U.S. patent application number 17/281068 was filed with the patent office on 2021-10-28 for over-expression of gds1 in yeast for increased ethanol and decreased acetate production.
The applicant listed for this patent is DANISCO US INC. Invention is credited to Zhongqiang CHEN, Min QI, Luan TAO, Quinn Qun ZHU.
Application Number | 20210332091 17/281068 |
Document ID | / |
Family ID | 1000005737643 |
Filed Date | 2021-10-28 |
United States Patent
Application |
20210332091 |
Kind Code |
A1 |
CHEN; Zhongqiang ; et
al. |
October 28, 2021 |
OVER-EXPRESSION OF GDS1 IN YEAST FOR INCREASED ETHANOL AND
DECREASED ACETATE PRODUCTION
Abstract
Described are compositions and methods relating to modified
yeast that over-express the glycerol-deficient suppressor, GDS1.
The yeast produces an increased amount of ethanol and a deceased
amount of acetate compared to parental cells. Such yeast is
particularly useful for large-scale ethanol production from starch
substrates where acetate in an undesirable end product.
Inventors: |
CHEN; Zhongqiang;
(Wilmington, DE) ; QI; Min; (Palo Alto, CA)
; TAO; Luan; (Wallingford, PA) ; ZHU; Quinn
Qun; (West Chester, PA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
DANISCO US INC |
Palo Alto |
CA |
US |
|
|
Family ID: |
1000005737643 |
Appl. No.: |
17/281068 |
Filed: |
September 26, 2019 |
PCT Filed: |
September 26, 2019 |
PCT NO: |
PCT/US2019/053061 |
371 Date: |
March 29, 2021 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
62738582 |
Sep 28, 2018 |
|
|
|
Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12P 7/06 20130101; C07K
14/395 20130101; C12N 1/16 20130101 |
International
Class: |
C07K 14/395 20060101
C07K014/395; C12P 7/06 20060101 C12P007/06; C12N 1/16 20060101
C12N001/16 |
Claims
1. Modified yeast cells derived from parental yeast cells, the
modified cells comprising a genetic alteration that causes the
modified cells to produce an increased amount of GDS1 polypeptides
compared to the parental cells, wherein the modified cells produce
during fermentation a decreased amount of acetate compared to the
amount of acetate produced by the parental cells under identical
fermentation conditions.
2. The modified yeast cells of claim 1, wherein the modified cells
produce during fermentation an increased amount of ethanol compared
to the amount of ethanol produced by the parental cells under
identical fermentation conditions.
3. The modified cells of claim 1 or 2, wherein the genetic
alteration comprises the introduction into the parental cells of a
nucleic acid capable of directing the expression of a GDS1
polypeptide to a level above that of the parental cell grown under
equivalent conditions.
4. The modified cells of claim 1 or 2, wherein the genetic
alteration comprises the introduction of an expression cassette for
expressing a GDS1 polypeptide.
5. The modified cells of any of claims 1-5, wherein the cells
further comprising one or more genes of the phosphoketolase
pathway.
6. The modified cells of claim 5, wherein the genes of the
phosphoketolase pathway are selected from the group consisting of
phosphoketolase, phosphotransacetylase and acetylating acetyl
dehydrogenase.
7. The modified cells of any of claims 1-6, wherein the amount of
increase in the expression of the GDS1 polypeptide is at least
about 500% compared to the level expression in the parental cells
grown under equivalent conditions.
8. The modified cells of any of claims 1-6, wherein the amount of
increase in the production of mRNA encoding the GDS1 polypeptide is
at least about 1000% compared to the level in the parental cells
grown under equivalent conditions.
9. The modified cells of any of claims 1-6, wherein the amount of
increase in the production of mRNA encoding the GDS1 polypeptide is
at least about 5000% compared to the level in the parental cells
grown under equivalent conditions.
10. The modified cells of any of claims 1-6, wherein the amount of
increase in the production of mRNA encoding the GDS1 polypeptide is
at least about 10000% compared to the level in the parental cells
grown under equivalent conditions.
11. The modified cells of any of claims 1-10, wherein the cells
further comprise an exogenous gene encoding a carbohydrate
processing enzyme.
12. The modified cells of any of claims 1-11, further comprising an
alteration in the glycerol pathway and/or the acetyl-CoA
pathway.
13. The modified cells of any of claims 1-12, further comprising an
alternative pathway for making ethanol.
14. The modified cells of any of claims 1-13, wherein the cells are
of a Saccharomyces spp.
15. A method for decreasing the production of acetate from yeast
cells grown on a carbohydrate substrate, comprising: introducing
into parental yeast cells a genetic alteration that increases the
production of GDS1 polypeptides compared to the amount produced in
the parental cells.
16. A method for increasing the production of ethanol from yeast
cells grown on a carbohydrate substrate, comprising: introducing
into parental yeast cells a genetic alteration that increases the
production of GDS1 polypeptides compared to the amount produced in
the parental cells.
17. The method of claim 15 or 16, wherein the cells having the
introduced genetic alteration are the modified cells are the cells
of any of claims 1-15.
18. The method of claim 15 or 17, wherein the decrease in acetate
production is at least 10%, at least 15%, at least 20%, or at least
25%. or at least 30% compared to the amount produced in the
parental cells.
19. The method of claim 16 or 17, wherein the increase in ethanol
production is at least 0.1%, at least 0.2%, at least 0.3%, or at
least 0.5%. or at least 1.0% compared to the amount produced in the
parental cells.
20. The method of any of claims 15-19, wherein GDS1 polypeptides
are over-expressed by at least 500%.
21. The method of any of claims 15-19, wherein GDS1 polypeptides
are over-expressed by at least 5-fold.
22. The method of any of claims 15-19, wherein GDS1 polypeptides
are over-expressed by at least 10-fold.
23. The method of any of claims 15-19, wherein GDS1 polypeptides
are over-expressed by at least 50-fold.
24. The method of any of claims 15-19, wherein GDS1 polypeptides
are over-expressed by at least 100-fold.
Description
CROSS REFERENCE
[0001] The present application claims the benefit of U.S.
Provisional Application Ser. No. 62/738,582, filed Sep. 28, 2018,
which is hereby incorporated by reference in its entirety.
TECHNICAL FIELD
[0002] The present compositions and methods relate to modified
yeast that over-expresses the glycerol-deficient suppressor, GDS1.
The yeast produces an increased amount of ethanol and a deceased
amount of acetate compared to parental cells. Such yeast is
particularly useful for large-scale ethanol production from starch
substrates, where acetate in an undesirable by-product.
BACKGROUND
[0003] First-generation yeast-based ethanol production converts
sugars into fuel ethanol. The annual fuel ethanol production by
yeast is about 90 billion liters worldwide (Gombert, A. K. and van
Maris. A. J. (2015) Curr. Opin. Biotechnol. 33:81-86). It is
estimated that about 70% of the cost of ethanol production is the
feedstock. Since the production volume is so large, even small
yield improvements have massive economic impact across the
industry.
