U.S. patent application number 14/873956 was filed with the patent office on 2016-01-28 for increased heterologous fe-s enzyme activity in yeast.
The applicant listed for this patent is Butamax Advanced Biofuels LLC. Invention is credited to Larry Cameron Anthony, Lori Ann Maggio-Hall, Steven Cary Rothman, Jean-Francois Tomb.
Application Number | 20160024534 14/873956 |
Document ID | / |
Family ID | 41267090 |
Filed Date | 2016-01-28 |
United States Patent
Application |
20160024534 |
Kind Code |
A1 |
Anthony; Larry Cameron ; et
al. |
January 28, 2016 |
Increased Heterologous Fe-S Enzyme Activity in Yeast
Abstract
Yeast strains were engineered that have increased activity of
heterologous proteins that require binding of an Fe--S cluster for
their activity. The yeast strains have reduced activity of an
endogenous Fe--S protein. Activities of heterologous fungal or
plant 2Fe-2S dihydroxy-acid dehydratases and Fe--S propanediol
dehydratase reactivase were increased for increased production of
products made using biosynthetic pathways including these enzymes,
such as valine, isoleucine, leucine, pantothenic acid (vitamin B5),
isobutanol, 2-butanone and 2-butanol.
Inventors: |
Anthony; Larry Cameron;
(Aston, PA) ; Maggio-Hall; Lori Ann; (Wilmington,
DE) ; Rothman; Steven Cary; (Princeton, NJ) ;
Tomb; Jean-Francois; (Wilmington, DE) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Butamax Advanced Biofuels LLC |
Wilmington |
DE |
US |
|
|
Family ID: |
41267090 |
Appl. No.: |
14/873956 |
Filed: |
October 2, 2015 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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12569069 |
Sep 29, 2009 |
9206447 |
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14873956 |
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61100801 |
Sep 29, 2008 |
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61100806 |
Sep 29, 2008 |
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Current U.S.
Class: |
435/136 ;
435/160; 435/254.2; 435/254.21; 435/254.22; 435/254.23 |
Current CPC
Class: |
C12N 9/88 20130101; Y02E
50/10 20130101; C12P 7/26 20130101; C12P 7/16 20130101; C12Y
402/01009 20130101; C12P 7/40 20130101 |
International
Class: |
C12P 7/40 20060101
C12P007/40; C12P 7/16 20060101 C12P007/16; C12N 9/88 20060101
C12N009/88 |
Claims
1-24. (canceled)
25. A recombinant yeast host cell comprising at least two
engineered modifications comprising: (i) a heterologous
dihydroxy-acid dehydratase Fe--S cluster protein expressed in the
cytosol of the recombinant yeast host cell, wherein the
heterologous dihydroxy-acid dehydratase Fe--S cluster protein is a
polypeptide having an amino acid sequence that is at least 90%
identical to SEQ ID NO: 183 or 185; and (ii) an endogenous Fe--S
cluster protein with reduced expression, wherein the endogenous
Fe--S cluster protein is dihydroxy-acid dehydratase.
26. The recombinant yeast host cell of claim 25, wherein the yeast
is selected from the group consisting of Saccharomyces,
Schizosaccharomyces, Hansenula, Candida, Kluyveromyces, Yarrowia,
and Pichia.
27. The recombinant yeast host cell of claim 25, wherein the
endogenous Fe--S cluster protein is expressed in the
mitochondria.
28. The recombinant yeast host cell of claim 25, wherein the host
cell is Saccharomyces that expresses a gene encoding a polypeptide
having the amino acid sequence as set forth in SEQ ID NO: 183 or
185.
29. The recombinant yeast host cell of claim 25, wherein the cell
comprises an isobutanol biosynthetic pathway.
30. The recombinant yeast host cell of claim 29, wherein the cell
produces isobutanol.
31. A method for the production of isobutanol comprising growing
the recombinant yeast host cell of claim 30, under conditions
wherein isobutanol is produced.
32. A method for the conversion of 2,3-dihydroxyisovalerate to
.alpha.-ketoisovalerate comprising: a) providing the recombinant
yeast host cell of claim 25 and a source of
2,3-dihydroxyisovalerate; and b) growing the recombinant host cell
of a) with said source of 2,3-dihydroxyisovalerate under conditions
where the 2,3-dihydroxyisovalerate is converted by the host cell to
.alpha.-ketoisovalerate.
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application is related to and claims the benefit of
priority to U.S. Provisional Application Nos. 61/100,801 filed Sep.
29, 2008 and 61/100,806 filed Sep. 29, 2008. The entirety of each
is hereby incorporated by reference.
FIELD OF THE INVENTION
[0002] The invention relates to the field of industrial
microbiology and the expression of proteins that require an
iron-sulfur cluster for activity. More specifically, expression of
heterologous Fe--S protein activity in yeast cells is improved
through specific host gene inactivation.
BACKGROUND OF THE INVENTION
[0003] Engineering of yeast for fermentative production of
commercial products is an active and growing field. Enzymatic
pathways engineered for biosynthesis of some products include
enzymes that require binding of an iron-sulfur (Fe--S) cluster for
activity. Dihydroxy-acid dehydratase (DHAD) is one example. DHAD is
part of naturally occurring biosynthetic pathways producing valine,
isoleucine, leucine and pantothenic acid (vitamin B5). Increased
expression of DHAD activity is desired for enhanced microbial
production of branched chain amino acids or of pantothenic acid. In
addition, DHAD catalyzed conversion of 2,3-dihydroxyisovalerate to
.alpha.-ketoisovalerate is a common step in the multiple isobutanol
biosynthetic pathways that are disclosed in co-pending US Patent
Pub No. US 20070092957 A1. Disclosed therein is engineering of
recombinant microorganisms for production of isobutanol, which is
useful as a fuel additive and whose availability may reduce the
demand for petrochemical fuels.
[0004] Diol dehydratase provides an enzyme activity in a
biosynthetic pathway for production of 2-butanone and 2-butanol
that is disclosed in co-pending US Patent Pub No. US
2007-0292927A1. Disclosed in US Patent Pub No. US20090155870 is a
butanediol dehydratase that is useful for expression in this
pathway due to its coenzyme B-12 independence. A diol dehydratase
reactivase that is an Fe--S cluster protein required for activity
of the B12-independent butanediol dehydratase, is also disclosed in
US Patent Pub No. US20090155870. 2-Butanone, also referred to as
methyl ethyl ketone (MEK), is a widely used solvent, extractant and
activator of oxidative reactions, as well as a substrate for
chemical synthesis of 2-butanol. 2-butanol is useful as a fuel
additive, whose availability may reduce the demand for
petrochemical fuels.
[0005] For improved production of compounds synthesized in pathways
including an Fe--S cluster containing enzyme, it is desirable to
provide a host cell capable of expressing high levels of this
enzymatic activity in the production host of interest. Whereas a
number of commercially relevant bacteria and yeast can express
activity of Fe--S cluster containing proteins, this activity is at
levels far below what is commercially useful for enhancing
introduced biosynthetic pathways. Consequently a need exists for
the discovery of host cells capable of expressing activity of Fe--S
cluster containing proteins at levels high enough to enhance
introduced pathways that have Fe--S requirements. Obtaining high
functional expression of heterologous Fe--S cluster containing
enzymes is problematic due to the Fe--S cluster requirement, which
involves availability and proper loading of the cluster into the
apo-protein.
SUMMARY OF THE INVENTION
[0006] Provided herein are recombinant yeast host cells comprising
at least one heterologous Fe--S cluster protein wherein the yeast
host has reduced expression of at least one endogenous Fe--S
cluster protein.
[0007] The recombinant yeast cell may be grown under suitable
conditions for the production of products including isobutanol,
2-butanol and 2-butanone.
[0008] In one aspect, the recombinant yeast cell comprises a
disruption in the gene encoding the at least one endogenous Fe--S
cluster protein.
[0009] In another aspect, the endogenous Fe--S cluster protein is
selected from the group consisting of dihydroxy-acid dehydratase,
isopropylmalate dehydratase, sulfite reductase, glutamate
dehyddrogenase, biotin synthase, aconitase, homoaconitase, lipoate
synthase, ferredoxin maturation, NADH ubiquinone oxidoreductase,
succinate dehydrogenase, ubiquinol-cytochrome-c reductase, ABC
protein Rli1, NTPase Nbp35, and hydrogenase-like protein.
[0010] In another aspect, the yeast is selected from the group
consisting of Saccharomyces, Schizosaccharomyces, Hansenula,
Candida, Kluyveromyces, Yarrowia and Pichia.
[0011] In another aspect, the endogenous Fe--S protein is expressed
in the mitochondria, and in another embodiment, the endogenous
Fe--S cluster protein has an activity selected from the group
consisting of: dihydroxy-acid dehydratase and isopropylmalate
dehydratase activity.
[0012] In another aspect, the host cell is Saccharomyces expressing
a gene encoding a polypeptide having the amino acid sequence as set
forth in SEQ ID NO:114.
[0013] In some embodiments, the at least one heterologous Fe--S
cluster protein is selected from the group consisting of fungal
2Fe-2S dihydroxy-acid dehydratases and plant 2Fe-2S dihydroxy-acid
dehydratases. In one embodiment, the heterologous fungal or plant
2Fe-2S cluster dihydroxy-acid dehydratase is expressed in the
cytosol. In one embodiment, the heterologous fungal or plant 2Fe-2S
cluster dihydroxy-acid dehydratase is a polypeptide having an amino
acid sequence that matches the Profile HMM of table 9 with an E
value of <10.sup.-5 wherein the polypeptide additionally
comprises all three conserved cysteines, corresponding to positions
56, 129, and 201 in the amino acids sequences of the Streptococcus
mutans DHAD enzyme corresponding to SEQ ID NO:179. In one
embodiment, the heterologous fungal or plant 2Fe-2S cluster
dihydroxy-acid dehydratase is a polypeptide having an amino acid
sequence that has at least about 95% sequence identity to an amino
acid sequence selected from the group consisting of SEQ ID NOs:46,
48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80,
82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110,
112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136,
138, 140, 142, 144, 146, 148, 150 and 152. In one embodiment, the
heterologous fungal or plant 2Fe-2S cluster dihydroxy-acid
dehydratase is a polypeptide having an amino acid sequence that is
at least about 90% identical to SEQ ID NO:114 using the Clustal W
method of alignment using the default parameters of GAP PENALTY=10,
GAP LENGTH PENALTY=0.1, and Gonnet 250 series of protein weight
matrix over the full length of the protein sequence.
[0014] In another aspect, a method for the conversion of
2,3-dihydroxyisovalerate to .alpha.-ketoisovalerate is provided,
said method comprising:
[0015] a) providing (1) a recombinant yeast host cell comprising at
least one heterologous gene encoding a 2Fe-2S dihydroxy-acid
dehydratase wherein the recombinant yeast host cell has reduced
activity of at least one endogenous Fe--S cluster protein; and (2)
a source of 2,3-dihydroxyisovalerate; and
[0016] b) growing the recombinant host cell of (a) with said source
of 2,3-dihydroxyisovalerate under conditions where the
2,3-dihydroxyisovalerate is converted by the host cell to
.alpha.-ketoisovalerate.
[0017] In another aspect, a method for the conversion of
2,3-butanediol to 2-butanone is provided, said method
comprising:
[0018] a) providing (1) a recombinant yeast host cell comprising at
least one heterologous gene encoding a Fe--S propanediol
dehydratase reactivase wherein the recombinant yeast host cell has
reduced activity of at least one endogenous Fe--S cluster protein;
and (2) a source of 2,3-butanediol; and
[0019] b) growing the recombinant host cell of (a) with said source
of 2,3-butanediol under conditions where 2,3-butanediol is
converted by the hots cell to 2-butanone.
[0020] Also provided is a method for the production of isobutanol
comprising growing a recombinant yeast host cell disclosed herein
under conditions wherein isobutanol is produced.
[0021] In other embodiments, the at least one heterologous Fe--S
cluster protein has Fe--S propanediol dehydratase reactivase
activity. In some embodiments, the at least one heterologous Fe--S
cluster protein having Fe--S propanediol dehydratase reactivase
activity is a propanediol dehydratase reactivase having an amino
acid sequence that is at least about 90% identical to the amino
acid sequence as set forth in SEQ ID NO:44 using the Clustal W
method of alignment using the default parameters of GAP PENALTY=10,
GAP LENGTH PENALTY=0.1, and Gonnet 250 series of protein weight
matrix over the full length of the protein sequence.
[0022] In some embodiments, the cell produces 2-butanol, and in
some embodiments the cell produces 2-butanone. In some embodiments,
the cell comprises a 2-butanol biosynthetic pathway, and in some
embodiments, the cell comprises a 2-butanone biosynthetic
pathway.
BRIEF DESCRIPTION OF THE FIGURES AND SEQUENCE DESCRIPTIONS
[0023] The invention can be more fully understood from the
following detailed description, figures, and the accompanying
sequence descriptions, which form a part of this application.
[0024] FIG. 1 shows biosynthetic pathways for isobutanol
production.
[0025] FIG. 2 shows a biosynthetic pathway for 2-butanone and
2-butanol production.
[0026] Table 9 is a table of the Profile HMM for dihydroxy-acid
dehydratases based on enzymes with assayed function prepared as
described in Example 1. Table 9 is submitted herewith
electronically and is incorporated herein by reference.
[0027] The following sequences conform with 37 C.F.R. 1.821-1.825
("Requirements for Patent Applications Containing Nucleotide
Sequences and/or Amino Acid Sequence Disclosures--the Sequence
Rules") and are consistent with World Intellectual Property
Organization (WIPO) Standard ST.25 (1998) and the sequence listing
requirements of the EPO and PCT (Rules 5.2 and 49.5(a-bis), and
Section 208 and Annex C of the Administrative Instructions). The
symbols and format used for nucleotide and amino acid sequence data
comply with the rules set forth in 37 C.F.R. .sctn.1.822.
