-deprivation revealed a novel negative regulator of lipid biosynthesis ZnCys-2845, a transcription factor of the fungal Zn(II)2Cys6 gene family. Using Cas9-mediated mutagenesis and RNAi technology, attenuated ZnCys strains were produced that were capable of partitioning approximately 45% of their total carbon content to lipids and of sustaining growth in a continuous growth system, resulting in a doubling of lipid productivity.

[0010] A first aspect of the invention is a mutant microorganism that produces at least 25% more lipid than is produced by a control microorganism while producing not less than 45% of the biomass produced by the control microorganism cultured under the same conditions, in which the culture conditions support production of biomass by the control microorganism. For example, a mutant microorganism as provided herein can produce at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 100% more lipid than is produced by a control microorganism cultured under the same conditions as the mutant microorganism, which can be batch, semi-continuous, or continuous culture conditions, and in various embodiments are culture conditions in which the control microorganism accumulates biomass. The control microorganism can be, in some examples, a wild type microorganism, i.e., a wild type microorganism from which the mutant microorganism is directly or indirectly derived. The mutant microorganism can produce, in various embodiments, at least about 50% of the biomass and at least about 50%, at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 110%, or at least 120% more lipid than is produced by a control microorganism cultured under the same conditions, where the control microorganism produces biomass, for example, produces biomass over the course of the culture or on a daily basis, under the culture conditions in which the mutant produces more lipid. In various examples a mutant microorganism as provided herein produces at least 50% of the biomass and at least 130%, at least 150%, at least 140%, at least 155%, at least 160%, at least 170%, at least 175%, at least 180%, at least 185%, at least 190%, at least 195%, at least 200%, at least 210%, or at least 215% of the amount of lipid produced by a wild type microorganism cultured under the same conditions, under which the wild type microorganism accumulates biomass. For example, the culture conditions can be nitrogen-replete with respect to the control or wild type microorganism.

[0011] A mutant microorganism as provided herein can produce at least 25% more FAME lipids than a control or wild type microorganism while producing at least 45% or at least about 50% as much biomass as the control or wild type microorganism over a culture period of at least three days, at least five days, at least seven days, at least eight days, at least ten days, at least twelve days, at least fifteen days, at least twenty days, at least thirty days, or at least sixty days. For example, the average daily FAME productivity can be at least 50% greater than that of a control or wild type microorganism while the average daily biomass (e.g., TOC) productivity can be at least 45% or at least about 50% that of the control or wild type microorganism over a culture period of at least three days, at least five days, at least seven days, at least ten days, at least twelve days, at least fifteen days, at least twenty days, at least thirty days, or at least sixty days. In particular examples, a mutant microorganism as provided herein can produce at least 50% more FAME lipids than a control or wild type microorganism while producing at least 60% as much biomass as the control microorganism over a culture period of at least seven days, at least eight days, or at least ten days where the daily amount of FAME produced by the mutant is not lower than the daily amount of FAME produced by the control or wild type microorganism on any day during the at least seven, at least eight, or at least ten day culture period. In further examples, the average daily FAME productivity of a mutant microorganism as provided herein can be at least 50% higher than the average daily FAME productivity of a control or wild type microorganism the average daily biomass productivity can be at least 50% of the average daily biomass productivity of the control microorganism over a culture period of at least seven days, at least eight days, or at least ten days where the daily amount of FAME produced by the mutant is not lower than the daily amount of FAME produced by the control or wild type microorganism on any day during the at least seven, at least eight, or at least ten day culture period.

[0012] For example, a mutant microorganism as provided herein can produce more FAME-derivatizable lipids ("FAME lipids" or "FAME") than a control microorganism while producing not less than 45% of the biomass produced by the control microorganism, when the mutant microorganism and control microorganism are cultured under the same culture conditions under which the control microorganism produces biomass. A mutant microorganism as provided herein can have greater average daily FAME productivity than a control microorganism while exhibiting at least 45% of the average daily biomass productivity of the control microorganism, when the mutant microorganism and control microorganism are cultured under the same culture conditions under which the control microorganism produces biomass. In various examples, a mutant microorganism as provided herein produces at least 50% more FAME lipids while producing not less than about 50%, not less than about 60%, or not less than about 70% of the biomass produced by the control microorganism, when the mutant microorganism and control microorganism are cultured under the same culture conditions under which the culture of the control microorganism produces biomass, which can be nitrogen-replete culture conditions with respect to the control microorganism. The control microorganism in various embodiments can be a wild type microorganism, e.g., a wild type microorganism from which the mutant microorganism is directly or indirectly derived.

[0013] In some examples, the culture conditions under which the mutant produces more lipid than a control or wild type microorganism can be culture conditions in which the concentration of ammonium in the culture medium is less than about 2.5 mM, for example, less than about 2 mM, less than about 1.5 mM, less than about 1 mM, or less than or equal to about 0.5 mM. In some examples the culture medium can include no added ammonium or substantially no ammonium. In some examples, the culture medium can include no added source of reduced nitrogen for the microorganism, e.g., no added ammonium, urea, or amino acids that can be metabolized by the microorganism. The culture medium can in some examples include a nitrogen source such as, but not limited to, nitrate. Alternatively or in addition, the culture medium can include urea. In some examples, the culture medium is nutrient replete with respect to a wild type microorganism of the species from which the mutant microorganism is derived.

[0014] In various embodiments, the mutant microorganism can be a photosynthetic microorganism and the mutant microorganism can produce at least 25% more FAME lipids than a control microorganism while producing at least 45%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 95% the amount of biomass as a control or wild type microorganism under photoautotrophic culture conditions. For example a mutant microorganism as provided herein can be an alga, such as a eukaryotic microalga, and can produce at least 25% more FAME lipids than a control or wild type microorganism while producing at least 45%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 95% the amount of biomass as a control microorganism when both the control microorganism are cultured using inorganic carbon as substantially the sole source of carbon in the cultures. The control microorganism can be, for example, a wild type microorganism.

[0015] Culture conditions in which a mutant microorganism as provided herein can produce more FAME lipids than a control or wild type microorganism while producing at least 45%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 95% the amount of biomass as a control or wild type microorganism include any of batch, continuous, or semi-continuous culture conditions in which the control or wild type microorganism produces biomass. In various embodiments, a mutant microorganism as provided herein can produce at least 50% more FAME lipids than a control or wild type microorganism while producing at least 45%, at least about 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% as much biomass as the control or wild type microorganism over a culture period of at least three days, at least four days, at least five days, at least seven days, at least eight days, at least ten days, or at least twelve days. In some embodiments the average daily FAME productivity of a mutant microorganism is at least 50% more than that of a control or wild type microorganism while the average daily biomass productivity (e.g., TOC productivity) is at least 45%, at least about 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% as great as that of the control or wild type microorganism over the culture period, for example, over a culture period of at least three days, at least four days, at least five days, at least seven days, at least ten days, or at least twelve days.

[0016] In some examples, a mutant microorganism as provided herein can produce at least 50% more FAME lipids while producing at least about 75% of the amount of biomass produced by a wild type or control microorganism during a culture period of at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, or at least thirteen days, for example, over a culture period of at least five, at least ten, at least fifteen, at least twenty, or at least thirty days where the mutant and control microorganism are cultured under the same conditions, under which both the mutant and control microorganisms produce biomass. For example, a mutant microorganism can demonstrate at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, or at least 110%, or at least 120% higher FAME productivity and exhibit no more than a 35%, 30%, 25%, 20%, 15%, 10%, 5%, 2%, or 1% decline in biomass (e.g., TOC) productivity with respect to a wild type or control microorganism cultured for at least five, at least six, at least seven, or at least eight days under conditions in which both the control and mutant microorganism cultures produce biomass. For example, the average daily FAME productivity of a mutant as provided herein can be at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, or at least 110% more than that of a wild type or control microorganism and the average daily biomass (e.g., TOC) productivity can be at least about 50%, at least about 60%, at least about 70%, or at least about 80% of the average daily biomass productivity of the control microorganism under conditions in which both the control and mutant microorganism cultures are producing biomass. In various embodiments, the average daily FAME productivity of a mutant as provided herein can be at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, or at least 110% more than that of a wild type or control microorganism and the average daily biomass (e.g., TOC) productivity can be at least about 50%, at least about 60%, at least about 70%, or at least about 80% of the average daily biomass productivity of the control microorganism under conditions in which both the control and mutant microorganism cultures are producing biomass on a daily basis. In some examples, a mutant microorganism can produce at least 100% more or at least 120% more FAME lipids than a wild type or control microorganism while producing at least about 75% or at least about 80% of the biomass produced by a control type microorganism cultured under identical conditions which are nitrogen replete with respect to the control microorganism. In other examples a mutant microorganism can produce at least 75%, at least 80%, at least 85% more FAME lipids than a wild type or control microorganism while producing approximately as much biomass as is produced by a wild type microorganism cultured under identical conditions under which the wild type or control microorganism produces biomass, e.g., within 10% or within 5% of the amount of biomass produced by the control microorganism. In various examples, the average daily FAME productivity for at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, or at least thirteen days of culturing, for example, at least five, at least ten, at least fifteen, at least twenty, or at least thirty days of culturing can be at least 80% greater than the average daily FAME productivity of a wild type or control microorganism and the average daily biomass productivity can be substantially the same as that of a control or wild type microorganism cultured under identical conditions under which the wild type or control microorganism produces biomass, e.g., within 10%, within 5%, or within 2% of the biomass productivity of the control microorganism. The conditions in which a mutant microorganism produces at least 80% more FAME lipids than a wild type or control microorganism while producing at least as much biomass as produced by a wild type microorganism can be nutrient replete with respect to the wild type or control microorganism, and can be nitrogen replete with respect to the wild type or control microorganism. In various embodiments the mutant microorganism can be a photosynthetic microorganism, e.g., an alga, and the culture conditions under which the mutant alga has greater FAME productivity while producing at least 50% of the TOC as a control microorganism are photoautotrophic conditions.

[0017] A mutant microorganism as provided herein can have a FAME lipids (FAME) to total organic carbon (TOC) ratio at least 30% higher than the FAME/TOC ratio of the control microorganism under culture conditions in which the mutant microorganism produces at least 45% more FAME lipids and at least 50% as much biomass as the control microorganism. The FAME/TOC ratio of a mutant microorganism as provided herein can be, for example, at least 30% higher, at least 40% higher, at least 50% higher, at least 60% higher, at least 70% higher, at least 80% higher, at least 90% higher, at least 100% higher, at least 110% higher, at least 120% higher, at least 130% higher, at least 140% higher, at least 150% higher, or at least 200% higher than the FAME/TOC ratio of a control or wild type microorganism cultured under identical conditions under which the control or wild type organism produces biomass, which may be nitrogen replete with respect to the wild type microorganism. In various embodiments, the FAME/TOC ratio of the mutant is at least 0.3, at least 0.4, at least 0.5, at least 0.6, at least 0.7, or at least 0.8 while the mutant microorganism culture is accumulating TOC. For example, a mutant microorganism as provided herein can have at least 25% higher lipid productivity than a control microorganism while exhibiting not less than 45% or not less than about 50% of the average daily biomass productivity of the control microorganism, and can further have FAME lipids (FAME)/total organic carbon (TOC) ratios at least 30%, at least 50%, at least 70%, or at least 90% higher than the FAME/TOC ratio of a wild type microorganism, for at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fifteen, at least twenty, at least twenty-five, at least thirty, or at least sixty days of culturing, when the mutant microorganism and control microorganism are cultured under the same culture conditions in which both the mutant microorganism and control microorganism accumulate biomass, e.g., accumulate biomass on a daily basis. In various embodiments, the FAME/TOC ratio of the mutant is at least 0.3, at least 0.4, at least 0.5, at least 0.6, at least 0.7, at least 0.8, or between about 0.35 and 0.85, or between about 0.4 and about 0.8 while the mutant microorganism produces at least 50% of the TOC produced by the control microorganism over a period of at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fifteen, at least twenty, at least twenty-five, at least thirty, or at least sixty days of culturing, where the mutant and control microorganism are cultured under the same conditions and the mutant produces more lipid than the control microorganism, and both the mutant microorganism and the control microorganism produce biomass.

[0018] Thus, a further aspect of the invention is a mutant microorganism that exhibits a higher FAME/TOC ratio than is exhibited by a control microorganism when both the mutant microorganism and control microorganism are cultured under substantially identical conditions under which both the mutant microorganism and the control microorganism culture are accumulating TOC. In various examples, a mutant microorganism has a higher FAME/TOC ratio than is exhibited by a control microorganism when the mutant microorganism and control microorganism are cultured under identical conditions under which both the control microorganism and the mutant microorganism produce biomass and the mutant microorganism culture produces at least about 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or about or substantially the same amount of TOC as the wild type microorganism culture. The FAME/TOC ratio of a mutant microorganism as provided herein can be, for example, at least 30% higher, at least 40% higher, at least 50% higher, at least 60% higher, at least 70% higher, at least 80% higher, at least 90% higher, at least 100% higher, at least 110% higher, at least 120% higher, at least 130% higher, at least 140% higher, or at least 150% higher than the FAME/TOC ratio of a control or wild type microorganism during a culture period in which the mutant microorganism produces at least about 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or substantially the same amount of TOC as the wild type microorganism culture. For example, the average daily biomass productivity of a mutant microorganism can be at least about 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, that of a control or wild type microorganism culture, while having a FAME/TOC ratio at least 30% higher, at least 40% higher, at least 50% higher, at least 60% higher, at least 70% higher, at least 80% higher, at least 90% higher, at least 100% higher, at least 110% higher, at least 120% higher, at least 130% higher, at least 140% higher, or at least 150% higher than the FAME/TOC ratio of a control or wild type microorganism averaged over the same time period.

[0019] A mutant microorganism as provided herein, e.g., a mutant microorganism such as any described herein that produces at least about 50% of the biomass and at least about 50%, at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 110%, or at least 120% more lipid than is produced by a control microorganism cultured under the same conditions, where the conditions support biomass accumulation by the control microorganism, can have a higher carbon to nitrogen (C:N) ratio than a control microorganism. For example, the C:N ratio can be from about 1.5 to about 2.5 times the C:N ratio of a control microorganism when the mutant microorganism and the control microorganism are cultured under conditions in which both the mutant and the control microorganisms accumulate biomass, and the mutant produces at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 100% more lipid that the control microorganism and at least 50%, at least 60%, at least 70%, at least 80%, or at least 85% of the TOC of the control microorganism. A mutant microorganism as provided herein, e.g., a mutant microorganism such as any described herein that produces at least about 50% of the biomass and at least about 50%, at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 110%, or at least 120% more lipid than is produced by a control microorganism cultured under the same conditions, where the conditions support daily biomass accumulation by the control microorganism, can have a higher carbon to nitrogen (C:N) ratio than a control microorganism. For example, the C:N ratio can be from about 1.5 to about 2.5 times the C:N ratio of a control microorganism when the mutant microorganism and the control microorganism are cultured under conditions in which both the mutant and the control microorganisms accumulate biomass on a daily basis, and the mutant produces at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 100% more lipid that the control microorganism and at least 50%, at least 60%, at least 70%, at least 80%, or at least 85% of the TOC of the control microorganism. In some embodiments the C:N ratio of a mutant as provided herein is between about 7 and between about 20, or between about 8 and about 17, or between about 10 and about 15, during the culture period in which mutant produces at least 50% more lipid that a control microorganism while producing at least 50% as much biomass as the control microorganism. A control microorganism in any of the embodiments or examples herein can be a wild type microorganism.

[0020] Alternatively or in addition, mutant microorganism as provided herein, e.g., a mutant microorganism such as any described herein that produces at least about 50% of the biomass and at least about 50%, at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 110%, or at least 120% more lipid than is produced by a control microorganism cultured under the same conditions, where the conditions support biomass accumulation by the control microorganism (e.g., where the conditions support daily biomass accumulation by the control microorganism), can have reduced protein content when compared with a control microorganism. For example, a mutant microorganism as provided herein can have a decrease in protein content of at least 10%, at least 20%, at least 30%, at least 40%, at least 45%, or at least 50% with respect to a control microorganism. The mutant microorganism can partition at least 35%, at least 40%, or at least about 45% of its total carbon to lipid while producing at least 50% more lipid than a control microorganism under the same culture conditions in which the mutant microorganims produces at least 65%, at least 70%, at least 75%, at least 80% as much biomass as the control microorganism.

[0021] Further, a mutant microorganism such as any provided herein can in some embodiments have attenuated expression of a gene encoding a protein whose expression affects the expression of other genes, e.g., at least ten, at least twenty, at least thirty, at least forty, at least fifty, at least sixty, at least seventy, at least eighty, at least ninety, or at least 100 additional genes. For example, a mutant as provided herein can have at least ten genes that are upregulated with respect to a wild type microorganism and at least ten genes that are downregulated with respect to a wild type microorganism under conditions in which the mutant phenotype (as disclosed herein) is displayed. A mutant as provided herein can have at least twenty, at least thirty, at least forty, at least fifty, at least sixty, at least seventy, at least eighty, at least ninety, or at least 100 genes that are upregulated with respect to a wild type microorganism and at least twenty, at least thirty, at least forty, at least fifty, at least sixty, at least seventy, at least eighty, at least ninety, or at least 100 genes that are downregulated with respect to a wild type microorganism under conditions in which the mutant phenotype (e.g., greater lipid production with respect to the wild type microorganism) is expressed. In some embodiments, genes encoding polypeptides involved in protein synthesis can be upregulated in a mutant as provided herein, for example, genes encoding ribosomal polypeptides or other polypeptides that function in protein translation, including, without limitation, those belonging to gene ontology (GO) groups such as "translation", "ribosome", and/or "regulation of translation initiation". Alternatively to or in combination with the upregulation of genes encoding polypeptides relating to protein synthesis, one or more genes encoding polypeptides involved in nitrogen assimilation such as one or more of a nitrite reductase, glutamine synthetase, ammonium transporter and/or an enzyme involved in molybdenum cofactor biosynthesis can be downregulated in a mutant as provided herein. Alternatively or in combination with any of the above, a mutant as provided herein can exhibit upregulation of one or more genes related to lipid biosynthesis including but not limited to desaturases, elongases, lipid droplet surface protein, and/or particular lipases, acyltransferases, and glyceraldehyde-3-phosphate dehydrogenases.

[0022] A mutant as described herein can be a mutant obtained by classical mutagenesis or can be a genetically engineered mutant. In various embodiments, a mutant microorganism as disclosed herein has been generated by introducing one or more genetic constructs (one or more nucleic acid molecules) into the microorganism. In some examples, one or more genetic constructs introduced into a microorganism are designed to attenuate expression of a native gene.

[0023] In various examples, mutants as disclosed herein can have attenuated expression of a fungal type Zn(2)Cys(6) transcription factor, i.e., a gene encoding a polypeptide that has a Zn(2)Cys(6) domain, e.g., has an amino acid sequence encoding a cd00067 "GAL4" domain or a "Zn_clus" domain belonging to pfam PF00172. For example, a mutant microorganism such as any disclosed herein having FAME production that is increased by at least 25% and biomass production that is reduced by no more than 50% with respect to a control microorganism for at least 3, at least 5, at least 7, at least 10, at least 12, at least 13, at least 15, at least 20, at least 25, or at least 30 days of culturing can have attenuated expression of a gene encoding a polypeptide that recruits to pfam PF00172. Alternatively or in addition, a mutant microorganism such as any disclosed herein having a FAME/TOC ratio that is at least 30% higher than the FAME/TOC ratio of a control microorganism under conditions in which the control microorganism is producing biomass can be a mutant microorganism that has attenuated expression of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, e.g., having an amino acid sequence encoding a domain belonging to pfam PF00172 or characterized as a cd00067 "GLA4" domain. In some examples, the Zn(2)Cys(6) domain can have at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:3.

[0024] Thus, another aspect of the invention is mutant microorganism having attenuated expression of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, wherein the mutant microorganism has increased partitioning of carbon to lipid with respect to a control microorganism that does not have attenuated expression of the gene encoding a polypeptide having a ZnCys domain. For example, a mutant microorganism as provided herein having attenuated expression of a polypeptide having a Zn(2)Cys(6) domain can have an increased FAME/TOC ratio with respect to a control cell when the mutant microorganism and control microorganism are cultured under identical conditions under which the control microorganism culture experiences an increase in TOC. In some examples, a mutant microorganism as provided herein can have a FAME/TOC ratio that is increased by at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 110%, at least 120%, at least 130%, at least 140%, or at least 150% as compared to the FAME/TOC ratio of a control microorganism when the mutant microorganism and control microorganism are cultured under identical conditions under which the control microorganism culture experiences an increase in TOC. Alternatively or in addition, a mutant microorganism as provided herein having attenuated expression of a gene encoding a polypeptide having a Zn(2)Cys(6) domain can have increased production of FAME lipids with respect to a control microorganism while demonstrating no more than a 45% reduction in TOC production with respect to the control microorganism when the mutant microorganism and control microorganism are cultured under identical conditions under which the control microorganism experiences an increase in TOC. For example, a mutant microorganism as provided herein having attenuated expression of a gene encoding a polypeptide having a Zn(2)Cys(6) domain can produce at least 25% or at least 50% more FAME lipids or at least 75% more FAME lipids with respect to a control microorganism while demonstrating no more than a 50% reduction in TOC production with respect to the control microorganism when the mutant microorganism and control microorganism are cultured under identical conditions under which the control microorganism experiences an increase in TOC. In various embodiments the mutant microorganism can display higher lipid productivity and/or carbon partitioning to lipid over a culture period of at least 3, at least 5, at least 7, at least 10, at least 12 days, at least 13, at least 15, at least 20, or at least 30 days. For example, mutant microorganism can have higher lipid productivity each day of the at least 5, at least 7, at least 10, at least 12 days, at least 15, at least 20, or at least 30-day culture period.

[0025] In some exemplary embodiments the amino acid sequence of the polypeptide having a Zn(2)Cys(6) domain is at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identical to any of SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO:17. In some examples, a mutant microorganism as provided herein can have attenuated expression of a gene encoding a polypeptide having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO: 11, or SEQ ID NO: 17. For example, a mutant microorganism as provided herein can have attenuated expression of a gene encoding a polypeptide having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2 or SEQ ID NO:17, or at least the N-terminal 517 amino acids of SEQ ID NO:2 or the N-terminal 540 amino acids of SEQ ID NO: 17. In further examples a mutant microorganism as provided herein has attenuated expression of a gene encoding a polypeptide that includes an amino acid sequence having at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to any of SEQ ID NO:2, SEQ ID NO:17, SEQ ID NO:18, or SEQ ID NO:19, or to amino acids 1-200 of SEQ ID NO:20. In some examples, a mutant microorganism as provided herein can have attenuated expression of a gene encoding a polypeptide having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2 or SEQ ID NO: 17. Alternatively or in addition, a mutant microorganism as provided herein can have attenuated expression of a gene having a coding sequence with at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:1 or any of SEQ ID NOs:72-84. In various embodiments the microorganism is a diatom or eustigmatophyte alga, and in some examples may be a species of Nannochloropsis.

[0026] Alternatively or in addition to any of the above, a mutant microorganism as provided herein can have attenuated expression of a gene encoding a polypeptide that has a Zn(2)Cys(6) domain and further includes a PAS3 domain. In some examples the PAS3 domain comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to any of SEQ ID NOs:21-25. The gene whose expression is attenuated can additionally encoding a polypeptide that further includes an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to at least 200 amino acids of any of SEQ ID NOs:18-20.

[0027] An attenuated gene encoding a polypeptide having a Zn(2)Cys(6) domain can be a gene that has an insertion, deletion, and/or one or more base changes with respect to the wild type gene. The insertion, deletion, or one or more base changes can be in a coding region, intron, 3' untranslated region, or 5' untranslated region of the gene, or can be upstream of the 5' untranslated region of the gene, e.g., in the promoter region of a gene, where the mutant produces less of an RNA corresponding to the gene and/or produces less of the encoded polypeptide. Alternatively or in addition, a mutant microorganism as provided herein can include an antisense construct, an RNAi construct, a guide RNA (gRNA) as part of a CRISPR system, or a ribozyme that targets the gene encoding the polypeptide having a Zn(2)Cys(6) domain, resulting in reduced expression of the gene.

[0028] A mutant microorganism as provided herein can be any eukaryotic microorganism, and in some examples is a heterokont or alga. For example, the mutant microorganism can be a Labyrinthulomycte species, such as, for example, a species of Labryinthula, Labryinthuloides, Thraustochytrium, Schizochytrium, Aplanochytrium, Aurantiochytrium, Oblongichytrium, Japonochytrium, Diplophrys, or Ulkenia. Alternatively a mutant microorganism can be an algal species such as for example, a species belonging to any of the genera Achnanthes, Amphiprora, Amphora, Ankistrodesmus, Asteromonas, Boekelovia, Bolidomonas, Borodinella, Botrydium, Botryococcus, Bracteococcus, Chaetoceros, Carteria, Chlamydomonas, Chlorococcum, Chlorogonium, Chlorella, Chroomonas, Chrysosphaera, Cricosphaera, Crypthecodinium, Cryptomonas, Cyclotella, Desmodesmus, Dunaliella, Elipsoidon, Emiliania, Eremosphaera, Ernodesmius, Euglena, Eustigmatos, Franceia, Fragilaria, Fragilaropsis, Gloeothamnion, Haematococcus, Hantzschia, Heterosigma, Hymenomonas, Isochrysis, Lepocinclis, Micractinium, Monodus, Monoraphidium, Nannochloris, Nannochloropsis, Navicula, Neochloris, Nephrochloris, Nephroselmis, Nitzschia, Ochromonas, Oedogonium, Oocystis, Ostreococcus, Parachlorella, Parietochloris, Pascheria, Pavlova, Pelagomonas, Phceodactylum, Phagus, Picochlorum, Platymonas, Pleurochrysis, Pleurococcus, Prototheca, Pseudochlorella, Pseudoneochloris, Pseudostaurastrum, Pyramimonas, Pyrobotrys, Scenedesmus, Schizochlamydella, Skeletonema, Spyrogyra, Stichococcus, Tetrachlorella, Tetraselmis, Thalassiosira, Tribonema, Vaucheria, Viridiella, Vischeria, and Volvox. In some embodiments a mutant microorganism is a diatom or eustigmatophyte alga. In some embodiments the mutant microorganism is a species of Nannochloropsis.

[0029] A further aspect of the invention is a method of producing lipid, comprising culturing a mutant microorganism as provided herein and isolating lipid from the microorganism, the culture medium, or both. The mutant microorganism can be cultured in a medium that comprises less than about 5 mM ammonium, less than about 2.5 mM ammonium, less than or equal to about 1 mM ammonium, or less than or equal to about 0.5 mM. The culture medium can include, for example, from about 0 to about 2.5 mM ammonium, from about 0.1 to about 2.5 mM ammonium, from about 0.5 to about 2.5 mM ammonium, from about 0 to about 1 mM ammonium, from about 0.1 to about 1 mM ammonium, or from about 0.2 to about 1 mM ammonium. The microorganism can be cultured in a medium that includes nitrate, which in some examples may be substantially the sole nitrogen source in the culture medium or may be present in addition to ammonium that may be present at a concentration of less than 5 mM, less than 2.5 mM, less than 2 mM, or less than 1 mM. Alternatively or in addition, the culture medium can comprise urea, which in some examples can be substantially the sole source of nitrogen in the culture medium. The mutant microorganism can be cultured under batch, continuous, or semi-continuous mode. The mutant microorganism can in some embodiments be a photosynthetic microorganism, e.g., and alga, and can be cultured photoautotrophically.

[0030] Yet another aspect of the invention is a method of producing lipid that includes culturing a microorganism under conditions in which the FAME to TOC ratio of the microorganism is maintained between about 0.3 and about 0.8, and isolating lipid from the microorganism, the culture medium, or both. For example, the microorganisms can be cultured such that the FAME to TOC ratio is maintained at between about 0.3 and about 0.8, between about 0.4 and about 0.7, between about 0.4 and about 0.6, or between about 0.45 and about 0.55. The ratio can be maintained at between about 0.3 and about 0.8, for example between about 0.4 and about 0.8, between about 0.4 and about 0.7, between about 0.4 and about 0.6, or between about 0.45 and about 0.55 for at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 15, at least 20, at least 30 days, or at least 60 days. The microorganism can be cultured under batch, continuous, or semi-continuous mode. The method of producing lipid can include culturing a mutant microorganism such as any provided herein under conditions in which the FAME to TOC ratio of the microorganism is maintained between about 0.3 and about 0.8, between about 0.3 and about 0.8, between about 0.4 and about 0.7, between about 0.4 and about 0.6, or between about 0.45 and about 0.55. For example, the microorganism can be a mutant microorganism having attenuated expression of a Zn(2)Cys(6) regulator gene, such as but not limited to a gene encoding a polypeptide having at least 55%, at least 65%, at least 75%, or at least 85% identity to a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:2 and SEQ ID NOs:5-17. Alternatively or in addition, the microorganism can be a mutant microorganism having attenuated expression of a gene that has a coding sequence having at least 50%, at least 55%, at least 60%, least 65%, at least 70%, at least 75%, at least 80%, at least 85% at least 90%, or at least 95% identity to SEQ ID NO: 1 or any of SEQ ID NOs:71-84. In any of the above methods for producing lipid, the mutant microorganism can be an alga, and the culturing can be under photoautotrophic conditions, i.e., conditions in which inorganic carbon is substantially the sole carbon source in the culture medium.

[0031] Yet another aspect of the invention is a nucleic acid molecule comprising a nucleic acid sequence encoding a polypeptide including an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, or SEQ ID NO: 17. The polypeptide having at least 60% identity to a nucleic acid sequence selected from the group consisting of SEQ ID NO:2 and SEQ ID NOs:5-17 can include an amino acid sequence encoding a Zn(2)Cys(6) domain. The nucleic acid molecule in various examples can be or comprise a cDNA that lacks one or more introns present in the naturally-occurring gene, or, alternatively, can include one or more introns not present in the naturally-occurring gene. The nucleic acid molecule in various examples can have a sequence that is not 100% identical to a naturally-occurring gene. The nucleic acid molecule in various examples can comprise a heterologous promoter operably linked to the sequence encoding a polypeptide that includes an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO: 15, SEQ ID NO: 16, or SEQ ID NO: 17 and/or can comprise a vector that includes a sequence encoding a polypeptide that includes an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, or SEQ ID NO:17.

[0032] A further aspect of the invention is a construct designed for attenuating expression of a gene encoding a polypeptide containing a Zn(2)Cys(6) domain. The construct can be or comprise, in various examples, a sequence encoding a guide RNA of a CRISPR system, an RNAi construct, an antisense construct, a ribozyme construct, or a construct for homologous recombination, e.g., a construct having one or more nucleotide sequences having homology to a naturally-occurring Zn(2)Cys(6) domain-encoding gene as disclosed herein and/or sequences adjacent thereto in the native genome from which the gene is derived. For example, the construct can include at least a portion of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, e.g., a sequence homologous to at least a portion of an gene that encodes a polypeptide that includes an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO:17. Alternatively or in addition, the construct can include a sequence having at least 50%, at least 55%, at least 60%, least 65%, at least 70%, at least 75%, at least 80%, at least 85% at least 90%, or at least 95% identity to SEQ ID NO:1 or any of SEQ ID NOs:71-84.

[0033] The construct can include, for example, at least a portion of the coding region of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, at least a portion of an intron of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, at least a portion of a 5'UTR of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, at least a portion of the promoter region of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, and/or at least a portion of a 3' UTR of a gene encoding a polypeptide having a Zn(2)Cys(6) domain. In some examples, the construct can be an RNAi, ribozyme, or antisense construct and can include a sequence from the transcribed region of the gene encoding a polypeptide having a Zn(2)Cys(6) domain in either sense or antisense orientation. In further examples a construct can be designed for the in vitro or in vivo expression of a guide RNA (e.g., of a CRISPR system) designed to target a gene encoding a polypeptide having a Zn(2)Cys(6) domain, and can include a sequence homologous to a portion of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, including, for example, an intron, a 5'UTR, a promoter region, and/or a 3' UTR of a gene encoding a polypeptide having a Zn(2)Cys(6) domain. In yet further examples, a construct for attenuating expression a gene encoding a Zn(2)Cys(6) domain-containing polypeptide can be a guide RNA of a CRISPR system or a CRISPRi system or can be an antisense oligonucleotide, where the sequence having homology to a transcribed region of a gene encoding a polypeptide having a Zn(2)Cys(6) domain is in antisense orientation.

[0034] These and other objects and features of the invention will become more fully apparent when the following detailed description of the invention is read in conjunction with the accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

[0035] FIG. 1A provides a graph showing lipid (FAME) accumulation of wild-type Nannochloropsis cultures grown in N replete (+N) and deplete (-N) conditions. The 3-hour time point samples were subjected to transcriptomic analysis (RNA-seq). FIG. 1B provides a plot of the differentially expressed genes in cells transferred to -N medium compared to cells provided with N replete medium. The genes (represented as dots) are plotted versus fold change (log.sub.2) in -N treated cells compared to replete cells. Putative transcription factors are represented as Xs. Genes present in the right side of the y-axis are upregulated and genes on the left side of the y-axis are downregulated. Only genes with a false discovery rate (FDR) less than or equal to 0.01 are displayed on the graph.

[0036] FIG. 2 is a schematic map of vector pSGE-6206 used to introduce the Cas9 gene into the N. gaditana Editor line.

[0037] FIG. 3A provides a map of the vector used in to generate the Cas9 expression strain Ng--CAS9+ in Nannochloropsis. FIG. 3B is an overlayed histogram from the Accuri C6 flow cytometer showing GFP fluorescence in the Ng-Cas9 editor strain (right peak, in red) compared to the wild type strain (left peak, in black). FIG. 3C is an image of a western blot with an anti-FLAG antibody demonstrating Cas9 expression in the Ng--CAS9+ line, with no background in the wild type control.

[0038] FIG. 4A provides a diagram of the donor fragment used for gene disruption at Cas9 target sites. The donor fragment construct includes the HygR (hygromycin resistance) gene driven by the EIF3 promoter and followed by the GNPDA terminator in inverted orientation. FIG. 4B is a schematic representation of a Cas9-mediated insertion of the hygromycin resistance (HygR) cassette into the ZnCys locus. The HygR cassette consisted of a promoter (Prom) driving the HygR gene followed by a terminator (T). The resulting mutant genotype (ZnCys-KO) was identified by PCR using primers that flank the insertion (arrows). The diagram is not to scale. FIG. 4C shows PCR genotyping of several Hyg resistant colonies transformed with a guide RNA designed to target the ZnCys locus. Presence of a 3 Kb band indicates insertion into the intended locus, while a 0.5 Kb band indicates an intact wild-type locus.

[0039] FIG. 5 is a schematic depiction of the N. gaditana ZnCys-2845 gene. A box denotes the position of the Zn(2)Cys(6) domain, which was the region targeted by the RNAi construct. Positions of insertions of the donor fragment in the BASH-3, knockout, and BASH-12 mutants are shown by arrows. The general location of the putative monopartite nuclear localization signal is also shown (NLS). The figure is not to scale.

[0040] FIG. 6A provides incident irradiance profiles for batch growth assessment and FIG. 6B is the Semi-continuous Productivity Assay.

[0041] FIG. 7A is a graph depicting FAME productivity of wild-type and ZnCys-2845 knockout N. gaditana cells cultured in batch mode in nitrate-only medium as determined from samples taken on odd days of the culture. FIG. 7B is a graph depicting TOC productivities for days 3-7 of the batch productivity assay. FIG. 7C is a graph depicting FAME/TOC ratios calculated from samples taken on odd days of the culture. FIG. 7D is a bar graph depicting the amount of fatty acids of various chain lengths present in the lipid isolated on day 7 of the batch assay from wild type WT-3730 and ZnCys 2845 knockout strain GE-8564. FIG. 7E is a bar graph depicting the level of TAG isolated from wild type and ZnCys 2845 knockout strain GE-8564 on day 7 of the batch assay. FIG. 7F is an electron micrograph of a wild type Nannochloropsis gaditana cell cultured in nitrate-only (nitrogen-replete) culture medium. FIG. 7G is an electron micrograph of a Nannochloropsis gaditana ZnCys knockout mutant GE-8564 cell cultured in nitrate-only culture medium. FIG. 7H is an electron micrograph of a wild type Nannochloropsis gaditana cell cultured in nitrogen-deplete culture medium. Error bars in graphs represent the standard deviation for the average value of three cultures (biological replicates). Symbols used in graphs: asterisks represent wild type WT-3730 cultured in nitrate plus ammonium medium PM124, black diamonds represent knockout mutant GE-8564 cultured in nitrate plus ammonium medium PM124, X's represent wild type WT-3730 cultured in nitrate-only medium PM074, and black circles represent knockout mutant GE-8564 cultured in nitrate-only medium PM074. N: nucleus; Ch: chloroplast; LD: lipid droplet; M: mitochondrion.

[0042] FIGS. 8A-8B provide graphs demonstrating repression of the lipid accumulation phenotype of ZnCys-KO by NH.sub.4.sup.+ supplementation in a five-day batch mode assay. FIG. 8A shows FAME (mg/L) per day. FIG. 8B shows TOC (mg/L) per day. FIG. 8C shows FAME/TOC values per day of ZnCys-KO (circles) and WT (diamonds) grown in batch mode on medium supplemented with NH.sub.4.sup.+ (SM-NH.sub.4.sup.+/NO.sub.3.sup.-). Error bars are standard deviations of 2 biological replicates (n=2).

[0043] FIG. 9 is an alignment of the PAS3 domain sequences of N. gaditana ZnCys-2845 and the PAS3 domain sequences of the ZnCys-2845 orthologs of N. oceanica, N. oculata, N. salina, and N. granulata.

[0044] FIG. 10 is an alignment of the N. gaditana polypeptide sequence encoded by the ZnCys-2845 gene and the N. oceanica polypeptide sequence encoded by the ortholog of the ZnCys-2845 gene, as well as partial N-terminal sequences of polypeptides encoded by orthologous genes in N. granulata, N. oculata, and N. salina.

[0045] FIGS. 11A-11C provide graphs depicting productivities of the N. gaditana wild type strain and GE-8564 knockout strain in a semi-continuous assay in which the culture medium includes urea as the sole nitrogen source. FIG. 11A shows daily FAME productivity over thirteen days of the assay. FIG. 11B shows daily TOC productivity over thirteen days of the assay. FIG. 11C) provides the FAME/TOC ratios for each day of the assay. Error bars in graphs represent the standard deviation of the three independent cultures (biological replicates). Symbols used in graphs: squares represent wild type WT-3730 cultured in urea-only medium PM125, triangles represent wild type WT-3730 cultured in nitrate-only medium PM074, circles represent ZnCys-2845 knockout mutant GE-8564 cultured in urea-only medium PM125, and diamonds represent ZnCys-2845 knockout mutant GE-8564 cultured in nitrate-only medium PM074.

[0046] FIG. 12A is a schematic depiction of the ZnCys-2845 gene with the positions of the nuclear localization signal (NLS), Zn(2)Cys(6) domain (Zn) and PAS3 domain shown as boxes and arrows depicting the sites of CRISPR-targeted mutations. FIG. 12B shows the relative transcript levels of the corresponding CRISPR-targeted mutants (position of primers used for transcript assessment shown in FIG. 12A. Normalized expression levels are relative to the average wild type level which was set to 1.0.

[0047] FIG. 13A is a graph depicting FAME productivity of wild-type and ZnCys-2845 knockdown N. gaditana cells cultured in batch mode in nitrate-only medium. FIG. 13B is a graph depicting TOC values for the odd days of the screen (days 1-3 and days 3-5). FIG. 13C is a graph providing FAME/TOC ratios of the cultures calculated on days 3, 5, and 7. Symbols used in graphs: open circles represent wild type WT-3730, a plus sign represents knockout mutant GE-13108, "BASH2"; an asterisk represents knockout mutant GE-13109, "BASH3"; Xs represent knockout mutant GE-13112, "BASH12"; open triangles represent ZnCys-2845 knockout mutant GE-8564; and dashes represent RNAi-7 strain GE-13103. The Error bars represent the standard deviation of two calculated productivity values of two separate cultures.

[0048] FIG. 14A provides the modular structure and salient features of the ZnCys locus. Abbreviations: NLS, nuclear localization sequence; Zn.sub.2Cys.sub.6, Zn(II)2Cys6 binuclear cluster domain (Pfam id: PF00172). The approximate location of the insertion in the original ZnCys-KO mutant is indicated with a black arrow. Patterned arrows indicate locations of successful Cas9 insertional mutants in putative 5'UTR (BASH-3 (strain GE-13109) .about.65 bp from the predicted start site) and 3'UTR regions (BASH-12 (strain GE-13112), approximately 30 bp from the predicted stop codon). Black horizontal arrows show the approximate location of the qRT-PCR primers used for assessing gene expression levels in panel B. The RNAi hairpin designed to silence ZnCys spanned the conserved Zn.sub.2Cys.sub.6 domain was homologous to the sequence denoted by the dotted double arrow. The figure is not to scale. FIG. 14B shows steady-state mRNA levels of the ZnCys locus in attenuated ZnCys lines (left to right on graph, wild type (WT) ZnCys-BASH-3, ZnCys-BASH-12, ZnCys-RNAi-7, and ZnCys-KO) relative to wild type (WT) as determined by qRT-PCR (left to right on graph, wild type (WT) ZnCys-BASH-3, ZnCys-BASH-12, ZnCys-RNAi-7, and ZnCys-KO). Expression levels were normalized to a housekeeping gene and were calculated relative to WT using the .DELTA..DELTA.C.sub.T method. Error bars are standard errors for 3 technical replicates. FIG. 14C shows TOC productivity and FAME/TOC values of ZnCys mutant lines assessed in batch mode in nitrate-replete medium (SM--NO3-). Individual data points used to calculate FAME/TOC and biomass productivity averages are shown in FIGS. 15A-15B. Error bars are standard deviations of two biological replicates.

[0049] FIG. 15A is a batch mode assessment of FAME (mg/L) produced by ZnCys attenuated lines (ZnCys-BASH-3 (GE-13109), ZnCys-BASH-12 (GE-13112), ZnCys-RNAi-7 (GE-13103)) grown in nitrate-replete medium. FIG. 15B is a batch mode assessment of TOC (mg/L) measurements corresponding to days 3, 5 and 7 of the screen.

[0050] FIGS. 16A-16D provide graphs and a table depicting productivities of the N. gaditana wild type strain and GE-8564 knockout strain in a semi-continuous assay in which the culture medium used for daily dilution includes nitrate as the sole nitrogen source. FIG. 16A shows daily FAME productivity over thirteen days of the assay (mg/L culture). FIG. 16B provides the daily productivities of the cultures in g/m2/day (standard deviation of three cultures provided in parentheses), along with the average daily productivity for each culture. FIG. 16C shows daily TOC productivity over thirteen days of the assay (mg/L culture). FIG. 16D provides the FAME/TOC ratios for each day of the assay Symbols used in graphs: diamonds represent wild type WT-3730 pre-cultured in nitrate-only medium; Xs represent knockdown mutant GE-13108 "BASH2" pre-cultured in nitrate plus ammonium medium; triangles represent knockdown mutant GE-13109 "BASH3" pre-cultured in nitrate plus ammonium medium; squares represent knockdown mutant GE-13112 "BASH12" pre-cultured in nitrate plus ammonium medium; open circles represent knockdown mutant GE-13103 "RNAi-7" pre-cultured in nitrate plus ammonium medium; closed circles represent knockdown mutant GE-13103 "RNAi-7" pre-cultured in nitrate-only medium; and dashes represent knockout mutant GE-8564 pre-cultured in nitrate plus ammonium medium. Error bars in graphs represent the standard deviation of the three independent cultures (biological replicates).

[0051] FIGS. 17A-17B. Productivity assessment of ZnCys mutants grown in semi-continuous mode for 8 days on NO.sub.3.sup.--containing culture medium. FIG. 17A shows daily FAME and FIG. 17B shows TOC (mg/L) measurements for ZnCys mutants (ZnCys-RNAi-7, ZnCys-BASH-12 and ZnCys-BASH-3) compared to their parental lines Ng--CAS9+ and WT. Cultures were grown in semi-continuous mode at a 30% daily dilution rate on SM--NO.sub.3.sup.-. Error bars represent standard deviations for 3 biological replicates (n=3).

[0052] FIG. 18 provides a bar graph of FAME and TOC productivities (g/m.sup.2/day) of ZnCys mutants (ZnCys-RNAi-7 (GE-13103), ZnCys-BASH-12 (GE-13112) and ZnCys-BASH-3 (GE-13109)) compared to their parental lines Ng--CAS9+(GE-6791) and WT in the assay whose daily FAME and TOC productivities are depicted in FIGS. 17A-17B. Productivity values are 8-day averages of daily measurements (n=3).

[0053] FIG. 19 provides a graph depicting the daily nitrogen content of the cells (mg/L culture, pellets only) in the semi-continuous assay whose daily FAME and TOC productivities are provided in FIGS. 16A-16D. Symbols used in graphs: diamonds represent wild type WT-3730 pre-cultured in nitrate-only medium; Xs represent knockdown mutant GE-13108 "BASH2" pre-cultured in nitrate plus ammonium medium; triangles represent knockdown mutant GE-13109 "BASH3" pre-cultured in nitrate plus ammonium medium; squares represent knockdown mutant GE-13112 "BASH12" pre-cultured in nitrate plus ammonium medium; open circles represent knockdown mutant GE-13103 "RNAi-7" pre-cultured in nitrate plus ammonium medium; closed circles represent knockdown mutant GE-13103 "RNAi-7" pre-cultured in nitrate-only medium; and dashes represent knockout mutant GE-8564 pre-cultured in nitrate plus ammonium medium. Error bars in graphs represent the standard deviation of the three independent cultures (biological replicates).

[0054] FIG. 20 provides a graph depicting total nitrogen and FAME levels of cultures of N. gaditana wild type strain WT-3730 and RNAi mutant GE-13103 in a semi-continuous assay using nitrate-only media, in which the GE-13103 knockdown strain was pre-cultured separately in either PM124 medium that included both nitrate and ammonium or in PM074 medium that included only nitrate. Wild type strain WT-3730 was pre-cultured in PM074 medium that included only nitrate. Solid diamonds and solid triangles represent the total nitrogen content of the cultures (cells plus culture medium) of GE-13103 pre-cultured in PM124 and PM074, respectively. Open diamonds and open triangles represent the FAME content of the cultures of GE-13103 pre-cultured in PM124 and PM074, respectively. Solid squares represent the FAME content of a culture of WT-3730 pre-cultured in nitrate-only medium. The calculated amount of ammonium on three days of the productivity assay is noted on the graph.

[0055] FIGS. 21A-21F provides graphs and a table depicting productivities of the N. gaditana wild type strain WT-3730 and GE-13103 knockdown strain in a semi-continuous assay in which the culture medium included three different concentrations of ammonium. FIG. 21A depicts FAME productivity (mg/L) in the semi-continuous assay in culture in which the ammonium level of the media used throughout the assay was 2.5, 1.0, or 0.5 mM. FIG. 21B provides daily FAME productivities (g/m.sup.2/day) (standard deviation of three cultures provided in parentheses), along with the average daily productivity for each culture condition in the semi-continuous assay in which the ammonium level of the media used throughout the assay was 2.5, 1.0, or 0.5 mM. FIG. 21C depicts TOC productivity (mg/L) in the semi-continuous assay in which the ammonium level of the media used throughout the assay was 2.5, 1.0, or 0.5 mM. FIG. 21D provides daily TOC productivities (g/m.sup.2/day) (standard deviation of three cultures for each ammonium concentration provided in parentheses), along with the average daily productivity for each culture condition in the semi-continuous assay in which the ammonium level of the media used throughout the assay was 2.5, 1.0, or 0.5 mM. FIG. 21E depicts daily FAME/TOC ratios in the semi-continuous assay in which the ammonium level of the media used throughout the assay was 2.5, 1.0, or 0.5 mM. FIG. 21F provides daily cell counts determined by flow cytometry of cultures analyzed for FAME and TOC productivities in FIGS. 21A-21E. Symbols used in graphs: Circles: WT-3730 cultured in nitrate-only medium; Squares: RNAi knockdown strain GE-13103 cultured in nitrate-containing medium that also included 2.5 mM ammonium; Triangles: RNAi knockdown strain GE-13103 cultured in nitrate-containing medium that also included 1.0 mM ammonium; Xs: RNAi knockdown strain GE-13103 cultured in nitrate-containing medium that also included 0.5 mM ammonium. Error bars in graphs represent the standard deviation of the three independent cultures (biological replicates).

[0056] FIGS. 22A-22E. Productivity assessment of ZnCys-KO and ZnCys-RNAi-7 grown in semi-continuous mode on nitrate-containing medium. FIG. 22A depicts daily FAME (mg/L). FIG. 22B depicts daily TOC (mg/L). FIG. 22C depicts C/N values derived from cellular N-content. FIG. 22D provides a bar graph comparing FAME. FIG. 22E depicts TOC productivities (g/m.sup.2/day) for WT and ZnCys-RNAi-7 calculated for the entire 13-day assay. ZnCys-KO failed to reach steady-state at a 30% daily dilution scheme and essentially washed away as the run progressed, therefore lipid and biomass productivity values were not calculated for this line (N/A, not available). ZnCys-KO was scaled up in culture medium that included NH.sub.4.sup.+ in addition to NO.sub.3.sup.- to obtain enough biomass for the assay.

[0057] FIG. 23 is a bar graph depicting the biomolecular composition of wild type Nannochloropsis strain WT-3730 and two ZnCys knockdown mutants, GE-13112 (BASH 12) and GE-13130 (RNAi).

[0058] FIG. 24 depicts hierarchical clustering by Euclidian distance of transcriptional fold changes of genes encoding proteins involved in N-assimilation from biological triplicates of ZnCys-KO, the nitrate reductase knockout mutant (NR--KO), RNAi-7 and WT grown in batch mode on nitrate-only medium (NO.sub.3, light green) or medium that included both ammonium and nitrate (NH.sub.4, dark green). Red indicates increased expression and blue indicates reduced expression, with black being neutral (neither increased nor decreased).

[0059] FIG. 25 provides images of immunoblot analysis of enzymes in the FAS cycle (KARl, KAS1/3, HAD and ENR), acetyl-CoA carboxylase (ACCase), glutamate synthase (GOGAT2) and nitrate reductase (NR) for duplicate cultures grown in batch mode on nitrate-only medium (WT, ZnCys-KO and ZnCys-RNAi-7 shown as RNAi-7). Coomassie brilliant blue stain (CBB) of a protein gel used for blotting is shown as a loading reference.

DETAILED DESCRIPTION OF THE INVENTION

Definitions

[0060] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. In case of conflict, the present application including the definitions will control. Unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. All ranges provided within the application are inclusive of the values of the upper and lower ends of the range unless specifically indicated otherwise.

[0061] All publications, patents and other references mentioned herein are incorporated by reference in their entireties for all purposes as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference.

[0062] The term "and/or" as used in a phrase such as "A and/or B" herein is intended to include "A and B", "A or B", "A", and "B".

[0063] "About" means either within 10% of the stated value, or within 5% of the stated value, or in some cases within 2.5% of the stated value, or, "about" can mean rounded to the nearest significant digit.

[0064] The term "gene" is used broadly to refer to any segment of a nucleic acid molecule (typically DNA, but optionally RNA) encoding a polypeptide or expressed RNA. Thus, genes include sequences encoding expressed RNA (which can include polypeptide coding sequences or, for example, functional RNAs, such as ribosomal RNAs, tRNAs, antisense RNAs, microRNAs, short hairpin RNAs, ribozymes, etc.). Genes may further comprise regulatory sequences required for or affecting their expression, as well as sequences associated with the protein or RNA-encoding sequence in its natural state, such as, for example, intron sequences, 5' or 3' untranslated sequences, etc. In some examples, "gene" may only refer to a protein-encoding portion of a DNA or RNA molecule, which may or may not include introns. A gene is preferably greater than 50 nucleotides in length, more preferably greater than 100 nucleotides in length, and can be, for example, between 50 nucleotides and 500,000 nucleotides in length, such as between 100 nucleotides and 100,000 nucleotides in length or between about 200 nucleotides and about 50,000 nucleotides in length, or about 200 nucleotides and about 20,000 nucleotides in length. Genes can be obtained from a variety of sources, including cloning from a source of interest or synthesizing from known or predicted sequence information.

[0065] The term "nucleic acid" or "nucleic acid molecule" refers to, a segment of DNA or RNA (e.g., mRNA), and also includes nucleic acids having modified backbones (e.g., peptide nucleic acids, locked nucleic acids) or modified or non-naturally-occurring nucleobases. The nucleic acid molecules can be double-stranded or single-stranded; a single stranded nucleic acid molecule that comprises a gene or a portion thereof can be a coding (sense) strand or a non-coding (antisense) strand.

[0066] A nucleic acid molecule may be "derived from" an indicated source, which includes the isolation (in whole or in part) of a nucleic acid segment from an indicated source. A nucleic acid molecule may also be derived from an indicated source by, for example, direct cloning, PCR amplification, or artificial synthesis from the indicated polynucleotide source or based on a sequence associated with the indicated polynucleotide source, which may be, for example, a species of organism. Genes or nucleic acid molecules derived from a particular source or species also include genes or nucleic acid molecules having sequence modifications with respect to the source nucleic acid molecules. For example, a gene or nucleic acid molecule derived from a source (e.g., a particular referenced gene) can include one or more mutations with respect to the source gene or nucleic acid molecule that are unintended or that are deliberately introduced, and if one or more mutations, including substitutions, deletions, or insertions, are deliberately introduced the sequence alterations can be introduced by random or targeted mutation of cells or nucleic acids, by amplification or other gene synthesis or molecular biology techniques, or by chemical synthesis, or any combination thereof. A gene or nucleic acid molecule that is derived from a referenced gene or nucleic acid molecule that encodes a functional RNA or polypeptide can encode a functional RNA or polypeptide having at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%, sequence identity with the referenced or source functional RNA or polypeptide, or to a functional fragment thereof. For example, a gene or nucleic acid molecule that is derived from a referenced gene or nucleic acid molecule that encodes a functional RNA or polypeptide can encode a functional RNA or polypeptide having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity with the referenced or source functional RNA or polypeptide, or to a functional fragment thereof.

[0067] As used herein, an "isolated" nucleic acid or protein is removed from its natural milieu or the context in which the nucleic acid or protein exists in nature. For example, an isolated protein or nucleic acid molecule is removed from the cell or organism with which it is associated in its native or natural environment. An isolated nucleic acid or protein can be, in some instances, partially or substantially purified, but no particular level of purification is required for isolation. Thus, for example, an isolated nucleic acid molecule can be a nucleic acid sequence that has been excised from the chromosome, genome, or episome that it is integrated into in nature, or has been synthesized apart from other sequences of the chromosome, genome, or episome that it is associated with in nature, or has been synthesized apart from other sequences with which it is juxtaposed in nature.

[0068] A "purified" nucleic acid molecule or nucleotide sequence, or protein or polypeptide sequence, is substantially free of cellular material and cellular components. The purified nucleic acid molecule or protein may be substantially free of chemicals beyond buffer or solvent, for example. "Substantially free" is not intended to mean that other components beyond the novel nucleic acid molecules are undetectable.

[0069] The terms "naturally-occurring" and "wild type" refer to a form found in nature. For example, a naturally occurring or wild type nucleic acid molecule, nucleotide sequence or protein may be present in and isolated from a natural source, and is not intentionally modified by human manipulation.

[0070] As used herein "attenuated" means reduced in amount, degree, intensity, or strength with respect to a control that does not have the manipulation or mutation that results in attenuated expression or activity. Attenuated gene expression may refer to a significantly reduced amount and/or rate of transcription of the gene in question, or of translation, folding, or assembly of the encoded protein. As nonlimiting examples, an attenuated gene may be an endogenous gene of the organism that is mutated or disrupted (e.g., a gene disrupted by partial or total deletion, truncation, frameshifting, or insertional mutation) that does not encode a complete functional open reading frame or that has decreased expression due to alteration or disruption of gene regulatory sequences. An attenuated gene may also be a gene targeted by a construct that reduces expression of the gene, such as, for example, an antisense RNA, microRNA, RNAi molecule, or ribozyme. Attenuated gene expression can be gene expression that is eliminated, for example, reduced to an amount that is insignificant or undetectable, or can be gene expression the is reduced by any amount with respect to the gene expression of a control microorganism, for example reduced from about 1% to about 99%, or from about 5% to about 95% of the level of gene expression of the control microorganism. Attenuated gene expression can also be gene expression that results in an RNA or protein that is not fully functional or nonfunctional, for example, attenuated gene expression can be gene expression that results in a truncated RNA and/or polypeptide.

[0071] "Exogenous nucleic acid molecule" or "exogenous gene" refers to a nucleic acid molecule or gene that has been introduced ("transformed") into a cell. A transformed cell may be referred to as a recombinant cell, into which additional exogenous gene(s) may be introduced. A descendent of a cell transformed with a nucleic acid molecule is also referred to as "transformed" if it has inherited the exogenous nucleic acid molecule. The exogenous gene may be from a different species (and so "heterologous"), or from the same species (and so "homologous"), relative to the cell being transformed. An "endogenous" nucleic acid molecule, gene or protein is a native nucleic acid molecule, gene or protein as it occurs in, or is naturally produced by, the host.

[0072] The term "native" is used herein to refer to nucleic acid sequences or amino acid sequences as they naturally occur in the host. The term "non-native" is used herein to refer to nucleic acid sequences or amino acid sequences that do not occur naturally in the host. A nucleic acid sequence or amino acid sequence that has been removed from a cell, subjected to laboratory manipulation, and introduced or reintroduced into a host cell such that it differs in sequence or location in the genome with respect to its position in a non-manipulated organism (i.e., is juxtaposed with or operably linked to sequences it is not juxtaposed with or operably linked to in a non-transformed organism) is considered "non-native". Thus non-native genes include genes endogenous to the host microorganism operably linked to one or more heterologous regulatory sequences that have been recombined into the host genome.

[0073] A "recombinant" or "engineered" nucleic acid molecule is a nucleic acid molecule that has been altered through human manipulation. As non-limiting examples, a recombinant nucleic acid molecule includes any nucleic acid molecule that: 1) has been partially or fully synthesized or modified in vitro, for example, using chemical or enzymatic techniques (e.g., by use of chemical nucleic acid synthesis, or by use of enzymes for the replication, polymerization, digestion (exonucleolytic or endonucleolytic), ligation, reverse transcription, transcription, base modification (including, e.g., methylation), integration or recombination (including homologous and site-specific recombination) of nucleic acid molecules); 2) includes conjoined nucleotide sequences that are not conjoined in nature; 3) has been engineered using molecular cloning techniques such that it lacks one or more nucleotides with respect to the naturally occurring nucleic acid molecule sequence; and/or 4) has been manipulated using molecular cloning techniques such that it has one or more sequence changes or rearrangements with respect to the naturally occurring nucleic acid sequence. As non-limiting examples, a cDNA is a recombinant DNA molecule, as is any nucleic acid molecule that has been generated by in vitro polymerase reaction(s), or to which linkers have been attached, or that has been integrated into a vector, such as a cloning vector or expression vector.

[0074] The term "recombinant protein" as used herein refers to a protein produced by genetic engineering regardless of whether the amino acid sequence varies from that of a wild-type protein.

[0075] When applied to organisms, the term recombinant, engineered, or genetically engineered refers to organisms that have been manipulated by introduction of a heterologous or exogenous recombinant nucleic acid sequence into the organism, and includes gene knockouts, targeted mutations, gene replacement, and promoter replacement, deletion, or insertion, as well as introduction of transgenes or synthetic genes into the organism. Recombinant or genetically engineered organisms can also be organisms into which constructs for gene "knockdown" have been introduced. Such constructs include, but are not limited to, RNAi, microRNA, shRNA, siRNA, antisense, and ribozyme constructs. Also included are organisms whose genomes have been altered by the activity of meganucleases, zinc finger nucleases, TALENs, or cas/CRISPR systems. An exogenous or recombinant nucleic acid molecule can be integrated into the recombinant/genetically engineered organism's genome or in other instances may not be integrated into the host genome. As used herein, "recombinant microorganism" or "recombinant host cell" includes progeny or derivatives of the recombinant microorganisms of the invention. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny or derivatives may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.

[0076] The term "promoter" refers to a nucleic acid sequence capable of binding RNA polymerase in a cell and initiating transcription of a downstream (3' direction) coding sequence. A promoter includes the minimum number of bases or elements necessary to initiate transcription at levels detectable above background. A promoter can include a transcription initiation site as well as protein binding domains (consensus sequences) responsible for the binding of RNA polymerase. Eukaryotic promoters often, but not always, contain "TATA" boxes and "CAT" boxes. Prokaryotic promoters may contain -10 and -35 prokaryotic promoter consensus sequences. A large number of promoters, including constitutive, inducible and repressible promoters, from a variety of different sources are well known in the art. Representative sources include for example, algal, viral, mammalian, insect, plant, yeast, and bacterial cell types, and suitable promoters from these sources are readily available, or can be made synthetically, based on sequences publicly available on line or, for example, from depositories such as the ATCC as well as other commercial or individual sources. Promoters can be unidirectional (initiate transcription in one direction) or bi-directional (initiate transcription in either direction). A promoter may be a constitutive promoter, a repressible promoter, or an inducible promoter. A promoter region can include, in addition to the gene-proximal promoter where RNA polymerase binds to initiate transcription, additional sequences upstream of the gene that can be within 1 kb, 2 kb, 3 kb, 4 kb, 5 kb or more of the transcriptional start site of a gene, where the additional sequences can influence the rate of transcription of the downstream gene and optionally the responsiveness of the promoter to developmental, environmental, or biochemical (e.g., metabolic) conditions.

[0077] The term "heterologous" when used in reference to a polynucleotide, gene, nucleic acid, polypeptide, or enzyme refers to a polynucleotide, gene, nucleic acid, polypeptide, or enzyme that is from a source or derived from a source other than the host organism species. In contrast a "homologous" polynucleotide, gene, nucleic acid, polypeptide, or enzyme is used herein to denote a polynucleotide, gene, nucleic acid, polypeptide, or enzyme that is derived from the host organism species. When referring to a gene regulatory sequence or to an auxiliary nucleic acid sequence used for maintaining or manipulating a gene sequence (e.g., a promoter, a 5' untranslated region, 3' untranslated region, poly A addition sequence, intron sequence, splice site, ribosome binding site, internal ribosome entry sequence, genome homology region, recombination site, etc.), "heterologous" means that the regulatory sequence or auxiliary sequence is not naturally associated with the gene with which the regulatory or auxiliary nucleic acid sequence is juxtaposed in a construct, genome, chromosome, or episome. Thus, a promoter operably linked to a gene to which it is not operably linked to in its natural state (i.e., in the genome of a non-genetically engineered organism) is referred to herein as a "heterologous promoter," even though the promoter may be derived from the same species (or, in some cases, the same organism) as the gene to which it is linked.

[0078] As used herein, the term "protein" or "polypeptide" is intended to encompass a singular "polypeptide" as well as plural "polypeptides," and refers to a molecule composed of monomers (amino acids) linearly linked by amide bonds (also known as peptide bonds). The term "polypeptide" refers to any chain or chains of two or more amino acids, and does not refer to a specific length of the product. Thus, peptides, dipeptides, tripeptides, oligopeptides, "protein," "amino acid chain," or any other term used to refer to a chain or chains of two or more amino acids, are included within the definition of "polypeptide," and the term "polypeptide" can be used instead of, or interchangeably with any of these terms.

[0079] Gene and protein Accession numbers, commonly provided in parenthesis after a gene or species name, are unique identifiers for a sequence record publicly available at the National Center for Biotechnology Information (NCBI) website (ncbi.nlm.nih.gov) maintained by the United States National Institutes of Health. The "GenInfo Identifier" (GI) sequence identification number is specific to a nucleotide or amino acid sequence. If a sequence changes in any way, a new GI number is assigned. A Sequence Revision History tool is available to track the various GI numbers, version numbers, and update dates for sequences that appear in a specific GenBank record. Searching and obtaining nucleic acid or gene sequences or protein sequences based on Accession numbers and GI numbers is well known in the arts of, e.g., cell biology, biochemistry, molecular biology, and molecular genetics.

[0080] As used herein, the terms "percent identity" or "homology" with respect to nucleic acid or polypeptide sequences are defined as the percentage of nucleotide or amino acid residues in the candidate sequence that are identical with the known polypeptides, after aligning the sequences for maximum percent identity and introducing gaps, if necessary, to achieve the maximum percent homology. N-terminal or C-terminal insertion or deletions shall not be construed as affecting homology, and internal deletions and/or insertions into the polypeptide sequence of less than about 50, less than about 40, less than about 30, less than about 20, or less than about 10 amino acid residues shall not be construed as affecting homology. Homology or identity at the nucleotide or amino acid sequence level can be determined by BLAST (Basic Local Alignment Search Tool) analysis using the algorithm employed by the programs blastp, blastn, blastx, tblastn, and tblastx (Altschul (1997), Nucleic Acids Res. 25, 3389-3402, and Karlin (1990), Proc. Natl. Acad. Sci. USA 87, 2264-2268), which are tailored for sequence similarity searching. The approach used by the BLAST program is to first consider similar segments, with and without gaps, between a query sequence and a database sequence, then to evaluate the statistical significance of all matches that are identified, and finally to summarize only those matches which satisfy a preselected threshold of significance. For a discussion of basic issues in similarity searching of sequence databases, see Altschul (1994), Nature Genetics 6, 119-129. The search parameters for histogram, descriptions, alignments, expect (i.e., the statistical significance threshold for reporting matches against database sequences), cutoff, matrix, and filter (low complexity) can be at the default settings. The default scoring matrix used by blastp, blastx, tblastn, and tblastx is the BLOSUM62 matrix (Henikoff (1992), Proc. Natl. Acad. Sci. USA 89, 10915-10919), recommended for query sequences over 85 in length (nucleotide bases or amino acids).

[0081] For blastn, designed for comparing nucleotide sequences, the scoring matrix can be set by the ratios of M (i.e., the reward score for a pair of matching residues) to N (i.e., the penalty score for mismatching residues), wherein the default values for M and N can be +5 and -4, respectively. Four blastn parameters can be adjusted as follows: Q=10 (gap creation penalty); R=10 (gap extension penalty); wink=1 (generates word hits at every winkth position along the query); and gapw=16 (sets the window width within which gapped alignments are generated). The equivalent Blastp parameter settings for comparison of amino acid sequences can be: Q=9; R=2; wink=1; and gapw=32. A Bestfit comparison between sequences, available in the GCG package version 10.0, can use DNA parameters GAP=50 (gap creation penalty) and LEN=3 (gap extension penalty), and the equivalent settings in protein comparisons can be GAP=8 and LEN=2. The preceding parameter settings are exemplary only and other parameter settings may be used.

[0082] Thus, when referring to the polypeptide or nucleic acid sequences of the present invention, included are sequence identities of at least 40%, at least 45%, at least 50%, at least 55%, of at least 70%, at least 65%, at least 70%, at least 75%, at least 80%, or at least 85%, for example at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or about 100% sequence identity with the full-length polypeptide or nucleic acid sequence, or to fragments thereof comprising a consecutive sequence of at least 50, at least 75, at least 100, at least 125, at least 150, at least 200, or more than 200 amino acid residues of the entire protein; variants of such sequences, e.g., wherein at least one amino acid residue has been inserted N- and/or C-terminal to, and/or within, the disclosed sequence(s) which contain(s) the insertion and substitution. Contemplated variants can additionally or alternately include those containing predetermined mutations by, e.g., homologous recombination or site-directed or PCR mutagenesis, and the corresponding polypeptides or nucleic acids of other species, including, but not limited to, those described herein, the alleles or other naturally occurring variants of the family of polypeptides or nucleic acids which contain an insertion and substitution; and/or derivatives wherein the polypeptide has been covalently modified by substitution, chemical, enzymatic, or other appropriate means with a moiety other than a naturally occurring amino acid which contains the insertion and substitution (for example, a detectable moiety such as an enzyme).

[0083] As used herein, the phrase "conservative amino acid substitution" or "conservative mutation" refers to the replacement of one amino acid by another amino acid with a common property. A functional way to define common properties between individual amino acids is to analyze the normalized frequencies of amino acid changes between corresponding proteins of homologous organisms (Schulz (1979) Principles of Protein Structure, Springer-Verlag). According to such analyses, groups of amino acids can be defined where amino acids within a group exchange preferentially with each other, and therefore resemble each other most in their impact on the overall protein structure (Schulz (1979) Principles of Protein Structure, Springer-Verlag). Examples of amino acid groups defined in this manner can include: a "charged/polar group" including Glu, Asp, Asn, Gln, Lys, Arg, and His; an "aromatic or cyclic group" including Pro, Phe, Tyr, and Trp; and an "aliphatic group" including Gly, Ala, Val, Leu, Ile, Met, Ser, Thr, and Cys. Within each group, subgroups can also be identified. For example, the group of charged/polar amino acids can be sub-divided into sub-groups including: the "positively-charged sub-group" comprising Lys, Arg and His; the "negatively-charged sub-group" comprising Glu and Asp; and the "polar sub-group" comprising Asn and Gln. In another example, the aromatic or cyclic group can be sub-divided into sub-groups including: the "nitrogen ring sub-group" comprising Pro, His, and Trp; and the "phenyl sub-group" comprising Phe and Tyr. In another further example, the aliphatic group can be sub-divided into sub-groups including: the "large aliphatic non-polar sub-group" comprising Val, Leu, and Ile; the "aliphatic slightly-polar sub-group" comprising Met, Ser, Thr, and Cys; and the "small-residue sub-group" comprising Gly and Ala. Examples of conservative mutations include amino acid substitutions of amino acids within the sub-groups above, such as, but not limited to: Lys for Arg or vice versa, such that a positive charge can be maintained; Glu for Asp or vice versa, such that a negative charge can be maintained; Ser for Thr or vice versa, such that a free --OH can be maintained; and Gln for Asn or vice versa, such that a free --NH2 can be maintained. A "conservative variant" is a polypeptide that includes one or more amino acids that have been substituted to replace one or more amino acids of the reference polypeptide (for example, a polypeptide whose sequence is disclosed in a publication or sequence database, or whose sequence has been determined by nucleic acid sequencing) with an amino acid having common properties, e.g., belonging to the same amino acid group or sub-group as delineated above.

