# Patent

## Title
Cell suitable for fermentation of a mixed sugar composition

## Abstract

The present invention relates to a cell suitable for production of one or more fermentation product from a sugar composition comprising glucose, galactose, arabinose and xylose, wherein the cell comprises two to fifteen copies of one or more xylose isomerase gene or two to fifteen copies of one or more xylose reductase and xylitol dehydrogenase, and two to ten copies of araA, araB and araD, genes, wherein these genes are integrated into the cell genome.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application is a §371 National Stage Application of PCT/EP2011/056232, filed Apr. 19, 2011, which claims priority to European Application Nos. 10160622.6, filed Apr. 21, 2010; and Ser. No. 10/160,647.3, filed Apr. 21, 2010, and U.S. Provisional Application Nos. 61/326,351, filed Apr. 21, 2010; and 61/326,358, filed Apr. 21, 2010.


BACKGROUND OF THE INVENTION
1. Field of the Invention
The invention relates to a cell (herein also designated as mixed sugar cell), suitable for fermentation of a sugar composition comprising multiple C5 and/or C6 sugars (such composition is herein also designated as mixed sugar composition). The mixed sugar composition may originate from ligno-cellulosic material. The invention also relates to a process for the production of fermentation product from the mixed sugar composition using the mixed sugar cell.
2. Description of Related Art
Most of the ethanol produced as alternative for fossil fuels is currently from fermentation of corn starch and sugar cane based sucrose. In order to reach the ambitious goals for producing renewable fuels, new technologies are being developed for converting non-food biomass into fermentation products such as ethanol. Saccharomyces cerevisiae is the organism of choice in the ethanol industry, but it cannot utilize five-carbon sugars contained in the hemicellulose component of biomass feedstocks. Hemicellulose can make up to 20-30% of biomass, with xylose and arabinose being the most abundant C5 sugars. Heterologous expression of a xylose isomerase (XI) is an option for enabling yeast cells to metabolize and ferment xylose. Likewise, expression of bacterial genes araA, araB, and araD in S. cerevisiae strains results in utilization and efficient alcoholic fermentation of arabinose. Galactose is a C6-sugar that is also a sugar that is often present in lignocellulose, often in amounts ( ̃4% of total sugars) that are not to be neglected for economic reasons.
J. van den Brink et al, Microbiology (2009)155, 1340-1350 discloses that glucose is the favoured carbon source for Saccharomyces cerevisiae and that upon switching from glucose limited fermentation conditions to galactose-excess condition under anaerobic condition, galactose was not consumed.
Sofar no process has been disclosed to convert glucose, arabinose, xylose and galactose, into a fermentation product in the same process with glucose.
SUMMARY
An object the invention is to provide a cell capable of converting glucose, xylose and galactose and mannose, i.e. a mix of four sugars, into a fermentation product. Another object of the invention is to such cell that is capable of converting glucose, xylose, arabinose, galactose and mannose, i.e. a mix of five sugars, into a fermentation product. A further object of the invention is to provide such above defined cell that is stable. A further object of the invention is to provide such above defined strain that is marker-free. A further object of the invention is to provide a process wherein glucose, xylose, arabinose, and galactose are simultaneously converted into a fermentation product. One or more of these objects are attained according to the invention.
The present invention provides a cell suitable for production of one or more fermentation product from a sugar composition comprising glucose, galactose, xylose, arabinose and mannose, wherein the cell comprises two to fifteen copies of one or more xylose isomerase gene or two to fifteen copies of one or more xylose reductase and xylitol dehydrogenase, and two to ten copies of araA, araB and araD, genes, wherein these genes are integrated into the cell genome.
The invention further provides to a process for the production of one or more fermentation product from a sugar composition comprising glucose, arabinose and xylose and optionally galactose and/or mannose comprising the following steps:

    
    
        a) fermentation of the sugar composition in the presence of a mixed sugar cell comprising two to fifteen copies of one or more xylose isomerase gene and/or two to fifteen copies of one or more xylose reductase and xylitol dehydrogenase, wherein these genes are integrated into the genome; and
        b) recovery of the fermentation product.
    
    