TABLE-US-00001 TABLE 1 Inactivation target Fe--S protein encoding
genes SEQ ID NO: SEQ ID NO: Organism and gene Nucleic Acid Peptide
Saccharomyces cerevisiae LEU1 1 2 Schizosaccharomyces pombe LEU1 3
4 Candida galbrata CBS 138 LEU1 5 6 Candida albicans SC 5314 LEU1 7
8 Kluyveromyces lactis LEU1 9 10 Yarrowia lipolytica LEU1 11 12
Pichia stipitis LEU1 13 14 Saccharomyces cerevisiae YJM789 111 112
ILV3 Schizosaccharomyces pombe ILV3 93 94 Candida galbrata CBS 138
ILV3 107 108 Candida albicans SC5314 ILV3 101 102 Kluyveromyces
lactis ILV3 113 114 Yarrowia lipolytica ILV3 105 106 Pichia
stipitis CBS 6054 ILV3 103 104 Saccharomyces cerevisiae ACO1 153
154 Schizosaccharomyces pombe 155 156 (chromosome II) ACO1
Schizosaccharomyces pombe 157 158 (chromosome I) ACO1 Kluyveromyces
lactis NRRL Y-1140 159 160 ACO1 Candida albicans SC5314 ACO1 161
162 Yarrowia lipolytica CLIB122 ACO1 163 164 Pichia stipitis CBS
6054 ACO1 165 166 Candida glabrata CBS138 167 168 (chromosome F)
ACO1 Candida glabrata CBS138 169 170 (chromosome D) ACO1 Candida
glabrata CBS138 171 172 (chromosome K) ACO1
TABLE-US-00002 TABLE 2 Fungal and plant 2Fe--2S DHADs in addition
to those in Table 1 SEQ ID NO: SEQ ID NO: Description Nucleic acid
Peptide Chlamydomonas reinhardtii 45 46 Ostreococcus lucimarinus
CCE9901 47 48 Vitis vinifera 49 50 (Unnamed protein product:
CAO71581.1) Vitis vinifera 51 52 (CAN67446.1) Arabidopsis thaliana
53 54 Oryza sativa (indica cultivar-group) 55 56 Physcomitrella
patens subsp. patens 57 58 Chaetomium globosum CBS 148.51 59 60
Neurospora crassa OR74A 61 62 Magnaporthe grisea 70-15 63 64
Gibberella zeae PH-1 65 66 Aspergillus niger 67 68 Neosartorya
fischeri NRRL 181 69 70 (XP_001266525.1) Neosartorya fischeri NRRL
181 71 72 (XP_001262996.1) Aspergillus niger 73 74 (An03g04520)
Aspergillus niger 75 76 (An14g03280) Aspergillus terreus NIH2624 77
78 Aspergillus clavatus NRRL 1 79 80 Aspergillus nidulans FGSC A4
81 82 Aspergillus oryzae 83 84 Ajellomyces capsulatus NAm1 85 86
Coccidioides immitis RS 87 88 Botryotinia fuckeliana B05.10 89 90
Phaeosphaeria nodorum SN15 91 92 Pichia guilliermondii ATCC 6260 95
96 Debaryomyces hansenii CBS767 97 98 Lodderomyces elongisporus
NRRL 99 100 YB-4239 Vanderwaltozyma polyspora DSM 109 110 70294
Ashbya gossypii ATCC 10895 115 116 Laccaria bicolor S238N-H82 117
118 Coprinopsis cinerea okayama7#130 119 120 Cryptococcus
neoformans var. 121 122 neoformans JEC21 Ustilago maydis 521 123
124 Malassezia globosa CBS 7966 125 126 Aspergillus clavatus NRRL 1
127 128 Neosartorya fischeri NRRL 181 129 130 (Putative)
Aspergillus oryzae 131 132 Aspergillus niger (An18g04160) 133 134
Aspergillus terreus NIH2624 135 136 Coccidioides immitis RS 137 138
(CIMG_04591) Paracoccidioides brasiliensis 139 140 Phaeosphaeria
nodorum SN15 141 142 Gibberella zeae PH-1 143 144 Neurospora crassa
OR74A 145 146 Coprinopsis cinerea okayama 7#130 147 148 Laccaria
bicolor S238N-H82 149 150 Ustilago maydis 521 151 152
TABLE-US-00003 TABLE 3 Expression genes SEQ ID NO: SEQ ID NO:
Description Nucleic acid Peptide Roseburia inulinivorans (RdhtA) 15
43 Roseburia inulinivorans (RdhtB) 16 44 Bacillus subtilis (alsS)
27 28 Vibrio cholerae (KARI) 35 36 Pseudomonas aeruginosa PAO1 37
38 (KARI) Pseudomonas fluorescens PF5 39 40 (KARI) Achromobacter
xylosoxidans (sadB) 41 42 B12-independent glycerol dehydratase 190
191 from Clostridium butyricum B-12 independent butanediol 192 193
dehydratase reactivase from Clostridium butyricum
[0028] SEQ ID NO:17 is a synthetic rdhtAB sequence.
[0029] SEQ ID NOs:18-21 and 30-33 are primers for PCR, cloning or
sequencing analysis used a described in the Examples herein.
[0030] SEQ ID NO:22 is a dual terminator sequence.
[0031] SEQ ID NO:23 is the Saccharomyces cerevisiae ADH
terminator.
[0032] SEQ ID NO:24 is the Saccharomyces cerevisiae CYC1
terminator.
[0033] SEQ ID NO:25 is the Saccharomyces cerevisiae FBA
promoter.
[0034] SEQ ID NO:26 is the Saccharomyces cerevisiae GPM
promoter.
[0035] SEQ ID NO:29 is the pNY13 vector.
[0036] SEQ ID NO:34 is the Saccharomyces cerevisiae CUP1
promoter.
[0037] SEQ ID NO:173 is the codon optimized coding region for ILV3
DHAD from Kluyveromyces lactis.
TABLE-US-00004 TABLE 4 Functionally verified DHADs used for Profile
HMM SEQ ID NO: SEQ ID NO: Organism Nucleic acid Peptide
Nitrosomonas europaea ATCC 19718 174 175 Synechocystis sp. PCC 6803
176 177 Streptococcus mutans UA159 178 179 Streptococcus
thermophilus LMG 180 181 18311 Ralstonia metallidurans CH34 182 183
Ralstonia eutropha JMP134 184 185 Lactococcus lactis subsp.
cremoris 186 187 SK11 Flavobacterium johnsoniae UW101 188 189
DETAILED DESCRIPTION OF THE INVENTION
[0038] Disclosed herein is the discovery that introduced Fe--S
containing proteins in yeast host cells have high activity levels
when expression of endogenous Fe--S containing proteins is
inhibited or disrupted. The present invention relates to
recombinant yeast cells engineered to provide expression of at
least one heterologous protein that is an Fe--S cluster protein,
and engineered for reduced expression of at least one endogenous
Fe--S cluster protein. In these cells the activity of the
heterologous Fe--S cluster protein is improved, such that there is
improved production of a product made in a biosynthetic pathway
that includes the enzyme activity. Examples of commercially useful
products from a pathway including an Fe--S protein include valine,
isoleucine, leucine, pantothenic acid, isobutanol, 2-butanone and
2-butanol.
[0039] The following abbreviations and definitions will be used for
the interpretation of the specification and the claims.
[0040] As used herein, the terms "comprises," "comprising,"
"includes," "including," "has," "having," "contains" or
"containing," or any other variation thereof, are intended to cover
a non-exclusive inclusion. For example, a composition, a mixture,
process, method, article, or apparatus that comprises a list of
elements is not necessarily limited to only those elements but may
include other elements not expressly listed or inherent to such
composition, mixture, process, method, article, or apparatus.
Further, unless expressly stated to the contrary, "or" refers to an
inclusive or and not to an exclusive or. For example, a condition A
or B is satisfied by any one of the following: A is true (or
present) and B is false (or not present), A is false (or not
present) and B is true (or present), and both A and B are true (or
present).
[0041] Also, the indefinite articles "a" and "an" preceding an
element or component of the invention are intended to be
nonrestrictive regarding the number of instances (i.e. occurrences)
of the element or component. Therefore "a" or "an" should be read
to include one or at least one, and the singular word form of the
element or component also includes the plural unless the number is
obviously meant to be singular.
[0042] The term "invention" or "present invention" as used herein
is a non-limiting term and is not intended to refer to any single
embodiment of the particular invention but encompasses all possible
embodiments as described in the specification and the claims.
[0043] As used herein, the term "about" modifying the quantity of
an ingredient or reactant of the invention employed refers to
variation in the numerical quantity that can occur, for example,
through typical measuring and liquid handling procedures used for
making concentrates or use solutions in the real world; through
inadvertent error in these procedures; through differences in the
manufacture, source, or purity of the ingredients employed to make
the compositions or carry out the methods; and the like. The term
"about" also encompasses amounts that differ due to different
equilibrium conditions for a composition resulting from a
particular initial mixture. Whether or not modified by the term
"about", the claims include equivalents to the quantities. In one
embodiment, the term "about" means within 10% of the reported
numerical value, preferably within 5% of the reported numerical
value
[0044] The term "Fe--S cluster protein" is a protein that binds an
iron-sulfur cluster and requires the binding of the cluster for its
activity.
[0045] The term "2Fe-2S DHAD" refers to DHAD enzymes requiring a
bound [2Fe-2S].sup.2+ cluster for activity.
[0046] The term "Fe--S propanediol dehydratase reactivase" refers
to propanediol dehydratase reactivases requiring a bound Fe--S
cluster for activity.
[0047] The term "isobutanol biosynthetic pathway" refers to an
enzyme pathway to produce isobutanol from pyruvate.
[0048] The term "2-butanol biosynthetic pathway" refers to an
enzyme pathway to produce 2-butanol from pyruvate.
[0049] The term "2-butanone biosynthetic pathway" refers to an
enzyme pathway to produce 2-butanone from pyruvate.
[0050] There term "Dihydroxy-acid dehydratase", also abbreviated
DHAD, will refer to an enzyme that converts
2,3-dihydroxyisovalerate to .alpha.-ketoisovalerate.
[0051] The term "butanediol dehydratase", also known as "diol
dehydratase" or "propanediol dehydratase" refers to a polypeptide
(or polypeptides) having an enzyme activity that catalyzes the
conversion of 2,3-butanediol to 2-butanone. Butanediol dehydratases
that do not utilize the cofactor adenosyl cobalamin (also known as
coenzyme B12, or vitamin B12; although vitamin B12 may refer also
to other forms of cobalamin that are not coenzyme B12) are coenzyme
B12-independent diol dehydratases that require association with a
diol dehydratase reactivase that is a Fe--S cluster protein.
Examples of B12-independent diol dehydratases include those from
Clostridium glycolicum (Hartmanis et al. (1986) Arch. Biochem.
Biophys. 245:144-152), Clostridium butyricum (protein SEQ ID
NO:191; coding region SEQ ID NO:190; O'Brien et al. (2004)
Biochemistry 43:4635-4645), and Roseburia inulinivorans (coding:
SEQ ID NO:15; protein: SEQ ID NO:43; disclosed in co-pending US
Patent Pub No. US20090155870.
[0052] The term "propanediol dehydratase reactivase", also known as
"diol dehydratase reactivase" or "butanediol dehydratase
reactivase" refers to a reactivating factor for diol dehydratase,
an enzyme which undergoes suicide inactivation during catalysis.
Diol dehydratase reactivases associated with coenzyme
B12-independent diol dehydratases may be Fe--S cluster proteins.
Examples include those from Clostridium glycolicum (Hartmanis et
al. (1986) Arch. Biochem. Biophys. 245:144-152), Clostridium
butyricum (protein SEQ ID NO:193; coding region SEQ ID NO:192;
O'Brien et al. (2004) Biochemistry 43:4635-4645), and Roseburia
inulinivorans (coding: SEQ ID NO:16; protein: SEQ ID NO:44;
disclosed in commonly owned and co-pending US Patent Pub No.
US20090155870).
[0053] The term "reduced expression" as it applies to the
expression of a protein in a cell host will include those
situations where the activity of the protein is diminished as
compared with a wildtype form (as with antisense technology for
example) or substantially eliminated as with gene disruption,
deletion or inactivation for example.
[0054] The term "carbon substrate" or "fermentable carbon
substrate" refers to a carbon source capable of being metabolized
by host organisms of the present invention and particularly carbon
sources selected from the group consisting of monosaccharides,
oligosaccharides, polysaccharides, and one-carbon substrates or
mixtures thereof.
[0055] The term "gene" refers to a nucleic acid fragment that is
capable of being expressed as a specific protein, optionally
including regulatory sequences preceding (5' non-coding sequences)
and following (3' non-coding sequences) the coding sequence.
"Native gene" refers to a gene as found in nature with its own
regulatory sequences. "Chimeric gene" refers to any gene that is
not a native gene, comprising regulatory and coding sequences that
are not found together in nature. Accordingly, a chimeric gene may
comprise regulatory sequences and coding sequences that are derived
from different sources, or regulatory sequences and coding
sequences derived from the same source, but arranged in a manner
different than that found in nature. "Endogenous gene" refers to a
native gene in its natural location in the genome of an organism. A
"foreign gene" or "heterologous gene" refers to a gene not normally
found in the host organism, but that is introduced into the host
organism by gene transfer. "Heterologous gene" includes a native
coding region, or portion thereof, that is reintroduced into the
source organism in a form that is different from the corresponding
native gene. For example, a heterologous gene may include a native
coding region that is a portion of a chimeric gene including
non-native regulatory regions that is reintroduced into the native
host. Also a foreign gene can comprise native genes inserted into a
non-native organism, or chimeric genes. A "transgene" is a gene
that has been introduced into the genome by a transformation
procedure.
[0056] As used herein the term "coding region" refers to a DNA
sequence that codes for a specific amino acid sequence. "Suitable
regulatory sequences" refer to nucleotide sequences located
upstream (5' non-coding sequences), within, or downstream (3'
non-coding sequences) of a coding sequence, and which influence the
transcription, RNA processing or stability, or translation of the
associated coding sequence. Regulatory sequences may include
promoters, translation leader sequences, introns, polyadenylation
recognition sequences, RNA processing site, effector binding site
and stem-loop structure.
[0057] The term "promoter" refers to a DNA sequence capable of
controlling the expression of a coding sequence or functional RNA.
In general, a coding sequence is located 3' to a promoter sequence.
Promoters may be derived in their entirety from a native gene, or
be composed of different elements derived from different promoters
found in nature, or even comprise synthetic DNA segments. It is
understood by those skilled in the art that different promoters may
direct the expression of a gene in different tissues or cell types,
or at different stages of development, or in response to different
environmental or physiological conditions. Promoters which cause a
gene to be expressed in most cell types at most times are commonly
referred to as "constitutive promoters". It is further recognized
that since in most cases the exact boundaries of regulatory
sequences have not been completely defined, DNA fragments of
different lengths may have identical promoter activity.