[0004] The phosphoketolase (PKL) pathway has been genetically
engineered into yeast to increase ethanol production, as described
in WO2015148272 (Miasnikov et al.). Unfortunately, the engineered
strains also produce more acetate than the parental yeast. Acetate
is not a desirable by-product as it has negative effects on yeast
growth and fermentation. In addition, acetate reduces the pH of
left-over water from fermentation and distillation, referred to as
backset, which is typically reused for liquefaction of a subsequent
batch of substrate. As a result, ethanol producers must adjust the
pH of the backset (or liquefact) or increase the amount of fresh
water used for liquefaction.
[0005] The need exists to control the amount of acetate produced by
yeast, particularly engineered yeast that tend to produce an
increased amount of acetate.
SUMMARY
[0006] The present compositions and methods relate to modified
yeast that over-express GDS1 polypeptides. Aspects and embodiments
of the compositions and methods are described in the following,
independently-numbered, paragraphs.
[0007] 1. In one aspect, modified yeast cells derived from parental
yeast cells are provided, the modified cells comprising a genetic
alteration that causes the modified cells to produce an increased
amount of GDS1 polypeptides compared to the parental cells, wherein
the modified cells produce during fermentation a decreased amount
of acetate compared to the amount of acetate produced by the
parental cells under identical fermentation conditions.
[0008] 2. In some embodiments of the modified yeast cells of
paragraph 1, the modified cells produce during fermentation an
increased amount of ethanol compared to the amount of ethanol
produced by the parental cells under identical fermentation
conditions.
[0009] 3. In some embodiments of the modified cells of paragraph 1
or 2, the genetic alteration comprises the introduction into the
parental cells of a nucleic acid capable of directing the
expression of a GDS1 polypeptide to a level above that of the
parental cell grown under equivalent conditions.
[0010] 4. In some embodiments of the modified cells of paragraph 1
or 2, the genetic alteration comprises the introduction of an
expression cassette for expressing a GDS1 polypeptide.
[0011] 5. In some embodiments of the modified cells of any of
paragraphs 1-5, the cells further comprising one or more genes of
the phosphoketolase pathway.
[0012] 6. In some embodiments of the modified cells of paragraph 5,
the genes of the phosphoketolase pathway are selected from the
group consisting of phosphoketolase, phosphotransacetylase and
acetylating acetyl dehydrogenase.
[0013] 7. In some embodiments of the modified cells of any of
paragraphs 1-6, the amount of increase in the expression of the
GDS1 polypeptide is at least about 500% compared to the level
expression in the parental cells grown under equivalent
conditions.
[0014] 8. In some embodiments of the modified cells of any of
paragraphs 1-6, the amount of increase in the production of mRNA
encoding the GDS1 polypeptide is at least about 1000% compared to
the level in the parental cells grown under equivalent
conditions.
[0015] 9. In some embodiments of the modified cells of any of
paragraphs 1-6, the amount of increase in the production of mRNA
encoding the GDS1 polypeptide is at least about 5000% compared to
the level in the parental cells grown under equivalent
conditions.
[0016] 10. In some embodiments of the modified cells of any of
paragraphs 1-6, the amount of increase in the production of mRNA
encoding the GDS1 polypeptide is at least about 10000% compared to
the level in the parental cells grown under equivalent
conditions.
[0017] 11. In some embodiments of the modified cells of any of
paragraphs 1-10, the cells further comprise an exogenous gene
encoding a carbohydrate processing enzyme.
[0018] 12. In some embodiments, the modified cells of any of
paragraphs 1-11 further comprise an alteration in the glycerol
pathway and/or the acetyl-CoA pathway.
[0019] 13. In some embodiments, the modified cells of any of
paragraphs 1-12 further comprise an alternative pathway for making
ethanol.
[0020] 14. In some embodiments of the modified cells of any of
paragraphs 1-13, the cells are of a Saccharomyces spp.
[0021] 15. In another aspect, a method for decreasing the
production of acetate from yeast cells grown on a carbohydrate
substrate is provided, comprising: introducing into parental yeast
cells a genetic alteration that increases the production of GDS1
polypeptides compared to the amount produced in the parental
cells.
[0022] 16. In another aspect. a method for increasing the
production of ethanol from yeast cells grown on a carbohydrate
substrate is provided, comprising: introducing into parental yeast
cells a genetic alteration that increases the production of GDS1
polypeptides compared to the amount produced in the parental
cells.
[0023] 17. In some embodiments of the method of paragraph 15 or 16,
the cells having the introduced genetic alteration are the modified
cells are the cells of any of paragraphs 1-15.
[0024] 18. In some embodiments of the method of paragraph 15 or 17,
the decrease in acetate production is at least 10%, at least 15%,
at least 20%, or at least 25%. or at least 30% compared to the
amount produced in the parental cells.
[0025] 19. In some embodiments of the method of paragraph 16 or 17,
the increase in ethanol production is at least 0.1%, at least 0.2%,
at least 0.3%, or at least 0.5%. or at least 1.0% compared to the
amount produced in the parental cells.
[0026] 20. In some embodiments of the method of any of paragraphs
15-19, GDS1 polypeptides are over-expressed by at least 500%.
[0027] 21. In some embodiments of the method of any of paragraphs
15-19, GDS1 polypeptides are over-expressed by at least 5-fold.
[0028] 22. In some embodiments of the method of any of paragraphs
15-19, GDS1 polypeptides are over-expressed by at least
10-fold.
[0029] 23. In some embodiments of the method of any of paragraphs
15-19, GDS1 polypeptides are over-expressed by at least
50-fold.
[0030] 24. In some embodiments of the method of any of paragraphs
15-19, GDS1 polypeptides are over-expressed by at least
100-fold.
[0031] These and other aspects and embodiments of present modified
cells and methods will be apparent from the description, including
any accompanying Drawings/Figures.
DETAILED DESCRIPTION
I. Definitions
[0032] Prior to describing the present yeast and methods in detail,
the following terms are defined for clarity. Terms not defined
should be accorded their ordinary meanings as used in the relevant
art.
[0033] As used herein, the term "alcohol" refers to an organic
compound in which a hydroxyl functional group (--OH) is bound to a
saturated carbon atom.
[0034] As used herein, the terms "yeast cells," "yeast strains," or
simply "yeast" refer to organisms from the phyla Ascomycota and
Basidiomycota. Exemplary yeast is budding yeast from the order
Saccharomycetales. Particular examples of yeast are Saccharomyces
spp., including but not limited to S. cerevisiae. Yeast include
organisms used for the production of fuel alcohol as well as
organisms used for the production of potable alcohol, including
specialty and proprietary yeast strains used to make
distinctive-tasting beers, wines, and other fermented
beverages.
[0035] As used herein, the phrase "engineered yeast cells,"
"variant yeast cells," "modified yeast cells," or similar phrases,
refer to yeast that include genetic modifications and
characteristics described herein. Variant/modified yeast do not
include naturally occurring yeast.