[0084] As used herein, "expression" includes the expression of a gene at least at the level of RNA production, and an "expression product" includes the resultant product, e.g., a polypeptide or functional RNA (e.g., a ribosomal RNA, a tRNA, a guide RNA, an antisense RNA, a micro RNA, an shRNA, a ribozyme, etc.), of an expressed gene. The term "increased expression" includes an alteration in gene expression to facilitate increased mRNA production and/or increased polypeptide expression. "Increased production" [of a gene product] includes an increase in the amount of polypeptide expression, in the level of the enzymatic activity of a polypeptide, or a combination of both, as compared to the native production or enzymatic activity of the polypeptide.

[0085] Some aspects of the present invention include the partial, substantial, or complete deletion, silencing, inactivation, or down-regulation of expression of particular polynucleotide sequences. The genes may be partially, substantially, or completely deleted, silenced, inactivated, or their expression may be down-regulated in order to affect the activity performed by the polypeptide they encode, such as the activity of an enzyme. Genes can be partially, substantially, or completely deleted, silenced, inactivated, or down-regulated by insertion of nucleic acid sequences that disrupt the function and/or expression of the gene (e.g., viral insertion, transposon mutagenesis, meganuclease engineering, homologous recombination, or other methods known in the art). The terms "eliminate," "elimination," and "knockout" can be used interchangeably with the terms "deletion," "partial deletion," "substantial deletion," or "complete deletion" and refer to substantially eliminating expression of the gene, for example, reducing the level of expression to less than 10%, less than 5%, less than 2%, or less than 1% of control levels or undetectable levels. The terms "attenuation" and "knockdown" can be used to describe mutations and manipulations resulting in a lower level of expression of a gene with respect to wild type levels of expression, or, in some cases, resulting in reduced activity of a gene product, such as by mutating a functional domain of the encoded polypeptide. Attenuation can be complete attenuation (e.g., "knockout") or can be partial attenuation, where, for example, RNA or protein levels are reduced or "knocked down" by from 1-99.5% of control levels, e.g., to a level where RNA or protein expression is detectable but reduced with respect to controls. In certain embodiments, a microorganism of interest may be engineered by site directed homologous recombination to knockout a particular gene of interest. In still other embodiments, RNAi or antisense DNA (asDNA) constructs may be used to partially, substantially, or completely silence, inactivate, or down-regulate a particular gene of interest.

[0086] These insertions, deletions, or other modifications of certain nucleic acid molecules or particular polynucleotide sequences may be understood to encompass "genetic modification(s)" or "transformation(s)" such that the resulting strains of the microorganisms or host cells may be understood to be "genetically modified", "genetically engineered" or "transformed."

[0087] As used herein, "up-regulated" or "up-regulation" includes an increase in expression of a gene or nucleic acid molecule of interest or the activity of an enzyme, e.g., an increase in gene expression or enzymatic activity as compared to the expression or activity in an otherwise identical gene or enzyme that has not been up-regulated.

[0088] As used herein, "down-regulated" or "down-regulation" includes a decrease in expression of a gene or nucleic acid molecule of interest or the activity of an enzyme, e.g., a decrease in gene expression or enzymatic activity as compared to the expression or activity in an otherwise identical gene or enzyme that has not been down-regulated.

[0089] As used herein, "mutant" refers to an organism that has a mutation in a gene that is the result of classical mutagenesis, for example, using gamma irradiation, UV, or chemical mutagens. "Mutant" as used herein also refers to a recombinant cell that has altered structure or expression of a gene as a result of genetic engineering that many include, as non-limiting examples, overexpression, including expression of a gene under different temporal, biological, or environmental regulation and/or to a different degree than occurs naturally and/or expression of a gene that is not naturally expressed in the recombinant cell; homologous recombination, including knock-outs and knock-ins (for example, gene replacement with genes encoding polypeptides having greater or lesser activity than the wild type polypeptide, and/or dominant negative polypeptides); gene attenuation via RNAi, antisense RNA, or ribozymes, or the like; and genome engineering using meganucleases, TALENs, and/or CRISPR technologies, and the like. A mutant is therefore not a naturally-occurring organism. A mutant organism of interest will typically have a phenotype different than that of the corresponding wild type or progenitor strain that lacks the mutation, where the phenotype can be assessed by growth assays, product analysis, photosynthetic properties, biochemical assays, etc. When referring to a gene "mutant" means the gene has at least one base (nucleotide) change, deletion, or insertion with respect to a native or wild type gene. The mutation (change, deletion, and/or insertion of one or more nucleotides) can be in the coding region of the gene or can be in an intron, 3' UTR, 5' UTR, or promoter region, e.g., within 2 kb of the transcriptional start site or within 3 kb or the translational start site. As nonlimiting examples, a mutant gene can be a gene that has an insertion within the promoter region that can either increase or decrease expression of the gene; can be a gene that has a deletion, resulting in production of a nonfunctional protein, truncated protein, dominant negative protein, or no protein; can be a gene that has one or more point mutations leading to a change in the amino acid of the encoded protein or results in aberrant splicing of the gene transcript, etc.

[0090] The term "Pfam" refers to a large collection of protein domains and protein families maintained by the Pfam Consortium and available at several sponsored world wide web sites, including: pfam.xfam.org/(European Bioinformatics Institute (EMBL-EBI). The latest release of Pfam is Pfam 30.0 (June 2016). Pfam domains and families are identified using multiple sequence alignments and hidden Markov models (HMMs). Pfam-A family or domain assignments, are high quality assignments generated by a curated seed alignment using representative members of a protein family and profile hidden Markov models based on the seed alignment. (Unless otherwise specified, matches of a queried protein to a Pfam domain or family are Pfam-A matches.) All identified sequences belonging to the family are then used to automatically generate a full alignment for the family (Sonnhammer (1998) Nucleic Acids Research 26, 320-322; Bateman (2000) Nucleic Acids Research 26, 263-266; Bateman (2004) Nucleic Acids Research 32, Database Issue, D138-D141; Finn (2006) Nucleic Acids Research Database Issue 34, D247-251; Finn (2010) Nucleic Acids Research Database Issue 38, D211-222). By accessing the Pfam database, for example, using the above-referenced website, protein sequences can be queried against the HMMs using HMMER homology search software (e.g., HMMER2, HMMER3, or a higher version, hmmer.org). Significant matches that identify a queried protein as being in a pfam family (or as having a particular Pfam domain) are those in which the bit score is greater than or equal to the gathering threshold for the Pfam domain. Expectation values (e values) can also be used as a criterion for inclusion of a queried protein in a Pfam or for determining whether a queried protein has a particular Pfam domain, where low e values (much less than 1.0, for example less than 0.1, or less than or equal to 0.01) represent low probabilities that a match is due to chance.

[0091] A "cDNA" is a DNA molecule that comprises at least a portion the nucleotide sequence of an mRNA molecule, with the exception that the DNA molecule substitutes the nucleobase thymine, or T, in place of uridine, or U, occurring in the mRNA sequence. A cDNA can be double stranded or single stranded and can be, for example, the complement of the mRNA sequence. In preferred examples, a cDNA does not include one or more intron sequences that occur in the naturally-occurring gene that the cDNA corresponds to (i.e., the gene as it occurs in the genome of an organism). For example, a cDNA can have sequences from upstream of an intron of a naturally-occurring gene juxtaposed to sequences downstream of the intron of the naturally-occurring gene, where the upstream and downstream sequences are not juxtaposed in a DNA molecule in nature (i.e., the sequences are not juxtaposed in the naturally occurring gene). A cDNA can be produced by reverse transcription of mRNA molecules, or can be synthesized, for example, by chemical synthesis and/or by using one or more restriction enzymes, one or more ligases, one or more polymerases (including, but not limited to, high temperature tolerant polymerases that can be used in polymerase chain reactions (PCRs)), one or more recombinases, etc., based on knowledge of the cDNA sequence, where the knowledge of the cDNA sequence can optionally be based on the identification of coding regions from genome sequences or compiled from the sequences multiple partial cDNAs.

[0092] Reference to properties that are "substantially the same" or "substantially identical" without further explanation of the intended meaning, is intended to mean the properties are within 10%, and preferably within 5%, and may be within 2.5%, within 1%, or within 0.5% of the reference value. Where the intended meaning of "substantially" in a particular context is not set forth, the term is used to include minor and irrelevant deviations that are not material to the characteristics considered important in the context of the invention.

[0093] Although methods and materials similar or equivalent to those described herein can be used in practice or testing of the present invention, suitable methods and materials are described below. The materials, methods, and examples are illustrative only and are not intended to be limiting. Other features and advantages of the invention will be apparent from the detailed description and from the claims.

[0094] A "control cell" or "control microorganism" is a cell or microorganism that is substantially identical to the manipulated, recombinant, or mutant cell referred to, with the exception that the control cell does not have the modification of the manipulated, recombinant, or mutant cell. A control cell can be a wild type cell, for example a wild type cell of the strain from which the manipulated, recombinant, or mutant cell is directly or indirectly derived.

[0095] "The same conditions" or "the same culture conditions", as used herein, means substantially the same conditions, that is, any differences between the referenced conditions are minor and not relevant to the function or properties of the microorganism that are material to the invention, e.g., lipid production or biomass production.

[0096] "Nitrogen replete" conditions, with respect to a particular cell type, are conditions under which the cell does not experience growth deficiency due to insufficient nitrogen.

[0097] As used herein "lipid" or "lipids" refers to fats, waxes, fatty acids, fatty acid derivatives such as fatty alcohols, wax esters, alkanes, and alkenes, sterols, monoglycerides, diglycerides, triglycerides, phospholipids, sphingolipids, saccharolipids, and glycerolipids. "FAME lipids" or "FAME" refers to lipids having acyl moieties that can be derivatized to fatty acid methyl esters, such as, for example, monoacylglycerides, diacylglycerides, triacylglycerides, wax esters, and membrane lipids such as phospholipids, galactolipids, etc. Lipid productivity can be assessed as FAME productivity in milligrams per liter (mg/L) over a given time period (e.g., per day) and for algae, may be reported as areal productivity, for example grams per meter.sup.2 per day (g/m.sup.2/day). In the semi-continuous assays provided herein, mg/L/day values are converted to g/m2/day by taking into account the area of incident irradiance (the SCPA flask rack aperture of 11/2''.times.33/8'', or 0.003145 m.sup.2) and the volume of the culture (550 ml). To obtain productivity values in g/m2/day, mg/L/day values are multiplied by the daily dilution rate (30%) and a conversion factor of 0.175. Where lipid or subcategories thereof (for example, TAG or FAME) are referred to as a percentage, the percentage is a weight percent unless indicated otherwise.

[0098] "Biomass" refers to cellular mass, whether of living or dead cells, and can be assessed, for example, as aspirated pellet weight, but is more preferably dry weight (e.g., lyophilate of a culture sample or pelleted cells), ash-free dry weight (AFDW), or total organic carbon (TOC), using methods known in the art. Biomass increases during the growth of a culture under growth permissive conditions and may be referred to as "biomass accumulation" in batch cultures, for example. In continuous or semi-continuous cultures that undergo steady or regular dilution, biomass that is produced that would otherwise accumulate in the culture is removed during culture dilution. Thus, daily biomass productivity (increases in biomass) by these cultures can also be referred to as "biomass accumulation". Biomass productivity can be assessed as TOC productivity in milligrams per liter (mg/L) per given time period (e.g., per day) and for algae, may be reported as grams per meter.sup.2 per day (g/m.sup.2/day). In the semi-continuous assays provided herein, mg/L values are converted to g/m2/day by taking into account the area of incident irradiance (the SCPA flask rack aperture of 11/2''.times. 33/8'', or 0.003145 m.sup.2) and the volume of the culture (550 ml). To obtain productivity values in g/m2/day, mg/L values are multiplied by the daily dilution rate (30%) and a conversion factor of 0.175. Where biomass is expressed as a percentage, the percentage is a weight percent unless indicated otherwise.

[0099] In the context of the invention, a "nitrogen source" is a source of nitrogen that can be taken up and metabolized by the subject microorganism and incorporated into biomolecules for growth. For example, compounds including nitrogen that cannot be taken up and/or metabolized by the microorganism for growth (e.g., nitrogen-containing biological buffers such as Hepes, Tris, etc.) are not considered nitrogen sources in the context of the invention.

[0100] "Reduced nitrogen", as used herein, is nitrogen in the chemical form of ammonium, ammonia, urea, or an amino acid that can be metabolized by the microorganism being cultured to provide a source of nitrogen for incorporation into biomolecules, thereby supporting growth. For example, in addition to ammonium/ammonia and urea, reduced nitrogen can include various amino acids where the amino acid(s) can serve as a nitrogen source to the subject microorganism. Examples of amino acids can include, without limitation, glutamate, glutamine, histidine, lysine, arginine, asparagine, alanine, and glycine. "Non-reduced nitrogen" in the context of a nitrogen source that can be present in a culture medium for microorganisms refers to nitrate or nitrite that must be reduced prior to assimilation into organic compounds by the microorganism.

[0101] "The sole source of nitrogen [in the culture medium]" is used interchangeably with "substantially the sole source of nitrogen" and indicates that no other nitrogen source is intentionally added to the culture medium and/or that no other nitrogen source is present in an amount sufficient to significantly increase the growth of the microorganisms or cells cultured in the referenced medium. Throughout this application, for brevity, the terms "nitrate-only" and "urea-only" are used to characterize culture media in which nitrate is the substantially the sole source of nitrogen that is available to the microorganisms for supporting growth or urea is the only source of nitrogen that is available to the microorganisms for supporting growth, respectively.

[0102] Similarly, "the sole source of carbon [in the culture medium]" is used interchangeably with "substantially the sole source of carbon" and indicates that where inorganic carbon is substantially the sole source of carbon in the culture medium no other carbon source is present in an amount sufficient to increase the productivity or growth of the microorganisms or cells cultured in the referenced medium or any other carbon source that may be present is not significantly incorporated into biomolecules such as lipids produced by the microorganisms or cells. "Inorganic carbon" refers to carbon dioxide, carbonate and carbonate salts, and carbonic acid.

[0103] Disclosed herein are methods for manipulating, assaying, culturing, and analyzing microorganisms. The invention set forth herein also makes use of standard methods, techniques, and reagents for cell culture, transformation of microorganisms, genetic engineering, and biochemical analysis that are known in the art.

[0104] All headings are for the convenience of the reader and do not limit the invention in any way.

Mutant Microorganisms Having Increased Lipid Productivity

[0105] The invention provides mutant microorganisms having at least 45% of the biomass productivity of a control microorganism and higher lipid productivity (e.g., higher productivity per day, preferably averaged over the culture period) with respect to the control microorganism when both the mutant microorganism and control microorganism are cultured under identical conditions in which the control microorganism culture is producing biomass. Biomass productivity can be assessed, for example, as ash-free dry weight (AFDW) production or productivity (i.e., amount produced per day) or total organic carbon (TOC) productivity. A mutant microorganism as provided herein can demonstrate greater lipid productivity than a control microorganism and at least 45% of the biomass productivity of the control microorganism over a culture period of at least three days, for example, a culture period of at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fourteen, at least fifteen, at least twenty, at least thirty, or at least sixty days when the mutant microorganism and the control microorganism are cultured under conditions that support growth of the control microorganism, i.e., under conditions in which the control microorganism culture produces biomass. In some examples the culture period in which a mutant microorganism as provided herein produces at least 45% of the biomass and produces more lipid with respect to a control microorganism can be less than 180 days, less than 120 days, or less than 90 days. In some examples, a mutant microorganism as provided herein produces higher amounts of lipid with respect to a control microorganism under culture conditions in which both the mutant and control microorganism are producing biomass and the mutant produces at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 105%, at least 110%, or at least 120% of the biomass produced by a control microorganism on a daily basis. In some examples, a mutant microorganism as provided herein produces higher amounts of lipid with respect to a control microorganism and at least 45% of the biomass but less than 300% or less than 325%, or less than 200% of the biomass produced by the control microorganism. In some examples, a mutant microorganism as provided herein produces higher amounts of lipid with respect to a control microorganism under culture conditions in which both the mutant and control microorganism are producing biomass and actively dividing.

[0106] Methods of measuring the amount of lipid produced by microorganisms are well-known in the art and provided in the examples herein. Total extractable lipid can be determined according to Folch et al. (1957) J. Biol. Chem. 226: 497-509; Bligh & Dyer (1959) Can. J. Biochem. Physiol. 37: 911-917; or Matyash et al. (2008) J. Lipid Res. 49:1137-1146, for example, and the percentage of biomass present as lipid can also be assessed using Fourier transform infrared spectroscopy (FT-IR) (Pistorius et al. (2008) Biotechnol & Bioengin. 103:123-129). Additional references for gravimetric analysis of FAME and TAGs are provided in U.S. Pat. No. 8,207,363 and WO 2011127118 for example, each incorporated herein by reference in its entirety. FAME analysis methods can also be found for example as American Oil Chemists' Society Methods Ce 1b-89 and Ce 1-62 (aocs.org/Methods/).

[0107] Biomass can be assessed by measuring total organic carbon (TOC) or by other methods, such as measuring ash-free dry weight (AFDW). Methods for measuring TOC are known in the art (e.g., U.S. Pat. No. 8,835,149) and are provided herein. Methods of measuring AFDW are also well-known and can be found, for example, in U.S. Pat. No. 8,940,508, incorporated herein by reference in its entirety.

[0108] A mutant microorganism can produce, for example, at least 25% more lipid than a control microorganism and at least 45% as much biomass as the control microorganism during a culture period of at least three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, twenty, thirty, or sixty days during which both the mutant and control microorganisms produce biomass. For example, the average daily lipid productivity can be at least 25% greater than the average daily lipid productivity of a control microorganism and the average daily biomass productivity can be at least 45% as much as the biomass productivity of the control microorganism during a culture period of at least three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, twenty, thirty, or sixty days. In additional examples, a mutant microorganism can produce at least about 50% more lipid than is produced by a control microorganism and at least 45% as much biomass as the control microorganism, i.e., can exhibit no more than a 55% reduction in biomass with respect to the control microorganism, under conditions in which the control microorganism is producing biomass. A mutant can in some examples produce less than 400% or less than 300% more lipid than a control microorganism while accumulating at least 45% as much biomass as the control microorganism during a culture period of at least three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, twenty, thirty, or sixty days.

[0109] The culture conditions under which a mutant as provided herein produces at least 25% or at least about 50% more FAME while producing at least 50% of the amount of TOC as a control microorganism can be nutrient replete, and can be nitrogen replete with respect to the control microorganism, that is, the culture conditions can be sufficient in nutrients with respect to the control microorganism such that additional nutrients do not increase the growth rate of the microorganism (where all other culture conditions and ingredients remain the same). For example, the culture conditions can be sufficient in nitrogen with respect to the control microorganism such that additional nitrogen do not increase the growth rate of the microorganism (where all other culture conditions and ingredients remain the same). Alternatively, in some embodiments the culture conditions under which a mutant as provided herein produces at least 25% or at least 50% more FAME (which can be the average daily FAME productivity) while producing at least 45% of the amount of TOC (e.g., the average daily TOC productivity) as a control microorganism can include nitrogen that supports biomass production, but at a lower rate than fully nitrogen replete culture media. For example, the culture conditions may allow for biomass (TOC or AFDW) production at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% the rate of biomass production in fully nitrogen replete culture media.

[0110] Mutant microorganisms disclosed herein can produce at least 25% more lipid, e.g., 25% more FAME, as is produced by a control microorganism, while producing at least 45% of the biomass of the control microorganism under conditions that support biomass production that is comparable to the levels of biomass of the control microorganism under nitrogen-replete conditions. For example, biomass production of the control microorganism can be within 20% or within 15% of the biomass production of the control microorganism under nitrogen-replete conditions. Alternatively or in addition, a mutant as provided herein can produce at least 45% of the biomass of the control microorganism while producing at least 25% more lipid than the control microorganism, where the mutant and control microorganism are cultured under conditions that are nitrogen replete with respect to the control microorganism. In various examples, the mutant can produce at least 45% of the biomass produced by a control cell and at least 25% more lipid than the control cell over the same time period in a culture that includes one or more of nitrate or urea, and in some examples can further optionally include less than about 5 mM ammonium, such as less than about 2.5 mM, ammonium, less than about 2 mM ammonium, less than about 1.5 mM ammonium, ammonium, less than about 1 mM ammonium, about 0.5 mM ammonium, or less than 0.5 mM ammonium.

[0111] In particular nonlimiting examples, a microorganism can be an algal or heterokont microorganism and can produce at least 25% more FAME while producing at least 45% of the amount of TOC as is produced by a control algal or heterokont microorganism in a culture medium that includes less than about 5 mM, less than about 4.5 mM, less than about 4 mM, less than about 3.5 mM, less than about 3 mM, less than about 2.5 mM, less than about 1 mM, or less than about 0.5 mM ammonium. For example, the ammonium concentration may be at a concentration ranging from about 0 to about 5 mM, from about 0 to about 4.0 mM, from about 0 to about 3 mM, from about 0 to about 2.5 mM, from about 0 to about 2.0 mM, from about 0 to about 1.5 mM, from about 0 to about 1.0 mM, or from about 0 to about 0.5 mM. The ammonium concentration may be at a concentration ranging from about from about 0.5 to about 5 mM, from about 0.5 to about 4 mM, from about 0.5 to about 3 mM, 0.5 to about 2.5 mM, from about 0.5 to about 2.0 mM, from about 0.5 to about 1.5 mM, about 0.5 to about 1 mM, or from about 1 to about 5 mM, about 1 to about 2.5 mM, or from about 0.1 to about 1 mM, from about 0.1 to about 1.5 mM, or from about 0.1 to about 2 mM. In further examples, the ammonium concentration may be at a concentration ranging from about 1 mM to about 2.5 mM or from about 0.2 to about 1.5 mM.

[0112] In some examples, a mutant microorganism can be an algal or heterokont cell that produces at least 25% more FAME while producing at least 45% of the amount of TOC as a control microorganism in a culture medium that includes about 2.5 mM ammonium or less, about 2.0 mM ammonium or less, about 1.5 mM ammonium or less, about 1.0 mM ammonium or less, about 0.5 mM ammonium or less, or substantially no ammonium, and can optionally include, for example, at least 1.0 mM, at least 2.0 mM, at least 3.0 mM, at least 4.0 mM, at least 5.0 mM, at least 6.0 mM, at least 7.0 mM, at least 8.0 mM, or at least 10.0 mM nitrate and/or urea. In further nonlimiting examples, a microorganism can be an algal or heterokont cell and can produce at least 50% more FAME while producing at least 45% of the amount of TOC as a control microorganism on a culture medium that includes less than about 5 mM, less than about 2.5 mM, less than about 1 mM, or less than about 0.5 mM ammonium. For example, a microorganism can be an algal or heterokont cell that produces at least 50% more FAME while producing at least 45% of the amount of TOC as a control microorganism in a culture medium that includes about 2.5 mM ammonium or less, about 1.0 mM ammonium or less, about 0.5 mM ammonium or less, or substantially no ammonium, and can include, for example, at least 1.0 mM, at least 2.0 mM, at least 3.0 mM, at least 4.0 mM, at least 5.0 mM, at least 6.0 mM, at least 7.0 mM, at least 8.0 mM, or at least 10.0 mM nitrate and/or urea.

[0113] The mutant microorganisms provided herein can have greater partitioning of carbon to lipid with respect to a control microorganism cultured under identical conditions in which both the control microorganism and the mutant microorganism are producing biomass. A mutant having increased partitioning of carbon to lipid with respect to a control microorganism can have increased partitioning of carbon to total extractable lipid, to total neutral lipids, to triglycerides, and/or to FAME-derivatizable lipids. For example, a mutant microorganism as provided herein can have a ratio of the amount of FAME-derivatizable lipids ("FAME") produced to biomass (TOC or ash-free dry weight (AFDW), for example) produced that is at least 50% higher than that of a control microorganism. Lipid and biomass production and/or production can be assessed, for example, by gravimetric analysis as known in the art and demonstrated in the examples herein. For example, a mutant microorganism as provided herein can have a ratio of FAME to TOC that is at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85, at least 90%, at least 95%, at least 100%, at least 110%, at least 120%, at least 130%, at least 140%, at least 150%, at least 160%, at least 170%, at least 180%, at least 190%, at least 200%, or at least 250% higher than the FAME/TOC ratio of a control microorganism when both the mutant microorganism and the control microorganism are cultured under conditions in which both the culture of the mutant microorganism and the culture of the control microorganism produce biomass. In some example, the FAME/TOC ratio of a mutant microorganism as provided herein can be increased with respect to the FAME/TOC ratio of a control microorganism cultured under identical conditions by less than about 300%.

[0114] In various examples a mutant microorganism as provided herein can have a ratio of the amount of FAME produced to TOC produced that is at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85, at least 90%, at least 95%, at least 100%, at least 110%, at least 120%, at least 130%, at least 140%, at least 150%, at least 160%, at least 170%, at least 180%, at least 190%, at least 200%, or at least 250% higher than the FAME/TOC ratio of a control microorganism when both the mutant microorganism and the control microorganism are cultured under conditions in which the control culture produces biomass (e.g., TOC) and the mutant culture produces at least 45%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95% of the amount of biomass that is produced by the control culture. In various examples, the FAME/TOC ratio of a mutant as provided herein can be at least 0.30, at least 0.35, at least 0.40, at least 0.45, at least 0.50, at least 0.55, at least 0.60, at least 0.65, at least 0.7, or at least 0.75 when cultured under conditions in which the mutant microorganism culture produces at least 45%, at least 50%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85, at least 90%, or at least 95% as much biomass (e.g., TOC) as a control microorganism culture, under conditions where both the control and mutant cultures produce biomass. In various examples, the FAME/TOC ratio of a mutant as provided herein can be at least 0.30, at least 0.35, at least 0.40, at least 0.45, at least 0.50, at least 0.55, at least 0.60, at least 0.65, at least 0.7, or at least 0.75 when cultured under conditions in which the mutant culture produces at least about 50%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85, at least 90%, at least 95%, or at least 100% as much biomass (e.g., TOC) as a control microorganism produces when cultured under nitrogen replete conditions.

[0115] In some examples, a mutant microorganism as provided herein can produce at least 50% more FAME while producing at least 80%, at least 85%, or at least 90% of the TOC produced by a control cell (such as a wild type cell) when cultured under conditions in which both the control and mutant microorganism produce biomass, and the FAME/TOC ratio of the mutant microorganism is at least 40%, at least 50%, at least 60%, at least 70%, or at least 75% higher than the FAME/TOC of the control microorganism. The FAME/TOC ratio of the mutant microorganism can be, for example, at least 0.30, at least 0.35, or at least 0.40. The culture conditions can include, for example, a culture medium that includes less than 5 mM, less than 2.5 mM, less than 2 mM, less than 1.5 mM, less than 1.0 mM, or less than 0.5 mM ammonium and can include at least 2 mM, at least 4 mM, or at least 6 mM urea or nitrate. In additional examples a mutant microorganism as provided herein can produce at least 60%, at least 70%, or at least 80% more FAME while producing at least 85%, at least 90%, or at least 95% of the TOC produced by a control cell (such as a wild type cell) when cultured under conditions in which both wild type and mutant microorganism are producing biomass, and the FAME/TOC ratio of the mutant microorganism is at least 50%, at least 60%, at least 70%, or at least 75% greater than the FAME/TOC ratio of the control microorganism. The FAME/TOC ratio of the mutant microorganism can be, for example, at least 0.35, at least 0.40, or at least 0.45. The culture conditions can include, for example, a culture medium that includes less than 2.5 mM, less than 1.0 mM, or less than 0.5 mM ammonium and can include at least 2 mM, at least 4 mM, or at least 6 mM urea or nitrate. The culture conditions can in some examples include substantially no ammonium, and in some examples can include substantially no reduced nitrogen as a nitrogen source.

[0116] In yet further examples a mutant microorganism as provided herein can produce at least 85%, at least 90%, at least 95%, at least 100%, at least 105%, at least 110%, or at least 115% more FAME while producing at least 70%, at least 75%, at least 80%, or at least 85% of the TOC produced by a control cell (such as a wild type cell) when cultured under conditions in which both wild type and mutant microorganism are producing biomass, and the FAME/TOC ratio of the mutant microorganism is at least 100%, at least 110%, at least 120%, at least 130%, at least 140%, at least 150%, at least 160%, at least 170%, or at least 180% greater than the FAME/TOC ratio of the control microorganism. FAME and TOC production can be assessed as average daily FAME productivity over the culture period, for example over a culture period of at least three, at least five, at least ten, at least twenty, at least thirty, or at least sixty days, or a culture period of between three and sixty days, or between three and thirty days, for example between three and fifteen days or between five and fifteen days. The FAME/TOC ratio of the mutant microorganism can be, for example, at least 0.50, at least 0.55, at least 0.60, at least 0.65, at least 0.70, or at least 0.75. The culture conditions can include, for example, a culture medium that includes less than 2.5 mM, less than 1.0 mM, or less than 0.5 mM ammonium and can include at least 2 mM, at least 4 mM, or at least 6 mM urea or nitrate.

[0117] In additional examples, a mutant microorganism can produce at least about 70% of the biomass produced by a wild type or control microorganism and at least 90% more lipid than is produced by a wild type or control microorganism when the mutant microorganism and wild type or control microorganism are cultured under the same conditions. FAME and TOC production can be assessed as average daily FAME productivity over the culture period, for example over a culture period of at least three, at least five, at least ten, at least twenty, at least thirty, or at least sixty days. For example the wild type and control microorganism can be cultured in batch, semi-continuous, or continuous culture for at least three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, twenty, thirty, or sixty days. In some examples the concentration of ammonium in the culture medium may be less than about 5 mM or less than about 2.5 mM. In some examples the culture medium may include at least 2 mM nitrate or at least 2 mM urea. The mutant microorganism can produce, in some examples, at least about 75% or at least about 80% of the biomass produced by a wild type or control microorganism and at least 100% or at least 110% more lipid than is produced by a wild type or control microorganism when the mutant microorganism and wild type or control microorganism are cultured under the same conditions. The FAME/TOC ratio can be at least 80%, at least 100%, at least 120%, or at least 150% greater than the FAME/TOC ratio of a wild type microorganism cultured under the same conditions. In some examples, the mutant microorganism can produce at least about 70% or at least about 75% of the biomass produced by a wild type or control microorganism and at least 100% or at least 120% more FAME lipids than are produced by a wild type or control microorganism when the mutant microorganism and wild type or control microorganism are cultured under the same conditions, and the mutant microorganism can have a FAME/TOC ratio at least 100% or at least 120% greater than the FAME/TOC ratio of a wild type microorganism cultured under the same conditions.

[0118] In various embodiments, a mutant microorganism as provided herein, e.g., a mutant microorganism such as any described herein that produces at least about 50% of the biomass and at least about 50%, at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 110%, at least 120%, at least 125%, or at least 130% more lipid than is produced by a control microorganism cultured under the same conditions, where the conditions support daily biomass accumulation by the control microorganism, can have a higher carbon to nitrogen (C:N) ratio than a control microorganism. For example, the C:N ratio can be from about 1.5 to about 2.5 the C:N ratio of a control microorganism when the mutant microorganism and the control microorganism are cultured under conditions in which both the mutant and the control microorganisms accumulate biomass, and the mutant produces at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 100% more lipid that the control microorganism and at least 50%, at least 60%, at least 70%, at least 80%, or at least 85% of the TOC of the control microorganism. In some embodiments the C:N ratio of a mutant as provided herein is between about 7 and about 20 or between about 8 and about 17, or between about 10 and about 15 during the culturing in which mutant produces at least 50% more lipid that a control microorganism while producing at least 50% as much biomass as the control microorganism. A control microorganism in any of the embodiments or examples herein can be a wild type microorganism.

[0119] Alternatively or in addition, mutant microorganism as provided herein, e.g., a mutant microorganism such as any described herein that produces at least about 50% of the biomass and at least about 50%, at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 110%, or at least 120% more lipid than is produced by a control microorganism cultured under the same conditions, where the conditions support daily biomass accumulation by the control microorganism, can have reduced protein content when compared with a control microorganism. For example, in some embodiments a mutant microorganism as provided herein can have a decrease in protein content of at least 10%, at least 20%, at least 30%, at least 40%, at least 45%, or at least 50% with respect to a control microorganism.

[0120] In various embodiments, a mutant microorganism as provided herein can have attenuated expression of a gene encoding a protein whose expression affects the expression of other genes, e.g., at least ten, at least twenty, at least thirty, at least forty, at least fifty, at least sixty, at least seventy, at least eighty, at least ninety, or at least 100 additional genes. For example, a mutant as provided herein can have at least ten genes that are upregulated with respect to a wild type microorganism and at least ten genes that are downregulated with respect to a wild type microorganism under conditions in which the mutant phenotype (greater lipid production) is expressed. A mutant as provided herein can have at least twenty, at least thirty, at least forty, at least fifty, at least sixty, at least seventy, at least eighty, at least ninety, or at least 100 genes that are upregulated with respect to a wild type microorganism and at least twenty, at least thirty, at least forty, at least fifty, at least sixty, at least seventy, at least eighty, at least ninety, or at least 100 genes that are downregulated with respect to a wild type microorganism under conditions in which the mutant phenotype (e.g., greater lipid production with respect to the wild type microorganism) is expressed. In some embodiments, genes encoding polypeptides involved in protein synthesis can be upregulated in a mutant as provided herein, for example, genes encoding ribosomal polypeptides or other polypeptides that function in translation, including, without limitation, those belonging to gene ontology (GO) groups such as "translation", "ribosome", "structural constituent of ribosome", "eukaryotic translation initiation factor 3 complex", "translation initiation factor activity", "translational initiation", "small ribosomal subunit", "formation of translation preinitiation complex", regulation of translation initiation, "eukaryotic 43S preinitiation complex", and "eukaryotic 48S preinitiation complex". Alternatively or in combination with the upregulation of genes encoding polypeptides relating to protein synthesis, any of various genes encoding polypeptides involved in nitrogen assimilation such as a molybdenum cofactor biosynthesis protein, a nitrate transporter, a nitrate reductase, a nitrite reductase, a glutamate synthase, a glutamine synthase, a glutamate dehydrogenase, and an ammonium transporter can be downregulated in a mutant as provided herein. Alternatively or in combination with any of the above, a mutant as provided herein can exhibit upregulation of certain genes related to lipid biosynthesis including but not limited to a lipid droplet surface protein and/or one or more desaturases, elongases, lipases, acyltransferases, and/or glyceraldehyde-3-phosphate dehydrogenases.

[0121] The properties of a mutant as provided herein having increased lipid production are compared to the same properties of a control microorganism that may be a wild type organism of the same species as the mutant, preferably the progenitor strain of the lipid-overproducing mutant. Alternatively, a control microorganism can be a microorganism that is substantially identical to the mutant microorganism with the exception that the control microorganism does not have the mutation that leads to higher lipid productivity. For example, a control microorganism can be a genetically engineered microorganism or classically mutated organism that has been further mutated or engineered to generate a mutant having increased lipid productivity and/or increased lipid partitioning as disclosed herein.

[0122] In some examples, a control microorganism can be a microorganism that is substantially identical to the mutant microorganism, with the exception that the control microorganism does not have a mutation in a gene or attenuated expression of a gene that regulates lipid induction (i.e., the gene whose mutation results in increased lipid production under conditions in which the mutant microorganism has at least about half the biomass productivity of the progenitor strain). The properties of a lipid-overproducing mutant having a disrupted, attenuated, or otherwise directly or indirectly genetically manipulated gene (resulting in altered structure or expression of the lipid induction regulator gene) are also be compared with the same properties of a control cell that does not have a disrupted, attenuated, or otherwise directly or indirectly genetically manipulated lipid induction regulator gene resulting in altered structure or expression of the lipid induction regulator gene (regardless of whether the cell is "wild-type"). For example, a control cell may be a recombinant cell or a cell mutated in a gene other than the lipid induction regulator gene whose effects are being assessed, etc.

[0123] Heterokont species considered for use in the invention include, but are not limited to, Bacillariophytes, Eustigmatophytes, Labrinthulids, and Thraustochytrids, such as, for example, species of Labryinthula, Labryinthuloides, Thraustochytrium, Schizochytrium, Aplanochytrium, Aurantiochytrium, Oblongichytrium, Japonochytrium, Diplophrys, or Ulkenia.

[0124] Mutant microorganisms having the properties disclosed herein, such as mutant microorganisms having attenuated expression of a gene that regulates lipid biosynthesis, such as the ZnCys-2845 gene of N. gaditana and orthologs thereof can be, in various examples, of any eukaryotic microalgal strain such as, for example, any species of any of the genera Achnanthes, Amphiprora, Amphora, Ankistrodesmus, Asteromonas, Boekelovia, Bolidomonas, Borodinella, Botrydium, Botryococcus, Bracteococcus, Chaetoceros, Carteria, Chlamydomonas, Chlorococcum, Chlorogonium, Chlorella, Chroomonas, Chrysosphaera, Cricosphaera, Crypthecodinium, Cryptomonas, Cyclotella, Desmodesmus, Dunaliella, Elipsoidon, Emiliania, Eremosphaera, Ernodesmius, Euglena, Eustigmatos, Franceia, Fragilaria, Fragilaropsis, Gloeothamnion, Haematococcus, Hantzschia, Heterosigma, Hymenomonas, Isochrysis, Lepocinclis, Micractinium, Monodus, Monoraphidium, Nannochloris, Nannochloropsis, Navicula, Neochloris, Nephrochloris, Nephroselmis, Nitzschia, Ochromonas, Oedogonium, Oocystis, Ostreococcus, Parachlorella, Parietochloris, Pascheria, Pavlova, Pelagomonas, Phceodactylum, Phagus, Picochlorum, Platymonas, Pleurochrysis, Pleurococcus, Prototheca, Pseudochlorella, Pseudoneochloris, Pseudostaurastrum, Pyramimonas, Pyrobotrys, Scenedesmus, Schizochlamydella, Skeletonema, Spyrogyra, Stichococcus, Tetrachlorella, Tetraselmis, Thalassiosira, Tribonema, Vaucheria, Viridiella, Vischeria, and Volvox. Non-limiting examples of particularly suitable species include, for instance, heterokont algae, such as but not limited to diatoms such as, for example, a species of any of the genera Amphora, Chaetoceros, Cyclotella, Fragilaria, Fragilaropsis, Hantzschia, Navicula, Nitzschia, Phceodactylum, or Thalassiosira, or Eustigmatophytes, e.g., Chloridella, Chlorobptrys, Ellipsoidion, Eustigmatos, Goniochloris, Monodopsis, Monodus, Nannochloropsis, Pseudocharaciopsis, Pseudostaruastrum, Pseudotetraedriella, or Vischeria. In some examples, the mutant alga cell is a species of Ellipsoidion, Eustigmatos, Monodus, Nannochloropsis, Pseudostaruastrum, Pseudotetraedriella, or Vischeria. In some examples, the mutant alga cell is a species of Nannochloropsis, e.g., N. gaditana, N. granulata, N. limnetica N. oceanica, N oculata, or N. salina.

[0125] The mutants can be spontaneous mutants, classically-derived mutants, or engineered mutants having attenuated expression of a regulator gene. For example, a mutant microorganism such as any described herein can be a mutant obtained by classical mutagenesis or genetic engineering. In particular embodiments, a mutant microorganism as provided herein is a genetically engineered mutant, for example, a microorganism into which at least one exogenous nucleic acid molecule has been introduced, e.g., into which at least one recombinant nucleic acid molecule has been introduced, where the mutant microorganism is genetically engineered to include the exogenous nucleic acid molecule and/or the exogenous nucleic acid molecule effects at least one alteration of the microorganism's genome.

[0126] In various examples, the mutant microorganism is an algal or heterokont species and has attenuated expression of a gene that encodes a polypeptide having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, or SEQ ID NO: 17 and/or has a coding region having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity SEQ ID NO: 1 or any of SEQ ID NOs:72-84. Alternatively or in addition, the mutant microorganism is an algal or heterokont species and has attenuated expression of a gene that encodes a polypeptide having an amino acid sequence with at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to amino acids 1-200 of SEQ ID NO:20 or to SEQ ID NO:18 or SEQ ID NO: 19. The mutant microorganism can in certain embodiments further include a domain having at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to any of SEQ ID NOs:21-25. The domain can be a PAS3 domain. The mutant microorganism can be engineered to attenuate expression of at least one gene encoding a polypeptide as set forth herein by any gene attenuation method, such as any disclosed herein or equivalents thereof.

[0127] The polypeptide encoded by the gene whose expression is attenuated can be a transcription factor protein of the Zn(II)2Cys6 fungal-type DNA-binding domain protein family. The polypeptide encoded by the gene whose expression is attenuated can include a Zn(2)Cys(6) domain, categorized as conserved domain cd00067 by the NCBI conserved domain database (ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml), referred to as the "GAL4-like Zn2Cys6 binuclear cluster DNA-binding domain" that is found in transcription factors such as GAL4, also characterized as smart00066: "GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain". This domain, which may be referred to herein as a Zn2Cys6, Zn.sub.2Cys.sub.6, or Zn(2)Cys(6) domain or simply a ZnCys domain, occurs at amino acids 190-219 of SEQ ID NO:2, is also characterized as pfam PF00172 ("Zn_Clus" or "Fungal Zn(2)-Cys(6) binuclear cluster domain") with a gathering cutoff for this family of 20.8. In some embodiments, a mutant as provided herein can have attenuated expression of a gene encoding a polypeptide having a Zn(2)Cys(6) domain having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:3.

[0128] Alternatively or in addition, the gene whose expression is attenuated can encode a polypeptide having a PAS_3 domain (pfam 08447, having a gathering cutoff of 25.6) also called "PAS fold domain" or simply a PAS domain, such as, for example, a PAS domain having at least at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to any of SEQ ID NOs:21-25.

[0129] The mutant microorganism having attenuated expression of a gene that regulates lipid production can be a "knockout" mutant, for example, in which the reading frame of the polypeptide is disrupted such that a functional protein is not produced. For example, the gene can include an insertion, deletion, or mutation in the reading frame that results in no functional protein being made. The insertion, deletion, or mutation can be made by various means, such as, for example, homologous recombination constructs, RNA-guided endonucleases that employ guide RNAs, optionally in combination with donor DNA fragments, etc. In other examples, the mutant microorganism can be a "knockdown" mutant in which expression of the gene is reduced with respect to a wild type cell. For example, transcript levels of the target gene, which may be, for example, a gene encoding a Zn(2)-C6 fungal-type DNA-binding domain protein, can be reduced between about 5% and about 95% or between about 10% and about 90% with respect to the transcript level in a control microorganism, such as a wild type microorganism. Knockdowns can be mutants in which a mutation, insertion, or deletion occurs in a non-coding region of the gene or can be effected by expressing constructs in the cells that reduce expression of the targeted gene, such as ribozyme, RNAi, or antisense constructs. In some embodiments gene attenuation can be effected by insertion of a DNA fragment into a noncoding region of the gene, such as a 5'UTR or 3' UTR. Insertion of a DNA fragment can optionally be by use of an RNA-guided endonuclease, e.g., a cas protein. The mutant microorganism having attenuated expression of a gene that regulates lipid production can include, for example, one or more of an RNAi construct for expressing RNAi or one or more RNAi molecules, an antisense construct for expressing antisense RNA or one or more antisense molecules, a ribozyme construct for expressing a ribozyme or one or more ribozymes, one or more guide RNAs, one or more constructs for expressing a guide RNA, one or more donor fragments for cas-mediated insertion, one or more homologous recombination constructs, one or more genes encoding a cas enzyme, or a cas enzyme, one or more genes encoding a TALEN, or one or more TALENs, or one or more meganucleases.

[0130] Thus, provided herein are microorganisms that have attenuated expression of a gene encoding a polypeptide of the Zn(II)2Cys6 family, i.e., a polypeptide that includes a "GAL4-like Zn2Cys6 binuclear cluster DNA-binding domain" (NCBI conserved domain cd00067) and/or recruits to pfam PF00172 ("Zn_Clus" or "Fungal Zn(2)-Cys(6) binuclear cluster domain") with a bit score greater than the gathering cutoff for this family of 20.8. Alternatively or in addition a mutant microorganism as provided herein may have attenuated expression of a gene encoding a polypeptide that includes a PAS domain (e.g., a "PAS3 domain" or "PAS fold domain") that may be characterized as PF08447 or PF00989. The mutant can produce more lipid that a control microorganism under culture conditions in which both the mutant and the control microorganism produce biomass and in which the mutant microorganism produces at least 50% of the biomass as is produced by the control microorganism. For example, the mutant microorganism can produce at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 110% or at least 120% more lipid that a control microorganism under culture conditions in which both the mutant and the control microorganism produce biomass and in which the mutant microorganism produces at least 50% of the biomass as is produced by the control microorganism. In various embodiments the microorganism that has attenuated expression of a gene encoding a polypeptide of the Zn(II)2Cys6 family and/or having a PAS domain produces at least 50% more the lipid and at least 50% of the biomass as is produced by a control microorganism on a daily basis for at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, or at least twelve-days of culturing. The mutant can include any of the properties described hereinabove, including, without limitation, increased FAME/TOC ratio under conditions in which the mutant produces more lipid that a control microorganism. The culture conditions under which the mutant produces a higher amount of lipid while producing at least 50% of the biomass as control microorganism can include less than 2.5 mM, less than 1.5 mM, less than 1 mM, or about 0.5 mM or less ammonium. The culture conditions under which the mutant produces a higher amount of lipid while producing at least 50% of the biomass as control microorganism can include a culture medium that includes nitrate, such as at least 2, 3, 4, or 5 mM nitrate. Alternatively or in addition, the culture conditions can include a culture medium that includes urea, such as at least 2, 3, 4, or 5 mM urea. The culture in some examples can provide nitrate as substantially the sole source of nitrogen available to the mutant and control microorganism. The control microorganism can be a wild type microorganism of the same species as the mutant, e.g., can be a wild type strain from which the mutant was derived. The microorganism can be an alga or a heterokont, and in some examples is a heterokont alga such as, but not limited to, a diatom or eustigmatophyte. In various examples lipid can be measured as FAME lipids, and biomass can be measured as, for example, TOC.

[0131] Alternatively or in addition, a mutant microorganism as provided herein having attenuated expression of a gene encoding a polypeptide of the Zn(II)2Cys6 family can demonstrate a FAME/TOC ratio that is at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85, at least 90%, at least 95%, at least 100%, at least 110%, at least 120%, at least 130%, at least 140%, at least 150%, at least 160%, at least 170%, at least 180%, at least 190%, at least 200%, or at least 250% higher than the FAME/TOC ratio of a control microorganism when both the mutant microorganism and the control microorganism are cultured under conditions in which the control culture produces biomass (e.g., TOC) and the mutant culture produces at least 45%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95% of the amount of biomass that is produced by the control culture. In an exemplary embodiment, a ZnCys attenuation strain can exhibit about twice the lipid productivity of a control strain (e.g., a wild type strain), while allocating approximately 35-70% of its carbon to lipid, for example, while allocating from about 40% to about 65% of its carbon to lipid, such as about 45%, 50%, 60%, or 65% of its carbon to lipid in a semicontinuous or continuous culture system. Further additionally or alternatively, a mutant microorganism as provided herein, e.g., a mutant microorganism having attenuated expression of a gene encoding a polypeptide of the Zn(II)2Cys6 family that produces at least about 50% of the biomass and at least about 50% more lipid than is produced by a control microorganism cultured under the same conditions, where the conditions support daily biomass accumulation by the control microorganism, can have a higher carbon to nitrogen (C:N) ratio than a control microorganism. For example, the C:N ratio can be from about 1.5 to about 2.5 the C:N ratio of a control microorganism when the mutant microorganism and the control microorganism are cultured under conditions in which both the mutant and the control microorganisms accumulate biomass, and the mutant produces at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 100% more lipid that the control microorganism and at least 50%, at least 60%, at least 70%, at least 80%, or at least 85% of the TOC of the control microorganism.

[0132] The gene whose expression is attenuated in a mutant that has higher lipid productivity than a control microorganism can be a gene encoding a polypeptide of the Zn(II)2Cys6 family that has at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, or SEQ ID NO: 18. Alternatively or in addition, the gene whose expression is attenuated can encode a polypeptide having a PAS3 domain (pfam08447), such as, for example, a PAS3 domain having at least at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to any of SEQ ID NOs:21-25.

[0133] A mutant microorganism as provided herein can be designed by targeting an endogenous gene of a microorganism of interest that encodes a polypeptide that includes a Zn2Cys6 domain as disclosed herein and/or a PAS3 domain as disclosed herein. Such genes can be identified in a microorganism of interest by bioinformatics methods, molecular biology techniques and combinations thereof. For example, a gene encoding a polypeptide that includes a Zn2Cys6 domain and/or a PAS3 domain can be identified using Southern hybridization, screening of cDNA libraries by hybridization or PCR, for example, using degenerate probes and/or primers. Genome sequences available in public or proprietary databases can be searched by any of a number of programs that perform sequence matching (blast programs) or analyze domain structures of encoded amino acid sequences. For example, hmmer.org provides software for analyzing structural and functional domains encoded by genes that can be used to scan genome sequences, including, for example, hmmsearch and hmmscan. Such searches can be done online. Programs such as MUSCLE and hmmalign can also be used to search for orthologs of proteins such as the proteins disclosed herein (e.g., ZnCys-2845 and orthologs) by constructing phylogenetic trees to determine relationships among proteins. In addition, sequence-based searches, including blastp, blastn, and tblastn (protein sequence queried against translated nucleotide sequence). Gene targeting can make use of the obtained sequences from the genome of the microorganism of interest. It is not necessary to resolve the complete structure of a gene to target the gene for attenuation. For example, using methods disclosed herein, including, without limitation, cas/CRISPR genome editing, RNAi constructs, antisense constructs, homologous recombination constructs, and ribozyme constructs, only a portion of a gene sequence can be employed in gene attenuation constructs and techniques.

Gene Attenuation

[0134] A mutant microorganism having attenuated expression of a gene that regulates lipid biosynthesis can be a mutant generated by any feasible method, including but not limited to UV irradiation, gamma irradiation, or chemical mutagenesis, and screening for mutants having increase lipid production, for example using the assays disclosed herein or by staining with lipophilic dyes such as Nile Red or BODIPY (e.g., Cabanelas et al. (2015) Bioresource Technology 184:47-52). Methods for generating mutants of microbial strains are well-known.

[0135] A mutant as provided herein that produces at least 25% more lipid while producing at least 50% of the biomass as the progenitor cell can also be a genetically engineered mutant, for example, a mutant in which a regulatory gene such as Zn(2)-C(6) fungal-type DNA-binding domain protein (e.g., ZnCys-2845 or an ortholog thereof, e.g., a gene encoding a polypeptide having at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2 or any of SEQ ID NOs:5-18) has been targeted by homologous recombination for knock-out or gene replacement (for example with mutated form of the gene that encodes a polypeptide having reduced activity with respect to the wild type polypeptide). For example, a microbial strain of interest may be engineered by site directed homologous recombination to insert a sequence into a genomic locus and thereby alter a gene and/or its expression, where the insertion can be, as nonlimiting examples, in the coding region of the gene, in an intron of the gene, in the 3' UTR or the gene, in the 5' UTR of the gene, or upstream of the transcriptional start site, i.e., in the promoter region of the gene.

[0136] For example, gene knockout or replacement by homologous recombination can be by transformation of a homologous recombination nucleic acid construct, i.e., a nucleic acid (e.g., DNA) fragment that includes a sequence homologous to the region of the genome to be altered, where the homologous sequence is interrupted by a foreign sequence, typically but not necessarily by a selectable marker gene that allows selection for the integrated construct. The genome-homologous flanking sequences on either side of the foreign sequence or mutated gene sequence can be for example, at least 20, at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1,000, at least 1,200, at least 1,500, at least 1,750, or at least 2,000 nucleotides in length. A gene knockout or gene "knock in" construct in which a foreign sequence is flanked by target gene sequences, can be provided in a vector that can optionally be linearized, for example, by cleavage at a site outside of the region that is to undergo homologous recombination, or can be provided as a linear fragment that is not in the context of a vector, for example, the knock-out or knock-in construct can be an isolated or synthesized fragment, including but not limited to a PCR product. In some instances, a split marker system can be used to generate gene knock-outs by homologous recombination, where two DNA fragments can be introduced that can regenerate a selectable marker and disrupt the gene locus of interest via three crossover events (Jeong et al. (2007) FEMSMicrobiol Lett 273: 157-163).

[0137] In one aspect the invention provides genetically modified organisms, e.g., microorganisms having one or more genetic modifications for attenuating expression of a lipid regulator gene such as a gene encoding a Zn(2)-C(6) fungal-type DNA-binding domain protein, that additionally may have at least 55% identity to any of SEQ ID NO:2 or SEQ ID NOs:5-18. As used herein "attenuating expression of a lipid regulator gene" means reducing or eliminating expression of the gene in any manner that reduces production of the fully functional lipid regulator protein. As used herein, "lipid regulator gene" refers to a gene whose attenuated expression in an organism or cell results in altered regulation of at least 50, at least 100, at least 200, or at least 300 genes in the organism or cell with respect to a control organism or cell and results in altered lipid productivity by the organism or cell. In an exemplary embodiment, a lipid regulator gene is a gene encoding a Zn(2)-C(6) fungal-type DNA-binding domain protein. Means for attenuating a lipid regulator gene include, for example, homologous recombination constructs; CRISPR systems, including one or more guide RNAs, a cas enzyme such but not limited to a Cas9 enzyme or a gene encoding a cas enzyme, and optionally, one or more donor fragments for insertion into a targeted site; RNAi constructs; shRNAs; antisense RNA constructs; ribozyme constructs; TALENS or genes encoding TALENs, Zinc Finger nucleases or genes encoding Zinc Finger nucleases; and meganucleases or genes encoding Zinc Finger nucleases.

[0138] For example, a recombinant microorganism engineered to have attenuated expression of a lipid regulator gene can have a disrupted lipid regulator gene that includes as least one insertion, mutation, or deletion that reduces or abolishes expression of the gene such that a fully functional lipid regulator gene is not produced or is produced in lower amounts than is produced by a control microorganism that does not include a disrupted lipid regulator gene. The disrupted lipid regulator gene can be disrupted by, for example, an insertion or gene replacement mediated by homologous recombination and/or by the activity of a meganuclease, zinc finger nuclease (Perez-Pinera et al. (2012) Curr. Opin. Chem. Biol. 16: 268-277), TALEN (WO 2014/207043; WO 2014/076571), or a cas protein (e.g., a Cas9 protein) of a CRISPR system.

[0139] CRISPR systems, reviewed recently by Hsu et al. (Cell 157:1262-1278, 2014) include, in addition to the cas nuclease polypeptide or complex, a targeting RNA, often denoted "crRNA", that interacts with the genome target site by complementarity with a target site sequence, a trans-activating ("tracr") RNA that complexes with the cas polypeptide and also includes a region that binds (by complementarity) the targeting crRNA.

[0140] The invention contemplates the use of two RNA molecules (a "crRNA" and a "tracrRNA") that can be co-transformed into a host strain (or expressed in a host strain) that expresses or is transfected with a cas protein for genome editing, or the use of a single guide RNA that includes a sequence complementary to a target sequence as well as a sequence that interacts with a cas protein. That is, in some strategies a CRISPR system as used herein can comprise two separate RNA molecules (a "tracr-RNA" and a "targeter-RNA" or "crRNA", see below) and referred to herein as a "two RNA molecule CRISPR system" "two RNA guide system" or a "Split guide RNA system". Alternatively, as illustrated in the examples, the DNA-targeting RNA can also include the trans-activating sequence for interaction with the cas protein (in addition to the target-homologous ("cr") sequences), that is, the DNA-targeting RNA can be a single RNA molecule and is referred to herein as a "chimeric guide RNA," a "single-guide RNA," or an "sgRNA." The terms "DNA-targeting RNA" and "gRNA" are inclusive, referring both to a two RNA guide system and to single-molecule DNA-targeting RNAs (i.e., sgRNAs). Both single-molecule guide RNAs and two RNA guide systems have been described in detail in the literature and for example, in U.S. Patent Application Publication No. US 2014/0068797, incorporated by reference herein in its entirety, and both are considered herein.

[0141] Any cas protein can be used in the methods herein, such as but not limited to, Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csn1 and Csx12), Cas10, Csy1, Csy2, Csy3, Cse1, Cse2, Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx15, Csf1, Csf2, Csf3, Csf4, homologs thereof, or modified versions thereof. The cas protein can be a Cas9 protein, such as a Cas9 protein of Staphylococcus pyogenes, S. thermophilus, S. pneumonia, S. aureus, or Neisseria meningitidis, as nonlimiting examples. Also considered are the Cas9 proteins provided as SEQ ID NOs: 1-256 and 795-1346 in U.S. Patent Application Publication No. US 2014/0068797, and chimeric Cas9 proteins that may combine domains from more than one cas9 protein, as well variants and mutants of identified Cas9 proteins. In additional examples, a cas protein used for genome modification can be a Cpf1 protein that uses a single RNA guide system, such as but not limited to a Cpf1 protein of Acidaminococcus or Lachnospiraceae (see for example Fagerlund et al. (2015) Genome Biol. 15:261; Zetsche et al. (2015) Cell 163:1-13); and European patent application EP3009511), as well as the C2c1, C2c2, C2c3 RNA-guided nucleases (Shmakov et al. (2015) Molecular Cell 60:1-13).

[0142] Cas nuclease activity cleaves target DNA to produce double strand breaks. These breaks are then repaired by the cell in one of two ways: non-homologous end joining or homology-directed repair. In non-homologous endjoining (NHEJ), the double-strand breaks are repaired by direct ligation of the break ends to one another. In this case, no new nucleic acid material is inserted into the site, although some nucleic acid material may be lost, resulting in a deletion, or altered, often resulting in mutation. In homology-directed repair, a donor polynucleotide (sometimes referred to as a "donor DNA" or "editing DNA") which may have homology to the cleaved target DNA sequence is used as a template for repair of the cleaved target DNA sequence, resulting in the transfer of genetic information from the donor polynucleotide to the target DNA. As such, new nucleic acid material may be inserted/copied into the site. The modifications of the target DNA due to NHEJ and/or homology-directed repair (for example using a donor DNA molecule) can lead to, for example, gene correction, gene replacement, gene tagging, transgene insertion, nucleotide deletion, gene disruption, gene mutation, etc.

[0143] In some instances, cleavage of DNA by a site-directed modifying polypeptide (e.g., a cas nuclease, zinc finger nuclease, meganuclease, or TALEN) may be used to delete nucleic acid material from a target DNA sequence by cleaving the target DNA sequence and allowing the cell to repair the sequence in the absence of an exogenously provided donor polynucleotide. Such NHEJ events can result in mutations ("mis-repair") at the site of rejoining of the cleaved ends that can resulting in gene disruption.

[0144] Alternatively, if a DNA-targeting RNA is co-administered to cells that express a cas nuclease along with a donor DNA, the subject methods may be used to add, i.e., insert or replace, nucleic acid material to a target DNA sequence (e.g., "knock out" by insertional mutagenesis, or "knock in" a nucleic acid that encodes a protein (e.g., a selectable marker and/or any protein of interest), an siRNA, an miRNA, etc., to modify a nucleic acid sequence (e.g., introduce a mutation), and the like.

[0145] A donor DNA can in particular embodiments include a gene regulatory sequence (e.g., a promoter) that can, using CRISPR targeting, be inserted upstream of the coding regions of the gene and upstream of the presumed proximal promoter region of the gene, for example, at least 50 bp, at least 100 bp, at least 120 bp, at least 150 bp, at least 200 bp, at least 250 bp, at least 300 bp, at least 350 bp, at least 400 bp, at least 450 bp, or at least 500 bp upstream of the initiating ATG of the coding region of the lipid regulator gene. The donor DNA can include a sequence, such as for example a selectable marker or any convenient sequence, that may be interfere with the native promoter. The additional sequence inserted upstream of the initiating ATG of the lipid regulator open reading frame (e.g., in the 5'UTR or upstream of the transcriptional start site of the lipid regulator gene) can decrease or even eliminate expression of the endogenous lipid regulator gene. Alternatively or in addition, the native lipid regulator gene can have its endogenous promoter wholly or partially replaced by a weaker or differently regulated promoter, or a non-promoter sequence.

[0146] In some examples, a nucleic acid molecule introduced into a host cell for generating a high efficiency genome editing cell line encodes a cas9 enzyme that is mutated to with respect to the corresponding wild-type enzyme such that the mutated cas9 enzyme lacks the ability to cleave one or both strands of a target polynucleotide containing a target sequence. For example, an aspartate-to-alanine substitution (D10A) in the RuvC I catalytic domain of Cas9 from S. pyogenes converts Cas9 from a nuclease that cleaves both strands to a nickase (an enzyme that cleaves a single strand). Other examples of mutations that render Cas9 a nickase include, without limitation, H840A, N854A, and N863A. In some embodiments, a Cas9 nickase may be used in combination with guide sequence(s), e.g., two guide sequences, which target respectively sense and antisense strands of the DNA target. This combination allows both strands to be nicked and used to induce NHEJ. Two nickase targets (within close proximity but targeting different strands of the DNA) can be used to inducing mutagenic NHEJ. Such targeting of a locus using enzymes that cleave opposite strains at staggered positions can also reduce nontarget cleavage, as both strands must be accurately and specifically cleaved to achieve genome mutation.

[0147] In additional examples, a mutant cas9 enzyme that is impaired in its ability to cleave DNA can be expressed in the cell, where one or more guide RNAs that target a sequence upstream of the transcriptional or translational start site of the targeted gene are also introduced. In this case, the cas enzyme may bind the target sequence and block transcription of the targeted gene (Qi et al. (2013) Cell 152:1173-1183). This CRISPR interference of gene expression can be referred to as RNAi and is also described in detail in Larson et al. (2013) Nat. Protoc. 8: 2180-2196.

[0148] In some cases, a cas polypeptide such as a Cas9 polypeptide is a fusion polypeptide, comprising, e.g.: i) a Cas9 polypeptide (which can optionally be variant Cas9 polypeptide as described above); and b) a covalently linked heterologous polypeptide (also referred to as a "fusion partner"). A heterologous nucleic acid sequence may be linked to another nucleic acid sequence (e.g., by genetic engineering) to generate a chimeric nucleotide sequence encoding a chimeric polypeptide. In some embodiments, a Cas9 fusion polypeptide is generated by fusing a Cas9 polypeptide with a heterologous sequence that provides for subcellular localization (i.e., the heterologous sequence is a subcellular localization sequence, e.g., a nuclear localization signal (NLS) for targeting to the nucleus; a mitochondrial localization signal for targeting to the mitochondria; a chloroplast localization signal for targeting to a chloroplast; an ER retention signal; and the like). In some embodiments, the heterologous sequence can provide a tag (i.e., the heterologous sequence is a detectable label) for ease of tracking and/or purification (e.g., a fluorescent protein, e.g., green fluorescent protein (GFP), YFP, RFP, CFP, mCherry, tdTomato, and the like; a hemagglutinin (HA) tag; a FLAG tag; a Myc tag; and the like).

[0149] Host cells can be genetically engineered (e.g., transduced or transformed or transfected) with, for example, a vector construct that can be, for example, a vector for homologous recombination that includes nucleic acid sequences homologous to a portion of a lipid regulator gene locus of the host cell or to regions adjacent thereto, or can be an expression vector for the expression of any or a combination of: a cas protein (e.g., a cas9 protein), a CRISPR chimeric guide RNA, a crRNA, and/or a tracrRNA, an RNAi construct (e.g., a shRNA), an antisense RNA, or a ribozyme. The vector can be, for example, in the form of a plasmid, a viral particle, a phage, etc. A vector for expression of a polypeptide or RNA for genome editing can also be designed for integration into the host, e.g., by homologous recombination. A vector containing a polynucleotide sequence as described herein, e.g., sequences having homology to host lipid regulator gene sequences (including sequences that are upstream and downstream of the lipid regulator-encoding sequences), as well as, optionally, a selectable marker or reporter gene, can be employed to transform an appropriate host to cause attenuation of a lipid regulator gene.

[0150] The recombinant microorganism in some examples can have reduced but not abolished expression of the lipid regulator gene, and the recombinant microorganism can have an increase in lipid production of from about 25% to about 200% or more, for example. A genetically modified microorganism as provided herein can in some examples include a nucleic acid construct for attenuating the expression of a lipid regulator gene, such as, for example, a gene encoding a polypeptide having at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2 or any of SEQ ID NO:5-18. For example, a host microorganism can include a construct for expressing an RNAi molecule, ribozyme, or antisense molecule that reduces expression of a lipid regulator gene encoding a polypeptide having at least 55% identity to SEQ ID NO:2 or any of SEQ ID NO:5-18. In some examples, a recombinant microorganism as provided herein can include at least one introduced (exogenous or non-native) construct for reducing expression of a lipid regulator gene.

[0151] In some examples, engineered strains can be selected for expression of a lipid regulator gene that is decreased with respect to a control cell that does not include a genetic modification for attenuating lipid regulator gene expression, but not eliminated, using methods known in the art, such as, for example, RNA-Seq or reverse transcription-PCR (RT-PCR).

[0152] A genetically engineered strain as provided herein can be engineered to include a construct for attenuating gene expression by reducing the amount, stability, or translatability of mRNA of a gene encoding a lipid regulator. For example, a microorganism such as an algal or heterokont strain can be transformed with an antisense RNA, RNAi, or ribozyme construct targeting an mRNA of a lipid regulator gene using methods known in the art. For example, an antisense RNA construct that includes all or a portion of the transcribed region of a gene can be introduced into a microorganism to decrease gene expression (Shroda et al. (1999) The Plant Cell 11:1165-78; Ngiam et al. (2000) Appl. Environ. Microbiol. 66: 775-782; Ohnuma et al. (2009) Protoplasma 236: 107-112; Lavaud et al. (2012) PLoS One 7:e36806). Alternatively or in addition, an RNAi construct (for example, a construct encoding a short hairpin RNA) targeting a gene having a Zn(2)Cys(6) domain can be introduced into a microorganism such as an alga or heterokont for reducing expression of the lipid regulator gene (see, for example, Cerruti et al. (2011) Eukaryotic Cell (2011) 10: 1164-1172; Shroda et al. (2006) Curr. Genet. 49:69-84).

[0153] Ribozymes are RNA-protein complexes that cleave nucleic acids in a site-specific fashion. Ribozymes have specific catalytic domains that possess endonuclease activity. For example, U.S. Pat. No. 5,354,855 reports that certain ribozymes can act as endonucleases with a sequence specificity greater than that of known ribonucleases and approaching that of the DNA restriction enzymes. Catalytic RNA constructs (ribozymes) can be designed to base pair with an mRNA encoding a gene as provided herein to cleave the mRNA target. In some examples, ribozyme sequences can be integrated within an antisense RNA construct to mediate cleavage of the target. Various types of ribozymes can be considered, their design and use is known in the art and described, for example, in Haseloff et al. (1988) Nature 334:585-591.

[0154] Ribozymes are targeted to a given sequence by virtue of annealing to a site by complimentary base pair interactions. Two stretches of homology are required for this targeting. These stretches of homologous sequences flank the catalytic ribozyme structure defined above. Each stretch of homologous sequence can vary in length from 7 to 15 nucleotides. The only requirement for defining the homologous sequences is that, on the target RNA, they are separated by a specific sequence which is the cleavage site. For hammerhead ribozyme, the cleavage site is a dinucleotide sequence on the target RNA is a uracil (U) followed by either an adenine, cytosine or uracil (A, C or U) (Thompson et al., (1995) Nucl Acids Res 23:2250-68). The frequency of this dinucleotide occurring in any given RNA is statistically 3 out of 16. Therefore, for a given target messenger RNA of 1,000 bases, 187 dinucleotide cleavage sites are statistically possible.

[0155] The general design and optimization of ribozyme directed RNA cleavage activity has been discussed in detail (Haseloff and Gerlach (1988) Nature 334:585-591; Symons (1992) Ann Rev Biochem 61: 641-71; Chowrira et al. (1994) J Biol Chem 269:25856-64; Thompson et al. (1995) supra), all incorporated by reference in their entireties. Designing and testing ribozymes for efficient cleavage of a target RNA is a process well known to those skilled in the art. Examples of scientific methods for designing and testing ribozymes are described by Chowrira et al., (1994) supra and Lieber and Strauss (1995) Mol Cell Biol. 15: 540-51, each incorporated by reference. The identification of operative and preferred sequences for use in down regulating a given gene is a matter of preparing and testing a given sequence, and is a routinely practiced "screening" method known to those of skill in the art.

[0156] The use of RNAi constructs is described in literature cited above as well as in US2005/0166289 and WO 2013/016267, for example. A double stranded RNA with homology to the target gene is delivered to the cell or produced in the cell by expression of an RNAi construct, for example, an RNAi short hairpin (sh) construct. The construct can include a sequence that is identical to the target gene, or at least 70%, 80%, 90%, 95%, or between 95% and 100% identical to a sequence of the target gene. The construct can have at least 20, at least 30, at least 40, at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, or at least 1 kb of sequence homologous to the target gene. Expression vectors can be engineered using promoters selected for continuous or inducible expression of an RNAi construct, such as a construct that produces an shRNA.