[0058] The term "operably linked" refers to the association of
nucleic acid sequences on a single nucleic acid fragment so that
the function of one is affected by the other. For example, a
promoter is operably linked with a coding sequence when it is
capable of effecting the expression of that coding sequence (i.e.,
that the coding sequence is under the transcriptional control of
the promoter). Coding sequences can be operably linked to
regulatory sequences in sense or antisense orientation.
[0059] The term "expression", as used herein, refers to the
transcription and stable accumulation of sense (mRNA) or antisense
RNA derived from the nucleic acid fragment of the invention.
Expression may also refer to translation of mRNA into a
polypeptide.
[0060] As used herein the term "transformation" refers to the
transfer of a nucleic acid fragment into a host organism, resulting
in genetically stable inheritance. Host organisms containing the
transformed nucleic acid fragments are referred to as "transgenic"
or "recombinant" or "transformed" organisms.
[0061] The terms "plasmid" and "vector" as used herein, refer to an
extra chromosomal element often carrying genes which are not part
of the central metabolism of the cell, and usually in the form of
circular double-stranded DNA molecules. Such elements may be
autonomously replicating sequences, genome integrating sequences,
phage or nucleotide sequences, linear or circular, of a single- or
double-stranded DNA or RNA, derived from any source, in which a
number of nucleotide sequences have been joined or recombined into
a unique construction which is capable of introducing a promoter
fragment and DNA sequence for a selected gene product along with
appropriate 3' untranslated sequence into a cell.
[0062] As used herein the term "codon degeneracy" refers to the
nature in the genetic code permitting variation of the nucleotide
sequence without effecting the amino acid sequence of an encoded
polypeptide. The skilled artisan is well aware of the "codon-bias"
exhibited by a specific host cell in usage of nucleotide codons to
specify a given amino acid. Therefore, when synthesizing a gene for
improved expression in a host cell, it is desirable to design the
gene such that its frequency of codon usage approaches the
frequency of preferred codon usage of the host cell.
[0063] The term "codon-optimized" as it refers to genes or coding
regions of nucleic acid molecules for transformation of various
hosts, refers to the alteration of codons in the gene or coding
regions of the nucleic acid molecules to reflect the typical codon
usage of the host organism without altering the polypeptide encoded
by the DNA.
[0064] As used herein, an "isolated nucleic acid fragment" or
"isolated nucleic acid molecule" will be used interchangeably and
will mean a polymer of RNA or DNA that is single- or
double-stranded, optionally containing synthetic, non-natural or
altered nucleotide bases. An isolated nucleic acid fragment in the
form of a polymer of DNA may be comprised of one or more segments
of cDNA, genomic DNA or synthetic DNA.
[0065] A nucleic acid fragment is "hybridizable" to another nucleic
acid fragment, such as a cDNA, genomic DNA, or RNA molecule, when a
single-stranded form of the nucleic acid fragment can anneal to the
other nucleic acid fragment under the appropriate conditions of
temperature and solution ionic strength. Hybridization and washing
conditions are well known and exemplified in Sambrook, J., Fritsch,
E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual,
2.sup.nd ed., Cold Spring Harbor Laboratory: Cold Spring Harbor,
N.Y. (1989), particularly Chapter 11 and Table 11.1 therein
(entirely incorporated herein by reference). The conditions of
temperature and ionic strength determine the "stringency" of the
hybridization. Stringency conditions can be adjusted to screen for
moderately similar fragments (such as homologous sequences from
distantly related organisms), to highly similar fragments (such as
genes that duplicate functional enzymes from closely related
organisms). Post-hybridization washes determine stringency
conditions. One set of preferred conditions uses a series of washes
starting with 6.times.SSC, 0.5% SDS at room temperature for 15 min,
then repeated with 2.times.SSC, 0.5% SDS at 45.degree. C. for 30
min, and then repeated twice with 0.2.times.SSC, 0.5% SDS at
50.degree. C. for 30 min. A more preferred set of stringent
conditions uses higher temperatures in which the washes are
identical to those above except for the temperature of the final
two 30 min washes in 0.2.times.SSC, 0.5% SDS was increased to
60.degree. C. Another preferred set of highly stringent conditions
uses two final washes in 0.1.times.SSC, 0.1% SDS at 65.degree. C.
An additional set of stringent conditions include hybridization at
0.1.times.SSC, 0.1% SDS, 65.degree. C. and washes with 2.times.SSC,
0.1% SDS followed by 0.1.times.SSC, 0.1% SDS, for example.
[0066] Hybridization requires that the two nucleic acids contain
complementary sequences, although depending on the stringency of
the hybridization, mismatches between bases are possible. The
appropriate stringency for hybridizing nucleic acids depends on the
length of the nucleic acids and the degree of complementation,
variables well known in the art. The greater the degree of
similarity or homology between two nucleotide sequences, the
greater the value of Tm for hybrids of nucleic acids having those
sequences. The relative stability (corresponding to higher Tm) of
nucleic acid hybridizations decreases in the following order:
RNA:RNA, DNA:RNA, DNA:DNA. For hybrids of greater than 100
nucleotides in length, equations for calculating Tm have been
derived (see Sambrook et al., supra, 9.50-9.51). For hybridizations
with shorter nucleic acids, i.e., oligonucleotides, the position of
mismatches becomes more important, and the length of the
oligonucleotide determines its specificity (see Sambrook et al.,
supra, 11.7-11.8). In one embodiment the length for a hybridizable
nucleic acid is at least about 10 nucleotides. Preferably a minimum
length for a hybridizable nucleic acid is at least about 15
nucleotides; more preferably at least about 20 nucleotides; and
most preferably the length is at least about 30 nucleotides.
Furthermore, the skilled artisan will recognize that the
temperature and wash solution salt concentration may be adjusted as
necessary according to factors such as length of the probe.
[0067] A "substantial portion" of an amino acid or nucleotide
sequence is that portion comprising enough of the amino acid
sequence of a polypeptide or the nucleotide sequence of a gene to
putatively identify that polypeptide or gene, either by manual
evaluation of the sequence by one skilled in the art, or by
computer-automated sequence comparison and identification using
algorithms such as BLAST (Altschul, S. F., et al., J. Mol. Biol.,
215:403-410 (1993)). In general, a sequence of ten or more
contiguous amino acids or thirty or more nucleotides is necessary
in order to putatively identify a polypeptide or nucleic acid
sequence as homologous to a known protein or gene. Moreover, with
respect to nucleotide sequences, gene specific oligonucleotide
probes comprising 20-30 contiguous nucleotides may be used in
sequence-dependent methods of gene identification (e.g., Southern
hybridization) and isolation (e.g., in situ hybridization of
bacterial colonies or bacteriophage plaques). In addition, short
oligonucleotides of 12-15 bases may be used as amplification
primers in PCR in order to obtain a particular nucleic acid
fragment comprising the primers. Accordingly, a "substantial
portion" of a nucleotide sequence comprises enough of the sequence
to specifically identify and/or isolate a nucleic acid fragment
comprising the sequence. The instant specification teaches the
complete amino acid and nucleotide sequence encoding particular
proteins. The skilled artisan, having the benefit of the sequences
as reported herein, may now use all or a substantial portion of the
disclosed sequences for purposes known to those skilled in this
art. Accordingly, the instant invention comprises the complete
sequences as reported in the accompanying Sequence Listing, as well
as substantial portions of those sequences as defined above.
[0068] The term "complementary" is used to describe the
relationship between nucleotide bases that are capable of
hybridizing to one another. For example, with respect to DNA,
adenosine is complementary to thymine and cytosine is complementary
to guanine.
[0069] The term "percent identity", as known in the art, is a
relationship between two or more polypeptide sequences or two or
more polynucleotide sequences, as determined by comparing the
sequences. In the art, "identity" also means the degree of sequence
relatedness between polypeptide or polynucleotide sequences, as the
case may be, as determined by the match between strings of such
sequences. "Identity" and "similarity" can be readily calculated by
known methods, including but not limited to those described in: 1)
Computational Molecular Biology (Lesk, A. M., Ed.) Oxford
University: NY (1988); 2) Biocomputing: Informatics and Genome
Projects (Smith, D. W., Ed.) Academic: NY (1993); 3) Computer
Analysis of Sequence Data, Part I (Griffin, A. M., and Griffin, H.
G., Eds.) Humania: NJ (1994); 4) Sequence Analysis in Molecular
Biology (von Heinje, G., Ed.) Academic (1987); and 5) Sequence
Analysis Primer (Gribskov, M. and Devereux, J., Eds.) Stockton: NY
(1991).
[0070] Preferred methods to determine identity are designed to give
the best match between the sequences tested. Methods to determine
identity and similarity are codified in publicly available computer
programs. Sequence alignments and percent identity calculations may
be performed using the MegAlign.TM. program of the LASERGENE
bioinformatics computing suite (DNASTAR Inc., Madison, Wis.).
Multiple alignment of the sequences is performed using the "Clustal
method of alignment" which encompasses several varieties of the
algorithm including the "Clustal V method of alignment"
corresponding to the alignment method labeled Clustal V (described
by Higgins and Sharp, CABIOS. 5:151-153 (1989); Higgins, D. G. et
al., Comput. Appl. Biosci., 8:189-191 (1992)) and found in the
MegAlign.TM. program of the LASERGENE bioinformatics computing
suite (DNASTAR Inc.). For multiple alignments, the default values
correspond to GAP PENALTY=10 and GAP LENGTH PENALTY=10. Default
parameters for pairwise alignments and calculation of percent
identity of protein sequences using the Clustal method are
KTUPLE=1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5. For
nucleic acids these parameters are KTUPLE=2, GAP PENALTY=5,
WINDOW=4 and DIAGONALS SAVED=4. After alignment of the sequences
using the Clustal V program, it is possible to obtain a "percent
identity" by viewing the "sequence distances" table in the same
program. Additionally the "Clustal W method of alignment" is
available and corresponds to the alignment method labeled Clustal W
(described by Higgins and Sharp, CABIOS. 5:151-153 (1989); Higgins,
D. G. et al., Comput. Appl. Biosci. 8:189-191(1992)) and found in
the MegAlign.TM. v6.1 program of the LASERGENE bioinformatics
computing suite (DNASTAR Inc.). Default parameters for multiple
alignment (GAP PENALTY=10, GAP LENGTH PENALTY=0.2, Delay Divergen
Seqs(%)=30, DNA Transition Weight=0.5, Protein Weight Matrix=Gonnet
Series, DNA Weight Matrix=IUB). After alignment of the sequences
using the Clustal W program, it is possible to obtain a "percent
identity" by viewing the "sequence distances" table in the same
program.
[0071] It is well understood by one skilled in the art that many
levels of sequence identity are useful in identifying polypeptides,
from other species, wherein such polypeptides have the same or
similar function or activity. Useful examples of percent identities
include, but are not limited to: 55%, 60%, 65%, 70%, 75%, 80%, 85%,
90%, or 95%, or any integer percentage from 55% to 100% may be
useful in describing the present invention, such as 55%, 56%, 57%,
58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%,
71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%,
84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%, 98% or 99%. Suitable nucleic acid fragments not only have the
above homologies but typically encode a polypeptide having at least
50 amino acids, preferably at least 100 amino acids, more
preferably at least 150 amino acids, still more preferably at least
200 amino acids, and most preferably at least 250 amino acids.
[0072] The term "sequence analysis software" refers to any computer
algorithm or software program that is useful for the analysis of
nucleotide or amino acid sequences. "Sequence analysis software"
may be commercially available or independently developed. Typical
sequence analysis software will include, but is not limited to: 1)
the GCG suite of programs (Wisconsin Package Version 9.0, Genetics
Computer Group (GCG), Madison, Wis.); 2.) BLASTP, BLASTN, BLASTX
(Altschul et al., J. Mol. Biol., 215:403-410 (1990)); 3.) DNASTAR
(DNASTAR, Inc. Madison, Wis.); 4.) Sequencher (Gene Codes
Corporation, Ann Arbor, Mich.); and 5) the FASTA program
incorporating the Smith-Waterman algorithm (W. R. Pearson, Comput.
Methods Genome Res., [Proc. Int. Symp.] (1994), Meeting Date 1992,
111-20. Editor(s): Suhai, Sandor. Plenum: New York, N.Y.). Within
the context of this application it will be understood that where
sequence analysis software is used for analysis, that the results
of the analysis will be based on the "default values" of the
program referenced, unless otherwise specified. As used herein
"default values" will mean any set of values or parameters that
originally load with the software when first initialized.
[0073] Standard recombinant DNA and molecular cloning techniques
used here are well known in the art and are described by Sambrook,
J., Fritsch, E. F. and Maniatis, T., Molecular Cloning: A
Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory
Press, Cold Spring Harbor, N.Y. (1989) (hereinafter "Maniatis");
and by Silhavy, T. J., Bennan, M. L. and Enquist, L. W.,
Experiments with Gene Fusions, Cold Spring Harbor Laboratory Press,
Cold Spring Harbor, N.Y. (1984); and by Ausubel, F. M. et al.,
Current Protocols in Molecular Biology, published by Greene
Publishing Assoc. and Wiley-Interscience (1987). Additional methods
used here are in Methods in Enzymology, Volume 194, Guide to Yeast
Genetics and Molecular and Cell Biology (Part A, 2004, Christine
Guthrie and Gerald R. Fink (Eds.), Elsevier Academic Press, San
Diego, Calif.).
Discovery of Improved Fe--S Cluster Protein Activity in Yeast
[0074] Proteins that contain a bound iron-sulfur cluster (Fe--S)
that is required for their activity may have low activity when used
in heterologous expression systems. Formation of Fe--S clusters and
their transfer to apo-proteins is a multistep process involving at
least several proteins including cysteine desulfurase, a scaffold
protein and a chaperone. Thus a heterologous Fe--S protein may not
be effectively composed by the endogenous host system. Applicants
have discovered a way to increase activity of an Fe--S protein
expressed as a heterologous protein in a yeast host cell.
Applicants have found that by reducing production of an endogenous
Fe--S protein in the yeast host cell, an improvement in activity of
an expressed heterologous Fe--S cluster protein can be achieved.