[0036] As used herein, the terms "polypeptide" and "protein" (and
their respective plural forms) are used interchangeably to refer to
polymers of any length comprising amino acid residues linked by
peptide bonds. The conventional one-letter or three-letter codes
for amino acid residues are used herein and all sequence are
presented from an N-terminal to C-terminal direction. The polymer
can comprise modified amino acids, and it can be interrupted by
non-amino acids. The terms also encompass an amino acid polymer
that has been modified naturally or by intervention; for example,
disulfide bond formation, glycosylation, lipidation, acetylation,
phosphorylation, or any other manipulation or modification, such as
conjugation with a labeling component. Also included within the
definition are, for example, polypeptides containing one or more
analogs of an amino acid (including, for example, unnatural amino
acids, etc.), as well as other modifications known in the art.
[0037] As used herein, functionally and/or structurally similar
proteins are considered to be "related proteins," or "homologs."
Such proteins can be derived from organisms of different genera
and/or species, or different classes of organisms (e.g., bacteria
and fungi), or artificially designed. Related proteins also
encompass homologs determined by primary sequence analysis,
determined by secondary or tertiary structure analysis, or
determined by immunological cross-reactivity, or determined by
their functions.
[0038] As used herein, the term "homologous protein" refers to a
protein that has similar activity and/or structure to a reference
protein. It is not intended that homologs necessarily be
evolutionarily related. Thus, it is intended that the term
encompass the same, similar, or corresponding enzyme(s) (i.e., in
terms of structure and function) obtained from different organisms.
In some embodiments, it is desirable to identify a homolog that has
a quaternary, tertiary and/or primary structure similar to the
reference protein. In some embodiments, homologous proteins induce
similar immunological response(s) as a reference protein. In some
embodiments, homologous proteins are engineered to produce enzymes
with desired activity(ies).
[0039] The degree of homology between sequences can be determined
using any suitable method known in the art (see, e.g., Smith and
Waterman (1981) Adv. Appl. Math. 2:482; Needleman and Wunsch (1970)
J Mol. Biol., 48:443; Pearson and Lipman (1988) Proc. Natl. Acad.
Sci. USA 85:2444; programs such as GAP, BESTFIT, FASTA, and TFASTA
in the Wisconsin Genetics Software Package (Genetics Computer
Group, Madison, Wis.); and Devereux et al. (1984) Nucleic Acids
Res. 12:387-95).
[0040] For example, PILEUP is a useful program to determine
sequence homology levels. PILEUP creates a multiple sequence
alignment from a group of related sequences using progressive,
pair-wise alignments. It can also plot a tree showing the
clustering relationships used to create the alignment. PILEUP uses
a simplification of the progressive alignment method of Feng and
Doolittle, (Feng and Doolittle (1987) J Mol. Evol. 35:351-60). The
method is similar to that described by Higgins and Sharp ((1989)
CABIOS 5:151-53). Useful PILEUP parameters including a default gap
weight of 3.00, a default gap length weight of 0.10, and weighted
end gaps. Another example of a useful algorithm is the BLAST
algorithm, described by Altschul et al. ((1990) J Mol. Biol.
215:403-10) and Karlin et al. ((1993) Proc. Natl. Acad. Sci. USA
90:5873-87). One particularly useful BLAST program is the
WU-BLAST-2 program (see, e.g., Altschul et al. (1996) Meth.
Enzymol. 266:460-80). Parameters "W," "T," and "X" determine the
sensitivity and speed of the alignment. The BLAST program uses as
defaults a word-length (W) of 11, the BLOSUM62 scoring matrix (see,
e.g., Henikoff and Henikoff (1989) Proc. Natl. Acad. Sci. USA
89:10915) alignments (B) of 50, expectation (E) of 10, M'S, N'-4,
and a comparison of both strands.
[0041] As used herein, the phrases "substantially similar" and
"substantially identical," in the context of at least two nucleic
acids or polypeptides, typically means that a polynucleotide or
polypeptide comprises a sequence that has at least about 70%
identity, at least about 75% identity, at least about 80% identity,
at least about 85% identity, at least about 90% identity, at least
about 91% identity, at least about 92% identity, at least about 93%
identity, at least about 94% identity, at least about 95% identity,
at least about 96% identity, at least about 97% identity, at least
about 98% identity, or even at least about 99% identity, or more,
compared to the reference (i.e., wild-type) sequence. Percent
sequence identity is calculated using CLUSTAL W algorithm with
default parameters. See Thompson et al. (1994) Nucleic Acids Res.
22:4673-4680. Default parameters for the CLUSTAL W algorithm are:
[0042] Gap opening penalty: 10.0 [0043] Gap extension penalty: 0.05
[0044] Protein weight matrix: BLOSUM series [0045] DNA weight
matrix: IUB [0046] Delay divergent sequences %: 40 [0047] Gap
separation distance: 8 [0048] DNA transitions weight: 0.50 [0049]
List hydrophilic residues: GPSNDQEKR [0050] Use negative matrix:
OFF [0051] Toggle Residue specific penalties: ON [0052] Toggle
hydrophilic penalties: ON [0053] Toggle end gap separation penalty
OFF
[0054] Another indication that two polypeptides are substantially
identical is that the first polypeptide is immunologically
cross-reactive with the second polypeptide. Typically, polypeptides
that differ by conservative amino acid substitutions are
immunologically cross-reactive. Thus, a polypeptide is
substantially identical to a second polypeptide, for example, where
the two peptides differ only by a conservative substitution.
Another indication that two nucleic acid sequences are
substantially identical is that the two molecules hybridize to each
other under stringent conditions (e.g., within a range of medium to
high stringency).
[0055] As used herein, the term "gene" is synonymous with the term
"allele" in referring to a nucleic acid that encodes and directs
the expression of a protein or RNA. Vegetative forms of filamentous
fungi are generally haploid, therefore a single copy of a specified
gene (i.e., a single allele) is sufficient to confer a specified
phenotype. The term "allele" is generally preferred when an
organism contains more than one similar genes, in which case each
different similar gene is referred to as a distinct "allele."
[0056] As used herein, "constitutive" expression refers to the
production of a polypeptide encoded by a particular gene under
essentially all typical growth conditions, as opposed to
"conditional" expression, which requires the presence of a
particular substrate, temperature, or the like to induce or
activate expression.
[0057] As used herein, the term "expressing a polypeptide" and
similar terms refers to the cellular process of producing a
polypeptide using the translation machinery (e.g., ribosomes) of
the cell.
[0058] As used herein, "over-expressing a polypeptide," "increasing
the expression of a polypeptide," and similar terms, refer to
expressing a polypeptide at higher-than-normal levels compared to
those observed with parental or "wild-type cells that do not
include a specified genetic modification.
[0059] As used herein, an "expression cassette" refers to a DNA
fragment that includes a promoter, and amino acid coding region and
a terminator (i.e., promoter::amino acid coding region::terminator)
and other nucleic acid sequence needed to allow the encoded
polypeptide to be produced in a cell. Expression cassettes can be
exogenous (i.e., introduced into a cell) or endogenous (i.e.,
extant in a cell).