[0157] A nucleic acid construct for gene attenuation, e.g., a ribozyme, RNAi, or antisense construct can include at least fifteen, at least twenty, at least thirty, at least forty, at least fifty, or at least sixty nucleotides having at least 80% identity, such as at least 85%, at least 90%, at least 95%, or at least 99% or complementarity to at least a portion of the sequence of an endogenous lipid regulator gene of the microorganism to be engineered. A nucleic acid construct for gene attenuation, e.g., a ribozyme, RNAi, or antisense construct can include at least fifteen, at least twenty, at least thirty, at least forty, at least fifty, or at least sixty nucleotides having at least 80%, such as at least 95% or about 100%, identity or complementarity to the sequence of a naturally-occurring gene, such as a gene having encoding a polypeptide having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80% or at least 85%, at least 90%, or at least 95% sequence identity to an endogenous lipid regulator gene. For example, a nucleic acid construct for gene attenuation, e.g., a ribozyme, RNAi, or antisense construct can include at least fifteen, at least twenty, at least thirty, at least forty, at least fifty, or at least sixty nucleotides having at least 80% identity or complementarity to the sequence of a naturally-occurring lipid regulator gene, such as any provided herein. The nucleotide sequence can be, for example, from about 30 nucleotides to about 3 kilobases or greater, for example, from 30-50 nucleotides in length, from 50 to 100 nucleotides in length, from 100 to 500 nucleotides in length, from 500 nucleotides to 1 kb in length, from 1 kb to 2 kb in length, or from 2 to 5 kb. For example, an antisense sequence can be from about 100 nucleotides to about 1 kb in length. For example, a nucleic acid construct for gene attenuation, e.g., a ribozyme, RNAi, or antisense construct can include at least fifteen, at least twenty, at least thirty, at least forty, at least fifty, at least sixty, or at least 100 nucleotides having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, or at least 85%, for example at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, or at least 95% identity or complementarity to an endogenous lipid regulator gene or a portion thereof.

[0158] Promoters used in antisense, RNAi, or ribozyme constructs can be any that are functional in the host organism and that are suitable for the levels of expression required for reducing expression of the target gene to a desired amount. Promoters functional in algae and heterokonts are known in the art and disclosed herein. The construct can be transformed into algae using any feasible method, include any disclosed herein. A recombinant organism or microorganism transformed with a nucleic acid molecule for attenuating lipid regulator gene expression, such as but not limited to an antisense, RNAi, or ribozyme construct, can have the properties of a lipid regulator mutant as described herein, including, for example, reduced chlorophyll, increased photosynthetic efficiency, and increased productivity in culture, with respect to a host organism or microorganism that does not include the exogenous nucleic acid molecule that results in attenuated gene expression.

[0159] In additional examples, such as disclosed in Examples herein, gene attenuation that decreases but does not eliminate expression of the target gene can be achieved through the use of homologous recombination or CRISPR/Cas9 genome editing where the donor fragment is targeted for insertion into a non-coding region of a gene. For example, a selectable marker cassette or other donor fragment can be targeted by the use of an appropriate guide RNA to the 5' UTR, 3' UTR, or an intron of a gene whose reduced expression is desired. Thus, another aspect of the invention is a method for attenuating expression of a gene the includes inserting a nucleic acid fragment into a site upstream of the translational start site or downstream of a translational termination site, wherein the expression level of the gene is reduced. As nonlimiting examples, a donor fragment insertion can be introduced into a region up to 2 kb upstream of the translational start site of a gene, or up to 2 kb downstream of the termination codon of a gene. For example, an insertion that is targeted to a site of between about 5 bp and 2 kb upstream of the translational start site, or between about 10 bp and 1.5 kb upstream of the translational start site, or between about 10 bp and about 1.2 kb upstream of the translational start site, or between about 20 bp and about 1 kb upstream of the translational start site. Alternatively or in addition, an insertion can be targeted to the 3' UTR of a gene. Alternatively or in addition, an insertion that is targeted to a site of between about 5 bp and 2 kb downstream of the translational termination site (stop codon), or between about 10 bp and 1.5 kb downstream of the stop codon, or between about 10 bp and about 1.2 kb downstream of the stop codon, or between about 20 bp and about 1 kb downstream of the stop codon. Without being limited to any particular mechanism, such insertions may reduce the rate or transcription of a gene or may reduce the stability of a resulting transcript.

Nucleic Acid Molecules and Constructs

[0160] Also provided herein are nucleic acid molecules encoding polypeptides that include amino acid sequences having at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO: 16, or SEQ ID NO: 17. Alternatively or in addition, a nucleic acid molecule as provided herein can include a sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO: 1 or any of SEQ ID NOs:72-84. The polypeptide having at least 60% identity to an amino acid sequence selected from the group consisting of SEQ ID NO:2 and SEQ ID NOs:5-17 or encoded by SEQ ID NO:1 or any of SEQ ID NOs:72-84 can include an amino acid sequence encoding a Zn(2)Cys(6) domain, e.g., a domain belonging to pfam PF00172. For example, the polypeptide encoded by the nucleic acid molecule can include a Zn(2)Cys(6) domain having an amino acid sequence with at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:3. Alternatively or in addition, a polypeptide encoded by a nucleic acid molecule as provided herein can optionally further include a PAS (or PAS3) domain. For example a polypeptide encoded by a nucleic acid molecule as provided herein can include a PAS domain having at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to any of SEQ ID NO:21-SEQ ID NO:25.

[0161] The nucleic acid molecule in various examples can be or comprise a cDNA that lacks one or more introns present in the naturally-occurring gene, or, alternatively, can include one or more introns not present in the naturally-occurring gene. The nucleic acid molecule in various examples can have a sequence that is not 100% identical to a naturally-occurring gene. For example, the nucleic acid molecule can include a mutation with respect to a naturally-occurring gene that reduces the activity of the encoded polypeptide or reduces expression of the mRNA or protein encoded by the gene.

[0162] The nucleic acid molecule in various examples can comprise a heterologous promoter operably linked to the sequence encoding a polypeptide that includes an amino acid sequence having at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, or SEQ ID NO: 17 and/or can comprise a heterologous promoter operably linked to a sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO: 1 or any of SEQ ID NOs:72-84. Alternatively or in addition, a nucleic acid molecule can comprise a vector that includes a sequence encoding a polypeptide that includes an amino acid sequence having at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO:17 and/or has at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:1 or any of SEQ ID NOs:72-84.

[0163] A further aspect of the invention is a construct designed for attenuating expression of a gene encoding a Zn(2)Cys(6) DNA-binding domain polypeptide. The construct can be or comprise, in various examples, a sequence encoding a guide RNA of a CRISPR system, an RNAi construct, an antisense construct, a ribozyme construct, or a construct for homologous recombination, e.g., a construct having one or more nucleotide sequences having homology to a naturally-occurring Zn(2)Cys(6) domain-encoding gene as disclosed herein and/or sequences adjacent thereto in the native genome from which the gene is derived. For example, the construct can include at least a portion of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, e.g., a sequence homologous to at least a portion of an gene that encodes a polypeptide that includes an amino acid sequence having at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, or SEQ ID NO: 17 or can include at least a portion of a nucleic acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:1 or any of SEQ ID NOs:72-84.

[0164] The construct for gene attenuation can include, for example, at least a portion of the coding region of a gene encoding a polypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17 or at least a portion of a gene having at least 50% identity to SEQ ID NO: 1 or any of SEQ ID NOs:72-84, at least a portion of an intron of a gene encoding a polypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17, at least a portion of a 5'UTR of a gene encoding a polypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17, at least a portion of the promoter region of a gene encoding a polypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17, and/or at least a portion of a 3' UTR of a gene encoding a polypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17. In some examples, the construct can be an RNAi, ribozyme, or antisense construct and can include a sequence from the transcribed region of the gene encoding a polypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17 in either sense or antisense orientation.

[0165] In further examples a construct can be designed for the in vitro or in vivo expression of a guide RNA (e.g., of a CRISPR system) designed to target a gene having a sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to at least a portion of SEQ ID NO: 1 or any of SEQ ID NOs:72-84 or coding a polypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17, and can include a sequence homologous to a portion of a gene encoding a polypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17, including, for example, an intron, a 5'UTR, a promoter region, and/or a 3' UTR of a gene encoding a polypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17. In yet further examples, a construct for attenuating expression a gene encoding a Zn(2)Cys(6) domain-containing polypeptide can be a guide RNA or antisense oligonucleotide, where the sequence having homology to a transcribed region of a gene encoding a polypeptide having a Zn(2)Cys(6) domain in antisense orientation.

[0166] Further provided are guide RNAs for attenuating expression of a Zn(2)Cys(6) gene or a gene encoding a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17, and DNA constructs encoding such guide RNAs. The guide RNAs can be chimeric or single guide RNAs or can be guide RNAs that include a tracr mate sequence but require an additional tracr RNA to effect genome editing. In various embodiments, provided herein is a nucleic acid molecule having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to at least a portion of SEQ ID NO: 1 or any of SEQ ID NOs:72-84, where the nucleic acid molecule encodes a guide RNA of a CRISPR system, that can be, as nonlimiting examples, a Cas9/CRISPR system or a Cpf1 CRISPR system. The nucleic acid molecule can include, for example at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 nucleotides of sequence of a naturally occurring Zn(2)Cys(6) gene, such as SEQ ID NO: 1 or any of SEQ ID NOs:72-84. In exemplary embodiments, the guide RNA or nucleic acid sequence encoding the guide RNA can include any of SEQ ID NOs:51-62 or sequences having at least 88% or 93% identity to any thereof.

[0167] In addition, provided herein are antisense, ribozyme, or RNAi constructs that include at least a portion of a gene having encoding a Zn(2)Cys(6) or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17, in which a promoter, such as a heterologous promoter, is operably linked to the Zn(2)Cys(6) gene sequence and the Zn(2)Cys(6) gene sequence is in antisense orientation.

[0168] Further, provided herein are constructs for homologous recombination that include at least one sequence from a Zn(2)Cys(6) gene locus of the genome of an alga juxtaposed with a heterologous nucleic acid sequence that can be, in nonlimiting examples, a selectable marker or detectable marker gene. In some examples a construct for homologous recombination includes two nucleic acid sequences from a Zn(2)Cys(6) gene locus of the genome of an alga where the two sequences flank a heterologous sequence for insertion into the Zn(2)Cys(6) gene locus.

[0169] One skilled in the art will appreciate that a number of transformation methods can be used for genetic transformation of microorganisms and, therefore, can be deployed for the methods of the present invention. "Stable transformation" is intended to mean that the nucleic acid construct introduced into an organism integrates into the genome of the organism or is part of a stable episomal construct and is capable of being inherited by the progeny thereof. "Transient transformation" is intended to mean that a polynucleotide is introduced into the organism and does not integrate into the genome or otherwise become established and stably inherited by successive generations.

[0170] Genetic transformation can result in stable insertion and/or expression of transgenes, constructs from either the nucleus or the plastid, and in some cases can result in transient expression of transgenes. The transformation methods can also be used for the introduction of guide RNAs or editing DNAs. Genetic transformation of microalgae has been reported successful for more than 30 different strains of microalgae, which belong to at least .about.22 species of green, red, and brown algae, diatoms, euglenids, and dianoflagellates (see, e.g., Radakovits et al., Eukaryotic Cell, 2010; and Gong et al., J Ind. Microbiol. Biotechnol., 2011). Non-limiting examples of such useful transformation methods include agitation of cells in the presence of glass beads or silicon carbide whiskers as reported by, for example, Dunahay, Biotechniques, 15(3):452-460, 1993; Kindle, Proc. Natl. Acad. Sci. U.S.A., 1990; Michael and Miller, Plant J., 13, 427-435, 1998. Electroporation techniques have been successfully used for genetic transformation of several microalgal species including Nannochloropsis sp. (see, e.g., Chen et al., J. Phycol., 44:768-76, 2008), Chlorella sp. (see, e.g., Chen et al., Curr. Genet., 39:365-370, 2001; Chow and Tung, Plant Cell Rep. Vol. 18, No. 9, 778-780, 1999), Chlamydomonas (Shimogawara et al., Genetics, 148: 1821-1828, 1998), Dunaliella (Sun et al., Mol. Biotechnol., 30(3): 185-192, 2005). Micro-projectile bombardment, also referred to as microparticle bombardment, gene gun transformation, or biolistic bombardment, has been used successfully for several algal species including, for example, diatoms species such as Phaeodactylum (Apt et al., Mol. Gen. Genet., 252:572-579, 1996), Cyclotella and Navicula (Dunahay et al., J. Phycol., 31:1004-1012, 1995), Cylindrotheca (Fischer et al., J Phycol., 35:113-120, 1999), and Chaetoceros sp. (Miyagawa-Yamaguchi et al., Phycol. Res. 59: 113-119, 2011), as well as green algal species such as Chlorella (El-Sheekh, Biologia Plantarum, Vol. 42, No. 2: 209-216, 1999), and Volvox species (Jakobiak et al., Protist, 155:381-93, 2004). Additionally, Agrobacterium-mediated gene transfer techniques can also be useful for genetic transformation of microalgae, as has been reported by, for example, Kumar, Plant Sci., 166(3):731-738, 2004, and Cheney et al., J Phycol., Vol. 37, Suppl. 11, 2001.

[0171] A transformation vector or construct as described herein will typically comprise a marker gene that confers a selectable or scorable phenotype on target host cells, e.g., algal cells or may be co-transformed with a construct that includes a marker. A number of selectable markers have been successfully developed for efficient isolation of genetic transformants of algae. Common selectable markers include antibiotic resistance, fluorescent markers, and biochemical markers. Several different antibiotic resistance genes have been used successfully for selection of microalgal transformants, including blastocydin, bleomycin (see, for example, Apt et al., 1996, supra; Fischer et al., 1999, supra; Fuhrmann et al., Plant J., 19, 353-61, 1999, Lumbreras et al., Plant J., 14(4):441-447, 1998; Zaslavskaia et al., J. Phycol., 36:379-386, 2000), spectinomycin (Cerutti et al., Genetics, 145: 97-110, 1997; Doetsch et al., Curr. Genet., 39, 49-60, 2001; Fargo, Mol. Cell. Biol., 19:6980-90, 1999), streptomycin (Berthold et al., Protist, 153:401-412, 2002), paromomycin (Jakobiak et al., Protist, supra.; Sizova et al., Gene, 277:221-229, 2001), nourseothricin (Zaslavskaia et al., 2000, supra), G418 (Dunahay et al., 1995, supra; Poulsen and Kroger, FEBS Lett., 272:3413-3423, 2005, Zaslavskaia et al., 2000, supra), hygromycin (Berthold et al., 2002, supra), chloramphenicol (Poulsen and Kroger, 2005, supra), and many others. Additional selectable markers for use in microalgae such as Chlamydomonas can be markers that provide resistance to kanamycin and amikacin resistance (Bateman, Mol. Gen. Genet. 263:404-10, 2000), zeomycin and phleomycin (e.g., ZEOCIN.TM. pheomycin D1) resistance (Stevens, Mol. Gen. Genet. 251:23-30, 1996), and paramomycin and neomycin resistance (Sizova et al., 2001, supra). Other fluorescent or chromogenic markers that have been used include luciferase (Falciatore et al., J. Mar. Biotechnol., 1: 239-251, 1999; Fuhrmann et al., Plant Mol. Biol., 2004; Jarvis and Brown, Curr. Genet., 19: 317-322, 1991), .beta.-glucuronidase (Chen et al., 2001, supra; Cheney et al., 2001, supra; Chow and Tung, 1999, supra; El-Sheekh, 1999, supra; Falciatore et al., 1999, supra; Kubler et al., J Mar. Biotechnol., 1:165-169, 1994), .beta.-galactosidase (Gan et al., J Appl. Phycol., 15:345-349, 2003; Jiang et al., Plant Cell Rep., 21:1211-1216, 2003; Qin et al., High Technol. Lett., 13:87-89, 2003), and green fluorescent protein (GFP) (Cheney et al., 2001, supra; Ender et al., Plant Cell, 2002, Franklin et al., Plant J., 2002; 56, 148, 210).

[0172] One skilled in the art will readily appreciate that a variety of known promoter sequences can be usefully deployed for transformation systems of microalgal species in accordance with the present invention. For example, the promoters commonly used to drive transgene expression in microalgae include various versions of the of cauliflower mosaic virus promoter 35S (CaMV35S), which has been used in both dinoflagellates and chlorophyta (Chow et al, Plant Cell Rep., 18:778-780, 1999; Jarvis and Brown, Curr. Genet., 317-321, 1991; Lohuis and Miller, Plant J., 13:427-435, 1998). The SV40 promoter from simian virus has also reported to be active in several algae (Gan et al., J. Appl. Phycol., 151 345-349, 2003; Qin et al., Hydrobiologia 398-399, 469-472, 1999). The promoters of RBCS2 (ribulose bisphosphate carboxylase, small subunit) (Fuhrmann et al., Plant J., 19:353-361, 1999) and PsaD (abundant protein of photosystem I complex; Fischer and Rochaix, FEBS Lett. 581:5555-5560, 2001) from Chlamydomonas can also be useful. The fusion promoters of HSP70A/RBCS2 and HSP70A/.beta.2TUB (tubulin) (Schroda et al., Plant J., 21:121-131, 2000) can also be useful for an improved expression of transgenes, in which HSP70A promoter may serve as a transcriptional activator when placed upstream of other promoters. High-level expression of a gene of interest can also be achieved in, for example diatoms species, under the control of a promoter of an fcp gene encoding a diatom fucoxanthin-chlorophyll a/b binding protein (Falciatore et al., Mar. Biotechnol., 1:239-251, 1999; Zaslavskaia et al., J. Phycol. 36:379-386, 2000) or the vcp gene encoding a eustigmatophyte violaxanthin-chlorophyll a/b binding protein (see U.S. Pat. No. 8,318,482). If so desired, inducible promoters can provide rapid and tightly controlled expression of genes in transgenic microalgae. For example, promoter regions of the NR genes encoding nitrate reductase can be used as such inducible promoters. The NR promoter activity is typically suppressed by ammonium and induced when ammonium is replaced by nitrate (Poulsen and Kroger, FEBS Lett 272:3413-3423, 2005), thus gene expression can be switched off or on when microalgal cells are grown in the presence of ammonium/nitrate. Additional algal promoters that can find use in the constructs and transformation systems provided herein include those disclosed in U.S. Pat. No. 8,883,993; U.S. Patent Appl. Pub. No. US 2013/0023035; U.S. Patent Application Pub. No. US 2013/0323780; and U.S. Patent Application Pub. No. US 2014/0363892.

[0173] Host cells can be either untransformed cells or cells that are already transfected with at least one nucleic acid molecule. For example, an algal host cell that is engineered to have attenuated expression of a lipid regulator gene can further include one or more genes that may confer any desirable trait, such as, but not limited to, increased production of biomolecules of interest, such as one or more proteins, pigments, alcohols, or lipids.

Methods of Producing Lipids

[0174] Also provided herein are methods of producing lipid by culturing a mutant microorganism as provided herein that has increased lipid productivity with respect to a control cell while producing at least 45% of the biomass produced by a control cell under the same culture conditions. The methods include culturing a mutant microorganism as provided herein in a suitable medium to produce lipid and recovering biomass or at least one lipid from the culture. The microorganism can in some examples be an alga, and the culture can be a photoautotrophic culture. Culturing can be in batch, semi-continuous, or continuous mode.

[0175] The mutant microorganism in some examples can be cultured in a medium that comprises less than about 5 mM ammonium, for example, less than about 2.5 mM ammonium, less than about 2 mM ammonium, less than about 1.5 mM ammonium, less than or equal to about 1 mM ammonium, or less than or equal to about 0.5 mM. The culture medium can include, for example, from about 0 to about 2.5 mM ammonium, from about 0.1 to about 2.5 mM ammonium, from about 0.5 to about 2.5 mM ammonium, from about 0 to about 1.5 mM ammonium, from about 0.1 to about 1 mM ammonium, or from about 0.2 to about 1 mM ammonium. The microorganism can be cultured in a medium that includes nitrate, which in some examples may be substantially the sole nitrogen source in the culture medium or may be present in addition to less than 5 mM ammonium, less than 2.5 mM ammonium, less than 1.0 mM ammonium, or less than or equal to about 0.5 mM ammonium. Alternatively or in addition, the culture medium can comprises urea, which in some examples can be substantially the sole source of nitrogen in the culture medium.

[0176] Yet another aspect of the invention is a method of producing lipid that includes culturing a microorganism under conditions in which the FAME to TOC ratio of the microorganism is maintained between about 0.3 and about 0.8, and isolating lipid from the microorganism, the culture medium, or both. For example, the microorganisms can be cultured such that the FAME to TOC ratio is maintained at between about 0.3 and about 0.8, between about 0.4 and about 0.7, between about 0.4 and about 0.6, or between about 0.45 and about 0.55. The ratio can be maintained at between about 0.3 and about 0.8, for example between about 0.4 and about 0.8, between about 0.4 and about 0.7, between about 0.4 and about 0.6, or between about 0.45 and about 0.55 for at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 15, at least 20, at least 30 days, or at least 60 days. In these methods the microorganism can be cultured under continuous or semi-continuous conditions. The method of producing lipid can include culturing a mutant microorganism such as any provided herein under conditions in which the FAME to TOC ratio of the microorganism is maintained between about 0.3 and about 0.8, between about 0.3 and about 0.8, between about 0.4 and about 0.7, between about 0.4 and about 0.6, or between about 0.45 and about 0.55. For example, the microorganism can be a mutant microorganism having attenuated expression of a gene encoding a polypeptide having at least 55%, at least 65%, at least 75%, or at least 85% identity to a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:2 and SEQ ID NOs:5-17. The FAME to TOC ratio may be adjusted, for example, by the type and concentration of nitrogen source present in the culture medium. For example, the method may include culturing a microorganism, such as a mutant microorganism as disclosed herein, in a culture medium that includes nitrate and less than 2.5 mM ammonium or less than 1.0 mM ammonium.

[0177] The culture conditions in the methods provided herein are preferably conditions in which a control microorganism (i.e., a microorganism that does not have the mutation leading to higher lipid productivity) produces biomass on a daily basis, for example, produces biomass on a daily basis for at least five, at least eight, at least ten, or at least twelve days, and in various embodiments the methods of producing lipid result in the mutant microorganism producing at least 50% more lipid than a control microorganism while exhibiting a decrease in biomass (e.g., TOC) accumulation of no more than 35%, 30%, 25%, 20%, 15%, 10%, 5%, 2%, or 1% with respect to the control microorganism. For example, the methods of producing lipid can include culturing a mutant microorganism as provided herein in a suitable medium to produce lipid and recovering biomass or at least one lipid from the culture, in which the mutant microorganism produces at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 110%, at least 120% more lipid than a control microorganism while producing at least 65%, 70%, 75%, 880%, 85%, 90%, 95%, 98%, or 99% of the biomass produced by the control microorganism, under conditions where both the mutant microorganism and the control microorganism are producing biomass on a daily basis. The microorganism can in some examples be an alga, and the culture can be a photoautotrophic culture. Culturing can be in batch, semi-continuous, or continuous mode.

[0178] The lipid producing microorganisms may be cultured in any suitable vessel(s), including flasks or bioreactors, where the algae may be exposed to artificial or natural light (or natural light supplemented with artificial light). The culture comprising mutant algae that are deregulated in their response to low light may be cultured on a light/dark cycle that may be, for example, a natural or programmed light/dark cycle, and as illustrative examples, may provide twelve hours of light to twelve hours of darkness, fourteen hours of light to ten hours of darkness, sixteen hours of light to eight hours of darkness, etc.

[0179] Culturing refers to the intentional fostering of growth (e.g., increases in cell size, cellular contents, and/or cellular activity) and/or propagation (e.g., increases in cell numbers via mitosis) of one or more cells by use of selected and/or controlled conditions. The combination of both growth and propagation may be termed proliferation. A microorganism as provided herein may be cultured for at least five, at least six, at least seven at least eight, at least nine, at least ten, at least eleven at least twelve, at least thirteen, at least fourteen, or at least fifteen days, or at least one, two three, four, five, six, seven, eight, nine, or ten weeks, or longer.

[0180] Non-limiting examples of selected and/or controlled conditions that can be used for culturing the recombinant microorganism can include the use of a defined medium (with known characteristics such as pH, ionic strength, and/or carbon source), specified temperature, oxygen tension, carbon dioxide levels, growth in a bioreactor, or the like, or combinations thereof. In some embodiments, the microorganism or host cell can be grown mixotrophically, using both light and a reduced carbon source. Alternatively, the microorganism or host cell can be cultured phototrophically. When growing phototrophically, the algal strain can advantageously use light as an energy source. An inorganic carbon source, such as CO.sub.2 or bicarbonate can be used for synthesis of biomolecules by the microorganism. "Inorganic carbon", as used herein, includes carbon-containing compounds or molecules that cannot be used as a sustainable energy source by an organism. Typically "inorganic carbon" can be in the form of CO.sub.2 (carbon dioxide), carbonic acid, bicarbonate salts, carbonate salts, hydrogen carbonate salts, or the like, or combinations thereof, which cannot be further oxidized for sustainable energy nor used as a source of reducing power by organisms. A microorganism grown photoautotrophically can be grown on a culture medium in which inorganic carbon is substantially the sole source of carbon. For example, in a culture in which inorganic carbon is substantially the sole source of carbon, any organic (reduced) carbon molecule or organic carbon compound that may be provided in the culture medium either cannot be taken up and/or metabolized by the cell for energy and/or is not present in an amount sufficient to provide sustainable energy for the growth and proliferation of the cell culture.

[0181] Microorganisms and host cells that can be useful in accordance with the methods of the present invention can be found in various locations and environments throughout the world. The particular growth medium for optimal propagation and generation of lipid and/or other products can vary and may be optimized to promote growth, propagation, or production of a product such as a lipid, protein, pigment, antioxidant, etc. In some cases, certain strains of microorganisms may be unable to grow in a particular growth medium because of the presence of some inhibitory component or the absence of some essential nutritional requirement of the particular strain of microorganism or host cell.

[0182] Solid and liquid growth media are generally available from a wide variety of sources, as are instructions for the preparation of particular media suitable for a wide variety of strains of microorganisms. For example, various fresh water and salt water media can include those described in Barsanti (2005) Algae: Anatomy, Biochemistry & Biotechnology, CRC Press for media and methods for culturing algae. Algal media recipes can also be found at the websites of various algal culture collections, including, as nonlimiting examples, the UTEX Culture Collection of Algae (www.sbs.utexas.edu/utex/media.aspx); Culture Collection of Algae and Protozoa (www.ccap.ac.uk); and Katedra Botaniky (botany.natur.cuni.cz/algo/caup-media.html).

[0183] The culture methods can optionally include inducing expression of one or more genes and/or regulating a metabolic pathway in the microorganism. Inducing expression can include adding a nutrient or compound to the culture, removing one or more components from the culture medium, increasing or decreasing light and/or temperature, and/or other manipulations that promote expression of the gene of interest. Such manipulations can largely depend on the nature of the (heterologous) promoter operably linked to the gene of interest.

[0184] In some embodiments of the present invention, the microorganisms having increased lipid productivity can be cultured in a "photobioreactor" equipped with an artificial light source, and/or having one or more walls that is transparent enough to light, including sunlight, to enable, facilitate, and/or maintain acceptable microorganism growth and proliferation. For production of fatty acid products or triglycerides, photosynthetic microorganisms or host cells can additionally or alternately be cultured in shake flasks, test tubes, vials, microtiter dishes, petri dishes, or the like, or combinations thereof.

[0185] Additionally or alternately, mutant or recombinant photosynthetic microorganisms or host cells may be grown in ponds, canals, sea-based growth containers, trenches, raceways, channels, or the like, or combinations thereof. In such systems, the temperature may be unregulated, or various heating or cooling method or devices may be employed As with standard bioreactors, a source of inorganic carbon (such as, but not limited to, CO.sub.2, bicarbonate, carbonate salts, and the like), including, but not limited to, air, CO.sub.2-enriched air, flue gas, or the like, or combinations thereof, can be supplied to the culture. When supplying flue gas and/or other sources of inorganic that may contain CO in addition to CO.sub.2, it may be necessary to pre-treat such sources such that the CO level introduced into the (photo)bioreactor do not constitute a dangerous and/or lethal dose with respect to the growth, proliferation, and/or survival of the microorganisms.

[0186] The mutant microorganisms can include one or more non-native genes encoding a polypeptide for the production of a product, such as but not limited to a lipid.

[0187] The methods include culturing a mutant microorganism as provided herein, such as a mutant microorganism as provided herein that has increased lipid productivity with respect to a control cell while producing at least 50% of the biomass produced by a control cell under the same culture conditions to produce biomass or lipid. Lipids can be recovered from culture by recovery means known to those of ordinary skill in the art, such as by whole culture extraction, for example, using organic solvents or by first isolating biomass from which lipids are extracted (see, for example, Hussein et al. Appl. Biochem. Biotechnol. 175:3048-3057; Grima et al. (2003) Biotechnol. Advances 20:491-515). In some cases, recovery of fatty acid products can be enhanced by homogenization of the cells (Gunerken et al. (2015) Biotechnol. Advances 33:243-260). For example, lipids such as fatty acids, fatty acid derivatives, and/or triglycerides can be isolated from algae by extraction of the algae with a solvent at elevated temperature and/or pressure, as described in the co-pending, commonly-assigned U.S. patent application Ser. No. 13/407,817 entitled "Solvent Extraction of Products from Algae", filed on Feb. 29, 2012, which is incorporated herein by reference in its entirety.

[0188] Biomass can be harvested, for example, by centrifugation or filtering. The biomass may be dried and/or frozen. Further products may be isolated from biomass, such as, for example, various lipids or one or more proteins. Also included in the invention is an algal biomass comprising biomass of lipid regulator mutant, such as any disclosed herein, such as but not limited to a lipid regulator mutant that includes a mutation in a gene encoding a polypeptide having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:2 and SEQ ID NOs:5-17.

Additional Embodiments

[0189] Alternatively or in addition to any of the forgoing embodiments, the invention provides the following embodiments:

[0190] Embodiment 1 is a mutant microorganism that produces at least 25% more lipid and at least 45% more biomass than is produced by a control microorganism cultured under substantially identical conditions in which the control microorganism produces biomass, optionally wherein any one or more of the following are fulfilled: [0191] (a) the control microorganism is a wild type microorganism; [0192] (b) the mutant microorganism produces at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, as much biomass, which can be assessed as average biomass (e.g., TOC) productivity per day, during a culture period of at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen days, at least fourteen, at least fifteen, at least twenty, at least thirty, or at least sixty days; [0193] (c) the mutant microorganism produces at least 25%, at least 30%, at least 55%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 110%, at least 115%, at least 120%, at least 150% more lipid, or at least 200% more lipid, which can be assessed as average lipid (e.g., FAME) productivity per day, than is produced by a control microorganism during a culture period of at least at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen days, at least fourteen, at least fifteen, at least twenty, at least thirty, or at least sixty days; [0194] (d) the substantially identical conditions in which the control microorganism produces biomass comprise a culture medium that comprises less than about 5 mM, less than about 4 mM, less than about 3 mM, less than 2.5 mM ammonium, less than 2 mM ammonium, less than 1.5 mM ammonium, less than or equal to about 1 mM ammonium, or less than or equal to about 0.5 mM ammonium; [0195] (e) the substantially identical conditions in which the control microorganism produces biomass comprise a culture medium that comprises nitrate or urea; and/or [0196] (f) the microorganism is a heterokont or alga.

[0197] Embodiment 2 is a mutant microorganism according to embodiment 1 in which the mutant has attenuated expression of a regulator gene wherein the regulator gene encodes a polypeptide having at least 50, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, or SEQ ID NO: 18 and/or regulator gene encodes a polypeptide that includes a Zn(2)Cys(6) domain, optionally wherein the polypeptide further includes a PAS3 domain.

[0198] Embodiment 3 is a mutant microorganism according to embodiment 1 or embodiment 2, wherein the mutant is a spontaneous mutant, a classically-derived mutant, or an engineered mutant, optionally wherein the mutant is an engineered mutants that: [0199] (a) has a disrupted gene, optionally wherein the gene is disrupted in a noncoding region; [0200] (b) is deleted in all or a portion of a gene; [0201] (c) includes an antisense construct, an RNAi construct, or a ribozyme construct that targets a gene; [0202] (d) includes an insertion, optionally wherein the insertion is generated by CRISPR/cas genome editing; and/or [0203] (e) includes a mutation generated by CRISPR/cas genome editing.

[0204] Embodiment 4 is a mutant microorganism according to any of embodiments 1-3, wherein: [0205] (a) the mutant produces at least 50% or at least 80% or at least 100% more FAME (e.g., average productivity per day) while producing at least 85% or at least 90% or at least 95% of the TOC produced by a control cell, e.g., TOC productivity on a per day basis, when cultured under conditions in which both the control and mutant microorganism produce biomass; and/or [0206] (b) wherein the FAME/TOC ratio of the mutant microorganism is at least 40%, at least 50%, at least 60%, at least 70%, or at least 75% higher than the FAME/TOC of the control microorganism while producing at least 85% or at least 90% of the TOC produced by a control cell (such as a wild type cell) when cultured under conditions in which both the control and mutant microorganism produce biomass; and/or [0207] (c) the FAME/TOC ratio of the mutant microorganism is at least 0.30, at least 0.35 at least 0.40, at least 0.5, or between about 0.3 and about 0.8 when cultured under conditions in which both the control and mutant microorganism produce biomass and/or [0208] (d) wherein the FAME/TOC ratio is maintained between about 0.3 and about 0.7 for a culture period of at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, or at least thirteen days during which the mutant microorganism produces at least 50%, at least 60%, at least 70%, or at least 75%, at least 80% or at least 85% of the biomass produced by a control microorganism cultured under the same conditions in which the control microorganism accumulates biomass.

[0209] Embodiment 6 is a mutant microorganism according to any of embodiments 1-3, wherein: [0210] (a) the mutant produces at least 85%, at least 90%, at least 95%, at least 100%, at least 105%, at least 110%, or at least 115% more FAME (e.g., on an average per day basis) while producing at least 70%, at least 75%, at least 80%, or at least 85% of the TOC produced (e.g., on an average per day basis) by a control microorganism (such as a wild type cell) when cultured under conditions in which both wild type and mutant microorganism are producing biomass; and/or [0211] (b) the FAME/TOC ratio of the mutant microorganism is at least 100%, at least 110%, at least 120%, at least 130%, at least 140%, at least 150%, at least 160%, at least 170%, or at least 180% greater than the FAME/TOC ratio of a control microorganism when cultured under conditions in which both wild type and mutant microorganism are producing biomass; and/or [0212] (c) the FAME/TOC ratio of the mutant microorganism is at least 0.50, at least 0.55, at least 0.60, at least 0.65, at least 0.70, or at least 0.75 and the mutant microorganism produces at least 70%, at least 75%, at least 80%, or at least 85% of the TOC produced by a control microorganism when cultured under conditions in which the wild type accumulates biomass.

[0213] Embodiment 7 is a mutant microorganism according to any of embodiments 1-6, wherein: [0214] (a) the culture conditions under which the mutant microorganism produces more lipid is batch, semi-continuous, or continuous culture; and/or (b) the daily lipid productivity of the mutant is greater than the daily lipid productivity of the control microorganism throughout the culture period.

[0215] Embodiment 8 is a mutant microorganism according to any of embodiments 1-7 in which the mutant microorganism comprises a mutation in a non-coding region of a gene that reduces expression of the gene, optionally wherein the mutation is an insertion.

[0216] Embodiment 9 is a mutant microorganism according to any of embodiments 1-7 in which the mutant microorganism comprises a construct that reduces expression of a gene, wherein the construct encodes an RNAi, antisense transcript, or ribozyme.

[0217] Embodiment 10 is a mutant microorganism according to any of embodiments 1-9, wherein the mutant microorganism is a Labyrinthulomycte species, [0218] (a) optionally wherein the mutant microorganism is a species belonging to any of the genera Labryinthula, Labryinthuloides, Thraustochytrium, Schizochytrium, Aplanochytrium, Aurantiochytrium, Oblongichytrium, Japonochytrium, Diplophrys, or Ulkenia; or wherein the mutant microorganism is an algal species, [0219] (b) optionally a species belonging to any of the genera Achnanthes, Amphiprora, Amphora, Ankistrodesmus, Asteromonas, Boekelovia, Bolidomonas, Borodinella, Botrydium, Botryococcus, Bracteococcus, Chaetoceros, Carteria, Chlamydomonas, Chlorococcum, Chlorogonium, Chlorella, Chroomonas, Chrysosphaera, Cricosphaera, Crypthecodinium, Cryptomonas, Cyclotella, Desmodesmus, Dunaliella, Elipsoidon, Emiliania, Eremosphaera, Ernodesmius, Euglena, Eustigmatos, Franceia, Fragilaria, Fragilaropsis, Gloeothamnion, Haematococcus, Hantzschia, Heterosigma, Hymenomonas, Isochrysis, Lepocinclis, Micractinium, Monodus, Monoraphidium, Nannochloris, Nannochloropsis, Navicula, Neochloris, Nephrochloris, Nephroselmis, Nitzschia, Ochromonas, Oedogonium, Oocystis, Ostreococcus, Parachlorella, Parietochloris, Pascheria, Pavlova, Pelagomonas, Phceodactylum, Phagus, Picochlorum, Platymonas, Pleurochrysis, Pleurococcus, Prototheca, Pseudochlorella, Pseudoneochloris, Pseudostaurastrum, Pyramimonas, Pyrobotrys, Scenedesmus, Schizochlamydella, Skeletonema, Spyrogyra, Stichococcus, Tetrachlorella, Tetraselmis, Thalassiosira, Tribonema, Vaucheria, Viridiella, Vischeria, and Volvox.

[0220] Embodiment 11 is biomass comprising any of the mutant microorganisms of any of embodiments 1-10.

[0221] Embodiment 12 is a nucleic acid molecule comprising a sequence encoding a polypeptide having at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO:17;

[0222] wherein any one or more of the following are satisfied: [0223] (a) the polypeptide includes an amino acid sequence encoding a Zn(2)Cys(6) domain, optionally wherein the Zn(2)Cys(6) domain has at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:3; [0224] the polypeptide includes an amino acid sequence encoding a PAS domain, optionally wherein the PAS domain has at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to any of SEQ ID NO:21-SEQ ID NO:25; [0225] (b) the nucleic acid molecule in various examples comprises a cDNA that lacks one or more introns present in the naturally-occurring gene or is a gene construct that includes one or more introns not present in the naturally-occurring gene; [0226] (c) the nucleic acid molecule in various examples can have a sequence that is not 100% identical to a naturally-occurring gene; [0227] (d) the nucleic acid molecule has at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO: 17; [0228] (e) the nucleic acid molecule comprises a heterologous promoter operably linked to the sequence; and/or [0229] (f) the nucleic acid molecule comprises a vector.

[0230] Embodiment 13 is a nucleic acid molecule construct for attenuating expression of a gene encoding a polypeptide according to having at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO:17; [0231] a sequence encoding a guide RNA of a CRISPR system, an RNAi construct, an antisense construct, a ribozyme construct, or a construct for homologous recombination, e.g., a construct having one or more nucleotide sequences having homology to a naturally-occurring Zn(2)Cys(6) domain-encoding gene as disclosed herein and/or sequences adjacent thereto in the native genome from which the gene is derived.

[0232] Embodiment 14 is method of engineering a cell for increased lipid production comprising attenuating expression of a gene encoding a polypeptide having at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, or SEQ ID NO: 17, optionally a gene encoding a polypeptide having an amino acid sequence having at least 55%, at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to any of SEQ ID NOs:21-25, into a microorganism to produce a mutant microorganism having higher lipid productivity than the progenitor microorganism, optionally wherein attenuating expression of the gene comprises introducing a nucleic acid molecule according to embodiment 13 into the microorganism.

[0233] Embodiment 15 is method for producing lipid comprising culturing a mutant according to any of embodiments 1-10 to produce lipid, optionally wherein any one or more of the following are satisfied: [0234] (a) the culture medium includes nitrate or urea; [0235] (b) the culture medium includes less than 5 mM, less than 4 mM, less than 3 mM, less than 2.5 mM ammonium, less than 2 mM ammonium, less than or equal to about 1.5 mM ammonium, less than or equal to about 1 mM ammonium, or less than or equal to about 0.5 mM ammonium; [0236] (c) the culture is a batch, semi-continuous, or continuous culture; [0237] (d) the culture period is at least 5, 7, 8, 9, 10, 11, 12, 13 day, at least 15, 20, 30, 40, 50, or 60 days; [0238] (e) the mutant is an algal mutant and the culture is photoautotrophic; [0239] (f) the mutant produces at least 25% more lipid, such as at least 50% more lipid, preferably FAME lipid, and at least 65% of the biomass of a control microorganism during the culture period; [0240] (g) the mutant produces more lipid, preferably FAME lipid, on each day of the culture period; and/or [0241] (h) the mutant accumulates biomass on each day of the culture period.

[0242] Embodiment 16 is method for producing lipid comprising culturing a microorganism under conditions in which the FAME/TOC ratio is maintained at between about 0.3 and about 0.8 throughout the culture period, optionally wherein any one or more of the following are satisfied: [0243] (a) the culture medium includes nitrate or urea; [0244] (b) the culture medium includes less than 5 mM, less than 4 mM, less than 3 mM, less than 2.5 mM ammonium, less than 2 mM ammonium, less than or equal to about 1.5 mM ammonium, less than or equal to about 1 mM ammonium, or less than or equal to about 0.5 mM ammonium; [0245] (c) the culture is a batch, semi-continuous, or continuous culture; [0246] (d) the culture period is at least 5, 7, 8, 9, 10, 11, 12, 13 day, at least 15, 20, 30, 40, 50, or 60 days; [0247] (e) the microorganism is an algal microorganism and the culture is photoautotrophic; [0248] (f) the microorganism accumulates biomass on each day of the culture period; and/or [0249] (g) the microorganism is a mutant microorganism according to any of embodiments 1-1

EXAMPLES

Media Used in Examples

[0250] The following media are used in the Examples.

[0251] PM066 medium (Example 1) includes 8.8 mM nitrate as the sole nitrogen source. PM066 medium included 10 mM nitrate (NO.sub.3) and 0.417 mM phosphate (PO.sub.4) along with trace metals and vitamins in Instant Ocean salts. PM066 media was made by adding 5.71 ml of a 1.75 M NaNO.sub.3 stock solution (148.7 g/L), and 5.41 ml of a 77 mM K.sub.2HPO.sub.4 3H.sub.2O stock solution (17.57 g/L) to 981 mls of Instant Ocean salts solution (35 g/L) along with 4 ml of Chelated Metals Stock Solution and ml of 4 ml Vitamin Stock Solution. Chelated Metals Stock Solution was prepared by adding to 400 mls of water 2.18 g Na.sub.2EDTA2H.sub.2O; 1.575 g FeCl.sub.36H.sub.2O; 500 .mu.l of 39.2 mM stock solution (0.98 g/100 ml) CuSO.sub.45H.sub.2O; 500 .mu.l of 77.5 mM stock solution (2.23 g/100 ml) ZnSO.sub.47H.sub.2O; 500 .mu.l of 42.0 mM stock solution (1.00 g/100 ml) CoCl.sub.26H.sub.2O; 500 .mu.l of 910.0 mM stock solution (18.0/100 ml) MnCl.sub.24H.sub.2O; 500 .mu.l of 26.0 mM stock solution (0.63 g/100 ml) Na.sub.2MoO.sub.42H.sub.2O; bringing up to 500 ml final volume, and filter sterilizing. Vitamin Stock Solution was prepared by adding to 400 mls of water 0.05 g Thiamine HCl; 500 .mu.l of 0.37 mM stock solution (0.05 g/100 ml) of cyanocobalamin; and 2.5 ml of 0.41 mM stock solution (0.01 g/100 ml) of biotin, bringing up to a final volume of 500 mls, and filter sterilizing.

[0252] PM067 medium included no nitrogen source (no nitrate, ammonium, or urea), and 0.417 mM phosphate (PO.sub.4) along with trace metals and vitamins in Instant Ocean salts. PM067 media was made by adding 5.41 ml of a 77 mM K.sub.2HPO.sub.4 3H.sub.2O stock solution (17.57 g/L) to 987 mls of Instant Ocean salts solution (35 g/L) along with 4 ml of Chelated Metals Stock Solution and ml of 4 ml Vitamin Stock Solution. Chelated Metals Stock Solution was prepared by adding to 400 mls of water 2.18 g Na.sub.2EDTA2H.sub.2O; 1.575 g FeCl.sub.36H.sub.2O; 500 .mu.l of 39.2 mM stock solution (0.98 g/100 ml) CuSO.sub.45H.sub.2O; 500 .mu.l of 77.5 mM stock solution (2.23 g/100 ml) ZnSO.sub.4 7H.sub.2O; 500 .mu.l of 42.0 mM stock solution (1.00 g/100 ml) CoCl.sub.26H.sub.2O; 500 .mu.l of 910.0 mM stock solution (18.0/100 ml) MnCl.sub.2-4H.sub.2O; 500 .mu.l of 26.0 mM stock solution (0.63 g/100 ml) Na.sub.2MoO.sub.4 2H.sub.2O; bringing up to 500 ml final volume, and filter sterilizing. Vitamin Stock Solution was prepared by adding to 400 mls of water 0.05 g Thiamine HCl; 500 .mu.l of 0.37 mM stock solution (0.05 g/100 ml) of cyanocobalamin; and 2.5 ml of 0.41 mM stock solution (0.01 g/100 ml) of biotin, bringing up to a final volume of 500 mls, and filter sterilizing.

[0253] PM074 is a nitrogen replete ("nitrate-only") medium (includes nitrate as substantially the sole nitrogen source) that is 10X F/2 made by adding 1.3 ml PROLINE.RTM. F/2 Algae Feed Part A (Aquatic Eco-Systems) and 1.3 ml PROLINE.RTM. F/2 Algae Feed Part B (Aquatic Eco-Systems) to a final volume of 1 liter of a solution of Instant Ocean salts (35 g/L) (Aquatic Eco Systems, Apopka, Fla.). Proline A and Proline B together include 8.8 mM NaNO.sub.3, 0.361 mM NaH.sub.2PO.sub.4.H.sub.2O, 10X F/2 Trace metals, and 10X F/2 Vitamins (Vuillard (1975) Culture of phytoplankton for feeding marine invertebrates in "Culture of Marine Invertebrate Animals." (eds: Smith W. L. and Chanley M. H.) Plenum Press, New York, USA. pp 26-60).

[0254] PM123 medium is PM074 medium supplemented with additional Proline B so that the concentration of nitrate was increased from approximately 8.8 mM to approximately 15 mM. This is also a "nitrate only" medium.

[0255] PM124 medium is PM074 supplemented with 5 mM ammonium and 10 mM HEPES pH 8.0. It is made by adding 10 mls of 1 M HEPES pH 8 and 5 mls of NH.sub.4Cl to the PM074 recipe (final volume of 1 L). In some examples, additional media with controlled ammonium levels was made by adjusting the ammonium concentration of PM074 and adding additional Hepes buffer.

[0256] PM125 medium (Example 5): includes 7.5 mM urea as the only source of nitrogen available to the cells. To 1.times. instant ocean was added (while mixing): 3.75 ml 2M Urea stock solution, 0.32 ml 1 M NaH.sub.2PO.sub.4 stock solution, 4 ml of Chelated Metals Stock Solution and ml of 4 ml Vitamin Stock Solution (see above). The media was filter sterilized through .ltoreq.0.1 m filter and stored at room temperature.

Example 1 Identification of A Zinc-Cys Domain Polypeptide Down-Regulated During Nitrogen Starvation

[0257] Various strains of Nannochloropsis accumulate high levels of triacylglycerols (TAG) storage lipid during nitrogen deprivation and correlations between increased TAG production and correlations between TAG accumulation and presumed underlying changes in gene expression in different metabolic pathways leading to TAG synthesis have been reported (Radakovits et al. (2012) Nat Commun 3: 686; Li et al. (2014) The Plant Cell 26: 1645-1665; Corteggiani Carpinelli et al. (2014) Mol Plant 7:1645-1665). To identify genes encoding regulators that influence lipid biosynthesis and accumulation, the early transcriptional response of Nannochloropsis cells subjected to N-deprivation (-N) was analyzed. A comparative transcriptomics experiment was performed in which the RNA transcript levels of genes of Nannochloropsis gaditana cells under nitrogen starvation, during which Nannochloropsis induces storage lipid biosynthesis, were compared with the levels of RNA transcripts of the same strain of Nannochloropsis gaditana grown under identical conditions except that the amount of nitrogen in the growth medium was not limiting.

[0258] Wild type N. gaditana (WT-3730) cells were grown in nutrient replete medium under a 16 hour light (120 .mu.E)/8 hour dark cycle to light limitation (to O.D. of 1.25) and at the beginning of the photoperiod were spun down and resuspended in either nitrogen replete medium PM066 or culture medium lacking a nitrogen source ("nitrogen deplete" or "-N" medium PM067) and incubated under the provided light conditions. RNA was isolated from samples removed at various time intervals after resuspension of the cells in nitrogen replete (+N) or nitrogen deplete (-N) medium. Lipid accumulation was determined from samples taken throughout the assay. Lipid accumulation (measured as FAME as described in Example 4) was indistinguishable between nitrogen deplete and nitrogen replete cultures at the 3 h timepoint, but at 10 h FAME accumulation in the nitrogen deplete culture was double that of the nitrogen replete culture (FIG. 1A). Treatments were performed in biological triplicates. Under the assumption that transcriptional changes should precede metabolic changes, the 3 h time-point was selected for mRNA sequencing. Two samples for each treatment were sequenced.

[0259] RNA was isolated by spinning down 10 mLs of each algal cell culture (4000.times.g for 5 minutes) and decanting the supernatant. The pellets were resuspended in 1.8 mL Buffer A (5 mL TLE Grinding Buffer, 5 mL phenol, 1 mL 1-bromo-3-chloropropane and L mercaptoethanol, where TLE Grinding Buffer includes 9 mL of 1M Tris pH 8, 5 mL of 10% SDS, 0.6 mL of 7.5 M LiCl, and 450 .mu.l 0.5 M EDTA in a final volume of 50 mL) and transferred to 2 mL microcentrifuge tubes containing approximately 0.5 mL of 200 .mu.m zirconium beads. The tubes were vortexed vigorously for 5 min at 4.degree. C. and then centrifuged for 2 min at 11.8.times.g. The aqueous layers were then removed and pipetted into new 2 mL tubes, to which 1 mL 25:24:1 phenol extraction buffer (25 mL phenol pH 8.1; 24 mL 1-bromo-3-chloropropane, and 1 mL isoamyl alcohol) was added. The tubes were shaken vigorously and centrifuged for 2 min at 11.8.times.g. After centrifugation, the aqueous layer was removed and pipetted into new 2 mL centrifuge tubes, to which 1 ml 1-bromo-3-chloropropane was added. The tubes were shaken and again centrifuged for 2 min at 11.8 x g. The aqueous layer was removed to a new tube and 0.356 volumes of 7.5 M LiCl were added. The tubes were inverted 10-12 times and stored at -20.degree. C. overnight. The next day, samples were allowed to come to room temperature without mixing and were centrifuged at 16,000.times.g for 30 minutes. The supernatants were removed and the pellets were washed with 1 mL of ice cold 80% ethanol. The tubes were centrifuged for 30 min at 16,000.times.g and allowed to air dry after the supernatants had been removed. Finally, the RNA pellets were resuspended in 50 .mu.l ultrapure water. The RNA quality was assessed by on-chip gel electrophoresis using an Agilent 2100 Bioanalyzer and RNA6000 LabChip according to manufacturer instructions.

[0260] Next-generation sequencing libraries were prepared from the isolated RNA utilizing the TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, Calif.) following manufacturer instructions. The TruSeq libraries were sequenced using sequencing-by-synthesis (Illumina MiSeq) to generate 100 bp paired-end reads using the mRNA-Seq procedure (described in Mortazavi et al. (2008) Nature Methods 5:621-628). Mappable reads were aligned to the N. gaditana reference genome sequence using TopHat (tophat.cbcb.umd.edu/). Expression levels were computed for every annotated gene using the Cuffdiff component of the Cufflinks software (cufflinks.cbcb.umd.edu). TopHat and Cufflinks are described in Trapnell et al. (2012) Nature Protocols 7: 562-578. Differential expression analysis was performed using the R package edgeR (McCarthy et al. (2012) Nucl. Acids Res. 40:doi:10/1093/nar/gks042)). Expression levels in units of fragments per kilobase per million (FPKM) were reported for every gene in each sample using standard parameters. FPKM is a measure of relative transcriptional levels that normalizes for differences in transcript length.

[0261] Global analysis of the transcriptome of -N and +N cultures at 3 h revealed 1064 differentially expressed genes having a difference in expression of greater than 1 fold and a false discovery rate (FDR) of less than 0.01. These genes are depicted as dots and Xs in the plot of FIG. 1B. Of these genes, 363 were upregulated (right side of the plot) and 701 were down-regulated in the -N condition (left side of the plot). The list of differentially expressed genes was compared with a bioinformatically curated list of putative Nannochloropsis transcription factors previously generated by mining the Nannochloropsis genome for proteins containing DNA binding domains and other conserved pfam domains typical of characterized transcription factors using the Plant Transcription Factor Database as a reference (Perez-Rodriguez et al. (2010) Nucl. Acids Res. 38: D822-D827; Jin et al. (2013) Nucl. Acids Res. 42: D1182-D1187). We found 20 transcription factors, represented as Xs in FIG. 1B and listed in Table 1, that were represented only in the down-regulated set of transcription factors. No transcription factors were found to be upregulated at the 3 h timepoint. N. gaditana gene identifiers are based on the genome sequence described in Corteggiani Carpinelli et al., Mol Plant 7, 323-335 (2014).

TABLE-US-00001 TABLE 1 Transcription Factors Targeted for Knockout by Cas9 PCR Positives Fold Lines/ Change Lines N. gaditana id Gene Description (log 2) FDR.sup..dagger. Screened Success.sup..dagger..dagger. Naga_100055g29 CCT domain protein -3.3 5.4E-15 13/31 Y Naga_100104g18 Zn(2)-C6 fungal-type DNA- -2.5 1.5E-19 19/29 Y binding domain protein Naga_100043g41 RpoD family RNApolymerase -1.6 5.3E-10 0/31 N sigma factor SigA Naga_100146g3 Fungal Zn(2)-Cys(6) binuclear -1.6 1.7E-02 24/31 Y cluster domain Naga_101321g2 Zinc finger, CCCH-type -1.5 4.5E-03 9/30 Y Naga_100489g1 Zinc finger, TAZ-type -1.4 3.6E-05 1/6 Y Naga_100042g29 SANT/Myb domain protein -1.4 1.1E-03 17/32 Y Naga_100248g8 Winged helix-turn-helix -1.3 3.1E-04 3/23 Y transcription repressor DNA-binding Naga_100066g21 CCT motif family protein -1.3 9.6E-06 5/30 Y Naga_100084g18 Myb-like DNA-binding shaqkyf -1.2 8.6E-06 17/32 Y class family protein Naga_100339g1 Nucleic acid-binding protein -1.2 1.6E-04 0/8 N Naga_100087g2 Activating transcription factor 6 -1.1 9.0E-05 16/29 Y Naga_100249g5 Fungal Zn(2)-Cys(6) binuclear -1.1 4.1E-06 19/31 Y cluster domain Naga_100329g4 Fungal specific transcription factor -1.1 9.1E-04 14/31 Y domain-containing region Naga_100028g52 Zn(2)-C6 fungal-type transcription -0.9 2.5E-03 10/31 Y factor Naga_100019g66 Winged helix-turn-helix -0.9 1.1E-03 22/31 Y transcription repressor Naga_100146g5 Fungal Zn(2)-Cys(6) binuclear -0.9 9.9E-04 14/31 Y cluster domain Naga_100086g13 Myb-like dna-binding domain -0.9 7.7E-04 25/32 Y containing protein Naga_100001g82 Fungal Zn(2)-Cys(6) binuclear -0.9 3.6E-03 2/32 Y cluster domain Naga_100001g77 Aureochromel-like protein -0.5 3.9E-02 16/32 Y .sup..dagger.FDR, False discovery rate .sup..dagger..dagger.Y, successful insertion of the selection cassette; N, unsuccessful insertion, as determined by PCR genotyping

Example 2 Knockout of Transcription Factor Genes in Nannochloropsis

[0262] All 20 transcription factor genes that were discovered to be differentially regulated under nitrogen deprivation (Table 1) were targeted for insertional knockout mutagenesis via the development of a high-efficiency Cas9-expressing editor line in Nannochloropsis (see WO 2016/109840 and corresponding U.S. application Ser. No. 14/986,492, filed Dec. 31, 2015, incorporated herein by reference in its entirety). As described in U.S. Ser. No. 14/986,492, a highly efficient Nannochloropsis Cas9 Editor line, N. gaditana strain GE-6791, expressing a gene encoding the Streptococcus pyogenes Cas9 nuclease, was used as a host for transformation with a chimeric guide RNA and donor DNA for insertional knockout.

[0263] To produce the high efficiency Nannochloropsis Cas9 Editor line, a Nannochloropsis strain was engineered and isolated that exhibited expression of the introduced cas9 gene in essentially 100% of the cell population of a growing culture. The vector pSGE-6206 (FIG. 2; SEQ ID NO:26), used to transform wild type N. gaditana strain WT-3730 included the following three elements: 1) a Cas9 expression cassette which contained a Cas9 gene from Streptococcus pyogenes codon optimized for Nannochloropsis gaditana (SEQ ID NO:27) that also included sequences encoding an N-terminal FLAG tag (SEQ ID NO:28), nuclear localization signal (SEQ ID NO:29), and peptide linker (entire FLAG, NLS, and linker sequence provided as SEQ ID NO:30), driven by the N. gaditana RPL24 promoter (SEQ ID NO:31) and terminated by N. gaditana bidirectional terminator 2 or "FRD" terminator (SEQ ID NO:32); 2) a selectable marker expression cassette, which contained the blasticidin deaminase ("blast" or "BSD") gene from Aspergillus terreus codon optimized for N. gaditana (SEQ ID NO:33), driven by the N. gaditana TCTP promoter (SEQ ID NO:34) and followed by the EIF3 terminator (SEQ ID NO:35); and 3) a GFP reporter expression cassette, which contained the TurboGFP gene (Evrogen, Moscow, Russia) codon optimized for Nannochloropsis gaditana (SEQ ID NO:36), driven by the N. gaditana 4A-III promoter (SEQ ID NO:37) and followed by the N. gaditana bidirectional terminator 5 or "GNPDA" terminator (SEQ ID NO:38). The Cas9 expression construct was assembled according to the Gibson Assembly.RTM. HiFi 1 Step Kit (Synthetic Genomics, La Jolla, Calif.) into a minimal pUC vector backbone; the confirmed DNA sequence of this plasmid is provided as SEQ ID NO:26.

[0264] The ZraI-linearized Cas9 expression construct (FIG. 3A) was transformed into Nannochloropsis cells by electroporation. 1.times.10.sup.9 cells were transformed in a 0.2 cm cuvette using a field strength of 7,000 V/cm delivered with the Gene Pulser II (Biorad, Carlsbad, Calif., USA). The transformation mixture was plated onto PM074 agar medium containing 100 mg/L of blasticidin. Resulting colonies were patched onto selection media for analysis and archiving. A small amount of biomass was taken from the patches and completely resuspended in 300 .mu.l of 1.times. Instant Ocean Salts solution (Aquatic Eco Systems; Apopka, Fla.). Care was taken to not add too much biomass so that a light green resuspension was obtained. This suspension was directly analyzed by flow cytometry using a BD Accuri C6 flow cytometer, using a 488 nm laser and 530/10 nm filter to measure GFP fluorescence per cell. 10,000-30,000 events were recorded for each sample using the slow fluidics setting. A strain having a single fluorescence peak that was shifted to a fluorescence level higher than that demonstrated by wild-type cells (FIG. 3B) and also demonstrating cas9 protein expression by Western blotting using an anti-FLAG antibody (Sigma # A9469) (FIG. 3C), designated strain GE-6791, was selected as a cas9 Editor strain and used in mutant generation by cas9/CRISPR genome editing as described herein. The Ng-Cas9 Editor line was found to be equivalent to wild-type in FAME and TOC productivity (see for example FIG. 18).

Generation of Targeted Insertional Mutants in the Ng-Cas9 Editor Line

[0265] All 20 identified transcription factors that were found to be downregulated under nitrogen starvation (Table 1) were targeted for knockout in the Cas9 Editor line. Guide RNAs (see Table 2 for the target sequences used for knockout of each of the 23 transcription factors) were synthesized in vitro according to (Cho et al. (2013) Nature Biotechnol. 31: 230-232) and described in Example 3, and co-electroporated with a PCR amplified expression cassette (pHygR, SEQ ID NO:45) containing a codon optimized hygromycin resistance gene (HygR, SEQ ID NO:44) driven by endogenous the EIF3_promoter (SEQ ID NO:46) and followed by N. gaditana NADH-dependent fumarate reductase bidirectional terminator (SEQ ID NO:32) in inverted orientation. Approximately 1 .mu.g each of the guide RNA targeting the particular transcription factor and the pHygR donor fragment (FIG. 4A) were added to the cuvette and electroporation was performed as described above. In general, loss-of-function "knockout" mutants were generated by selecting a guide RNA target locus in the first half of exonic coding sequence. Selection of HygR transformants was as above except that 500 mg/L hygromycin was added to agar plates instead of blasticidin. Targeted insertion of the pHygR fragment via NHEJ-mediated repair of the double stranded DNA break catalyzed by Cas9 in loci targeted by guide RNAs was assessed by colony PCR using primers that flanked the guide RNA target site by .about.200 bp on either side (Table 3). Using these primers, PCR amplification of wild-type loci would result in .about.400 bp products, whereas pHygR targeted insertional mutants would result in .about.2800 bp products-accounting for the insertion of the 2400 bp pHygR fragment. PCR products were sequence-confirmed for all mutants allowing for the determination of insert orientation and detection of any loss of chromosomal and/or insert DNA, or the gain of small insertions generated during the NHEJ-mediated dsDNA break repair process (see FIGS. 4B and 4C for a diagram of the insertion process and exemplary colony PCR results).

[0266] Eighteen of the 20 targeted transcription factors (Table 1) were disrupted at the intended locus as confirmed by PCR genotyping. Based on the high overall editing efficiency observed it is likely that the remaining 2 loci were essential for viability. To test the knockouts for effects on lipid induction, two independent mutants per locus were screened for lipid and biomass productivities by assessing FAME and TOC levels throughout multiple time-points of a 7-day culture as described in detail in Example 4, below.

TABLE-US-00002 TABLE 2 Guide RNA Sequences and Screening Primers Used in Cas9-Mediated Mutagenesis Target Sequence Adjacent to PAM N. gaditana id Description (NGG) Naga_100055g29 CCT domain protein TTCCGAAGTACTGGTTC (SEQ ID NO: 87) Naga_100104g18 Zn(2)-C6 fungal-type DNA-binding domain AGTAGGCCATTCCCGGAG protein (ZnCys-2845) (SEQ ID NO: 88) Naga_100489g1 Zinc finger, TAZ-type TGTGGCAGACGCCGACGG (SEQ ID NO: 89) Naga_100043g41 RpoD family RNA polymerase sigma factor SigA GTACTGCCTGACAAACTAGG (SEQ ID NO: 90) Naga_100146g3 Fungal Zn(2)-Cys(6) binuclear cluster domain TGAGCAGTCGTACGAAA (SEQ ID NO: 91) Naga_101321g2 Zinc finger, CCCH-type CGAAGTCAACCATGGGGC (SEQ ID NO: 92) Naga_100248g8 Winged helix-turn-helix transcription repressor TCCTGTGACTTGACGGTG DNA-binding (SEQ ID NO: 93) Naga_100042g29 SANT/Myb domain protein GGCAATACAAGCAGTGGAAG (SEQ ID NO: 94) Naga_100066g21 CCT motif family protein CTGATCTCGAGATGGCTG (SEQ ID NO: 95) Naga_100329g4 Fungal specific transcription factor domain- GTGAAGATTGGTCCCACT containing protein (SEQ ID NO: 96) Naga_100084g18 Myb-like DNA-binding shaqkyf class family GGACGCTACGACCGTGCGGG protein (SEQ ID NO: 97) Naga_100339g1 Nucleic acid-binding protein CTGCACCAGACACAAATT (SEQ ID NO: 98) Naga_100087g2 Activating transcription factor 6 GGGAAATATTAAGACTGGAG (SEQ ID NO: 99) Naga_100249g5 Fungal Zn(2)-Cys(6) binuclear cluster domain TCACGGGAGATGTCCTGT (SEQ ID NO: 100) Naga_100028g52 Zn(2)-C6 fungal-type transcription factor AGGACTCTCCTCAGCTGA (SEQ ID NO: 101) Naga_100019g66 Winged helix-turn-helix transcription repressor TCTTCATCTGCGACAACG (SEQ ID NO: 102) Naga_100146g5 Fungal Zn(2)-Cys(6) binuclear cluster domain ACGTCCGAATATACCGAA (SEQ ID NO: 103) Naga_100086g13 Myb-like dna-binding domain containing protein GTAGAACAAGCGTTAGACC (SEQ ID NO: 104) Naga_100001g82 Fungal Zn(2)-Cys(6) binuclear cluster domain CGCCACCCTCGCACGTGTC (SEQ ID NO: 105) Naga_100001g77 Aureochrome1-like protein GGCACCATCCCCACCGGTTT (SEQ ID NO: 106) Naga_100104g18 ZnCys-2845 (Guide targets 5'UTR resulting in GGGACTGTCCCATTGTGC strain ZnCys-2845 BASH-3) (SEQ ID NO: 54) Naga_100104g18 ZnCys-2845 (Guide targets 3'UTR resulting in AACTCGCTCGTCGATCAC strain ZnCys-2845 BASH-12) (SEQ ID NO: 62) Naga_100699g1 Nitrate Reductase GGGTTGGATGGAAAAAGGCA (SEQ ID NO: 193)

TABLE-US-00003 TABLE 3 Screening Primers Used in Cas9-Mediated Mutagenesis N. gaditana id Genotyping Primer (Sense) Genotyping Primer (Antisense) Naga_100055g29 AAGTGCGCAAGACGCTCCAG TTTGAATATCTGCACATGCA (SEQ ID NO: 107) (SEQ ID NO: 108) Naga_100104g18 ACCTCCTTGTCACTGAGCAG GATCCCAAAGGTCATATCCGT ZnCys-2845 (SEQ ID NO: 109) (SEQ ID NO: 110) Naga_100489g1 ACTCTGTGCTACCAATTGCTG CGTCAGCAAATCTTGCACCA (SEQ ID NO: 111) (SEQ ID NO: 112) Naga_100043g41 GAGATGCTGTCCGAGACACG GTATCTCGGACAGGGCACTG (SEQ ID NO: 113) (SEQ ID NO: 114) Naga_100146g3 ATCCATGTAAAGACGATGTGC TGATATCACATGCTCAAGGTC (SEQ ID NO: 115) (SEQ ID NO: 116) Naga_101321g2 AGATGAGGATCAAGCACCGAGCCA GGAAGAAATAGTAGTTGCGTG (SEQ ID NO: 117) (SEQ ID NO: 118) Naga_100248g8 AGGCGCTCTGATTGCTGTGGC TCTTCCACGTCGGATGGCCAG (SEQ ID NO: 119) (SEQ ID NO: 120) Naga_100042g29 ATTGTGGAGGGTAACAAACTACG TGAGTCCCGTGGAGAGGAGTCG (SEQ ID NO: 121) (SEQ ID NO: 122) Naga_100066g21 AGGTTCCAATGGAGGCCGCA CACTTTCCTTCGTACGCTCAGC (SEQ ID NO: 123) (SEQ ID NO: 124) Naga_100329g4 CTCGAGGTAGGTGGTGAAAG GTGATTCGCATGGACGAAC (SEQ ID NO: 125) (SEQ ID NO: 126) Naga_100084g18 ATGGGTACGGACTTGTTCG ACAGCGATACGGACAGTGAC (SEQ ID NO: 127) (SEQ ID NO: 128) Naga_100339g1 GACGTTGCATGAGAAAGGAG GATGCACAGGTGCTTGTTAG (SEQ ID NO: 129) (SEQ ID NO: 130) Naga_100087g2 TGCAAAGCCTATTTCCGACG CTCATTCGTGAGGTGACCAT (SEQ ID NO: 131) (SEQ ID NO: 132) Naga_100249g5 GAGCAAACTGACATTGATAC GTACCACACATACACATG (SEQ ID NO: 133) (SEQ ID NO: 134) Naga_100028g52 CACATCCACCATCATTCCAC GAGTGTTCCCAGTGAGCCAG (SEQ ID NO: 135) (SEQ ID NO: 136) Naga_100019g66 CTGACAAGAAGATGGACATG CTTTAGTTATACGTCTGAAG (SEQ ID NO: 137) (SEQ ID NO: 138) Naga_100146g5 GAGAGGATAGTTCTCAGAG GTCCCACAATCTATTGTG (SEQ ID NO: 139) (SEQ ID NO: 140) Naga_100086g13 ATGAGTACTTGCGCGCTTTG GCATGCCTCCGTCACAGAGT (SEQ ID NO: 141) (SEQ ID NO: 142) Naga_100001g82 ATCCATTGAGCATGCCGACG GCAACATGTTAATGCATCGT (SEQ ID NO: 143) (SEQ ID NO: 144) Naga_100001g77 TCGTCCTCGAACTCTTCCTC CGGGAACAACCAAGGTGTAA (SEQ ID NO: 145) (SEQ ID NO: 146) Naga_100104g18 TAGCAGAGCAGGCTCATCAC GAATATGTGGTCTAGCTCGT ZnCys-2845 (SEQ ID NO: 147) (SEQ ID NO: 148) BASH-3 Naga_100104g18 ATGGCTCCACCCTCTGTAAG CTGACTACAGCTAGCACGAT ZnCys-2845 (SEQ ID NO: 149) (SEQ ID NO: 150) BASH-12 Naga_100699g1 AAGACTTTGGAGGATGTCTGAGTGG ACGAAGCTACATCCAGTGCAAGG (SEQ ID NO: 151) (SEQ ID NO: 152)

Example 3 ZnCys-2845 Knockout Mutant

[0267] The ZnCys-2845 gene (Naga_100104 g18, second row of Table 1) was targeted for disruption by first making a DNA construct for producing a guide RNA in which the construct included the sequence of a chimeric guide engineered downstream of a T7 promoter. The chimeric guide sequence included an 18 bp target sequence (SEQ ID NO:39) homologous to a sequence within the ZnCys-2845 gene sequence that was immediately upstream of an S. pyogenes cas9 PAM sequence (NGG), and also included the transactivating CRISPR (tracr) sequence. The chimeric guide sequence was synthesized by first making a DNA template made up of complementary DNA oligonucleotides that included the T7 promoter sequence (SEQ ID NO:40 and SEQ ID NO:41, made by SGI-DNA, La Jolla, Calif.) that incorporated the T7 promoter sequence and were annealed to create a double-stranded DNA template which was used in in vitro transcription reactions using the MEGAshortscript.TM. T7 Kit (Life Technologies # AM1354M) according to the manufacturer's instructions to synthesize the guide RNA. The resulting RNA was purified using Zymo-Spin.TM. V-E columns (Zymo Research # C1024-25) according to manufacturer's protocol.