Expression in yeast of either heterologous fungal or plant 2Fe-2S
dihydroxy-acid dehydratase (DHAD) or Fe--S propanediol dehydratase
reactivase (RdhtB) was improved when an endogenous gene encoding
isopropylmalate dehydratase (LEU1) or an endogenous gene encoding
dihydroxy-acid dehydratase (ILV3) was inactivated in the yeast host
cells.
[0075] In yeast host cells with inactivation of a gene encoding an
endogenous Fe--S protein, the activity of the expressed
heterologous Fe--S protein may be increased to at least about 1.4
fold of the activity in a yeast host cell with no inactivation of
Fe--S protein encoding gene. For example, the Kluyveromyces lactis
DHAD had 1.4 fold activity in a LEU1 deletion host as compared to a
host without the deletion; the Roseburia inulinivorans RdhtB had
1.7 fold comparative activity in a LEU deletion host as measured by
the activated RdhtA protein activity (described below);
Saccharomyces cerevisiae DHAD expressed in the cytosol had 1.5 fold
comparative activity in a mitochondrial ILV3 deletion host; and
Kluyveromyces lactis DHAD expressed in the cytosol had 7.4 fold
comparative activity in a mitochondrial ILV3 deletion host.
Yeast Host Cells with Reduced Expression of Endogenous Fe--S
Protein
[0076] Reduced endogenous Fe--S protein expression may be
engineered in any yeast cell that is amenable to genetic
manipulation. Examples include yeasts of Saccharomyces,
Schizosaccharomyces, Hansenula, Candida, Kluyveromyces, Yarrowia
and Pichia. Suitable strains include, but are not limited to,
Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces
lactis, Kluyveromyces thermotolerans, Candida glabrata, Candida
albicans, Pichia stipitis and Yarrowia lipolytica. Particularly
suitable is Saccharomyces cerevisiae.
[0077] In any of these yeasts, any endogenous Fe--S protein may be
a target for reduced expression. Fe--S proteins in yeast that may
be targeted for reduced expression include, for example, the
following proteins (with encoding gene): aconitase (ACO1),
homoaconitase (LYS4), DHAD (ILV3), lipoate synthase (LIPS), biotin
synthase (BIO2), ferredoxin maturation (YAH1), NADH ubiquinone
oxidoreductase (NDI1), succinate dehydrogenase (SDH2),
ubiquinol-cytochrome-c reductase (RIP1), isopropylmalate isomerase
(LEU1), sulfite reductase (ECMI7), glutamate dehydrogenase (GLT1),
ABC protein Rli1 (RLI1), NTPase Nbp35 (NBP35), and hydrogenase-like
protein (NARI1). Yeast cells with reduced expression of individual
Fe--S proteins may require special conditions for growth such as
supplementation of the growth medium with a particular nutrient, as
is well known to one skilled in the art. For example, a strain with
disruption of LEU1 is supplemented with leucine, a strain with
disruption of DHAD is supplemented with leucine, isoleucine, and
valine, and a strain with disruption of LYS4 is supplemented with
lysine. Some strains with a disruption require no supplementation
for growth. Particularly suitable Fe--S proteins that may be
targeted for reduced expression include Isopropylmalate isomerase
(LEU1), Dihydroxyacid dehydratase (ILV3), Sulfite reductase
(ECM17), Glutamate dehydrogenase (GLT1), and Biotin synthase
(BIO2). Reduced expression is engineered for at least one
endogenous Fe--S protein, and two or more endogenous Fe--S proteins
may be reduced.
[0078] LEU1 encodes isopropylmalate dehydratase, an enzyme
belonging to EC 4.2.1.33 that is involved in branched chain amino
acid biosynthesis, specifically synthesis of leucine. Any gene
encoding an isopropylmalate dehydratase, which is an enzyme
requiring a 4Fe-4S cluster for activity, may be inactivated in a
yeast host cell of this disclosure. Examples of yeast LEU1
inactivation target genes and their encoded proteins are those from
Saccharomyces cerevisiae (coding SEQ ID NO:1; protein SEQ ID NO:2),
Schizosaccharomyces pombe (coding SEQ ID NO:3; protein SEQ ID
NO:4), Candida galbrata strain CBS 138 (coding SEQ ID NO:5; protein
SEQ ID NO:6), Candida albicans SC5314 (coding SEQ ID NO:7; protein
SEQ ID NO:8), Kluyveromyces lactis (coding SEQ ID NO: protein SEQ
ID NO:10), Yarrowia lipolytica (coding SEQ ID NO:11; protein SEQ ID
NO:12) and Pichia stipitis (coding SEQ ID NO:13; protein SEQ ID
NO:14).
[0079] Similarly in any of the yeast hosts described herein, an
endogenous ILV3 gene may be inactivated to reduce endogenous Fe--S
protein expression. ILV3 encodes mitochondrial DHAD that is
involved in branched chain amino acid biosynthesis. Mitochondrial
DHAD is encoded by a nuclear gene, and has a mitochondrial
targeting signal sequence so that it is transported to and
localized in the mitochondrion. Any ILV3 gene may be inactivated in
a yeast host cell of this disclosure. Examples of yeast ILV3
inactivation target genes and their encoded proteins are those from
Saccharomyces cerevisiae YJM78 (coding SEQ ID NO:111; protein SEQ
ID NO:112), Schizosaccharomyces pombe (coding SEQ ID NO:93; protein
SEQ ID NO:94), Candida galbrata strain CBS 138 (coding SEQ ID
NO:107; protein SEQ ID NO:108), Candida albicans SC5314 (coding SEQ
ID NO:101; protein SEQ ID NO:102), Kluyveromyces lactis (coding SEQ
ID NO:113; protein SEQ ID NO:114), Yarrowia lipolytica (coding SEQ
ID NO:105; protein SEQ ID NO:106) and Pichia stipitis CBS 6054
(coding SEQ ID NO:103; protein SEQ ID NO:104).
[0080] Because genes encoding isopropylmalate dehydratases and DHAD
enzymes genes are well known, and because of the prevalence of
genomic sequencing, additional suitable species of these enzymes
can be readily identified by one skilled in the art on the basis of
sequence similarity using bioinformatics approaches. Typically
BLAST (described above) searching of publicly available databases
with known isopropylmalate dehydratase amino acid sequences, such
as those provided herein, is used to identify these enzymes and
their encoding sequences that may be targeted for inactivation in
the present strains. For example, endogenous yeast isopropylmalate
dehydratase and DHAD proteins having amino acid sequence identities
of at least about 70-75%, 75%-80%, 80-85%, 85%-90%, 90%-95% or 98%
sequence identity to any of the isopropylmalate dehydratase
proteins of SEQ ID NOs:2, 4, 6, 8, 10, 12 and 14 and the DHAD
proteins of SEQ ID NOs:94, 102, 104, 106, 108, 112, and 114 may
have reduced expression in the present strains. Identities are
based on the Clustal W method of alignment using the default
parameters of GAP PENALTY=10, GAP LENGTH PENALTY=0.1, and Gonnet
250 series of protein weight matrix.
[0081] Additionally, the sequences of LEU1 coding regions and ILV3
provided herein may be used to identify other homologs in nature.
For example each of the coding regions described herein may be used
to isolate genes encoding homologous proteins. Isolation of
homologous genes using sequence-dependent protocols is well known
in the art. Examples of sequence-dependent protocols include, but
are not limited to: 1) methods of nucleic acid hybridization; 2)
methods of DNA and RNA amplification, as exemplified by various
uses of nucleic acid amplification technologies [e.g., polymerase
chain reaction (PCR), Mullis et al., U.S. Pat. No. 4,683,202;
ligase chain reaction (LCR), Tabor, S. et al., Proc. Acad. Sci. USA
82:1074 (1985); or strand displacement amplification (SDA), Walker,
et al., Proc. Natl. Acad. Sci. U.S.A., 89:392 (1992)]; and 3)
methods of library construction and screening by
complementation.
[0082] For example, genes encoding similar proteins or polypeptides
to the isopropylmalate dehydratase and DHAD encoding genes provided
herein could be isolated directly by using all or a portion of the
instant nucleic acid fragments as DNA hybridization probes to
screen libraries from any desired organism using methodology well
known to those skilled in the art. Specific oligonucleotide probes
based upon the disclosed nucleic acid sequences can be designed and
synthesized by methods known in the art (Maniatis, supra).
Moreover, the entire sequences can be used directly to synthesize
DNA probes by methods known to the skilled artisan (e.g., random
primers DNA labeling, nick translation or end-labeling techniques),
or RNA probes using available in vitro transcription systems. In
addition, specific primers can be designed and used to amplify a
part of (or full-length of) the instant sequences. The resulting
amplification products can be labeled directly during amplification
reactions or labeled after amplification reactions, and used as
probes to isolate full-length DNA fragments by hybridization under
conditions of appropriate stringency.
[0083] Typically, in PCR-type amplification techniques, the primers
have different sequences and are not complementary to each other.
Depending on the desired test conditions, the sequences of the
primers should be designed to provide for both efficient and
faithful replication of the target nucleic acid. Methods of PCR
primer design are common and well known in the art (Thein and
Wallace, "The use of oligonucleotides as specific hybridization
probes in the Diagnosis of Genetic Disorders", in Human Genetic
Diseases: A Practical Approach, K. E. Davis Ed., (1986) pp 33-50,
IRL: Herndon, Va.; and Rychlik, W., In Methods in Molecular
Biology, White, B. A. Ed., (1993) Vol. 15, pp 31-39, PCR Protocols:
Current Methods and Applications. Humania: Totowa, N.J.).
[0084] Generally two short segments of the described sequences may
be used in polymerase chain reaction protocols to amplify longer
nucleic acid fragments encoding homologous genes from DNA or RNA.
The polymerase chain reaction may also be performed on a library of
cloned nucleic acid fragments wherein the sequence of one primer is
derived from the described nucleic acid fragments, and the sequence
of the other primer takes advantage of the presence of the
polyadenylic acid tracts to the 3' end of the mRNA precursor
encoding microbial genes.
[0085] Alternatively, the second primer sequence may be based upon
sequences derived from the cloning vector. For example, the skilled
artisan can follow the RACE protocol (Frohman et al., PNAS USA
85:8998 (1988)) to generate cDNAs by using PCR to amplify copies of
the region between a single point in the transcript and the 3' or
5' end. Primers oriented in the 3' and 5' directions can be
designed from the instant sequences. Using commercially available
3' RACE or 5' RACE systems (e.g., BRL, Gaithersburg, Md.), specific
3' or 5' cDNA fragments can be isolated (Ohara et al., PNAS USA
86:5673 (1989); Loh et al., Science 243:217 (1989)).
[0086] Alternatively, the provided isopropylmalate dehydratase and
DHAD encoding sequences can be employed as hybridization reagents
for the identification of homologs. The basic components of a
nucleic acid hybridization test include a probe, a sample suspected
of containing the gene or gene fragment of interest, and a specific
hybridization method. Probes are typically single-stranded nucleic
acid sequences that are complementary to the nucleic acid sequences
to be detected. Probes are "hybridizable" to the nucleic acid
sequence to be detected. The probe length can vary from 5 bases to
tens of thousands of bases, and will depend upon the specific test
to be done. Typically a probe length of about 15 bases to about 30
bases is suitable. Only part of the probe molecule need be
complementary to the nucleic acid sequence to be detected. In
addition, the complementarity between the probe and the target
sequence need not be perfect. Hybridization does occur between
imperfectly complementary molecules with the result that a certain
fraction of the bases in the hybridized region are not paired with
the proper complementary base.
[0087] Hybridization methods are well defined. Typically the probe
and sample must be mixed under conditions that will permit nucleic
acid hybridization. This involves contacting the probe and sample
in the presence of an inorganic or organic salt under the proper
concentration and temperature conditions. The probe and sample
nucleic acids must be in contact for a long enough time that any
possible hybridization between the probe and sample nucleic acid
may occur. The concentration of probe or target in the mixture will
determine the time necessary for hybridization to occur. The higher
the probe or target concentration, the shorter the hybridization
incubation time needed. Optionally, a chaotropic agent may be
added. The chaotropic agent stabilizes nucleic acids by inhibiting
nuclease activity. Furthermore, the chaotropic agent allows
sensitive and stringent hybridization of short oligonucleotide
probes at room temperature (Van Ness and Chen, Nucl. Acids Res.
19:5143-5151 (1991)). Suitable chaotropic agents include
guanidinium chloride, guanidinium thiocyanate, sodium thiocyanate,
lithium tetrachloroacetate, sodium perchlorate, rubidium
tetrachloroacetate, potassium iodide and cesium trifluoroacetate,
among others. Typically, the chaotropic agent will be present at a
final concentration of about 3 M. If desired, one can add formamide
to the hybridization mixture, typically 30-50% (v/v).
[0088] Various hybridization solutions can be employed. Typically,
these comprise from about 20 to 60% volume, preferably 30%, of a
polar organic solvent. A common hybridization solution employs
about 30-50% v/v formamide, about 0.15 to 1 M sodium chloride,
about 0.05 to 0.1 M buffers (e.g., sodium citrate, Tris-HCl, PIPES
or HEPES (pH range about 6-9)), about 0.05 to 0.2% detergent (e.g.,
sodium dodecylsulfate), or between 0.5-20 mM EDTA, FICOLL
(Pharmacia Inc.) (about 300-500 kdal), polyvinylpyrrolidone (about
250-500 kdal) and serum albumin. Also included in the typical
hybridization solution will be unlabeled carrier nucleic acids from
about 0.1 to 5 mg/mL, fragmented nucleic DNA (e.g., calf thymus or
salmon sperm DNA, or yeast RNA), and optionally from about 0.5 to
2% wt/vol glycine. Other additives may also be included, such as
volume exclusion agents that include a variety of polar
water-soluble or swellable agents (e.g., polyethylene glycol),
anionic polymers (e.g., polyacrylate or polymethylacrylate) and
anionic saccharidic polymers (e.g., dextran sulfate).
[0089] Nucleic acid hybridization is adaptable to a variety of
assay formats. One of the most suitable is the sandwich assay
format. The sandwich assay is particularly adaptable to
hybridization under non-denaturing conditions. A primary component
of a sandwich-type assay is a solid support. The solid support has
adsorbed to it or covalently coupled to it immobilized nucleic acid
probe that is unlabeled and complementary to one portion of the
sequence.