[0060] As used herein, the terms "fused" and "fusion" with respect
to two DNA fragments, such as a promoter and the coding region of a
polypeptide refer to a physical linkage causing the two DNA
fragments to become a single molecule.
[0061] As used herein, the terms "wild-type" and "native" are used
interchangeably and refer to genes, proteins or strains found in
nature, or that are not intentionally modified for the advantage of
the presently described yeast.
[0062] As used herein, the term "protein of interest" refers to a
polypeptide that is desired to be expressed in modified yeast. Such
a protein can be an enzyme, a substrate-binding protein, a
surface-active protein, a structural protein, a selectable marker,
a signal transducer, a receptor, a transporter, a transcription
factor, a translation factor, a co-factor, or the like, and can be
expressed. The protein of interest is encoded by an endogenous gene
or a heterologous gene (i.e., gene of interest") relative to the
parental strain. The protein of interest can be expressed
intracellularly or as a secreted protein.
[0063] As used herein, "disruption of a gene" refers broadly to any
genetic or chemical manipulation, i.e., mutation, that
substantially prevents a cell from producing a function gene
product, e.g., a protein, in a host cell. Exemplary methods of
disruption include complete or partial deletion of any portion of a
gene, including a polypeptide-coding sequence, a promoter, an
enhancer, or another regulatory element, or mutagenesis of the
same, where mutagenesis encompasses substitutions, insertions,
deletions, inversions, and combinations and variations, thereof,
any of which mutations substantially prevent the production of a
function gene product. A gene can also be disrupted using CRISPR,
RNAi, antisense, or any other method that abolishes gene
expression. A gene can be disrupted by deletion or genetic
manipulation of non-adjacent control elements. As used herein,
"deletion of a gene," refers to its removal from the genome of a
host cell. Where a gene includes control elements (e.g., enhancer
elements) that are not located immediately adjacent to the coding
sequence of a gene, deletion of a gene refers to the deletion of
the coding sequence, and optionally adjacent enhancer elements,
including but not limited to, for example, promoter and/or
terminator sequences, but does not require the deletion of
non-adjacent control elements. Deletion of a gene also refers to
the deletion a part of the coding sequence, or a part of promoter
immediately or not immediately adjacent to the coding sequence,
where there is no functional activity of the interested gene
existed in the engineered cell.
[0064] As used herein, the terms "genetic manipulation" and
"genetic alteration" are used interchangeably and refer to the
alteration/change of a nucleic acid sequence. The alteration can
include but is not limited to a substitution, deletion, insertion
or chemical modification of at least one nucleic acid in the
nucleic acid sequence.
[0065] As used herein, a "functional polypeptide/protein" is a
protein that possesses an activity, such as an enzymatic activity,
a binding activity, a surface-active property, a signal transducer,
a receptor, a transporter, a transcription factor, a translation
factor, a co-factor, or the like, and which has not been
mutagenized, truncated, or otherwise modified to abolish or reduce
that activity. Functional polypeptides can be thermostable or
thermolabile, as specified.
[0066] As used herein, "a functional gene" is a gene capable of
being used by cellular components to produce an active gene
product, typically a protein. Functional genes are the antithesis
of disrupted genes, which are modified such that they cannot be
used by cellular components to produce an active gene product, or
have a reduced ability to be used by cellular components to produce
an active gene product.
[0067] As used herein, yeast cells have been "modified to prevent
the production of a specified protein" if they have been
genetically or chemically altered to prevent the production of a
functional protein/polypeptide that exhibits an activity
characteristic of the wild-type protein. Such modifications
include, but are not limited to, deletion or disruption of the gene
encoding the protein (as described, herein), modification of the
gene such that the encoded polypeptide lacks the aforementioned
activity, modification of the gene to affect post-translational
processing or stability, and combinations, thereof.
[0068] As used herein, "attenuation of a pathway" or "attenuation
of the flux through a pathway," i.e., a biochemical pathway, refers
broadly to any genetic or chemical manipulation that reduces or
completely stops the flux of biochemical substrates or
intermediates through a metabolic pathway. Attenuation of a pathway
may be achieved by a variety of well-known methods. Such methods
include but are not limited to: complete or partial deletion of one
or more genes, replacing wild-type alleles of these genes with
mutant forms encoding enzymes with reduced catalytic activity or
increased Km values, modifying the promoters or other regulatory
elements that control the expression of one or more genes,
engineering the enzymes or the mRNA encoding these enzymes for a
decreased stability, misdirecting enzymes to cellular compartments
where they are less likely to interact with substrate and
intermediates, the use of interfering RNA, and the like.
[0069] As used herein, "aerobic fermentation" refers to growth in
the presence of oxygen.
[0070] As used herein, "anaerobic fermentation" refers to growth in
the absence of oxygen.
[0071] As used herein, the expression "end of fermentation" refers
to the stage of fermentation when the economic advantage of
continuing fermentation to produce a small amount of additional
alcohol is exceeded by the cost of continuing fermentation in terms
of fixed and variable costs. In a more general sense, "end of
fermentation" refers to the point where a fermentation will no
longer produce a significant amount of additional alcohol, i.e., no
more than about 1% additional alcohol, or no more substrate left
for further alcohol production.
[0072] As used herein, the expression "carbon flux" refers to the
rate of turnover of carbon molecules through a metabolic pathway.
Carbon flux is regulated by enzymes involved in metabolic pathways,
such as the pathway for glucose metabolism and the pathway for
maltose metabolism.
[0073] As used herein, the singular articles "a," "an" and "the"
encompass the plural referents unless the context clearly dictates
otherwise. All references cited herein are hereby incorporated by
reference in their entirety. The following abbreviations/acronyms
have the following meanings unless otherwise specified: [0074] EC
enzyme commission [0075] PKL phosphoketolase [0076] PTA
phosphotransacetylase [0077] AADH acetaldehyde dehydrogenases
[0078] ADH alcohol dehydrogenase [0079] EtOH ethanol [0080] GDS1
glycerol-deficient suppressor [0081] AA .alpha.-amylase [0082] GA
glucoamylase [0083] .degree. C. degrees Centigrade [0084] bp base
pairs [0085] DNA deoxyribonucleic acid [0086] ds or DS dry solids
[0087] g or gm gram [0088] g/L grams per liter [0089] H.sub.2O
water [0090] HPLC high performance liquid chromatography [0091] hr
or h hour [0092] kg kilogram [0093] M molar [0094] mg milligram
[0095] mL or ml milliliter [0096] min minute [0097] mM millimolar
[0098] N normal [0099] nm nanometer [0100] PCR polymerase chain
reaction [0101] ppm parts per million [0102] .DELTA. relating to a
deletion [0103] .mu.g microgram [0104] .mu.L and .mu.l microliter
[0105] .mu.M micromolar
II. Modified Yeast Cells Having Increased GDS1 Expression
[0106] Described are modified yeast and methods having a genetic
alteration that results in the production of increased amounts of
GDS1 polypeptides compared to corresponding (i.e.,
otherwise-identical) parental cells. GDS1 is a 522-amino acid
residue, serine-rich polypeptide identified as a suppressor of
certain glycerol-deficient phenotypes. GDS1 appears to have no
obvious homology to other know yeast proteins (see, e.g.,
Konopinska, A. et al. (1995) Yeast 11:1513-18). GDS1 is important
for yeast cells to grow on medium containing glycerol as the carbon
source. However, no association has been made between GDS1
over-expression and acetate reduction and/or ethanol increase in
engineered yeast.