[0268] The donor fragment for insertion into the targeted ZnCys-2845 locus (SEQ ID NO:44) included a selectable marker cassette that included the hygromycin resistance gene (HygR, SEQ ID NO:45) downstream of the N. gaditana EIF3 promoter (SEQ ID NO:46) and followed by N. gaditana bidirectional terminator 2 (SEQ ID NO:32), with the entire promoter-hygromycin resistance gene-terminator sequence flanked by 27 base pair identification sequences on the 5' (SEQ ID NO:47 5'ID) and 3' (SEQ ID NO:48 3'ID) ends to yield the DNA fragment referred to as the "Hyg Resistance Cassette" (SEQ ID NO:44, HygR Cassette).

[0269] For targeted knockout of the ZnCys-2845 (Naga_100104 g18) locus, Cas9 Editor line GE-6791 was transformed by electroporation using 5 .mu.g of purified chimeric guide RNA targeting the ZnCys-2845 gene and 1 .mu.g of the selectable donor DNA (Hyg Resistance Cassette; SEQ ID NO:44, shown in FIG. 4A) essentially as described in US 2014/0220638. Following electroporation, cells were plated on PM124 agar media containing hygromycin to select for transformants that incorporated the hygromycin resistance cassette. Transformants were patched onto a fresh plate and screened by colony PCR for insertion of the donor fragment into the ZnCys-2845 gene.

[0270] For colony PCR screening, a small amount of cells from a colony to be screened was suspended into 100 .mu.l of 5% Chelex 100 Resin (BioRad)/TE solution and the suspension was boiled for 10 minutes at 99.degree. C., after which the tubes were briefly spun. One microliter of the lysate supernatant was added to a PCR reaction mix, in which the PCR mixture and reactions were set up and performed according to the QIAGEN Fast Cycling PCR Master Mix Protocol from the manufacturer (Handbook available at qiagen.com). The primers used to detect the insertion of the donor fragment into the targeted locus of the ZnCys-2845 gene were SEQ ID NO:49 and SEQ ID NO:50. Based on the PCR-based colony screening, two knockout strains, GE-8564 and GE-8565, were tested in productivity assays.

[0271] As described below, mutants harboring the HygR cassette in the coding sequence of genome locus Naga_100104 g18 had an insertion of the donor cassette in a gene encoding a predicted Zn(II)2Cys6 binuclear cluster domain protein (Pfam PF00173, see FIG. 5) and is referred to as ZnCys-2845. These mutants exhibited a marked increase in lipid accumulation with respect to wild type as assessed by FAME/TOC (Example 4, FIG. 7C). As described below, the lipid accumulation phenotype in these ZnCys-2845 KO mutants was further confirmed to be similar to that observed in nitrogen-starved wild type cells by the appearance of prominent lipid droplets (FIGS. 7F-H).

Example 4 ZnCys-2845 Knockout Mutants in Batch Productivity Assay

[0272] To determine the effect of knocking out the ZnCys-2845 gene on growth and lipid production, ZnCys-2845 knockout strain GE-8564 and the wild type progenitor strain WT-3730 were cultured in a batch productivity assay in nitrogen replete medium PM123 that included 15 mM nitrate as the sole nitrogen source available to the cells, i.e., the culture medium had no source of reduced nitrogen. Because it had been determined that the ZnCys-2845 mutant does not grow in the absence of reduced nitrogen, the production cultures were inoculated to an initial OD730 of 0.5 from seed (scale-up) cultures that were grown in PM124 medium that included 5 mM ammonium in addition to 8.8 mM nitrate.

[0273] After inoculation, ZnCys knockout strain GE-8564 and wild type strain WT-3730 were grown in triplicate cultures in a batch assay in 75 cm.sup.2 rectangular tissue culture flasks containing 175 ml of PM123 medium, which includes 15 mM nitrate as the sole nitrogen source, for seven days. The flasks were positioned with their narrowest "width" dimension against an LED light. The culture flasks were masked with an opaque white plastic to provide a 21.1 cm.sup.2 rectangular opening for irradiance to reach the cultures. Incident irradiance was programmed at a 16 h light: 8 hour dark cycle with a linear ramp up of irradiance from 0 to 1200 uE over 4 hours, after which the irradiance was held at for six hours at 1200 uE, and then a linear ramp down in irradiance from 1200 to 0 uE over a 4 h period (increasing in 15 min intervals) (FIG. 6A). Deionized H.sub.2O was added to the cultures daily to replace evaporative losses. The temperature of the cultures was regulated by a water bath set at 25.degree. C. Cultures were inoculated at OD730 of 0.5 on day 0 and samples (5 mls) were removed on days 3, 5, and 7 for assessing cell density, fatty acid methyl esters (FAME) as a measure of lipid, and total organic carbon (TOC). Sampling was done 30 minutes prior to the end of the light cycle. FAME analysis was performed on 2 mL samples that were dried using a GeneVac HT-4X. To each of the dried pellets the following were added: 500 .mu.L of 500 mM KOH in methanol, 200 .mu.L of tetrahydrofuran containing 0.05% butylated hydroxyl toluene, 40 .mu.L of a 2 mg/ml C11:0 free fatty acid/C13:0 triglyceride/C23:0 fatty acid methyl ester internal standard mix and 500 .mu.L of glass beads (425-600 .mu.m diameter). The vials were capped with open top PTFE septa-lined caps and placed in an SPEX GenoGrinder at 1.65 krpm for 7.5 minutes. The samples were then heated at 80.degree. C. for five minutes and allowed to cool. For derivatization, 500 .mu.L of 10% boron trifluoride in methanol was added to the samples prior to heating at 80.degree. C. for 30 minutes. The tubes were allowed to cool prior to adding 2 mL of heptane and 500 .mu.L of 5 M NaCl. The samples were vortexed for five minutes at 2K rpm and finally centrifuged for three minutes at 1K rpm. The heptane layer was sampled using a Gerstel MPS Autosampler. Quantitation used the 80 .mu.g of C23:0 FAME internal standard. The samples were run on an Agilent 7890A gas chromatography system using an Agilent 127-3212 DB-FFAP, 10 .mu.m.times.100 .mu.m.times.100 nm column and an FID detector at 260.degree. C. The flow rate was 500 .mu.L/minute using H.sub.2 as a carrier with constant flow control. The oven was set at 90.degree. C. for 0.98 min, then 15.301.degree. C./minute to 230.degree. C. and held for 1.66 min. The inlet contained a 4 mm glass wool packed liner (Agilent P/N 5183-4647), and was set at 250.degree. C. and used a split ratio of 40:1. The injection volume was 900 nL.

[0274] Total organic carbon (TOC) was determined by diluting 2 mL of cell culture to a total volume of 20 mL with DI water. Three injections per measurement were injected into a Shimadzu TOC-Vcsj Analyzer for determination of Total Carbon (TC) and Total Inorganic Carbon (TIC). The combustion furnace was set to 720.degree. C., and TOC was determined by subtracting TIC from TC. The 4 point calibration range was from 2 ppm to 200 ppm corresponding to 20-2000 ppm for non-diluted cultures with a correlation coefficient of r.sup.2>0.999.

[0275] The results of these analyses are shown in Tables 4-6. Values provided for wild type and knockout GE-8564 mutant are the average of three cultures with standard deviations (sd). The "% increase" column refers to the percentage increase of the ZnCys knockout mutant with respect to wild type values.

TABLE-US-00004 TABLE 4 Lipid (FAME) Produced by ZnCys-2845 Knockout Mutant and Wild Type Cultures in Batch Assay with Nitrate-Only Culture Medium WT-3730 (NO3) ZnCys-KO GE-8564 (NO.sub.3) Day .mu.g/ml sd .mu.g/ml sd % increase 3 105.03 9.71 188.56 6.52 79.53 5 140.01 13.48 223.41 0.28 59.57 7 198.49 2.04 250.76 3.22 26.33

TABLE-US-00005 TABLE 5 Biomass (TOC) Produced by ZnCys-2845 Knockout Mutant and Wild Type Cultures in Batch Assay with Nitrate-Only Culture Medium WT-3730 (NO3) ZnCys-KO GE-8564 (NO3) Day .mu.g/ml s.d. .mu.g/ml s.d. % diff 3 375.6 10.18 261.7 7.07 -30.3 4 474.6 8.34 283.95 3.61 -40.2 5 534.45 43.20 269.5 3.68 -49.6 6 644.8 48.65 311.75 3.18 -51.7 7 804.35 36.13 329.3 1.70 -59.1

TABLE-US-00006 TABLE 6 FAME/TOC Ratios of ZnCys-2845 Knockout Mutant and Wild Type Strains in Batch Assay with Nitrate-Only Culture Medium WT-3730 (NO3) ZnCys-KO GE-8564 (NO3) Day s.d. s.d. % increase 3 0.28 0.018 0.72 0.044 157 5 0.26 0.004 0.83 0.012 219 7 0.25 0.009 0.76 0.006 204

[0276] The same batch productivity assay was performed on ZnCys-2845 cas9 knockout mutant GE-8564 using PM124 medium that included 5 mM ammonium in addition to 8.8 mM nitrate. Samples were removed as described and analyzed for FAME and TOC as provided above. The "% difference" column refers to the percentage difference of the ZnCys knockout mutant with respect to wild type values.

TABLE-US-00007 TABLE 7 FAME Produced by ZnCys-2845 Knockout Mutant and Wild Type Cultures in Batch Assay with Nitrate Plus Ammonium Culture Medium WT-3730 (NO3 + NH4) ZnCys-KO GE-8564 (NO3 + NH4) DAY .mu.g/ml s.d. .mu.g/ml s.d. % diff 3 93.03 6.943 88.43 1.827 -4.9 4 120.14 8.427 124.41 0.472 3.6 5 121.31 0.7895 123.31 3.702 1.6 6 169.70 6.0668 181.6 3.397 7.0 7 198.11 7.954 225.6 4.548 13.88

TABLE-US-00008 TABLE 8 Biomass (TOC) Produced by ZnCys-2845 Knockout Mutant and Wild Type Cultures in Batch Assay with Nitrate Plus Ammonium Culture Medium WT-3730 (NO3 + NH4) ZnCys-KO GE-8564 (NO3 + NH4) DAY .mu.g/ml s.d. .mu.g/ml s.d. % diff 3 321.5 35.07 302.7 6.36 -5.8 4 392.3 16.69 415.65 11.10 6.0 5 464 4.384 502.3 5.80 8.3 6 556.45 20.15 637.65 14.21 14.59 7 679.95 6.01 728.6 32.10 7.15

TABLE-US-00009 TABLE 9 FAME/TOC Ratios of ZnCys-2845 Knockout Mutant and Wild Type Strains in Batch Assay with Nitrate Plus Ammonium Culture Medium WT-3730 (NO3 + NH4) ZnCys-KO GE-8564 (NO3 + NH4) Day s.d. s.d. % diff 3 0.29 0.0100 0.29 0.0001 0 4 0.31 0.0085 0.30 0.0091 -3.2 5 0.26 0.0008 0.25 0.0045 -3.8 6 0.31 0.0220 0.29 0.0117 -6.5 7 0.29 0.0091 0.31 0.0074 6.9

[0277] The graphs in FIGS. 7A-7D show the results of this analysis. FIG. 7A demonstrates that cultures of ZnCys-2845 knockout strain GE-8564 (average values for triplicate cultures depicted as circles on the graph) grown in a medium that included only nitrate as a nitrogen source had higher FAME content than wild type cultures every day tested. As can be seen in Table 4, these FAME values were considerably higher than wild type on a volumetric basis. Although the FAME content of the ZnCys-2845 knockout mutant culture in nitrate-only medium was at a higher level on day 3 of the culture, which was the first day assayed, as well as on days 5 and 7 (Table 4 and FIG. 7A), the increase in FAME per day between days 3 and 7 was less for the ZnCys-2845 knockout strain than for the wild type strain. FIG. 7B demonstrates that over this time period the ZnCys-2845 gene disruption mutant cultured in nitrate-only medium (circles) increased its total organic carbon very little as compared to wild type (Xs), which showed steady growth as assessed by TOC accumulation (as also seen in Table 5). Thus, the ZnCys-2845 knockout strain, when cultured in a medium that included nitrate as the sole nitrogen source, behaved as though it were in nitrogen starvation, increasing lipid production but also decreasing in biomass accumulation. FIG. 7C confirms this, demonstrating that over the course of the one week productivity assay, the FAME/TOC ratio of the ZnCys-2845 knockout strain GE-8564 was elevated over wild type (approximately three-fold that of wild type, Table 6), with greater than 60% (and up to at least about 80%) of TOC being allocated to FAME lipids. FIG. 7D shows that the C16 and C18 fatty acids that were overproduced in knockout strain GE-8564 (black bars) with respect to wild type in nitrogen replete conditions (diagonally striped bars), while C20 fatty acids were underrepresented with respect to their abundance in wild type cells, as expected for selective overproduction of storage lipids (i.e., triglycerides). The fatty acid profile of the GE-8564 knockout strain was very similar to that of wild type cells under nitrogen starvation (dotted bars).

[0278] Direct demonstration of TAG production was determined by analysis of extracted lipids. Extracted lipids of knockout mutant GE-8564 and wild type progenitor strain WT-3730 from samples taken on Day 7 of the batch assay in the nitrate-only PM074 medium were identified and quantitated by HPLC. For HPLC analysis of lipids, 2 mL samples of each culture were spun down at maximum speed for 5 minutes, the supematants were removed, and pellets were re-suspended in 400 .mu.L of H.sub.2O. The cell suspensions (approximately 500 .mu.L) were transferred to 4 mL glass vials with Teflon lined caps. 500 .mu.L of glass beads (212-300 .mu.m diameter) were added to each of the cell suspensions, after which 50 .mu.L of 50% H.sub.2SO.sub.4 and 100 .mu.L of 5M NaCl were added. Bead beating was performed for 5 minutes at 1 krpm, then 2 mL of hexane was added to each sample, and bead beating was repeated for 5 minutes at 1 krpm. The samples were loaded onto a multi-tube vortexer and shaken for 30 minutes at 1 krpm, and then vortexed for 30 seconds at 2.5 krpm. 500 uL of the organic layer was transferred to an HPLC vial, and 50 .mu.L of internal standard solution (1 mg/mL 6-ketocholestanol in toluene) was added to each vial. Standards were from NuCheck, Sigma-Aldrich, or Supelco. The vials were capped and vortexed briefly (5 seconds at 2.5 krpm) prior to HPLC analysis. The HPLC was run at a flow rate of 2 mL/minute on a Chromegasphere SI-60 150 mm.times.4.6 mm.times.10 .mu.m column (ES Industries), with a column compartment set at 40.degree. C. The injection volume was 25 .mu.L with a draw and eject speed of 200 .mu.L/minute. Eluent A was hexane and Eluent B was a 80:10:10:1 mixture of hexane, isopropanol, ethyl acetate, and 10% formic acid in isopropanol, run as a gradient program as follows: 2% B at 0.0 min; 2% B at 1.0 min; 25% B at 5.0 min; 98% B at 5.5 min; 98% B at 8.99 min; 2% B at 9.00 min; stop time: 9.0 minutes; 4 minutes post time. The detector was ELSD at 30.degree. C. and 3.5 bar N.sub.2, with a gain of 5.

[0279] FIG. 7E shows that the amount of TAG in the ZnCys-2845 knockout cells in nitrate only medium was more than 5-fold that of the wild type cells, that is, the observed increase in FAME lipid could be attributed to the increase in TAGs. Electron microscopy also showed the dramatic lipid accumulation characteristic of the nitrogen starvation response. FIG. 7F shows a wild type cell grown under nitrogen replete conditions (nitrate-only culture medium), with a prominent nucleus (N), chloroplast (Ch), and mitochondrion (M), as well as a few small lipid droplets (LD). FIG. 7G shows the ZnCys knockout mutant grown in nitrate-only medium, in which a prominent lipid droplet (LD) is the largest cellular structure visible, a cellular morphology highly similar to the nitrogen starved wild type cell shown in FIG. 7H. Thus, the ZnCys-2845 polypeptide acts as a negative regulator of lipid biosynthesis, as attenuating expression of the ZnCys-2845 gene results in increased lipid production.

[0280] The increase in FAME exhibited by the ZnCys-2845 knockout strain cultured in nitrate-only medium was not apparent when the ZnCys-2845 knockout strain was grown in a culture medium that also included ammonium however (Table 7). In this case, the amount of FAME produced was very similar to that produced by wild type cells grown in nitrate plus ammonium medium, with lipid production of the knockout mutant increasing somewhat relative to wild type toward the end in the run, probably indicating depletion of ammonium from the batch culture (Table 7). FIG. 8A shows that the amount of FAME produced by wild type (diamonds) and the ZnCys-2845 knockout strain (circles) cultured in ammonium-only medium was virtually identical over the one week batch assay, as was TOC accumulation, shown in FIG. 8B (also evident from Table 8). FAME/TOC values of the wild-type and ZnCys-2845 knockout strain were correspondingly similar (FIG. 8C, Table 9).

[0281] Thus, the ZnCys-2845 gene disruption mutant behaved like the wild type strain when ammonium was replete in the culture medium (Tables 7-9 and FIGS. 8A-8C), but appeared to be impaired in nitrate assimilation, behaving as though the cells were in nitrogen depleted medium when nitrate was the sole source of nitrogen present by inducing storage lipid biosynthesis (FIGS. 7A-7H).

Example 5 Bioinformatic Analysis of the ZnCys-2845 Protein: Domains and Orthologs

[0282] As described in Example 1, the ZnCys-2845 gene at locus Naga_100104 g18 that was differentially expressed between the N-replete and N-deplete samples was a gene (cDNA sequence provided as SEQ ID NO: 1) encoding a polypeptide (SEQ ID NO:2) that appeared on a bioinformatics-generated Nannochloropsis putative transcription factor list. The polypeptide was observed to have a Zinc(2)Cys(6) domain characteristic of some transcription factors and is therefore classified as a Zn(2)-C(6) fungal-type DNA-binding domain protein. In addition to the Zn(2)-Cys(6) domain, the Nannochloropsis polypeptide ZnCys-2845 contains a distinct nuclear localization sequence with a confidence score of 1.0 (which equates to 100% confidence), consistent with its characterization as transcription factor (FIG. 5).

[0283] ZnCys-2845 is a 1065 amino acid protein (SEQ ID NO:2) identified by transcriptomics analysis of genes differentially regulated during lipid induction and annotated as a putative transcription factor due to the Zn(2)-Cys(6) binuclear cluster domain extending from amino acid 190 to 219 (SEQ ID NO:3). The protein recruits to Pfam PF00172 ("Zn_Clus" or "Fungal Zn(2)-Cys(6) binuclear cluster domain" with a bit score of 25.2 (the gathering cutoff for this family is 20.8) and an e value of 1.1 e-05. Thus, ZnCys-2845 is a member of the Zn(II)2Cys6 fungal-type DNA-binding domain protein family. Members of this family contain the well-conserved motif CysX.sub.2CysX.sub.6CysX.sub.5-12CysX.sub.2CysX.sub.6-8Cys (a cysteine residue followed by two amino acid residues of any identity, followed by second cysteine residue followed by six amino acid residues of any identity, followed by a third cysteine residue followed by between five and twelve amino acid residues of any identity, followed by a fourth cysteine residue followed by two amino acid residues of any identity, followed by a fifth cysteine residue followed by between six and eight amino acid residues of any identity, followed by a sixth cysteine residue; SEQ ID NO:4). It has been demonstrated that the cysteine residues can bind two zinc atoms, which coordinate folding of the domain involved in DNA binding. Other identifiers for this domain include the conserved domain database (cdd) domain cd00067, the interpro protein domain database domain IPR001138, the SMART protein domain `GAL4`, and the PROSITE protein domain PS00463.

[0284] This class of "ZnCys" transcription factors was originally thought to be exclusively fungal, but more recently members have been identified among chromalveolates, in particular stramenopiles/heterokonts (including non-photosynthetic labyrinthulomycetes or "chytrids") and haptophytes (e.g., E. huxleyi). The first and best studied protein in this family is Gal4p, a Saccharomyces transcriptional activator of genes involved in galactose catabolism (Leverentz & Reece (2006) Biochem Soc Transac 34:794-797; Breunig (2000) Food Technol. Biotechnol. 38:287-293). The terms "Zn(2)-C(6) fungal-type DNA-binding domain protein", "Zn(II)2Cys6 fungal-type DNA-binding domain protein", "Zn(2)-Cys(6) domain polypeptide", "Zn(2)Cys(6) protein/polypeptide" and "Zn2Cys6 protein/polypeptide" are used interchangeably herein.

[0285] Examination of genome databases revealed genes encoding polypeptides having Zn(2)-Cys(6) domains in plants and fungi. Interestingly, several heterokont species were found to include Zn(2)-Cys(6) domain polypeptides, including labyrinthulomycete species such as from the genera Schizochytrium and Aplanochytrium and diatom species, including members of the Navicula, Cyclotella, Thalassiosira, Phaeodactylum, Fragilariopsis genera.

TABLE-US-00010 TABLE 10 Putative Orthologs of N. gaditana Lipid Regulator ZnCys-2845 Translation SEQ ID Species Library ID NO Phaeodactylum triconutum Phatr2_2 337562 5 Navicula sp. wt0229_cDNA_clc 4242909 6 Navicula sp. wt0229_cDNA_clc 4243087 7 Navicula sp. wt0229_cDNA_clc 4238609 8 Cyclotella sp. wt0293_nuclear_v1.3 5077789 9 Cyclotella sp. wt0293_nuclear_v1.3 5083384 10 Cyclotella sp. wt0293_nuclear_v1.3 5084316 11 Thalassiosira pseudonana thaps3_2 322124 12 Thalassiosira pseudonana thaps3_2 326683 13 Thalassiosira pseudonana thaps3_2 326937 14 Fragilariopsis cylindrus fracy1_2 386612 15 Fragilariopsis cylindrus fracy1_2 386837 16 Nannochloropsis oceanica Wt-5473 17

[0286] The N. oceanica gene (coding sequence provided as SEQ ID NO:84, encoded polypeptide provided as SEQ ID NO: 17) was found by scanning the predicted protein set of a proprietary Nannochloropsis genome for matches to the PF00172 HMM model using hmmsearch (hmmer.org) and the trusted cutoff for the match score; however, no additional Nannochloropsis orthologs were found by scanning Nannochloropsis genomes downloaded from singlecellcenter.org/en/NannoRegulationDatabase/Download/S 11.zip, probably due to incomplete protein sets of the genomes. Additional putative orthologs of the Nannochloropsis gaditana ZnCys-2845 protein (SEQ ID NO:2) were found by BLAST (tblastn) against public genome assemblies of Nannochloropsis strains and species, including N. gaditana strain CCMP526, N. oceanica strain IMET1, N. oceanica strain CCMP531, N. oculata strain CCMP525, N. salina strain CCMP537, and N. granulata strain CCMP529. However, in each case the alignment matches were observed to break within the PF00172 Zn_Clus domain, such that all of the sequences were found to be incomplete, lacking the 5' end of the coding region and N-terminal sequence of the proteins. An additional conserved region, approximately 170 amino acids in length from the ZnCys-2845 polypeptide (positions 345-51 of SEQ ID NO:27), was clearly identified in all Nannochloropsis genomes analyzed and examined further. The delta-blast tool in NCBI was used to evaluate the highly conserved region between N. gaditana WT-3730 ZnCys-2845 (SEQ ID NO:2) putative orthologs in other Nannochloropsis species.

[0287] This domain, a PAS3_fold domain (pfam PF08447), is found in many signaling proteins where it functions as a signal sensor. Using this approach putative matches to ZnCys-28345 could be clearly identified in each of the six Nannochloropsis genomes searched. Unfortunately, the alignment matches in all cases appeared to break within the putative match to the PF00172 Zn_Clus domain. However, from the blast alignments, an approximately 170 aa region from ZnCys-28345 (positions 345-517) was observed and clearly identifiable across all strains (single copy). An alignment of the PAS3 domains in the identified ZnCys-2845 orthologs from Nannochloropsis is provided in FIG. 9, where the high degree of conservation of the domain sequence among different Nannochloropsis species is evident. The PAS3 domain of ZnCys-2845 (identified in the gene diagram of FIG. 12A) extends from amino acid 345 to amino acid 517 of SEQ ID NO:2, and is provided as SEQ ID NO:21. SEQ ID NO:21 also represents the sequence of the PAS3 domain of N. gaditana strain CCMP526. The sequence of the PAS3 domain of N. oceanica strain WT-5473, N. oceanica strain IMET1, and N. oceanica strain CCMP531 ZnCys-2845 orthologs is provided as SEQ ID NO:22. The N. oceanica ZnCys-2845 ortholog PAS3 domain (SEQ ID NO:22) is 86% identical in sequence to the N. gaditana PAS3 domain (SEQ ID NO:21). The PAS3 domain of the N. salina strain CCMP537 ZnCys-2845 ortholog is provided as SEQ ID NO:23, which is 98% identical to the N. gaditana ZnCys-2845 PAS3 domain (SEQ ID NO:21). The PAS3 domain of the N. oculata strain CCMP539 ZnCys-2845 ortholog is provided as SEQ ID NO:24, and it demonstrates 86% sequence identity to the PAS3 domain of N. gaditana ZnCys-2845 (SEQ ID NO:21). As provided above, the PAS3 domain of the ZnCys-2845 ortholog of N. granulata strain CCMP529 is provided as SEQ ID NO:22, which is approximately 86% identical to the PAS3 domain of N. gaditana ZnCys-2845 (SEQ ID NO:21).

[0288] An alignment of the amino acid sequence encoded by the N. gaditana ZnCys-2845 gene and the amino acid sequence (SEQ ID NO: 17) encoded by the N. oceanica strain WT-5473 ortholog of the ZnCys-2845 gene, both of which were determined by in-house genome sequencing and gene assignment, is provided in FIG. 10. Genome sequences of three additional Nannochloropsis species, N. granulata strain CCMP529, N. oculata strain CCMP539, and N. salina strain CCMP537, were further examined to attempt to stitch together protein-encoding sequences of putative ZnCys-28545 orthologs as characterized by the PAS3 domains. The six Nannochloropsis genomes were curated to find regions of homology extending outward from the PAS3 domains. Blastn was utilized to identify homologous sequences, which were linked together with gaps introduced to maximize homology.

[0289] The Zn(2)-Cys(6) domain of N. oceanica is identical to the Zn(2)-Cys(6) domain of N. gaditana (SEQ ID NO:3). The polypeptides encoded by the two genes (N. gaditana ZnCys-2845 and the N. oceanica ortholog) have 56% identity across the entire deduced polypeptide sequence, and 71% identity across the first 517 amino acids of N. gaditana ZnCys-2845 (SEQ ID NO:2), a portion of the amino acid sequence that extends from the N-terminus of the protein through the Zn(2)-Cys(6) domain and through the PAS3 domain (see FIG. 5). Amino acids 1-200 encoded by the N. salina ZnCys-2845 homologous sequence (SEQ ID NO:20) have approximately 98% identity to corresponding amino acid sequence of N. gaditana ZnCys-2845 (SEQ ID NO:2); whereas the incomplete polypeptide sequence of a putative ortholog of N. granulata (SEQ ID NO: 18) is approximately 61% identical to N. gaditana ZnCys-2845 (SEQ ID NO:2) and the incomplete polypeptide sequence of a putative ortholog of N. oculata (SEQ ID NO: 19) is approximately 61% identical to N. gaditana ZnCys-2845 (SEQ ID NO:2). These partial polypeptide sequences do not include the PAS3 domains of the Nannochloropsis orthologs, which, as noted above, have much higher % identities to the PAS3 domain of N. gaditana ZnCys-2845 (SEQ ID NO:21).

Example 6 Growth and Lipid Biosynthesis of ZnCys-2845 Knockout Mutant in Semi-Continuous Production System Using Urea Nitrogen Source

[0290] To determine whether the ZnCys-2845 gene disruption knockout mutant could utilize other sources of nitrogen, a semi-continuous productivity assay was set up in which the culture medium included urea as the sole nitrogen source.

[0291] For assays in cultures that included urea as the sole nitrogen source, seed cultures (also referred to as "starter cultures" or "scale-up cultures") of ZnCys-2845 knockout strain GE-8564 and wild type strain WT-3730 were grown in PM125 medium that included 7.5 mM urea as the sole nitrogen source. For assays in which wild type cells were cultured in nitrate-only medium (PM074), the wild type cells were scaled up in cultures that included the PM074 nitrate-only medium. The GE-8564 ZnCys-2845 knockout mutants were scaled up in cultures that included the PM124 medium that included both nitrate (8.8 mM) and ammonium (5 mM) for the semi-continuous assays that included only nitrate as the nitrogen source in the assay culture medium.

[0292] The scale-up cultures were used to inoculate 225 cm.sup.2 rectangular tissue culture flasks, each of which contained a final total volume of 550 ml of culture after inoculation. The cultures were inoculated so that each 550 ml culture had an initial OD.sub.730 of 0.9. A typical inoculum volume was approximately 200 ml of scale-up culture that was added to approximately 350 ml of assay culture medium, which was either PM074 (nitrate-only medium) or PM125 (urea-only medium). Cultures were diluted daily at mid-day, when the light intensity was at its peak, by removing 30% of the volume (165 mls) and replacing it with the same volume of the assay medium (either PM074 or PM125) plus an additional 10 ml of deionized water to make up for evaporation (included in the make-up medium). Semi-continuous assays were typically run for 10-14 days. Daily lipid and biomass productivities were only calculated for cultures that had reached steady state (where the increase in growth was equal to the dilution factor for the assay).

[0293] Three cultures were initiated per strain. The flasks included stir bars and had stoppers having inserted tubing connected with syringe filters for delivering CO.sub.2 enriched air (1% CO.sub.2, flow rate, 300 ml per min) that was bubbled through the cultures. The flasks were set in a water bath programmed to maintain a constant temperature of 25.degree. C. on stir plates set to 575 rpm during the assay period. Culture flasks were masked with an opaque white plastic to provide a 31.5 cm.sup.2 rectangular opening for irradiance to reach the culture. The flasks were aligned with the width (narrowest dimension) against an LED light bank that was programmed with a light/dark cycle and light profile that increased until "solar noon" and then declined to the end of the light period. The light profile was designed to mimic a spring day in Southern California: 14 h light: 10 h dark, with the light peaking at approximately 2000 .mu.E (FIG. 6B). The flasks included stir bars and had stoppers with inserted tubing connected with syringe filters for delivering CO.sub.2 enriched air (1% CO.sub.2, flow rate, 300 ml per min). The flasks were set in a water bath programmed to maintain a constant temperature of 25.degree. C. on stir plates set to 575 rpm during the assay period.

[0294] Cultures were diluted daily at mid-day, when the light intensity was at its peak by removing 30% of the volume (165 ml) and replacing it with the same volume of the assay medium plus an additional 10 ml of deionized water to make up for evaporation. A 30% dilution rate was empirically determined as the most productive dilution rate for Nannochloropsis, as 50, 30, and 15% daily dilutions resulted in average TOC productivities of 6.5, 9 and 8 g/m.sup.2/day, respectively. Semi-continuous assays were typically run for 7-14 days. Daily lipid (FAME) and biomass (TOC) productivities were calculated from cultures that had reached steady state standing crop TOC and FAME density. Volumetric FAME and TOC productivities in (mg/L/day) were calculated by multiplying the volumetric FAME and TOC amounts by the 30% dilution rate. Aerial productivities (g/m2/day) were calculated by dividing the total productivity of the culture by the size of the aperture through which irradiance was permitted:

( volumetric productivity ) mg L * day * 0.55 L 0.00315 m 2 * g 1000 mg = g m 2 * day ##EQU00001##

[0295] FIG. 11A shows that the ZnCys-2845 knockout mutant GE-8564, when cultured in the semi-continuous assay where nitrate is the sole source of nitrogen (diamonds), showed a large induction of lipid production at the outset of the assay which subsequently declined steeply after day 3 of the assay such that lipid production fell below that of the non-induced wild type culture by day 10 of the assay, after which it declined to even lower levels. This pattern is consistent with the results of the batch assay of Example 4 which indicated the ZnCys-2845 knockout mutant GE-8564 is induced for lipid production in nitrate-only media.

[0296] In contrast, the cultures of the GE-8564 mutant having a disrupted ZnCys-2845 gene cultured in urea-only medium (FIG. 11A, circles) had consistently higher daily FAME productivity than the wild type strain cultured in either nitrate only medium (triangles) or urea-only medium (squares), both of which are conditions in which the wild type strain is not induced for lipid production (as evidenced by the FAME/TOC ratios of these cultures throughout the assay, see FIG. 11C and Table 14, below). Table 11 provides the daily amounts of FAME produced on an areal basis by all strains in the semi-continuous assay along with the percentage increase of the amount of FAME produced by the knockout mutant GE-8564 strain over wild type FAME levels when both were cultured in urea-only culture medium also provided. Average areal FAME productivity for each strain, expressed as g/m.sup.2/day, is provided in Table 12. The increase in FAME productivity of the knockout mutant strain GE-8564 over the wild type strain averaged 58% over the course of the thirteen-day assay when both strains were cultured in urea-only medium. It can also be seen that wild type cells cultured in urea-only medium showed, on average, 16% less FAME productivity than wild type cells in nitrate-only medium. The GE-8564 knockout mutant in nitrate-only medium showed increased FAME production with respect to wild type in the first 8 days of the assay and then experienced declines in daily FAME production as the assay progressed, consistent with a nitrogen depletion response.

TABLE-US-00011 TABLE 11 FAME (g/m.sup.2/day) Produced by ZnCys Knockout and Wild type Strains Cultured with Nitrate or Urea as Nitrogen Source in Semi-Continuous Assay ZnCys- ZnCys-KO ZnCys- ZnCys-KO KO/ % difference WT/ KO/ % increase DAY WT/NO3 NO3 NO3 UREA UREA UREA 1 2.48 5.46 120% 1.84 2.64 43% 2 2.41 5.86 143% 2.24 2.70 20% 3 2.45 6.68 172% 2.18 3.08 41% 4 2.23 6.40 187% 2.00 2.80 40% 5 2.45 5.41 121% 1.98 3.05 54% 6 2.40 4.72 97% 2.12 3.57 69% 7 2.46 3.85 57% 1.90 3.55 87% 8 2.47 3.18 28% 2.11 3.46 64% 9 2.54 2.43 -5% 2.07 3.39 64% 10 2.38 1.77 -26% 1.90 3.16 66% 11 2.25 1.27 -43% 1.74 3.25 87% 12 2.35 0.90 -62% 1.89 3.09 63% 13 2.09 0.69 -67% 1.90 3.05 60% Avg. 2.38 3.74 57% 1.99 3.14 57%

[0297] Table 12 provides the average daily FAME productivities of the cultures over the thirteen day semi-continuous culture. The average daily FAME productivity for the ZnCys knockout GE-8564 grown in a urea-only medium was 32% higher than the average daily FAME productivity of the wild type strain (WT-3730) grown in nitrate medium (rightmost column). The high FAME productivity value of the ZnCys-2435 knockout in nitrate-only medium is due to the very high FAME production in the first 7 days of the culture. The daily FAME productivity is already declining by day 5 of the culture however, after which it declines well below wild type cultured in nitrate-only medium (FIG. 11A).

TABLE-US-00012 TABLE 12 Average Daily FAME Productivity of Semi-Continuous Cultures in Urea-Only or Nitrate-Only Media g/m.sup.2/day Avg change Strain FAME v. WT (NO.sub.3) WT-3730 2.38 0% (NO3) WT-3730 1.99 -16% (Urea) ZnCys-KO GE-8564 3.14 32% (Urea) ZnCys-KO GE-8564 3.74 57% (NO3)

[0298] FIG. 11B shows that the ZnCys-2845 knockout mutant (GE-8564) cultured in the semi-continuous assay in a nitrate-only medium (diamonds) demonstrated a precipitous drop in biomass production over the course of the assay, declining to levels that were only a fraction of the biomass produced by wild type cells cultured in nitrate medium by the end of the assay. In contrast, during this semi-continuous productivity assay, there was little decline in biomass (TOC) productivity in the ZnCys-2845 gene disruption mutant cultured in urea medium (circles) with respect to the wild type strain cultured in nitrate medium (triangles), and the ZnCys-2845 knockout mutant even demonstrated slightly better productivity than wild type cultured in urea medium (squares), all three of which remained in fairly consistent over the entire course of the assay.

[0299] Table 13 provides the TOC content of these semi-continuous cultures and the percentage difference in the daily amount of TOC produced between the ZnCys-2845 knockout mutant cultured in nitrate-only medium with respect to wild type cells cultured in nitrate-only medium, and the percentage difference in daily TOC produced between the ZnCys-2845 knockout mutant cultured in urea medium with respect to wild type cells cultured in urea medium. In Table 13 the reduction in the amount of biomass produced on a daily basis can be seen in ZnCys-2845 knockout mutant cultured in nitrate only medium as the assay progresses. The biomass production levels of the other cultures, including the ZnCys-2845 knockout mutant cultured in urea medium that had a 58% increase in daily FAME productivity with respect to wild type in urea medium, remains quite consistent throughout the thirteen day assay, and has a slightly better average TOC productivity than does the wild type strain cultured in urea medium. Thus, the ZnCys-2845 knockout mutant was able to accumulate biomass at levels at least equivalent to the wild type strain while demonstrating nearly 60% higher daily FAME productivity when cultured in a medium that included urea as the sole source of nitrogen.

TABLE-US-00013 TABLE 13 Biomass (g/m.sup.2/day TOC) Produced by Strains Grown in Nitrate or Urea in a Semi-Continuous Assay ZnCys- ZnCys- KO % ZnCys- KO % WT/ ZnCys- difference WT/ KO/ increase, NO3 KO/NO3 NO3 UREA UREA UREA DAY medium medium medium medium medium medium 1 9.65 11.00 14% 8.06 8.86 10% 2 9.24 9.69 5% 7.94 8.25 4% 3 9.42 9.61 2% 8.35 8.80 5% 4 10.28 8.72 -15% 9.21 8.86 -4% 5 10.08 7.19 -29% 8.85 8.88 0% 6 9.97 6.18 -38% 8.72 9.09 4% 7 9.99 5.07 -49% 8.79 9.29 6% 8 9.42 3.83 -59% 8.03 8.55 6% 9 9.34 3.22 -66% 7.99 8.84 11% 10 9.12 2.46 -73% 7.94 8.57 8% 11 9.32 2.00 -79% 7.74 8.74 13% 12 9.53 1.77 -81% 8.11 8.59 6% 13 9.57 1.45 -85% 8.28 9.25 12% Avg 9.61 5.55 -42% 8.31 8.81 6%

[0300] In fact, despite the increased lipid production by the ZnCys-2845 knockout mutant in urea-only medium with respect to wild type cells in nutrient replete (nitrate-only) medium (FIG. 11A and Table 11) the average amount of TOC produced throughout the course of the assay by the ZnCys knockout mutant in urea-containing medium was at least 90% that of wild type cells cultured in nitrate medium, i.e., only about 10% less than that of nitrogen replete wild type cells.

[0301] FIG. 11C shows the daily FAME to TOC ratios of the cultures in the semi-continuous assay. These ratios stay fairly consistent for all samples with the exception of the ZnCys-2845 gene disruption mutant ("ZnCys-KO") cultured in nitrate-only medium (diamonds), which shows FAME to TOC ratios climbing from the first day of culturing up to day 8, after which the ratio begins to decline. These FAME:TOC ratios of the ZnCys-2845 gene disruption mutant cultured in nitrate-only medium are far higher than the FAME:TOC ratios of wild type cultured in both nitrate-only and urea-only medium and the ZnCys-2845 knockout mutant cultured in urea-only medium and are indicative of the classic lipid induction response to nitrogen depletion. FAME to TOC ratios of the mutant and wild type semicontinuous assay cultures are provided in Table 14.

TABLE-US-00014 TABLE 14 FAME/TOC Ratios of Cultures Cultured in Nitrate or Urea WT/ ZnCys-KO/ WT/ ZnCys-KO/ DAY NO3 NO3 UREA UREA 1 0.3 0.5 0.2 0.3 2 0.3 0.6 0.3 0.3 3 0.3 0.7 0.3 0.3 4 0.2 0.7 0.2 0.3 5 0.2 0.8 0.2 0.3 6 0.2 0.8 0.2 0.4 7 0.2 0.8 0.2 0.4 8 0.3 0.8 0.3 0.4 9 0.3 0.8 0.3 0.4 10 0.3 0.7 0.3 0.4 11 0.2 0.6 0.2 0.4 12 0.2 0.5 0.2 0.4 13 0.2 0.5 0.2 0.3

[0302] The ZnCys-2845 gene disruption mutant cultured in urea-only shows consistently higher FAME:TOC ratios with respect to wild type cells cultured in either nitrate-only or urea only medium, but the FAME:TOC ratio is fairly stable throughout the culture period, in the range of 0.3 to less than 0.5, representing an increase of on average about 45% over wild type. Thus, when urea was used as the sole source of reduced nitrogen in the assay, the ZnCys-2845 gene disruption mutant demonstrated significantly increased partitioning of carbon to lipid (Table 14, FIG. 11C) without a substantial loss of overall carbon assimilation (Table 13, FIG. 11B), resulting in an approximately 57% increase in FAME produced on a daily basis and only an approximately 6% decrease in TOC produced with respect to wild type cells cultured under the same (urea-only) conditions over the course of the assay.

Example 7 CAS9 ZnCys-2845 Knockdown Constructs

[0303] Since the ZnCys-2845 knockout line exhibited a significant deficit in TOC productivity concomitant with increased carbon partitioning to lipid in batch growth (Example 4, FIG. 7B), we next investigated whether varying the degree of attenuation of ZnCys-2845 expression would result in engineered strains in which lipid and TOC productivity were better optimized. Additional mutant strains were engineered to have decreased expression of the ZnCys-2845 gene using Cas9/CRISPR genome engineering. Twelve chimeric guide RNAs were designed to target sequences upstream of the ATG, within an intron of the gene, in the 3' end of the gene but still within the coding sequence, or in the 3' untranslated region of the gene (FIG. 12A). These constructs described here as "Bash Knockdown constructs" or simply "Bash constructs" because they are designed to insert the donor fragment into a site in a region of the gene where the insertion is expected to allow the targeted gene to be expressed at a lower level than in wild type. (Correspondingly, the strains that include such insertions are referred to as "Bash strains", "Bashers", or "Bash Knockdown mutants".) The twelve 18-nucleotide sequences having homology to the ZnCys-2845 gene (target site sequences) are provided in Table 15.

TABLE-US-00015 TABLE 15 Target and Chimeric Guide Sequences for Attenuating ZnCys-2845 Expression "Bash" Gene Attenuation Gene Region Target Sequence Target Site Targeted (18 nt) -1 5' UTR SEQ ID NO: 51 1 5' UTR SEQ ID NO: 52 2 5' UTR SEQ ID NO: 53 3 5' UTR SEQ ID NO: 54 4 5' UTR SEQ ID NO: 55 6 Intron in SEQ ID NO: 56 PAS3 domain sequence 7 Intron in SEQ ID NO: 57 PAS3 domain sequence 8 C-terminus SEQ ID NO: 58 9 C-terminus SEQ ID NO: 59 10 C-terminus SEQ ID NO: 60 11 3' UTR SEQ ID NO: 61 12 3' UTR SEQ ID NO: 62

[0304] Chimeric guide DNA constructs were synthesized as two complementary strands that were annealed to produce a double-stranded construct with a T7 promoter positioned upstream of the guide sequence (that included the 18-nucleotide target sequence in addition to the tracr sequence), and used to produce the chimeric guide RNAs by in vitro transcription and purified as described in Example 3. SEQ ID NO:42 is an example of a generic "sense" strand for producing a guide RNA and SEQ ID NO:43 is an example of a generic "complementary" strand that would be annealed to the sense strand (where the target sequence is again represented by 18 Ns,) for producing the guide RNA by in vitro transcription.

[0305] In the present experiments, each chimeric guide RNA was individually transformed into Nannochloropsis Editor strain GE-6791 along with the donor fragment that included a Hyg resistance ("HygR") cassette (FIG. 4A, SEQ ID NO:44) as described in Example 3. Hygromycin resistant colonies were selected and screened by colony PCR as described using primers adjacent to the targeted regions of the ZnCys-2845 gene. Primers MA-ZnCys-FP (SEQ ID NO:49) and MA-ZnCys-RP (SEQ ID NO:50) were used to confirm the knockout (GE-8564) and donor fragment insertion into introns; primers MA-5'Bash-ZnCys-FP (SEQ ID NO:63) and MA-5'Bash-ZnCys-RP (SEQ ID NO:64) were used to confirm the insertion of the donor fragment into the 5' regions of the ZnCys-2845 gene; and primers MA-3'Bash-ZnCys-FP (SEQ ID NO:65) and MA-3'Bash-ZnCys-RP (SEQ ID NO:66) were used to confirm the insertion of the donor fragment into the 3' regions of the ZNCys-2845 gene. Eleven of the twelve guide RNAs resulted in isolates that by colony PCR appeared to have the Hyg gene inserted at the targeted locus (insertion into 5' UTR target site -1 was not observed.)

[0306] Quantitative reverse transcription-PCR (qRT-PCR) was performed on RNA isolated from the knockdown lines to determine whether expression of the ZnCys-2845 gene was in fact reduced in these lines. The ZnCys-2845 Bash Knockdown strains were grown under standard nitrogen replete conditions (PM074 (nitrate-only) medium) and harvested during early stationary phase. Total RNA was isolated from ZnCys-2845 Bash Knockdown cells, using methods provided in Example 1, above. RNA was converted to cDNA BioRad's iScript.TM. Reverse Transcription Supermix kit according to the manufacturer's protocol. For PCR, Ssofast EvaGreen Supermix (Bio-Rad, Hercules, Calif.) was used along with gene-specific primers. The PCR reaction was carried out on C1000 Thermal Cycler coupled with a CFX Real-time System (BioRad). Primer and cDNA concentrations were according to the manufacturer's recommendation. Primers for amplifying a sequence of the ZnCys-2845 transcript were SEQ ID NO:67 and SEQ ID NO:68. Transcript levels for each sample were normalized against a housekeeping gene with consistent expression levels under different culture conditions (1T5001704; SEQ ID NO:69) and relative expression levels were calculated using the ddCT method using BioRad's CFX Manager software.

[0307] FIG. 12B shows that several of the strains had reduced levels of ZnCys-2845 transcript. Of these, strains GE-13108 (ZnCys-2845 Bash-2) and GE-13109 (ZnCys-2845 Bash-3), targeting the 5' end of the ZnCys-2845 gene, and strain GE-13112 (ZnCys-2845 Bash-12), targeting the 3' end of the ZnCys-2845 gene, were selected for productivity assays.

Example 8 RNAi Knockdown Construct

[0308] In another strategy to determine whether decreasing expression of the ZnCys-2845 gene would allow the cells to accumulate more carbon than the Cas9 knockout while still producing increased amounts of lipid with respect to wild type, an interfering RNA (RNAi) construct was designed for expression in Nannochloropsis cells. The construct included a sequence designed to form a hairpin that included a sequence homologous to a region of the ZnCys-2845 gene (SEQ ID NO:70), followed by a loop sequence and then followed by the inverse sequence to the ZnCys-2845 gene-homologous sequence, driven by the N. gaditana EIF3 promoter (SEQ ID NO:46) and followed by N. gaditana "terminator 9" (SEQ ID NO:71). The construct also included a gene encoding GFP codon optimized for Nannochloropsis (SEQ ID NO:36) under the control of the Nannochloropsis 4AIII promoter (SEQ ID NO:37) and followed by "terminator 5" (SEQ ID NO:38), as well as a gene conferring hygromycin resistance (SEQ ID NO:45) driven by the TCTP promoter (SEQ ID NO:34) and terminated by the EIF3 terminator (SEQ ID NO:35). The construct was linearized and transformed into wild type Nannochloropsis gaditana WT-3730 by electroporation as described.

[0309] Hygromycin resistant colonies were screened for the presence of the RNAi construct and positive strains were further screened by qRT-PCR as described in Example 7 for knockdown of the ZnCys-2845 transcript levels.

Example 9 Knockdown Constructs in Batch Assay

[0310] ZnCys-2845 RNAi strain GE-13103 and ZnCys-2845 knockdown "basher" strains GE-13108, GE-13109, and GE-13112 were tested in the batch productivity assay described in Example 4 by scaling up the cultures in culture medium PM124 (which includes both NH.sub.4 and NO.sub.3 as nitrogen sources) and by carrying out the assay in PM123 culture medium that includes nitrate as the sole nitrogen source. The ZnCys-2845 Knockout strain GE-8564 and the wild type background strain were run in the same assay as controls.

[0311] The results, provided in Tables 16-18 and shown in FIGS. 13A-13C, were startling. All gene attenuation mutants, including original knockout mutant GE-8564 (triangles), produced FAME in amounts greater than wild type (circles) when cultured with nitrate as the sole nitrogen source on all days sampled (FIG. 13A, data provided in Table 16). However, while the original knockout strain GE-8564 (triangles) had a significantly reduced rate of total organic carbon accumulation with respect to wild type (FIG. 13B), in these conditions, the attenuated knockdown strains--the "bash" strains and RNAi strain having reduced expression of the ZnCys-2845 gene--had rates of TOC accumulation close to or (for example in the case of GE-13112 (represented as Xs)) essentially identical to, wild type (FIG. 13B, data provided in Table 17). Remarkably, these ZnCys-2845 knockdown mutants demonstrated FAME to TOC ratios that were significantly enhanced with respect to wild type (FIG. 13C and Table 18), although not as high as the FAME to TOC ratios of the ZnCys-2845 knockout mutant GE-8564, i.e., the carbon partitioning to lipid in these knockdown attenuation strains was intermediate between that of wild type and the ZnCys-2845 knockout strain.

TABLE-US-00016 TABLE 16 FAME Productivity of ZnCys-2845 Knockdown Strains Compared to Wild Type in Batch Assay with NO3-Containing Culture Medium (mg/L Culture) BASH-2 BASH-3 BASH-12 RNAi-7 ZnCys-KO (GE-13108) (GE-13109) (GE-13112) (GE-13103) (GE-8564) Day WT % incr % incr %incr %incr %incr 3 159.22 279.72 75.68 260.14 233.36 233.36 40.64 233.36 46.56 242.05 52.02 5 191.33 446.40 133.31 377.8 368.41 368.41 55.98 368.41 92.55 360.89 88.67 7 270.37 599.06 121.57 431.41 460.69 460.69 27.96 460.69 70.39 473.53 75.14

TABLE-US-00017 TABLE 17 TOC Productivity of ZnCys-2845 Knockdown Strains Compared to Wild Type in Batch Assay with NO.sub.3-Containing Culture Medium (mg/L Culture) BASH-2 BASH-3 BASH-12 RNAi-7 ZnCys-KO (GE-13108) (GE-13109) (GE-13112) (GE-13103) (GE-8564) Day WT % diff % diff % diff % diff % diff 3 642.4 608.1 -5.34 615.05 -4.26 627.2 -2.37 497.4 -22.57 281.5 -56.18 5 920.75 827.9 -10.09 836.9 -9.11 913.95 -0.74 713.4 -22.52 408.8 -55.01 7 1188 1044.5 -12.08 1044 -12.12 1175.5 -1.05 929.2 -21.78 558.15 -53.18

TABLE-US-00018 TABLE 18 FAME/TOC Ratios of ZnCys-2845 Knockdown Strains Compared to Wild Type in Batch Assay with NO.sub.3-Containing Culture Medium BASH-2 BASH-3 BASH-12 RNAi-7 ZnCys-KO WT 3730 (GE-13108) (GE-13109) (GE-13112) (GE-13103) (GE-8564) Day s.d. s.d. s.d. s.d. s.d. s.d. 3 0.2478 0.0092 0.4599 0.0090 0.4229 0.0096 0.3570 0.0043 0.4690 0.0146 0.8608 0.0334 5 0.2078 0.0012 0.5391 0.0059 0.4514 0.0025 0.3263 0.0106 0.5161 0.0230 0.8824 0.0393 7 0.2276 0.0012 0.5735 0.0051 0.4132 0.0036 0.2942 0.0033 0.4959 0.0069 0.8491 0.0593

[0312] FIG. 14A provides a diagram of the ZnCys-2845 gene and FIG. 14B provides a graph showing normalized ZnCys-2845 RNA levels in cultured strains having insertional BASH mutations ("basher" strains GE-13109 and GE-13112), the RNAi construct (ZnCys-2845 RNAi strain GE-13103), or the knockout (KO) mutation (ZnCys-2845 knockout mutant GE-8564) as quantitated by PCR using the methods provided in Example 7. The ZnCys BASH-3 strain GE-13109 demonstrated an approximately 20% reduction in ZnCys-2845 transcript level, the ZnCys BASH-12 strain GE-13112 demonstrated an approximately 50% reduction in ZnCys-2845 transcript level, and the ZnCys-2845 RNAi isolate (GE-13103) demonstrated an approximately 70% reduction in ZnCys-2845 transcript level. FIG. 14C provides a graph of the FAME/TOC ratio and TOC productivity of each strain based on a batch assay in nitrate-only medium as described above, except that in the assay of FIG. 14C, the ZnCys-2845 knockout strain GE-8564) was not precultured in the presence of ammonium but in nitrate-only medium. As summarized in FIG. 14C, in batch growth with no nitrate, all three ZnCys-2845 gene attenuation lines exhibited increases in carbon partitioning to lipid evident at FAME/TOC ratios (see also Table 18) that were intermediate between wild type and ZnCys knockout (strain GE-8564) FAME/TOC ratios. TOC accumulation in the knockdown mutants were nearly equivalent to wild type (the ZnCys RNAi-7 strain GE-13103 having the greatest impairment of only about 20%), showing a substantial improvement over the reduction shown in the ZnCys-2845 knockout mutant which demonstrates an approximately 85% reduction in average daily TOC productivity (FIG. 14C). The daily FAME and TOC values of the batch assay from which the data of FIG. 14C is derived are provided in the graphs of FIGS. 15A and 15B.

Example 10 ZnCys-2845 Knockdown Mutants in the Semi-Continuous Productivity Assay

[0313] ZnCys-2845 RNAi strain GE-13103, BASH2 strain GE-13108, BASH3 strain GE-13109, and BASH12 strain GE-13112 were then assayed in the semi-continuous productivity assay described in Example 6, except that in this case the assay medium, PM074, included nitrate as the sole nitrogen source and the knockdown strains were pre-cultured in PM124 medium that included 5 mM ammonium in addition to 8.8 mM nitrate. For the GE-13103 ZnCys-2845 RNAi strain, productivity was assayed in two ways: a first set of semi-continuous assay cultures was inoculated using starter cultures that included the PM074 nitrate-only culture medium, and a second set of GE-13103 semi-continuous assay cultures was inoculated using starter cultures that included 5 mM ammonium in addition to 8.8 mM nitrate (PM124 medium).

[0314] The starter cultures were used to inoculate 225 cm.sup.2 rectangular tissue culture flasks, each of which contained a final total volume of 550 ml of culture after inoculation. The cultures were inoculated so that each 550 ml culture had an initial OD.sub.730 of 0.9. A typical inoculum volume was approximately 200 ml of scale-up culture that was added to approximately 350 ml of assay culture medium, which was PM074 (nitrate-only medium). Cultures were diluted daily at mid-day, when the light intensity was at its peak, by removing 30% of the volume (165 mls) and replacing it with the same volume of the assay medium (PM074) plus an additional 10 ml of deionized water to make up for evaporation (included in the make-up medium). Thus, assay cultures inoculated from scale-up ZnCys-2845 RNAi cultures that included 5 mM ammonium in the culture medium (PM124 medium) started out with a significant amount of ammonium (e.g., about 2 mM ammonium or less) that progressively declined and was diluted out further during the course of the assay. Semi-continuous assays were typically run for 10-14 days. Daily lipid and biomass productivities were only calculated for cultures that had reached steady state (where the increase in growth was equal to the dilution factor for the assay).

[0315] During the course of the semi-continuous assay, daily 30% dilutions were with nitrate-only medium (PM074) for all cultures. In these assays, much more lipid was produced on a daily basis by the GE-13103 RNAi knockdown cells scaled up in nitrate-only medium in the semi-continuous assay (filled-in circles, FIG. 16A) as compared with wild type cells, which were in nitrogen replete conditions (diamonds). The amount of lipid produced on a daily basis by the GE-13103 strain was even higher when the scale-up culture medium included ammonium in addition to nitrate (open circles in FIG. 16A). BASH2 strain GE-13108 (Xs), BASH3 strain GE-13109 (triangles), and BASH12 strain GE-13112 (squares) also produced considerably more FAME in the semi-continuous assay than did the wild type strain.

[0316] FIG. 16B provides the daily amount of FAME produced by the knockdown strains in the semi-continuous assay that included nitrate as the sole nitrogen source in the culture medium (PM074 medium). The knockdown strains, which included GE-13108 (5' Bash2), GE-13109 (5' Bash3), GE-13112 (3' Bash12), and GE-13103 (RNAi-7) were pre-cultured in nitrate plus ammonium medium PM124. The RNAi knockdown strain GE-13103 was also assayed after being pre-cultured in nitrate-only medium (PM074), alongside wild type strain WT-3730 pre-cultured in nitrate-only medium (PM074) (which is a nitrogen replete medium for the wild type strain). Knockout strain GE-8564 was cultured separately in nitrate-only (PM074) medium as the culture medium used in the semi-continuous assay. The table of FIG. 16B demonstrates that all of the knockdown strains had higher productivities than the wild type strain when cultured in the semi-continuous assay with regular dilution using a culture medium in which nitrate was substantially the sole nitrogen source (PM074). In this assay, knockdown strain GE-13112 (BASH12), demonstrated production of an average daily amount of FAME that was 83% greater than wild type, and knockdown strain GE-13109 (BASH3), demonstrated production of an average daily amount of FAME that was 81% greater than wild type on nitrate. Knockdown strain GE-13108 (BASH2), demonstrated production of an average daily amount of FAME that was 88% greater than wild type diluted with the same culture medium (PM074) over the course of the assay. Thus, all of the insertional knockdown mutants targeting non-coding regions of the ZnCys-2845 gene demonstrated substantial increases in areal FAME productivity of at least 70% higher (and approximately 80%-90% higher), than wild type cells in nitrate-only culture medium, with only minimal TOC productivity decreases of approximately 5-15% in the GE-13108 (BASH2), GE-13112 (BASH12), and RNAi-7 GE-13103 strains compared to the wild type strain (FIG. 16C). The RNAi-7 strain GE-13103 pre-cultured in nitrate-only medium produced on average is 107% more FAME on a daily basis than wild type cultured under the same conditions. The RNAi-7 strain GE-13103 pre-cultured in a medium that included both ammonium plus nitrate produced on average is 122% more FAME on a daily basis than wild type cultured under the same conditions. Thus, the GE-13103 gene attenuation mutant produced at least twice as much lipid as wild type in a semi-continuous assay in which the cultures were regularly diluted with nitrate-only medium, regardless of the nitrogen source in the pre-culture medium. The knockout mutant, GE-8564, also produced somewhat more FAME than wild type in the assay, although the increase was not as great as for the knockdown mutants (approximately 40% greater than when both were cultured in nitrate-only medium). The amount of FAME produced by knockout mutant GE-8564 cultured in nitrate-only medium fell off drastically beginning at about day 6 of the culture, reflecting large losses in biomass (Table 20).

[0317] These improvements in FAME productivity by the knockdown strains are presented as a percentage increase over wild type, averaged over the duration of the culture, in Table 19. All of the knockdown strains (GE-13103, GE-13108, GE-13109, and GE13112) had increases in FAME productivity (i.e., g/m.sup.2/day) with respect to wild type over the course of the culture, ranging from 81% to 122% over the course of the entire culture, with even greater productivity increases seen in the first four days of culturing, ranging from 100% (i.e., twice the wild type productivity) to 160%. GE-13103, the RNAi knockdown strain, had the largest productivity increase with respect to wild type over the course of the semi-continuous culture, approximately 100% improvement (when pre-cultured in PM074) and approximately 120% improvement (when pre-cultured in PM124).

TABLE-US-00019 TABLE 19 FAME Productivity of Knockdown and Knockout Strains (g/m.sup.2/day) Day 1-Day 4 Day 8-Day 11 Day 1-Day 11 Strain s.d. % impr s.d. % impr % impr WT-3730 2.37 0.11 -- 2.41 0.08 -- 2.43 -- GE-13112 (BASH-12) 4.75 0.20 100% 4.14 0.10 72% 4.44 83% GE-13109 (BASH-4) 4.89 0.16 107% 3.90 0.13 62% 4.39 81% GE-13108 (BASH-3) 6.15 0.43 160% 2.84 0.46 18% 4.55 88% GE-13103 (RNAi-7) 5.45 0.17 130% 4.39 0.19 82% 4.95 104% (pre-cultured in NO3) GE-13103 (RNAi-7) 5.83 0.32 146% 4.82 0.26 100% 5.40 122% (pre-cultured in NH4 + NO3) GE-8564 (ZnCys-KO) 2.98 0.20 26% 3.14 0.12 30% 3.22 33% Urea medium GE-8564 (ZnCys-KO) 5.80 0.84 145% 1.16 0.43 -52% 3.39 40% Nitrate medium

[0318] The amount of TOC accumulated on a daily basis by the knockdown strains was only slightly to modestly less than the TOC accumulated by wild type in knockdown cultures, GE-13109 (5' Bash-3), and GE13112 (3' Bash-12) although it was significantly lower in GE-13108 (5' Bash-2) and knockout strain GE-8564 cultured in nitrate-only medium (FIG. 16C and Table 20). Nevertheless, the TOC productivity in the RNAi knockdown strain (GE-13103) that exhibited an approximately 100% increase in FAME productivity over 11 days (and approximately 120% increased when precultured with ammonium) was only about 18% reduced with respect to wild type, and the TOC productivities of BASH-12 and BASH-4 knockdown mutant strains GE-13112 and GE-13109 (that demonstrated increases of at least 80% in FAME productivity over eleven days) were decreased by only 5% or less.

TABLE-US-00020 TABLE 20 Daily Average TOC Productivity of Knockdown and Knockout Strains Strain g/m.sup.2/day s.d. % diff WT 9.50 0.30 0% GE-13112 (BASH-12) 9.43 0.60 -1% GE-13109 (BASH-3) 9.06 0.56 -5% GE-13108 (BASH-2) 6.33 2.32 -33% GE-13103 (RNAi-7) 7.75 0.87 -18% (pre-cultured in NO3) GE-13103 (RNAi-7) 8.27 1.09 -13% (pre-cultured in NH4 + NO3) GE-8564 (ZnCys-KO) 8.86 0.26 -7% Cultured in Urea GE-8564 (ZnCys-KO) 4.68 2.88 -51% Cultured in NO3

[0319] The ZnCys-2845 knockdown and knockout cultures all demonstrated increased FAME to TOC ratios as compared to wild type (solid diamonds) in the semicontinuous assay in nitrate medium (FIG. 16D and Table 21). When scaled up in nitrate only medium, the RNAi knockdown strain GE-13103 (closed circles) demonstrated a greater than 100% increase, approximately a 150% increase, in FAME/TOC ratio with respect to wild type and the same GE-13103 strain scaled up in nitrate plus ammonium medium (open circles) demonstrated an 153% increase in their FAME to TOC ratio in the semi-continuous productivity assay (Table 21).

TABLE-US-00021 TABLE 21 FAME/TOC Ratios of Knockdown and Knockout Strains Strain fame/toc s.d. % impr WT-3730 0.26 0.02 0% GE-13112 (BASH-12) 0.47 0.01 82% GE-13109 (BASH-3) 0.48 0.02 87% GE-13108 (BASH-2) 0.73 0.05 180% RNAi-7 (precultured 0.64 0.02 147% in NO3) RNAi-7 (precultured 0.66 0.04 153% in NO3 + NH4) GE-8564 (ZnCys-KO) 0.36 0.03 41% Cultured in Urea GE-8564 (ZnCys-KO) 0.69 0.11 168% Cultured in NO3

[0320] These genetically engineered knockdown cells were able to partition more of their carbon to lipid than wild type (FIG. 16D). The increased FAME/TOC ratios were particularly notable in the ZnCys RNAi attenuation strain GE13103, as it had only modest reductions in TOC (between about 15% and about 20%, Table 20) coupled with increased FAME with respect to wild type throughout the assay (greater than 100% increase, an approximately 120% increase, Table 19).

[0321] Graphs of volumetric FAME and TOC productivities of wild type, Cas9 Editor line GE-6791, and ZnCys-2845 knockdown lines GE-13112 (BASH-12A), GE-13109 (BASH-3A), and GE-13108 (BASH-2A) assayed in a separate semicontinuous assay using nitrate-only medium are provided in FIGS. 17A and 17B (data provided in Table 22 and Table 23), and the average areal (g/m.sup.2/day) TOC and FAME productivities of the wild type strain and Cas9 editor line (as controls) and the BASH-3, BASH-12, and RNAi mutants (all pre-cultured in nitrate-only medium) in this assay are summarized in the graph of FIG. 18, where it can be seen that the RNAi strain has the highest FAME productivity of the tested mutants.

TABLE-US-00022 TABLE 22 Average Daily FAME Productivity of Knockdown Strains in Semi-Continuous Assay Using Nitrate-only Medium AV DAILY FAME % PRODUCTIVTY INCREASE STRAIN (sd) FROM WT WT 2.42 0 (0.13) ZnCys-BASH-12 4.19 73.1 (0.25) ZnCys-BASH-3 4.48 85.1 (0.35) ZnCys-RNAi-7 4.88 101.7 (0.44) Ng-Cas9+ 2.53 4.5 (0.10)

TABLE-US-00023 TABLE 23 Average Daily FAME Productivity of Knockdown Strains in Semi-Continuous Assay Using Nitrate-only Medium AV DAILY TOC % PRODUCTIVITY DECREASE STRAIN (sd) FROM WT WT 9.96~(0.47) 0 ZnCys-BASH-12 9.48~(0.42) 4.8 ZnCys-BASH-3 9.04~(0.40) 9.2 ZnCys-RNAi-7 8.09~(0.58) 18.8 Ng-Cas9+ 9.80~(0.45) 1.6

[0322] The increases in FAME/TOC were significantly less at the outset of the culture period in the ZnCys RNAi attenuation cultures that had been pre-cultured in a medium containing a mixture of nitrate and ammonium than in the ZnCys RNAi attenuation cultures that had been pre-cultured in a medium containing only nitrate (FIG. 16D). Thus it appeared that strains pre-cultured in nitrate plus ammonium media included reduced nitrogen (ammonium) from the pre-culture that was introduced into the assay cultures, and this residual ammonium repressed lipid biosynthesis to some degree. This effect disappeared by the fifth day of the assay (see FIG. 16A, open circles (RNAi strain precultured with ammonium in the medium) versus solid circles (RNAi strain precultured with only nitrate in the medium)), by which time the rate of production of lipid by the ZnCys RNAi attenuation strain did not significantly differ between cultures that had been inoculated with a seed culture that included ammonium and nitrate and cultures that had been inoculated with a seed culture that included only nitrate as a nitrogen source. At this point presumably the cultures that had been pre-cultured in medium that included ammonium ran out of their reduced nitrogen source and induced lipid biosynthesis to approximately the same degree as the cultures that had not been pre-cultured in an ammonium-containing medium. This interpretation was supported by analysis of the nitrogen present in the cultures. For total nitrogen (TN) analysis of cell pellets, 10 ml culture samples were spun down, the media removed from the pellets, and each pellet was resuspended in 1 ml nanopure H.sub.2O, which was then transferred to a 22 ml vial, to which 19 ml of nanopure H.sub.2O was added. Total nitrogen analysis was performed using a Shimadzu TOC-V.sub.CSH/VN.sub.M-1 analyzer. FIG. 19 shows that the amount of total nitrogen in the cell pellets was significantly higher in the GE-13103 cultures that had been inoculated with a pre-culture that included ammonium in the medium (open circles) than in the cultures that had been inoculated with a pre-culture that included only nitrate (NO.sub.3) (e.g., closed circles). Thus it appeared that the ZnCys RNAi attenuation cells, while able to utilize nitrate for growth (as evidenced by continued TOC accumulation, e.g., FIG. 16C), still induced lipid biosynthesis as long as ammonium was present at low concentrations, for example, of less than about 2 mM or less than about 1.5 mM.