[0090] Protein and nucleic acid encoding sequences for any of the
other Fe--S proteins that may be targeted for reduced activity in a
yeast cell of the invention may be identified using bioinformatics
and other methods well known to one skilled in the art. For
example, aconitase sequences are identified by keyword searching in
bioinformatics databases. Several sequences identified by this
method are those from Saccharomyces cerevisiae (coding SEQ ID
NO:153; protein SEQ ID NO:154), Schizosaccharomyces pombe on
chromosome II (coding SEQ ID NO:155; protein SEQ ID NO:156),
Schizosaccharomyces pombe on chromosome I (coding SEQ ID NO:157;
protein SEQ ID NO:158), Kluyveromyces lactis (coding SEQ ID NO:15;
protein SEQ ID NO:160), Candida albicans SC5314 (coding SEQ ID
NO:161; protein SEQ ID NO:162), Yarrowia lipolytica (coding SEQ ID
NO:163; protein SEQ ID NO:164), Pichia stipitis CBS 6054 (coding
SEQ ID NO:165; protein SEQ ID NO:166), Candida galbrata CBS 138
chromosome F (coding SEQ ID NO:167; protein SEQ ID NO:168), Candida
galbrata CBS 138 chromosome D (coding SEQ ID NO:169; protein SEQ ID
NO:170), and Candida galbrata CBS 138 chromosome K (coding SEQ ID
NO:171; protein SEQ ID NO:172).
[0091] Genes encoding Fe--S proteins, for example LEU1, ILV3, or
ACO1 may be disrupted in any yeast cell using genetic modification.
Many methods for genetic modification of target genes are known to
one skilled in the art and may be used to create the present yeast
strains. Modifications that may be used to reduce or eliminate
expression of a target protein are disruptions that include, but
are not limited to, deletion of the entire gene or a portion of the
gene, inserting a DNA fragment into the gene (in either the
promoter or coding region) so that the protein is not expressed or
expressed at lower levels, introducing a mutation into the coding
region which adds a stop codon or frame shift such that a
functional protein is not expressed, and introducing one or more
mutations into the coding region to alter amino acids so that a
non-functional or a less enzymatically active protein is expressed.
In addition, expression of a gene may be blocked by expression of
an antisense RNA or an interfering RNA, and constructs may be
introduced that result in cosuppression. In addition, the synthesis
or stability of the transcript may be lessened by mutation.
Similarly the efficiency by which a protein is translated from mRNA
may be modulated by mutation. All of these methods may be readily
practiced by one skilled in the art making use of the known or
identified coding sequences such as LEU1 or ILV3.
[0092] DNA sequences surrounding a LEU1, ILV3, or ACO1 coding
sequence are also useful in some modification procedures and are
available for yeasts such as for Saccharomycse cerevisiae in the
complete genome sequence coordinated by Genome Project ID9518 of
Genome Projects coordinated by NCBI (National Center for
Biotechnology Information) with identifying GOPID 13838. Additional
examples of yeast genomic sequences include that of Yarrowia
lipolytica, GOPIC 13837, and of Candida albicans, which is included
in GPID 10771, 10701 and 16373. Additional genomes have been
completely sequenced and annotated and are publicly available for
the following yeast strains Candida glabrata CBS 138, Kluyveromyces
lactis NRRL Y-1140, Pichia stipitis CBS 6054, and
Schizosaccharomyces pombe 972h-.
[0093] In particular, DNA sequences surrounding a target coding
sequence, such as LEU1 or ILV3, are useful for modification methods
using homologous recombination. For example, in this method
flanking sequences are placed bounding a selectable marker gene to
mediate homologous recombination whereby the marker gene replaces
the target gene. Also partial target gene sequences and flanking
sequences bounding a selectable marker gene may be used to mediate
homologous recombination whereby the marker gene replaces a portion
of the target gene. In addition, the selectable marker may be
bounded by site-specific recombination sites, so that following
expression of the corresponding site-specific recombinase, the
resistance gene is excised from the target gene without
reactivating the latter. The site-specific recombination leaves
behind a recombination site which disrupts expression of the target
gene encoded protein. The homologous recombination vector may be
constructed to also leave a deletion in the target gene following
excision of the selectable marker, as is well known to one skilled
in the art.
[0094] Deletions may be made using mitotic recombination as
described in Wach et al. ((1994) Yeast 10:1793-1808). This method
involves preparing a DNA fragment that contains a selectable marker
between genomic regions that may be as short as 20 bp, and which
bound a target DNA sequence. This DNA fragment can be prepared by
PCR amplification of the selectable marker gene using as primers
oligonucleotides that hybridize to the ends of the marker gene and
that include the genomic regions that can recombine with the yeast
genome. The linear DNA fragment can be efficiently transformed into
yeast and recombined into the genome resulting in gene replacement
including with deletion of the target DNA sequence (as described in
Methods in Enzymology, v194, pp 281-301 (1991)).
[0095] Moreover, promoter replacement methods may be used to
exchange the endogenous transcriptional control elements allowing
another means to modulate expression such as described in Mnaimneh
et al. ((2004) Cell 118(1):31-44) and in Example 12 herein.
[0096] In addition, a target gene in any yeast cell may be
disrupted using random mutagenesis, which is followed by screening
to identify strains with reduced target gene encided activity.
Using this type of method, the DNA sequence of for example the
LEU1, ILV3, or any other region of the genome affecting expression
of a target Fe--S protein, need not be known.
[0097] Methods for creating genetic mutations are common and well
known in the art and may be applied to the exercise of creating
mutants. Commonly used random genetic modification methods
(reviewed in Methods in Yeast Genetics, 2005, Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, N.Y.) include spontaneous
mutagenesis, mutagenesis caused by mutator genes, chemical
mutagenesis, irradiation with UV or X-rays, or transposon
mutagenesis.
[0098] Chemical mutagenesis of yeast commonly involves treatment of
yeast cells with one of the following DNA mutagens: ethyl
methanesulfonate (EMS), nitrous acid, diethyl sulfate, or
N-methyl-N'-nitro-N-nitroso-guanidine (MNNG). These methods of
mutagenesis have been reviewed in Spencer et al (Mutagenesis in
Yeast, 1996, Yeast Protocols: Methods in Cell and Molecular
Biology. Humana Press, Totowa, N.J.). Chemical mutagenesis with EMS
may be performed as described in Methods in Yeast Genetics, 2005,
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
Irradiation with ultraviolet (UV) light or X-rays can also be used
to produce random mutagenesis in yeast cells. The primary effect of
mutagenesis by UV irradiation is the formation of pyrimidine dimers
which disrupt the fidelity of DNA replication. Protocols for
UV-mutagenesis of yeast can be found in Spencer et al (Mutagenesis
in Yeast, 1996, Yeast Protocols: Methods in Cell and Molecular
Biology. Humana Press, Totowa, N.J.). Introduction of a mutator
phenotype can also be used to generate random chromosomal mutations
in yeast. Common mutator phenotypes can be obtained through
disruption of one or more of the following genes: PMS1, MAG1, RAD18
or RAD51. Restoration of the non-mutator phenotype can be easily
obtained by insertion of the wildtype allele. Collections of
modified cells produced from any of these or other known random
mutagenesis processes may be screened for reduced Fe--S protein
activity.
Heterologous Fe--S Proteins
[0099] Any fungal or plant 2Fe-2S cluster dihydroxy-acid
dehydratase (DHAD) and any Fe--S propanediol dehydratase reactivase
may be expressed as a heterologous protein in a yeast host cell
engineered as disclosed herein for reduced endogenous Fe--S cluster
protein expression, and increased activity may be obtained. A
heterologous protein includes one that is expressed in a manner
differently from expression of a corresponding endogenous protein.
For example in yeast, endogenous DHAD is encoded by ILV3 in the
nucleus and the expressed DHAD protein has a mitochondrial
targeting signal sequence such that the protein is localized in the
mitochondrion. An Fe--S cluster is added to the DHAD protein in the
mitochondrion for its activity in branched chain amino acid
biosynthesis. It is desirable to express DHAD activity in the
cytosol for participation in biosynthetic pathways that are
localized in the cytosol. Cytosolic expression of DHAD in yeast is
heterologous expression since the native protein is localized in
the mitochondrion. For example, heterologous expression of the
Saccharomyces cerevisiae DHAD in S. cerevisiae is obtained by
expressing the S. cerevisiae DHAD coding region with the
mitochondrial targeting signal removed, such that the protein
remains in the cytosol. 2Fe-2S DHADs that may be used in the
present disclosure include those from fungi and plants.
Representative fungal or plant 2Fe-2S DHADs are listed in Tables 1
and 2. Fungal or plant 2Fe-2S DHADs with amino acid sequence
identities of 95% or greater were removed from the analysis
providing this list for simplification. However, any sequences with
95% or greater amino acid identities to any of these sequences are
useful in the present invention. The analysis used to obtain 2Fe-2S
DHADs is described in commonly owned and co-pending U.S. Patent
Application 61/100,792, which is herein incorporated by reference.
The analysis is as follows: Therein a Profile Hidden Markov Model
(HMM) was prepared based on amino acid sequences of eight
functionally verified DHADs. These DHADs are from Nitrosomonas
europaea (DNA SEQ ID NO:174; Protein SEQ ID NO:175), Synechocystis
sp. PCC6803 (DNA SEQ ID:176; Protein SEQ ID NO:177), Streptococcus
mutans (DNA SEQ ID NO:178; Protein SEQ ID NO:179), Streptococcus
thermophilus (DNA SEQ ID NO:180; protein SEQ ID No:181), Ralstonia
metallidurans (DNA SEQ ID NO:182; protein SEQ ID NO:183), Ralstonia
eutropha (DNA SEQ ID NO:184; protein SEQ ID NO:185), and
Lactococcus lactis (DNA SEQ ID NO:186; protein SEQ ID NO:187). In
addition the DHAD from Flavobacterium johnsoniae (DNA SEQ ID
NO:188; protein SEQ ID NO:189) was found to have dihydroxy-acid
dehydratase activity when expressed in E. coli and was used in
making the Profile. The Profile HMM is prepared using the HMMER
software package (The theory behind profile HMMs is described in R.
Durbin, S. Eddy, A. Krogh, and G. Mitchison, Biological sequence
analysis: probabilistic models of proteins and nucleic acids,
Cambridge University Press, 1998; Krogh et al., 1994; J. Mol. Biol.
235:1501-1531), following the user guide which is available from
HMMER (Janelia Farm Research Campus, Ashburn, Va.). The output of
the HMMER software program is a Profile Hidden Markov Model (HMM)
that characterizes the input sequences, given in Table 9.
[0100] Any protein that matches the Profile HMM with an E value of
<10.sup.-5 is a DHAD related protein, which includes 4Fe-4S
DHADs, 2Fe-2S DHADs, arabonate dehydratases, and phosphogluconate
dehydratases. Sequences matching the Profile HMM are then analyzed
for the presence of the three conserved cysteines, corresponding to
positions 56, 129, and 201 in the Streptococcus mutans DHAD. The
presence of all three conserved cysteines is characteristic of
proteins having a [2Fe-2S].sup.2+ cluster. Proteins having the
three conserved cysteines include arabonate dehydratases and 2Fe-2S
DHADs. The 2Fe-2S DHADs may be distinguished from the arabonate
dehydratases by analyzing for signature conserved amino acids found
to be present in the 2Fe-2S DHADs or in the arabonate dehydratases
at positions corresponding to the following positions in the
Streptococcus mutans DHAD amino acid sequence. These signature
amino acids are in 2Fe-2S DHADs or in arabonate dehydratases,
respectively, at the following positions (with greater than 90%
occurrence): 88 asparagine vs glutamic acid; 113 not conserved vs
glutamic acid; 142 arginine or asparagine vs not conserved; 165:
not conserved vs glycine; 208 asparagine vs not conserved; 454
leucine vs not conserved; 477 phenylalanine or tyrosine vs not
conserved; and 487 glycine vs not conserved.
[0101] The proteins identified by this process that have a fungal
or plant origin, such as SEQ ID NOs:46, 48, 50, 52, 54, 56, 58, 60,
62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94,
96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122,
124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148,
150 and 152 may be used in the present invention, as well as any
protein with amino acid identity of at least about 95%, 96%, 97%,
98%, or 99% to any of these sequences. Particularly suitable is the
DHAD from Kluyveromyces lactis (SEQ ID NO:114) and DHADs with at
least about 90% amino acid sequence identity to SEQ ID NO:114 using
the Clustal W method of alignment using the default parameters of
GAP PENALTY=10, GAP LENGTH PENALTY=0.1, and Gonnet 250 series of
protein weight matrix over the full length of the protein
sequence.
[0102] In addition, fungal or plant 2Fe-2S DHADs that may be used
in the present invention may be identified by their position in a
fungal or plant 2Fe-2S DHAD branch of a phylogenetic tree of DHAD
related proteins. In addition, 2Fe-2S DHADs that may be used may be
identified using sequence comparisons with any of the fungal or
plant 2Fe-2S DHADs whose sequences are provided herein, where
sequence identity may be at least about 80%-85%, 85%-90%, 90%-95%
or 95%-99%.
[0103] Additionally, the sequences of fungal or plant 2Fe-2S DHADs
provided herein may be used to identify other homologs in nature.
For example each of the DHAD encoding nucleic acid fragments given
herein as SEQ ID NOs:45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65,
67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99,
101, 103, 105, 107, 109, 111, 113, 115, 117, 11, 121, 123, 125,
127, 129, 131, 133, 135, 137, 13, 141, 143, 145, 147, 149 and 151
may be used to isolate genes encoding homologous proteins as
described above for the LEU1 coding region.
[0104] The coenzyme B12-independent propanediol dehydratase
reactivase of Roseburia inulinivorans is a protein requiring an
Fe--S cluster for activity. This protein, RdhtB, is disclosed in
co-pending US Patent Pub No. US20090155870, which is herein
incorporated by reference. RdhtB reactivates a coenzyme
B12-independent propanediol dehydratase of Roseburia inulinivorans,
which is named RdhtA and is also disclosed in commonly owned and
co-pending US Patent Pub No. US20090155870. The activity of RdhtB
may be assessed by assaying the activity of RdhtA, since RdhtB is
required for RdhtA activity. Activity of RdhtB, and therefore of
RdhtA, is improved by expressing in a yeast host with reduced
endogenous Fe--S protein expression disclosed herein. Heterologous
expression of any coenzyme B12-independent propanediol dehydratase
reactivase that requires an Fe--S cluster for activity may be
improved in a yeast strain having reduced endogenous Fe--S protein
expression. A coenzyme B12-independent propanediol dehydratase
reactivase may be readily identified by one skilled in the art by
assessing propanediol dehydratase activity of the associated
propanediol dehydratase enzyme in the presence or absence of
coenzyme B12. An example is a diol dehydratase reactivase of
Clostridium butyricum (coding region SEQ ID NO:192; protein SEQ ID
NO:193).