[0107] Applicants have discovered that yeast cells over-expressing
GDS1 polypeptides produce a decreased amount of acetate and an
increased amount of ethanol compared to otherwise-identical
parental cells. Decreased acetate is desirable as acetate adversely
affects yeast growth and fermentation and additionally results in
backset that has a lower than desirable pH, requiring pH adjustment
or the use of more fresh water to dilute the backset.
[0108] In some embodiments, the increase in the amount of GDS1
polypeptides produced by the modified cells is an increase of at
least 1000%, at least 2500%, at least 5000%, at least at least
10000%, or more, especially at early stage of fermentation,
compared to the amount of GDS1 polypeptides produced by parental
cells grown under the same conditions.
[0109] In some embodiments, the increase in the amount of GDS1
polypeptides produced by the modified cells is at least 10-fold, at
least 25-fold, at least 50-fold, at least 100-fold, or more,
compared to the amount of GDS1 polypeptides produced by parental
cells grown under the same conditions.
[0110] In some embodiments, the increase in the strength of the
promoter used to control expression of the GDS1 polypeptides
produced by the modified cells is at least 10-fold, at least
25-fold, at least 50-fold, at least 100-fold, or more, compared to
strength of the native promoter controlling GDS1 expression, based
on the amount of mRNA produced. As shown in Table 1, RNAseq data
(see, e.g., Wang, Z. et al. (2009) Nature Rev. Gen. 10:57-63)
indicates that the TPI1 promoter used for the exemplified GDS1
expression cassette is at least 76-times stronger than the normal
native GDS1 promoter during early-stage fermentation in the
parental FERMAX.TM. Gold strain (Martrex Inc., Minnesota, USA;
herein abbreviated, "FG," a well-known commercially-available
fermentation yeast used in the grain ethanol industry).
TABLE-US-00001 TABLE 1 RNAseq analyses of GDS1 and TPI1 in the FG
strain Promoter 0 hr 6 hr 24 hr native GDS1 764 965 89 RHO1 58337
98377 23003
[0111] In some embodiments, the decrease in acetate production by
the modified cells is a decrease of at least 10%, at least 15%, at
least 20%, at least 25%, at least 30%, at least 35%, at least 40%,
or at least 50%, more, compared to the amount of acetate produced
by parental cells grown under the same conditions.
[0112] In some embodiments, the increase in ethanol production by
the modified cells is an increase of at least 0.1%, at least 0.3%,
or at least 0.5%, or at least 1%, or more, compared to the amount
of ethanol produced by parental cells grown under the same
conditions.
[0113] Preferably, increased GDS1 expression is achieved by genetic
manipulation using sequence-specific molecular biology techniques,
as opposed to chemical mutagenesis, which is generally not targeted
to specific nucleic acid sequences. However, chemical mutagenesis
is not excluded as a method for making modified yeast cells.
[0114] In some embodiments, the present compositions and methods
involve introducing into yeast cells a nucleic acid capable of
directing the over-expression, or increased expression, of a GDS1
polypeptide. Particular methods include but are not limited to (i)
introducing an exogenous expression cassette for producing the
polypeptide into a host cell, optionally in addition to an
endogenous expression cassette, (ii) substituting an exogenous
expression cassette with an endogenous cassette that allows the
production of an increased amount of the polypeptide, (iii)
modifying the promoter of an endogenous expression cassette to
increase expression, (iv) increase copy number of the same or
different cassettes for over-expression of GDS1, and/or (v)
modifying any aspect of the host cell to increase the half-life of
the polypeptide in the host cell.
[0115] In some embodiments, the parental cell that is modified
already includes a gene of interest, such as a gene encoding a
selectable marker, carbohydrate-processing enzyme, or other
polypeptide. In some embodiments, a gene of introduced is
subsequently introduced into the modified cells.
[0116] In some embodiments, the parental cell that is modified
already includes an engineered pathway of interest, such as a PKL
pathway to increases ethanol production, or any other pathway to
increase alcohol production.
[0117] The amino acid sequence of the exemplified S. cerevisiae
GDS1 polypeptide is shown, below, as SEQ ID NO: 1:
TABLE-US-00002 MALANSRPLQIPTLENEILHNSNSPVFQLNSMGFTTRADTISNPGTDLI
GNQPGMALDDNNLAGSSFSSSQEIKATKPKKDFGAPKKDNPLLEISKLI
PVTGERPKPENRDSPLDDDVLHAVFLILWEMDPNQQGMTVKQLCDLLLQ
KHPDMSNLSTKLSNLISAKLNAYVKKIEKGEKTLTYALSREWSNSSPRR
MLYIYRGILSPDYKEHAQAVTMQLKQQLETSGDTSDFNSNGKKKRESSS
NQLVNNDSYSSSMTDMKNMSSNSSFSKNLNVGNLAFSLSPEFNIPYSTS
PVSLNLSPSMSNNQQQLLTPNSASKSKNNNKKRNYMDEDTNESMTEPKK
TKTTKPGKQTKSQSLSVLSTPKKGSSASLSTFASSKNISPDSSLSHNAS
SNTYVTAAAAAPRLSKLLPKNGFKKNSRSSSELAAIHKVISTQTPIESS
SESSQYNSSSSSPVNSAAASSAESLSDINSSQDNGRESNPSSQESRNEV
TNWMKIVRNGFLTHDIESPESITLDDLENIFN
[0118] The NCBI database includes over 100 entries for S.
cerevisiae GDS1 polypeptides. Natural variations in the amino acid
sequence are not expected to affect its function. In addition,
based on such BLAST and Clustal W data, it is apparent that the
exemplified S. cerevisiae GDS1 polypeptide shares a high degree of
sequence identity to polypeptides from other organisms, and
over-expression of functionally and/or structurally similar
proteins, homologous proteins and/or substantially similar or
identical proteins, is expected to produce similar beneficial
results.
[0119] In particular embodiments of the present compositions and
methods, the amino acid sequence of the GDS1 polypeptide that is
over-expressed in modified yeast cells has at least about 70%, at
least about 75%, at least about 80%, at least about 85%, at least
about 90%, at least about 91%, at least about 92%, at least about
93%, at least about 94%, at least about 95%, at least about 96%, at
least about 97%, at least about 98%, or even at least about 99%
identity, to SEQ ID NO: 1.