In an embodiment, the mixed sugar cell is of the genus Saccharomyces. In an embodiment the mixed sugar cell is of the species Saccharomyces cerevisiae. In an embodiment, the fermentation product is ethanol.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 sets out a physical map of plasmid pPWT006.
FIG. 2 sets out a physical map of plasmid pPWT018.
FIG. 3 sets out a Southern blot autoradiogram. Chromosomal DNA of wild-type strain CEN.PK113-7D (lane 1) and BIE104A2 (lane 2) was digested with both EcoRI and HindIII. The blot was hybridized with a specific SIT2-probe.
FIG. 4 sets out a physical map of plasmid pPWT080, the sequence of which is given in SEQ ID NO: 8
FIG. 5 sets out a growth curves under aerobic conditions of BIE104P1A2 on different media. Strain BIE104A2P1 was pregrown on YNB 2% galactose. Growth curve was started on 2% galactose and 1% arabinose, followed by event indicated in the graph by number (1) transfer to YNB with 2% arabinose as sole carbon source. After reaching an OD 600 more than 1, the culture was transferred to fresh medium with a starting OD 600 of 0.2. Upon three transfers on pure arabinose medium the resulting strain was designated BIE104P1A2c.
FIG. 6 sets out a growth curves under anaerobic conditions of BIE104P1A2c on YNB 2% arabinose as sole carbon source. After reaching an OD 600 higher than 1, the culture was transferred to fresh medium with a starting OD 600 of 0.2. After several transfers the resulting strain was named BIE104P1A2d (=BIE201).
FIG. 7 sets out a physical map of the plasmid pPWT042, the sequence of which is given in SEQ ID NO:14.
FIG. 8 sets out a growth curve under aerobic conditions of a transformation mixture. Strain BIE201X9 was transformed with fragment X18-Ty1 and the transformation mixture was used to inoculate Verduyn-medium supplemented with 2% xylose. After reaching an OD 600 of approximately 35, an aliquot of the culture was used to inoculate a second flask with fresh medium. From the second flask, colonies were isolated for further analysis.
FIG. 9 sets out the growth of single colony isolates on Verduyn-medium supplemented with either 2% glucose, or 2% xylose, or 2% arabinose or 2% galactose.
FIG. 10 sets out the growth of selected single colony isolates on Verduyn-medium supplemented with either 2% xylose or 2% arabinose.
FIG. 11 sets out the sugar conversion and product formation of a mixed culture of strains BIE104P1Y9mc and BIE201 on synthetic medium, in a fed-batch experiment. CO2 production was measured constantly. Growth was monitored by following optical density of the culture. Preculture was grown on 2% glucose.
FIG. 12 sets out the sugar conversion and product formation of strain BIE252 on synthetic medium, in a fed-batch experiment. CO2 production was measured constantly. Growth was monitored by following optical density of the culture. Preculture was grown on 2% glucose.
FIG. 13 sets out the total CO2 that was produced in the fed-batch experiments.
FIG. 14 sets out the sugar conversion and product formation of a mixed culture of strains BIE104P1Y9mc and BIE201 on synthetic medium, in a batch experiment. CO2 production was measured constantly. Growth was monitored by following optical density of the culture. Preculture was grown on 2% glucose.
FIG. 15 sets out the sugar conversion and product formation of a mixed culture of strain BIE252 on synthetic medium, in a batch experiment. CO2 production was measured constantly. Growth was monitored by following optical density of the culture. Preculture was grown on 2% glucose.
FIG. 16 sets out the total CO2 that was produced in the batch experiments.
FIG. 17 sets out the performance of strain BIE252 in hydrolyzed corn fiber at 13.8% d.m. CO2 production rate, ethanol production and sugar conversion are shown.
FIG. 18 sets out the performance of strain BIE252 in hydrolyzed corn stover at 10% d.m. CO2 production rate, ethanol production and sugar conversion are shown.
FIG. 19 sets out the performance of strain BIE252 in hydrolyzed wheat straw at 10% d.m. CO2 production rate, ethanol production and sugar conversion are shown.
FIG. 20a sets out the sugar conversion (rate) of strain BIE252.
FIG. 20b sets out the sugar conversion (rate) of a single colony isolate of strain BIE252 after cultivation for more than 100 generations in YEP-medium with 2% glucose.
FIG. 20c sets out the sugar conversion (rate) of a single colony isolate of strain BIE252 after cultivation for more than 100 generations in YEP-medium with 2% glucose.
FIG. 21 sets out the physical map of plasmid pPWT148.
FIG. 22 sets out the physical map of plasmid pPWT152.
FIG. 23 sets out a CHEF gel, stained with ethidium bromide. Chromosomes were separated on their size using the CHEF technique. Strains analyzed are BIE104 (untransformed yeast cell), BIE104A2P1a (primary transformant unable to consume arabinose, synonym of BIE104A2P1), BIE104A2P1c, a strain derived from BIE104A2P1 by adaptive evolution, which is able to grow on arabinose, strain BIE201, derived from BIE104A2P1c by adaptive evolution, which can grow on arabinose under anaerobic conditions and strain BIE252, that is a mixed sugar strain. Shifts in chromosomes are observed (see text). Strain YNN295 is a marker strain (Bio-Rad), used as a reference for the size of the chromosomes.