[0105] Other coenzyme B12-independent propanediol dehydratase
reactivases that may be used may be identified through
bioinformatics analysis of sequences as compared to that of RdhtB
SEQ ID NO:44 by one skilled in the art. Proteins with coenzyme
B12-independent propanediol dehydratase reactivase activity and
sequence identity to SEQ ID NO:44 of at least about 80%-85%,
85%-90%, 90%-95% or 95%-99% may be used. Particularly suitable are
those that are at least about 90% identical to the amino acid
sequence as set forth in SEQ ID NO:44 using the Clustal W method of
alignment using the default parameters of GAP PENALTY=10, GAP
LENGTH PENALTY=0.1, and Gonnet 250 series of protein weight matrix
over the full length of the protein sequence.
[0106] In addition, other coenzyme B12-independent propanediol
dehydratase reactivase homologs that may be used may be identified
using the RdhtB coding region (SEQ ID NO:16) by methods as
described above for the LEU1 coding region.
Expression of Heterologous Fe--S Proteins
[0107] Expression is achieved by transforming with a sequence
encoding an Fe--S protein. The coding region to be expressed may be
codon optimized for the target host cell, as well known to one
skilled in the art. Methods for gene expression in yeast are known
in the art (see for example Methods in Enzymology, Volume 194,
Guide to Yeast Genetics and Molecular and Cell Biology (Part A,
2004, Christine Guthrie and Gerald R. Fink (Eds.), Elsevier
Academic Press, San Diego, Calif.).
[0108] Expression of genes in yeast typically requires a promoter,
operably linked to a coding region of interest, and a
transcriptional terminator. A number of yeast promoters can be used
in constructing expression cassettes for genes in yeast, including,
but not limited to promoters derived from the following genes:
CYC1, HIS3, GAL1, GAL10, ADH1, PGK, PHO5, GAPDH, ADC1, TRP1, URA3,
LEU2, ENO, TPI, CUP1, FBA, GPD, GPM, and AOX1. Suitable
transcriptional terminators include, but are not limited to FBAt,
GPDt, GPMt, ERG10t, GAL1t, CYC1, and ADH1.
[0109] Suitable promoters, transcriptional terminators, and coding
regions may be cloned into E. coli-yeast shuttle vectors, and
transformed into yeast cells. These vectors allow strain
propagation in both E. coli and yeast strains. Typically the vector
used contains a selectable marker and sequences allowing autonomous
replication or chromosomal integration in the desired host.
Typically used plasmids in yeast are shuttle vectors pRS423,
pRS424, pRS425, and pRS426 (American Type Culture Collection,
Rockville, Md.), which contain an E. coli replication origin (e.g.,
pMB1), a yeast 2.mu. origin of replication, and a marker for
nutritional selection. The selection markers for these four vectors
are His3 (vector pRS423), Trp1 (vector pRS424), Leu2 (vector
pRS425) and Ura3 (vector pRS426). Construction of expression
vectors with a chimeric gene encoding the described Fe--S protein
coding regions may be performed by either standard molecular
cloning techniques in E. coli or by the gap repair recombination
method in yeast.
[0110] The gap repair cloning approach takes advantage of the
highly efficient homologous recombination in yeast. Typically, a
yeast vector
[0111] DNA is digested (e.g., in its multiple cloning site) to
create a "gap" in its sequence. A number of insert DNAs of interest
are generated that contain a .gtoreq.21 bp sequence at both the 5'
and the 3' ends that sequentially overlap with each other, and with
the 5' and 3' terminus of the vector DNA. For example, to construct
a yeast expression vector for "Gene X`, a yeast promoter and a
yeast terminator are selected for the expression cassette. The
promoter and terminator are amplified from the yeast genomic DNA,
and Gene X is either PCR amplified from its source organism or
obtained from a cloning vector comprising Gene X sequence. There is
at least a 21 bp overlapping sequence between the 5' end of the
linearized vector and the promoter sequence, between the promoter
and Gene X, between Gene X and the terminator sequence, and between
the terminator and the 3' end of the linearized vector. The
"gapped" vector and the insert DNAs are then co-transformed into a
yeast strain and plated on the medium containing the appropriate
compound mixtures that allow complementation of the nutritional
selection markers on the plasmids. The presence of correct insert
combinations can be confirmed by PCR mapping using plasmid DNA
prepared from the selected cells. The plasmid DNA isolated from
yeast (usually low in concentration) can then be transformed into
an E. coli strain, e.g. TOP10, followed by mini preps and
restriction mapping to further verify the plasmid construct.
Finally the construct can be verified by sequence analysis.
[0112] Like the gap repair technique, integration into the yeast
genome also takes advantage of the homologous recombination system
in yeast. Typically, a cassette containing a coding region plus
control elements (promoter and terminator) and auxotrophic marker
is PCR-amplified with a high-fidelity DNA polymerase using primers
that hybridize to the cassette and contain 40-70 base pairs of
sequence homology to the regions 5' and 3' of the genomic area
where insertion is desired. The PCR product is then transformed
into yeast and plated on medium containing the appropriate compound
mixtures that allow selection for the integrated auxotrophic
marker. For example, to integrate "Gene X" into chromosomal
location "Y", the promoter-coding regionX-terminator construct is
PCR amplified from a plasmid DNA construct and joined to an
autotrophic marker (such as URA3) by either SOE PCR or by common
restriction digests and cloning. The full cassette, containing the
promoter-coding regionX-terminator-URA3 region, is PCR amplified
with primer sequences that contain 40-70 bp of homology to the
regions 5' and 3' of location "Y" on the yeast chromosome. The PCR
product is transformed into yeast and selected on growth media
lacking uracil. Transformants can be verified either by colony PCR
or by direct sequencing of chromosomal DNA.
[0113] Any coding regions expressed in the present yeast cells may
be codon optimized for expression in the specific host yeast cell
being engineered as is well known to one skilled in the art. For
example, for expression of the K. lactis and P. stipitis ILV3
coding regions in S. cerevisiae, each was codon optimized for S.
cerevisiae expression in Example 1 herein.
Product Biosynthesis with Improved Heterologous Fe--S Protein
Activity
[0114] Production of any product that has an Fe--S protein
contributing to its biosynthetic pathway may benefit from the
improved activity disclosed herein of a heterologous expressed
Fe--S protein in a yeast host with reduced endogenous Fe--S protein
expression. For example, DHAD provides a step in pathways for
biosynthesis of isobutanol, and RdhtB contributes to a biosynthetic
pathway to produce 2-butanone or 2-butanol.
[0115] Biosynthetic pathways including a step performed by DHAD for
synthesis of isobutanol are disclosed in commonly owned and
co-pending US Patent Application publication US 20070092957 A1,
which is herein incorporated by reference. A diagram of the
disclosed isobutanol biosynthetic pathways is provided in FIG. 1.
Production of isobutanol in a strain disclosed herein benefits from
increased DHAD activity. As described in US Patent Pub No.
US20070092957 A1, steps in an example isobutanol biosynthetic
pathway include conversion of: [0116] pyruvate to acetolactate
(FIG. 1 pathway step a) as catalyzed for example by acetolactate
synthase; [0117] acetolactate to 2,3-dihydroxyisovalerate (FIG. 1
pathway step b) as catalyzed for example by acetohydroxy acid
isomeroreductase; [0118] 2,3-dihydroxyisovalerate to
.alpha.-ketoisovalerate (FIG. 1 pathway step c) as catalyzed for
example by acetohydroxy acid dehydratase also called DHAD; [0119]
.alpha.-ketoisovalerate to isobutyraldehyde (FIG. 1 pathway step d)
as catalyzed for example by branched-chain .alpha.-keto acid
decarboxylase; and [0120] isobutyraldehyde to isobutanol (FIG. 1
pathway step e) as catalyzed for example by branched-chain alcohol
dehydrogenase.
[0121] The substrate to product conversions, and enzymes involved
in these reactions, for steps f, g, h, I, j, and k of alternative
pathways are described in US 20070092957 A1.
[0122] Genes that may be used for expression of the enzymes for the
isobutanol pathways are described in US 20070092957 A1, and
additional genes that may be used can be identified by one skilled
in the art through bioinformatics or experimentally as described
above. The preferred use in all three pathways of ketol-acid
reductoisomerase (KARI) enzymes with particularly high activities
are disclosed in commonly owned and co-pending US Patent Pub No.
US20080261230. Examples of high activity KARIs disclosed therein
are those from Vibrio cholerae (DNA: SEQ ID NO:35; protein SEQ ID
NO:36), Pseudomonas aeruginosa PAO1, (DNA: SEQ ID NO:37; protein
SEQ ID NO:38), and Pseudomonas fluorescens PF5 (DNA: SEQ ID NO:39;
protein SEQ ID NO:40).
[0123] Additionally described in US 20070092957 A1 are construction
of chimeric genes and genetic engineering of yeast, exemplified by
Saccharomyces cerevisiae, for isobutanol production using the
disclosed biosynthetic pathways.
[0124] A biosynthetic pathway including propanediol dehydratase for
synthesis of 2-butanone and 2-butanol is disclosed in commonly
owned and co-pending US Patent Pub No. US20070292927A1, which is
herein incorporated by reference. A diagram of the disclosed
2-butanone and 2-butanol biosynthetic pathway is provided in FIG.
2. 2-Butanone is the product made when the last depicted step of
converting 2-butanone to 2-butanol is omitted. Production of
2-butanone or 2-butanol in a strain disclosed herein benefits from
increased coenzyme B12-independent propanediol dehydratase
reactivase activity. As described in US Patent Pub No.
US20070292927A1, steps in the disclosed biosynthetic pathway
include conversion of: [0125] pyruvate to acetolactate (FIG. 2 step
a) as catalyzed for example by acetolactate synthase; [0126]
acetolactate to acetoin (FIG. 2 step b) as catalyzed for example by
acetolactate decarboxylase; [0127] acetoin to 2,3-butanediol (FIG.
2 step i) as catalyzed for example by butanediol dehydrogenase;
[0128] 2,3-butanediol to 2-butanone (FIG. 2 step j) as catalyzed
for example by diol dehydratase glycerol dehydratase, or
propanediol dehydratase; and [0129] 2-butanone to 2-butanol (FIG. 2
step f) as catalyzed for example by butanol dehydrogenase.
[0130] Genes that may be used for expression of these enzymes are
described in US Patent Pub No. US20070292927A1. The use in this
pathway in yeast of the butanediol dehydratase from Roseburia
inulinivorans, RdhtA, (protein SEQ ID NO:43, coding region SEQ ID
NO:15) is disclosed in commonly owed and co-pending US Patent Pub
No. US20090155870. This enzyme is used in conjunction with the
butanediol dehydratase reactivase from Roseburia inulinivorans,
RdhtB, (protein SEQ ID NO:44, coding region SEQ ID NO:16). This
butanediol dehydratase is desired in many hosts because it does not
require coenzyme B.sub.12.
[0131] Additionally described in US Patent Pub No. US20090155870
are construction of chimeric genes and genetic engineering of yeast
for 2-butanol production using the US 20070292927A1 disclosed
biosynthetic pathway.
Fermentation Media
[0132] Yeasts disclosed herein may be grown in fermentation media
for production of a product having an Fe--S protein as part of the
biosynthetic pathway. Fermentation media must contain suitable
carbon substrates. Suitable substrates may include but are not
limited to monosaccharides such as glucose and fructose,
oligosaccharides such as lactose or sucrose, polysaccharides such
as starch or cellulose or mixtures thereof and unpurified mixtures
from renewable feedstocks such as cheese whey permeate, cornsteep
liquor, sugar beet molasses, and barley malt. Additionally the
carbon substrate may also be one-carbon substrates such as carbon
dioxide, or methanol for which metabolic conversion into key
biochemical intermediates has been demonstrated. In addition to one
and two carbon substrates methylotrophic organisms are also known
to utilize a number of other carbon containing compounds such as
methylamine, glucosamine and a variety of amino acids for metabolic
activity. For example, methylotrophic yeast are known to utilize
the carbon from methylamine to form trehalose or glycerol (Bellion
et al., Microb. Growth C1 Compd., [Int. Symp.], 7th (1993), 415-32.
Editor(s): Murrell, J. Collin; Kelly, Don P. Publisher: Intercept,
Andover, UK). Similarly, various species of Candida will metabolize
alanine or oleic acid (Sulter et al., Arch. Microbiol. 153:485-489
(1990)). Hence it is contemplated that the source of carbon
utilized in the present invention may encompass a wide variety of
carbon containing substrates and will only be limited by the choice
of organism.
[0133] Although it is contemplated that all of the above mentioned
carbon substrates and mixtures thereof are suitable in the present
invention, preferred carbon substrates are glucose, fructose, and
sucrose.
[0134] In addition to an appropriate carbon source, fermentation
media must contain suitable minerals, salts, cofactors, buffers and
other components, known to those skilled in the art, suitable for
the growth of the cultures and promotion of the enzymatic pathway
necessary for production of the desired product.
Culture Conditions
[0135] Typically cells are grown at a temperature in the range of
about 20.degree. C. to about 37.degree. C. in an appropriate
medium. Suitable growth media in the present invention are common
commercially prepared media such as broth that includes yeast
nitrogen base, ammonium sulfate, and dextrose as the carbon/energy
source) or YPD Medium, a blend of peptone, yeast extract, and
dextrose in optimal proportions for growing most Saccharomyces
cerevisiae strains. Other defined or synthetic growth media may
also be used and the appropriate medium for growth of the
particular microorganism will be known by one skilled in the art of
microbiology or fermentation science.
[0136] Suitable pH ranges for the fermentation are between pH 3.0
to pH 7.5, where pH 4.5.0 to pH 6.5 is preferred as the initial
condition.
[0137] Fermentations may be performed under aerobic or anaerobic
conditions, where anaerobic or microaerobic conditions are
preferred.
[0138] The amount of butanol produced in the fermentation medium
can be determined using a number of methods known in the art, for
example, high performance liquid chromatography (HPLC) or gas
chromatography (GC).
Industrial Batch and Continuous Fermentations
[0139] The present process employs a batch method of fermentation.