III. Modified Yeast Cells Having Increased GDS1 Expression in
Combination with Genes of an Exogenous PKL Pathway
[0120] Increased expression of GDS1 can be combined with expression
of genes in the PKL pathway to further increase ethanol production
and reduce the production of elevated amounts of acetate that is
associated with introducing an exogenous PKL pathway into
yeast.
[0121] Engineered yeast cells having a heterologous PKL pathway
have been previously described in WO2015148272 (Miasnikov et al.).
These cells express heterologous phosphoketolase (PKL),
phosphotransacetylase (PTA) and acetylating acetyl dehydrogenase
(AADH), optionally with other enzymes, to channel carbon flux away
from the glycerol pathway and toward the synthesis of acetyl-CoA,
which is then converted to ethanol. Such modified cells are capable
of increased ethanol production in a fermentation process when
compared to otherwise-identical parent yeast cells.
IV. Combination of Increased Active GDS1 Production with Other
Mutations that Alter Alcohol or Acetate Production
[0122] In some embodiments, in addition to expressing increased
amounts of active GDS1 polypeptides, optionally in combination with
introducing an exogenous PKL pathway, the present modified yeast
cells include additional modifications that increase ethanol or
reduce acetate production.
[0123] The modified cells may further include mutations that result
in attenuation of the native glycerol biosynthesis pathway and/or
reuse glycerol pathway, which are known to increase alcohol
production. Methods for attenuation of the glycerol biosynthesis
pathway in yeast are known and include reduction or elimination of
endogenous NAD-dependent glycerol 3-phosphate dehydrogenase (GPD)
or glycerol phosphate phosphatase activity (GPP), for example by
disruption of one or more of the genes GPD1, GPD2, GPP1 and/or
GPP2. See, e.g., U.S. Pat. No. 9,175,270 (Elke et al.), 8,795,998
(Pronk et al.) and 8,956,851 (Argyros et al.). Methods to enhance
the reuse glycerol pathway by over expression of glycerol
dehydrogenase (GCY1) and dihydroxyacetone kinase (DAK1) to convert
glycerol to dihydroxyacetone phosphate (Zhang et al; J Ind
Microbiol Biotechnol (2013) 40:1153-1160).
[0124] The modified yeast may further feature increased acetyl-CoA
synthase (also referred to acetyl-CoA ligase) activity (EC 6.2.1.1)
to scavenge (i.e., capture) acetate produced by chemical or
enzymatic hydrolysis of acetyl-phosphate (or present in the culture
medium of the yeast for any other reason) and converts it to
Ac-CoA. This partially reduces the undesirable effect of acetate on
the growth of yeast cells and may further contribute to an
improvement in alcohol yield. Increasing acetyl-CoA synthase
activity may be accomplished by introducing a heterologous
acetyl-CoA synthase gene into cells, increasing the expression of
an endogenous acetyl-CoA synthase gene and the like.
[0125] In some embodiments the modified cells may further include a
heterologous gene encoding a protein with NAD.sup.+-dependent
acetylating acetaldehyde dehydrogenase activity and/or a
heterologous gene encoding a pyruvate-formate lyase. The
introduction of such genes in combination with attenuation of the
glycerol pathway is described, e.g., in U.S. Pat. No. 8,795,998
(Pronk et al.). In some embodiments of the present compositions and
methods the yeast expressly lacks a heterologous gene(s) encoding
an acetylating acetaldehyde dehydrogenase, a pyruvate-formate lyase
or both.
[0126] In some embodiments, the present modified yeast cells may
further over-express a sugar transporter-like (STL1) polypeptide to
increase the uptake of glycerol (see, e.g., Ferreira et al. (2005)
Mol. Biol. Cell. 16:2068-76; Du{grave over (s)}kova et al. (2015)
Mol. Microbiol. 97:541-59 and WO 2015023989 A1) to increase ethanol
production and reduce acetate.
[0127] In some embodiments, the present modified yeast cells
further include a butanol biosynthetic pathway. In some
embodiments, the butanol biosynthetic pathway is an isobutanol
biosynthetic pathway. In some embodiments, the isobutanol
biosynthetic pathway comprises a polynucleotide encoding a
polypeptide that catalyzes a substrate to product conversion
selected from the group consisting of: (a) pyruvate to
acetolactate; (b) acetolactate to 2,3-dihydroxyisovalerate; (c)
2,3-dihydroxyisovalerate to 2-ketoisovalerate; (d)
2-ketoisovalerate to isobutyraldehyde; and (e) isobutyraldehyde to
isobutanol. In some embodiments, the isobutanol biosynthetic
pathway comprises polynucleotides encoding polypeptides having
acetolactate synthase, keto acid reductoisomerase, dihydroxy acid
dehydratase, ketoisovalerate decarboxylase, and alcohol
dehydrogenase activity.
[0128] In some embodiments, the modified yeast cells comprising a
butanol biosynthetic pathway further comprise a modification in a
polynucleotide encoding a polypeptide having pyruvate decarboxylase
activity. In some embodiments, the yeast cells comprise a deletion,
mutation, and/or substitution in an endogenous polynucleotide
encoding a polypeptide having pyruvate decarboxylase activity. In
some embodiments, the polypeptide having pyruvate decarboxylase
activity is selected from the group consisting of: PDC1, PDC5,
PDC6, and combinations thereof. In some embodiments, the yeast
cells further comprise a deletion, mutation, and/or substitution in
one or more endogenous polynucleotides encoding FRA2, ALD6, ADH1,
GPD2, BDH1, and YMR226C.
V. Combination of Increased Expression GDS1 with Other Beneficial
Mutations
[0129] In some embodiments, in addition to increased expression of
GDS1 polypeptides, optionally in combination with other genetic
modifications that benefit alcohol production, the present modified
yeast cells further include any number of additional genes of
interest encoding proteins of interest. Additional genes of
interest may be introduced before, during, or after genetic
manipulations that result in the increased production of GDS1
polypeptides. Proteins of interest, include selectable markers,
carbohydrate-processing enzymes, and other commercially-relevant
polypeptides, including but not limited to an enzyme selected from
the group consisting of a dehydrogenase, a transketolase, a
phosphoketolase, a transladolase, an epimerase, a phytase, a
xylanase, a .beta.-glucanase, a phosphatase, a protease, an
.alpha.-amylase, a .beta.-amylase, a glucoamylase, a pullulanase,
an isoamylase, a cellulase, a trehalase, a lipase, a pectinase, a
polyesterase, a cutinase, an oxidase, a transferase, a reductase, a
hemicellulase, a mannanase, an esterase, an isomerase, a
pectinases, a lactase, a peroxidase and a laccase. Proteins of
interest may be secreted, glycosylated, and otherwise-modified.
VI. Use of the Modified Yeast for Increased Alcohol Production
[0130] The present compositions and methods include methods for
increasing alcohol production and/or reducing glycerol production,
in fermentation reactions. Such methods are not limited to a
particular fermentation process. The present engineered yeast is
expected to be a "drop-in" replacement for convention yeast in any
alcohol fermentation facility. While primarily intended for fuel
alcohol production, the present yeast can also be used for the
production of potable alcohol, including wine and beer.