[0323] The relationship between the amount of ammonium present in the ZnCys-2845 RNAi strain GE-13103 cultures during semi-continuous assays was investigated in semi-continuous productivity assays performed as described above in which daily samples were analyzed for nitrogen content of the whole culture (culture medium plus cells) as well as FAME content as described in the examples above.

[0324] FIG. 20 shows the amount of FAME and nitrogen present in the culture on successive days of semi-continuous culture graphically. Whole culture total nitrogen (TN) was determined by removing a 2 ml sample of the culture to a 22 ml vial, to which 18 ml of nanopure H.sub.2O was added, and analyzing the sample using a Shimadzu TOC-V.sub.CSH/VN.sub.M-1 analyzer. The amount of nitrate that could be accounted for in the PM074 medium was subtracted from the total nitrogen of the sample to arrive at the amount of nitrogen present as ammonium indicated in FIG. 19. Because the ammonium present in the PM124 starter culture was progressively diluted out of the cultures that were inoculated with PM124 (NH.sub.4+NO.sub.3) starter cultures, it can be seen that for this sample, FAME production (open diamonds) rises as ammonium concentration (solid diamonds) falls. Ammonium levels in the culture below about 2.5 mM, and especially below about 2 mM, appeared to result in induction of FAME production in the attenuated RNAi strain (open diamonds).

Example 11 Relationship of Productivity of ZnCys-2845 Attenuation Mutants to Available NH.sub.4 Concentration

[0325] The relationship between nitrogen availability and FAME productivity in the ZnCys-2845 RNAi strain GE-13103 was further investigated in a semi-continuous productivity assay as described in Example 10 except that the semi-continuous assay was performed in three separate culture media in which the concentration of ammonium was held constant at three different levels. Wild type Nannochloropsis gaditana (WT-3730) was also included in the assay, where the wild type strain was cultured in the standard PM074 medium that included no ammonium (but included 8.8 mM nitrate as the sole source of nitrogen).

[0326] In this experiment, starter cultures that included culture medium containing either 0.5 mM, 1.0 mM, or 2.5 mM ammonium in addition to 8.8 mM nitrate were used to inoculate assay flasks that included culture media that included the corresponding amount of ammonium (in addition to 8.8 mM nitrate). After reaching steady state the cultures were diluted back daily with the ammonium-supplemented media, such that one set of triplicate cultures in which the assay medium included 0.5 mM ammonium was inoculated from a seed culture that included 0.5 mM ammonium and was diluted daily with a medium containing 0.5 mM ammonium throughout the assay, another set of triplicate cultures was inoculated from a seed culture that included 1.0 mM ammonium and included 1.0 mM throughout the assay, and a third set of triplicate cultures was inoculated from a seed culture that included 2.5 mM ammonium and included 2.5 mM ammonium throughout the assay. In each case, the medium was PM074 that includes 8.8 mM nitrate as the sole source of nitrogen that can be used by the microorganisms, supplemented with the appropriate amount of NH.sub.4Cl as well as with 5 mM Hepes, pH 7.5. The results can be seen in Tables 22-24. All samples were assayed in triplicate, and provided values are the average of the three cultures.

[0327] FIG. 21A shows the amount of FAME present in the culture on successive days of semicontinuous culture for cultures held at 0.5 mM, 1.0 mM, and 2.5 mM ammonium (solid diamond and triangles, representing RNAi symbols). It can be clearly seen that reducing the ammonium concentration of the culture from 2.5 mM (squares) to 1.0 mM (triangles) increases FAME productivity, which is increased even further when the ammonium concentration is maintained at 0.5 mM (Xs) (see also Table 24).

TABLE-US-00024 TABLE 24 Daily FAME Content (mg/L) of Cultures: Average of Triplicate FAME Values (sd) Strain Day1 Day2 Day3 Day4 Day5 Day6 Day7 Day8 Day9 Day10 WE-3730 44.3 46.31 48.63 48.27 45.91 44.35 45.73 46.48 45.07 41.15 (0.32) (1.53) (1.87) (0.76) (1.66) (1.47) (0.16) (0.81) (0.91) (5.94) GE-13103 35.9 35.5 39.0 35.3 32.5 29.7 35.1 42.3 57.8 41.2 2.5 mM NH4C1 (2.92) 3.24 0.16 0.46 3.36 4.15 2.01 5.09 0.80 3.17 GE-13103 60.0 58.3 58.8 55.3 51.7 48.2 52.5 57.6 60.9 54.5 1.0 mM NH4C1 (1.85) (1.20) 94.290 (0.79) (5.83) (5.75) (6.97) (1.92) (1.11) (1.41) GE-13103 83.5 85.8 87.4 84.4 81.1 75.4 73.9 78.4 83.6 76.9 0.5 mM NH4C1 (0.86) (0.290 (0.980 (0.550 (5.130 (3.37) (3.80) (3.35) (4.60) (3.11)

[0328] The FAME productivity is provided in the table of FIG. 21B. The FAME productivity of the GE13103 knockdown strain in 2.5 mM NH.sub.4 medium is reduced by about 15% with respect to wild type FAME productivity in nitrate-only medium (which does not induce lipid production in the wild type strain). At lower ammonium concentrations however, the knockdown mutant shows greater FAME productivity over the course of the assay than does the wild type strain. For example, in culture medium in which the ammonium concentration is 1 mM, the knockdown mutant strain demonstrates an increased average daily FAME productivity of 22%, while at 0.5 mM ammonium, GE-13103 demonstrates an increased average daily FAME productivity of 77% with respect to the wild type strain, that is, the GE-13103 knockdown strain at very low ammonium concentration produces almost twice as much FAME lipids as wild type.

[0329] Nevertheless, FIG. 21C shows that reducing the ammonium concentration of the culture medium below 2.5 mM NH.sub.4 does not have a major effect on TOC accumulation by the GE13103 knockdown mutant (Table 25).

TABLE-US-00025 TABLE 25 Daily TOC Content (g/m.sup.2/day): Average of Triplicate Values (sd) Strain Day1 Day2 Day3 Day4 Day5 Day6 Day7 Day8 Day9 Day10 Day 11 WT-3730 179.3 177.35 181.7 181.57 172.43 173.7 172.13 171.67 174.1 185 189.47 (7.56) (3.04) (1.56) (7.38) (6.09) (5.36) (3.50) (4.44) (4.36) (2.19) (4.35) GE-13103 137.7 131.1 132.5 123.2 118.6 125.2 127.9 134.9 143.2 153.0 167.5 2.5 mM NH4 (5.59) (6.92) (1.70) (10.63) (13.35) (13.36) (11.15) (5.61) (4.55) (7.74) (12.62) GE-13103 155.2 155.7 152.2 153.0 147.3 163.2 151.2 155.3 162.8 170.0 176.1 1.0 mM NH4 (10.53) (14.08) (12.84) (15.22) (16.67) (8.20) (19.97) (15.51) (13.06) (11.60) (10.77) GE-13103 164.4 167.7 169.1 166.2 160.2 159.7 155.8 160.2 164.3 169.1 172.4 0.5 mM NH4 (4.95) (4.74) (6.86) (5.11) 7.06) (6.33) (7.68) (5.65) (6.22) (1.99) (7.35)

[0330] For example, the average daily TOC productivity of the knockdown mutant strain cultured in 0.5 mM ammonium was essentially identical to that of wild type cultured under nitrogen replete (nitrate only) conditions (FIG. 21D). Thus, the GE-13103 knockdown mutant demonstrated at least 75% more lipid productivity while demonstrating no reduction in biomass productivity with respect to wild type cells in nitrogen replete conditions over a period of at least 10 days of culturing. As shown in FIG. 21F, cell counts, as determined by flow cytometry, remained reasonably consistent for a given ammonium concentration throughout the assay, indicating that the cells were actively dividing throughout the semi-continuous assay under all conditions, including conditions in which the low-ammonium cultures were induced for lipid biosynthesis, as indicated by the elevated FAME/TOC ratios of the 1 mM ammonium and 0.5 mM ammonium-containing cultures (as demonstrated in FIG. 21E).

[0331] The FAME to TOC ratio of the GE-13103 knockdown mutant cultured in medium having varying ammonium concentrations is shown in FIG. 21E. The FAME to TOC ratio remains between about 0.3 and 0.4 when the ammonium concentration is between about 1 mM and about 2.5 mM, but increases further when the ammonium concentration drops from about 1.0 mM to about 0.5 mM, remaining close to 0.5 throughout the assay using 0.5 mM ammonium in the medium, for example well within the range of between about 4.0 and about 6.0, and within the region of between about 4.5 and about 5.5 (see Table 26).

TABLE-US-00026 TABLE 26 FAME/TOC Ratios: Average of Triplicate FAME/TOC Values (sd) Strain Day1 Day2 Day3 Day4 Day5 Day6 Day7 Day8 Day9 Day10 WT-3730 0.2 0.3 0.27 0.27 0.27 0.26 0.27 0.27 0.26 0.22 (0.01) (0.01) (0.01) (0.01) (0.00) (0.00) (0.01) (0.01) (0.00) (0.03) GE-13103 0.3 0.3 0.3 0.3 0.3 0.2 0.3 0.3 0.4 0.3 2.5 mM NH4Cl (0.01) (0.01) (0.00) (0.00) (0.01) (0.01) (0.01) (0.03) (0.01) (0.01) GE-13103 0.4 0.4 0.4 0.3 0.4 0.3 0.3 0.4 0.4 0.3 1.0 mM NH4C1 (0.00) (0.00) (0.01) (0.01) (0.00) (0.00) (0.00) (0.03) (0.03) (0.01) GE-13103 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 mM NH4Cl (0.02) (0.01) (0.01) (0.01) (0.01) (0.02) (0.02) (0.00) (0.01) (0.01)

[0332] Thus, the strains obtained by attenuating expression of a gene as provided here that regulates lipid biosynthesis are able to actively divide while producing considerably more lipid than wild type. The ability to sustain elevated levels of lipid production without a decline in TOC accumulation throughout the assay (FIGS. 22A-22E), indicates the mutants provided herein can provide sustained high-level lipid production such as in continuous and semi-continuous cultures.

Example 12 Analysis of Protein, Carbohydrate, and Lipid Content of ZnCys Mutants

[0333] In the above experiments (e.g., Example 4), FAME and TOC productivities of knockout mutant strain GE-8564 were found to be essentially equal to those of the wild type strain when both were cultured in the presence of ammonium (FIGS. 8A-8C), suggesting that a bottleneck in nitrate assimilation led to the marked phenotypes of increased lipid production that were observed only when nitrate was used as the sole nitrogen source. Knockdown mutants of ZnCys-2845 were observed to exhibit substantial increases in FAME productivity (Table 16 and FIG. 13A as well as FIGS. 16A and 16B) with minimal TOC decreases of from about 1% to about 33% (Table 17 and FIG. 13B; FIG. 16C). FAME and TOC productivities for a semi-continuous assay that included wild-type, ZnCys-2845 BASH-3, ZnCys-2845 BASH-12, and ZnCys-2845 RNAi strain GE-13103 are shown in the graphs of FIGS. 17A and 17B, respectively. ZnCys BASH-3, ZnCys BASH-12, and ZnCys RNAi all exhibited substantial increases in aerial FAME productivity (up to 103% for ZnCys RNAi-7) with only minimal TOC decreases of approximately 5-15% compared to the wild type strain and the Cas9 progenitor line (FIG. 18). To determine how carbon was allocated to major categories of biomolecules, the strains were grown in the semi-continuous assay system as described in Example 10, where the PM074 dilution medium included nitrate as the sole nitrogen source. In this assay the RNAi line demonstrates increased FAME productivity and the knockout line is unable to maintain growth (FIGS. 22A-E). The strains from these cultures were assessed for carbohydrate, lipid, and protein, which together accounted for about 75% of TOC.

[0334] For HPLC analysis of lipids, 2 ml samples of each culture were spun down at maximum speed for 5 minutes, the supernatants were removed, and pellets were re-suspended in 400 .mu.L of H.sub.2O. The cell suspensions (approximately 500 .mu.L) were transferred to 4 ml glass vials with Teflon lined caps. 500 .mu.L of glass beads (212-300 m diameter) were added to each of the cell suspensions, after which 50 .mu.L of 50% H.sub.2SO.sub.4 and 100 .mu.L of 5M NaCl were added. Bead beating was performed for 5 minutes at 1 krpm, then 2 ml of hexane was added to each sample, and bead beating was repeated for 5 minutes at 1 krpm. The samples were loaded onto a multi-tube vortexer and shaken for 30 minutes at 1 krpm, and then vortexed for 30 seconds at 2.5 krpm. 500 .mu.L of the organic layer was transferred to an HPLC vial, and 50 .mu.L of internal standard solution (1 mg/ml 6-ketocholestanol in toluene) was added to each vial. Standards were from NuCheck, Sigma-Aldrich, or Supelco. The vials were capped and vortexed briefly (5 seconds at 2.5 krpm) prior to HPLC analysis. The HPLC was run at a flow rate of 2 ml/minute on a Chromegasphere SI-60 150 mm.times.4.6 mm.times.10 m column (ES Industries), with a column compartment set at 40.degree. C. The injection volume was 25 .mu.L with a draw and eject speed of 200 .mu.L/minute. Eluent A was hexane and Eluent B was an 80:10:10:1 mixture of hexane, isopropanol, ethyl acetate, and 10% formic acid in isopropanol, run as a gradient program as follows: 2% B at 0.0 min; 2% B at 1.0 min; 35% B at 8.0 min; 98% B at 8.5 min; 98% B at 11.5 min; 2% B at 11.6 min; stop time: 11.6 minutes; 5 minutes post time. The detector was ELSD at 30.degree. C. and 3.5 bar N2, with a gain of 5.

[0335] Total carbohydrate analysis was conducted on .about.0.7 mg TOC equivalent of cell culture concentrated to 0.5 ml in phosphate buffered saline (PBS) after three centrifugations followed by washing with PBS. Acid hydrolysis was used to convert carbohydrates to their constituent monomers by the addition of 0.5 ml deionized H.sub.2O and 1 ml 6 N HCl and U-.sup.13C-glucose and -galactose as internal standards at a final concentration of 50 .mu.g/ml each. Samples were heated at 105.degree. C. for one hour in glass vials with PTFE-lined capped. One hundred .mu.l aliquots of the room temperature cooled, 3,000 g centrifuged (1 min) samples were dried in an EZ-2 Genevac (Stoneridge, N.Y.) and derivatized with MSTFA/TMCS and analyzed by GC-MS according to Ruiz-Matute et al. (2011) J. Chromatogr B Analyt Technol Biomed Life Sci 879: 1226-1240. Internal .sup.13C labeled standards were used to quantify the concentration of the major carbohydrate monomers, glucose and galactose, and estimate the concentration of less abundant sugars (arabinose, rhamnose, xylose, and mannose). These were summed to yield a total saccharide concentration in ug/ml which was converted to the carbon content of total carbohydrates by a multiplication factor of 0.45 (i.e., .about.45% of carbohydrate mass is represented by carbon. This value was divided by the amount of TOC detected in an identical aliquot of concentrated cell culture to estimate the percent of carbon allocated to carbohydrate.

[0336] Total amino acid analysis was conducted by derivatization of whole amino acid hydrolysate to propoxycarbonyl propyl esters using a modified method according to the EZ:faast kit from Phenomenex (Torrance, Calif.). Briefly, to 0.5 ml concentrated cells (as described for carbohydrate analysis above) 800 .mu.l of 6 N HCl containing 200 .mu.l/ml thioglycolic acid, 10 .mu.l of .beta.-mecraptoethanol, and 200 .mu.l of 2 mM norvaline (internal standard) were added and the vortexed sample was incubated at 110.degree. C. for 24 h. Samples cooled to room temperature were centrifuged at 1,500 g for 1 minute and a 50 .mu.l aliquot was transferred to a fresh 2 ml GC vial. Aliquots were derivatized and analyzed by GC-MS according to the EZ-faast manual and (8). This method allowed for the quantification of Ala, Gly, Val, Leu, Ile, Pro, Asp+Asn, Met, Glu+Gln, Phe, Lys, Tyr, and Cys; Trp, Thr, Ser, Arg, and His were excluded. Volumetric concentrations of each detected hydrolyzed amino acid was converted to the carbon content present in that amount. These values were summed to and normalized to TOC as described for total carbohydrates above to give an estimate of carbon allocated to protein.

[0337] The results are seen in FIG. 23, where it can be seen that both attenuated ZnCys mutants ZnCys-BASH-12 and ZnCys RNAi had decreases of approximately 45-50% in protein compared to the wild type strain, accompanying an approximately 90-125% increase in lipids in the strains. Consistently, the ZnCys knockout strain were observed to have the highest C:N ratios while ZnCys RNAi displayed more intermediate levels (FIG. 22C), suggesting there may be a threshold C:N value that maximizes lipid productivity. The ZnCys knockout strain appears to be beyond that threshold, partitioning so much carbon into lipid that overall biomass and lipid productivity are negatively affected. In contrast, in this set of gene attenuation mutants, the ZnCys RNAi appears to have the optimal C:N value for lipid productivity in the range of about 10-15.

TABLE-US-00027 TABLE 27 Protein, Carbohydrate, and Lipid (FAME) % Composition of Wild Type and ZnCys Knockdown Strains Change Change Change Change STRAIN Protein from wt Carb from wt FAME from wt Other from wt WT 40.2 0 11.2 0 19.6 0 29.1 0 (0.55) (0.50) (0.32) (0.27) ZnCys- 22.5 -44% 12.7 +13% 37.6 +92% 27.2 -6.5% BASH-12 (0.70) (0.12) (2.19) (2.94) ZnCys- 20.1 -50% 12.7 +13% 42.7 +118% 24.9 -14% RNAi-7 (2.43) (0.70) (4.73) (1.59)

[0338] BASH-12 strain GE-1112 allocated approximately 38% of its carbon to FAME lipids, and approximately 22% of its carbon to protein, while RNAi strain GE-13103 allocated approximately 43% of its carbon to lipid, and approximately 20% of its carbon to protein. This is distinguished from wild type cells in nitrate-only medium that allocate approximately 20% of carbon to lipid, and approximately 40% of carbon to protein. (In both mutants and wild type cells, approximately 10-15% of carbon is allocated to carbohydrates.) Thus both ZnCys gene attenuation ("knockdown") mutants increased carbon allocation to lipid by 90-120% (doubling lipid productivity with respect to wild type) largely at the expense of allocation of carbon to protein, which dropped by about 40-50% with respect to the carbon allocation to protein in wild type cells cultured under the same conditions.

Example 13 Transcriptomic Analysis of the ZnCys-2845 Knockout and Knockdown Mutants

[0339] The ability of ZnCys-2845 knockout strain GE-8564 to accumulate FAME and TOC at levels essentially identical to wild type cells when the culture medium was supplemented with ammonium (Tables 7-9, FIG. 8), indicated the mutant was impaired in nitrate assimilation. To further investigate nitrogen assimilation in these mutants, steady-state mRNA levels of key N-assimilation genes by qRT-PCR were determined to gain a better understanding of N-deficiency in the mutants under induced (nitrate-only medium) and non-induced (ammonium supplementation) conditions.

[0340] A nitrate reductase mutant was engineered using the same Cas9 Editor line described in Example 2. Briefly, a guide RNA was designed having the target sequence of a portion of the coding region of the N. gaditana nitrate reductase gene Naga_100699 g1. The guide RNA (having target sequence SEQ ID NO: 193) was synthesized as disclosed in Example 3, and transformed into the Cas9 editor line along with the donor fragment (SEQ ID NO:44) as described in Example 2. The resulting nitrate reductase knockout strain (NR--KO) served as a control for the inability to assimilate nitrate, as a functional nitrate reductase enzyme is necessary to assimilate nitrogen when nitrate is the sole nitrogen source. Effectively, the NR--KO strain is under nitrogen starvation when cultured in nitrate-only medium.

[0341] Steady-state mRNA levels of key N-assimilation genes were assessed by qRT-PCR to gain a better understanding of N-deficiency in the mutants under induced (NO.sub.3--) and non-induced (NH.sub.4+) conditions, where the nitrate reductase mutant (NR--KO) created by Cas9-mediated mutagenesis was used as an N-starvation control under growth on NO.sub.3.sup.-. When grown on medium that included ammonium all strains shared similar gene expression profiles for the N-assimilation gene set, consistent with their wild type phenotype with regard to biomass and FAME accumulation when cultured with ammonium-containing medium (FIG. 24, ammonium transcriptional profiles of the ZnCys knockout, the ZnCys RNAi knockdown, wild type, and the NR knockout shown in columns 2-5).

TABLE-US-00028 TABLE 28 Primer Sequences for Transcripts Measured by Quantitative Real-Time PCR N. gaditana qRT-PCR sense primer / Gene Description genome ID qRT-PCR antisense primer NAR1 Formate Nitrite Naga_100100g7 GCCAACCTGCCAGTAAAATTC Transporter (SEQ ID NO: 153) AGAGCGGGATTCTGTTCTTG (SEQ ID NO: 154) Amt2 Ammonium Transporter Naga_100099g15 AGAACGTGGGTAAGATGCAAC (SEQ ID NO: 155) ACCAGCCAAACCAGAGAAG (SEQ ID NO: 156) GS2 Glutamine Synthase Naga_100003g1 19 GGCATACCTATTCATCCGCTAG (SEQ ID NO: 157) CAAATGACCAAGCACCAACTC (SEQ ID NO: 158) NAR2 Nitrite Transporter Naga_100046g36 GCGAGGCATCTTGTGAATTG (NAR1) (SEQ ID NO: 159) ACGGAGTGTTCAAATCCCAG (SEQ ID NO: 160) GS1 Glutamine Synthase Naga_100056g25 CATGGACTCATTCTCCTACGG (SEQ ID NO: 161) ATCCTCGAAATATCCGCACC (SEQ ID NO: 162) GOGAT1 Glutamate Synthase Naga_101084g2 TGGATGCAAACGAGATGCTAG (SEQ ID NO: 163) AGGAAAGCGGGAATAGTGTG (SEQ ID NO: 164) GDH Glutamate Naga_100063g22 GGGACTCGTTGGAAGGTAAG Dehydrogenase (SEQ ID NO: 165) CATTTCCACAAGTTTCTCCGC (SEQ ID NO: 166) GOGAT2 Glutamate Synthase Naga_100005g23 AAGGGAATGTCTTGGAACCG (plastid) (SEQ ID NO: 167) AGTGGGTAGACAGTGGAGAG (SEQ ID NO: 168) NRT2 Nitrate high affinity Naga_100699g1 AGTGCTATGGAGTTTTGCGG Transporter (SEQ ID NO: 169) TTGGGATTTGGTCAAGGAGAG (SEQ ID NO: 170) NiR Nitrite Reductase Naga_100852g1 GCCGATCCTTTCTTGCAAAC (SEQ ID NO: 171) AGCGTTCAATCAGGTCCAAG (SEQ ID NO: 172) NR Nitrate Reductase Naga_100699g1 GCTATATTGGAGAATCCGGCG (SEQ ID NO: 173) GGGAACGTCAACAGTGATAGTG (SEQ ID NO: 174) Amt1 Ammonium Transporter Naga_100551g3g1 CCTTCGGTGCCTATTTCGG AmtB-like protein (SEQ ID NO: 175) CATGTCGCTGGTATAGGATGC (SEQ ID NO: 176) UreT Urea active transporter- Naga_100311g2 ATGGCAGTAGAAATGGACCC like protein (SEQ ID NO: 177) AGTAAGAGAACGAAAAGGGCG (SEQ ID NO: 178) qRT-PCR Protein of Unknown Naga_100004g25 CTCTCCTATTGCTTTCCCTCG control Function (SEQ ID NO: 179) CTACCAACACCTCTACACTTCC (SEQ ID NO: 180)

[0342] However, when grown on nitrate as the sole nitrogen source, NR--KO showed a radically different expression profile from the ZnCys mutant lines (FIG. 24, column 1 compared with columns 6 & 7 showing transcriptional profiles of the ZnCys-2845 knockout and RNAi knockdown mutants). Consistent with previous reports on N-deprived N. gaditana (Radakovitz et al. 2012), a large number of genes involved in N-assimilation were severely upregulated in the NR--KO (shown in red color), including two ammonium transporters (AMT1 and AMT2), a glutamate synthase (GOGAT1), a NO.sub.3.sup.- transporter (NRT2) and nitrite reductase (NiR). Interestingly, this response was not observed for ZnCys mutants. In fact, gene expression profiles for the ZnCys-2845 knockout and the ZnCys-2845 RNAi knockdown engineered mutants more closely resembled wild type under these conditions, though NiR and NRT2 were significantly down regulated in the ZnCys-2845 knockout with respect to wild type, thus offering a possible explanation to the N-deficiency of the cells (FIG. 22C). Analysis of protein levels by Western blotting showed that nitrate reductase could not be detected in extracts of ZnCys-2845 knockout strain GE-8564, while a signal was detected in ZnCys-2845 RNAi knockdown strain GE-13103 extracts as well as wild-type extracts (FIG. 25). Likewise, a very weak signal was observed for the nitrogen assimilation enzyme glutamine oxoglutarate aminotransferase (GOGAT1) in GE-8564, while it was more apparent for GE-13103.

[0343] Protein level changes in the plastid lipid biosynthetic machinery were also assessed using specific peptide antibodies against ACCase and fatty acid synthesis (FAS) pathway components (FIG. 25). For antibody production, two peptides (#1 and #2 in Table 29) were synthesized and injected into rabbits. Terminal cysteines are shown for reference.

TABLE-US-00029 TABLE 29 Peptide Sequences Used to Generate Antibodies Detecting Fatty Acid Biosynthesis Enzymes in N. gaditana N. gaditana Gene Description genome ID Peptide #1 Peptide #2 ACCase Acetyl-CoA Naga_100605g1 C-FKFADTPDEESPLR C-AENFKEDPLRRDMR Carboxylase (SEQ ID NO: 181) (SEQ ID NO: 182) HAD 3-Hydroxyacyl Naga_100113g7 C-TANEPQFTGHFPER C-IDGVFRKPVVPGD ACP Dehydrase (SEQ ID NO: 183) (SEQ ID NO: 184) ENR Enoyl-ACP Naga_101053g1 C-PEDVPEAVKTNKRY C-AIGGGEKGKKTFIE Reductase (SEQ ID NO: 185) (SEQ ID NO: 186) KAR .beta.-Ketoacyl-ACP Naga_100037g12 C-VAIKADMSKPEEVE C-SDMTEKLDLDGIKK Reductase (SEQ ID NO: 187) (SEQ ID NO: 188) KAS1 .beta.-Ketoacyl-ACP Naga_100002g173 C-YMRGSKGQIYMKEK C-DAKPYFKDRKSAVR Synthase 1 (SEQ ID NO: 189) (SEQ ID NO: 190) KAS3 .beta.-Ketoacyl-ACP NG_scf10: MGKRSTASSTGLAY-C C-PPSIREVTPYKGKY Synthase 3 19284 . . . 18979 (SEQ ID NO: 191) (SEQ ID NO: 192)

[0344] Compared to wild type, levels of these enzymes were not noticeably higher in ZnCys mutants, and in the case in NR--KO, ACCase and KARl were reduced. These data suggest that under N-replete conditions the plastid lipid biosynthetic machinery is already present at a capacity that is capable of at least double the flux to fatty acid given the -100% increase in FAME productivity observed in ZnCys-2845 RNAi knockdown strain GE-13103. This conclusion is consistent with transcriptional changes observed for N-deprived Nannochloropsis, where pathways involved in providing carbon precursors to lipid biosynthesis appear to be more differentially expressed than "core" lipid biosynthetic pathways (Radakovitz et al 2012, Carpinelli et al 2014, Li et al 2014).

[0345] In order to gain further insight into the mechanisms that allow for ZnCys-2845 attenuated lines to constitutively produce lipid and sustain growth, we analyzed the global transcriptional profiles of ZnCys-2845 RNAi strain GE-13103 during steady-state growth conditions (e.g., FIGS. 17A-17B). Using a 2-fold cut-off and FDR <0.05, 1118 genes were found to be differentially expressed between ZnCys-RNAi-7 and wild type in nitrate-only culture medium. Of these, 790 were up-regulated and 328 down-regulated in the mutant. Analysis of the down-regulated gene set for enriched gene ontology (GO) categories by "molecular function", "biological process" or "cellular component" revealed that genes involved in photosynthesis and light harvesting were overrepresented in the mutant with respect to the wild type (Table 30).

TABLE-US-00030 TABLE 30 Overrepresented Gene Ontology Categories Corresponding to Genes that are Down-Regulated in ZnCys_RNAi-7 Over- FDR # genes # genes in represented adjusted Category Ontology.sup..dagger. GO Term DE.sup..dagger..dagger. category pvalue pvalue.sup..dagger..dagger..dagger. GO:0009765 BP photosynthesis, light 15 17 4.3E-11 7.4E-08 harvesting GO:0016168 MF chlorophyll binding 15 22 4.3E-08 2.4E-05 GO:0018298 BP protein-chromophore 15 22 4.3E-08 2.4E-05 linkage GO:0009523 CC photosystem II 18 39 1.3E-06 5.7E-04 GO:0003824 MF catalytic activity 98 399 2.6E-05 8.9E-03 .sup..dagger.BP, Biological process; CC, cellular component; MF, molecular function .sup..dagger..dagger.DE, Differentially expressed genes .sup..dagger..dagger..dagger.FDR, False Discovery Rate

[0346] The same analysis conducted on the up-regulated gene set revealed that components of protein synthesis were significantly enriched for in the attenuated ZnCys-2845 RNAi strain GE-13103 (Table 31). Considering that our analysis of biomass composition indicated an approximately 45% decrease in total protein content in GE-13103 (FIG. 23), the up-regulation of translation machinery and down-regulation of photosynthetic apparatus is likely a response to that deficit.

TABLE-US-00031 TABLE 31 Overrepresented Gene Ontology (GO) Categories Corresponding to Genes that are Up-Regulated in ZnCys-2845 RNAi Strain GE-13103 Over- FDR # genes # genes in represented adjusted Category Ontology.sup..dagger. GO Term DE.sup..dagger..dagger. category pvalue pvalue.sup..dagger..dagger..dagger. GO:0006412 BP translation 88 175 1.9E-26 3.1E-23 GO:0005840 CC ribosome 77 160 5.1E-24 4.4E-21 GO:0003735 MF structural constituent of 68 138 1.2E-22 6.5E-20 ribosome GO:0005622 CC intracellular 85 226 1.1E-11 4.6E-09 GO:0005737 CC cytoplasm 70 183 3.4E-07 1.2E-04 GO:0000166 MF nucleotide binding 175 525 5.5E-07 1.4E-04 GO:0005524 MF ATP binding 206 636 5.6E-07 1.4E-04 GO:0005852 CC eukaryotic translation 10 11 2.2E-06 4.6E-04 initiation factor 3 complex GO:0003743 MF translation initiation 26 55 1.5E-05 2.8E-03 factor activity GO:0005694 CC chromosome 12 18 2.3E-05 3.5E-03 GO:0006413 BP translational initiation 26 56 2.3E-05 3.5E-03 GO:0030529 CC Ribonucleo-protein 34 109 2.9E-05 4.1E-03 complex GO:0006260 BP DNA replication 20 37 1.1E-04 1.4E-02 GO:0015935 CC small ribosomal subunit 8 13 2.0E-04 2.4E-02 GO:0005874 CC microtubule 17 30 4.3E-04 4.3E-02 GO:0001731 BP formation of translation 5 5 4.9E-04 4.3E-02 preinitiation complex GO:0006446 BP regulation of 5 5 4.9E-04 4.3E-02 translational initiation GO:0016282 CC eukaryotic 43S 5 5 4.9E-04 4.3E-02 preinitiation complex GO:0033290 CC eukaryotic 48S 5 5 4.9E-04 4.3E-02 preinitiation complex GO:0051082 MF unfolded protein 14 28 5.4E-04 4.4E-02 binding GO:0007155 BP cell adhesion 8 10 5.5E-04 4.4E-02 .sup..dagger.BP, Biological process; CC, cellular component; MF, molecular function .sup..dagger..dagger.DE, Differentially expressed genes .sup..dagger..dagger..dagger.FDR, False Discover Rate

[0347] Consistent with our qRT-PCR findings (FIG. 24), analysis of N-assimilation genes revealed a few key down-regulated genes that could account for the low N-levels in the mutant, including nitrite reductase, two glutamine synthetases (GS1 and GS2), an ammonium transporter (AMT1) and a key enzyme involved in molybdenum cofactor biosynthesis (MoeA/CNX1), a cofactor that is essential for nitrate reductase activity (Table 29).

TABLE-US-00032 TABLE 32 Average Transcript Levels and Fold Changes of Differentially Expressed Genes Involved in N-Assimilation ZnCys WT RNAi-7t FC.dagger..dagger. Gene Alias N. gaditana id Description (FPKM).dagger. (FPKM).dagger. (log.sub.2) FDR.dagger..dagger..dagger. Amt3 Naga_102173g1 Ammonium transporter 2.3 14.7 2.5 3.8E-06 AmtB-like protein Amt2 Naga_100099g15 Ammonium transporter 635.9 841.4 0.4 5.5E-02 NAR2 Naga_100100g7 Formate nitrite transporter 40.3 42.7 0.1 8.3E-01 UreT Naga_100311g2 Urea active transporter- 6.4 6.5 -0.1 7.9E-01 like protein NAR1 Naga_100046g36 Nitrite transporter 137.1 128.2 -0.1 5.2E-01 GOGAT2 Naga_100005g23 Glutamate synthase 54.1 48.9 -0.2 5.0E-01 (plastid) GOGAT1 Naga_101084g2 Glutamate synthase 8.7 7.2 -0.3 7.3E-01 NR Naga_100699g1 Nitrate reductase 336.1 283.2 -0.3 2.4E-01 NRT2 NG_SCF17:5277-7851 Nitrate high affinity 1650.0 1368.4 -0.3 1.0E-02 transporter GS1 Naga_100056g25 Glutamine synthetase 2084.4 1529.3 -0.5 3.4E-03 GDH1 Naga_100063g22 Glutamate dehydrogenase 317.5 205.4 -0.7 9.7E-06 GS2 Naga_100003g119 Glutamine synthetase 6.5 3.9 -0.7 4.3E-02 NiR Naga_100852g1 Nitrite reductase 783.2 499.2 -0.7 2.3E-04 MoeA/CNX1 Naga_101167g3 Molybdenum cofactor 207.0 83.0 -1.4 6.2E-14 biosynthesis protein Amt1 Naga_100551g3 Ammonium transporter 126.9 16.7 -2.9 7.9E-36 AmtB-like protein .dagger.FPKM, Fragments per kilobase of transcript per million mapped reads .dagger..dagger.FC, Fold change of genes in ZnCys-RNAi-7 relative to WT .dagger..dagger..dagger.FDR, False Discovery Rate

[0348] The GO category analysis did not find a statistical enrichment for genes involved in lipid biosynthesis. However, when the list was manually curated, 26 genes related to glycerolipid biosynthesis were identified as upregulated using the same filtering criterium as above (Table 30). These genes included six fatty acid desaturases, elongases, lipases and acyltransferases of unknown substrate specificity, and the lipid droplet surface protein (LDSP) which is believed to be the main structural component of the lipid droplet (Vieler et al. (2012) Plant Physiol. 158:1562-1569).

TABLE-US-00033 TABLE 33 Average Transcript Levels and Fold Changes of Differentially Expressed Genes Involved in Glycerolipid Biosynthesis ZnCys- WT RNAi-7 FC.sup..dagger..dagger. N. gaditana id Description (FPKM).sup..dagger. (FPKM).sup..dagger. (log.sub.2) FDR.sup..dagger..dagger..dagger. Naga_100092g4 Omega-6 fatty acid desaturase delta-12 1.0 13.8 4.0 1.0E-11 Naga_100004g102 Elongation of fatty acids protein (EC 19.6 120.0 2.6 2.9E-14 2.3.1.199) Naga_100086g4 Lipid droplet surface protein 280.3 1608.6 2.5 7.4E-34 Naga_100040g9 Acyl transferase/acyl 0.7 2.0 2.2 7.9E-04 hydrolase/lysophospholipase Naga_100042g43 Nadp-dependent glyceraldehyde-3- 14.2 63.0 2.1 5.2E-08 phosphate dehydrogenase Naga_100042g12 Delta 5 fatty acid desaturase 11.3 46.8 2.0 5.0E-11 Naga_100035g27 CDP-diacylglycerol pyrophosphatase 1.0 4.3 2.0 3.2E-06 Naga_100162g4 Elongation of fatty acids protein (EC 7.3 28.5 1.9 5.9E-07 2.3.1.199) Naga_100257g1 Glyceraldehyde-3-phosphate 20.0 74.9 1.8 2.2E-14 dehydrogenase (EC 1.2.1.12) Naga_100937g1 Acyltransferase 3 (Fragment) 1.6 6.2 1.8 1.9E-04 Naga_100273g7 Delta 5 fatty acid desaturase 12.2 42.2 1.8 2.4E-08 Naga_100001g58 Glyceraldehyde-3-phosphate 25.8 87.8 1.7 4.8E-17 dehydrogenase (EC 1.2.1.12) Naga_100426g5 Lipase, class 3 1.0 4.6 1.7 7.5E-05 Naga_100012g35 Lipase domain-containing protein 0.3 1.6 1.6 2.8E-03 Naga_100226g14 Acyltransferase 3 2.3 6.6 1.6 6.5E-07 Naga_100241g4 Lipase 0.7 2.6 1.4 2.0E-03 Naga_100075g9 Delta(5) fatty acid desaturase B 6.0 16.1 1.4 9.0E-05 Naga_100115g11 Stearoyl-CoA 9-desaturase 23.8 63.1 1.4 4.0E-14 Naga_102092g1 Acyl-CoA Synthase 5.3 13.1 1.3 8.5E-04 Naga_100063g13 Delta 3 fatty acid desaturase 25.6 59.7 1.2 6.0E-09 Naga_100530g1 Lipase-like protein 1.7 3.9 1.1 2.1E-02 Naga_100028g54 Acetyl-coenzyme A synthetase (EC 16.9 36.8 1.1 1.3E-10 6.2.1.1) Naga_101607g1 Triglyceride lipase-cholesterol esterase 53.7 115.3 1.1 1.9E-06 Naga_100247g4 Patatin-like phospholipase domain- 114.3 54.5 -1.1 2.0E-09 containing protein 2 Naga_100529g6 Lipase, class 3 (Fragment) 291.2 134.6 -1.1 2.1E-13 Naga_100771g2 Acyltransferase 3 14.1 3.6 -2.0 5.4E-15 .sup..dagger.FPKM, Fragments per kilobase of transcript per million mapped reads .sup..dagger..dagger.FC, Fold change of genes in ZnCys-RNAi-7 relative to WT .sup..dagger..dagger..dagger.FDR, False Discovery Rate (transcript levels are shown for genes with FDR < 0.05)

[0349] Consistent with our Western blot data for ACCase and FAS (FIG. 25), transcripts encoding these enzymes were not found to be differentially expressed in the mutant with respect to wild type, nor was differential regulation of genes encoding diacylglycerol acyltransferases (DGATs) or other enzymatic steps leading to TAG biosynthesis observed.

Sequence CWU 1

1

19313198DNANannochloropsis gaditanamisc_featureZnCys-2845 protein-encoding sequence (cDNA) 1atgaccacct tcttgaatcc aggcccggca agggagaaac tcgtgggcag tggcgtcttt 60ttcgaaggca gcatcggggt cgtcgggcac gagtcaggcg ggggagttgg gagccaggac 120gagatggaca cggaccattt caacgagcta gaccacatat tcgacttgtc gtacagcgcg 180gaacaggacc cttttggctc gggcagcggg cacgcgcaga gtcagggcac tgggtatggg 240catccgcccc agacgcagct cgggggcgcc agtctcttga tgccccaccc acacaacagc 300catggcgcga tcagccacga cggctctcgc atgcacaacg atggcatgga ttggcgcgcg 360aaggatgagg actgctcgta ccacaccgcc gtggacgcca gctgccacat cgacagtagc 420taccaccatg ttgatgcctc aggccactcc atggtcgacg cctcgggtca cagcacgata 480gacgcgtcgg gccacgactc cctcatcgac tcaagcggcc attacgacga ctatctggcg 540cacaaggggg acgcccgcta catggagcac agttgtgaag cctgcaagcg ctcgaagaaa 600cgatgcaacc gccgcaaccc ctgccagatc tgcacctcca ggggcatcaa gtgtgtgccg 660caaatccggg gtcctgggcg ccccccgggc agtaaaagca gtcggggctg cacctccttg 720tcactgagca gctcacggca tggaagctcc aggggtgaca tacgcgccgc gaacggaagc 780gggcagagcc acaacagcag tgccacgaca tcggccgcct cctccacctc ctcctccttg 840tcccgctccc tctccgggaa tggcctactc caacagggcc aggagttggc cgtcggcgcc 900cggcggcact ctcccccccg cgacccctgg cactgtcgct ttttcttcga ggccgcccgc 960cactgcaaag aggccttcct gcggacgtgg cacgataacg agctggacac cgccaagtgc 1020atcatgctca ggaatttgtg gacgaaagtc tcgtcgcaac tggcctctgg cacggatatg 1080acctttggga tctgcgacca gctgcaagag gtggtggggc ccgcccccac gggctctggt 1140cccatggccg ggagccccgc cacgcgctcc aagagccacg cggcgcagca ggcgcaactc 1200ctcacgcacc ccggttcgaa agaggccatg ggccctcact gcctgcccct ggacttgcga 1260agaatggagg acggcgtctc catgctgtgc ggcttcatgt tcttgcagga cgagcttttc 1320gtctacacgg acgagcgttt cgcggccacc ttcatgacgc gggaagaggt ggagtccaag 1380gtcggctccc tcgcggtgct gcccatcctc ctgctcgcgg agatcttcca ccccgacgac 1440ctccctgaca tctacgcggc catcggtgct tactggtttt ctcgccgctc ctctaccacg 1500tcagagagcg ggagcagcag cagcagcagc acaaacagca gtgtcagcag tgcggggagt 1560cgggagtcgg cggcctcggc cacaggcacc ccggaggcgt cctggatctg caaatgcatc 1620gacaaggcga acacggaagt gacggccttc gtgcgcttcc gctctttcgt cgcacctgcg 1680gagggctacc ccggggcggc catgctctcc atcctgccct taaaaccgag caagtatctc 1740gcggacccgg acactaaggg gagtgtcagg tctggggtgt cgtcgcgctt gcagatgagg 1800gacaccttcg gagccttgcc cacagccctg ccggagcaag acgacgagga ccttggcgac 1860gatttggtcg ggcggcgacc gtcggtggat cgcatggagg gcctggggcc cggggccggg 1920gagggccagg accctgagag cgacgacgcc ttattccggc cccttcggag gggcatgacc 1980gtgctctcgg atgagacgag cgggccgcag gctgtgcctg tcgcaaagca ggtttcagac 2040cccggcgtac agcaccagga tcacgcctgc tacagccagc ctaccataca catatcccag 2100ctgtcgagcg cccttcggag cacggtgggc ttgtcgtggg ggggggaggg gaccgaccgc 2160agtggggaat cttttccatc gtcgcagttc tcctcccatg ctcagacgca aggtggacaa 2220tcatcttctg gtctcccgca agatggcaaa agctgtggtg gttaccctgc ctcggatgat 2280ggtcgtgggg gggacatgac ggacggggtt ctgcccattg cacaacttac caaggcccaa 2340attttccttc tgcaagaaga gggtggtgtt tctggtcgag acctccccgc tgccggcgac 2400aattcatcat atggcgattt agccagcggg agagagggcc aagggggtcg ccgtcatcaa 2460cgaaaggaac aagagtcgcg gaagcaccct gaccctcggg atggacacac cctccctgca 2520agtggattga cgatggacga ggaggataca ggaagcgtgg ttacagactt tgagatttac 2580ggctccagtc ccagtccgga gcccggccag tcccttaata cttcctcacg aggctcggca 2640aggttgcaga tgcaggcctc gagccagggg gggcaccaaa cgtactttgg acgacacgag 2700cacatggaaa agcaaaatcg agaggaggtg cagcgactgc cgatggctcc accctctgta 2760agtttcgccc aggcggggga gctatccagt gatcgacgag cgagttgcgc gggcttgagc 2820atcctaggcg gacctgctgg gaaagtggaa ggctccaggg gatccctgag ccacagtaag 2880agtaacaacg acctggacat atcgtgtcat gggcccgccg atcccaacgg ctacggtggg 2940ttgcagtgga cgccggctcc actggcgtct ctgctggggg ccaagggcct actagaggcg 3000gggaacgggg tgggcgatca cgcgatctcg tcggttcacg ccaatcaggg gcctgcccac 3060cagaagcgtc ggacgagccg cgcggggtcg cggaccgttc ctgccaacaa tggtggcgat 3120aataccgcgg ggagcgcagc gatcgcgggc gcgaaggatg aagaggcgga gccaggcttt 3180cttgcccgct ctttgtga 319821065PRTNannochloropsis gaditanamisc_featureZnCys-2845 protein sequence 2Met Thr Thr Phe Leu Asn Pro Gly Pro Ala Arg Glu Lys Leu Val Gly1 5 10 15Ser Gly Val Phe Phe Glu Gly Ser Ile Gly Val Val Gly His Glu Ser 20 25 30Gly Gly Gly Val Gly Ser Gln Asp Glu Met Asp Thr Asp His Phe Asn 35 40 45Glu Leu Asp His Ile Phe Asp Leu Ser Tyr Ser Ala Glu Gln Asp Pro 50 55 60Phe Gly Ser Gly Ser Gly His Ala Gln Ser Gln Gly Thr Gly Tyr Gly65 70 75 80His Pro Pro Gln Thr Gln Leu Gly Gly Ala Ser Leu Leu Met Pro His 85 90 95Pro His Asn Ser His Gly Ala Ile Ser His Asp Gly Ser Arg Met His 100 105 110Asn Asp Gly Met Asp Trp Arg Ala Lys Asp Glu Asp Cys Ser Tyr His 115 120 125Thr Ala Val Asp Ala Ser Cys His Ile Asp Ser Ser Tyr His His Val 130 135 140Asp Ala Ser Gly His Ser Met Val Asp Ala Ser Gly His Ser Thr Ile145 150 155 160Asp Ala Ser Gly His Asp Ser Leu Ile Asp Ser Ser Gly His Tyr Asp 165 170 175Asp Tyr Leu Ala His Lys Gly Asp Ala Arg Tyr Met Glu His Ser Cys 180 185 190Glu Ala Cys Lys Arg Ser Lys Lys Arg Cys Asn Arg Arg Asn Pro Cys 195 200 205Gln Ile Cys Thr Ser Arg Gly Ile Lys Cys Val Pro Gln Ile Arg Gly 210 215 220Pro Gly Arg Pro Pro Gly Ser Lys Ser Ser Arg Gly Cys Thr Ser Leu225 230 235 240Ser Leu Ser Ser Ser Arg His Gly Ser Ser Arg Gly Asp Ile Arg Ala 245 250 255Ala Asn Gly Ser Gly Gln Ser His Asn Ser Ser Ala Thr Thr Ser Ala 260 265 270Ala Ser Ser Thr Ser Ser Ser Leu Ser Arg Ser Leu Ser Gly Asn Gly 275 280 285Leu Leu Gln Gln Gly Gln Glu Leu Ala Val Gly Ala Arg Arg His Ser 290 295 300Pro Pro Arg Asp Pro Trp His Cys Arg Phe Phe Phe Glu Ala Ala Arg305 310 315 320His Cys Lys Glu Ala Phe Leu Arg Thr Trp His Asp Asn Glu Leu Asp 325 330 335Thr Ala Lys Cys Ile Met Leu Arg Asn Leu Trp Thr Lys Val Ser Ser 340 345 350Gln Leu Ala Ser Gly Thr Asp Met Thr Phe Gly Ile Cys Asp Gln Leu 355 360 365Gln Glu Val Val Gly Pro Ala Pro Thr Gly Ser Gly Pro Met Ala Gly 370 375 380Ser Pro Ala Thr Arg Ser Lys Ser His Ala Ala Gln Gln Ala Gln Leu385 390 395 400Leu Thr His Pro Gly Ser Lys Glu Ala Met Gly Pro His Cys Leu Pro 405 410 415Leu Asp Leu Arg Arg Met Glu Asp Gly Val Ser Met Leu Cys Gly Phe 420 425 430Met Phe Leu Gln Asp Glu Leu Phe Val Tyr Thr Asp Glu Arg Phe Ala 435 440 445Ala Thr Phe Met Thr Arg Glu Glu Val Glu Ser Lys Val Gly Ser Leu 450 455 460Ala Val Leu Pro Ile Leu Leu Leu Ala Glu Ile Phe His Pro Asp Asp465 470 475 480Leu Pro Asp Ile Tyr Ala Ala Ile Gly Ala Tyr Trp Phe Ser Arg Arg 485 490 495Ser Ser Thr Thr Ser Glu Ser Gly Ser Ser Ser Ser Ser Ser Thr Asn 500 505 510Ser Ser Val Ser Ser Ala Gly Ser Arg Glu Ser Ala Ala Ser Ala Thr 515 520 525Gly Thr Pro Glu Ala Ser Trp Ile Cys Lys Cys Ile Asp Lys Ala Asn 530 535 540Thr Glu Val Thr Ala Phe Val Arg Phe Arg Ser Phe Val Ala Pro Ala545 550 555 560Glu Gly Tyr Pro Gly Ala Ala Met Leu Ser Ile Leu Pro Leu Lys Pro 565 570 575Ser Lys Tyr Leu Ala Asp Pro Asp Thr Lys Gly Ser Val Arg Ser Gly 580 585 590Val Ser Ser Arg Leu Gln Met Arg Asp Thr Phe Gly Ala Leu Pro Thr 595 600 605Ala Leu Pro Glu Gln Asp Asp Glu Asp Leu Gly Asp Asp Leu Val Gly 610 615 620Arg Arg Pro Ser Val Asp Arg Met Glu Gly Leu Gly Pro Gly Ala Gly625 630 635 640Glu Gly Gln Asp Pro Glu Ser Asp Asp Ala Leu Phe Arg Pro Leu Arg 645 650 655Arg Gly Met Thr Val Leu Ser Asp Glu Thr Ser Gly Pro Gln Ala Val 660 665 670Pro Val Ala Lys Gln Val Ser Asp Pro Gly Val Gln His Gln Asp His 675 680 685Ala Cys Tyr Ser Gln Pro Thr Ile His Ile Ser Gln Leu Ser Ser Ala 690 695 700Leu Arg Ser Thr Val Gly Leu Ser Trp Gly Gly Glu Gly Thr Asp Arg705 710 715 720Ser Gly Glu Ser Phe Pro Ser Ser Gln Phe Ser Ser His Ala Gln Thr 725 730 735Gln Gly Gly Gln Ser Ser Ser Gly Leu Pro Gln Asp Gly Lys Ser Cys 740 745 750Gly Gly Tyr Pro Ala Ser Asp Asp Gly Arg Gly Gly Asp Met Thr Asp 755 760 765Gly Val Leu Pro Ile Ala Gln Leu Thr Lys Ala Gln Ile Phe Leu Leu 770 775 780Gln Glu Glu Gly Gly Val Ser Gly Arg Asp Leu Pro Ala Ala Gly Asp785 790 795 800Asn Ser Ser Tyr Gly Asp Leu Ala Ser Gly Arg Glu Gly Gln Gly Gly 805 810 815Arg Arg His Gln Arg Lys Glu Gln Glu Ser Arg Lys His Pro Asp Pro 820 825 830Arg Asp Gly His Thr Leu Pro Ala Ser Gly Leu Thr Met Asp Glu Glu 835 840 845Asp Thr Gly Ser Val Val Thr Asp Phe Glu Ile Tyr Gly Ser Ser Pro 850 855 860Ser Pro Glu Pro Gly Gln Ser Leu Asn Thr Ser Ser Arg Gly Ser Ala865 870 875 880Arg Leu Gln Met Gln Ala Ser Ser Gln Gly Gly His Gln Thr Tyr Phe 885 890 895Gly Arg His Glu His Met Glu Lys Gln Asn Arg Glu Glu Val Gln Arg 900 905 910Leu Pro Met Ala Pro Pro Ser Val Ser Phe Ala Gln Ala Gly Glu Leu 915 920 925Ser Ser Asp Arg Arg Ala Ser Cys Ala Gly Leu Ser Ile Leu Gly Gly 930 935 940Pro Ala Gly Lys Val Glu Gly Ser Arg Gly Ser Leu Ser His Ser Lys945 950 955 960Ser Asn Asn Asp Leu Asp Ile Ser Cys His Gly Pro Ala Asp Pro Asn 965 970 975Gly Tyr Gly Gly Leu Gln Trp Thr Pro Ala Pro Leu Ala Ser Leu Leu 980 985 990Gly Ala Lys Gly Leu Leu Glu Ala Gly Asn Gly Val Gly Asp His Ala 995 1000 1005Ile Ser Ser Val His Ala Asn Gln Gly Pro Ala His Gln Lys Arg 1010 1015 1020Arg Thr Ser Arg Ala Gly Ser Arg Thr Val Pro Ala Asn Asn Gly 1025 1030 1035Gly Asp Asn Thr Ala Gly Ser Ala Ala Ile Ala Gly Ala Lys Asp 1040 1045 1050Glu Glu Ala Glu Pro Gly Phe Leu Ala Arg Ser Leu 1055 1060 1065330PRTNannochloropsis gaditanamisc_featureZn(2)-Cys(6) binuclear cluster domain of ZnCys-2845 3His Ser Cys Glu Ala Cys Lys Arg Ser Lys Lys Arg Cys Asn Arg Arg1 5 10 15Asn Pro Cys Gln Ile Cys Thr Ser Arg Gly Ile Lys Cys Val 20 25 30418PRTArtificial SequenceSyntheticmisc_featureConserved motif of Zn(2)-Cys(6) binuclear cluster domainmisc_feature(2)..(3)Xaa can be any naturally occurring amino acidmisc_feature(5)..(10)Xaa can be any naturally occurring amino acidmisc_feature(12)..(12)Xaa can be any naturally occurring amino acidmisc_feature(14)..(15)Xaa can be any naturally occurring amino acidmisc_feature(17)..(17)Xaa can be any naturally occurring amino acid 4Cys Xaa Xaa Cys Xaa Xaa Xaa Xaa Xaa Xaa Cys Xaa Cys Xaa Xaa Cys1 5 10 15Xaa Cys5696PRTPhaeodactylum tricornutum 5Met Asn Glu Asp Ser Thr Glu Asp Pro Asp Asp Gly Ser Val Ala Leu1 5 10 15Cys Ala Ser Cys Asp Arg Cys Arg Ser Arg Lys Thr Lys Cys Asp Gly 20 25 30Gln Arg Pro Cys Gly Asn Cys Leu Ala Lys Tyr Met Lys Lys Asn Lys 35 40 45Leu Ser Ser Ala Asp Gly Ile Asp Phe Thr Glu Cys Glu Cys Val Tyr 50 55 60Ser Pro Ala Lys Arg Arg Gly Pro Ile Pro Gly Arg Thr Ala Gly Gln65 70 75 80Ala Arg Lys Ala Thr Glu Leu Gln His His Gln Gln Gln Gln Pro Asn 85 90 95Asp Trp Pro Gln Asn Tyr His Asn Asn Pro Ser Thr Gly Val Asn Leu 100 105 110Asn Gly Thr Gly Leu Asp Ala Gln Met Thr Ala Ala Leu Phe Ser Gly 115 120 125Gln Thr Glu Gln Ala Ser Leu Gln Gln Lys Leu Asn Phe Leu Gln Ser 130 135 140Leu Gln Asn Gln Asp Glu Asp His Leu Met Met Gln Gln Gln Gln Gln145 150 155 160Gln His Gln Met Asp Glu Pro Ala Asn Arg Arg Val Lys Arg Glu Asp 165 170 175Ala Gly Gln Asn Thr Ser Thr Asn Gly Ile Pro Arg Thr Ile Thr Thr 180 185 190His Thr His Leu Leu Glu Arg Ser Asn Pro Asp Gly Ala Arg Leu Arg 195 200 205Ala Tyr Tyr Gln Leu Ser Ile Asp Glu Leu Tyr Arg Leu Pro Pro Ile 210 215 220Pro Thr Asp Glu Glu Tyr Cys Ala Arg Leu Asn Val Pro Gly Met Thr225 230 235 240Pro Gln Met Ile Pro Gly Pro His Leu Ala Ala Leu Ser Ala Ala Arg 245 250 255Phe Ala Glu Ile Ala Leu Gly Ala Leu Val His Asn Glu Val Ser Leu 260 265 270Ala Met Glu Leu Cys Asn Ala Val Val His Cys Leu Arg Glu Ser Val 275 280 285Gln Glu Pro Val Gln Thr Pro Val Met Phe Glu Val Ala Lys Ala Tyr 290 295 300Phe Leu Leu Gly Val Phe Arg Ala Cys Arg Gly Asp Met Glu Arg Tyr305 310 315 320Phe Lys Tyr Arg Arg Val Cys Met Thr Tyr Leu Ala Lys Leu Glu Asn 325 330 335Asp Asp Lys Thr Ala Val Leu Leu Ala Ala Val Ala Tyr Leu Asp Ser 340 345 350Trp Ala Pro Tyr Ala Thr Gln Thr Glu Leu Lys Tyr Asp Val Lys Leu 355 360 365Asp Ala Gly Ala Ile Ala Ser Asp Pro Lys Asn Gln Asn Trp Ile Gln 370 375 380Gly Ala Pro Pro Val Tyr Leu Asn Asn Glu Ala Pro Leu His Ala Arg385 390 395 400Ala Leu Asp Ala Leu Ala Cys Ala Val Arg Thr Cys Cys Asp Gln Ala 405 410 415Asn Ser Arg Phe Ala Leu Ile Ser Lys Glu Ala Asn Ile Glu Gly Leu 420 425 430Asp Thr Ile Pro Ser Glu Ser Ile Ser Ser Ala Thr Tyr Asn Ala Val 435 440 445Leu Ser His Glu Asn Glu Leu Cys Ser Arg Asn Ile Val Leu Ser Ala 450 455 460Tyr Thr Leu Met Gln Gln His Glu Ser Thr Asp Ser Ser Arg His Lys465 470 475 480Asn Glu Gly Gln His Met Val Ile Ser Ala Met Asp Ala Phe Leu Glu 485 490 495Asn Ser Asp Glu Asp Gly Asn Gly Gly Phe Thr Asp Ser Gln Ile Gln 500 505 510Ser Leu Leu Ser Val Cys Asn Thr Ala Ile Glu Asn Pro Phe Leu Leu 515 520 525His His Ala Gly Pro Thr Tyr His Met Val Ser Asn Ala Ala Val Leu 530 535 540Leu Cys His Leu Leu Asn Gly Leu His Met Ala Lys Met Asn Gly Gln545 550 555 560Asp Phe Gly Arg Met Glu Gln Ser Met Phe Glu Glu Val Phe Asp Ala 565 570 575Phe Ile Ser Ile Arg Lys Leu Leu Thr Ile His Arg Arg Lys Leu Pro 580 585 590Val Lys Leu Arg Cys His Ala Ile Pro Arg Pro Ser Met Asp Gly Leu 595 600 605Lys Glu Gly Gln Pro Leu Ile Asp Leu Gly Glu Thr Ile Leu Cys Ala 610 615 620Cys Arg Gly Cys Gln Gly Phe Val Leu Met Ala Cys Ser Pro Cys Val625 630 635 640Ala Ala Glu Arg Ala Gln Ala Ala Gln His Asp Leu Ser Val Glu Ala 645 650 655Ala Lys Glu Ala Glu Ala Ile Glu Met Gly Glu Leu Asp Asn Glu Leu 660 665 670Asp Asn Leu Gly Ala Glu Phe Asp Met Asp Asp Asp Met Leu Leu Gly 675 680 685Met Ile Ser Asn Leu Ile Ser Ser 690 6956248PRTNavicula sp. 6Met Ala Cys Thr Ala Cys His Leu Ala Lys Arg Lys Cys Asp Lys Lys1 5 10