A classical batch fermentation is a closed system where the
composition of the medium is set at the beginning of the
fermentation and not subject to artificial alterations during the
fermentation. Thus, at the beginning of the fermentation the medium
is inoculated with the desired organism or organisms, and
fermentation is permitted to occur without adding anything to the
system. Typically, however, a "batch" fermentation is batch with
respect to the addition of carbon source and attempts are often
made at controlling factors such as pH and oxygen concentration. In
batch systems the metabolite and biomass compositions of the system
change constantly up to the time the fermentation is stopped.
Within batch cultures cells moderate through a static lag phase to
a high growth log phase and finally to a stationary phase where
growth rate is diminished or halted. If untreated, cells in the
stationary phase will eventually die. Cells in log phase generally
are responsible for the bulk of production of end product or
intermediate.
[0140] A variation on the standard batch system is the Fed-Batch
system. Fed-Batch fermentation processes are also suitable in the
present invention and comprise a typical batch system with the
exception that the substrate is added in increments as the
fermentation progresses. Fed-Batch systems are useful when
catabolite repression is apt to inhibit the metabolism of the cells
and where it is desirable to have limited amounts of substrate in
the media. Measurement of the actual substrate concentration in
Fed-Batch systems is difficult and is therefore estimated on the
basis of the changes of measurable factors such as pH, dissolved
oxygen and the partial pressure of waste gases such as CO.sub.2.
Batch and Fed-Batch fermentations are common and well known in the
art and examples may be found in Thomas D. Brock in Biotechnology:
A Textbook of Industrial Microbiology, Second Edition (1989)
Sinauer Associates, Inc., Sunderland, Mass., or Deshpande, Mukund
V., Appl. Biochem. Biotechnol., 36:227, (1992), herein incorporated
by reference.
[0141] Although the present invention is performed in batch mode it
is contemplated that the method would be adaptable to continuous
fermentation methods. Continuous fermentation is an open system
where a defined fermentation medium is added continuously to a
bioreactor and an equal amount of conditioned media is removed
simultaneously for processing. Continuous fermentation generally
maintains the cultures at a constant high density where cells are
primarily in log phase growth.
[0142] Continuous fermentation allows for the modulation of one
factor or any number of factors that affect cell growth or end
product concentration. For example, one method will maintain a
limiting nutrient such as the carbon source or nitrogen level at a
fixed rate and allow all other parameters to moderate. In other
systems a number of factors affecting growth can be altered
continuously while the cell concentration, measured by media
turbidity, is kept constant. Continuous systems strive to maintain
steady state growth conditions and thus the cell loss due to the
medium being drawn off must be balanced against the cell growth
rate in the fermentation. Methods of modulating nutrients and
growth factors for continuous fermentation processes as well as
techniques for maximizing the rate of product formation are well
known in the art of industrial microbiology and a variety of
methods are detailed by Brock, supra.
[0143] The present invention may be practiced using either batch,
fed-batch or continuous processes and known modes of fermentation
are suitable. Additionally, it is contemplated that cells may be
immobilized on a substrate as whole cell catalysts and subjected to
fermentation conditions for 1-butanol production.
Methods for Butanol Isolation from the Fermentation Medium
[0144] Bioproduced butanol may be isolated from the fermentation
medium using methods known in the art. For example, solids may be
removed from the fermentation medium by centrifugation, filtration,
decantation, or the like. Then, the butanol may be isolated from
the fermentation medium, which has been treated to remove solids as
described above, using methods such as distillation, liquid-liquid
extraction, or membrane-based separation. Because butanol forms a
low boiling point, azeotropic mixture with water, distillation can
only be used to separate the mixture up to its azeotropic
composition. Distillation may be used in combination with another
separation method to obtain separation around the azeotrope.
Methods that may be used in combination with distillation to
isolate and purify butanol include, but are not limited to,
decantation, liquid-liquid extraction, adsorption, and
membrane-based techniques. Additionally, butanol may be isolated
using azeotropic distillation using an entrainer (see for example
Doherty and Malone, Conceptual Design of Distillation Systems,
McGraw Hill, New York, 2001).
[0145] The butanol-water mixture forms a heterogeneous azeotrope so
that distillation may be used in combination with decantation to
isolate and purify the butanol. In this method, the butanol
containing fermentation broth is distilled to near the azeotropic
composition. Then, the azeotropic mixture is condensed, and the
butanol is separated from the fermentation medium by decantation.
The decanted aqueous phase may be returned to the first
distillation column as reflux. The butanol-rich decanted organic
phase may be further purified by distillation in a second
distillation column.
[0146] The butanol may also be isolated from the fermentation
medium using liquid-liquid extraction in combination with
distillation. In this method, the butanol is extracted from the
fermentation broth using liquid-liquid extraction with a suitable
solvent. The butanol-containing organic phase is then distilled to
separate the butanol from the solvent.
[0147] Distillation in combination with adsorption may also be used
to isolate butanol from the fermentation medium. In this method,
the fermentation broth containing the butanol is distilled to near
the azeotropic composition and then the remaining water is removed
by use of an adsorbent, such as molecular sieves (Aden et al.
Lignocellulosic Biomass to Ethanol Process Design and Economics
Utilizing Co-Current Dilute Acid Prehydrolysis and Enzymatic
Hydrolysis for Corn Stover, Report NREL/TP-510-32438, National
Renewable Energy Laboratory, June 2002).
[0148] Additionally, distillation in combination with pervaporation
may be used to isolate and purify the butanol from the fermentation
medium. In this method, the fermentation broth containing the
butanol is distilled to near the azeotropic composition, and then
the remaining water is removed by pervaporation through a
hydrophilic membrane (Guo et al., J. Membr. Sci. 245, 199-210
(2004)).
EXAMPLES
[0149] The present invention is further defined in the following
Examples. It should be understood that these Examples, while
indicating preferred embodiments of the invention, are given by way
of illustration only. From the above discussion and these Examples,
one skilled in the art can ascertain the essential characteristics
of this invention, and without departing from the spirit and scope
thereof, can make various changes and modifications of the
invention to adapt it to various uses and conditions.
General Methods
[0150] Standard recombinant DNA and molecular cloning techniques
used in the Examples are well known in the art and are described by
Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A
Laboratory Manual; Cold Spring Harbor Laboratory Press: Cold Spring
Harbor, N.Y. (1989) (Maniatis) and by T. J. Silhavy, M. L. Bennan,
and L. W. Enquist, Experiments with Gene Fusions, Cold Spring
Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1984) and by
Ausubel, F. M. et al., Current Protocols in Molecular Biology, pub.
by Greene Publishing Assoc. and Wiley-Interscience (1987), and by
Methods in Yeast Genetics, 2005, Cold Spring Harbor Laboratory
Press, Cold Spring Harbor, N.Y.
[0151] Materials and methods suitable for the maintenance and
growth of bacterial cultures are well known in the art. Techniques
suitable for use in the following Examples may be found as set out
in Manual of Methods for General Bacteriology (Phillipp Gerhardt,
R. G. E. Murray, Ralph N. Costilow, Eugene W. Nester, Willis A.
Wood, Noel R. Krieg and G. Briggs Phillips, eds), American Society
for Microbiology, Washington, D.C. (1994)) or by Thomas D. Brock in
Biotechnology: A Textbook of Industrial Microbiology, Second
Edition, Sinauer Associates, Inc., Sunderland, Mass. (1989). All
reagents, restriction enzymes and materials used for the growth and
maintenance of microbial cells were obtained from Aldrich Chemicals
(Milwaukee, Wis.), BD Diagnostic Systems (Sparks, Md.), Life
Technologies (Rockville, Md.), or Sigma Chemical Company (St.
Louis, Mo.) unless otherwise specified. Microbial strains were
obtained from The American Type Culture Collection (ATCC),
Manassas, Va., unless otherwise noted. All the oligonucleotide
primers were synthesized by Sigma-Genosys (Woodlands, Tex.) or
Integrated DNA Technologies (Coralsville, Iowa).
[0152] Synthetic complete medium is described in Amberg, Burke and
Strathern, 2005, Methods in Yeast Genetics, Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, N.Y.
HPLC
[0153] Analysis for fermentation by-product composition is well
known to those skilled in the art. For example, one high
performance liquid chromatography (HPLC) method utilizes a Shodex
SH-1011 column with a Shodex SH-G guard column (both available from
Waters Corporation, Milford, Mass.), with refractive index (RI)
detection. Chromatographic separation is achieved using 0.01 M
H.sub.2SO.sub.4 as the mobile phase with a flow rate of 0.5 mL/min
and a column temperature of 50.degree. C. Isobutanol retention time
is 47.6 minutes.
[0154] The meaning of abbreviations is as follows: "s" means
second(s), "min" means minute(s), "h" means hour(s), "psi" means
pounds per square inch, "nm" means nanometers, "d" means day(s),
".mu.L" means microliter(s), "mL" means milliliter(s), "L" means
liter(s), "mm" means millimeter(s), "nm" means nanometers, "mM"
means millimolar, "M" means molar, "mmol" means millimole(s),
".mu.mol" means micromole(s)", "g" means gram(s), ".mu.g" means
microgram(s) and "ng" means nanogram(s), "PCR" means polymerase
chain reaction, "OD" means optical density, "OD.sub.600" means the
optical density measured at a wavelength of 600 nm, "kDa" means
kilodaltons, "g" means the gravitation constant, "bp" means base
pair(s), "kbp" means kilobase pair(s), "% w/v" means weight/volume
percent, % v/v" means volume/volume percent, "wt %" means percent
by weight, "HPLC" means high performance liquid chromatography, and
"GC" means gas chromatography. The term "molar selectivity" is the
number of moles of product produced per mole of sugar substrate
consumed and is reported as a percent.
Example 1
Expression of DHAD from K. lactis in LEU1 Deletion Strain of S.
cerevisiae
[0155] The yeast LEU1 gene encodes isopropylmalate dehydratase, an
enzyme that requires an Fe--S cluster for its function. The impact
of LEU1 deletion on DHAD activity expressed from the Kluyveromyces
lactis DHAD coding region was examined in this example. For gene
expression in yeast, the shuttle vector pNY13 (SEQ ID NO:29)
derived from pRS423 was used. This shuttle vector contained an F1
origin of replication (1423 to 1879) for maintenance in E. coli and
a 2 micron origin (nt 7537 to 8881) for replication in yeast. The
vector has an FBA promoter (nt 2111 to 3110) and FBA terminator (nt
4316 to 5315). In addition, it carries the HIS3 marker (nt 504 to
1163) for selection in yeast and ampicillin resistance marker (nt
6547 to 7404) for selection in E. coli. pNY9 is the same vector
with a URA3 marker replacing the HIS3 marker.
[0156] The ILV3 coding region for DHAD from Kluyveromyces lactis
was synthesized with codon-optimization for expression in S.
cerevisiae by DNA 2.0 (Menlo Park, Calif.). The cloned synthesized
sequence was PCR amplified. During amplification, a portion of the
mitochondrial signal peptide for the DHAD at the N-terminus was
deleted by using ilv3(K)(0)-F(delet) as the forward primer with
ilv3(K)(o)-R as the reverse primer, resulting in a coding region
for cytoplasmic expression (SEQ ID NO:173). In addition, an SphI
site was incorporated in the forward primer, while a NotI site was
included in the reverse primer. The PCR product was cloned into the
shuttle vectors pNY9 and pNY13 so that the ILV3 coding region was
under the control of the FBA promoter. Both PCR product and each
vector (pNY9, pNY13) were digested with SphI and NotI. After
digestion, the components were ligated, and the ligation mixture
was transformed into TOP10 competent cells (Invitrogen).
Transformants were selected in LB agar plates supplemented with 100
.mu.g/ml of ampicillin. Positive clones were screened by PCR with
the forward and reverse primers described above. The resulting
plasmids were designated as pRS423::FBAp-ILV3(KL) and
pRS426::FBAp-ILV3(KL), derived from plasmids pNY13 and pNY9,
respectively.
[0157] To study the expression of the DHAD from K. lactis in S.
cerevisiae the expression vector pRS423::FBAp-ILV3(KL) along with
an empty vector pRS426 were transformed into strains BY4743 and
BY4743 leu1::kanMX4 (ATCC 4034377). The competent cell preparation
and transformation were based on the Frozen Yeast Transformation
kit from Zymo Research. The transformants were selected on agar
plates with yeast synthetic medium lacking histidine and uracil
(Teknova). For enzymatic assays, the strains carrying the
expression construct and the empty vector pRS426 were first grown
overnight in 5 ml synthetic complete yeast medium lacking histidine
and uracil. The 5 ml overnight cultures were transferred into 100
ml of medium in a 250 ml flask. The cultures were harvested when
they reached 1 to 2 O.D. at 600 nm. The samples were washed with 10
ml of 20 mM Tris (pH 7.5) and then resuspended in 1 ml of the same
Tris buffer. The samples were transferred into 2.0 ml tubes
containing 0.1 mm silica (Lysing Matrix B, MP biomedicals). The
cells were then broken in a bead-beater (BIO101). The supernatant
was obtained by centrifugation in a microfuge at 13,000 rpm at
4.degree. C. for 30 minutes. Typically, 0.06 to 0.1 mg of crude
extract protein was used in a DHAD assay. Protein in the crude
extracts was determined by Bradford assay with Coomassie stain.
Dihydroxy-Acid Dehydratase Enzyme Assay
[0158] The in vitro DHAD enzyme assay is a variation on the assay
described in Flint et al. (J. Biol. Chem. (1993) 268:14732-14742).