BRIEF DESCRIPTION OF THE SEQUENCE LISTING
SEQ ID NO: 1 sets out the sequence of plasmid pPWT018
SEQ ID NO: 2 sets out the sequence of primer for checking the integration of pPWT018
SEQ ID NO: 3 sets out the sequence of primer for checking the integration of pPWT018 (with SEQ ID NO: 2) and for checking copy number pPWT018 (with SEQ ID NO: 4)
SEQ ID NO: 4 sets out the sequence of primer for checking copy number pPWT018
SEQ ID NO: 5 sets out the sequence of primer for checking the presence of pPWT018 in genome in combination with SEQ ID NO: 4
SEQ ID NO: 6 sets out the sequence of forward primer for generating the SIT2 probe
SEQ ID NO: 7 sets out the sequence of reverse primer for generating the SIT2 probe
SEQ ID NO: 8 sets out the sequence of plasmid pPWT080
SEQ ID NO: 9 sets out the sequence of forward primer for checking correct integration of pPWT080 at the end of the GRE3-locus (with SEQ ID NO: 10) and for checking the copy number plasmid pPWT080 (with SEQ ID NO: 11)
SEQ ID NO: 10 sets out the sequence of reverse primer for checking correct integration of pPWT080 at the end of the GRE3-locus
SEQ ID NO: 11 sets out the sequence of reverse primer for checking the copy number plasmid pPWT080
SEQ ID NO: 12 sets out the sequence of forward primer for generating an RKI1-probe
SEQ ID NO: 13 sets out the sequence of reverse primer for generating an RKI1-probe
SEQ ID NO: 14 sets out sequence of plasmid pPWT042
SEQ ID NO: 15 sets out the sequence of primer for checking integration of pPWT042
SEQ ID NO: 16 sets out the sequence of primer for checking integration of pPWT042
SEQ ID NO: 17 sets out the sequence of primer for checking integration of pPWT042
SEQ ID NO: 18 sets out the sequence of primer for checking marker loss of pPWT042
SEQ ID NO: 19 sets out the sequence of primer for amplification of xylA-cassette
SEQ ID NO: 20 sets out the sequence of primer for amplification of xylA-cassette
SEQ ID NO: 21 sets out the sequence of primer for the amplification of kanMX-cassette
SEQ ID NO: 22 sets out the sequence of primer for the amplification of the kanMX-cassette
SEQ ID NO: 23 sets out the sequence of primer for quantitative PCR
SEQ ID NO: 24 sets out the sequence of primer for quantitative PCR.
SEQ ID NO: 25 sets out the sequence of primer for quantitative PCR
SEQ ID NO: 26 sets out the sequence of primer for quantitative PCR.
DETAILED DESCRIPTION OF A PREFERRED EMBODIMENT
Throughout the present specification and the accompanying claims, the words “comprise” and “include” and variations such as “comprises”, “comprising”, “includes” and “including” are to be interpreted inclusively. That is, these words are intended to convey the possible inclusion of other elements or integers not specifically recited, where the context allows.
The articles “a” and “an” are used herein to refer to one or to more than one (i.e. to one or at least one) of the grammatical object of the article. By way of example, “an element” may mean one element or more than one element.
The various embodiments of the invention described herein may be cross-combined.
The Sugar Composition
The sugar composition according to the invention comprises glucose, arabinose and xylose. Any sugar composition may be used in the invention that suffices those criteria. Optional sugars in the sugar composition are galactose and mannose. In a preferred embodiment, the sugar composition is a hydrolysate of one or more lignocellulosic material. Lignocellulose herein includes hemicellulose and hemicellulose parts of biomass. Also lignocellulose includes lignocellulosic fractions of biomass. Suitable lignocellulosic materials may be found in the following list: orchard primings, chaparral, mill waste, urban wood waste, municipal waste, logging waste, forest thinnings, short-rotation woody crops, industrial waste, wheat straw, oat straw, rice straw, barley straw, rye straw, flax straw, soy hulls, rice hulls, rice straw, corn gluten feed, oat hulls, sugar cane, corn stover, corn stalks, corn cobs, corn husks, switch grass, miscanthus, sweet sorghum, canola stems, soybean stems, prairie grass, gamagrass, foxtail; sugar beet pulp, citrus fruit pulp, seed hulls, cellulosic animal wastes, lawn clippings, cotton, seaweed, trees, softwood, hardwood, poplar, pine, shrubs, grasses, wheat, wheat straw, sugar cane bagasse, corn, corn husks, corn hobs, corn kernel, fiber from kernels, products and by-products from wet or dry milling of grains, municipal solid waste, waste paper, yard waste, herbaceous material, agricultural residues, forestry residues, municipal solid waste, waste paper, pulp, paper mill residues, branches, bushes, canes, corn, corn husks, an energy crop, forest, a fruit, a flower, a grain, a grass, a herbaceous crop, a leaf, bark, a needle, a log, a root, a sapling, a shrub, switch grass, a tree, a vegetable, fruit peel, a vine, sugar beet pulp, wheat midlings, oat hulls, hard or soft wood, organic waste material generated from an agricultural process, forestry wood waste, or a combination of any two or more thereof.
An overview of some suitable sugar compositions derived from lignocellulose and the sugar composition of their hydrolysates is given in table 1. The listed lignocelluloses include: corn cobs, corn fiber, rice hulls, melon shells, sugar beet pulp, wheat straw, sugar cane bagasse, wood, grass and olive pressings.







TABLE 1







Overview of sugar compositions from lignocellulosic materials.
















Lignocellulosic







%.



material
Gal
Xyl
Ara
Man
Glu
Rham
Sum
Gal.
Lit.



