VII. Yeast Cells Suitable for Modification
[0131] Yeasts are unicellular eukaryotic microorganisms classified
as members of the fungus kingdom and include organisms from the
phyla Ascomycota and Basidiomycota. Yeast that can be used for
alcohol production include, but are not limited to, Saccharomyces
spp., including S. cerevisiae, as well as Kluyveromyces, Lachancea
and Schizosaccharomyces spp. Numerous yeast strains are
commercially available, many of which have been selected or
genetically engineered for desired characteristics, such as high
alcohol production, rapid growth rate, and the like. Some yeasts
have been genetically engineered to produce heterologous enzymes,
such as glucoamylase or .alpha.-amylase.
VII. Substrates and Products
[0132] Alcohol production from a number of carbohydrate substrates,
including but not limited to corn starch, sugar cane, cassava, and
molasses, is well known, as are innumerable variations and
improvements to enzymatic and chemical conditions and mechanical
processes. The present compositions and methods are believed to be
fully compatible with such substrates and conditions.
[0133] Alcohol fermentation products include organic compound
having a hydroxyl functional group (--OH) is bound to a carbon
atom. Exemplary alcohols include but are not limited to methanol,
ethanol, n-propanol, isopropanol, n-butanol, isobutanol,
n-pentanol, 2-pentanol, isopentanol, and higher alcohols. The most
commonly made fuel alcohols are ethanol, and butanol.
[0134] These and other aspects and embodiments of the present yeast
strains and methods will be apparent to the skilled person in view
of the present description. The following examples are intended to
further illustrate, but not limit, the compositions and
methods.
EXAMPLES
Example 1
Materials and Methods
Liquefact Preparation:
[0135] Liquefact (corn mash slurry) was prepared by adding 600 ppm
of urea, 0.124 SAPU/g ds acid fungal protease, 0.33 GAU/g ds
variant Trichoderma glucoamylase and 1.46 SSCU/g ds Aspergillus
kawachii .alpha.-amylase, adjusted to a pH of 4.8 with sulfuric
acid.
AnKom Assays:
[0136] 300 .mu.L of concentrated yeast overnight culture was added
to each of a number ANKOM bottles filled with 50 g prepared
liquefact (see above) to a final OD of 0.3. The bottles were then
incubated at 32.degree. C. with shaking at 150 RPM for 55
hours.
HPLC Analysis:
[0137] Samples of the cultures from AnKom assays were collected in
Eppendorf tubes by centrifugation for 12 minutes at 14,000 RPM. The
supernatants were filtered using 0.2 PTFE filters and then used for
HPLC (Agilent Technologies 1200 series) analysis with the following
conditions: Bio-Rad Aminex HPX-87H columns, running at a
temperature of 55.degree. C. with a 0.6 ml/min isocratic flow in
0.01 N H2SO4 and a 2.5 .mu.l injection volume. Calibration
standards were used for quantification of the of acetate, ethanol,
glycerol, glucose and other molecules. Unless otherwise indicated,
all values are reported in g/L.
Example 2
Preparation of a GDS1 Expression Cassette
[0138] The GDS1 coding region at the YOR355W locus (SEQ ID NO:2) of
S. cerevisiae was synthesized and operably linked to the TPI1
promoter (YDR050C locus; SEQ ID NO: 3) and GDS1 terminator (YOR355W
locus; SEQ ID NO: 4) to generate the TPI1Pro::GDS1s::Gds1Ter
expression cassette, referred to herein as GDS1s. The expression
cassette was introduced between positions 476541 and 476599 of
yeast chromosome IV either (i) FERMAX.TM. Gold (Martrex Inc.,
Minnesota, USA; herein abbreviated, "FG"), which is a well-known
fermentation yeast used in the grain ethanol industry, or (ii)
FG-PKR, which is an engineered FG yeast having a heterologous
phosphoketolase (PKL) pathway involving the expression of
phosphoketolase (PKL), phosphotransacetylase (PTA) and acetylating
acetyl dehydrogenase (AADH) as described in WO2015148272 (Miasnikov
et al.). The expected insertion of the GDS1s expression cassette in
the two parental strains was confirmed by PCR analyses.
[0139] The amino acid sequence of the S. cerevisiae GDS1
polypeptide is shown, below, as SEQ ID NO: 1:
TABLE-US-00003 MALANSRPLQIPTLENEILHNSNSPVFQLNSMGFTTRADTISNPGTDLI
GNQPGMALDDNNLAGSSFSSSQEIKATKPKKDFGAPKKDNPLLEISKLI
PVTGERPKPENRDSPLDDDVLHAVFLILWEMDPNQQGMTVKQLCDLLLQ
KHPDMSNLSTKLSNLISAKLNAYVKKIEKGEKTLTYALSREWSNSSPRR
MLYIYRGILSPDYKEHAQAVTMQLKQQLETSGDTSDFNSNGKKKRESSS
NQLVNNDSYSSSMTDMKNMSSNSSFSKNLNVGNLAFSLSPEFNIPYSTS
PVSLNLSPSMSNNQQQLLTPNSASKSKNNNKKRNYMDEDINESMTEPKK
TKTTKPGKQTKSQSLSVLSTPKKGSSASLSTFASSKNISPDSSLSHNAS
SNTYVTAAAAAPRLSKLLPKNGFKKNSRSSSELAAIHKVISTQTPIESS
SESSQYNSSSSSPVNSAAASSAESLSDINSSQDNGRESNPSSQESRNEV
TNWMKIVRNGFLTHDIESPESITLDDLENIFN