15Ser Pro Cys Ser Arg Cys Ile Ser Lys Ser Leu Glu Cys Ile Pro His 20 25 30Ile Ser Arg Gln Gly Lys Lys Lys Val Arg Arg Val Glu Glu Lys Lys 35 40 45Asp Asp Gly Leu Asp Arg Leu Leu Leu Glu Gln Leu Thr Gly Thr Glu 50 55 60Pro Val Gln Gly His Thr His His Phe Gly Leu Lys Tyr Leu Val Arg65 70 75 80Ser Trp Ile Ser Phe Ala Phe Lys Arg Arg Ser Phe Phe Leu Met Gln 85 90 95Arg Gly Cys Ala Leu Ala Ile Lys Val Gly Phe Ser Met Asp Glu Ile 100 105 110Phe Cys Glu Gln Ser Asn Ser Arg Glu Met Asp Phe Leu Lys Asn Ile 115 120 125Ile Leu Val Pro Lys Glu Ala Gln His Leu Tyr Val Pro Thr Pro Leu 130 135 140Gln Trp Thr Glu Ile Pro Glu Arg Leu Leu Arg Asn Thr Asp Thr Ile145 150 155 160Gly Ser Ser Gly Asn Arg Glu Gly Arg Trp Ile Trp Met Arg Glu Met 165 170 175Ile Lys Gly Glu Ser Arg Tyr Leu Val Ser Glu Ala Phe Glu Arg Asp 180 185 190Val Ala Pro Trp Ser Ser Leu His Lys Ala Trp Glu Asp Asn Arg Gly 195 200 205Ala Val Ile Asp Leu Phe Val Ile Glu Glu Asp Lys His Lys His Thr 210 215 220Lys Ser Phe Ala His Gln Ile Ser Leu Tyr Lys Glu Gln Ala Val Asn225 230 235 240Gly Glu Gly Asn Arg Leu Thr Arg 2457333PRTNavicula sp. 7Met Val Cys Ile Gly Cys His Glu Ser Lys Arg Lys Cys Asp Lys Gln1 5 10 15Thr Pro Cys Ser Arg Cys Leu Lys Leu Gly Ile Pro Cys Ile Pro His 20 25 30Leu Ser Gln Gln Gly Lys Arg Lys Arg Gly Ser Pro Asp Glu Thr Pro 35 40 45Glu Asp Val Thr Ile Leu Arg Gln Val Ser Leu Pro Lys Asp His Tyr 50 55 60Gly Leu Cys His Leu Ile Arg Ser Trp Ile Ser Ile Ala Phe Val Arg65 70 75 80Arg Ser Phe Pro Leu Leu Asn Lys Ala Thr Thr Met Ala Asn Gln Leu 85 90 95Gly Val Thr Met Asp Glu Ile Met Ser Arg Ser Met Thr Gln Gln Gly 100 105 110Met His Trp Leu Gly Pro Val Val Ala Thr Pro Gln Ser Glu Gln Met 115 120 125Ala Gly Gly Pro Arg Leu Gln Trp Asn Glu Leu Pro Glu Gly Leu Leu 130 135 140Val Ala Thr Arg Thr Leu His Ser Val Asp Cys Glu Ala Arg Trp Ile145 150 155 160Trp Ile Arg Glu Leu Ser Gln Gly Arg Ser Arg Tyr Leu Val Thr Gln 165 170 175Ala Phe Glu Arg Asp Ile Ala Thr Trp Ala Leu Val Gln Ser Thr Trp 180 185 190Asn Glu Asn Arg Ile Ser Val Val Asp Leu Phe Leu Asp Gly Ala Ala 195 200 205Arg Glu Lys His Ala Lys Ser Val Ala His Gln Tyr Ser Leu His Ala 210 215 220Lys Pro Pro Thr Pro His Ser Ala Arg Cys Ser Arg Gln Arg Ser Gln225 230 235 240Val Lys Leu Arg Asn Gly Asp Met Ile Ser Val Glu Glu Ile Ser Cys 245 250 255Met Asp Phe Val His Met Asp Leu Ser Tyr His Phe Val Glu Tyr Val 260 265 270Pro Val Cys Ile Gln Pro Ile Arg Ser Gln Ala Cys Ile Gln Asn Lys 275 280 285Val Gln Ser Thr Gln Ser Leu Phe Gln Glu Met Ser Lys Val Met Trp 290 295 300Asp Asp Tyr Pro Leu Met Val Asn Val Asp Asp Ile Pro Ala Glu Gly305 310 315 320Asn Glu Leu Asp Gln Ile Leu Gln Leu Leu Asn Gly Gly 325 3308729PRTNavicula sp. 8Met Glu Asp Phe Asn Asn Asn Asn Thr Gln Gln Ala Asp Asp Glu Lys1 5 10 15Leu Cys Ala Ser Cys Asp Arg Cys Arg Ser Arg Lys Thr Lys Cys Asp 20 25 30Gly Lys Arg Pro Cys Gly Asn Cys Val Ala Lys Tyr Met Lys Lys Tyr 35 40 45Lys Val Met Ser Val Glu Gly Val Pro Glu Ser Ala Phe Glu Cys Val 50 55 60Tyr Ser Pro Ala Lys Arg Arg Gly Pro Val Pro Gly Arg Thr Pro Ser65 70 75 80Gln Ala Arg Ser Leu Asn Asp Val Thr Gly Gly Asn Met Asn Val Asn 85 90 95Met Thr Gly Gly Asn Asn Phe Asp Trp Asn Met Asp Leu Met Ser Gln 100 105 110Gln Gln Gln Gln Gln His His Gln Gln Gln Gln Gln Pro Met Met Ser 115 120 125Ser Leu Ile Gly Gly Leu Asp Gly Asn Asn Ile Leu Asn Gln Phe Asn 130 135 140Leu Met Arg Gln Met Gln Leu Gln Gln Gln Leu Pro Leu Gln Pro Gln145 150 155 160Gln Met Ala Met Gln Gln His Met Met Asp Thr Ser Glu Val Gly Glu 165 170 175Arg Ser Ala Arg Arg Met Lys Met Glu Asp Val Pro Ser Ala Pro Gly 180 185 190Gly Val Pro Arg Thr Val Ser Asp His Thr His Leu Leu Asp Arg Asn 195 200 205Asp Pro Asp Gly Ser Arg Leu Phe Ser Tyr Phe Lys Leu Ser Ile Asp 210 215 220Glu Leu Phe Arg Leu Pro Pro Thr Pro Thr Asp Glu Glu Tyr Cys Leu225 230 235 240Arg Leu Asn Ile Pro Gly Met Thr Pro Arg Met Ile Pro Gly Thr His 245 250 255Leu Ala Ala Leu Ser Ala Ala Arg Phe Ala Glu Ile Ala Leu Gly Ala 260 265 270Met Val His Asn Glu Ile Ser Leu Ala Met Glu Leu Cys Asn Ala Val 275 280 285Val His Cys Leu Arg Glu Ser Val Lys Glu Pro Val Gln Thr Pro Ile 290 295 300Met Leu Glu Val Ser Lys Ala Tyr Phe Leu Leu Gly Val Phe Arg Ala305 310 315 320Cys Arg Gly Asp Met Ala Arg Tyr Phe Lys Tyr Arg Arg Val Cys Met 325 330 335Thr Tyr Leu Gly Lys Leu Glu Asn Ser Ser Arg Thr Ala Thr Leu Thr 340 345 350Ser Ala Ile Ser Tyr Leu Asp Ala Trp Ala Tyr Met Ile Tyr Asn Gly 355 360 365Asn Glu Lys Gln Val Pro Asp Val Asp Arg Thr Leu Pro Pro Pro Ser 370 375 380Gly Cys Ala Thr Asn Gly Met Ile Asn Pro Ile Glu Ala Lys Tyr Asn385 390 395 400Thr Lys Thr Ser Val Pro Ala Val Val Ser Asp Pro Lys Asn Lys Asn 405 410 415Trp Ile Gln Gly Ala Pro Pro Val Tyr Leu Asn Asn Glu Ala Pro Pro 420 425 430His Ala Arg Ser Leu Asp Ala Leu Ala Cys Ala Val Arg Ser Cys Cys 435 440 445Asp Gln Ala Asn Ser Arg Phe Ala Gln Met Met Lys Thr Glu Gly Asn 450 455 460Pro Ser Asp Asn Thr Met Ile Pro Gln Ser Thr Ile Ile Thr Pro Thr465 470 475 480Ala Thr Ala Val Met Asn His Glu Asn Glu Leu Cys Ser Arg Asn Met 485 490 495Val Leu Ser Ala Tyr Thr Leu Met Gln Gln Gln Glu Ser Ser Thr Lys 500 505 510Gly Arg His His Ser Glu Gly His Gln Met Val Ile Ser Ala Met Asp 515 520 525Ala Phe Leu Glu Asn Ser Asp Glu Asp Gly Gly Thr Gly Phe Thr Asp 530 535 540Ser Gln Ile Gln Ser Leu Leu Ser Val Cys Asn Thr Ala Ile Ala Asn545 550 555 560Pro Phe Leu Leu His His Ala Gly Pro Thr Tyr His Met Val Thr Asn 565 570 575Ala Thr Ile Leu Leu Cys His Leu Leu Asn Ala Met His Ala Met Lys 580 585 590Gln Ser Gly Gln Val Glu Asp Met Glu Val Ala Met Phe Glu Glu Val 595 600 605Leu Asp Thr Phe Ile Ala Ile Arg Lys Leu Leu Thr Ile His Arg Arg 610 615 620Lys Leu Pro Val Lys Leu Arg Cys His Gly Ile Pro Arg Pro Gln Leu625 630 635 640Thr Asn Thr Asp Ala Ser Ala Pro Ile Val Asp Leu Gly Glu Thr Phe 645 650 655Leu Cys Ala Cys Arg Gly Cys Gln Gly Phe Val Leu Met Ala Cys Ser 660 665 670Pro Cys Val Ala Ala Glu Arg Ala Arg Asp Ala Thr Lys Arg Met Glu 675 680 685Met Glu Leu Gln His Glu Ala Gln Ala Ile Glu Met Gly Glu Leu Asp 690 695 700Thr Asp Ile Asp Asn Ile Gly Ala Glu Phe Asp Leu Asp Asp Asp Ala705 710 715 720Leu Leu Ser Met Ile Ser Ser Leu Ile 7259723PRTCyclotella sp. 9Met Asp Asp Thr Val Ala Ala Glu Glu Ala Lys Glu Ala Thr Asp Leu1 5 10 15Gln Ser Ser Asp Ser Lys Pro Thr Ser Pro Ser Ser Thr Pro Leu Asn 20 25 30Arg Asp Ser Thr Ser Leu Cys Ser Ser Cys Asp Pro Cys Arg Ala Arg 35 40 45Lys Thr Lys Cys Asp Gly Leu Arg Pro Cys Arg Ala Cys Ile Ser Lys 50 55 60His Val Lys Lys His Lys Leu Ser Ser Tyr Glu Gly Ile Thr Ala Glu65 70 75 80Asp Cys Gly Cys Thr Tyr Ser Val Ala Lys Arg Arg Gly Pro Val Pro 85 90 95Gly Phe Lys Asn Ala Lys Asp Glu Lys Gly Asp Gly Asn Leu Ser Thr 100 105 110Ser Lys Lys Arg Gly Pro Thr Gln Asp Gly Thr Leu His Ser Tyr Pro 115 120 125Pro Lys Lys Lys Lys Glu Lys Arg Ser Val Asp Val Leu Ala Arg Phe 130 135 140Pro His Ser Ala Ala Gln Asp Ala Met Ala Ala Ala Ser Asp Ser Ala145 150 155 160Arg Gln Gln Leu Gly Phe Ile Glu Arg Leu Gln Gln Gln Gln Gln Glu 165 170 175Phe Gln Arg Gln Gln Gln Gln Gln Met Gln Met Gln Gln Met Ala Gln 180 185 190Ala Gln Asn Ala Gln Ala Met Pro Phe Met Ser Arg Asp Gly Asp Asn 195 200 205Ser Ala Ile Ser Arg Gln Met Asn Asn Asn Tyr Asn Glu Gln Val Ser 210 215 220Gly His Lys Pro Ser Gln Gln Phe Ser Ser Thr Glu Gln Thr Ser Ala225 230 235 240Val Gly Cys Glu Lys Thr Thr Val Arg Glu Leu Leu His Val Leu Asp 245 250 255Pro Lys Asp Pro Leu Gly Ser Arg Phe Arg Ala Cys Tyr Gly Ile Ser 260 265 270Phe Gly Ser Ile Phe Gly Leu Pro Pro Ile Leu Thr Tyr Asp Glu Tyr 275 280 285Cys Arg Gln Phe Thr Pro Thr Ile Ala Ser Thr Ser Met Pro Lys Tyr 290 295 300Asp Val Ala Ala Leu Gln Ala Ala Gln Phe Ala Glu Leu Ala Leu Gly305 310 315 320Ala Leu Ala Asp Gly Asp Arg Cys Met Met Phe Ala Leu Ile Asn Ala 325 330 335Ser Ile Phe Cys Leu Gln Asp Thr Val Lys Glu Pro Val His Arg Ser 340 345 350Cys Gln Phe Glu Leu Ala Lys Ala Phe Phe Phe His Ser Leu Ile Arg 355 360 365Cys His Asn Gly Asp Met Glu Arg Tyr Phe Lys Tyr Arg Arg Ala Ala 370 375 380Met His Thr Leu Ala His Leu Asp Gly Tyr Pro Asn Val Glu Thr Leu385 390 395 400Met Ala Ala Val Gly Phe Gln Asp Ala Leu Ala Phe Met Leu Tyr Asn 405 410 415Gly Cys Asp Asp Asp Val Pro Asp Ile Asp Ser Asp Tyr Pro Gln Val 420 425 430Leu Asp Arg Phe Asp Thr Lys Glu Ser Ser Ser Val Ser Phe Thr Pro 435 440 445Ser Lys Leu Ala Ser Asp Pro Thr Asn Lys Thr Trp Ile Thr Gly Pro 450 455 460Pro Met Phe Ser Ser Glu Ser Ser Ala Pro Leu Lys Ser Arg Ile Leu465 470 475 480Asp Ile Leu Ala Cys Ala Thr Arg Ser Phe Val Glu Glu Ser Gln Phe 485 490 495Lys Lys Glu Ile Lys Ser Val Glu Thr Ser Thr Arg Lys Arg Arg Asn 500 505 510Phe Ile Thr Ala Glu Asp Lys Arg Ile Lys Tyr Lys Ile Cys Leu Gly 515 520 525His Leu Asn Glu Ala Gly Arg Leu Leu Ala Val Ala Asn Cys Lys Ser 530 535 540Ser Ser Ser Ser Ile Tyr Asp Val Tyr His Val Leu Val Met Ala Phe545 550 555 560Arg Val Met Ile His Glu Asp Thr Ser Glu Pro Glu Glu Ser Gln Val 565 570 575Gln Asn Ala Phe His Val Leu Lys Ala Ile Ile Arg Gln Pro Ser Leu 580 585 590Leu Asn Ile Gly Pro Ile Asn Ile Phe Val His Lys Cys Val Ile Phe 595 600 605Val Ala Arg Leu Ile Asn Lys Ser His Lys Ala Gly Leu Glu Asp Gln 610 615 620Ser Ala Arg Asp Leu Phe Glu Glu Ser Ile Asp Leu Tyr His Ala Ser625 630 635 640Arg Thr Ile Leu Asn Ile His Asn Ser Lys Leu Pro Asp Gln Leu Arg 645 650 655Cys His Glu Ile Pro Arg Pro Lys Ser Ile Thr Ala Lys Glu Cys Asp 660 665 670Thr Ile Ile Thr Leu Gly Asp Glu Ser Met Met Pro His Arg Met Ala 675 680 685Ser Val Lys Glu Glu Thr Ser Ala Ser Thr Ser Asp Thr Glu Lys Glu 690 695 700Cys His Ile Asn Asp Lys Ala Phe Leu Val Phe Leu Ser Gly Leu Tyr705 710 715 720Leu Ala Arg101515PRTCyclotella sp. 10Met His Phe Ser Ala Gln Pro Pro Gln Gly Asn Gly Asp Met Ala Gln1 5 10 15Leu Asp Gly Val Ser Thr Ala Ser Lys Lys Thr Arg Ala Cys Thr Glu 20 25 30Cys His Arg Ala Lys Ser Lys Cys Val Phe Ser Glu Glu Gly Gln Glu 35 40 45Lys Cys Asp Arg Cys Phe Arg Leu Asn Lys Asp Cys Val Pro His Leu 50 55 60Ser Arg Gln Gly Gln Arg Lys Lys Lys Ser Glu Lys Gly Met Met Lys65 70 75 80Ser Ser Val Ala Thr Ser Leu Ala Glu Val Ser Lys Gly Ser Asn Val 85 90 95Ala Ser Lys Ala Pro Met Ser Gly Glu Ser Lys Ser Thr Ser Pro Phe 100 105 110Phe Pro Asp Asn Ala Val Glu Gly Asn Arg Pro Phe Ser Phe His Ala 115 120 125Ala Ser Gln Asp Thr Ser Leu Asn Arg Leu Ala Ala Thr Ala Thr Gly 130 135 140Gly Pro Ser Met Ser Gln Met Ala Pro Leu Ala Lys Phe Ile Pro Gln145 150 155 160Lys His Met Phe Ser Ser Asn His Pro Thr Phe His Asn Thr Gly Pro 165 170 175Cys Gly Leu Tyr Glu Ala Arg Leu Arg Arg Thr Gln Ala Gly Thr Ala 180 185 190Leu Pro Val Asp Gln Thr Asn Ile Thr Val Thr Glu Gln Arg Gln Ala 195 200 205Ala Met Ser Met Phe Ser Asn Ser Asp Arg Thr Ile Thr Asp Ser Thr 210 215 220His Gln Gly Val Thr Phe Arg Glu Asp Leu Ser Ser Ser Arg Ser Leu225 230 235 240Pro Leu Arg Glu Trp Met Lys Cys Ala Leu Asn Ser Asn Lys Ile Arg 245 250 255Asp Ser Ser Gly Ser Ser Pro Ile Ser Ser Lys Tyr Ile Ala Ser Cys 260 265 270Leu Lys Ile Ala Leu Ser Leu Ala Lys Gln Ile Ser Asp Ala Glu Val 275 280 285Thr Ser Ser Arg Glu Ile Leu Gln Trp Leu Pro Arg Asp Ser Ile Asp 290 295 300Trp Pro Gln Tyr Ile Thr Val Lys Leu Thr Gly Asn Glu Thr Gln Val305 310 315 320Pro Pro His Asp Ala Arg Thr Gly Ser Leu Asp His Ser Ser Val Ala 325 330 335Asp Asp Glu Leu Asp Met Leu Glu Ala Leu Leu Asp Ser Ile Cys Glu 340 345 350Glu Asn Glu Val Asp Thr Thr Asp Val Phe Asp Ile Tyr Ser Ala Ala 355 360 365Ile Leu Leu Asp Tyr Ser Lys Asn Ser Asp Asp Gly Val Asp Pro Leu 370 375 380Ser Phe Pro Gly Gln Glu Tyr Arg Ile His Ala Leu Gly Leu Val Phe385 390 395 400Cys Glu Leu Phe Ser Gly Gly Arg Val Pro Ser Thr Glu Leu Val Ser 405 410 415Asp Gly Leu Cys Gln Asp Asp Val Val Thr Pro Ala Ile Ser Glu Arg 420 425 430Leu Glu Phe Thr Gly Met Leu Lys Leu Glu Pro Asn Glu Asn Asp Ile 435 440 445Tyr Lys Asp Thr

Ser Cys Lys Tyr Val Gly Thr Arg Lys Lys Thr Arg 450 455 460Glu Leu Asp Glu Ser Leu His Ser Ser Ile Glu Ser Leu Arg Arg Leu465 470 475 480Gly Ile Ser Cys Pro Leu Cys Asp Leu Ile Phe Asn Ile Leu Asp Ser 485 490 495Ile Asn Gly Asp Leu Gly Arg Asp Asp Ser Tyr Arg Lys Met Ser Asp 500 505 510Val Ala Ile Asp Leu Gln Asn Met Val Asp Lys Pro Lys Thr Phe Leu 515 520 525Asn Asp Leu Asp Val Ile Thr Leu Ser Ser Thr Gly Leu Gln Leu Thr 530 535 540Asp Asn Leu Phe Met Arg Asp Glu Glu Val Ala Leu Leu Gln His Ala545 550 555 560Tyr Tyr Arg Ser Thr Leu Gly Ser Ser Glu Phe Ala Val Ile Thr Gly 565 570 575Gly Ser Gly Thr Gly Lys Ser His Leu Ala Phe Arg Leu Gly Ser His 580 585 590Ile Thr Ser His Gly Gly Ile Phe Leu Ser Val Lys Phe Asn Gln Met 595 600 605Lys Gln Ala Asp Pro Tyr Ser Ala Leu Val Ser Ala Phe Asn Glu Tyr 610 615 620Phe Asn Asn Phe Thr Met Thr Lys Gln Leu Asp Ser Met Lys Arg Ile625 630 635 640Ala Ser Lys Leu Arg Asp Glu Leu Gly Gln Asp Ala Leu Leu Leu Ala 645 650 655Lys Val Ile Pro Asn Leu Ala Glu Val Leu Asp Phe Ala Ala Val Asp 660 665 670Thr Ala Phe Asp Gly Asp Cys Val Asn Gly His Glu Lys Met His Tyr 675 680 685Ile Leu Val Cys Phe Val Glu Val Met Ser Ala Cys Ser His Val Thr 690 695 700Leu Thr Leu Phe Leu Asp Asp Leu Gln Trp Ala Asp Ala Phe Ser Leu705 710 715 720Ser Val Leu Gln Gln Ile Met Ile Met Pro Asp Glu His Lys Gln Phe 725 730 735Phe Phe Val Gly Cys Tyr Arg Asp Asp Gln Met Glu Asp Asp His Pro 740 745 750Phe Lys Lys Met Ile Ser Arg Cys Gly Asp Phe Gly Val Arg Leu Thr 755 760 765Met Val Tyr Leu Glu Cys Met Asp Lys Asp Gly Met Asn Thr Met Ile 770 775 780Ser Glu Leu Leu Cys Leu Pro Pro Arg Leu Val Lys Ser Leu Ser Glu785 790 795 800Leu Val Tyr Ser Lys Thr Lys Gly Asn Pro Leu Phe Leu Ser Arg Leu 805 810 815Leu Ile Ser Leu Asn Lys Asp Gly Leu Leu Asn Leu Ser Leu Gly Arg 820 825 830Arg Arg Trp Val Trp Asp Glu Lys Gln Ile Gln Ser Lys Glu Leu Pro 835 840 845Asp Asp Val Ala Ser Phe Phe Ser Ser Arg Val Gly Lys Leu Ser Pro 850 855 860Glu Val Gln Ala Ala Leu Gln Val Leu Ser Cys Phe Gly Ser Val Asn865 870 875 880Thr Tyr Glu Leu Ser Ile Leu Glu Ser Gly Leu Ser Leu Asn Val Val 885 890 895Lys Pro Leu Glu Arg Ala Val Asn Glu Gly Phe Val Ser Lys Asn Gly 900 905 910Asn Asp Tyr Arg Phe Ser His Asp Lys Ile His Glu Ala Val Tyr Gly 915 920 925Met Val Glu Leu Glu Glu Arg Arg Phe Gln His Leu Asn Tyr Ala Ile 930 935 940Ser Leu Val Lys Phe Ala Leu Gly Gln Asp Asp Ser Ile Ile Phe Thr945 950 955 960Ala Ile Gly Gln Ala Asn Leu Ala Gly Pro Ser Ile Thr Thr Asp Ala 965 970 975Leu Gln Ser Ala Glu Phe Ala Arg Cys Asn Met Val Ala Gly Lys Lys 980 985 990Ala Met Ser Leu Ser Asp Phe Ser Cys Ala Ala Ile Cys Phe Ser Lys 995 1000 1005Gly Leu Ser Phe Leu Asp Glu Asn Arg Trp Ser Asp Tyr Tyr Asn 1010 1015 1020Leu Ser Leu Glu Leu Phe Glu Leu Ala Ala Lys Cys Ala Leu Val 1025 1030 1035Leu Gly Asp Phe Ala Ser Leu Ala Thr Met Ser Glu Gln Val Glu 1040 1045 1050Lys His Ser Arg Cys Phe Glu Asp Lys Leu Glu Val Ser Phe Leu 1055 1060 1065Val Met Cys Ser Leu Ala Tyr Ala Ser Lys Ile Ser Asp Ser Val 1070 1075 1080His Ile Gly Leu Ser Ile Leu Ser Gln Leu Gly His Glu Leu Pro 1085 1090 1095Thr Asn Phe Thr Arg Ala Glu Ile Ile Phe His Ile Glu Gln Thr 1100 1105 1110Lys Thr Val Leu His Ser Ile Ser Asp Lys Asp Leu Met Phe Tyr 1115 1120 1125Lys Lys Met Thr Asp Pro Lys His Ile Met Ala Met Arg Cys Leu 1130 1135 1140Ala Lys Leu Glu Leu Ile Val Leu Gln Ile Asn Pro Asp Leu Gln 1145 1150 1155Pro Ile Ile Thr Leu Lys Met Val Asn Met Thr Met Asp Leu Gly 1160 1165 1170Val Ser His Met Ser Ser Val Gly Met Ala Tyr Phe Ala Gly Leu 1175 1180 1185Val Ala Lys Leu Asp Glu Ile Gln Asp Gly Ile Arg Phe Ala Arg 1190 1195 1200Leu Ala Lys Met Leu Leu Asp Lys Ser Gly Ser Lys Glu Ile Thr 1205 1210 1215Gly Asp Val Ile Phe Thr Thr Ser Glu Val Leu Cys Phe His Glu 1220 1225 1230Pro Leu Gln Ser Val Asn Glu Tyr Arg Phe Tyr Gly Gln Thr Thr 1235 1240 1245Ala Leu Ala Ala Gly Asp Met Tyr Phe Ala Cys Val Leu Lys Met 1250 1255 1260Ser Asn Cys Gly Thr Met Leu Trp Met Gly Ser Asn Leu Leu Ser 1265 1270 1275Val Lys Asp Ala Phe Val Gln Val Ala Arg Tyr Leu Lys Ala Lys 1280 1285 1290Asn His Leu Ser Thr Tyr Asn Leu Leu Leu Leu Ser Lys Arg Ser 1295 1300 1305Ile Leu Met Leu Met Gly Leu Ala Asp Glu Asp Glu Pro Leu Thr 1310 1315 1320Val Asp Gln Leu Thr Asn Pro Tyr Gln Leu Lys Tyr Phe Tyr Phe 1325 1330 1335Gln Lys Met Phe Gln Ser Phe Val Phe Asn Arg Asn Asp Asp Met 1340 1345 1350Lys Gln Tyr Thr Glu Lys Phe Leu Gln Phe Lys Met Pro Ser Trp 1355 1360 1365Leu Leu Leu Ser Val His Ala Arg His Glu Phe Tyr Val Gly Leu 1370 1375 1380Ile Ser Phe Gln Ile Tyr Arg Glu Ser Gly Ile Ser Leu Trp Phe 1385 1390 1395Glu Arg Gly Gln Gln Cys Lys Ser Lys Val Gln Leu Trp Lys Glu 1400 1405 1410Gln Gly Ser Val Trp Asn Phe Glu His Lys Leu Tyr Leu Leu Gln 1415 1420 1425Ala Glu Glu Tyr Tyr Cys Asn Asp Asp Phe Glu Arg Ala Gly Glu 1430 1435 1440Ser Phe Lys Asn Ser Ile Thr Ser Ala Lys Ser His Lys Phe Leu 1445 1450 1455Asn Asp Glu Ala Leu Ala Cys Glu Leu Ala Ala Asn Phe Tyr Leu 1460 1465 1470Gly Thr Gly Asp Leu Thr Ser Ser Met Lys Tyr Phe Arg Leu Ala 1475 1480 1485His Asp Lys Tyr Asn Glu Trp Gly Ala Leu Gly Lys Ala Ala Gln 1490 1495 1500Leu Val Thr Phe Met Thr Glu Lys Phe Ala Ser Cys 1505 1510 151511873PRTCyclotella sp. 11Met Thr Asn His Phe Asp Asn Asn Gln Trp Ser Ser Pro Ser Pro Pro1 5 10 15Met Met Glu Ala His Asp Asp Asn Gln His Gln Gln His Glu Gly Gly 20 25 30Val Leu Leu Cys Ala Ser Cys Asp Arg Cys Arg Ala Arg Lys Thr Lys 35 40 45Cys Asp Gly Met Arg Pro Cys Gly Asn Cys Lys Thr Lys Tyr Met Lys 50 55 60Ser Lys Lys Leu Asp Ser Val Glu Gly Ile Asp Leu Ala Glu Phe Asp65 70 75 80Cys Ile Tyr Ser Pro Ala Lys Arg Arg Gly Pro Val Pro Gly Lys Ser 85 90 95Ala Thr Arg Lys Ala Ser Glu Met Met Ser Tyr Ser Asn Pro Asp Val 100 105 110Met His Phe Gly Ala Gly Gly Gly Gly Thr Gln Gly Gly Gly Tyr His 115 120 125Ser Gln Val Gly Phe Asp Gly Thr Met Asn Thr Gly Gly Gly Phe Asn 130 135 140Pro Gln Gln Gln Gln Gln Leu Gln Gln Phe Asn Asn Asn Ser Ser Ala145 150 155 160Gln Phe Ser Ala Glu Glu Leu Lys Gln Met Leu Leu Leu Gln Gln Gln 165 170 175Leu Leu Leu Gln Gln Gln Glu Met Gln Met Gln Gln Gln Gln Gln His 180 185 190Gln Gln Gly Leu Leu Gln Gln Leu Thr Asn Val Ala Gly Gly Gly Asn 195 200 205Ile Asn Ile Ala Asn Thr Leu Arg Arg Ala Ser Met Asn Gly Gly Ile 210 215 220Thr Ala Asn Gly Glu Thr Met Gly Ala Met Asn Asn Asp Val Gly Ser225 230 235 240Val Asp Arg Ser Gly Met Gly Gly Asn Asn Gly His Val Asp Glu Gln 245 250 255Ser Leu Gln Leu Ile Gln Gln Tyr Gln Asn Gln Leu Asn Ile Gly Ser 260 265 270Asn His Gly Met Thr Ser Gly Asn Ala Ser Ile Ile Gly Ser Val Val 275 280 285Gly Gly Leu Pro Val Gln Pro Ser Pro Met Pro Ser Gln Gln Tyr Val 290 295 300Gln Glu Gln Gln Pro Ala Lys Arg Ala His Arg Ile Asp Ser Ala Met305 310 315 320Ser Ser Asn Asn Asp Gly Thr Leu Pro Lys Ser Val Ile Ser His Leu 325 330 335Pro Leu Leu Asp Arg His Asp Gly Asp Gly Asn Val Leu Arg Ala Tyr 340 345 350Tyr Asp Leu Ser Val Asn Asp Ile Leu Asn Leu Pro Pro Ile Pro Ser 355 360 365Asp Glu Glu Tyr Cys Ser Arg Leu Ala Arg Asn Asn Tyr His Cys Leu 370 375 380Pro Ser Asn Leu Pro Thr Tyr Asp His Ser Ala Leu Gln Ala Ala Arg385 390 395 400Phe Ala Glu Leu Ala Leu Gly Ala Leu Ala Asn Asn Gln Ile Pro Leu 405 410 415Ala Leu Glu Leu Ser Asn Ala Ser Val Met Cys Met Arg Asn Cys Ala 420 425 430Glu Glu Pro Ser Asp Glu Ser Cys Met Tyr Glu Val Ala Arg Ala Tyr 435 440 445Leu Leu His Gly Ile Phe Arg Ser Phe Arg Gly Asp Phe Val Arg Tyr 450 455 460Phe Lys Tyr Arg Arg Val Cys Met Thr His Val Gly Gln Leu Ala Asn465 470 475 480Thr Pro His Val Glu Ala Leu Leu Ala Ala Val Ser Phe His Asp Ala 485 490 495Leu Ala Tyr Met Met His Asn Ala Lys Glu Glu Ser Leu Pro Asp Ile 500 505 510Asp Gln Val Leu Pro Arg Leu Asn Pro Gly Asn Cys Asp Phe Asp Asp 515 520 525Ser Asp Glu Val Glu Ala Lys Tyr Gly Ile Ser Thr Asn Ala Lys Ser 530 535 540Val Ala Ser Asp Pro Asn Asn Gln Met Trp Ile Gln Gly Ala Pro Pro545 550 555 560Val Phe Leu Asn Asn Glu Ala Asn Leu Ala Asn Arg Ser Leu Asp Gly 565 570 575Leu Ala Cys Ala Ile Arg Ser Cys Cys Asp His Ala Asn Ser Gln Phe 580 585 590Glu Glu Met Ala Lys Ala Val Gly Ala Asp Phe Val Gly Gly Ser Gly 595 600 605Ser Cys Gly Met Ser Ala Thr Thr Lys Ala Val Thr Ala Asn Glu Asn 610 615 620Glu Leu Cys Ser Arg Asn Ile Val Leu Ser Ala Arg Thr Leu Leu Asp625 630 635 640Gln Tyr Asn Gly Val Ser His Glu Lys Ala Lys Lys His Gly Leu Gln 645 650 655Met Leu Ala Leu Ala Met Glu Ala Phe Leu Glu Asn Ser Gly Glu Ser 660 665 670Asp Gly Val Gly Gly Phe Thr Asp Lys Gln Ile Lys Asn Leu Leu Thr 675 680 685Val Cys Asp Thr Ile Val Lys Asn Pro Leu Leu Leu His Ala Pro Gly 690 695 700Pro Val Tyr His Met Met Thr Asn Ser Ala Ile Met Leu Cys His Leu705 710 715 720Leu Asn Gly Met His Ala Asn Cys Gly Glu Gly Ser Asn Ser Ser Gly 725 730 735Lys Ser Gly Ile Glu Glu Val Leu Phe Asp Glu Val Leu Asp Ser Phe 740 745 750Met Ala Thr Arg Lys Ile Leu Asn Ala His Arg Lys Ser Leu Pro Val 755 760 765Lys Leu Arg Cys His Gly Ile Pro Arg Pro Asn Val Gly Pro Phe Lys 770 775 780Lys Ser Asp Pro Glu Ala Pro Phe Val Asp Leu Gly Glu Thr Leu Leu785 790 795 800Cys Ala Cys Arg Gly Cys Gln Gly Phe Val Leu Met Gly Cys Ser Pro 805 810 815Cys Val Ala Ala Glu Arg Ser Ala Ala Ala Ala Lys Ala Gln His Ala 820 825 830His Ser Ser Ser Thr Asn Gly Asn Tyr Asn Glu Asp Glu Phe Glu Arg 835 840 845Glu Leu Gln Asp Met Gly Ala Phe Asp Met Asp Asp Asp Ala Leu Leu 850 855 860Asn Val Leu Ser Arg Phe Val Gln Asn865 87012379PRTThalassiosira pseudonana 12Met Ala Thr Thr Thr Glu Val Gln Lys His Ala Val Ser Ala Pro Leu1 5 10 15Pro Ala Ser Ala Ala Thr Thr Thr Thr Gly Gly Gly Asn Asn Glu Ser 20 25 30Thr Val Leu Cys Ala Ser Cys Asp Arg Cys Arg Ala Arg Lys Thr Lys 35 40 45Cys Asn Gly Ala His Pro Cys Ser Gly Cys Val Ser Lys Tyr Met Lys 50 55 60Lys His Lys Leu Glu Ser Phe Asp Gly Ile Asp His Ala Leu Val Glu65 70 75 80Cys His Tyr Ser Val Ala Arg Lys Arg Gly Pro Gln Pro Gly Ser Ser 85 90 95Lys Ser Pro Thr Ala Pro Arg Gly Ser Ile Pro Ala Asp Gly Thr Thr 100 105 110Ile Tyr Gln Gln Pro Ala Lys Lys Lys Pro Lys Lys Ala Lys Gln Ala 115 120 125Ala Pro Met Met His Asp Leu Ala Ala Met Ala Ser Ala Phe Gly Gly 130 135 140Gly Asn Leu Gly Gln Met Pro Leu Pro Leu Asp Pro Ala Ala Ala Ala145 150 155 160Leu Gln Gln Gln Ile Leu Ser Ser Leu Gly Ala Ile Gly Leu Gly Leu 165 170 175Tyr Ala Asn Phe Thr Ala Gly Gly Gly Ser Ala Met Thr Ala Ala Ser 180 185 190Asn Asn Ala Arg Gln Gln Leu Ala Ala Val Glu Ser Leu Leu Ser Asn 195 200 205Asn Lys Ser Asp Val Asp Ser Val Thr Asn Pro Leu Ser Ser Glu Glu 210 215 220Glu Ala His Phe Arg Ala Cys Tyr Thr Leu Ser Val Gly Ser Leu Phe225 230 235 240Gly Leu Pro Asp Val Leu Lys Lys Glu Asp Tyr Phe Pro Lys Tyr Asp 245 250 255Val Ala Val Leu Gln Ala Ala Arg Phe Ala Glu Leu Ala Ile Gly Ala 260 265 270Leu Val Asp Gly Asn Gly Ser Lys Met Thr Lys Leu Ala Asn Ala Thr 275 280 285Val Leu Cys Leu Lys Glu Ala Ala Gln Glu Pro Val His Pro Ser Cys 290 295 300Lys Phe Asp Val Ala Arg Ala Tyr Phe Phe Leu Ala Ile Cys Glu Leu305 310 315 320Asn Ile Gly Asp Val Glu Gly Tyr Leu Lys Tyr Arg Arg Glu Ser Met 325 330 335Arg Arg Leu Ser Glu Met Asn Asp Ala Ser Gly Ala Asp Thr Leu Leu 340 345 350Ala Ala Met Ser Leu Gln Asp Ser Phe Val Tyr Ile Leu Tyr Lys Gly 355 360 365Leu Asp Asp Thr Leu Pro Asn Ile Asp Ser Ala 370 37513896PRTThalassiosira pseudonana 13Met Ser Thr Asp Asp Asn Asn Ile Met Pro Glu Asp Trp Gln Asn Asn1 5 10 15Pro Pro Pro Leu Pro Gln Asp Asn Trp Gln Asn Asn Glu Gln Thr Ser 20 25 30Asn Tyr Asp Asn Gly Asn Ser Asn Gly Gly Gln Tyr Ser Thr His His 35 40 45Gln Gln Gln Pro Pro Gln Glu Gln Val Asn Arg Ala Gln Ser Ser Tyr 50 55 60Asn Asn Gln Tyr Ser Thr Ser Gln Tyr Asn Ser Asn Gln Gln Gln Glu65 70 75 80Gln His Tyr Gln Gln Gln Gln Gln Gln Gln Gln Leu Gln Leu Cys Ala 85 90 95Ser Cys Asp Arg Cys Arg Ala Arg Lys Thr Lys Cys Asp Gly Glu Arg 100 105 110Pro Cys Gly Asn Cys Val Asn Lys Leu Lys Lys Lys Leu Lys Leu Asp 115 120 125Asn Val Asp Gly Ile Asp Ile Ala Glu Phe Asp Cys Val Tyr Ser Pro 130

135 140Ala Lys Arg Arg Gly Pro Ile Pro Gly Lys Thr Gly Gln Ser Arg Lys145 150 155 160Ser Ser Glu Met Met Tyr Gln Gln Pro Gln Gln Arg Gly Gly Gly Tyr 165 170 175Leu Gly Ser Gly Gly Gly Gly Gly Tyr Pro Gln Gln Gln His Gly Leu 180 185 190Gln Gly Gly Gly Tyr Asn Phe Gly Gly Gly Gln Gln Gln Gln Gln Gln 195 200 205Gln Gln Trp Ile Asn Ser Asn Asn Asn Gln Gly Ser Gln Phe Ser Ser 210 215 220Glu Glu Leu Lys Gln Met Leu Ser Leu Gln Gln Gln Leu Leu Ile Gln225 230 235 240Gln Gln Gln Met Gln Gln Gln Gln Gln Gln Gln Gly Met Leu Gln Gln 245 250 255Leu Ala Thr Val Thr Ser Gly Val Gly Ser Ser Gly Ile Gly Gly Ala 260 265 270Gly Gly Ile Gly Gly Met Gly Asn Thr Asn Asn Val Gln Val Glu Asn 275 280 285Gly Ala Leu Gln Leu Leu Gln Gln Tyr Gln Gln Gln Leu Asn Ser Gly 290 295 300Asn Asn Thr Leu Gly Ser Ser Gly Ser Ile Asn Met Gly Leu Gly Ser305 310 315 320Gln Pro Ser Pro Met Pro Ser Ser Ser Tyr Asn Gln Glu Gln Gln Gln 325 330 335Gln Pro Thr Lys Arg Ala His Arg Leu Glu Pro Val Leu Ser Asn Ala 340 345 350Asn Ser Thr Asn Leu Pro Asn Ser Val Ala Ser His Leu Pro Leu Leu 355 360 365Ser Leu His Asn Pro Asp Gly Asn Val Leu Arg Ser Tyr Tyr Gln Leu 370 375 380Ser Val Asn Asp Leu Leu Asn Leu Pro Pro Ile Pro Ser Asp Glu Asp385 390 395 400Tyr Cys Thr Ile Leu Ser Gln Asn Asn Tyr Asn Cys Leu Pro Ser Asn 405 410 415Leu Pro Thr Tyr Asp Gln Ser Ala Leu Gln Ala Ala Arg Phe Ala Glu 420 425 430Leu Ala Leu Gly Ala Leu Ala Asn Asn Gln Val Pro Leu Ala Leu Glu 435 440 445Leu Ser Asn Ala Ser Val Met Cys Met Arg Asn Cys Val Glu Glu Pro 450 455 460Ser His Lys Ser Cys Ile Tyr Asp Val Ala Arg Ala Tyr Leu Leu His465 470 475 480Gly Ile Phe Arg Ser Phe Arg Gly Asp Phe Val Arg Tyr Phe Lys Tyr 485 490 495Arg Arg Val Cys Met Ser His Leu Ser Gln Leu Asn Asn Glu Pro Asn 500 505 510Val Glu Ala Leu Leu Ala Ala Ile Ser Tyr His Asp Ala Leu Ala Tyr 515 520 525Met Met His Asn Ala Ser Glu Asp Ala Leu Pro Asp Ile Asp Glu Val 530 535 540Leu Pro Arg Leu Asn Asp Cys Gly Lys Asn Asp Ser Gly Cys Asp Ile545 550 555 560Glu Ala Lys Tyr Gly Ile Ser Thr Asn Ala Ser Ser Val Val Thr Asn 565 570 575Ala Asn Asn Gln Met Trp Met Gln Gly Ala Pro Pro Val Phe Leu Asn 580 585 590Asn Glu Ala Ser Leu Val Asn Arg Ser Leu Asp Ala Leu Ala Cys Ala 595 600 605Val Arg Ser Cys Cys Asp Gln Ala Asn Ser Ser Phe Glu Glu Met Ala 610 615 620Lys Glu Ala Gly Val Asp Leu Pro Ala Gly Gly Gly Ser Cys Gly Thr625 630 635 640Ser Ala Thr Thr Gln Ala Val Met Ala Asn Glu Asn Glu Leu Cys Ser 645 650 655Arg Asn Ile Val Leu Ser Ala Gln Thr Leu Leu Ser Gln His Ala Gly 660 665 670Thr Ser His Glu Lys Ser Lys Lys His Gly Leu Val Met Val Ala Thr 675 680 685Ala Met Glu Ala Phe Leu Glu Asn Gly Gly Gly Asp Glu Glu Gly Met 690 695 700Gly Gly Phe Thr Asp Lys Gln Ile Lys Asn Leu Leu Ala Val Cys Asn705 710 715 720Thr Ile Val Lys Asn Pro Leu Leu Leu Phe Ala Pro Gly Pro Thr Tyr 725 730 735His Met Val Ser Asn Val Ala Ile Leu Leu Cys His Leu Leu Asn Gly 740 745 750Ile His Ala Asn Cys Gly Gly Ser Ser Gly Asn Ala Lys Ser Gly Met 755 760 765Glu Glu Val Leu Phe Asp Glu Val Leu Asp Ala Phe Met Ala Ile Arg 770 775 780Lys Leu Leu Asn Leu His Arg Lys Asn Leu Pro Val Lys Leu Arg Cys785 790 795 800His Gly Ile Pro Arg Pro Lys Leu Gly Pro Phe Lys Lys Ser Asp Pro 805 810 815Glu Thr Pro Phe Ile Asp Leu Gly Asp Thr Leu Met Cys Val Cys Arg 820 825 830Gly Cys Gln Gly Phe Val Leu Met Gly Cys Ser Pro Cys Val Ala Ala 835 840 845Glu Arg Ser Ala Ser Ser Ala Arg Met His Ala Asn Gln Ser Glu Asp 850 855 860Asp Asp Asp Glu Phe Glu Arg Glu Leu Gly Gln Leu Asp Asp Phe Asn865 870 875 880Leu Asp Asp Asp Ala Leu Leu Ser Leu Leu Ser Arg Ile Val Gln Asn 885 890 89514689PRTThalassiosira pseudonana 14Met Ser Gln Thr Ser Asn Thr Glu Pro Lys Gly Ala Lys Arg Lys Thr1 5 10 15Gln Ala Cys Thr Glu Cys His Lys Ser Lys Ser Lys Cys Thr Tyr Pro 20 25 30Asp Pro Thr Thr Thr Ala Ala Gly Gly Thr Ala Lys Leu Cys Cys Asn 35 40 45Arg Cys Ile Arg Leu Gly Arg Asp Cys Ile Pro His Ile Ser Gln Gln 50 55 60Gly Lys Arg Asn Lys Lys Thr Glu Glu Glu Thr Met Lys Asn Glu Lys65 70 75 80Arg Val Asn Glu Asp Asp Met Gln Asp Gly Leu Cys Lys Ser Thr Met 85 90 95Cys Ala Ala Ala Ile Gly Asn Gln Asp Lys Ile Leu Lys Glu Asn Asn 100 105 110Leu Ser Leu Glu Leu Pro Arg His Ile Thr Asn Ser Met Ala Gly Gln 115 120 125Phe Pro Ala Gly Gly Gly Gly Gly Met Met Gly Gly Gln Phe Ala Gly 130 135 140Arg Ser Gly Ala Gly Ile Leu His Pro Ala Asp Ile Leu Ser Gly Gly145 150 155 160Met Asn Ser Ser Gln Leu Ser Leu Met Leu Asn His Phe Ser Gly Thr 165 170 175Ser Gly Gly Gln Ser Asp Thr Met Ser Thr Leu Asn Asn Ile Met Ser 180 185 190Ser Ser Ala Met Gly Ala Thr Gly Pro Pro Pro Ser Val Asp Ala Leu 195 200 205Leu Met Leu Ala Ser Arg Ser Thr Ser Ile Gly Ser Asn Ser Gly Val 210 215 220Asn Leu Gly Gly Thr Ala Ser Ala Ala Pro Ala Leu Pro Gly Thr Ser225 230 235 240Gln His Leu Ile Gln Gln Trp Gln His Gln Gln Asn Gln Leu Arg Tyr 245 250 255Ala Val Met Gly Gly Met Gln Thr Ala Thr Met Met Gly Met Thr Gln 260 265 270Ala Ser Gly Asp Gly Ser Ala Thr Gly Asn Gln Leu Asp Ser Ala Ile 275 280 285Ile Thr Lys Lys Glu Arg Thr Ser Ser Phe Gly Ser Glu Asn Asp Gln 290 295 300Pro Lys Asn Lys Lys Gln Lys Ala Ile Gln Glu Ala Lys Glu Trp Cys305 310 315 320Ala Gly Gly Gly Gly Asp Asp Gln Lys Gln Ser Val Leu Glu Ala Leu 325 330 335Ala Ala Ala Thr Lys Asn Glu Thr Thr Pro Lys Phe Val Pro Pro His 340 345 350Ile His Tyr Pro Pro Val Ser Leu Leu Ala Glu Thr Thr Thr Thr Ala 355 360 365Ile Asn Asp Asn Ala Ser Ser Ser Ala Ala Ala Ala Ala Asp Asn Thr 370 375 380Thr Asp Thr Gln Glu Ser Gln Leu Arg Arg Ser Ser Tyr Asn Ala Gln385 390 395 400Phe Val Thr Pro Glu Asp Ala Ile Gly Asn His Ile Thr Gly Gln Lys 405 410 415Leu Pro Cys Leu Gln Asn His Tyr Gly Leu Gln Cys Gln Ile Arg Glu 420 425 430Trp Ile Ser Met Ala Leu Val Arg Arg Ser Phe Ala Leu Leu Ser Lys 435 440 445Ala Ser Ser Leu Ala Asn Arg Cys Gly Ile Ser Met Asp Arg Ile Phe 450 455 460Cys Gly Val Val Glu Glu Val Glu Lys Lys Gly Gly Ala Glu Lys Lys465 470 475 480Thr Lys Gly Gly Cys Lys Met Asn Val Gly Gly Lys Met Asn Tyr Leu 485 490 495Leu Ser Val Phe Leu Glu Pro Arg Thr Ala Gln Val Val Pro Met Glu 500 505 510Gln Pro Phe Glu Arg Asn Leu Leu Cys Trp Arg His Ile Ser Gln Ile 515 520 525Phe Glu Asp Asn Leu Ala Asp Gly Phe Ser Leu Met Phe Ala Lys Glu 530 535 540Asp Phe Arg Arg Phe Leu Ala Cys Tyr Ala His Gln Ile Ser Ser Gln545 550 555 560Pro Ser Ala Glu Ser Pro Ile Arg Pro Val Tyr Ala Pro Lys Ile Thr 565 570 575Val Arg Leu Leu Ser Arg Asp Trp Gly Gln Thr Glu Ala Val Thr Glu 580 585 590Glu Met Ile Glu Gly Val Gly Lys Asn Glu Ala Glu Thr Thr Glu Met 595 600 605Asp Ala Leu Phe Val Val Val Pro Thr Met Asp Lys Val Thr Tyr Tyr 610 615 620Leu Glu Leu Phe His Pro Asn Leu Glu Ser Asp Ala Lys Asp Cys Glu625 630 635 640Ala Asp Asp Asn Asp Glu Gly Thr Glu Thr Pro Glu Ser Asn Pro Pro 645 650 655Ala Leu Asp Thr Val Met Glu Gly Glu Asp Trp Gln Gly Ile Asp Glu 660 665 670Ile Leu Ala Ser Gly Asp Asp Met Asp Ala Leu Met Lys Ala Leu Leu 675 680 685Asp15410PRTFragilariopsis cylindrus 15Met Gly Thr Ser Ala Asn Arg Ala Cys Thr Glu Cys His Lys Ala Lys1 5 10 15Val Lys Cys Val Arg Asp Asp Asp Gly Asn Ile Ile Cys Lys Arg Cys 20 25 30Glu Arg Ile Gly Leu Lys Cys Val Glu His Ile Ser Arg Gln Gly Gln 35 40 45Gly Thr Arg Arg Arg Lys Lys Val Lys Lys Glu Thr Thr Thr Ala Thr 50 55 60Gly Ala Ala Asn Lys Asn Asn Glu Asp Lys Thr Val Asp Glu Ala Leu65 70 75 80Ala Ile Thr Ile Ala Leu Ser Ser Pro Ser Pro Met Pro Ser Cys Pro 85 90 95Val Ser Gly Gly Ser Asn Ile Val Phe Ser Gly Asn Gly Asn Val Asn 100 105 110Gly Val Pro Ser Ser Ala Cys Asn Ala Leu Thr Ala Met Asn Gly Gln 115 120 125Ala Met Thr Asn Asn Lys Glu Gly Leu Cys Asn Gly Met Ala Ser Leu 130 135 140Gln Val Glu Asp Ser Ile Ile Cys Lys Ser Ile Thr Asn Gly Leu Gly145 150 155 160Lys Glu His Tyr Gly Ile His His Leu Ile Arg Met Trp Val Ala Leu 165 170 175Ser Phe Thr Arg Arg Ser Phe Ser Leu Leu Ala Arg Ala Ser Phe Ile 180 185 190Ala Ser Arg Met Gly Ile Ser Met Asp Glu Ile Ile Ser Asn Gln Ser 195 200 205Asn Phe Ala Ile Asp Ser Gly Ser Gln Pro Met Tyr Phe Leu Gly Arg 210 215 220Asp Ile Leu Val Pro Lys Ser Gln Arg Lys Thr Ile Gly Leu Pro Leu225 230 235 240Asn Ile Glu Glu Ile Pro Trp Asp Leu Leu Glu Ala Val Gln Ile Asp 245 250 255Pro Val Arg Pro Asp Glu Thr Phe Arg Asn Arg Trp Cys Ala Ile Arg 260 265 270Met Thr Val Gln Gly Thr Ser Arg Phe Leu Thr Ser Pro Leu Phe Ser 275 280 285Arg Asp Phe Ser Ser Val Asp Glu Ile Asn Lys Val Trp Asp Glu Asn 290 295 300Lys Pro Asn Lys Glu Val Val Asp Leu Trp Met Pro Lys Ser Glu Lys305 310 315 320Gly Asn Ile Asn Asn Asp Asn Asn Asn Asn Asn Asn Ser Ser Asp Arg 325 330 335Asn Ser Gln Tyr Gly Gly Thr Thr Ser Ser Ala Lys Lys Arg Asp Ile 340 345 350Ile Asp Val Ala Gly Gly Thr Ser Asn Asn Glu Ile Glu Ser Asp Val 355 360 365Cys Asp Pro Ile Met His Asp Asp Gly Ile Glu Phe Thr Asp Leu Val 370 375 380Val Thr Glu Glu Met Gln Glu Phe Phe Gln Leu Leu Ala Gly Asp Gln385 390 395 400Arg Val Gln Ala Asp Leu Asn Ser Leu Phe 405 41016805PRTFragilariopsis cylindrus 16Met Thr Thr Ser Thr Arg Leu Arg Gly Lys Arg Gly Lys Lys Asp Ser1 5 10 15Arg Asn Asp Ala Val Ala Thr Ser Asp Asn Gly Val Ala Met Thr Thr 20 25 30Ala Asn Ala Val Val Val Val Asn Asp Glu Lys Asn Lys Gln Asp Asn 35 40 45Tyr Asn Asn Glu Gly Asp Pro Val Glu Phe Lys Val Arg Val Glu Leu 50 55 60Glu Val Glu Ala Pro Ile Asn Glu Gln Lys Ala Val Asp Asn Asn Glu65 70 75 80Lys Lys Lys Ser Ser Ala Glu Thr Thr Lys Ala Glu Ala Ala Val Val 85 90 95Asn Ser Asp Glu Asp Val Asn Asp Asp Val Asn Asp Asp Val Asn Asp 100 105 110Gly Glu Asp Asp Ala Val Val Val Val Lys Asn Ser Lys Glu Asn Asn 115 120 125Asp Asp Asp Asn Asp Ser Asp Thr Lys Lys Met Gln Asp Ala Thr Lys 130 135 140Lys Lys Met Ala Pro His Gln Asp Asp Ala Cys Val Val Glu Val Val145 150 155 160Gln Val Ser Asp Arg Pro Ser Phe Leu Gly Gly Thr Val Leu Lys Arg 165 170 175Asp Thr Val Gly Leu Gly Leu Arg Tyr Lys Thr Glu Lys Glu Lys Glu 180 185 190Lys Val His Glu Asn Asp Ile Leu Phe Ser Ser Val Asp Leu Gly Leu 195 200 205Gln Ser Gly Ser Gly Gly Ser Ser Ser Ser Gln Phe Leu Asn His Thr 210 215 220Asp His Ser Gly Asn Lys Lys Leu Gln Ser Ile Ile Lys Ala Arg Lys225 230 235 240Ser Asn Tyr Phe Val Asn Asp Val Thr Asn Ile Asp Ser Cys Ser Ile 245 250 255Ala Val Asn Glu Glu Glu Arg Thr Lys Ile Ala Lys Glu Ile Phe His 260 265 270Glu Ile Thr Thr Thr Thr Thr Thr Thr Gly Lys Asp Val Gly Ile Gly 275 280 285Val Gly Arg Phe Leu Asn Phe Lys Ser Met Thr Lys Ala Lys Tyr Glu 290 295 300Asn Leu Gly Cys Asp Phe Val Trp Glu Ile Met Asp Glu Ile Thr Ser305 310 315 320Ile Ile Lys Ile Cys Gln Thr Met Asn Tyr Ile Phe Met Ser Asp Gln 325 330 335Glu Arg Thr Glu Arg Ser Leu Ala Ile Glu Thr Gln Gln Lys Gln Gln 340 345 350Gln Asn Asp Tyr Arg Asn Glu Arg Gln Gln Lys Asn Gly Lys Thr Leu 355 360 365Ser Ser Ser Asp Lys Lys Ser Lys Thr Lys Lys Ser Thr Lys Gln Asn 370 375 380Lys Ile Leu Leu Gln Gln Arg Gln Gln Glu Gln Glu Gln Arg Glu Asn385 390 395 400Ala Gln Ile Gln Glu Gln Gln Leu Gln Gln Gln Gln Gln Gln Gln Gln 405 410 415Gln Cys Gln Gln Val Gln Met Arg Ile Tyr Gln Leu Gln Gln Gln Leu 420 425 430Gln Gln Gln Gln Val Tyr Tyr Pro Pro Thr Pro Leu Ile Gln Gln Tyr 435 440 445Pro Thr Ala Met Pro Met Pro Met Pro Leu Ser Ser Pro Ser Pro Leu 450 455 460Leu Pro Lys Asp Gly Lys Lys Lys Lys Thr Lys Gly Glu Lys Arg Lys465 470 475 480Ala Pro Val Pro Ala Ala Met Ala Ser Glu Arg Ser Gly Ile Ile Glu 485 490 495Gly Arg Val Ile Val Asp Thr Ile Val Gly Gly Asp Ser Asp Glu His 500 505 510Ile Gly Asn Glu Asn Leu Val Lys Leu Ile Val Lys Lys Lys Ser Glu 515 520 525Tyr Asp Tyr Ile Glu Val Lys Asp Ile Lys Lys Leu Gly Ile Ala Arg 530 535 540Val Arg Gln Asn Val Ser Leu Asn Ile Val Lys Ser Ile Val Lys Glu545 550 555 560Asn Gly Gly Arg Phe Leu Phe Arg Arg Lys Lys Asp Val Asp Asp Asp 565 570 575Leu Leu Glu Thr Pro Thr Val Glu Ala Thr Ile Ala Val Ile Lys Asp 580 585 590Gly Glu Asp Ala Ile Ala Arg Ala Glu Ala Ala Leu Arg Gly Glu Lys 595

600 605Thr Pro Thr Lys Thr Ser Asn Asp Ile Glu Asp Glu Asp Glu Asp Asp 610 615 620Asn Ile Lys Asn Glu Asp Ser Gly Pro Val Val Trp Glu Glu Leu Lys625 630 635 640Asp Glu Ser Met Ile Gln Ala Ile Val Trp Arg Cys Met Lys Asp Ile 645 650 655Tyr Glu Leu Ala Asp Glu Asn Lys Thr Glu Ile Leu Glu Lys Arg Lys 660 665 670Glu Ala Lys Lys Glu Arg Lys Arg Leu His Glu Tyr Asp His Asp Asp 675 680 685Glu Ser Ala Gly Pro Ala Ala Ala Ala Thr Ala Arg Lys Lys Gln Ala 690 695 700Val Glu Glu Asp Pro Ser Gly Arg Lys Asn Lys Ser Cys Asp Phe Cys705 710 715 720Arg Asp Lys Lys Leu Lys Cys Asn Arg Thr Ser Pro Cys Glu Asn Cys 725 730 735Thr Thr Lys Tyr Met Lys Asp His Asn Leu Thr Ser Glu Glu Val Glu 740 745 750Glu Ser Lys Ile Ala Asn Ser Ile Asn Ala Val Ala Val Val Ala Lys 755 760 765Val Glu Glu Ala Lys Lys Leu Glu Ser Met Pro Glu Thr Lys Arg Pro 770 775 780Arg Thr Arg Ser Ile Phe His Phe Leu Val Phe Leu Ile Leu Glu Cys785 790 795 800Ser Val Pro Met Glu 805171039PRTNannochloropsis oceanicamisc_featureZnCys-2845 Orthologmisc_featureStrain 5473 17Met Thr Thr Leu Leu Gly Gln Pro Pro Ser Ser Leu Gly Ala Met Gly1 5 10 15Ser Ala Phe Tyr Asp Glu Asp Ala Gln Ser Val Val Ala Leu Gly Gln 20 25 30His Ala Ala Gly Ser Gly Thr Glu Asp Glu Met Asp Thr Asp His Phe 35 40 45Asp Glu Leu Asp Arg Ile Ile Phe Asp Met Pro Tyr Val Ser Glu Gln 50 55 60Asp Pro Leu Ser Ser Cys Ser Val Gly Gly Gln Ser Gln Gly Gln Thr65 70 75 80Asn Gly Gln Gly His Gly His Gln Glu Arg Gly Ala Ser Gln His Gly 85 90 95Gly Ala Gly Leu Leu Met Pro Asn Pro His Asn Gly His Ile His Gly 100 105 110Asp Gly Gly His His Ile Asn His Asn Asn His Gly Ser Val Arg Gly 115 120 125Gly Gly Met Asp Trp His Ala Lys Glu Glu Asp Ala Ser Tyr His Thr 130 135 140Ala Val Asp Ser Ser Cys His Thr Asp Arg Ser Tyr His Arg Val Asp145 150 155 160Ala Ser Gly His Ser Met Ile Asp Ala Ser Ser His Ser Met Met Asp 165 170 175Ala Ser Gly His Glu Ser Leu Ile Asp Ser Ser Gly His Tyr Asp Asp 180 185 190Phe Ala Ala His Lys Gly Asp Pro Arg Tyr Met Glu His Ser Cys Glu 195 200 205Ala Cys Lys Arg Ser Lys Lys Arg Cys Asn Arg Arg Asn Pro Cys Gln 210 215 220Ile Cys Thr Ser Arg Gly Ile Lys Cys Val Pro Gln Ile Arg Gly Pro225 230 235 240Gly Arg Pro Pro Gly Ser Lys Ser Ser Arg Gly Ser Ser Ser Ser Ser 245 250 255Ser Leu Thr Leu Gly Ser Ser Arg His Gly Gly Ser Arg Gly Asp Val 260 265 270Arg Ser Ser Leu Asn Ser Thr Gln His Ser Thr Asn Ser Ser Ala Thr 275 280 285Thr Ser Ala Ala Ser Ser Thr Ala Ser Ser Leu Ser Arg Ser Leu Ser 290 295 300Gly Asn Gly Leu Leu Gln Gln Glu Gln Asp Leu Val Val Val Ala Ala305 310 315 320Ala Ala Ser Thr Arg Gln Ser Pro Pro Arg Asp Pro Trp His Cys Arg 325 330 335Phe Phe Phe Glu Ala Ala Arg His Cys Lys Glu Ala Phe Leu Lys Ala 340 345 350Trp His Asp Asn Glu Leu Asp Thr Ser Lys Cys Ile Met Leu Arg Asn 355 360 365Leu Trp Thr Lys Thr Ser Ser Ile Leu Ala Ser Gly Val Asp Met Thr 370 375 380Phe Gly Ile Cys Asp Gln Leu Gln Glu Val Val Gly Pro Ala Pro Thr385 390 395 400Gly Ser Gly Pro Ile Ala Cys Ser Pro Ala Thr Arg Ser Lys Ser Gln 405 410 415Ala Ala Gln Gln Ala Gln Leu Leu Ser His Pro Gly Ser Lys Glu Gly 420 425 430Met Gly Pro Trp Asn Leu Pro Asp Asp Leu Arg Lys Met Asp Asp Gly 435 440 445Val Ser Met Leu Cys Gly Phe Met Phe Ile Gln Asp Glu Leu Phe Val 450 455 460Phe Thr Asp Glu Arg Phe Ala Ala Thr Phe Met Thr Arg Glu Glu Val465 470 475 480Glu Gly Lys Val Glu Ser Phe Ala Val Leu Pro Ile Leu Leu Leu Ala 485 490 495Glu Ile Phe His Pro Asp Asp Leu Pro Asp Val Tyr Ala Ala Ile Gly 500 505 510Ala His Trp Phe Arg Arg Arg Pro Ser Ser Gly Val Gly Val Gly Gly 515 520 525Ser Asn Gly Ser Ile Ser Ser Met Asn Ser Ser Ser Gly Ser Thr Ser 530 535 540Ser Arg Asp Ser Ala Ser Pro Gly Pro Val Ser Arg Glu Val Pro Glu545 550 555 560Ala Ala Trp Ile Cys Lys Cys Ile Asp Lys Arg Asn Thr Glu Ile Thr 565 570 575Ala Leu Val Arg Phe Arg Ser Phe Ala Ala Pro Thr Glu Gly Tyr Ala 580 585 590Gly Ala Ala Met Leu Ser Ile Leu Pro Leu Thr Arg Ser Lys Tyr Ile 595 600 605Ala Asp Pro Asp Val Gln Thr Asn Met Arg Ser Gly Val Ser Ser Arg 610 615 620His His Leu Arg Asp Thr Phe Gly Ala Leu Pro Thr Ala Leu Pro Glu625 630 635 640His Asp Asp Glu Asp Asp Asp Asp Glu His His His Leu Val Leu Glu 645 650 655Arg Arg Gly Glu Arg Val Gly Ala Ser Gly His Gly Gln Asp Leu Leu 660 665 670Asn Glu Glu Glu Asp Asp Glu Ile Phe Leu Asp Ala His Gly Asp Asp 675 680 685Ala Met Phe Arg Pro Leu Arg Arg Gly Met Thr Val Leu Ser Ala Glu 690 695 700Thr Ser Gly Pro Gln Pro Val Pro Leu Ser Lys His Ala Ser Asp Pro705 710 715 720Leu Pro His His Asn Glu His His Phe His Ser Gln Pro Gln His Thr 725 730 735Ser Ser His Leu Ser Ser Leu Ser Ser Met Ala Ser His Gln Thr Gly 740 745 750Val Ser Trp Gly Gly Gly Arg Ile Ser Glu Cys Leu Gly Asn Gln Asn 755 760 765Arg Ser Ala Ser Gln Phe Tyr Asn Thr Val Gln His Gln Glu Arg Pro 770 775 780Lys Arg Glu Gln Glu Glu Pro His Gln Gln His Arg Glu Glu Gln Gln785 790 795 800Gln His Arg Leu Pro Gly Asn Asn Ser Leu Asp Gly Ser Ser Ser His 805 810 815Gly Gly Ala Met Asp Gln Asp Leu Pro Thr Val Gln Leu Thr Gln Ala 820 825 830Gln Leu Phe Leu Leu Gln Gly Gly Thr Gly Ser Gly Ile Gly Leu Phe 835 840 845Lys Asp Ile Gln Gln Glu Gln Gln His Met Cys Asn Gln Ile Ser Pro 850 855 860Asp Gly Val Thr Ala Ala Glu Glu Ser Ala Glu Arg Val Ala Thr Glu865 870 875 880Leu Tyr Gly Ser Ser Pro Ser Pro Glu Pro His Leu Leu Gly His Ser 885 890 895Arg His Ser Pro Thr Gln Arg Ala Gln Gln Gln Gln Gln Gln Gln Lys 900 905 910Arg Gln Gln Glu Arg Gln Gln Glu Asp Gln Gln Gln Glu Gln Gly His 915 920 925Gln Gln Gln Gln Gln Gln Gln Gln Gln Gln Gly Met Val Leu Pro Leu 930 935 940Pro His Leu Pro Gly Met Val Pro Ser Leu Val Arg Thr Val Ser Ser945 950 955 960Ser Ala Met Leu Gly Ala Arg Pro Thr Thr Ile Ser Gln Gly Lys Asp 965 970 975Glu Gly Gly Arg Gly Gly Ala Leu Ser His Ser Asn Ser Ser Thr Asp 980 985 990Leu Asp Met Ser Cys His Gly Pro Ala Asp Pro Asn Gly Tyr Gly Gly 995 1000 1005Leu His Trp Thr Pro Ala Pro Leu Ala Ser Phe Leu Gly Val Ser 1010 1015 1020Ser Trp Gly Ser Arg Arg Gly Ser Arg Lys Glu Glu Arg Ser Lys 1025 1030 1035Asp18364PRTNannochloropsis granulatamisc_featureZnCys-2845 Orthologmisc_featurePartial sequencemisc_feature(211)..(211)Xaa can be any naturally occurring amino acid 18Met Thr Thr Leu Ile Gly Gln Pro Pro Pro Ser Leu Arg Ala Met Gly1 5 10 15Ser Ala Phe Tyr Asp Glu Asp Ala Gln Ser Val Val Ala Leu Ser Gln 20 25 30His Ala Ser Gly Ser Gly Thr Glu Asp Glu Met Asp Thr Asp His Phe 35 40 45Asp Glu Leu Asp Arg Ile Ile Phe Asp Met Pro Tyr Val Ala Asp Gln 50 55 60Asp Pro Phe Ser Ser Gly Ser Gly Gly Gly Gln Ser Gln Gly Gln Thr65 70 75 80Asn Gly Gln Gly His Gly His Gln Gln Arg Gly Gly Ala Ser Gln His 85 90 95Gly Gly Ala Gly Leu Leu Met Pro Thr Pro His Asn Gly His Thr His 100 105 110Gly Asp Gly Gly His His Ser Asn His Ser Asn His Gly Ser Ala Arg 115 120 125Gly Gly Gly Ile Asp Trp His Val Lys Glu Glu Asp Ala Ser Tyr His 130 135 140Thr Ala Val Asp Ser Ser Cys His Ile Asp Arg Ser Tyr His Arg Val145 150 155 160Asp Val Ser Gly His Ser Met Ile Asp Ala Ser Gly His Ser Met Met 165 170 175Asp Ala Ser Gly His Glu Ser Leu Ile Asp Ser Ser Gly His Tyr Asp 180 185 190Asp Phe Ala Ala His Lys Gly Asp Pro Arg Tyr Met Glu His Ser Cys 195 200 205Glu Ala Xaa Pro Cys Gln Ile Cys Thr Ser Arg Gly Ile Lys Cys Val 210 215 220Pro Gln Ile Arg Gly Pro Gly Arg Pro Pro Gly Ser Lys Ser Ser Arg225 230 235 240Gly Ser Ser Ser Ser Ser Ser Leu Ala Leu Ser Ser Ser Arg His Gly 245 250 255Gly Ser Arg Gly Asp Val Arg Ser Ser Leu Asn Ser Thr Gln His Ser 260 265 270Thr Asn Ser Ser Ala Thr Thr Ser Ala Ala Ser Ser Thr Ala Ser Ser 275 280 285Leu Ser Arg Ser Leu Ser Gly Asn Gly Leu Leu Gln Gln Glu Gln Glu 290 295 300Leu Ala Ala Val Ala Ala Gly Ala Ala Arg Gln Ser Pro Pro Arg Asp305 310 315 320Pro Trp His Cys Arg Phe Phe Phe Glu Ala Ala Arg His Cys Lys Glu 325 330 335Ala Phe Leu Lys Ala Trp His Asp Asn Glu Leu Asp Thr Ser Lys Cys 340 345 350Ile Met Leu Arg Tyr Val Leu Thr Ser Phe Gly Asp 355 36019333PRTNannochloropsis oculatamisc_featureZnCys-2845 Orthologmisc_featurePartial sequencemisc_feature(65)..(65)Xaa can be any naturally occurring amino acidmisc_feature(176)..(176)Xaa can be any naturally occurring amino acidmisc_feature(316)..(316)Xaa can be any naturally occurring amino acid 19Met Thr Thr Leu Leu Gly Gln Pro Pro Pro Ser Leu Arg Ala Met Gly1 5 10 15Ser Ala Phe Tyr Asp Glu Asp Ala Gln Ser Val Val Ala Leu Ser Gln 20 25 30His Ala Ala Gly Ser Gly Thr Glu Asp Glu Met Asp Thr Asp His Phe 35 40 45Asp Glu Leu Asp Arg Ile Ile Phe Asp Met Pro Tyr Val Ala Glu Gln 50 55 60Xaa Leu Leu Met Pro Thr Pro His Asn Gly His Thr His Gly Asp Gly65 70 75 80Gly Tyr His Ser Asn His Ser Asn His Gly Ser Ala Arg Gly Gly Gly 85 90 95Met Asp Trp His Val Lys Glu Glu Asp Ala Ser Tyr His Thr Ala Val 100 105 110Asp Ser Ser Cys His Ile Asp Arg Ser Tyr His Arg Val Asp Ala Ser 115 120 125Gly His Ser Met Ile Asp Ala Ser Gly His Ser Met Met Asp Ala Ser 130 135 140Gly His Glu Ser Leu Ile Asp Ser Ser Gly His Tyr Asp Asp Phe Ala145 150 155 160Ala His Lys Gly Asp Pro Arg Tyr Met Glu His Ser Cys Glu Ala Xaa 165 170 175Pro Cys Gln Ile Cys Thr Ser Arg Gly Ile Lys Cys Val Pro Gln Ile 180 185 190Arg Gly Pro Gly Arg Pro Pro Gly Ser Lys Ser Ser Arg Gly Ser Ser 195 200 205Ser Ser Ser Ser Leu Ala Leu Ser Ser Ser Arg His Gly Gly Ser Arg 210 215 220Gly Asp Val Arg Ser Ser Leu Asn Asn Thr Gln His Ser Thr Asn Ser225 230 235 240Ser Ala Thr Thr Ser Ala Ala Ser Ser Thr Ala Ser Ser Leu Ser Arg 245 250 255Ser Leu Ser Gly Asn Gly Leu Leu Gln Gln Glu Gln Glu Leu Ala Ala 260 265 270Val Ala Ala Ala Ala Ala Ala Ala Ala Ala Arg Gln Ser Pro Pro Arg 275 280 285Asp Pro Trp His Cys Arg Phe Phe Phe Glu Ala Ala Arg His Cys Lys 290 295 300Glu Ala Phe Leu Lys Ala Trp His Asp Asn Glu Xaa Lys Ala Trp His305 310 315 320Asp Asn Glu Leu Asp Thr Ser Lys Cys Ile Met Leu Arg 325 33020255PRTNannochloropsis salinamisc_featureZnCys-2845 Ortholog 20Met Thr Thr Phe Leu Asn Pro Gly Pro Ala Arg Glu Lys Leu Val Gly1 5 10 15Ser Gly Val Phe Phe Glu Asp Ser Ile Gly Leu Val Gly His Glu Ser 20 25 30Gly Gly Gly Val Gly Ser Gln Asp Glu Met Asp Thr Asp His Phe Asn 35 40 45Glu Leu Asp His Ile Phe Asp Leu Ser Tyr Ser Ala Glu Gln Asp Pro 50 55 60Phe Gly Ser Gly Ser Gly His Ala Gln Ser Gln Gly Thr Gly Tyr Gly65 70 75 80His Pro Pro Gln Thr Gln Leu Gly Gly Ala Gly Leu Leu Met Pro His 85 90 95Pro His Asn Ser His Gly Ala Thr Ser His Asp Gly Ser Arg Met His 100 105 110Asn Asp Gly Met Asp Trp Arg Ala Lys Asp Glu Asp Cys Ser Tyr His 115 120 125Thr Ala Val Asp Ala Ser Cys His Ile Asp Ser Ser Tyr His His Val 130 135 140Asp Ala Ser Gly His Ser Met Val Asp Ala Ser Gly His Ser Thr Ile145 150 155 160Asp Ala Ser Gly His Asp Ser Leu Ile Asp Ser Ser Gly His Tyr Asp 165 170 175Asp Tyr Leu Ala His Lys Gly Asp Ala Arg Tyr Met Glu His Ser Cys 180 185 190Glu Ala Cys Lys Arg Ser Lys Val Arg Arg Val Ala Thr Ser Leu Trp 195 200 205Arg Ala Gln Pro Arg Arg Tyr Phe His Ala Leu Pro His Gln Ser His 210 215 220Phe Val Leu Leu Asn Pro Lys Phe Cys Val Leu Arg Asn Ile Val Ala225 230 235 240Cys Pro Thr Ala Pro His Ser Ser Leu Tyr Phe His Ile Pro Ser 245 250 25521173PRTNannochloropsis gaditanamisc_featurePAS3 domain of ZnCys-2845 21Asn Leu Trp Thr Lys Val Ser Ser Gln Leu Ala Ser Gly Thr Asp Met1 5 10 15Thr Phe Gly Ile Cys Asp Gln Leu Gln Glu Val Val Gly Pro Ala Pro 20 25 30Thr Gly Ser Gly Pro Met Ala Gly Ser Pro Ala Thr Arg Ser Lys Ser 35 40 45His Ala Ala Gln Gln Ala Gln Leu Leu Thr His Pro Gly Ser Lys Glu 50 55 60Ala Met Gly Pro His Cys Leu Pro Leu Asp Leu Arg Arg Met Glu Asp65 70 75 80Gly Val Ser Met Leu Cys Gly Phe Met Phe Leu Gln Asp Glu Leu Phe 85 90 95Val Tyr Thr Asp Glu Arg Phe Ala Ala Thr Phe Met Thr Arg Glu Glu 100 105 110Val Glu Ser Lys Val Gly Ser Leu Ala Val Leu Pro Ile Leu Leu Leu 115 120 125Ala Glu Ile Phe His Pro Asp Asp Leu Pro Asp Ile Tyr Ala Ala Ile 130 135 140Gly Ala Tyr Trp Phe Ser Arg Arg Ser Ser Thr Thr Ser Glu Ser Gly145 150 155 160Ser Ser Ser Ser Ser Ser Thr Asn Ser Ser Val Ser Ser 165 17022173PRTNannochloropsis oceanicamisc_featurePAS3 domain of