Corn cob a
10
286
36

227
11
570
1.7
(1)


Corn cob b
131
228
160

144

663
19.8
(1)


Rice hulls a
9
122
24
18
234
10
417
2.2
(1)


Rice hulls b
8
120
28

209
12
378
2.2
(1)


Melon Shells
6
120
11

208
16
361
1.7
(1)


Sugar beet pulp
51
17
209
11
211
24
523
9.8
(2)


Wheat straw Idaho
15
249
36

396

696
2.2
(3)


Corn fiber
36
176
113

372

697
5.2
(4)


Cane Bagasse
14
180
24
5
391

614
2.3
(5)


Corn stover
19
209
29

370

626

(6)


Athel (wood)
5
118
7
3
493

625
0.7
(7)


Eucalyptus (wood)
22
105
8
3
445

583
3.8
(7)


CWR (grass)
8
165
33

340

546
1.4
(7)


JTW (grass)
7
169
28

311

515
1.3
(7)


MSW
4
24
5
20
440

493
0.9
(7)


Reed Canary Grass
16
117
30
6
209
1
379
4.2
(8)


Veg











Reed Canary Grass
13
163
28
6
265
1
476
2.7
(9)


Seed











Olive pressing residu
15
111
24
8
329

487
3.1
(9)





Gal = galactose,


Xyl = xylose,


Ara = arabinose,


Man = mannose,


Glu = glutamate,


Rham = rhamnose.


The percentage galactose (% Gal) and literature source is given.






It is clear from table 1 that in these lignocelluloses a high amount of sugar is presence in de form of glucose, xylose, arabinose and galactose. The conversion of glucose, xylose, arabinose and galactose to fermentation product is thus of great economic importance. Also mannose is present in some lignocellulose materials be it usually in lower amounts than the previously mentioned sugars. Advantageously therefore also mannose is converted by the mixed sugar cell.
The Mixed Sugar Cell
The mixed sugar cell comprises two to fifteen copies of one or more xylose isomerase gene or two to fifteen copies of one or more xylose reductase and xylitol dehydrogenase, and two to ten copies of araA, araB and araD, genes, wherein these genes are integrated into the cell genome. I
In one embodiment, the mixed sugar cell comprises about eight copies or eight copies of xylose isomerase, wherein these genes are integrated into the mixed sugar cell genome. In another embodiment, the mixed sugar cell comprises eight copies of a xylose reductase and xylitol dehydrogenase, wherein these genes are integrated into the mixed sugar cell genome.
The number of copies may be determined by the skilled person by any known method. In the examples, a suitable method is described.
The mixed sugar cell comprises two to ten copies of araA, araB and araD, genes, wherein these genes are integrated into the cell genome. t is able to ferment glucose, arabinose, xylose and galactose.
In an embodiment, the mixed sugar cell comprises two copies, three copies, four copies five copies, six copies, seven copies, eight copies, nine copies or ten copies, two to ten, two to nine, two to eight, two to seven, two to six, two to five, two to four, three to ten, three to nine, three to eight, three to seven, three to six, three to five, four to ten, four to nine, four to eight, four to seven or four to six copies of each of araA, araB and araD, genes, wherein these genes are integrated into the cell genome. In an embodiment the mixed sugar cell comprises about four, or four copies of each of araA, araB and araD genes, wherein these genes are integrated into the cell genome.
In an embodiment the number of copies of xylose isomerase gene or xylose reductase and xylitol dehydrogenase in to mixed sugar cell is eight or nine. In an embodiment the number of copies of araA, araB and araD genes in the mixed sugar cell is 3 or 4.
In an embodiment, the cell is capable of converting 90% or more glucose, xylose arabinose, galactose and mannose available, into a fermentation product. In an embodiment, cell is capable of converting 91% or more, 92% or more, 94% or more, 95% or more, 96% or more, 97% or more, 98% or more or 100% of all glucose, xylose arabinose, galactose and mannose available, into a fermentation product.
In an embodiment, the cell has a disruption or deletion of the GAL80 gene.
In one embodiment of the invention the mixed sugar cell is able to ferment one or more additional sugar, preferably C5 and/or C6 sugar e.g. mannose. In an embodiment of the invention the mixed sugar cell comprises one or more of: a xylA-gene, XYL1 gene and XYL2 gene and/or XKS1-gene, to allow the mixed sugar cell to ferment xylose; deletion of the aldose reductase (GRE3) gene; overexpression of PPP-genes TAL1, TKL1, RPE1 and RKI1 to allow the increase of the flux through the pentose phosphate pass-way in the cell.
In an embodiment, the mixed sugar cell is an industrial cell, more preferably an industrial yeast. An industrial cell and industrial yeast cell may be defined as follows. The living environments of (yeast) cells in industrial processes are significantly different from that in the laboratory. Industrial yeast cells must be able to perform well under multiple environmental conditions which may vary during the process. Such variations include change in nutrient sources, pH, ethanol concentration, temperature, oxygen concentration, etc., which together have potential impact on the cellular growth and ethanol production of Saccharomyces cerevisiae. Under adverse industrial conditions, the environmental tolerant strains should allow robust growth and production. Industrial yeast strains are generally more robust towards these changes in environmental conditions which may occur in the applications they are used, such as in the baking industry, brewing industry, wine making and the ethanol industry. In one embodiment, the industrial mixed sugar cell is constructed on the basis of an industrial host cell, wherein the construction is conducted as described hereinafter. Examples of industrial yeast (S. cerevisiae) are ETHANOL RED® (S. cerevisiae; Fermentis) FERMIOL® (S. cerevisiae; DSM) and THERMOSACC® (S. cerevisiae; Lallemand).
In an embodiment the mixed sugar cell is inhibitor tolerant. Inhibitor tolerance is resistance to inhibiting compounds. The presence and level of inhibitory compounds in lignocellulose may vary widely with variation of feedstock, pretreatment method hydrolysis process. Examples of categories of inhibitors are carboxylic acids, furans and/or phenolic compounds. Examples of carboxylic acids are lactic acid, acetic acid or formic acid. Examples of furans are furfural and hydroxy-methylfurfural. Examples or phenolic compounds are vanillin, syringic acid, ferulic acid and coumaric acid. The typical amounts of inhibitors are for carboxylic acids: several grams per liter, up to 20 grams per liter or more, depending on the feedstock, the pretreatment and the hydrolysis conditions. For furans: several hundreds of milligrams per liter up to several grams per liter, depending on the feedstock, the pretreatment and the hydrolysis conditions. For phenolics: several tens of milligrams per liter, up to a gram per liter, depending on the feedstock, the pretreatment and the hydrolysis conditions.
The mixed sugar strains according to the invention are inhibitor tolerant, i.e. they can withstand common inhibitors at the level that they typically have with common pretreatment and hydrolysis conditions, so that the mixed sugar strains can find broad application, i.e. it has high applicability for different feedstock, different pretreatment methods and different hydrolysis conditions.
In one embodiment, the industrial mixed sugar cell is constructed on the basis of an inhibitor tolerant host cell, wherein the construction is conducted as described hereinafter. Inhibitor tolerant host cells may be selected by screening strains for growth on inhibitors containing materials, such as illustrated in Kadar et al, Appl. Biochem. Biotechnol. (2007), Vol. 136-140, 847-858, wherein an inhibitor tolerant S. cerevisiae strain ATCC 26602 was selected.
In an embodiment, the mixed sugar cell is marker-free. As used herein, the term “marker” refers to a gene encoding a trait or a phenotype which permits the selection of, or the screening for, a host cell containing the marker. Marker-free means that markers are essentially absent in the mixed sugar cell. Being marker-free is particularly advantageous when antibiotic markers have been used in construction of the mixed sugar cell and are removed thereafter. Removal of markers may be done using any suitable prior art technique, e.g intramolecular recombination. A suitable method of marker removal is illustrated in the examples.
A mixed sugar cell may be able to convert plant biomass, celluloses, hemicelluloses, pectins, rhamnose, galactose, frucose, maltose, maltodextrines, ribose, ribulose, or starch, starch derivatives, sucrose, lactose and glycerol, for example into fermentable sugars. Accordingly, a mixed sugar cell may express one or more enzymes such as a cellulase (an endocellulase or an exocellulase), a hemicellulase (an endo- or exo-xylanase or arabinase) necessary for the conversion of cellulose into glucose monomers and hemicellulose into xylose and arabinose monomers, a pectinase able to convert pectins into glucuronic acid and galacturonic acid or an amylase to convert starch into glucose monomers.
The mixed sugar cell further may comprise those enzymatic activities required for conversion of pyruvate to a desired fermentation product, such as ethanol, butanol, lactic acid, 3-hydroxy-propionic acid, acrylic acid, acetic acid, succinic acid, citric acid, fumaric acid, malic acid, itaconic acid, an amino acid, 1,3-propane-diol, ethylene, glycerol, a β-lactam antibiotic or a cephalosporin.
In an embodiment, the mixed sugar cell a cell that is naturally capable of alcoholic fermentation, preferably, anaerobic alcoholic fermentation. A mixed sugar cell preferably has a high tolerance to ethanol, a high tolerance to low pH (i.e. capable of growth at a pH lower than about 5, about 4, about 3, or about 2.5) and towards organic and/or a high tolerance to elevated temperatures.
Any of the above characteristics or activities of a mixed sugar cell may be naturally present in the cell or may be introduced or modified by genetic modification.
Construction of the Mixed Sugar Strain
According to an embodiment, the genes may be introduced in the mixed sugar cell by introduction into a host cell:

    a) a cluster consisting of the genes araA, araB and araD under control of a strong constitutive promoter
    b) a cluster consisting of PPP-genes TAL1, TKL1, RPE1 and RKI1, optionally under control of strong constitutive promoter; and deletion of an aldose reductase gene;
    c) a cluster consisting of a xylA-gene and a XKS1-gene under control of strong constitutive promoter;
    d) a construct comprising a xylA gene under control of a strong constitutive promoter, which has the ability to integrate into the genome on multiple loci;

and adaptive evolution to produce the mixed sugar cell. The above cell may be constructed using recombinant expression techniques.



Recombinant Expression
The mixed sugar cell is a recombinant cell. That is to say, a mixed sugar cell comprises, or is transformed with or is genetically modified with a nucleotide sequence that does not naturally occur in the cell in question.
Techniques for the recombinant expression of enzymes in a cell, as well as for the additional genetic modifications of a mixed sugar cell are well known to those skilled in the art. Typically such techniques involve transformation of a cell with nucleic acid construct comprising the relevant sequence. Such methods are, for example, known from standard handbooks, such as Sambrook and Russel (2001) “Molecular Cloning: A Laboratory Manual (3rd edition), Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, or F. Ausubel et al., eds., “Current protocols in molecular biology”, Green Publishing and Wiley Interscience, New York (1987). Methods for transformation and genetic modification of fungal host cells are known from e.g. EP-A-0635 574, WO 98/46772, WO 99/60102, WO 00/37671, WO90/14423, EP-A-0481008, EP-A-0635574 and U.S. Pat. No. 6,265,186.
Typically, the nucleic acid construct may be a plasmid, for instance a low copy plasmid or a high copy plasmid. The cell according to the present invention may comprise a single or multiple copies of the nucleotide sequence encoding a enzyme, for instance by multiple copies of a nucleotide construct or by use of construct which has multiple copies of the enzyme sequence.
The nucleic acid construct may be maintained episomally and thus comprise a sequence for autonomous replication, such as an autosomal replication sequence sequence. A suitable episomal nucleic acid construct may e.g. be based on the yeast 2p or pKD1 plasmids (Gleer et al., 1991, Biotechnology 9: 968-975), or the AMA plasmids (Fierro et al., 1995, Curr Genet. 29:482-489). Alternatively, each nucleic acid construct may be integrated in one or more copies into the genome of the cell. Integration into the cell's genome may occur at random by non-homologous recombination but preferably, the nucleic acid construct may be integrated into the cell's genome by homologous recombination as is well known in the art (see e.g. WO90/14423, EP-A-0481008, EP-A-0635 574 and U.S. Pat. No. 6,265,186).
Most episomal or 2μ plasmids are relatively unstable, being lost in approximately 10−2 or more cells after each generation. Even under conditions of selective growth, only 60% to 95% of the cells retain the episomal plasmid. The copy number of most episomal plasmids ranges from 20-100 per cell of cir+ hosts. However, the plasmids are not equally distributed among the cells, and there is a high variance in the copy number per cell in populations. Strains transformed with integrative plasmids are extremely stable, even in the absence of selective pressure. However, plasmid loss can occur at approximately 10−3 to 10−4 frequencies by homologous recombination between tandemly repeated DNA, leading to looping out of the vector sequence. Preferably, the vector design in the case of stable integration is thus, that upon loss of the selection marker genes (which also occurs by intramolecular, homologous recombination) that looping out of the integrated construct is no longer possible. Preferably the genes are thus stably integrated. Stable integration is herein defined as integration into the genome, wherein looping out of the integrated construct is no longer possible. Preferably selection markers are absent. Typically, the enzyme encoding sequence will be operably linked to one or more nucleic acid sequences, capable of providing for or aiding the transcription and/or translation of the enzyme sequence.
The term “operably linked” refers to a juxtaposition wherein the components described are in a relationship permitting them to function in their intended manner. For instance, a promoter or enhancer is operably linked to a coding sequence the said promoter or enhancer affects the transcription of the coding sequence.
As used herein, the term “promoter” refers to a nucleic acid fragment that functions to control the transcription of one or more genes, located upstream with respect to the direction of transcription of the transcription initiation site of the gene, and is structurally identified by the presence of a binding site for DNA-dependent RNA polymerase, transcription initiation sites and any other DNA sequences known to one of skilled in the art. A “constitutive” promoter is a promoter that is active under most environmental and developmental conditions. An “inducible” promoter is a promoter that is active under environmental or developmental regulation.
The promoter that could be used to achieve the expression of a nucleotide sequence coding for an enzyme according to the present invention, may be not native to the nucleotide sequence coding for the enzyme to be expressed, i.e. a promoter that is heterologous to the nucleotide sequence (coding sequence) to which it is operably linked. The promoter may, however, be homologous, i.e. endogenous, to the host cell.