[0140] The GDS1-coding region of the GDS1s gene is shown, below, as
SEQ ID NO: 2:
TABLE-US-00004 ATGGCATTGGCAAATTCCAGACCTTTGCAAATACCAACTTTAGAGAATG
AAATTCTTCATAACTCAAATTCTCCAGTATTTCAGTTGAATTCAATGGG
ATTTACAACTAGAGCTGACACTATTTCGAATCCAGGCACGGATCTTATC
GGCAACCAGCCAGGCATGGCCCTTGATGATAATAATTTGGCCGGTTCTT
CGTTTTCCTCATCTCAGGAAATAAAAGCTACCAAACCTAAGAAGGACTT
TGGTGCTCCCAAAAAAGACAATCCATTATTAGAAATTTCTAAGCTAATA
CCTGTTACTGGTGAGAGGCCAAAACCCGAAAATAGAGACTCCCCTCTGG
ATGATGACGTTCTTCACGCAGTTTTTTTAATATTATGGGAAATGGATCC
GAATCAACAAGGCATGACCGTCAAACAACTGTGTGACTTGCTTTTGCAA
AAACATCCAGATATGTCCAATTTATCAACCAAGTTGTCAAATTTAATTT
CCGCAAAACTGAACGCTTATGTTAAAAAAATTGAAAAAGGTGAGAAAAC
GTTAACTTATGCTTTATCAAGGGAATGGTCTAATTCATCTCCTAGAAGG
ATGCTCTATATATACAGAGGCATATTATCTCCCGATTACAAGGAGCATG
CTCAAGCTGTTACGATGCAACTTAAACAACAATTGGAGACCTCCGGTGA
TACAAGCGACTTTAATTCAAATGGCAAGAAAAAAAGGGAGTCCAGCAGT
AACCAGCTAGTTAACAATGACAGTTATTCAAGTTCTATGACGGACATGA
AAAATATGTCTTCTAACAGTTCCTTCTCAAAAAATTTGAATGTAGGGAA
TCTGGCCTTTTCATTAAGTCCAGAATTCAACATACCTTATTCCACTTCT
CCAGTGTCACTAAATCTTTCCCCATCGATGAGTAATAATCAGCAACAAT
TACTGACACCTAATTCGGCATCGAAGAGTAAAAACAATAATAAAAAAAG
AAATTACATGGATGAAGATACTAACGAGTCAATGACCGAGCCAAAGAAA
ACCAAAACTACTAAACCTGGCAAACAAACAAAATCCCAATCTTTATCAG
TTTTATCCACCCCCAAAAAGGGTTCCTCTGCATCTCTTTCTACATTTGC
AAGCTCCAAGAATATTTCGCCAGATTCTTCTCTGTCGCATAATGCATCG
TCAAATACTTATGTTACTGCCGCTGCCGCTGCACCAAGGCTTTCTAAGC
TTTTGCCGAAAAATGGGTTTAAGAAAAATTCACGTAGCTCTTCTGAACT
GGCTGCTATCCATAAAGTAATCTCTACACAGACTCCAATTGAGAGCTCT
TCAGAGAGCTCTCAATATAACAGTAGTAGTAGTTCACCAGTTAATAGTG
CAGCTGCTTCTTCTGCTGAATCTTTATCCGACATCAATTCCAGTCAGGA
TAACGGAAGAGAATCAAACCCAAGTTCCCAAGAATCACGAAACGAAGTT
ACGAATTGGATGAAAATTGTGAGAAATGGATTTTTGACACATGATATTG
AATCTCCTGAATCAATCACATTAGATGACCTAGAAAATATATTCAATTG A
[0141] The TPI1 promoter region used for GDS1s over-expression
shown, below, as SEQ ID NO: 3:
TABLE-US-00005 TCTTCAGATTCCCTCATGGAGAAAGTGCGGCAGATGTATATGACAGAGT
CGCCAGTTTCCAAGAGACTTTATTCAGGCACTTCCATGATAGGCAAGAG
AGAAGACCCAGAGATGTTGTTGTCCTAGTTACACATGGTATTTATTCCA
GAGTATTCCTGATGAAATGGTTTAGATGGACATACGAAGAGTTTGAATC
GTTTACCAATGTTCCTAACGGGAGCGTAATGGTGATGGAACTGGACGAA
TCCATCAATAGATACGTCCTGAGGACCGTGCTACCCAAATGGACTGATT
GTGAGGGAGACCTAACTACATAGTGTTTAAAGATTACGGATATTTAACT
TACTTAGAATAATGCCATTTTTTTGAGTTATAATAATCCTACGTTAGTG
TGAGCGGGATTTAAACTGTGAGGACCTTAATACATTCAGACACTTCTGC
GGTATCACCCTACTTATTCCCTTCGAGATTATATCTAGGAACCCATCAG
GTTGGTGGAAGATTACCCGTTCTAAGACTTTTCAGCTTCCTCTATTGAT
GTTACACCTGGACACCCCTTTTCTGGCATCCAGTTTTTAATCTTCAGTG
GCATGTGAGATTCTCCGAAATTAATTAAAGCAATCACACAATTCTCTCG
GATACCACCTCGGTTGAAACTGACAGGTGGTTTGTTACGCATGCTAATG
CAAAGGAGCCTATATACCTTTGGCTCGGCTGCTGTAACAGGGAATATAA
AGGGCAGCATAATTTAGGAGTTTAGTGAACTTGCAACATTTACTATTTT
CCCTTCTTACGTAAATATTTTTCTTTTTAATTCTAAATCAATCTTTTTC
AATTTTTTGTTTGTATTCTTTTCTTGCTTAAATCTATAACTACAAAAAA
CACATACATAAACTAAA
[0142] The TGDS1 terminator region used for GDS1s over-expression
shown, below, as SEQ ID NO: 4:
TABLE-US-00006 TTTTTATCTCCCTTTACAAGAGCATAACGGCTGCTCTACACCTATGTCG
TTGTTTTTTTTTTTTCAACTAATAATATGTGTTCCTCTCATTTGGACAA
TTTTTAGCTAGTTCTAACTTTCACTACAATATTTAAATAAATAAACAAC
CATAAATAAATAAATGAAAAACAATTAAACCGTTAGAGGTGGACTAATT
TACTGTTAATGACAGTAATTTTTTTTTTTTTGGCTGTTTTCGGTTATTC
CGGATATATATGGATTGATCTTCATTTACCCCACAGTTAGTTTATCCGA AATTTA
Example 3
Alcohol Production Using Yeast that Over-Express GDS1
[0143] Strains over-expressing GDS1 were tested in an Ankom assay,
containing 50 g liquefact, as described in Example 1. Fermentations
were performed at 32.degree. C. for 55 hours. Samples from the end
of fermentation were analyzed by HPLC. The results are summarized
in Tables 2 and 3.
TABLE-US-00007 TABLE 2 HPLC results with strains FG and FG-TS using
an Ankom assay EtOH Acetate Glycerol Acetate Ethanol increase
reduction Strain (g/L) (g/L) (g/L) (%) (%) FG 14.7 0.74 137.7 -0-
-0- FG-TS 14.8 0.53 138.2 0.3% 28.4%
TABLE-US-00008 TABLE 3 HPLC results with strains FG-PKL and
FG-PKL-TS using an Ankom assay EtOH Acetate Glycerol Acetate
Ethanol increase reduction Strain (g/L) (g/L) (g/L) (%) (%) FG-PKL
12.1 1.31 144.0 -0- -0- FG-PKL-TS 11.9 1.09 144.7 0.5% 16.8%
[0144] Over-expression of GDS1 resulted in a decrease of acetate
production of about 28% in FG yeast, which is recognized as a
robust, non-genetically-engineered, high-ethanol-producing yeast
for the fuel ethanol industry. Over-expression of GDS1 resulted in
a decrease of acetate production by of about 16.8% in FG yeast
engineered to have an exogenous PKL pathway. Furthermore,
over-expression GDS1 resulted in an increase of 0.3% and 0.5% in
ethanol production in FG and FG-PKL, respectively. These results
demonstrate that GDS1 over-expression is beneficial for reducing
acetate, and increasing ethanol production in engineered yeast
strains.
* * * * *