ZnCys-2845 orthologmisc_featureStrain IMET1 22Asn Leu Trp Thr Lys Thr Ser Ser Ile Leu Ala Ser Gly Val Asp Met1 5 10 15Thr Phe Gly Ile Cys Asp Gln Leu Gln Glu Val Val Gly Pro Ala Pro 20 25 30Thr Gly Ser Gly Pro Ile Ala Cys Ser Pro Ala Thr Arg Ser Lys Ser 35 40 45Gln Ala Ala Gln Gln Ala Gln Leu Leu Ser His Pro Gly Ser Lys Glu 50 55 60Gly Met Gly Pro Trp Asn Leu Pro Asp Asp Leu Arg Lys Met Asp Asp65 70 75 80Gly Val Ser Met Leu Cys Gly Phe Met Phe Ile Gln Asp Glu Leu Phe 85 90 95Val Phe Thr Asp Glu Arg Phe Ala Ala Thr Phe Met Thr Arg Glu Glu 100 105 110Val Glu Gly Lys Val Glu Ser Phe Ala Val Leu Pro Ile Leu Leu Leu 115 120 125Ala Glu Ile Phe His Pro Asp Asp Leu Pro Asp Val Tyr Ala Ala Ile 130 135 140Gly Ala His Trp Phe Arg Arg Arg Pro Ser Ser Gly Val Gly Val Gly145 150 155 160Gly Ser Asn Gly Ser Ile Ser Ser Met Asn Ser Ser Ser 165 17023173PRTNannochloropsis salinamisc_featureStrain CCMPmisc_featurePAS3 domain of ZnCys-2845 ortholog 23Asn Leu Trp Thr Lys Val Ser Ser Gln Leu Ala Ser Gly Thr Asp Met1 5 10 15Thr Phe Gly Ile Cys Asp Gln Leu Gln Glu Val Val Gly Pro Ala Pro 20 25 30Thr Gly Ser Gly Pro Met Ala Gly Ser Pro Ala Thr Arg Ser Lys Ser 35 40 45His Ala Ala Gln Gln Ala Gln Leu Leu Thr His Pro Gly Ser Lys Glu 50 55 60Ala Met Gly Pro His Cys Leu Pro Leu Asp Leu Arg Arg Met Glu Asp65 70 75 80Gly Val Ser Met Leu Cys Gly Phe Met Phe Leu Gln Asp Glu Leu Phe 85 90 95Val Tyr Thr Asp Glu Arg Phe Ala Ala Thr Phe Met Thr Arg Glu Glu 100 105 110Val Glu Ser Lys Val Gly Ser Leu Ala Val Leu Pro Ile Leu Leu Leu 115 120 125Ala Glu Ile Phe His Pro Asp Asp Leu Pro Asp Ile Tyr Ala Ala Ile 130 135 140Gly Ala Tyr Trp Phe Ser Arg Arg Ser Ser Thr Met Ser Asp Ser Gly145 150 155 160Ser Ser Ser Ser Ser Thr Ser Ser Ser Val Ser Ser Ala 165 17024173PRTNannochloropsis oculatamisc_featureStrain CCMP525misc_featurePAS3 domain of ZnCys-2845 ortholog 24Asn Leu Trp Thr Lys Thr Ser Ser Val Leu Ala Ser Gly Val Asp Met1 5 10 15Thr Phe Gly Ile Cys Glu Gln Leu Gln Glu Val Val Gly Pro Ala Pro 20 25 30Thr Gly Thr Gly Pro Ile Ala Cys Ser Pro Ala Thr Arg Ser Lys Ser 35 40 45Gln Ala Val Gln Gln Ala Gln Leu Leu Thr His Pro Gly Ser Lys Glu 50 55 60Gly Met Gly Pro Trp Asn Leu Pro Asp Asp Leu Arg Lys Met Asp Asp65 70 75 80Gly Val Ser Met Leu Cys Gly Phe Met Phe Ile Gln Asp Glu Leu Phe 85 90 95Val Tyr Thr Asp Glu Arg Phe Ala Ala Thr Phe Met Thr Arg Glu Glu 100 105 110Val Glu Gly Lys Val Glu Ser Phe Ala Val Leu Pro Ile Leu Leu Leu 115 120 125Ala Glu Ile Phe His Pro Asp Asp Leu Pro Asp Val Tyr Ala Ala Ile 130 135 140Gly Ala His Trp Phe Arg Arg Arg Pro Ser Ser Gly Gly Gly Val Gly145 150 155 160Gly Ser Asn Gly Ser Ile Ser Ser Met Thr Ser Asn Gly 165 17025173PRTNannochloropsis granulatamisc_featureStrain CCMP529misc_featurePAS3 domain of ZnCys-2845 ortholog 25Asn Leu Trp Thr Lys Thr Ser Ser Val Leu Ala Ser Gly Val Asp Met1 5 10 15Thr Phe Gly Ile Cys Asp Gln Leu Gln Glu Val Val Gly Pro Ala Pro 20 25 30Thr Gly Ser Gly Pro Ile Ala Cys Ser Pro Ala Thr Arg Ser Lys Ser 35 40 45Gln Ala Ala Gln Gln Ala Gln Leu Leu Ser His Pro Gly Ser Lys Glu 50 55 60Gly Met Gly Pro Trp Asn Leu Pro Asp Asp Leu Arg Lys Met Asp Asp65 70 75 80Gly Val Ser Met Leu Cys Gly Phe Met Phe Ile Gln Asp Glu Leu Phe 85 90 95Val Tyr Thr Asp Glu Arg Phe Ala Ala Thr Phe Met Thr Arg Glu Glu 100 105 110Val Glu Gly Lys Val Glu Ser Phe Ala Val Leu Pro Ile Leu Leu Leu 115 120 125Ala Glu Ile Phe His Pro Asp Asp Leu Pro Asp Val Tyr Ala Ala Ile 130 135 140Gly Ala His Trp Phe Arg Arg Arg Pro Ser Ser Gly Val Gly Val Gly145 150 155 160Gly Ser Asn Gly Ser Ile Ser Ser Met Asn Ser Ser Ser 165 1702611263DNAArtificial SequenceSyntheticmisc_featurevector pSGE-6206 26gcggccgccg tatggtcgac ggttgctcgg atgggggggg cggggagcga tggagggagg 60aagatcaggt aaggtctcga cagactagag aagcacgagt gcaggtataa gaaacagcaa 120aaaaaagtaa tgggcccagg cctggagagg gtatttgtct tgtttttctt tggccaggaa 180cttgttctcc tttcttcgtt tctaggaccc cgatccccgc tcgcatttct ctcttcctca 240gccgaagcgc agcggtaaag catccatttt atcccaccga aagggcgctc ccagccttcg 300tcgagcggaa ccggggttac agtgcctcaa ccctcccaga cgtagccaga gggaagcaac 360tccctgatgc caaccgctgt gggctgccca tcggaatctt tgacaattgc cttgatcccc 420gggtgcaagt caagcagcac ctgccgacat cgcccgcacg gagacagaat gccgcggttt 480tcgttcccga tggccactat gcacgtcaga tttccggcag cagccgcagc ggccgttccg 540aggaccacga gctccgcgca tggccctccg gtgaaatgat atacattcac gccggtaaag 600atccgaccgt cggacgagag ggctgcactg gccaccgagt agtcctcgct aataggtatg 660ctgttgatgg tcgcagttgc acgttcgatc agcgtggatt cctcttggga taaaggcttg 720gccatcgagc tcggtacccg gggatccatg attgttgtat tatgtaccta tgtttgtgat 780gagacaataa atatgagaag agaacgttgc ggccactttt ttctccttcc ttcgcgtgct 840catgttggtg gtttgggagg cagaagatgc atggagcgcc acacattcgg taggacgaaa 900cagcctcccc cacaaaggga ccatgggtag ctaggatgac gcacaagcga gttcccgctc 960tcgaagggaa acccaggcat ttccttcctc ttttcaagcc acttgttcac gtgtcaacac 1020aattttggac taaaatgccc ctcggaactc ggcaggcctc cctctgctcc gttgtcctgg 1080tcgccgagaa cgcgagaccg tgccgcatgc catcgatctg ctcgtctgta ctactaatcg 1140tgtgcgtgtt cgtgcttgtt tcgcacgaaa ttgtcctcgt tcggccctca caacggtgga 1200aatcggtgct agaataaagt gaggtggctt atttcaatgg cggccgtcat catgcgggat 1260caactgaagt acggcgggtt ctcgagattt catcgtgctc gtccagagca ggtgttttgc 1320ctgcagctct tcatgtttag gggtcatgat ttcatctgat atgccgtaag aaaaccaata 1380ttcacttctc aattttccat ggaaaggtga aggcctaggt tgtgtgcgag gcaacgactg 1440gggagggatc gcaacattct tgctaacctc ccctctatct tggccgctgt gaatcggcat 1500atttaccggg ctgaattgag aaagtgtttt gagggaatta aaaggtggct gtcttgcaag 1560cttggcttca gtgcctgctt aattcgaacc gatccagctt gtgatgaggc cttcctaagc 1620ctggtagtca gaagcgacat ggcgctataa atttcgtctc agttggagag tagaaaagca 1680tgattcgaac acggttttca actgccaaag atatctccat tgtttccttc aatctgtaca 1740cctgcacggt gcaccagttg gtacggcata ttatggttta ataagcatac atcatatgaa 1800tacaattcag cttaaattta tcatacaaag atgtaagtgc agcgtgggtc tgtaacgatc 1860gggcgtaatt taagataatg cgagggaccg ggggaggttt tggaacggaa tgaggaatgg 1920gtcatggccc ataataataa tatgggtttg gtcgcctcgc acagcaaccg tacgtgcgaa 1980aaaggaacag atccatttaa taagttgaac gttattcttt cctatgcaat gcgtgtatcg 2040gaggcgagag caagtcatag gtggctgcgc acaataattg agtctcagct gagcgccgtc 2100cgcgggtggt gtgagtggtc atcctcctcc cggcctatcg ctcacatcgc ctctcaatgg 2160tggtggtggg gcctgatatg acctcaatgc cgacccatat taaaacccag taaagcattc 2220accaacgaac gaggggctct tttgtgtgtg ttttgagtat gattttacac ctctttgtgc 2280atctctctgg tcttccttgg ttcccgtagt ttgggcatca tcactcacgc ttccctcgac 2340cttcgttctt cctttacaac cccgacacag gtcagagttg gagtaatcaa aaaaggggtg 2400cacgaatgag atacattaga ttttgacaga tatcctttta ctggagaggg ttcaagggat 2460caaatgaaca gcgggcgttg gcaatctagg gagggatcgg aggttggcag cgagcgaaag 2520cgtgtccatc cttttggctg tcacacctca cgaaccaact gttagcaggc cagcacagat 2580gacatacgag aatctttatt atatcgtaga ccttatgtgg atgacctttg gtgctgtgtg 2640tctggcaatg aacctgaagg cttgataggg aggtggctcc cgtaaaccct ttgtcctttc 2700cacgctgagt ctcccccgca ctgtccttta tacaaattgt tacagtcatc tgcaggcggt 2760ttttctttgg caggcaaaga tgcccaagaa aaagcggaag gtcggcgact acaaggatga 2820cgatgacaag ttggagcctg gagagaagcc ctacaaatgc cctgagtgcg gaaagagctt 2880cagccaatct ggagccttga cccggcatca acgaacgcat acacgagaca agaagtactc 2940catcgggctg gacatcggga cgaactccgt gggatgggcc gtgatcacag acgaatacaa 3000ggtgccttcc aagaagttca aggtgctggg gaacacggac agacactcca tcaagaagaa 3060cctcatcggg gccttgctct tcgactccgg agaaaccgcc gaagcaacgc gattgaaaag 3120aaccgccaga agacgataca cacgacggaa gaaccgcatc tgctacctcc aggagatctt 3180cagcaacgag atggccaagg tggacgactc gttctttcat cgcctggagg agagcttcct 3240ggtggaggaa gacaagaaac atgagcgcca cccgatcttc gggaacatcg tggacgaagt 3300ggcctaccac gagaaatacc ccacgatcta ccacttgcgc aagaaactcg tggactccac 3360ggacaaagcg gacttgcggt tgatctactt ggccttggcc cacatgatca aatttcgggg 3420ccacttcctg atcgagggcg acttgaatcc cgacaattcc gacgtggaca agctcttcat 3480ccagctggtg cagacctaca accagctctt cgaggagaac cccatcaatg cctccggagt 3540ggacgccaaa gccatcttgt ccgcccgatt gtccaaatcc agacgcttgg agaacttgat 3600cgcacaactt cctggcgaga agaagaacgg cctcttcggc aacttgatcg cgctgtcgct 3660gggattgacg cctaacttca agtccaactt cgacttggcc gaggacgcca agttgcaact 3720gtccaaggac acctacgacg acgacctcga caacctgctg gcccaaattg gcgaccaata 3780cgcggacttg tttttggcgg ccaagaactt gagcgacgcc atcttgttga gcgacatctt 3840gcgcgtgaat acggagatca ccaaagcccc tttgtccgcc tctatgatca agcggtacga 3900cgagcaccac caagacttga ccctgttgaa agccctcgtg cggcaacaat tgcccgagaa 3960gtacaaggag atcttcttcg accagtccaa gaacgggtac gccggctaca tcgacggagg 4020agcctcccaa gaagagttct acaagttcat caagcccatc ctggagaaga tggacggcac 4080cgaggagttg ctcgtgaagc tgaaccgcga agacttgttg cgaaaacagc ggacgttcga 4140caatggcagc atcccccacc aaatccattt gggagagttg cacgccatct tgcgacggca 4200agaggacttc tacccgttcc tgaaggacaa ccgcgagaaa atcgagaaga tcctgacgtt 4260cagaatcccc tactacgtgg gacccttggc ccgaggcaat tcccggtttg catggatgac 4320gcgcaaaagc gaagagacga tcaccccctg gaacttcgaa gaagtggtcg acaaaggagc 4380atccgcacag agcttcatcg agcgaatgac gaacttcgac aagaacctgc ccaacgagaa 4440ggtgttgccc aagcattcgc tgctgtacga gtacttcacg gtgtacaacg agctgaccaa 4500ggtgaagtac gtgaccgagg gcatgcgcaa acccgcgttc ctgtcgggag agcaaaagaa 4560ggccattgtg gacctgctgt tcaagaccaa ccggaaggtg accgtgaaac agctgaaaga 4620ggactacttc aagaagatcg agtgcttcga ctccgtggag atctccggcg tggaggaccg 4680attcaatgcc tccttgggaa cctaccatga cctcctgaag atcatcaagg acaaggactt 4740cctggacaac gaggagaacg aggacatcct ggaggacatc gtgctgaccc tgaccctgtt 4800cgaggaccga gagatgatcg aggaacggtt gaaaacgtac gcccacttgt tcgacgacaa 4860ggtgatgaag cagctgaaac gccgccgcta caccggatgg ggacgattga gccgcaaact 4920gattaatgga attcgcgaca agcaatccgg aaagaccatc ctggacttcc tgaagtccga 4980cgggttcgcc aaccgcaact tcatgcagct catccacgac gactccttga ccttcaagga 5040ggacatccag aaggcccaag tgtccggaca aggagactcc ttgcacgagc acatcgccaa 5100tttggccgga tcccccgcaa tcaaaaaagg catcttgcaa accgtgaaag tggtcgacga 5160actggtgaag gtgatgggac ggcacaagcc cgagaacatc gtgatcgaaa tggcccgcga 5220gaaccaaacc acccaaaaag gacagaagaa ctcccgagag cgcatgaagc ggatcgaaga 5280gggcatcaag gagttgggct cccagatcct gaaggagcat cccgtggaga atacccaatt 5340gcaaaacgag aagctctacc tctactacct ccagaacggg cgggacatgt acgtcgacca 5400agagctggac atcaaccgcc tctccgacta cgatgtggat catattgtgc cccagagctt 5460cctcaaggac gacagcatcg acaacaaggt cctgacgcgc agcgacaaga accggggcaa 5520gtctgacaat gtgccttccg aagaagtcgt gaagaagatg aagaactact ggcggcagct 5580gctcaacgcc aagctcatca cccaacggaa gttcgacaac ctgaccaagg ccgagagagg 5640aggattgtcc gagttggaca aagccggctt cattaaacgc caactcgtgg agacccgcca 5700gatcacgaag cacgtggccc aaatcttgga ctcccggatg aacacgaaat acgacgagaa 5760tgacaagctg atccgcgagg tgaaggtgat cacgctgaag tccaagctgg tgagcgactt 5820ccggaaggac ttccagttct acaaggtgcg ggagatcaac aactaccatc acgcccatga 5880cgcctacctg aacgccgtgg tcggaaccgc cctgatcaag aaatacccca agctggagtc 5940cgaattcgtg tacggagatt acaaggtcta cgacgtgcgg aagatgatcg cgaagtccga 6000gcaggagatc ggcaaagcca ccgccaagta cttcttttac tccaacatca tgaacttctt 6060caagaccgag atcacgctcg ccaacggcga gatccgcaag cgccccctga tcgagaccaa 6120cggcgagacg ggagagattg tgtgggacaa aggaagagat tttgccacag tgcgcaaggt 6180gctgtccatg cctcaggtga acatcgtgaa gaagaccgag gtgcaaacag gagggttttc 6240caaagagtcc attttgccta agaggaattc cgacaagctc atcgcccgca agaaggactg 6300ggaccccaag aagtacgggg gcttcgactc ccccacggtg gcctactccg tgttggtggt 6360ggccaaagtg gagaaaggga agagcaagaa gctgaaatcc gtgaaggagt tgctcggaat 6420cacgatcatg gaacgatcgt cgttcgagaa aaaccccatc gacttcctcg aagccaaagg 6480gtacaaagag gtgaagaagg acctgatcat caagctgccc aagtactccc tgttcgagct 6540ggagaacggc cgcaagcgga tgctggcctc cgccggggaa ctgcagaaag ggaacgaatt 6600ggccttgccc tccaaatacg tgaacttcct ctacttggcc tcccattacg aaaagctcaa 6660aggatcccct gaggacaatg agcagaagca actcttcgtg gaacaacaca agcactacct 6720ggacgagatc atcgagcaga tcagcgagtt ctccaagcgc gtgatcctcg ccgacgccaa 6780cctggacaag gtgctctccg cctacaacaa gcaccgcgac aagcctatcc gcgagcaagc 6840cgagaatatc attcacctgt ttaccctgac gaatttggga gcccctgccg cctttaaata 6900ctttgacacc accatcgacc gcaaaagata cacctccacc aaggaagtct tggacgccac 6960cctcatccac cagtccatca cgggcctcta cgagacgcgc atcgacctct cccaattggg 7020cggcgactaa agtgatgcgg cctttaggaa acaccacaaa agtaattgac aatctcagga 7080acgatctgcg tgtttacagc ttcccaaata acaattatac cacgtaccaa aaggggttta 7140atgtatctca caaattcttc taataggtac agcttctcaa attgggtgta tgatgtgaca 7200cttcgtctca cacacgtcac gataattcag cgtatggctt cccttcatca cattcacgca 7260aacttctaca caaccctggg catatttctt gtgttggcaa cactcccgaa atcgattctg 7320cacacaatgg ttcattcaat gattcaagta cgttttagac ggactaggca gtttaattaa 7380aaacatctat cctccagatc accagggcca gtgaggccgg cataaaggac ggcaaggaaa 7440gaaaagaaag aaagaaaagg acacttatag catagtttga agttataagt agtcgcaatc 7500tgtgtgcagc cgacagatgc tttttttttc cgtttggcag gaggtgtagg gatgtcgaag 7560accagtccag ctagtatcta tcctacaagt caatcatgct gcgacaaaaa tttctcgcac 7620gaggcctctc gataaacaaa actttaaaag cacacttcat tgtcatgcag agtaataact 7680cttccgcgtc gatcaattta tcaatctcta tcatttccgc ccctttcctt gcatagagca 7740agaaaagcga cccggatgag gataacatgt cctgcgccag tagtgtggca ttgcctgtct 7800ctcatttaca cgtactgaaa gcataatgca cgcgcatacc aatatttttc gtgtacggag 7860atgaagagac gcgacacgta agatcacgag aaggcgagca cggttgccaa tggcagacgc 7920gctagtctcc attatcgcgt tgttcggtag cttgctgcat gtcttcagtg gcactatatc 7980cactctgcct cgtcttctac acgagggcca catcggtgca agttcgaaaa atcatatctc 8040aatcttcaga tcctttccag aaacggtgct caggcgggaa agtgaaggtt ttctactcta 8100gtggctaccc caattctctc cgactgtcgc agacggtcct tcgttgcgca cgcaccgcgc 8160actacctctg aaattcgaca accgaagttc aattttacat ctaacttctt tcccattctc 8220tcaccaaaag cctagcttac atgttggaga gcgacgagag cggcctgccc gccatggaga 8280tcgagtgccg catcaccggc accctgaacg gcgtggagtt cgagctggtg ggcggcggag 8340agggcacccc cgagcagggc cgcatgacca acaagatgaa gagcaccaaa ggcgccctga 8400ccttcagccc ctacctgctg agccacgtga tgggctacgg cttctaccac ttcggcacct 8460accccagcgg ctacgagaac cccttcctgc acgccatcaa caacggcggc tacaccaaca 8520cccgcatcga gaagtacgag gacggcggcg tgctgcacgt gagcttcagc taccgctacg 8580aggccggccg cgtgatcggc gacttcaagg tgatgggcac cggcttcccc gaggacagcg 8640tgatcttcac cgacaagatc atccgcagca acgccaccgt ggagcacctg caccccatgg 8700gcgataacga tctggatggc agcttcaccc gcaccttcag cctgcgcgac ggcggctact 8760acagctccgt ggtggacagc cacatgcact tcaagagcgc catccacccc agcatcctgc 8820agaacggggg ccccatgttc gccttccgcc gcgtggagga ggatcacagc aacaccgagc 8880tgggcatcgt ggagtaccag cacgccttca agaccccgga tgcagatgcc ggtgaagaat 8940aagggtggga aggagtcggg gagggtcctg gcagagcggc gtcctcatga tgtgttggag 9000acctggagag tcgagagctt cctcgtcacc tgattgtcat gtgtgtatag gttaaggggg 9060cccactcaaa gccataaaga cgaacacaaa cactaatctc aacaaagtct actagcatgc 9120cgtctgtcca tctttatttc ctggcgcgcc tatgcttgta aaccgttttg tgaaaaaatt 9180tttaaaataa aaaaggggac ctctagggtc cccaattaat tagtaatata atctattaaa 9240ggtcattcaa aaggtcatcc agacgaaagg gcctcgtgat acgcctattt ttataggtta 9300atgtcatgat aataatggtt tcttagacgt caggtggcac ttttcgggga aatgtgcgcg 9360gaacccctat ttgtttattt ttctaaatac attcaaatat gtatccgctc atgagacaat 9420aaccctgata aatgcttcaa taatattgaa aaaggaagag tatgagtatt caacatttcc 9480gtgtcgccct tattcccttt tttgcggcat tttgccttcc tgtttttgct cacccagaaa 9540cgctggtgaa agtaaaagat gctgaagatc agttgggtgc acgagtgggt tacatcgaac 9600tggatctcaa cagcggtaag atccttgaga gttttcgccc cgaagaacgt tttccaatga 9660tgagcacttt taaagttctg ctatgtggcg cggtattatc ccgtattgac gccgggcaag 9720agcaactcgg tcgccgcata cactattctc agaatgactt ggttgagtac tcaccagtca 9780cagaaaagca tcttacggat ggcatgacag taagagaatt atgcagtgct gccataacca 9840tgagtgataa cactgcggcc aacttacttc tgacaacgat cggaggaccg aaggagctaa 9900ccgctttttt gcacaacatg ggggatcatg taactcgcct tgatcgttgg gaaccggagc 9960tgaatgaagc cataccaaac gacgagcgtg acaccacgat gcctgtagca atggcaacaa 10020cgttgcgcaa actattaact ggcgaactac ttactctagc ttcccggcaa caattaatag 10080actggatgga ggcggataaa gttgcaggac cacttctgcg ctcggccctt ccggctggct 10140ggtttattgc tgataaatct ggagccggtg agcgtgggtc tcgcggtatc attgcagcac 10200tggggccaga tggtaagccc tcccgtatcg tagttatcta cacgacgggg agtcaggcaa 10260ctatggatga acgaaataga cagatcgctg agataggtgc ctcactgatt aagcattggt 10320aactgtcaga ccaagtttac tcatatatac tttagattga tttaaaactt catttttaat 10380ttaaaaggat ctaggtgaag atcctttttg ataatctcat gaccaaaatc ccttaacgtg 10440agttttcgtt ccactgagcg tcagaccccg tagaaaagat caaaggatct

tcttgagatc 10500ctttttttct gcgcgtaatc tgctgcttgc aaacaaaaaa accaccgcta ccagcggtgg 10560tttgtttgcc ggatcaagag ctaccaactc tttttccgaa ggtaactggc ttcagcagag 10620cgcagatacc aaatactgtc cttctagtgt agccgtagtt aggccaccac ttcaagaact 10680ctgtagcacc gcctacatac ctcgctctgc taatcctgtt accagtggct gctgccagtg 10740gcgataagtc gtgtcttacc gggttggact caagacgata gttaccggat aaggcgcagc 10800ggtcgggctg aacggggggt tcgtgcacac agcccagctt ggagcgaacg acctacaccg 10860aactgagata cctacagcgt gagctatgag aaagcgccac gcttcccgaa gggagaaagg 10920cggacaggta tccggtaagc ggcagggtcg gaacaggaga gcgcacgagg gagcttccag 10980ggggaaacgc ctggtatctt tatagtcctg tcgggtttcg ccacctctga cttgagcgtc 11040gatttttgtg atgctcgtca ggggggcgga gcctatggaa aaacgccagc aacgcggcct 11100ttttacggtt cctggccttt tgctggcctt ttgctcacat gttctttcct gcgttatccc 11160ctgattctgt ggataaccgt attaccgcct ttgagtgagc tgataccgct cgccgcagcc 11220gaacgaccga gcgcagcgag tcagtgagcg aggaagcgga aga 11263274101DNAArtificial SequenceSyntheticmisc_featureCas9 from S. pyogenes codon optimized for Nannochloropsis 27gacaagaagt actccatcgg gctggacatc gggacgaact ccgtgggatg ggccgtgatc 60acagacgaat acaaggtgcc ttccaagaag ttcaaggtgc tggggaacac ggacagacac 120tccatcaaga agaacctcat cggggccttg ctcttcgact ccggagaaac cgccgaagca 180acgcgattga aaagaaccgc cagaagacga tacacacgac ggaagaaccg catctgctac 240ctccaggaga tcttcagcaa cgagatggcc aaggtggacg actcgttctt tcatcgcctg 300gaggagagct tcctggtgga ggaagacaag aaacatgagc gccacccgat cttcgggaac 360atcgtggacg aagtggccta ccacgagaaa taccccacga tctaccactt gcgcaagaaa 420ctcgtggact ccacggacaa agcggacttg cggttgatct acttggcctt ggcccacatg 480atcaaatttc ggggccactt cctgatcgag ggcgacttga atcccgacaa ttccgacgtg 540gacaagctct tcatccagct ggtgcagacc tacaaccagc tcttcgagga gaaccccatc 600aatgcctccg gagtggacgc caaagccatc ttgtccgccc gattgtccaa atccagacgc 660ttggagaact tgatcgcaca acttcctggc gagaagaaga acggcctctt cggcaacttg 720atcgcgctgt cgctgggatt gacgcctaac ttcaagtcca acttcgactt ggccgaggac 780gccaagttgc aactgtccaa ggacacctac gacgacgacc tcgacaacct gctggcccaa 840attggcgacc aatacgcgga cttgtttttg gcggccaaga acttgagcga cgccatcttg 900ttgagcgaca tcttgcgcgt gaatacggag atcaccaaag cccctttgtc cgcctctatg 960atcaagcggt acgacgagca ccaccaagac ttgaccctgt tgaaagccct cgtgcggcaa 1020caattgcccg agaagtacaa ggagatcttc ttcgaccagt ccaagaacgg gtacgccggc 1080tacatcgacg gaggagcctc ccaagaagag ttctacaagt tcatcaagcc catcctggag 1140aagatggacg gcaccgagga gttgctcgtg aagctgaacc gcgaagactt gttgcgaaaa 1200cagcggacgt tcgacaatgg cagcatcccc caccaaatcc atttgggaga gttgcacgcc 1260atcttgcgac ggcaagagga cttctacccg ttcctgaagg acaaccgcga gaaaatcgag 1320aagatcctga cgttcagaat cccctactac gtgggaccct tggcccgagg caattcccgg 1380tttgcatgga tgacgcgcaa aagcgaagag acgatcaccc cctggaactt cgaagaagtg 1440gtcgacaaag gagcatccgc acagagcttc atcgagcgaa tgacgaactt cgacaagaac 1500ctgcccaacg agaaggtgtt gcccaagcat tcgctgctgt acgagtactt cacggtgtac 1560aacgagctga ccaaggtgaa gtacgtgacc gagggcatgc gcaaacccgc gttcctgtcg 1620ggagagcaaa agaaggccat tgtggacctg ctgttcaaga ccaaccggaa ggtgaccgtg 1680aaacagctga aagaggacta cttcaagaag atcgagtgct tcgactccgt ggagatctcc 1740ggcgtggagg accgattcaa tgcctccttg ggaacctacc atgacctcct gaagatcatc 1800aaggacaagg acttcctgga caacgaggag aacgaggaca tcctggagga catcgtgctg 1860accctgaccc tgttcgagga ccgagagatg atcgaggaac ggttgaaaac gtacgcccac 1920ttgttcgacg acaaggtgat gaagcagctg aaacgccgcc gctacaccgg atggggacga 1980ttgagccgca aactgattaa tggaattcgc gacaagcaat ccggaaagac catcctggac 2040ttcctgaagt ccgacgggtt cgccaaccgc aacttcatgc agctcatcca cgacgactcc 2100ttgaccttca aggaggacat ccagaaggcc caagtgtccg gacaaggaga ctccttgcac 2160gagcacatcg ccaatttggc cggatccccc gcaatcaaaa aaggcatctt gcaaaccgtg 2220aaagtggtcg acgaactggt gaaggtgatg ggacggcaca agcccgagaa catcgtgatc 2280gaaatggccc gcgagaacca aaccacccaa aaaggacaga agaactcccg agagcgcatg 2340aagcggatcg aagagggcat caaggagttg ggctcccaga tcctgaagga gcatcccgtg 2400gagaataccc aattgcaaaa cgagaagctc tacctctact acctccagaa cgggcgggac 2460atgtacgtcg accaagagct ggacatcaac cgcctctccg actacgatgt ggatcatatt 2520gtgccccaga gcttcctcaa ggacgacagc atcgacaaca aggtcctgac gcgcagcgac 2580aagaaccggg gcaagtctga caatgtgcct tccgaagaag tcgtgaagaa gatgaagaac 2640tactggcggc agctgctcaa cgccaagctc atcacccaac ggaagttcga caacctgacc 2700aaggccgaga gaggaggatt gtccgagttg gacaaagccg gcttcattaa acgccaactc 2760gtggagaccc gccagatcac gaagcacgtg gcccaaatct tggactcccg gatgaacacg 2820aaatacgacg agaatgacaa gctgatccgc gaggtgaagg tgatcacgct gaagtccaag 2880ctggtgagcg acttccggaa ggacttccag ttctacaagg tgcgggagat caacaactac 2940catcacgccc atgacgccta cctgaacgcc gtggtcggaa ccgccctgat caagaaatac 3000cccaagctgg agtccgaatt cgtgtacgga gattacaagg tctacgacgt gcggaagatg 3060atcgcgaagt ccgagcagga gatcggcaaa gccaccgcca agtacttctt ttactccaac 3120atcatgaact tcttcaagac cgagatcacg ctcgccaacg gcgagatccg caagcgcccc 3180ctgatcgaga ccaacggcga gacgggagag attgtgtggg acaaaggaag agattttgcc 3240acagtgcgca aggtgctgtc catgcctcag gtgaacatcg tgaagaagac cgaggtgcaa 3300acaggagggt tttccaaaga gtccattttg cctaagagga attccgacaa gctcatcgcc 3360cgcaagaagg actgggaccc caagaagtac gggggcttcg actcccccac ggtggcctac 3420tccgtgttgg tggtggccaa agtggagaaa gggaagagca agaagctgaa atccgtgaag 3480gagttgctcg gaatcacgat catggaacga tcgtcgttcg agaaaaaccc catcgacttc 3540ctcgaagcca aagggtacaa agaggtgaag aaggacctga tcatcaagct gcccaagtac 3600tccctgttcg agctggagaa cggccgcaag cggatgctgg cctccgccgg ggaactgcag 3660aaagggaacg aattggcctt gccctccaaa tacgtgaact tcctctactt ggcctcccat 3720tacgaaaagc tcaaaggatc ccctgaggac aatgagcaga agcaactctt cgtggaacaa 3780cacaagcact acctggacga gatcatcgag cagatcagcg agttctccaa gcgcgtgatc 3840ctcgccgacg ccaacctgga caaggtgctc tccgcctaca acaagcaccg cgacaagcct 3900atccgcgagc aagccgagaa tatcattcac ctgtttaccc tgacgaattt gggagcccct 3960gccgccttta aatactttga caccaccatc gaccgcaaaa gatacacctc caccaaggaa 4020gtcttggacg ccaccctcat ccaccagtcc atcacgggcc tctacgagac gcgcatcgac 4080ctctcccaat tgggcggcga c 41012824DNAArtificial SequenceSyntheticmisc_featureEncodes FLAG tag 28gactacaagg atgacgatga caag 242924DNAArtificial SequenceSyntheticmisc_featureEncodes NLS 29cccaagaaaa agcggaaggt cggc 2430147DNAArtificial SequenceSyntheticmisc_featureEncodes peptide linker 30atgcccaaga aaaagcggaa ggtcggcgac tacaaggatg acgatgacaa gttggagcct 60ggagagaagc cctacaaatg ccctgagtgc ggaaagagct tcagccaatc tggagccttg 120acccggcatc aacgaacgca tacacga 147311000DNANannochloropsis gaditanamisc_featureRPL24 promoter 31aataagcata catcatatga atacaattca gcttaaattt atcatacaaa gatgtaagtg 60cagcgtgggt ctgtaacgat cgggcgtaat ttaagataat gcgagggacc gggggaggtt 120ttggaacgga atgaggaatg ggtcatggcc cataataata atatgggttt ggtcgcctcg 180cacagcaacc gtacgtgcga aaaaggaaca gatccattta ataagttgaa cgttattctt 240tcctatgcaa tgcgtgtatc ggaggcgaga gcaagtcata ggtggctgcg cacaataatt 300gagtctcagc tgagcgccgt ccgcgggtgg tgtgagtggt catcctcctc ccggcctatc 360gctcacatcg cctctcaatg gtggtggtgg ggcctgatat gacctcaatg ccgacccata 420ttaaaaccca gtaaagcatt caccaacgaa cgaggggctc ttttgtgtgt gttttgagta 480tgattttaca cctctttgtg catctctctg gtcttccttg gttcccgtag tttgggcatc 540atcactcacg cttccctcga ccttcgttct tcctttacaa ccccgacaca ggtcagagtt 600ggagtaatca aaaaaggggt gcacgaatga gatacattag attttgacag atatcctttt 660actggagagg gttcaaggga tcaaatgaac agcgggcgtt ggcaatctag ggagggatcg 720gaggttggca gcgagcgaaa gcgtgtccat ccttttggct gtcacacctc acgaaccaac 780tgttagcagg ccagcacaga tgacatacga gaatctttat tatatcgtag accttatgtg 840gatgaccttt ggtgctgtgt gtctggcaat gaacctgaag gcttgatagg gaggtggctc 900ccgtaaaccc tttgtccttt ccacgctgag tctcccccgc actgtccttt atacaaattg 960ttacagtcat ctgcaggcgg tttttctttg gcaggcaaag 100032317DNANannochloropsis gaditanamisc_featurebidirectional terminator 2 32agtgatgcgg cctttaggaa acaccacaaa agtaattgac aatctcagga acgatctgcg 60tgtttacagc ttcccaaata acaattatac cacgtaccaa aaggggttta atgtatctca 120caaattcttc taataggtac agcttctcaa attgggtgta tgatgtgaca cttcgtctca 180cacacgtcac gataattcag cgtatggctt cccttcatca cattcacgca aacttctaca 240caaccctggg catatttctt gtgttggcaa cactcccgaa atcgattctg cacacaatgg 300ttcattcaat gattcaa 31733399DNAArtificial SequenceSyntheticmisc_featureblast gene from Aspergillus terreus codon optimized for N. gaditana 33atggccaagc ctttatccca agaggaatcc acgctgatcg aacgtgcaac tgcgaccatc 60aacagcatac ctattagcga ggactactcg gtggccagtg cagccctctc gtccgacggt 120cggatcttta ccggcgtgaa tgtatatcat ttcaccggag ggccatgcgc ggagctcgtg 180gtcctcggaa cggccgctgc ggctgctgcc ggaaatctga cgtgcatagt ggccatcggg 240aacgaaaacc gcggcattct gtctccgtgc gggcgatgtc ggcaggtgct gcttgacttg 300cacccgggga tcaaggcaat tgtcaaagat tccgatgggc agcccacagc ggttggcatc 360agggagttgc ttccctctgg ctacgtctgg gagggttga 39934999DNANannochloropsis gaditanamisc_featureTCTP promoter 34cgtgcaggtg tacagattga aggaaacaat ggagatatct ttggcagttg aaaaccgtgt 60tcgaatcatg cttttctact ctccaactga gacgaaattt atagcgccat gtcgcttctg 120actaccaggc ttaggaaggc ctcatcacaa gctggatcgg ttcgaattaa gcaggcactg 180aagccaagct tgcaagacag ccacctttta attccctcaa aacactttct caattcagcc 240cggtaaatat gccgattcac agcggccaag atagagggga ggttagcaag aatgttgcga 300tccctcccca gtcgttgcct cgcacacaac ctaggccttc acctttccat ggaaaattga 360gaagtgaata ttggttttct tacggcatat cagatgaaat catgacccct aaacatgaag 420agctgcaggc aaaacacctg ctctggacga gcacgatgaa atctcgagaa cccgccgtac 480ttcagttgat cccgcatgat gacggccgcc attgaaataa gccacctcac tttattctag 540caccgatttc caccgttgtg agggccgaac gaggacaatt tcgtgcgaaa caagcacgaa 600cacgcacacg attagtagta cagacgagca gatcgatggc atgcggcacg gtctcgcgtt 660ctcggcgacc aggacaacgg agcagaggga ggcctgccga gttccgaggg gcattttagt 720ccaaaattgt gttgacacgt gaacaagtgg cttgaaaaga ggaaggaaat gcctgggttt 780cccttcgaga gcgggaactc gcttgtgcgt catcctagct acccatggtc cctttgtggg 840ggaggctgtt tcgtcctacc gaatgtgtgg cgctccatgc atcttctgcc tcccaaacca 900ccaacatgag cacgcgaagg aaggagaaaa aagtggccgc aacgttctct tctcatattt 960attgtctcat cacaaacata ggtacataat acaacaatc 99935318DNANannochloropsis gaditanamisc_featureEIF3 terminator 35ggcactgtaa ccccggttcc gctcgacgaa ggctgggagc gccctttcgg tgggataaaa 60tggatgcttt accgctgcgc ttcggctgag gaagagagaa atgcgagcgg ggatcggggt 120cctagaaacg aagaaaggag aacaagttcc tggccaaaga aaaacaagac aaataccctc 180tccaggcctg ggcccattac ttttttttgc tgtttcttat acctgcactc gtgcttctct 240agtctgtcga gaccttacct gatcttcctc cctccatcgc tccccgcccc ccccatccga 300gcaaccgtcg accatacg 31836702DNAArtificial SequenceSyntheticmisc_featureTurboGFP gene codon optimized for Nannochloropsis gaditana 36atgttggaga gcgacgagag cggcctgccc gccatggaga tcgagtgccg catcaccggc 60accctgaacg gcgtggagtt cgagctggtg ggcggcggag agggcacccc cgagcagggc 120cgcatgacca acaagatgaa gagcaccaaa ggcgccctga ccttcagccc ctacctgctg 180agccacgtga tgggctacgg cttctaccac ttcggcacct accccagcgg ctacgagaac 240cccttcctgc acgccatcaa caacggcggc tacaccaaca cccgcatcga gaagtacgag 300gacggcggcg tgctgcacgt gagcttcagc taccgctacg aggccggccg cgtgatcggc 360gacttcaagg tgatgggcac cggcttcccc gaggacagcg tgatcttcac cgacaagatc 420atccgcagca acgccaccgt ggagcacctg caccccatgg gcgataacga tctggatggc 480agcttcaccc gcaccttcag cctgcgcgac ggcggctact acagctccgt ggtggacagc 540cacatgcact tcaagagcgc catccacccc agcatcctgc agaacggggg ccccatgttc 600gccttccgcc gcgtggagga ggatcacagc aacaccgagc tgggcatcgt ggagtaccag 660cacgccttca agaccccgga tgcagatgcc ggtgaagaat aa 70237822DNANannochloropsis gaditanamisc_feature4A-III promoter 37ggcataaagg acggcaagga aagaaaagaa agaaagaaaa ggacacttat agcatagttt 60gaagttataa gtagtcgcaa tctgtgtgca gccgacagat gctttttttt tccgtttggc 120aggaggtgta gggatgtcga agaccagtcc agctagtatc tatcctacaa gtcaatcatg 180ctgcgacaaa aatttctcgc acgaggcctc tcgataaaca aaactttaaa agcacacttc 240attgtcatgc agagtaataa ctcttccgcg tcgatcaatt tatcaatctc tatcatttcc 300gcccctttcc ttgcatagag caagaaaagc gacccggatg aggataacat gtcctgcgcc 360agtagtgtgg cattgcctgt ctctcattta cacgtactga aagcataatg cacgcgcata 420ccaatatttt tcgtgtacgg agatgaagag acgcgacacg taagatcacg agaaggcgag 480cacggttgcc aatggcagac gcgctagtct ccattatcgc gttgttcggt agcttgctgc 540atgtcttcag tggcactata tccactctgc ctcgtcttct acacgagggc cacatcggtg 600caagttcgaa aaatcatatc tcaatcttca gatcctttcc agaaacggtg ctcaggcggg 660aaagtgaagg ttttctactc tagtggctac cccaattctc tccgactgtc gcagacggtc 720cttcgttgcg cacgcaccgc gcactacctc tgaaattcga caaccgaagt tcaattttac 780atctaacttc tttcccattc tctcaccaaa agcctagctt ac 82238200DNANannochloropsis gaditanamisc_featurebidirectional terminator 5 38gggtgggaag gagtcgggga gggtcctggc agagcggcgt cctcatgatg tgttggagac 60ctggagagtc gagagcttcc tcgtcacctg attgtcatgt gtgtataggt taagggggcc 120cactcaaagc cataaagacg aacacaaaca ctaatctcaa caaagtctac tagcatgccg 180tctgtccatc tttatttcct 2003918DNANannochloropsis gaditanamisc_feature18 bp sequence homologous to a sequence within the ZnCys-2845 gene and upstream of a cas9 PAM sequence 39agtaggccat tcccggag 1840120DNAArtificial SequenceSyntheticmisc_featureChimeric guide targeting ZnCys-2845 (knockout), first strand 40taatacgact cactatagga gtaggccatt cccggaggtt ttagagctag aaatagcaag 60ttaaaataag gctagtccgt tatcaacttg aaaaagtggc accgagtcgg tgcttttttt 12041120DNAArtificial SequenceSyntheticmisc_featureChimeric guide targeting ZnCys-2845 (knockout), opposite strand 41aaaaaaagca ccgactcggt gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa aacctccggg aatggcctac tcctatagtg agtcgtatta 12042120DNAArtificial SequenceSyntheticmisc_featureGeneric first strand for construct to produce chimeric guide by in vitro transcriptionmisc_feature(20)..(37)n is a, c, g, or t 42taatacgact cactataggn nnnnnnnnnn nnnnnnngtt ttagagctag aaatagcaag 60ttaaaataag gctagtccgt tatcaacttg aaaaagtggc accgagtcgg tgcttttttt 12043120DNAArtificial SequenceSyntheticmisc_featureGeneric opposite strand for construct to produce chimeric guide by in vitro transcriptionmisc_feature(84)..(101)n is a, c, g, or t 43aaaaaaagca ccgactcggt gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa aacnnnnnnn nnnnnnnnnn ncctatagtg agtcgtatta 120442400DNAArtificial SequenceSyntheticmisc_featureDonor Fragment with HygR cassette 44tccacagccc gaacccatga gagagaatca taatcaaaga tgagccagcc acgaagctac 60cggagaattc tgtaagaaaa atgtttaaag ttgaaaatgc taacagtgaa gtgatatcct 120tttttaatgg agtgttgagg tgaagtctag catcgtaggg gaaaacagga ttctgtgtct 180tccattctac tccttgataa agcgaagaaa tccgacaaaa ccaaagagat tgttcaagtt 240taagatttgt aagcgtacaa ctatgaactt cttctctttg taggcctgag tggtcgtatg 300catacgattc atgaagtgaa tcagtatcgc tggattttgc ttaggagtaa agcacaacta 360agaaaatatg ctgcctggca ggcatcctga gacatgaggc aagcgacgta gcaattgaat 420cctaatttaa gccagggcat ctgtatgact ctgttagtta attgatgaac caatgagctt 480taaaaaaaaa tcgttgcgcg taatgtagtt ttaattctcc gccttgaggt gcggggccat 540ttcggacaag gttctttgga cggagatggc agcatgtgtc ccttctccaa attggtccgt 600gtggtagttg agatgctgcc ttaaaattct gctcggtcat cctgccttcg cattcactcc 660tttcgagctg tcgggttcct cacgaggcct ccgggagcgg attgcgcaga aaggcgaccc 720ggagacacag agaccataca ccgactaaat tgcactggac gatacggcat ggcgacgacg 780atggccaagc attgctacgt gattattcgc cttgtcattc agggagaaat gatgacatgt 840gtgggacggt ctttacatgg gaagagggca tgaaaataac atggcctggc gggatggagc 900gtcacacctg tgtatgcgtt cgatccacaa gcaactcacc atttgcgtcg gggcctgtct 960ccaatctgct ttaggctact tttctctaat ttagcctatt ctatacagac agagacacac 1020agggatcatg gggaagaaac cggaactgac cgctacgtcc gtggagaaat tccttattga 1080gaagttcgac tctgtctccg acttgatgca actgagcgag ggagaggaga gtagggcgtt 1140ctcgtttgac gtagggggtc ggggatacgt gttgagggtt aatagttgtg cggacgggtt 1200ctacaaggat cggtatgtct accgtcattt cgcctccgcc gctctcccca taccagaggt 1260actggacatt ggggagttta gcgaatctct cacgtactgc atctcgcgcc gagcccaggg 1320agtgacgttg caagatctgc ccgaaactga attgcctgcc gttttgcaac ccgtggccga 1380ggccatggac gcgatcgctg ccgcagatct gtctcagacg tccggctttg gaccttttgg 1440gccccagggc atcgggcagt acacgacctg gcgagacttc atctgcgcca ttgccgatcc 1500tcacgtctat cattggcaga cagtcatgga tgacaccgtg tctgcatccg tggcccaagc 1560actggacgaa ctcatgttgt gggccgagga ttgccctgag gtcaggcacc tggtgcacgc 1620ggatttcggc agcaataacg tacttacaga caatggtcgg attactgctg tcatcgactg 1680gtccgaagcg atgtttggtg atagccaata cgaagtggcg aacatattct tctggcgtcc 1740ctggttggcg tgcatggagc agcagacacg ctactttgaa cggaggcacc cggagctggc 1800cggctcccca cgactccgcg cctatatgtt gcgtatcgga ctcgatcagc tttaccagtc 1860tctcgtcgac ggcaacttcg acgacgccgc gtgggcgcag ggccgctgcg acgcgatagt 1920ccgcagcggg gctgggacgg tgggtcggac ccaaatcgca cgccggtcgg ctgcggtgtg 1980gacagacggc tgtgttgagg tgcttgcgga ctcgggcaac cgtaggccga gcacccgacc 2040gcgtgcaaag gagtgattga atcattgaat gaaccattgt gtgcagaatc gatttcggga 2100gtgttgccaa cacaagaaat atgcccaggg ttgtgtagaa gtttgcgtga atgtgatgaa 2160gggaagccat acgctgaatt atcgtgacgt gtgtgagacg aagtgtcaca tcatacaccc 2220aatttgagaa gctgtaccta ttagaagaat ttgtgagata cattaaaccc cttttggtac 2280gtggtataat tgttatttgg gaagctgtaa acacgcagat cgttcctgag attgtcaatt 2340acttttgtgg tgtttcctaa aggccgcatc actgcccgaa tcgagttgat ggcccgcaaa 2400451029DNAArtificial SequenceSyntheticmisc_featureHygromycin resistance gene 45atggggaaga aaccggaact gaccgctacg tccgtggaga aattccttat tgagaagttc 60gactctgtct ccgacttgat gcaactgagc gagggagagg agagtagggc gttctcgttt 120gacgtagggg

gtcggggata cgtgttgagg gttaatagtt gtgcggacgg gttctacaag 180gatcggtatg tctaccgtca tttcgcctcc gccgctctcc ccataccaga ggtactggac 240attggggagt ttagcgaatc tctcacgtac tgcatctcgc gccgagccca gggagtgacg 300ttgcaagatc tgcccgaaac tgaattgcct gccgttttgc aacccgtggc cgaggccatg 360gacgcgatcg ctgccgcaga tctgtctcag acgtccggct ttggaccttt tgggccccag 420ggcatcgggc agtacacgac ctggcgagac ttcatctgcg ccattgccga tcctcacgtc 480tatcattggc agacagtcat ggatgacacc gtgtctgcat ccgtggccca agcactggac 540gaactcatgt tgtgggccga ggattgccct gaggtcaggc acctggtgca cgcggatttc 600ggcagcaata acgtacttac agacaatggt cggattactg ctgtcatcga ctggtccgaa 660gcgatgtttg gtgatagcca atacgaagtg gcgaacatat tcttctggcg tccctggttg 720gcgtgcatgg agcagcagac acgctacttt gaacggaggc acccggagct ggccggctcc 780ccacgactcc gcgcctatat gttgcgtatc ggactcgatc agctttacca gtctctcgtc 840gacggcaact tcgacgacgc cgcgtgggcg cagggccgct gcgacgcgat agtccgcagc 900ggggctggga cggtgggtcg gacccaaatc gcacgccggt cggctgcggt gtggacagac 960ggctgtgttg aggtgcttgc ggactcgggc aaccgtaggc cgagcacccg accgcgtgca 1020aaggagtga 1029461000DNAArtificial SequenceSyntheticmisc_featureEIF3 promoter 46tcataatcaa agatgagcca gccacgaagc taccggagaa ttctgtaaga aaaatgttta 60aagttgaaaa tgctaacagt gaagtgatat ccttttttaa tggagtgttg aggtgaagtc 120tagcatcgta ggggaaaaca ggattctgtg tcttccattc tactccttga taaagcgaag 180aaatccgaca aaaccaaaga gattgttcaa gtttaagatt tgtaagcgta caactatgaa 240cttcttctct ttgtaggcct gagtggtcgt atgcatacga ttcatgaagt gaatcagtat 300cgctggattt tgcttaggag taaagcacaa ctaagaaaat atgctgcctg gcaggcatcc 360tgagacatga ggcaagcgac gtagcaattg aatcctaatt taagccaggg catctgtatg 420actctgttag ttaattgatg aaccaatgag ctttaaaaaa aaatcgttgc gcgtaatgta 480gttttaattc tccgccttga ggtgcggggc catttcggac aaggttcttt ggacggagat 540ggcagcatgt gtcccttctc caaattggtc cgtgtggtag ttgagatgct gccttaaaat 600tctgctcggt catcctgcct tcgcattcac tcctttcgag ctgtcgggtt cctcacgagg 660cctccgggag cggattgcgc agaaaggcga cccggagaca cagagaccat acaccgacta 720aattgcactg gacgatacgg catggcgacg acgatggcca agcattgcta cgtgattatt 780cgccttgtca ttcagggaga aatgatgaca tgtgtgggac ggtctttaca tgggaagagg 840gcatgaaaat aacatggcct ggcgggatgg agcgtcacac ctgtgtatgc gttcgatcca 900caagcaactc accatttgcg tcggggcctg tctccaatct gctttaggct acttttctct 960aatttagcct attctataca gacagagaca cacagggatc 10004727DNAArtificial SequenceSyntheticmisc_feature5'ID sequence 47tccacagccc gaacccatga gagagaa 274827DNAArtificial SequenceSyntheticmisc_feature3'ID sequence 48gcccgaatcg agttgatggc ccgcaaa 274920DNAArtificial SequenceSyntheticmisc_featureMA-ZnCys-FP 49acctccttgt cactgagcag 205021DNAArtificial SequenceSyntheticmisc_featureMA-ZnCys-RP 50gatcccaaag gtcatatccg t 215118DNAArtificial SequenceSyntheticmisc_featureBash-(-1) CRISPR target sequence 51ctgtcaaatc aacaaaac 185218DNAArtificial SequenceSynthetic 52agctcagata tcttccag 185318DNAArtificial SequenceSyntheticmisc_featureBash-2 CRISPR target sequence 53atcttccagt ggtgggcg 185418DNAArtificial SequenceSyntheticmisc_featureBash-3 CRISPR target sequence 54gggactgtcc cattgtgc 185518DNAArtificial SequenceSyntheticmisc_featureBash-4 CRISPR target sequence 55tctgtctaaa tcagcaca 185618DNAArtificial SequenceSyntheticmisc_featureBash-6 CRISPR target sequence 56gccaagtgca tcatgctc 185718DNAArtificial SequenceSyntheticmisc_featureBash-7 CRISPR target sequence 57gctcaggtac gcatctca 185818DNAArtificial SequenceSyntheticmisc_featureBash-8 CRISPR target sequence 58attggaatca attttgaa 185918DNAArtificial SequenceSyntheticmisc_featureBash-9 CRISPR target sequence 59gctgttcatc acaaagag 186018DNAArtificial SequenceSyntheticmisc_featureBash-10 CRISPR target sequence 60ctctttgtga tgaacagc 186118DNAArtificial SequenceSyntheticmisc_featureBash-11 CRISPR target sequence 61cgtcggttca cgccaatc 186218DNAArtificial SequenceSyntheticmisc_featureBash-12 CRISPR target sequence 62aactcgctcg tcgatcac 186320DNAArtificial SequenceSyntheticmisc_featurePrimer MA-5'Bash-ZnCys-FP 63tagcagagca ggctcatcac 206420DNAArtificial SequenceSyntheticmisc_featurePrimer MA-5'Bash-ZnCys-RP 64gaatatgtgg tctagctcgt 206520DNAArtificial SequenceSyntheticmisc_featurePrimer MA-3'Bash-ZnCys-FP 65atggctccac cctctgtaag 206620DNAArtificial SequenceSyntheticmisc_featurePrimer MA-3'Bash-ZnCys-RP 66ctgactacag ctagcacgat 206721DNAArtificial SequenceSyntheticmisc_featurePrimer ZnCys-2845 Forward primer 67atacaggaag cgtggttaca g 216821DNAArtificial SequenceSyntheticmisc_featurePrimer ZnCys-2845 Reverse primer 68gaagtattaa gggactggcc g 2169849DNANannochloropsis gaditanamisc_feature1T5001704 Housekeeping gene 69atgtcacggt cgcggtcctg ttccgaagct tctgcggcct cttcgtcatc ggcagcagca 60gcgtcttcga ctcacgcccc ttcttcgcgc ggagcttcgg tggccgacgg tgctgcaagg 120gagcgagaag ataatggcaa acgcctgagg tcaccgagcc ctgccggtgg tgaagcttct 180ggttccgagg aagcggaaga ggatgatgag cccgccaaat tgcatgtttc tggtctaaca 240agaaacgtga cagaggagca tctcaacgag atattcgcca catttgggaa gctgtcgcgt 300gtggaactgg tacttgaccg acgagtgggc ttatcgcggg gcttcgccta tgttgagtac 360gatcatcgga aggacgctga ggaagcccag ctgtacatgg acggtggtca gcttgacggc 420gcacctttga aagtgaactt tgtgcttttg ggcggagccg cagccgatct cctgtatccc 480gtggcggtgg tcgagaaagg gacctttacg atcgcaatgg cggtccgccg gagaggaggg 540gcgggggagc tcaatgggag gggcggcggg gccggtctcg ttctccgcct cgggggggtc 600gacacgaccg aggtcggttg ccgccagggc ggtttactcg aggagagcgc ggacgcagcc 660ccccctaccg tcgccagcca gaccctcgcg gctggtcgcc gccacggcgc gggccgggtg 720ggcgggcatc tccgcctcgg gccgcggtcg cagccggagc agccgctcct cacgcagccg 780ttcctagatg gagggggcgg cgccaacagg gaaggcaagc aggagtctca cccgccgctt 840gaggcttga 84970408DNANannochloropsis gaditanamisc_featureRegion of ZnCys-2845 gene 70gtttaaacga tcagccacga cggctctcgc atgcacaacg atggcatgga ttggcgcgcg 60aaggatgagg actgctcgta ccacaccgcc gtggacgcca gctgccacat cgacagtagc 120taccaccatg ttgatgcctc aggccactcc atggtcgacg cctcgggtca cagcacgata 180gacgcgtcgg gccacgactc cctcatcgac tcaagcggcc attacgacga ctatctggcg 240cacaaggggg acgcccgcta catggagcac agttgtgaag cctgcaagcg ctcgaagaaa 300cgatgcaacc gccgcaaccc ctgccagatc tgcacctcca ggggcatcaa gtgtgtgccg 360caaatccggg gtcctgggcg ccccccgggc agtaaaagca gtcggggc 40871163DNANannochloropsis gaditanamisc_featureTerminator 9 71gagtcaaggg ggaaggtgca tagtgtgcaa caacagcatt aacgtcaaag aaaactgcac 60gttcaagccc gcgtgaacct gccggtcttc tgatcgccta catatagcag atactagttg 120tacttttttt tccaaaggga acattcatgt atcaatttga aat 163722091DNAPhaeodactylum tricornutummisc_featureEncodes ZnCys polypeptide of SEQ ID NO5 72atgaacgaag acagtaccga agacccggat gatggcagtg tggcgctctg tgcatcatgc 60gatcgttgcc gctcgcgaaa gaccaagtgt gacggccagc gcccctgtgg aaactgcttg 120gccaagtaca tgaagaagaa taaactcagt agcgcggatg gaatcgattt taccgagtgt 180gagtgtgtct attcacccgc taagcgtcgt ggccctattc cgggtcgtac cgctggccaa 240gctcggaagg ccaccgagct gcaacatcac caacagcagc agccgaatga ttggcctcaa 300aattatcaca acaacccttc gactggggtg aacttgaacg ggacaggatt ggacgcccaa 360atgactgctg ctttattttc cggccaaacc gaacaggcgt cgttgcagca aaaactgaac 420tttttgcagt cactgcaaaa tcaagacgaa gatcatctca tgatgcaaca gcagcagcag 480cagcatcaga tggacgagcc tgccaatcga cgagtgaaac gtgaagatgc tggacagaat 540accagcacga acgggattcc tcgcactatc accacccaca cgcacctttt ggaacgctcc 600aatccagatg gagcccgtct tcgtgcgtac taccagctat cgatcgacga actctatcgt 660ttgcctccga taccgacgga cgaagaatac tgtgcccgcc ttaacgttcc ggggatgacg 720cctcaaatga tcccaggtcc acatctggcc gccctgagtg ccgcacgctt tgctgagatc 780gcgctcggcg cacttgttca caacgaagtg tcgttagcga tggaattgtg taatgcagtt 840gttcactgct tgcgggaatc cgtacaggaa cccgtgcaga caccagtgat gttcgaagtt 900gccaaggcgt actttttgct cggcgttttc cgtgcctgtc gcggagacat ggaacggtat 960ttcaaatatc gccgggtctg tatgacgtat ttggcgaagc tggagaacga tgataaaacg 1020gcggtgctcc ttgccgcagt ggcctacttg gactcttggg ctccgtacgc tactcagact 1080gagctcaagt atgatgtcaa gttggatgct ggtgccattg ctagcgatcc caagaatcaa 1140aactggattc aaggtgctcc gccggtgtac ctgaataatg aggccccgtt gcatgcacgg 1200gctttggatg ctttggcttg tgccgttcgc acttgttgcg atcaagccaa cagccgtttc 1260gctcttatta gcaaggaggc taatatcgaa ggtctggaca cgattccttc cgaatccatt 1320tcttctgcaa cgtacaatgc agttctatcg cacgagaatg agctctgcag tcgcaatatt 1380gttctttcag cgtacactct gatgcaacag cacgaatcta ctgacagttc tcgacacaaa 1440aacgagggac agcacatggt catttctgcg atggacgcgt ttctggaaaa tagtgacgaa 1500gatggcaatg gtggattcac cgacagtcag attcagagtt tgctttctgt ttgtaacact 1560gcgattgaga atccgttcct cttgcaccat gctggtccaa catatcacat ggtgtccaac 1620gcggccgtac tattgtgtca tttattaaac ggccttcata tggccaagat gaacggtcaa 1680gatttcggtc ggatggaaca gtccatgttt gaagaagtct ttgacgcttt tatatcgatt 1740cgcaaactct tgacgattca tcgacgtaaa ctaccggtca aactgcgttg ccatgctatt 1800ccgagaccaa gcatggacgg tttaaaggaa gggcagccgt taattgattt gggggaaaca 1860attctttgtg cgtgccgtgg atgccagggt tttgtcctta tggcttgcag tccctgtgta 1920gcggcggagc gtgcccaggc ggcgcaacat gatttgtcag tcgaagcggc gaaggaagcc 1980gaagcgattg aaatgggcga gctcgacaac gaattggaca acttgggagc ggaatttgat 2040atggacgacg atatgttgtt gggaatgatt agcaatctca tttcaagttg a 209173744DNANavicula sp.misc_featureEncodes ZnCys polypeptide of SEQ ID NO6 73atggcttgca cggcgtgtca tcttgccaaa cgaaaatgcg acaagaaatc gccatgctcg 60cgctgtatca gcaaatcgct cgaatgcatt cctcacattt cccgtcaagg gaaaaagaag 120gtccggcggg tcgaagagaa gaaagatgac ggtcttgatc gtttgcttct cgagcagttg 180acggggaccg aaccagtgca aggtcataca caccatttcg gattgaagta tttggttcgg 240tcttggattt cgtttgcgtt caaacggcgg agctttttcc tgatgcaacg aggatgtgca 300ctggcaataa aagttggctt ttcgatggat gagatattct gcgaacaatc taattctcgc 360gaaatggatt ttctcaaaaa tattatttta gtacccaagg aagcgcagca tttgtatgtc 420ccgacaccac ttcagtggac ggaaattccc gaacgccttc tcaggaacac ggatacaata 480ggctcgtctg gaaacagaga gggtcggtgg atatggatgc gggagatgat caagggagaa 540tctcggtatc ttgtatcgga agcatttgaa cgagacgttg caccctggag ctcactgcac 600aaggcgtggg aagacaaccg gggggctgtg attgacctat tcgtcattga agaagataag 660cacaagcaca ccaagtcatt cgcacatcaa atttcgctct acaaagaaca agccgtcaac 720ggggaaggaa accgcttgac tcgt 744741002DNANavicula sp.misc_featureEncodes ZnCys polypeptide of SEQ ID NO7 74atggtttgta ttggttgtca cgaatcgaaa cgcaagtgtg ataagcaaac tccgtgttcg 60cgttgcctga aactaggaat tccttgcatc cctcaccttt cgcagcaagg caaacgcaag 120agaggttcgc ccgacgagac accagaagat gtgacgattt tgcgccaagt ttccttgccg 180aaagatcact atggtttgtg ccatttgatt cgttcgtgga tatcgattgc ctttgtacga 240cggagctttc ctttgcttaa caaagccacg acaatggcca atcaattggg cgtcacgatg 300gacgaaatca tgagtcgttc gatgacccag cagggcatgc attggctggg tccggtcgta 360gcgaccccgc aatccgaaca aatggcgggt ggtccacgct tgcaatggaa cgaactgccc 420gagggtctct tggtggcgac acgcacgctt catagtgttg actgcgaagc acggtggatt 480tggattcgcg aattgagtca agggcgttct cgttatttgg tgacgcaagc ctttgaacga 540gatatcgcta catgggcact ggtgcaaagc acgtggaatg agaaccgcat ttcggtcgtc 600gatctctttt tggacggtgc ggctcgtgaa aaacacgcca aatcagtggc gcatcagtat 660tcgctgcatg cgaagcctcc gacgccgcac agtgcgcgct gcagtcgcca acgcagtcag 720gtaaaactgc gcaacggaga catgatttca gtggaagaaa tttcctgcat ggatttcgtc 780catatggatt tgtcgtacca ttttgtggaa tacgtcccgg tgtgtataca accgattcgc 840tcccaagctt gtatccagaa caaagtccag agcacgcagt cgttatttca agaaatgtcc 900aaggtcatgt gggatgatta tcctctcatg gtgaatgtcg atgatattcc ggcggaagga 960aacgagctgg atcagattct gcaattgtta aatggaggtt aa 100275512DNANavicula sp.misc_featureEncodes ZnCys polypeptide of SEQ ID NO8 75atggaagact tcaacaacaa caacacgcaa caagccgatg atgaaaagtt gtgtgcaagt 60tgcgatcgct gccgatcgcg taaaacgaaa tgcgatggga aacgtccctg tggaaactgt 120gtggcaaagt acatgaagaa gtacaaagtc atgagtgtcg aaggcgtacc cgaatctgcc 180tttgagtgcg tctattcacc ggccaagcgt cgcggccccg tccctggacg tacgccttcg 240caagctcgtt ccttgaacga tgtaacgggt ggcaacatga atgtgaacat gacgggtggg 300aataactttg attggaacat ggatctcatg tcgcaacaac aacagcagca gcaccaccaa 360caacaacaac aaccaatgat gtcatcgtta attggtggat tggatgggaa caacattttg 420aatcagttca atttgatgcg acaaatgcaa cttcagcagc aattgccgct ccagccacaa 480caaatggcaa tgcagcagca catgatggac ac 512762172DNACyclotella sp.misc_featureEncodes ZnCys polypeptide of SEQ ID NO9misc_feature(447)..(447)n is a, c, g, or t 76atggacgaca ccgtcgccgc agaggaagca aaagaagcaa ccgacctaca gtcatccgac 60tccaaaccca cttccccatc atcgacaccc ctcaatcgcg attccaccag cctctgctcc 120tcctgtgatc cctgccgcgc tcgtaagacg aaatgcgatg gtcttcgccc ctgccgcgcg 180tgcatcagca agcatgtcaa gaaacataag ctgtcgtctt acgaggggat taccgccgaa 240gattgcggat gcacctattc cgtagccaaa cggaggggtc cggtgcctgg ctttaagaat 300gcgaaggacg aaaagggcga tgggaattta tcgacatcga agaagagagg tcccacgcaa 360gacgggacgt tgcattctta ccctcccaaa aagaagaaag agaagagaag tgttgatgtt 420ctagcacgat ttcctcactc ggctgcncag gatgcgatgg ctgccgcttc ggacagcgcg 480aggcaacaac ttgggttcat tgaacggctg cagcaacaac agcaggagtt tcagcgtcaa 540cagcagcagc agatgcaaat gcaacagatg gcacaagcac aaaatgctca ggccatgcct 600ttcatgtctc gggacggtga caacagcgct atttcgcgcc aaatgaataa taattataat 660gagcaggtct ctgggcataa gccgtcgcag cagttttcgt ccactgaaca aacatctgca 720gtgggttgcg agaaaaccac ggtgcgcgaa ctgcttcacg tcctcgaccc aaaagatccg 780ctgggatcac gattccgcgc atgctacggc atctcctttg gatcaatatt tggacttcct 840ccaattctta cctatgacga atactgtcgt cagttcactc caacgattgc ttcaacttca 900atgccaaaat acgacgtagc ggcacttcaa gcggcacaat ttgcagagct tgccttgggt 960gccctcgctg atggagaccg ttgcatgatg ttcgccttaa ttaatgctag catattttgt 1020cttcaggata cggtgaagga acctgttcat cgtagctgcc aattcgagct cgcaaaggct 1080ttcttcttcc attccttaat tagatgtcac aatggggata tggagcggta tttcaagtat 1140cgacgtgcag ctatgcacac tttggctcac ttggatgggt atcccaatgt tgaaacactg 1200atggctgccg ttggatttca agacgcactg gcattcatgc tctacaatgg atgtgatgat 1260gatgtaccgg acattgatag tgactatcct caagtgttag atcgattcga taccaaggaa 1320tcgagcagcg tatccttcac accctcgaaa ctcgcatcag atcccacgaa taagacctgg 1380atcactggcc ccccgatgtt ttcctcggag agttccgccc cacttaaaag tcgtattcta 1440gatattctgg cctgtgcaac tcgatcgttt gttgaagagt ctcagttcaa gaaggagatc 1500aaaagcgttg aaacgagcac tcgcaaacgt aggaatttca taactgcaga agacaagagg 1560attaagtata aaatttgtct cggtcatcta aacgaggctg gaagactgct ggctgtagca 1620aattgcaagt catcctccag ttccatttac gatgtgtacc atgtactggt tatggctttt 1680cgtgtgatga ttcatgaaga tacttcggag ccggaagaat cacaagtcca aaatgcattt 1740catgttttga aagctatcat cagacaacca agcctattga atattggccc cattaatata 1800tttgtccaca aatgcgtaat ttttgtagca cgccttatca acaagtcgca taaggcagga 1860ctcgaggatc aatcggcaag ggacctcttt gaagaatcaa ttgatttgta ccatgcctcc 1920agaactattc tcaatataca caatagtaaa ctccccgacc aacttcgatg ccacgaaatt 1980ccgaggccga aatccatcac tgcgaaagaa tgtgacacaa tcattacgtt aggcgacgag 2040tcgatgatgc cccacaggat ggccagtgtg aaggaggaaa ccagcgcttc cacatctgac 2100actgaaaagg aatgccacat caacgataaa gcctttttgg tgtttttgag tggtctatat 2160cttgcgcgtt aa 2172774548DNACyclotella sp.misc_featureEncodes ZnCys polypeptide of SEQ ID NO10 77atgcatttct ctgcgcagcc gccccagggg aacggggaca tggcccagct cgacggcgta 60tccacagcct ccaaaaagac tcgcgcctgc acggaatgcc acagagccaa gagcaaatgt 120gtcttttccg aagagggcca agaaaagtgt gatcgatgct tcaggttgaa caaggattgc 180gtgcctcatt tatcgaggca gggccagagg aagaagaaaa gcgagaaagg tatgatgaaa 240tcctccgtgg ccacctcgtt ggcggaggtc tcgaaaggga gcaacgtcgc cagtaaagcc 300ccgatgtctg gcgaaagcaa aagtacaagc ccctttttcc cagacaacgc agtggaaggc 360aaccggccct tttcattcca cgccgctagt caggatacgt cattgaacag gcttgctgca 420acggcaactg gaggtccgtc aatgagccaa atggctcctc tagcaaaatt cattcctcaa 480aagcacatgt tctcatccaa tcaccccact tttcataata ctggcccatg cggtctctac 540gaagcccggc tcaggaggac tcaagccggc actgccttac cggtggatca aacaaacata 600actgtcacag agcaacggca agccgcaatg tcaatgtttt ctaatagtga tagaaccata 660acggactcga cccatcaagg cgtcacattt cgtgaggact tgtcgtcgtc caggtcattg 720ccactgagag agtggatgaa atgtgcactc aattcgaaca aaatccgtga cagcagcggg 780agcagtccta tttcttccaa gtatattgca tcttgcctca aaatcgcact ctcgttggct 840aaacaaatca gtgatgcaga ggttacttct tcgcgagaga tacttcaatg gctgcctcgc 900gacagtatag attggccaca gtatattaca gtgaaattga caggaaatga aactcaagtt 960cctccccatg atgctcggac tggatcttta gaccattcat ccgtggcgga tgatgagttg 1020gacatgctcg aagcactttt ggactcaatc tgcgaagaaa atgaagtgga tacaacagat 1080gttttcgata tttattcggc tgcaattctg ctggattata gcaaaaatag cgatgatggg 1140gttgatcctc tttcgtttcc cgggcaagaa tatcgaatcc atgcccttgg actggtgttt 1200tgcgaactgt tttcaggtgg acgagtcccg tccactgaac tagtgtcgga tggcctttgt 1260caggacgatg tagtcacccc agcgatttct gaaaggttgg agtttacagg tatgctgaag 1320ctcgagccaa acgagaacga catttacaag gacacaagct gcaaatatgt aggcacaaga 1380aaaaaaacac gtgagcttga cgaatcgttg cactcgtcca ttgagtcact