Promoters are widely available and known to the skilled person. Suitable examples of such promoters include e.g. promoters from glycolytic genes, such as the phosphofructokinase (PFK), triose phosphate isomerase (TPI), glyceraldehyde-3-phosphate dehydrogenase (GPD, TDH3 or GAPDH), pyruvate kinase (PYK), phosphoglycerate kinase (PGK) promoters from yeasts or filamentous fungi; more details about such promoters from yeast may be found in (WO 93/03159). Other useful promoters are ribosomal protein encoding gene promoters, the lactase gene promoter (LAC4), alcohol dehydrogenase promoters (ADH1, ADH4, and the like), and the enolase promoter (ENO). Other promoters, both constitutive and inducible, and enhancers or upstream activating sequences will be known to those of skill in the art. The promoters used in the host cells of the invention may be modified, if desired, to affect their control characteristics. Suitable promoters in this context include both constitutive and inducible natural promoters as well as engineered promoters, which are well known to the person skilled in the art. Suitable promoters in eukaryotic host cells may be GAL7, GAL10, or GAL1, CYC1, HIS3, ADH1, PGL, PH05, GAPDH, ADC1, TRP1, URA3, LEU2, ENO1, TPI1, and AOX1. Other suitable promoters include PDC1, GPD1, PGK1, TEF1, and TDH3.
In a mixed sugar cell, the 3′-end of the nucleotide acid sequence encoding enzyme preferably is operably linked to a transcription terminator sequence. Preferably the terminator sequence is operable in a host cell of choice, such as e.g. the yeast species of choice. In any case the choice of the terminator is not critical; it may e.g. be from any yeast gene, although terminators may sometimes work if from a non-yeast, eukaryotic, gene. Usually a nucleotide sequence encoding the enzyme comprises a terminator. Preferably, such terminators are combined with mutations that prevent nonsense mediated mRNA decay in the host mixed sugar cell (see for example: Shirley et al., 2002, Genetics 161:1465-1482).
The transcription termination sequence further preferably comprises a polyadenylation signal.
Optionally, a selectable marker may be present in a nucleic acid construct suitable for use in the invention. As used herein, the term “marker” refers to a gene encoding a trait or a phenotype which permits the selection of, or the screening for, a host cell containing the marker. The marker gene may be an antibiotic resistance gene whereby the appropriate antibiotic can be used to select for transformed cells from among cells that are not transformed. Examples of suitable antibiotic resistance markers include e.g. dihydrofolate reductase, hygromycin-B-phosphotransferase, 3′-O-phosphotransferase II (kanamycin, neomycin and G418 resistance). Antibiotic resistance markers may be most convenient for the transformation of polyploid host cells, Also non-antibiotic resistance markers may be used, such as auxotrophic markers (URA3, TRP1, LEU2) or the S. pombe TPI gene (described by Russell P R, 1985, Gene 40: 125-130). In a preferred embodiment the host cells transformed with the nucleic acid constructs are marker gene free. Methods for constructing recombinant marker gene free microbial host cells are disclosed in EP-A-0 635 574 and are based on the use of bidirectional markers such as the A. nidulans amdS (acetamidase) gene or the yeast URA3 and LYS2 genes. Alternatively, a screenable marker such as Green Fluorescent Protein, lacL, luciferase, chloramphenicol acetyltransferase, beta-glucuronidase may be incorporated into the nucleic acid constructs of the invention allowing to screen for transformed cells.
Optional further elements that may be present in the nucleic acid constructs suitable for use in the invention include, but are not limited to, one or more leader sequences, enhancers, integration factors, and/or reporter genes, intron sequences, centromers, telomers and/or matrix attachment (MAR) sequences. The nucleic acid constructs of the invention may further comprise a sequence for autonomous replication, such as an ARS sequence.
The recombination process may thus be executed with known recombination techniques. Various means are known to those skilled in the art for expression and overexpression of enzymes in a mixed sugar cell. In particular, an enzyme may be overexpressed by increasing the copy number of the gene coding for the enzyme in the host cell, e.g. by integrating additional copies of the gene in the host cell's genome, by expressing the gene from an episomal multicopy expression vector or by introducing a episomal expression vector that comprises multiple copies of the gene.
Alternatively, overexpression of enzymes in the host cells of the invention may be achieved by using a promoter that is not native to the sequence coding for the enzyme to be overexpressed, i.e. a promoter that is heterologous to the coding sequence to which it is operably linked. Although the promoter preferably is heterologous to the coding sequence to which it is operably linked, it is also preferred that the promoter is homologous, i.e. endogenous to the host cell. Preferably the heterologous promoter is capable of producing a higher steady state level of the transcript comprising the coding sequence (or is capable of producing more transcript molecules, i.e. mRNA molecules, per unit of time) than is the promoter that is native to the coding sequence. Suitable promoters in this context include both constitutive and inducible natural promoters as well as engineered promoters.
In an embodiment, the mixed sugar cell is markerfree, which means that no auxotrophic or dominant markers, in particular antibiotic resistance markers, are present in the genome or extra-chromosomally.
The coding sequence used for overexpression of the enzymes mentioned above may preferably be homologous to the host cell. However, coding sequences that are heterologous to the host may be used.