The assay was performed in a 1.6 ml total volume and consisted of:
800 .mu.l 2.times. buffer (100 mM Tris pH 8.0, 20 mM MgCl.sub.2),
160 .mu.l 10.times. substrate (15.6 mg/ml dihydroxyisovalerate),
crude extract (typically 50-200 .mu.g protein), and water. The
reaction was incubated at 37.degree. C. At 0, 30, 60, and 90 minute
time intervals, 350 .mu.l aliquots of the reaction were removed and
incubated with 350 .mu.l of 0.05% dinitrophenyhydrazine in 1N HCl
for 30 minutes at 25.degree. C. To quench the reaction, 350 .mu.l
of 4N sodium hydroxide was added to the reaction mixture, and the
reaction was centrifuged at 15,000.times.g for 2 minutes. The
supernatant was transferred to a plastic disposable cuvette and
absorbance at 540 nm was measured in a spectrophotometer. The
amount of .alpha.-ketoisovalerate (KIV) produced was determined by
entering the absorbance into the linear regression equation
obtained from a standard curve of .alpha.-ketoisovalerate. The
amount of KIV produced at each time point was plotted to determine
the rate of production. The slope of the linear regression was then
used to calculate specific activity using the formula:
Specific activity calculation=(slope of KIV production/1000)/mg
protein per 1.6 mL reaction=mmol/min*mg
The dehydratase from K. lactis had a specific activity in the range
of 0.2 to 0.35 .mu.mol min.sup.-1 mg.sup.-1 when expressed in yeast
strain BY4743 (.DELTA.leu1). In contrast, this enzyme had a
specific activity in the range of only 0.14 .mu.mol min.sup.-1
mg.sup.-1 when expressed in the parent yeast strain BY4743. Strains
BY4743 (.DELTA.leu1) and wildtype BY4743 containing empty vectors
pRS423 or pRS426 had a background of activity in the range of 0.03
to 0.1 .mu.mol min.sup.-1 mg.sup.-1.
Example 2
Expression of Diol Dehydratase in LEU1 Deletion Strain of S.
cerevisiae
[0159] A coenzyme B12-independent propanediol dehydratase is
disclosed in commonly owned and co-pending US Patent Pub No.
US20090155870. The sequences encoding this coenzyme B12-independent
(S-adenosylmethionine (SAM)-dependent) propanediol dehydratase (SEQ
ID NO:15) and its putative associated reactivase (SEQ ID NO:16) in
the bacterium Roseburia inulinivorans [Scott et al. (2006) J.
Bacteriol. 188:4340-9], hereafter referred to as rdhtA and rdhtB,
respectively, were synthesized as one DNA fragment (SEQ ID NO:17)
by standard methods and cloned into an E. coli vector (by DNA2.0,
Inc., Menlo Park, Calif.). This clone was used as a PCR template to
prepare separate RdhtA and RdhtB coding region fragments. The RdhtA
coding region for the diol dehydratase was amplified by PCR using
primers N695 and N696 (SEQ ID NOs:18 and 19). The RdhtB coding
region for the diol dehydratase activase, was amplified by PCR
using primers N697 and N698 (SEQ ID NOs:20 and 21). The two DNA
fragments were combined with a dual terminator DNA fragment (SEQ ID
NO:22) that has an ADH terminator (SEQ ID NO:23) and a CYC1
terminator (SEQ ID NO:24) adjacent to each other in opposing
orientation using SOE PCR (Horton et al. (1989) Gene 77:61-68). The
dual terminator fragment was isolated as a 0.6 kb fragment
following PacI digestion of pRS426::FBA-ILV5+GPM-kivD (described in
co-owned and co-pending US Patent Publication 20070092957 A1,
Example 17). The resulting 4 kb DNA fragment had the RdhtA and
RdhtB coding regions in opposing orientation on either side of the
dual terminator, with the 3'end of each coding region adjacent to
the dual terminator sequence. This DNA fragment was then cloned by
gap repair methodology (Ma et al. (1987) Genetics 58:201-216) into
the S. cerevisiae shuttle vector pRS426::FBA-ILV5+GPM-kivD that was
prepared by digestion with BbvCI to remove the ILV5 and kivD coding
regions and dual terminator sequence between their 3' ends. The
resulting plasmid, pRS426::RdhtAB (below), contained the RdhtA gene
under the control of the S. cerevisiae FBA promoter (SEQ ID NO:25)
and the RdhtB gene under control of the S. cerevisiae GPM promoter
(SEQ ID NO:26).
[0160] Plasmids pRS426 and pRS426::RdhtAB were introduced into S.
cerevisiae strains BY4743 (ATCC 201390) and BY4743 leu1::kanMX4
(ATCC 4034377) by standard techniques (Methods in Yeast Genetics,
2005, Cold Spring Harbor Laboratory Press, Cold Spring Harbor,
N.Y., pp. 201-202). Cells were plated on synthetic complete medium
lacking uracil to select for transformants. Transformants were
tested for diol dehydratase activity using an in vivo assay as
follows. Patched cells grown on solid medium were used to inoculate
liquid media (20 ml) in petri plates. Media used were synthetic
complete minus uracil with and without addition of 5 g/L
1,2-propanediol 9Aldrich Cat. No. 398039). The petri plates were
transferred to an Anaeropack.TM. System jar (Mitsubishi Gas
Chemical Co. Cat. No. 50-70). An anaerobic environment (<0.1%
oxygen) was generated using Pack-Anaero sachets (Mitsubishi Gas
Chemical Co. Cat. No. 10-01). After 48 hours, culture supernatants
were sampled, filtered and analyzed by HPLC as described in General
Methods. Propanol, which has a retention time of 38.8 minutes, was
observed in culture supernatants of strains carrying pRS426::RdhtAB
when 1,2-propanediol was provided in the medium. The results given
in Table 5 show that more propanol was produced in the supernatants
of the strain also carrying the LEU1 deletion than in the strain
without the LEU1 deletion. Statistical analysis gave a P score of
less than 0.0005.
TABLE-US-00005 TABLE 5 Propanol production with propanediol
dehydratase/reactivase expression in yeast with and without LEU1
knockout. 1,2-propanediol Propanol Peak Strain Added Area BY4743 5
g/L 19472 .+-. 1403 .DELTA.leu1::kanMX4/pRS426::RdhtAB (n = 6)
BY4743 0 g/L 2478 (n = 1) .DELTA.leu1::kanMX4/pRS426::RdhtAB
BY4743/pRS426::RdhtAB 5 g/L 11830 .+-. 1963 (n = 6)
BY4743/pRS426::RdhtAB 0 g/L 2369 (n = 1) BY4743
.DELTA.leu1::kanMX4/pRS426 5 g/L 2633 (n = 1) BY4743/pRS426 5 g/L
2841 (n = 1)
Example 3
Improving Cytosolic Dihydroxy-Acid Dehydratase (DHAD) Activity in
S. cerevisiae Through a Disruption of Mitochondrial ILV3
Vector/Host Construction
[0161] In S. cerevisiae ILV3 encodes the mitochondrial
dihydroxy-acid dehydratase that is involved in branched chain amino
acid biosynthesis. To reduce background from endogenous ILV3
expression for in vitro enzymatic assays in S. cerevisiae, an
ilv3::URA3 disruption cassette was constructed by PCR amplification
of the URA3 marker from pRS426 (ATCC No. 77107) with primers
"ILV3::URA3 F" and "ILV3::URA3 R", given as SEQ ID NO:30 and 31.
These primers produced a 1.4 kb URA3 PCR product that contained 70
bp 5' and 3' extensions identical to sequences upstream and
downstream of the ILV3 chromosomal locus for homologous
recombination. The PCR product was transformed into BY4741 cells
(ATCC 201388) using standard genetic techniques (Methods in Yeast
Genetics, 2005, Cold Spring Harbor Laboratory Press, Cold Spring
Harbor, N.Y., pp. 201-202) and resulting transformants were
maintained on synthetic complete media lacking uracil and
supplemented with 2% glucose at 30.degree. C. Transformants were
screened by PCR using primers "ILV3 F Check" and "URA3 REV Check",
given as SEQ ID NOs:32 and 33, to verify integration at the correct
site and disruption of the endogenous ILV3 locus. The correct
transformants had the genotype: BY4741 ilv3::URA3.
[0162] Construction of plasmid pRS423::FBAp-ILV3(KL) and
pRS426::FBAp-ILV3(KL) were described in Example 1. Construction of
pRS423::CUP1-alsS+FBA-ILV3 has been described in co-owned and
co-pending US Patent Publication US20070092957 A1, Example 17 which
is herein incorporated by reference. pRS423::CUP1-alsS+FBA-ILV3 is
the same plasmid as pRS423::CUP1p-alsS-FBAp-ILV3. This construction
contains a chimeric gene containing the S. cerevisiae CUP1 promoter
(SEQ ID NO:34), alsS coding region from Bacillus subtilis (SEQ ID
NO:27), and CYC1 terminator (SEQ ID NO:24); and also a chimeric
gene containing the S. cerevisiae FBA promoter (SEQ ID NO:25), ILV3
coding region from S. cerevisiae lacking the mitochondrial
targeting signal coding sequence (SEQ ID NO:111) and ADH1
terminator (SEQ ID NO:23).
Preparation of Samples
[0163] Plasmid vectors pRS423::CUP1p-alsS-FBAp-ILV3 and
pRS423::FBAp-ILV3(KL) were transformed into strain BY4741
ilv3::URA3 using standard genetic techniques (Methods in Yeast
Genetics, 2005, Cold Spring Harbor Laboratory Press, Cold Spring
Harbor, N.Y.) and maintained on synthetic complete media lacking
histidine. Plasmid vectors pRS423::CUP1p-alsS-FBAp-ILV3 and
pRS426::FBAp-ILV3(KL) were also transformed into strain BY4741.
Aerobic cultures were grown in 1000 ml flasks containing 200 ml
synthetic complete media lacking histidine and supplemented with 2%
glucose in an Innova4000 incubator (New Brunswick Scientific,
Edison, N.J.) at 30.degree. C. and 225 rpm. Cultures were harvested
at OD600 measurements of 1.0-2.0 and pelleted by centrifugation at
6000.times.g for 10 minutes. Cell pellets were washed with 10 mM
Tris-HCl, pH 8.0 and pellets were stored at -80.degree. C. until
assayed for activity. Cell free extracts were prepared by standard
bead beating method using 1 ml of 0.5 mm beads and 1.5 ml of yeast
cell suspension. Protein concentration in the extracts was
determined by Bradford assay with Coomassie stain. DHAD enzyme
assays and specific activity calculations were performed as
described in Example 1. The results given in Table 6 show that
there was higher DHAD activity in the ILV3 deletion cells than in
cells without the ILV3 deletion.
TABLE-US-00006 TABLE 6 DHAD activity in yeast with and without ILV3
deletion. Average Specific Specific Activity Activity Strain
(.mu.mol/min * mg) (.mu.mol/min * mg) BY4741 0.018 0.013 0.014
0.008 BY4741 pRS423::CUP1p-alsS- 0.018 0.019 FBAp-ILV3 0.020 BY4741
pRS426::FBAp-ILV3(KL) 0.040 0.038 0.036 BY4741 ilv3::URA3 0.00006
0.00041 0.00075 BY4741 ilv3::URA3 0.030 0.029
pRS423::CUP1p-alsS-FBAp-ILV3 0.028 BY4741 ilv3::URA3 0.317 0.281
pRS423::FBAp-ILV3(KL) 0.244
Verification of Alpha-Ketoisovalerate Formation by HPLC
[0164] Formation of alpha-ketoisovalerate from the in vitro DHAD
enzyme assays was accomplished using HPLC and semicarbizide
derivatization. DHAD enzyme assays were performed in a 1.6 ml total
volume and consisted of: 800 .mu.l 2.times. buffer (100 mM Tris pH
8.0, 20 mM MgCl.sub.2), 160 .mu.l 10.times. substrate (15.6 mg/ml
dihydroxyisovalerate), crude extract (typically 50-200 .mu.g
protein), and water. The reactions were incubated at 37.degree. C.
At time intervals of zero and 90 minutes 350 .mu.l aliquots of the
reactions were removed, transferred to ice, and centrifuged at
13,000.times.g for 2 minutes at 4.degree. C. to remove precipitated
protein. The supernatants were transferred to ice-chilled Microcon
YM-10 (Sigma) spin columns and centrifuged at 13,000.times.g for 20
minutes at 4.degree. C. to remove enzymes and soluble proteins. The
flowthroughs were mixed with 100 .mu.l derivatizing reagent (1%
semicarbizide hydrochloride and 1.5% sodium acetate trihydrate) and
incubated at room temperature for 15 minutes. The reactions were
spun through CoStar spin filters (CoStar, 0.22 .mu.m filter) at
13,000.times.g for 5 minutes at 4.degree. C. to remove any
precipitates. The flowthroughs were transferred to HPLC vials for
analysis.
[0165] Analysis of derivatized alpha-ketoisovalerate was conduced
using reverse phase chromatography on a Supelco LC-18 column with
Superguard LC-18-DB guard column (Supelco; 25 cm.times.4.6 mm, 5
.mu.m). Injection volumes were 10 .mu.l. Mobile phases were
methanol (A) and 50 mM NaOAc pH 7.2. The gradient program utilized
is given in Table 7, with detection at 250 nm.
TABLE-US-00007 TABLE 7 Gradient used for derivatized
alpha-ketoisovalerate HPLC assay Time (min) Flow (ml/min) % NaOAc
(50 mM) % MEOH Curve Initial 1.0 95 5 5 1.0 95 5 6 20 1.0 70 30 6
21 1.0 0 100 6 25 1.0 0 100 6 26 1.0 95 5 6 35 1.0 95 5 6
The retention time of semicarbizide-derivatized
alpha-ketoisovalerate was 11.5 minutes.
[0166] The results, which are given in Table 8, confirmed that KIV
was produced in the cells, as detected in the indirect assay for
specific activity above. The amount of KIV listed in the DHAD Assay
column is the amount determined indirectly in the 90 min sample for
the activity assay described above in determining the specific
activity. This amount of KIV correlates well with the amount
detected in the HPLC assay.
TABLE-US-00008 TABLE 8 Comparison of KIV detected in DHAD activity
asay and by HPLC. keto-isovalerate production (.mu.M) Strain DHAD
Assay HPLC BY4741 ilv3::URA3 pRS423::FBAp- 256 256 ILV3(KL) BY4741
ilv3::URA3 pRS423::FBAp- 162 163 ILV3(KL)
Sequence CWU 0 SQTB SEQUENCE LISTING The patent application
contains a lengthy "Sequence Listing" section. A copy of the
"Sequence Listing" is available in electronic form from the USPTO
web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20160024534A1).
An electronic copy of the "Sequence Listing" will also be available
from the USPTO upon request and payment of the fee set forth in 37
CFR 1.19(b)(3).
0 SQTB SEQUENCE LISTING The patent application contains a lengthy
"Sequence Listing" section. A copy of the "Sequence Listing" is
available in electronic form from the USPTO web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20160024534A1).
An electronic copy of the "Sequence Listing" will also be available
from the USPTO upon request and payment of the fee set forth in 37
CFR 1.19(b)(3).
* * * * *
References