caggcggctt 1440ggcatttcct gcccactgtg tgacttgatc ttcaacatac tagattccat caacggagac 1500ttgggcagag atgactcgta ccgaaaaatg tcagacgtag ctatcgattt gcaaaacatg 1560gtagacaaac caaaaacatt cctcaatgat ctcgatgtta ttactttatc gtcgacgggc 1620ttgcaattga cggacaactt attcatgcga gatgaggagg tcgccttgct gcaacacgct 1680tattatcgtt ccacattggg gtcgtctgag tttgctgtca tcactggcgg gtcggggaca 1740gggaagtcac atttagcctt tcgtctaggc agtcacataa catctcatgg tggtatattc 1800ctctccgtaa agttcaatca aatgaaacag gccgaccctt actcagcttt agtttcagcg 1860ttcaatgagt atttcaacaa tttcacgatg acgaagcagt tagactcgat gaaacggatc 1920gctagcaagc tgcgagatga actgggacaa gacgcacttc ttttagcgaa agtcattccc 1980aatttagcag aggttcttga ttttgctgcg gttgatacag cctttgatgg agactgtgta 2040aatgggcacg agaagatgca ttatatatta gtgtgttttg tcgaagtcat gtctgcttgt 2100tcacacgtga cattgaccct gtttcttgac gatcttcaat gggcagatgc cttctcattg 2160tcagtactcc aacagataat gattatgcct gatgagcaca aacaattctt ctttgtagga 2220tgctatcgag acgaccagat ggaagatgac catccgttca agaaaatgat cagcagatgc 2280ggtgattttg gtgtcaggct gacgatggtt tatttagaat gcatggacaa ggacggaatg 2340aacacaatga tttcagaatt gctttgccta ccccctcggc tggtcaagag tctatctgag 2400ttggtttact caaagacgaa aggaaaccca ttgttcttat cgcggttgtt gatatcgttg 2460aataaggatg ggctgctcaa tctgagtctg ggccgccgcc gttgggtatg ggacgaaaaa 2520cagattcaat cgaaagagtt gcctgatgat gtagcatcat tcttttctag cagggtgggc 2580aagctatcac cagaggttca ggcagcgctt caggttttat catgttttgg ctctgttaac 2640acgtacgaat tatcaatact cgagtcaggc cttagcctga atgtagtcaa accacttgaa 2700agagccgtaa atgaaggatt cgtctccaag aatggcaatg attaccgttt ttctcatgac 2760aagattcacg aagcggtcta tggtatggtt gagttagaag agcgtcgctt ccagcatcta 2820aactacgcga ttagtttggt caagttcgca ttgggacaag atgatagcat catttttacc 2880gctattggcc aagctaatct cgctggccca tcgattacta ctgatgcact tcagtctgct 2940gaatttgcga ggtgcaatat ggtagcgggg aaaaaagcaa tgagtctgtc agatttctcg 3000tgtgcagcga tttgcttcag caagggctta tcatttctgg acgaaaatcg ttggagtgat 3060tactataacc ttagccttga actgtttgag ttggcagcca aatgtgcgct ggtgctcgga 3120gactttgcca gtcttgccac gatgtctgaa caggttgaaa aacatagccg ttgtttcgaa 3180gacaaactcg aggtgtcttt cttggttatg tgttcattgg catatgcatc taaaatctcg 3240gattctgtcc atattggttt atcaattctt tcccaacttg gtcatgaatt acccacaaat 3300tttactcgag cggagatcat ctttcacatc gaacaaacta aaacagttct tcactccatt 3360tctgataaag acctaatgtt ctacaagaaa atgactgacc ctaaacacat catggcaatg 3420aggtgtttgg ctaagttgga acttattgtg ctacagatca atccagattt gcaacctatc 3480ataactttga aaatggtcaa catgaccatg gatctcgggg tgtcacacat gtcttcagtt 3540ggaatggcct actttgctgg acttgttgct aaactagatg aaatccaaga cggcattcga 3600tttgcaagac ttgcaaaaat gttgcttgac aaaagtgggt ccaaagagat cacaggagat 3660gtcatcttta caacatcaga agttctctgc tttcatgagc cattacagag tgtcaacgag 3720tatcgttttt acggacaaac tactgcattg gcagcaggtg acatgtactt tgcatgtgtg 3780ctcaagatgt cgaattgtgg gacgatgctc tggatgggat caaatctcct gagtgtgaaa 3840gatgcctttg ttcaggttgc tcgctactta aaagcgaaga accacttgtc aacgtacaat 3900ctcttgctac tctcaaagcg tagtattttg atgctcatgg ggctagcaga tgaagatgaa 3960cccctcactg ttgatcaact gaccaatccc taccaactga agtattttta ttttcaaaaa 4020atgtttcaat ccttcgtatt taatcgaaat gatgatatga aacaatacac tgagaaattc 4080ttgcaattca agatgccctc gtggttattg ctctcagtcc atgcgagaca tgagttttac 4140gtaggcctta tttcatttca gatttaccgt gagtctggta tctctttgtg gtttgagagg 4200ggccaacagt gcaagtcaaa agtgcaacta tggaaagagc aaggatcagt gtggaatttt 4260gaacataaac tctatttgtt acaggccgaa gaatattatt gcaacgatga cttcgagagg 4320gctggagaat ctttcaagaa ttcgataaca tctgctaagt cacacaaatt cttaaatgat 4380gaagctctgg cttgtgagct tgctgcaaac ttctatcttg gcaccggtga tttaacatct 4440tcgatgaaat attttcgcct cgcccatgat aagtacaatg aatggggtgc tcttggtaag 4500gctgcacaac tggttacatt catgacagaa aagtttgcca gctgttga 4548782622DNACyclotella sp.misc_featureEncodes ZnCys polypeptide of SEQ ID NO11 78atgacaaacc atttcgacaa caaccaatgg tccagcccct caccccccat gatggaagcc 60cacgacgaca atcagcatca gcaacacgaa ggaggcgttc tcctctgcgc ctcgtgcgat 120cgctgtcgtg cacgtaagac gaagtgcgat ggaatgagac cttgtgggaa ttgtaaaacc 180aagtacatga agtctaagaa gctggacagc gtggaaggaa tcgaccttgc cgaattcgac 240tgcatctact ctcccgccaa acgccgcggt cccgtccctg gcaaaagcgc tacgcgcaag 300gcctccgaaa tgatgtctta cagcaaccca gatgtcatgc actttggagc cgggggagga 360ggcacccaag gagggggata tcattctcaa gtgggattcg acggaaccat gaatactgga 420gggggattca atccgcagca gcagcagcag cttcagcaat tcaacaacaa ttcaagtgct 480caattttcgg cggaagaatt gaaacagatg cttcttcttc agcaacagtt gttgttgcag 540caacaagaga tgcagatgca gcagcagcaa cagcatcagc agggtttgtt gcagcagttg 600actaatgtgg cgggaggggg gaacatcaat attgctaaca ctctaaggcg ggcgagcatg 660aatgggggga ttactgcaaa tggcgagaca atgggagcaa tgaacaacga tgttggttcc 720gtggacaggt caggcatggg aggaaacaat gggcacgtgg atgagcagtc actccaactc 780attcagcaat atcagaatca gttgaatatc gggtcaaatc atggcatgac atcaggcaat 840gcgtctatca ttggctctgt tgtcggagga ttgccagtgc agccatctcc tatgccttct 900caacagtatg ttcaagagca gcagccagct aagcgtgctc accgtattga ttctgccatg 960tctagcaata acgatggcac tcttccaaag tctgtgatta gccatctccc tctcctcgac 1020cgtcatgacg gagacggcaa tgtccttcga gcctactacg acctcagtgt gaatgatatc 1080ctcaacctcc cccccatccc ctcagatgaa gaatactgca gtcgtcttgc ccgcaataat 1140tatcactgcc tacccagtaa tcttcccacc tatgatcact cagcgttaca agccgcacga 1200tttgcggaac tagccttggg agcactcgcg aacaatcaga ttcccttggc gctagagttg 1260agcaacgcct ctgtcatgtg catgaggaat tgtgcagagg aaccaagtga tgagagttgt 1320atgtatgagg ttgcgcgggc gtatttgctg catggaattt ttaggagttt caggggagac 1380ttcgtcaggt atttcaaata tcgacgagtt tgcatgacgc atgttgggca gttggcgaac 1440acaccacatg tggaggcact ccttgccgcg gtgtctttcc acgatgcact cgcgtatatg 1500atgcataacg ccaaggaaga atctcttccg gatattgatc aggtcttgcc gcgtctaaat 1560cccggcaact gtgattttga cgacagtgat gaagttgagg ctaaatatgg catctcgact 1620aatgccaaat cggtcgcttc agaccctaac aatcaaatgt ggattcaagg tgcgcctcct 1680gtgtttctga ataacgaagc aaatctagcc aatcggtcat tggacggact ggcatgcgca 1740atccgttctt gttgtgatca tgcaaattca caattcgaag aaatggcaaa agctgtcggg 1800gctgactttg ttggcggatc tggttcttgc ggaatgtccg ctacaactaa ggctgttacg 1860gcaaatgaaa atgagctctg tagtcgaaat attgtgttgt cggctcgtac tctcctcgac 1920cagtataatg gggtcagtca cgaaaaagcc aaaaaacatg ggctccaaat gttagcgtta 1980gcgatggaag cattcttgga aaactctggg gaaagtgatg gtgttggagg gttcactgac 2040aagcagatca agaacttgct tactgtgtgt gatactattg ttaagaatcc attacttctg 2100catgctcctg gtcccgtata tcacatgatg acgaattcgg ctatcatgct ttgtcatctt 2160ttgaatggca tgcatgcgaa ttgtggagaa ggatcaaact cgtcgggcaa atcaggcatc 2220gaagaagttc tgtttgatga agtcctcgat tcattcatgg caacgaggaa gatattgaac 2280gcccatcgaa aatccctacc agtaaaactc cgttgccatg gcatcccacg accaaatgtc 2340ggacccttca aaaagtctga ccccgaagct ccatttgtag accttggcga aacattgctc 2400tgtgcttgca gaggatgtca aggattcgta ttgatgggat gcagtccttg cgttgctgct 2460gagagatcgg ctgcagcggc caaagcacaa catgcacatt cgtcttctac aaatggcaat 2520tacaatgaag atgagtttga gagagaatta caagacatgg gagcttttga tatggacgat 2580gatgccctgt tgaatgtcct ttctcggttt gtacagaact ag 2622791137DNAThalassiosira pseudonanamisc_featureEncodes ZnCys polypeptide of SEQ ID NO12 79atggcaacaa ctactgaagt acaaaaacat gcagtctctg ctcctctccc cgcatcagca 60gcaacaacta caacaggagg aggaaataat gaatccaccg tcctttgcgc atcatgtgat 120cgctgtcgtg ctcgtaaaac gaagtgcaac ggcgctcatc cttgctcggg atgtgtttca 180aagtacatga agaagcacaa gttggaaagc tttgatggga ttgatcatgc attggttgaa 240tgtcactata gtgttgcgag aaaaagaggg cctcaacctg gttccagtaa gagcccaact 300gcgcccagag gatcaattcc ggcggatggg acgacgatct accaacagcc tgccaagaag 360aagccaaaga aagcgaagca ggcagctcca atgatgcacg atttggctgc catggcaagt 420gcatttggag gaggaaacct tgggcagatg cctcttcctc ttgaccctgc tgccgcggct 480ttgcaacagc agattctttc cagtctagga gctatcggtc tggggctcta tgcgaacttt 540accgctggtg gtggcagtgc gatgactgca gcttcgaata acgcaaggca gcagttggca 600gctgtggaat cgttgttgtc aaacaacaag tccgatgtgg acagtgtcac gaatccatta 660tccagcgaag aagaggctca tttccgtgca tgttacactc tctccgttgg cagtctcttt 720ggtcttcctg atgttcttaa gaaggaagac tacttcccga agtacgacgt ggctgtcttg 780caagctgctc gctttgcaga attggcaatc ggagcgttgg tcgacggaaa tggttccaag 840atgaccaagt tggccaatgc aactgttttg tgtctgaagg aagccgcgca agagcctgtc 900cacccgagct gcaagtttga tgttgcaagg gcatacttct tcctcgctat ttgtgagctc 960aacattggtg acgtggaagg gtacttgaag tacagaaggg agagtatgag acgtctgtcc 1020gagatgaatg atgcctctgg agccgatact cttttggcag caatgtccct tcaggactcg 1080ttcgtgtaca ttctttacaa gggcttggat gatacccttc ctaacatcga ttctgca 1137802691DNAThalassiosira pseudonanamisc_featureEncodes ZnCys polypeptide of SEQ ID NO13 80atgagcaccg acgacaacaa catcatgcca gaagactggc agaataatcc acctcccctg 60ccacaggaca attggcagaa taatgagcag acaagcaact acgacaacgg caacagcaat 120ggagggcagt acagcacgca tcatcaacaa caaccaccgc aggagcaggt gaaccgtgct 180caatcgtcgt acaacaatca atacagcacc tcccaataca actccaacca acaacaagaa 240caacactacc aacagcagca gcaacaacag cagcttcaac tatgcgcctc gtgcgatcga 300tgccgcgctc gaaaaacgaa atgcgatgga gaacgaccgt gtgggaactg tgtcaataag 360ctcaagaaga agttgaagct tgacaacgtg gacggaatcg acattgccga attcgactgt 420gtttactccc ccgccaaacg acgtggcccc atccccggta agacggggca gtctcgtaaa 480tcgagtgaaa tgatgtatca gcagccgcag cagaggggag gaggatatct cggtagtggg 540gggggaggag gataccccca gcagcagcat ggtctgcaag ggggagggta taattttggg 600ggaggacagc agcagcaaca acaacaacag tggatcaaca gcaacaacaa ccaaggaagt 660caattctcct ccgaagaatt gaaacaaatg ctatcactcc aacagcagct tctcattcaa 720cagcagcaaa tgcagcaaca gcaacaacag caggggatgc ttcaacagtt ggctactgtg 780acgagtggtg ttggaagtag tggtattgga ggggcaggtg gtattggagg aatggggaac 840accaacaatg tccaggtgga aaatggagca ttgcagcttc ttcagcagta tcaacagcag 900ttgaacagtg gaaacaacac gctgggtagt agtggaagca tcaacatggg actgggatct 960caaccctctc ccatgccgtc atcctcctac aatcaagaac aacaacagca acctaccaaa 1020cgtgcccatc gccttgagcc tgtactatcc aacgccaact ccaccaatct ccccaactcg 1080gtcgcctcac acctccccct cctctccctc cacaaccccg acggcaacgt cctccgctcc 1140tactaccaac tcagcgtcaa cgatctcctc aacctccccc ccatccccag cgacgaagac 1200tactgcacca tcctctctca aaataactac aactgcctcc cgagcaatct tcccacctac 1260gaccaatcgg cattgcaagc ggcgcggttt gcagagttgg cattgggagc gttggcgaac 1320aatcaggttc cgttggcttt ggagttgagt aatgcttcgg taatgtgtat gagaaattgt 1380gtggaggagc cgagtcacaa gagttgtatc tatgatgtgg cgagggcgta tttgttgcat 1440gggatattta ggagttttag gggagacttt gtgaggtatt tcaagtatcg cagggtatgc 1500atgagtcatc tttcgcagtt gaataacgaa cccaacgtgg aagctctcct cgctgccatt 1560tcctatcacg atgccctcgc atacatgatg cacaacgcaa gtgaagatgc cctccccgac 1620attgacgaag tattgcctcg tctcaacgac tgcggtaaga acgattctgg ctgtgacatt 1680gaggccaagt acggcatttc caccaatgct tcgtccgttg taacaaacgc caacaaccaa 1740atgtggatgc agggtgctcc tcccgtcttc ttgaacaatg aagccagtct cgtcaatcgt 1800tcgttagatg ccttggcttg cgctgtccgt tcgtgctgtg atcaagccaa ttccagcttt 1860gaggagatgg cgaaggaagc aggagttgat ttgcctgcag ggggaggatc ttgtggaacg 1920agtgctacca cgcaagctgt gatggcgaat gaaaacgagt tgtgcagtcg caacattgtg 1980ctttcggctc agactcttct cagtcagcat gcgggcacga gtcacgagaa gagtaagaag 2040catgggcttg tcatggtagc tacggcaatg gaagcctttt tggagaatgg gggaggagat 2100gaggaaggaa tgggaggttt caccgacaag cagattaaga acttgttggc tgtgtgtaat 2160acgattgtca agaatccgtt gctactcttt gcgcctggac cgacgtatca tatggttagc 2220aacgtggcga ttttgttgtg ccatctgttg aatggaatac atgccaactg tggagggtct 2280tctggcaatg ccaaatctgg gatggaagaa gttctatttg atgaggtact tgatgctttc 2340atggcaataa ggaagctatt gaacctccac cgaaagaatc ttccagtcaa actccgctgt 2400catggcattc ctcgccccaa attgggacct ttcaaaaagt cggatcccga gacacccttt 2460attgatttgg gcgatacttt aatgtgtgtt tgtcggggtt gtcagggctt tgtgctcatg 2520ggatgctcgc cttgtgtggc tgcagagaga tcggcatcct cggcaaggat gcatgccaat 2580caaagtgaag atgacgacga tgagtttgaa cgggaacttg gacaattgga cgatttcaac 2640ctggacgacg atgctttgtt gagtctgctt tctcgcatcg ttcagaattg a 2691812070DNAThalassiosira pseudonanamisc_featureEncodes ZnCys polypeptide of SEQ ID NO14 81atgtcccaaa caagcaacac cgaacccaaa ggcgccaaac gcaaaaccca agcatgcacc 60gaatgccaca agtccaaatc caaatgcacc tatcccgatc ccaccacaac cgccgccggc 120ggcaccgcta aactgtgttg caatcgttgc atacggctgg gacgagactg cattcctcac 180atctcacagc agggcaagag gaacaaaaag accgaggagg agacgatgaa gaatgagaag 240agagtgaacg aagatgatat gcaagatggc ttatgcaagt cgaccatgtg tgctgccgcg 300attggtaatc aagataagat tttgaaggag aataatctga gcttggaatt gcccagacat 360attaccaatt caatggctgg tcagtttcct gctggtggag gtggaggtat gatgggtggt 420cagtttgccg ggagaagtgg tgcgggtata cttcaccctg cggatattct atcgggtggg 480atgaattcga gtcagttgag tctaatgttg aatcatttca gtggtactag tggaggtcag 540agcgatacaa tgtcgacact gaataatatc atgtcttcat ctgcaatggg agctacggga 600cctccacctt cggtagatgc attgctcatg ttggcttctc gtagtactag tattgggagc 660aacagtggag tgaacttggg ggggacagca tcagcagcac ccgctttgcc ggggacaagt 720cagcatctca ttcaacaatg gcaacatcag caaaaccaac ttcgttatgc tgtcatgggg 780ggtatgcaga ctgcgactat gatgggcatg actcaggcat ctggagatgg cagtgctact 840ggaaatcagt tggatagtgc cattattacg aaaaaggaac gcacttcatc atttggcagc 900gagaatgatc agccgaagaa taagaagcaa aaggcgatcc aggaggcgaa ggagtggtgt 960gctggtggag gtggcgacga tcagaaacaa tcagtgctgg aagcattggc tgctgctacg 1020aaaaatgaaa cgacgccaaa gttcgtgcca cctcacattc attaccctcc cgtatccctc 1080cttgccgaga ccaccaccac tgctatcaac gacaacgctt cttcttctgc agcagcagca 1140gcagataaca ctacagacac tcaagaaagc caactccgac gttcgtccta caacgctcaa 1200ttcgtcacac ccgaagatgc aatcggcaat cacataactg gtcaaaagct cccatgtctc 1260caaaatcact atgggcttca atgtcaaatc cgtgaatgga tctcaatggc tttagtacga 1320cgaagctttg cattgttaag caaggcgtcg tctttggcga atcgatgtgg tattagtatg 1380gataggatat tttgtggggt tgtagaggaa gtggagaaga agggtggcgc tgaaaagaaa 1440acgaaggggg gttgcaagat gaacgttggt gggaagatga actatctgct ttctgtcttt 1500ctggagccaa ggactgcaca ggttgttccc atggaacagc cttttgagcg aaacttattg 1560tgttggcgtc acatctctca aatctttgag gacaacctgg cagatggctt ctctttgatg 1620tttgcaaaag aggactttcg tagatttttg gcttgttatg ctcatcagat ttcatcgcaa 1680ccgagcgcag agagtcctat tcgtccagta tatgcaccga agattactgt tcgtttgttg 1740agcagggatt ggggccagac ggaagctgtg acggaggaaa tgatcgaggg tgtgggtaag 1800aacgaagcgg agactactga aatggacgct ctctttgtcg tcgttccaac aatggacaag 1860gttacatact acttggagct gtttcatccc aaccttgagt cggatgcgaa ggattgcgag 1920gccgatgata atgacgaggg aactgaaact cccgagtcca accctcccgc cttggatacc 1980gtcatggagg gcgaagattg gcaaggaatc gatgagattt tggccagtgg tgatgacatg 2040gatgctttga tgaaggcatt gttggattaa 2070821233DNAFragilariopsis cylindrusmisc_featureEncodes ZnCys polypeptide of SEQ ID NO15 82atggggacgt ctgctaatag agcctgtact gaatgccata aggctaaggt caagtgtgtc 60agggatgatg atggaaacat aatatgcaaa cgatgtgaaa gaattggact gaaatgcgtc 120gaacatatct ctagacaagg acaaggtaca agacgccgaa aaaaggtaaa gaaggaaaca 180acgacggcga cgggagcggc aaataaaaac aatgaagata agacggtaga tgaagctcta 240gcgatcacga tagcactatc ttctccaagt cccatgccct cgtgtccagt atctggtgga 300tcaaacatcg tgttcagcgg taatggtaac gttaacggcg ttccatcgtc cgcatgcaat 360gcacttacgg ctatgaatgg acaagctatg accaacaaca aagagggact atgtaatggt 420atggcttcgt tacaagttga agatagtatt atctgtaaga gtattactaa tggattaggt 480aaagaacatt atgggattca tcatctaatc cgtatgtggg ttgcattatc atttacacgt 540cgaagttttt cattacttgc ccgtgcgtca tttattgcat ccagaatggg gatttcgatg 600gacgaaatta tatcgaatca atcgaatttt gctatcgatt ctggttcaca accgatgtac 660ttcttgggga gagatatatt ggtaccgaag agtcaaagaa agacgatcgg tcttccactt 720aatatcgaag aaattccctg ggatcttctc gaagctgttc agatcgatcc ggtacgtcct 780gatgagacct tccgtaatcg atggtgtgct attcgaatga cagtacaggg cacttcccga 840ttcttgacat cccctctttt ttctagagac ttttcttctg ttgacgaaat caataaggtt 900tgggacgaaa acaaaccaaa taaagaagtt gttgatctat ggatgccaaa gtctgaaaag 960gggaatatta ataatgataa taataataat aataattcct cggaccgtaa tagtcaatat 1020ggaggaacaa catcaagtgc caagaaacgc gacattattg atgtagcagg aggcacatca 1080aataatgaaa ttgaaagcga tgtttgcgat cccatcatgc atgatgatgg tatcgaattt 1140actgatttgg ttgttacaga agaaatgcag gaattttttc aattacttgc tggtgatcaa 1200agagtgcaag cagatctgaa tagtctattc tag 1233832418DNAFragilariopsis cylindrusmisc_featureEncodes ZnCys polypeptide of SEQ ID NO16 83atgactacta gtactagatt aagaggcaaa agggggaaaa aagattcgag aaatgatgcc 60gtcgccacca gcgacaacgg cgtagctatg acaacggcga atgctgtagt agtggtcaac 120gatgagaaga ataagcaaga taattataac aacgaaggcg atccagttga atttaaagtt 180agagtagaat tagaagtaga agctcccatc aatgaacaaa aagctgtcga taataatgag 240aagaagaaga gcagtgccga gactactaag gctgaggctg ctgttgtgaa ttcagatgag 300gatgtaaatg atgatgtaaa tgatgatgta aatgatggag aggacgatgc agtcgttgta 360gtaaagaaca gtaaagaaaa caatgacgat gacaatgata gtgataccaa aaagatgcag 420gacgcaacga agaagaagat ggcgcctcat caagatgatg cttgtgtagt tgaagttgtt 480caagtttctg acagaccatc atttcttggt gggactgtat taaaacgtga tactgttgga 540ttaggattac gatataaaac agaaaaagaa aaagagaaag tacatgaaaa tgatattcta 600ttttcaagtg ttgatcttgg tttacaatca ggatcaggag gatcatcttc tagtcaattt 660ttgaatcata cagatcatag tggtaataag aaattacaat ctataatcaa ggcaagaaaa 720tcaaattatt ttgtgaatga tgttactaat attgattcat gtagtattgc agtaaatgaa 780gaagaacgta ctaaaattgc aaaagaaatc tttcatgaaa taacaacaac aacaacaaca 840actggtaaag atgtaggtat tggtgttggt cgatttttaa attttaaatc aatgactaaa 900gcaaagtatg agaatttagg ttgtgatttt gtatgggaaa ttatggatga aataacatca 960ataataaaaa tatgtcaaac tatgaattat atctttatgt ccgatcaaga acgtactgaa 1020cgtagtcttg caatagaaac acagcaaaaa caacaacaaa atgactatcg gaatgaacga 1080caacaaaaga atgggaagac tttatcatca tctgataaaa agtcgaaaac gaaaaagtca 1140acaaaacaaa ataaaattct tttacaacaa cgtcaacaag aacaagaaca acgtgaaaac 1200gctcagatac aagaacaaca gcttcaacaa caacaacaac aacaacaaca atgtcaacaa 1260gttcagatgc gaatatacca attacagcaa cagttacagc agcagcaagt gtattaccct 1320ccaacaccgc ttattcaaca gtatccgacg gcaatgccaa tgccaatgcc attatcaagt 1380ccttcaccac tactaccaaa agacggtaag aagaagaaga cgaagggaga gaagagaaag 1440gcaccagttc cagcagcaat ggcaagtgaa agaagtggta ttattgaagg ccgtgttatt 1500gttgatacta ttgttggtgg tgatagtgat gaacacattg ggaatgaaaa tttagttaaa

1560ttaattgtca agaaaaaatc agaatatgat tatattgaag ttaaggatat aaaaaagtta 1620ggtatagcaa gagtacgtca aaatgtatca ttgaatatag tcaaatctat tgttaaagaa 1680aatggtggcc gattcttatt ccgtagaaag aaagacgttg atgatgattt gttagagact 1740cctacagtag aggcgacgat cgctgtaatt aaagatggag aagatgctat agcaagagca 1800gaagcagcat tacgaggaga aaaaacacca acgaagacgt cgaacgatat tgaggatgag 1860gatgaggatg ataacatcaa aaatgaagat tctggtcctg ttgtttggga ggaattgaaa 1920gatgaaagta tgatacaagc gattgtatgg agatgtatga aagatatata tgaattagct 1980gacgaaaata agacagagat attagaaaag agaaaggaag caaaaaagga aagaaaacgt 2040ttacatgaat atgatcatga tgatgaatca gcaggcccag cagcagcagc aaccgcacgg 2100aaaaaacaag cagtagagga agatccatct ggtcgtaaga ataaaagttg tgatttttgt 2160cgtgataaaa aactgaaatg caatcgtaca agcccttgtg aaaactgtac tacaaagtac 2220atgaaggatc acaatttgac tagtgaggaa gtcgaagaat ccaaaattgc caatagtatt 2280aatgcggtag cggtggtcgc aaaagttgaa gaagcaaaga aactggaatc aatgccagaa 2340acgaagcgtc ctcgtacgag aagtatattc cattttttag tatttttaat actagaatgt 2400tccgtgccga tggagtaa 2418843120DNANannochloropsis oceanicamisc_featureEncodes ZnCys polypeptide of SEQ ID NO17 84atgacgaccc tccttggaca gcccccctcc tcgttggggg cgatggggag tgcattttac 60gatgaggacg ctcagagcgt cgtggccctc ggccaacacg ctgcaggcag tggcacggag 120gacgagatgg atacagacca tttcgatgag ttggaccgca tcatcttcga catgccgtac 180gtgtcagagc aggatccctt gagcagctgt agcgtcggag ggcagtcgca agggcaaacc 240aacgggcagg gccatgggca ccaagagcgg ggggcgtcac agcacggggg cgcgggtctc 300ttgatgccta acccccacaa tggccacatc cacggtgatg ggggtcacca cataaatcac 360aacaaccatg gaagcgtccg agggggaggg atggactggc acgcgaagga ggaggacgcc 420tcatatcata ctgcggtgga ctccagctgt cacactgacc ggagctacca tcgtgtggat 480gcctcggggc attccatgat cgacgcctcc agccatagca tgatggatgc atcggggcac 540gagtccctga ttgattcgag tgggcattac gacgacttcg ccgcgcacaa gggcgacccc 600agatatatgg agcacagctg cgaggcctgc aagcgatcca agaaacgctg taaccgtcgc 660aacccctgcc aaatatgcac ctcccgaggc atcaagtgcg tgccccaaat ccgcggaccc 720ggtcgtcctc caggcagtaa gagcagcaga ggctcctcct cctcttcctc cctcactctg 780ggcagttccc gccatggtgg ctcccgggga gatgtgcgct cttccctcaa cagcacccag 840catagcacca acagcagtgc caccacctcc gccgcatctt ccactgcctc ctccctctct 900cgctctttgt ctggtaacgg gttgttacag caagagcagg acttggtggt agtggctgct 960gctgcttcta cgagacaatc ccctccaagg gacccttggc actgtcgatt cttcttcgag 1020gcggcgcggc attgcaagga ggcgtttctg aaggcctggc atgacaatga gttggatacg 1080tccaagtgta ttatgctcag gaacctctgg accaagacgt cctccatcct cgcctcaggg 1140gtcgacatga ccttcggtat ctgtgaccag ctccaagaag tggttgggcc cgccccaacg 1200ggctcgggcc cgattgcctg tagtcctgcg acgagaagca agagccaggc ggcgcaacaa 1260gcccagctct tgtcgcaccc ggggtcgaag gagggaatgg gtccttggaa tctgcccgat 1320gatttgagga agatggatga tggagtgtcg atgttgtgtg ggttcatgtt tatccaggac 1380gagttgttcg tgtttacaga cgagaggttc gccgctacat tcatgacacg cgaggaggtg 1440gaggggaagg tggagagctt cgcagtgttg ccgatactgt tgttggcgga gatattccac 1500cctgacgacc tacctgatgt ttatgcagca attggcgcgc attggtttag gcggcggccg 1560agctctggtg taggggtggg gggaagtaat gggagtatca gcagcatgaa cagcagtagc 1620ggtagtacga gcagtaggga ctcggcaagc ccggggccag tgtctcggga ggtacctgag 1680gcggcttgga tttgcaaatg cattgataag cggaatacgg agataacggc cttggtgcgg 1740tttcggtcat ttgcggcacc gacggagggt tacgcgggtg cggctatgtt atcgatcttg 1800ccgttgacaa gaagcaagta tattgcggat ccggatgtac agacgaacat gaggtcgggg 1860gtgtcgtcga ggcaccactt gagggataca tttggggcat tgcctactgc tttgccggag 1920cacgatgacg aagacgatga cgacgagcat caccatctgg tgttagaaag gagaggggaa 1980agagtggggg cgtcggggca tggccaggat ttgttaaatg aggaggagga cgatgaaatt 2040tttttggatg cacacggtga cgacgctatg ttccggccct tgcggcgggg gatgacggtg 2100ttgtcggctg agacgagcgg tcctcaaccg gtgcctcttt ccaagcatgc ctctgaccct 2160ctacctcatc acaacgagca ccacttccac agccagcccc agcacacctc ttctcatttg 2220tctagtttga gtagcatggc gtcgcatcag acaggcgtgt cgtggggggg tggaaggatt 2280tctgaatgcc tggggaacca aaaccgcagc gcctcgcaat tctacaacac agtgcagcat 2340caagagcggc ctaagcggga gcaagaggag ccgcaccagc agcaccgtga agaacaacag 2400caacatcgcc ttccaggcaa caatagcttg gacgggagca gcagccacgg aggcgccatg 2460gaccaagacc tccctactgt tcagctgacc caggcgcagc tcttcctctt gcaggggggc 2520actggcagtg gcatcggttt atttaaagat atacagcagg agcagcagca catgtgcaac 2580cagatttcgc cagacggcgt gacagcagcg gaggagagcg cagagagagt cgctactgag 2640ctgtacggtt cgagtcccag tccggagccg cacctccttg gccattcccg tcacagccca 2700acgcaacgtg cacagcagca gcagcagcag cagaaaaggc aacaagaacg ccagcaagaa 2760gatcagcaac aagaacaagg acatcaacag cagcaacagc agcaacagca gcaggggatg 2820gtgctgcccc tgccacacct gcctgggatg gtgccgtcgc ttgtccgcac cgtgagcagc 2880agcgccatgt tgggtgcccg ccccacaacc atatcccaag gaaaggacga agggggacgt 2940ggaggggcgt tgagtcacag caatagcagc accgacctgg atatgtcttg tcatggcccg 3000gcggatccga atgggtatgg tggattgcat tggacgccgg cgccattggc ttcttttttg 3060ggggtttcct cttggggatc aaggcgtggc tcaaggaagg aggagagatc taaagattag 3120858315DNAArtificial SequenceSyntheticmisc_featureKnockdown construct 85gcggccgccg tatggtcgac ggttgctcgg atgggggggg cggggagcga tggagggagg 60aagatcaggt aaggtctcga cagactagag aagcacgagt gcaggtataa gaaacagcaa 120aaaaaagtaa tgggcccagg cctggagagg gtatttgtct tgtttttctt tggccaggaa 180cttgttctcc tttcttcgtt tctaggaccc cgatccccgc tcgcatttct ctcttcctca 240gccgaagcgc agcggtaaag catccatttt atcccaccga aagggcgctc ccagccttcg 300tcgagcggaa ccggggttac agtgcctcac tcctttgcac gcggtcgggt gctcggccta 360cggttgcccg agtccgcaag cacctcaaca cagccgtctg tccacaccgc agccgaccgg 420cgtgcgattt gggtccgacc caccgtccca gccccgctgc ggactatcgc gtcgcagcgg 480ccctgcgccc acgcggcgtc gtcgaagttg ccgtcgacga gagactggta aagctgatcg 540agtccgatac gcaacatata ggcgcggagt cgtggggagc cggccagctc cgggtgcctc 600cgttcaaagt agcgtgtctg ctgctccatg cacgccaacc agggacgcca gaagaatatg 660ttcgccactt cgtattggct atcaccaaac atcgcttcgg accagtcgat gacagcagta 720atccgaccat tgtctgtaag tacgttattg ctgccgaaat ccgcgtgcac caggtgcctg 780acctcagggc aatcctcggc ccacaacatg agttcgtcca gtgcttgggc cacggatgca 840gacacggtgt catccatgac tgtctgccaa tgatagacgt gaggatcggc aatggcgcag 900atgaagtctc gccaggtcgt gtactgcccg atgccctggg gcccaaaagg tccaaagccg 960gacgtctgag acagatctgc ggcagcgatc gcgtccatgg cctcggccac gggttgcaaa 1020acggcaggca attcagtttc gggcagatct tgcaacgtca ctccctgggc tcggcgcgag 1080atgcagtacg tgagagattc gctaaactcc ccaatgtcca gtacctctgg tatggggaga 1140gcggcggagg cgaaatgacg gtagacatac cgatccttgt agaacccgtc cgcacaacta 1200ttaaccctca acacgtatcc ccgaccccct acgtcaaacg agaacgccct actctcctct 1260ccctcgctca gttgcatcaa gtcggagaca gagtcgaact tctcaataag gaatttctcc 1320acggacgtag cggtcagttc cggtttcttc cccatcgagc tcggtacccg gggatccatg 1380attgttgtat tatgtaccta tgtttgtgat gagacaataa atatgagaag agaacgttgc 1440ggccactttt ttctccttcc ttcgcgtgct catgttggtg gtttgggagg cagaagatgc 1500atggagcgcc acacattcgg taggacgaaa cagcctcccc cacaaaggga ccatgggtag 1560ctaggatgac gcacaagcga gttcccgctc tcgaagggaa acccaggcat ttccttcctc 1620ttttcaagcc acttgttcac gtgtcaacac aattttggac taaaatgccc ctcggaactc 1680ggcaggcctc cctctgctcc gttgtcctgg tcgccgagaa cgcgagaccg tgccgcatgc 1740catcgatctg ctcgtctgta ctactaatcg tgtgcgtgtt cgtgcttgtt tcgcacgaaa 1800ttgtcctcgt tcggccctca caacggtgga aatcggtgct agaataaagt gaggtggctt 1860atttcaatgg cggccgtcat catgcgggat caactgaagt acggcgggtt ctcgagattt 1920catcgtgctc gtccagagca ggtgttttgc ctgcagctct tcatgtttag gggtcatgat 1980ttcatctgat atgccgtaag aaaaccaata ttcacttctc aattttccat ggaaaggtga 2040aggcctaggt tgtgtgcgag gcaacgactg gggagggatc gcaacattct tgctaacctc 2100ccctctatct tggccgctgt gaatcggcat atttaccggg ctgaattgag aaagtgtttt 2160gagggaatta aaaggtggct gtcttgcaag cttggcttca gtgcctgctt aattcgaacc 2220gatccagctt gtgatgaggc cttcctaagc ctggtagtca gaagcgacat ggcgctataa 2280atttcgtctc agttggagag tagaaaagca tgattcgaac acggttttca actgccaaag 2340atatctccat tgtttccttc aatctgtaca cctgcacggt gcaccagttg gtacggcata 2400ttatggttta aagttgaaaa tgctaacagt gaagtgatat ccttttttaa tggagtgttg 2460aggtgaagtc tagcatcgta ggggaaaaca ggattctgtg tcttccattc tactccttga 2520taaagcgaag aaatccgaca aaaccaaaga gattgttcaa gtttaagatt tgtaagcgta 2580caactatgaa cttcttctct ttgtaggcct gagtggtcgt atgcatacga ttcatgaagt 2640gaatcagtat cgctggattt tgcttaggag taaagcacaa ctaagaaaat atgctgcctg 2700gcaggcatcc tgagacatga ggcaagcgac gtagcaattg aatcctaatt taagccaggg 2760catctgtatg actctgttag ttaattgatg aaccaatgag ctttaaaaaa aaatcgttgc 2820gcgtaatgta gttttaattc tccgccttga ggtgcggggc catttcggac aaggttcttt 2880ggacggagat ggcagcatgt gtcccttctc caaattggtc cgtgtggtag ttgagatgct 2940gccttaaaat tctgctcggt catcctgcct tcgcattcac tcctttcgag ctgtcgggtt 3000cctcacgagg cctccgggag cggattgcgc agaaaggcga cccggagaca cagagaccat 3060acaccgacta aattgcactg gacgatacgg catggcgacg acgatggcca agcattgcta 3120cgtgattatt cgccttgtca ttcagggaga aatgatgaca tgtgtgggac ggtctttata 3180tgggaagagg gcatgaaaat aacatggcct ggcgggatgg agcgtcacac ctgtgtatgc 3240gttcgatcca caagcaactc accatttgcg tcggggcctg tctccaatct gctttaggct 3300acttttctct aatttagcct attctataca gacagagaca cacagggatc gtttaaacga 3360tcagccacga cggctctcgc atgcacaacg atggcatgga ttggcgcgcg aaggatgagg 3420actgctcgta ccacaccgcc gtggacgcca gctgccacat cgacagtagc taccaccatg 3480ttgatgcctc aggccactcc atggtcgacg cctcgggtca cagcacgata gacgcgtcgg 3540gccacgactc cctcatcgac tcaagcggcc attacgacga ctatctggcg cacaaggggg 3600acgcccgcta catggagcac agttgtgaag cctgcaagcg ctcgaagaaa cgatgcaacc 3660gccgcaaccc ctgccagatc tgcacctcca ggggcatcaa gtgtgtgccg caaatccggg 3720gtcctgggcg ccccccgggc agtaaaagca gtcggggctg cacctccttg tcactgagca 3780gctcacggca tggaagctcc aggggtgaca tacgcgccgc gaacggaagc gggcagagcc 3840acaacagcag tgccacgaac cgccccgact gcttttactg cccggggggc gcccaggacc 3900ccggatttgc ggcacacact tgatgcccct ggaggtgcag atctggcagg ggttgcggcg 3960gttgcatcgt ttcttcgagc gcttgcaggc ttcacaactg tgctccatgt agcgggcgtc 4020ccccttgtgc gccagatagt cgtcgtaatg gccgcttgag tcgatgaggg agtcgtggcc 4080cgacgcgtct atcgtgctgt gacccgaggc gtcgaccatg gagtggcctg aggcatcaac 4140atggtggtag ctactgtcga tgtggcagct ggcgtccacg gcggtgtggt acgagcagtc 4200ctcatccttc gcgcgccaat ccatgccatc gttgtgcatg cgagagccgt cgtggctgat 4260cgtttaaacg agtcaagggg gaaggtgcat agtgtgcaac aacagcatta acgtcaaaga 4320aaactgcacg ttcaagcccg cgtgaacctg ccggtcttct gatcgcctac atatagcaga 4380tactagttgt actttttttt ccaaagggaa cattcatgta tcaatttgaa ataaacatct 4440atcctccaga tcaccagggc cagtgaggcc ggcataaagg acggcaagga aagaaaagaa 4500agaaagaaaa ggacacttat agcatagttt gaagttataa gtagtcgcaa tctgtgtgca 4560gccgacagat gctttttttt tccgtttggc aggaggtgta gggatgtcga agaccagtcc 4620agctagtatc tatcctacaa gtcaatcatg ctgcgacaaa aatttctcgc acgaggcctc 4680tcgataaaca aaactttaaa agcacacttc attgtcatgc agagtaataa ctcttccgcg 4740tcgatcaatt tatcaatctc tatcatttcc gcccctttcc ttgcatagag caagaaaagc 4800gacccggatg aggataacat gtcctgcgcc agtagtgtgg cattgcctgt ctctcattta 4860cacgtactga aagcataatg cacgcgcata ccaatatttt tcgtgtacgg agatgaagag 4920acgcgacacg taagatcacg agaaggcgag cacggttgcc aatggcagac gcgctagtct 4980ccattatcgc gttgttcggt agcttgctgc atgtcttcag tggcactata tccactctgc 5040ctcgtcttct acacgagggc cacatcggtg caagttcgaa aaatcatatc tcaatcttca 5100gatcctttcc agaaacggtg ctcaggcggg aaagtgaagg ttttctactc tagtggctac 5160cccaattctc tccgactgtc gcagacggtc cttcgttgcg cacgcaccgc gcactacctc 5220tgaaattcga caaccgaagt tcaattttac atctaacttc tttcccattc tctcaccaaa 5280agcctagctt acatgttgga gagcgacgag agcggcctgc ccgccatgga gatcgagtgc 5340cgcatcaccg gcaccctgaa cggcgtggag ttcgagctgg tgggcggcgg agagggcacc 5400cccgagcagg gccgcatgac caacaagatg aagagcacca aaggcgccct gaccttcagc 5460ccctacctgc tgagccacgt gatgggctac ggcttctacc acttcggcac ctaccccagc 5520ggctacgaga accccttcct gcacgccatc aacaacggcg gctacaccaa cacccgcatc 5580gagaagtacg aggacggcgg cgtgctgcac gtgagcttca gctaccgcta cgaggccggc 5640cgcgtgatcg gcgacttcaa ggtgatgggc accggcttcc ccgaggacag cgtgatcttc 5700accgacaaga tcatccgcag caacgccacc gtggagcacc tgcaccccat gggcgataac 5760gatctggatg gcagcttcac ccgcaccttc agcctgcgcg acggcggcta ctacagctcc 5820gtggtggaca gccacatgca cttcaagagc gccatccacc ccagcatcct gcagaacggg 5880ggccccatgt tcgccttccg ccgcgtggag gaggatcaca gcaacaccga gctgggcatc 5940gtggagtacc agcacgcctt caagaccccg gatgcagatg ccggtgaaga ataagggtgg 6000gaaggagtcg gggagggtcc tggcagagcg gcgtcctcat gatgtgttgg agacctggag 6060agtcgagagc ttcctcgtca cctgattgtc atgtgtgtat aggttaaggg ggcccactca 6120aagccataaa gacgaacaca aacactaatc tcaacaaagt ctactagcat gccgtctgtc 6180catctttatt tcctggcgcg cctatgcttg taaaccgttt tgtgaaaaaa tttttaaaat 6240aaaaaagggg acctctaggg tccccaatta attagtaata taatctatta aaggtcattc 6300aaaaggtcat ccagacgaaa gggcctcgtg atacgcctat ttttataggt taatgtcatg 6360ataataatgg tttcttagac gtcaggtggc acttttcggg gaaatgtgcg cggaacccct 6420atttgtttat ttttctaaat acattcaaat atgtatccgc tcatgagaca ataaccctga 6480taaatgcttc aataatattg aaaaaggaag agtatgagta ttcaacattt ccgtgtcgcc 6540cttattccct tttttgcggc attttgcctt cctgtttttg ctcacccaga aacgctggtg 6600aaagtaaaag atgctgaaga tcagttgggt gcacgagtgg gttacatcga actggatctc 6660aacagcggta agatccttga gagttttcgc cccgaagaac gttttccaat gatgagcact 6720tttaaagttc tgctatgtgg cgcggtatta tcccgtattg acgccgggca agagcaactc 6780ggtcgccgca tacactattc tcagaatgac ttggttgagt actcaccagt cacagaaaag 6840catcttacgg atggcatgac agtaagagaa ttatgcagtg ctgccataac catgagtgat 6900aacactgcgg ccaacttact tctgacaacg atcggaggac cgaaggagct aaccgctttt 6960ttgcacaaca tgggggatca tgtaactcgc cttgatcgtt gggaaccgga gctgaatgaa 7020gccataccaa acgacgagcg tgacaccacg atgcctgtag caatggcaac aacgttgcgc 7080aaactattaa ctggcgaact acttactcta gcttcccggc aacaattaat agactggatg 7140gaggcggata aagttgcagg accacttctg cgctcggccc ttccggctgg ctggtttatt 7200gctgataaat ctggagccgg tgagcgtggg tctcgcggta tcattgcagc actggggcca 7260gatggtaagc cctcccgtat cgtagttatc tacacgacgg ggagtcaggc aactatggat 7320gaacgaaata gacagatcgc tgagataggt gcctcactga ttaagcattg gtaactgtca 7380gaccaagttt actcatatat actttagatt gatttaaaac ttcattttta atttaaaagg 7440atctaggtga agatcctttt tgataatctc atgaccaaaa tcccttaacg tgagttttcg 7500ttccactgag cgtcagaccc cgtagaaaag atcaaaggat cttcttgaga tccttttttt 7560ctgcgcgtaa tctgctgctt gcaaacaaaa aaaccaccgc taccagcggt ggtttgtttg 7620ccggatcaag agctaccaac tctttttccg aaggtaactg gcttcagcag agcgcagata 7680ccaaatactg tccttctagt gtagccgtag ttaggccacc acttcaagaa ctctgtagca 7740ccgcctacat acctcgctct gctaatcctg ttaccagtgg ctgctgccag tggcgataag 7800tcgtgtctta ccgggttgga ctcaagacga tagttaccgg ataaggcgca gcggtcgggc 7860tgaacggggg gttcgtgcac acagcccagc ttggagcgaa cgacctacac cgaactgaga 7920tacctacagc gtgagctatg agaaagcgcc acgcttcccg aagggagaaa ggcggacagg 7980tatccggtaa gcggcagggt cggaacagga gagcgcacga gggagcttcc agggggaaac 8040gcctggtatc tttatagtcc tgtcgggttt cgccacctct gacttgagcg tcgatttttg 8100tgatgctcgt caggggggcg gagcctatgg aaaaacgcca gcaacgcggc ctttttacgg 8160ttcctggcct tttgctggcc ttttgctcac atgttctttc ctgcgttatc ccctgattct 8220gtggataacc gtattaccgc ctttgagtga gctgataccg ctcgccgcag ccgaacgacc 8280gagcgcagcg agtcagtgag cgaggaagcg gaaga 831586111DNANannochloropsis gaditanamisc_featureSNARE terminator (inverted orientation) 86tatgcttgta aaccgttttg tgaaaaaatt tttaaaataa aaaaggggac ctctagggtc 60cccaattaat tagtaatata atctattaaa ggtcattcaa aaggtcatcc a 1118717DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding CCT domain-containing protein 87ttccgaagta ctggttc 178818DNAArtificial SequenceSyntheticmisc_featureTarget sequence for guide RNA targeting gene encoding Zn(2)-C6 fungal-type DNA-binding domain protein (ZnCys-2845) 88agtaggccat tcccggag 188918DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding Zinc finger, TAZ-type protein 89tgtggcagac gccgacgg 189020DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding RpoD family RNA polymerase sigma factor SigA protein 90gtactgcctg acaaactagg 209117DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding Fungal Zn(2)-Cys(6) binuclear cluster domain-containing protein 91tgagcagtcg tacgaaa 179218DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding Zinc finger, CCCH-type-containing protein 92cgaagtcaac catggggc 189318DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding Winged helix-turn-helix transcription repressor DNA-binding protein 93tcctgtgact tgacggtg 189420DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding SANT/Myb domain protein 94ggcaatacaa gcagtggaag 209518DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding CCT motif family protein 95ctgatctcga gatggctg 189618DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding Fungal specific transcription factor domain-containing protein 96gtgaagattg gtcccact 189720DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding Myb-like DNA-binding shaqkyf class family protein 97ggacgctacg accgtgcggg 209818DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding Nucleic acid-binding protein 98ctgcaccaga cacaaatt

189920DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding Activating transcription factor 6 99gggaaatatt aagactggag 2010018DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding Fungal Zn(2)-Cys(6) binuclear cluster domain-containing protein 100tcacgggaga tgtcctgt 1810118DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding Zn(2)-C6 fungal-type transcription factor 101aggactctcc tcagctga 1810218DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding Winged helix-turn-helix transcription repressor 102tcttcatctg cgacaacg 1810318DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding Fungal Zn(2)-Cys(6) binuclear cluster domain-containing protein 103acgtccgaat ataccgaa 1810419DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding Myb-like dna-binding domain-containing protein 104gtagaacaag cgttagacc 1910519DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding Fungal Zn(2)-Cys(6) binuclear cluster domain-containing protein 105cgccaccctc gcacgtgtc 1910620DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA targeting gene encoding Aureochrome1-like protein 106ggcaccatcc ccaccggttt 2010720DNANannochloropsis gaditanamisc_featureSense Primer from gene encoding CCT domain- containing protein 107aagtgcgcaa gacgctccag 2010821DNANannochloropsis gaditanamisc_featureAntisense Primer from gene encoding CCT domain-containing protein 108gatcccaaag gtcatatccg t 2110920DNAArtificial SequenceSyntheticmisc_featurePrimer 109acctccttgt cactgagcag 2011021DNAArtificial SequenceSyntheticmisc_featurePrimer 110gatcccaaag gtcatatccg t 2111121DNAArtificial SequenceSyntheticmisc_featurePrimer 111actctgtgct accaattgct g 2111220DNAArtificial SequenceSyntheticmisc_featurePrimer 112cgtcagcaaa tcttgcacca 2011320DNAArtificial SequenceSyntheticmisc_featurePrimer 113gagatgctgt ccgagacacg 2011420DNAArtificial SequenceSyntheticmisc_featurePrimer 114gtatctcgga cagggcactg 2011521DNAArtificial SequenceSyntheticmisc_featurePrimer 115atccatgtaa agacgatgtg c 2111621DNAArtificial SequenceSyntheticmisc_featurePrimer 116tgatatcaca tgctcaaggt c 2111724DNAArtificial SequenceSyntheticmisc_featurePrimer 117agatgaggat caagcaccga gcca 2411821DNAArtificial SequenceSyntheticmisc_featurePrimer 118ggaagaaata gtagttgcgt g 2111921DNAArtificial SequenceSyntheticmisc_featurePrimer 119aggcgctctg attgctgtgg c 2112021DNAArtificial SequenceSyntheticmisc_featurePrimer 120tcttccacgt cggatggcca g 2112123DNAArtificial SequenceSynthetic 121attgtggagg gtaacaaact acg 2312222DNAArtificial SequenceSyntheticmisc_featurePrimer 122tgagtcccgt ggagaggagt cg 2212320DNAArtificial SequenceSyntheticmisc_featurePrimer 123aggttccaat ggaggccgca 2012422DNAArtificial SequenceSyntheticmisc_featurePrimer 124cactttcctt cgtacgctca gc 2212520DNAArtificial SequenceSyntheticmisc_featurePrimer 125ctcgaggtag gtggtgaaag 2012619DNAArtificial SequenceSyntheticmisc_featurePrimer 126gtgattcgca tggacgaac 1912719DNAArtificial SequenceSyntheticmisc_featurePrimer 127atgggtacgg acttgttcg 1912820DNAArtificial SequenceSyntheticmisc_featurePrimer 128acagcgatac ggacagtgac 2012920DNAArtificial SequenceSyntheticmisc_featurePrimer 129gacgttgcat gagaaaggag 2013020DNAArtificial SequenceSyntheticmisc_featurePrimer 130gatgcacagg tgcttgttag 2013120DNAArtificial SequenceSyntheticmisc_featurePrimer 131tgcaaagcct atttccgacg 2013220DNAArtificial SequenceSyntheticmisc_featurePrimer 132ctcattcgtg aggtgaccat 2013320DNAArtificial SequenceSyntheticmisc_featurePrimer 133gagcaaactg acattgatac 2013418DNAArtificial SequenceSyntheticmisc_featurePrimer 134gtaccacaca tacacatg 1813520DNAArtificial SequenceSyntheticmisc_featurePrimer 135cacatccacc atcattccac 2013620DNAArtificial SequenceSyntheticmisc_featurePrimer 136gagtgttccc agtgagccag 2013720DNAArtificial SequenceSyntheticmisc_featurePrimer 137ctgacaagaa gatggacatg 2013820DNAArtificial SequenceSyntheticmisc_featurePrimer 138ctttagttat acgtctgaag 2013919DNAArtificial SequenceSyntheticmisc_featurePrimer 139gagaggatag ttctcagag 1914018DNAArtificial SequenceSyntheticmisc_featurePrimer 140gtcccacaat ctattgtg 1814120DNAArtificial SequenceSyntheticmisc_featurePrimer 141atgagtactt gcgcgctttg 2014220DNAArtificial SequenceSyntheticmisc_featurePrimer 142gcatgcctcc gtcacagagt 2014320DNAArtificial SequenceSyntheticmisc_featurePrimer 143atccattgag catgccgacg 2014420DNAArtificial SequenceSyntheticmisc_featurePrimer 144gcaacatgtt aatgcatcgt 2014520DNAArtificial SequenceSyntheticmisc_featurePrimer 145tcgtcctcga actcttcctc 2014620DNAArtificial SequenceSyntheticmisc_featurePrimer 146cgggaacaac caaggtgtaa 2014720DNAArtificial SequenceSyntheticmisc_featurePrimer 147tagcagagca ggctcatcac 2014820DNAArtificial SequenceSyntheticmisc_featurePrimer 148gaatatgtgg tctagctcgt 2014920DNAArtificial SequenceSyntheticmisc_featurePrimer 149atggctccac cctctgtaag 2015020DNANannochloropsis gaditanamisc_featurePrimer 150ctgactacag ctagcacgat 2015125DNANannochloropsis gaditanamisc_featurePrimer 151aagactttgg aggatgtctg agtgg 2515223DNAArtificial SequenceSyntheticmisc_featurePrimer 152acgaagctac atccagtgca agg 2315321DNANannochloropsis gaditanamisc_featureNAR1 gene, sense Primer 153gccaacctgc cagtaaaatt c 2115420DNANannochloropsis gaditanamisc_featureNAR1 gene, antisense Primer 154agagcgggat tctgttcttg 2015521DNANannochloropsis gaditanamisc_featureAmt2 gene, sense Primer 155agaacgtggg taagatgcaa c 2115619DNANannochloropsis gaditanamisc_featureAmt2 gene, antisense Primer 156accagccaaa ccagagaag 1915722DNANannochloropsis gaditanamisc_featureGS2 gene, sense Primer 157ggcataccta ttcatccgct ag 2215821DNANannochloropsis gaditanamisc_featureGS2 gene, antisense Primer 158caaatgacca agcaccaact c 2115920DNANannochloropsis gaditanamisc_featureNAR2 gene, sense Primer 159gcgaggcatc ttgtgaattg 2016020DNANannochloropsis gaditanamisc_featureNAR2 gene, antisense Primer 160acggagtgtt caaatcccag 2016121DNANannochloropsis gaditanamisc_featureGS1 gene, sense Primer 161catggactca ttctcctacg g 2116220DNANannochloropsis gaditanamisc_featureGS1 gene, antisense Primer 162atcctcgaaa tatccgcacc 2016321DNANannochloropsis gaditanamisc_featureGOGAT1 gene, sense primer 163tggatgcaaa cgagatgcta g 2116420DNANannochloropsis gaditanamisc_featureGOGAT1 gene, antisense primer 164aggaaagcgg gaatagtgtg 2016520DNANannochloropsis gaditanamisc_featureGDH gene, sense primer 165gggactcgtt ggaaggtaag 2016621DNANannochloropsis gaditanamisc_featureGDH gene, antisense primer 166catttccaca agtttctccg c 2116720DNANannochloropsis gaditanamisc_featureGOGAT2 gene, sense primer 167aagggaatgt cttggaaccg 2016820DNANannochloropsis gaditanamisc_featureGOGAT2 gene, antisense primer 168agtgggtaga cagtggagag 2016920DNANannochloropsis gaditanamisc_featureNRT2 gene, sense primer 169agtgctatgg agttttgcgg 2017020DNANannochloropsis gaditanamisc_featureNRT2 gene, antisense primer 170agtgggtaga cagtggagag 2017120DNANannochloropsis gaditanamisc_featureNiR gene, sense primer 171gccgatcctt tcttgcaaac 2017220DNANannochloropsis gaditanamisc_featureNiR gene, antisense primer 172agcgttcaat caggtccaag 2017321DNANannochloropsis gaditanamisc_featureNR gene, sense primer 173gctatattgg agaatccggc g 2117422DNANannochloropsis gaditanamisc_featureNR gene, antisense primer 174gggaacgtca acagtgatag tg 2217519DNANannochloropsis gaditanamisc_featureAmt1 gene, sense primer 175ccttcggtgc ctatttcgg 1917621DNANannochloropsis gaditanamisc_featureAmt1 gene, antisense primer 176catgtcgctg gtataggatg c 2117720DNANannochloropsis gaditanamisc_featureUreT gene, sense primer 177atggcagtag aaatggaccc 2017821DNANannochloropsis gaditanamisc_featureUreT gene, sense primer 178agtaagagaa cgaaaagggc g 2117921DNANannochloropsis gaditanamisc_featureSense primer, gene of unkown function 179ctctcctatt gctttccctc g 2118022DNANannochloropsis gaditanamisc_featureAntisense primer, gene of unkown function 180ctaccaacac ctctacactt cc 2218114PRTNannochloropsis gaditanamisc_featureAcetyl-CoA Carboxylase peptide 1 181Phe Lys Phe Ala Asp Thr Pro Asp Glu Glu Ser Pro Leu Arg1 5 1018214PRTNannochloropsis gaditanamisc_featureAcetyl-CoA Carboxylase peptide 2 182Ala Glu Asn Phe Lys Glu Asp Pro Leu Arg Arg Asp Met Arg1 5 1018314PRTNannochloropsis gaditanamisc_feature3-Hydroxyacyl ACP Dehydrase peptide 1 183Thr Ala Asn Glu Pro Gln Phe Thr Gly His Phe Pro Glu Arg1 5 1018413PRTNannochloropsis gaditanamisc_feature3-Hydroxyacyl ACP Dehydrase peptide 2 184Ile Asp Gly Val Phe Arg Lys Pro Val Val Pro Gly Asp1 5 1018514PRTNannochloropsis gaditanamisc_featureEnoyl-ACP Reductase peptide 1 185Pro Glu Asp Val Pro Glu Ala Val Lys Thr Asn Lys Arg Tyr1 5 1018614PRTNannochloropsis gaditanamisc_featureEnoyl-ACP Reductase peptide 2 186Ala Ile Gly Gly Gly Glu Lys Gly Lys Lys Thr Phe Ile Glu1 5 1018714PRTNannochloropsis gaditanamisc_featureBeta-Ketoacyl-ACP Reductase peptide 1 187Val Ala Ile Lys Ala Asp Met Ser Lys Pro Glu Glu Val Glu1 5 1018814PRTNannochloropsis gaditanamisc_featureBeta-Ketoacyl-ACP Reductase peptide 2 188Ser Asp Met Thr Glu Lys Leu Asp Leu Asp Gly Ile Lys Lys1 5 1018914PRTNannochloropsis gaditanamisc_featureBeta-Ketoacyl-ACP Synthase 1 peptide 1 189Tyr Met Arg Gly Ser Lys Gly Gln Ile Tyr Met Lys Glu Lys1 5 1019014PRTNannochloropsis gaditanamisc_featureBeta-Ketoacyl-ACP Synthase 1 peptide 2 190Asp Ala Lys Pro Tyr Phe Lys Asp Arg Lys Ser Ala Val Arg1 5 1019114PRTNannochloropsis gaditanamisc_featureBeta-Ketoacyl-ACP Synthase 3 peptide 1 191Met Gly Lys Arg Ser Thr Ala Ser Ser Thr Gly Leu Ala Tyr1 5 1019214PRTNannochloropsis gaditanamisc_featureBeta-Ketoacyl-ACP Synthase 3 peptide 2 192Pro Pro Ser Ile Arg Glu Val Thr Pro Tyr Lys Gly Lys Tyr1 5 1019320DNANannochloropsis gaditanamisc_featureTarget sequence for guide RNA, nitrate reductase gene 193gggttggatg gaaaaaggca 20

Claims

1. A classically-derived or genetically engineered mutant algal or heterokont microorganism that produces at least 50% more fatty acid methyl ester-derivatizable lipids (FAME lipids) than a control microorganism and at least 70% of the amount of biomass produced by the control microorganism when the mutant microorganism and control microorganism are cultured under identical conditions under which the control microorganism is producing biomass, wherein the mutant microorganism has attenuated expression of a gene encoding a polypeptide comprising an amino acid sequence having at least 80% identity to an amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO: 14, SEQ ID NO:15, and SEQ ID NO: 16.

2. A mutant algal or heterokont microorganism according to claim 1, wherein the mutant microorganism and control microorganism are cultured under identical conditions which are nitrogen replete with respect to the control microorganism.

3. A mutant algal or heterokont microorganism according to claim 1, wherein the control microorganism is a wild type microorganism.

4. A mutant algal or heterokont microorganism according to claim 1, wherein the mutant microorganism produces at least 50% more FAME lipids than a control microorganism while accumulating at least 70% the amount of biomass accumulated by the control microorganism over a culture period of at least five days.

5. A mutant algal or heterokont microorganism according to claim 4, wherein the mutant microorganism produces at least 50% more FAME lipids than a control microorganism while accumulating at least 70% the amount of biomass accumulated by the control microorganism over a culture period of at least ten days.

6. A mutant algal or heterokont microorganism according to claim 4, wherein the mutant microorganism accumulates at least 80% the amount of biomass accumulated by the control microorganism.

7. A mutant algal or heterokont microorganism according to claim 6, wherein the mutant microorganism accumulates at least 90% the amount of biomass accumulated by the control microorganism.

8. A mutant algal or heterokont microorganism according to claim 7, wherein the mutant microorganism accumulates at least 95% the amount of biomass accumulated by the control microorganism.

9. A mutant algal or heterokont microorganism according to claim 4, wherein the mutant microorganism produces at least 75% more FAME lipids than the wild type microorgamsm.

10. A mutant algal or heterokont microorganism according to claim 9, wherein the mutant microorganism produces at least 100% more FAME lipids than the control microorganism.

11. A mutant algal or heterokont microorganism according to claim 1, wherein the mutant microorganism exhibits a F AME/TOC ratio at least 30% higher than the FAME/TOC ratio of the control microorganism.

12. A mutant algal or heterokont microorganism according to claim 1, wherein the polypeptide further comprises a PAS3 domain.

13. A mutant algal or heterokont microorganism according to claim 2, wherein the P AS3 domain has at least 65% identity to a sequence selected from the group consisting of SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, and SEQ ID NO:25.

14. A mutant heterokont microorganism according to claim 1, wherein the heterokont microorganism is a Labyrinthulomycite species of Labryinthula, Labryinthuloides, Thraustochytrium, Schizochytrium, Aplanochytrium, Aurantiochytrium, Oblongichytrium, Japonochytrium, Diplophrys, or Ulkenia.

15. A mutant algal microorganism according to claim 1, wherein the algal microorganism is an algal species of Achnanthes, Amphiprora, Amphora, Ankistrodesmus, Asteromonas, Boekelovia, Bolidomonas, Borodinella, Botrydium, Botryococcus, Bracteococcus, Chaetoceros, Carteria, Chlamydomonas, Chlorococcum, Chlorogonium, Chlorella, Chroomonas, Chrysosphaera, Cricosphaera, Crypthecodinium, Cryptomonas, Cyclotella, Desmodesmus, Dunaliella, Elipsoidon, Emiliania, Eremosphaera, Ernodesmius, Euglena, Eustigmatos, Franceia, Fragilaria, Fragilaropsis, Gloeothamnion, Haematococcus, Hantzschia, Heterosigma, Hymenomonas, Isochrysis, Lepocinclis, Micractinium, Monodus, Monoraphidium, Nannochloris, Nannochloropsis, Navicula, Neochloris, Nephrochloris, Nephroselmis, Nitzschia, Ochromonas, Oedogonium, Oocystis, Ostreococcus, Parachlorella, Parietochloris, Pascheria, Pavlova, Pelagomonas, Phceodactylum, Phagus, Picochlorum, Platymonas, Pleurochrysis, Pleurococcus, Prototheca, Pseudochlorella, Pseudoneochloris, Pseudostaurastrum, Pyramimonas, Pyrobotrys, Scenedesmus, Schizochlamydella, Skeletonema, Spyrogyra, Stichococcus, Tetrachlorella, Tetraselmis, Thalassiosira, Tribonema, Vaucheria, Viridiella, Vischeria, or Volvox.

16. A method of producing lipid, comprising culturing the microorganism of claim 1 and isolating lipid from the microorganism, the culture medium, or both.

17. A method of producing lipid, comprising culturing a microorganism according to claim 1 under conditions in which the FAME to TOC ratio of the microorganism is maintained between 0.3 and 0.9, and isolating lipid from the microorganism, the culture medium, or both.

18. A method according to claim 17, wherein the FAME to TOC ratio is maintained between about 0.4 and about 0.8.

19. An RNAi construct comprising a sequence homologous to at least a portion of a gene that encodes a polypeptide having at least 80% identity to SEQ ID NO:2, SEQ ID NO: 17, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, or SEQ ID NO: 16.

20. A method of producing lipid, comprising culturing a classical mutagenesis derived or genetically engineered mutant algal or heterokont microorganism that produces at least 30% more fatty acid methyl ester-derivatizable lipids (FAME lipids) than a control algal or heterokont microorganism and at least 45% of the amount of biomass produced by the control microorganism when the mutant microorganism and control microorganism are cultured under identical conditions under which the control microorganism is producing biomass, wherein the mutant microorganism has attenuated expression of a gene encoding a polypeptide comprising an amino acid sequence having at least 80% identity to an amino acid sequence selected from the group consisting of: SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO: 14, SEQ ID NO:15, and SEQ ID NO: 16.

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