Overexpression of an enzyme, when referring to the production of the enzyme in a genetically modified cell, means that the enzyme is produced at a higher level of specific enzymatic activity as compared to the unmodified host cell under identical conditions. Usually this means that the enzymatically active protein (or proteins in case of multi-subunit enzymes) is produced in greater amounts, or rather at a higher steady state level as compared to the unmodified host cell under identical conditions. Similarly this usually means that the mRNA coding for the enzymatically active protein is produced in greater amounts, or again rather at a higher steady state level as compared to the unmodified host cell under identical conditions. Preferably in a host, an enzyme to be overexpressed is overexpressed by at least a factor of about 1.1, about 1.2, about 1.5, about 2, about 5, about 10 or about 20 as compared to a strain which is genetically identical except for the genetic modification causing the overexpression. It is to be understood that these levels of overexpression may apply to the steady state level of the enzyme's activity, the steady state level of the enzyme's protein as well as to the steady state level of the transcript coding for the enzyme.
Adaptation
Adaptation is the evolutionary process whereby a population becomes better suited (adapted) to its habitat or habitats. This process takes place over several to many generations, and is one of the basic phenomena of biology.
The term adaptation may also refer to a feature which is especially important for an organism's survival. Such adaptations are produced in a variable population by the better suited forms reproducing more successfully, by natural selection.
Changes in environmental conditions alter the outcome of natural selection, affecting the selective benefits of subsequent adaptations that improve an organism's fitness under the new conditions. In the case of an extreme environmental change, the appearance and fixation of beneficial adaptations can be essential for survival. A large number of different factors, such as e.g. nutrient availability, temperature, the availability of oxygen, etcetera, can drive adaptive evolution.
Fitness
There is a clear relationship between adaptedness (the degree to which an organism is able to live and reproduce in a given set of habitats) and fitness. Fitness is an estimate and a predictor of the rate of natural selection. By the application of natural selection, the relative frequencies of alternative phenotypes will vary in time, if they are heritable.
Genetic Changes
When natural selection acts on the genetic variability of the population, genetic changes are the underlying mechanism. By this means, the population adapts genetically to its circumstances. Genetic changes may result in visible structures, or may adjust the physiological activity of the organism in a way that suits the changed habitat.
It may occur that habitats frequently change. Therefore, it follows that the process of adaptation is never finally complete. In time, it may happen that the environment changes gradually, and the species comes to fit its surroundings better and better. On the other hand, it may happen that changes in the environment occur relatively rapidly, and then the species becomes less and less well adapted. Adaptation is a genetic process, which goes on all the time to some extent, also when the population does not change the habitat or environment.
The Adaptive Evolution
The mixed sugar cells may in their preparation be subjected to adaptive evolution. A mixed sugar cell may be adapted to sugar utilisation by selection of mutants, either spontaneous or induced (e.g. by radiation or chemicals), for growth on the desired sugar, preferably as sole carbon source, and more preferably under anaerobic conditions. Selection of mutants may be performed by techniques including serial transfer of cultures as e.g. described by Kuyper et al. (2004, FEMS Yeast Res. 4: 655-664) or by cultivation under selective pressure in a chemostat culture. E.g. in a preferred host cell at least one of the genetic modifications described above, including modifications obtained by selection of mutants, confer to the host cell the ability to grow on the xylose as carbon source, preferably as sole carbon source, and preferably under anaerobic conditions. When XI is used as gene to convert xylose, preferably the cell produce essentially no xylitol, e.g. the xylitol produced is below the detection limit or e.g. less than about 5, about 2, about 1, about 0.5, or about 0.3% of the carbon consumed on a molar basis.
Adaptive evolution is also described e.g. in Wisselink H. W. et al, Applied and Environmental Microbiology August 2007, p. 4881-4891
In one embodiment of adaptive evolution a regimen consisting of repeated batch cultivation with repeated cycles of consecutive growth in different media is applied, e.g. three media with different compositions (glucose, xylose, and arabinose; xylose and arabinose. See Wisselink et al. (2009) Applied and Environmental Microbiology, February 2009, p. 907-914.
Yeast Transformation and Genetic Stability
Genetic engineering, i.e. transformation of yeast cells with recombinant DNA, became feasible for the first time in 1978 [Beggs, 1978; Hinnen et al., 1978]. Recombinant DNA technology in yeast has established itself since then. A multitude of different vector constructs are available. Generally, these plasmid vectors, called shuttle vectors, contain genetic material derived from E. coli vectors consisting of an origin of replication and a selectable marker (often the βlactamase gene, ampR), which enable them to be propagated in E. coli prior to transformation into yeast cells. Additionally, the shuttle vectors contain a selectable marker for selection in yeast. Markers can be genes encoding enzymes for the synthesis of a particular amino acid or nucleotide, so that cells carrying the corresponding genomic deletion (or mutation) are complemented for auxotrophy or auxotrophy. Alternatively, these vectors contain heterologous dominant resistance markers, which provides recombinant yeast cells (i.e. the cells that have taken up the DNA and express the marker gene) resistance towards certain antibiotics, like g418 (Geneticin), hygromycinB or phleomycin. In addition, these vectors may contain a sequence of (combined) restriction sites (multiple cloning site or MCS) which will allow to clone foreign DNA into these sites, although alternative methods exist as well.
Traditionally, four types of shuttle vectors can be distinguished by the absence or presence of additional genetic elements:

    
    
        Integrative plasmids (YIp) which by homologous recombination are integrated into the host genome at the locus of the marker or another gene, when this is opened by restriction and the linearized DNA is used for transformation of the yeast cells. This generally results in the presence of one copy of the foreign DNA inserted at this particular site in the genome.
        Episomal plasmids (YEp) which carry part of the 2μ plasmid DNA sequence necessary for autonomous replication in yeast cells. Multiple copies of the transformed plasmid are propagated in the yeast cell and maintained as episomes.
        Autonomously replicating plasmids (YRp) which carry a yeast origin of replication (ARS, autonomously replicated sequence) that allows the transformed plasmids to be propagated several hundred-fold.
        CEN plasmids (YCp) which carry in addition to an ARS sequence a centromeric sequence (derived from one of the nuclear chromosomes) which normally guarantees stable mitotic segregation and usually reduces the copy number of self-replicated plasmid to just one.
    
    


These plasmids are being introduced into the yeast cells by transformation. Transformation of yeast cells may be achieved by several different techniques, such as permeabilization of cells with lithium acetate (Ito et al, 1983) and electroporation methods.
In commercial application of recombinant microorganisms, plasmid instability is the most important problem. Instability is the tendency of the transformed cells to lose their engineered properties because of changes to, or loss of, plasmids. This issue is discussed in detail by Zhang et al (Plasmid stability in recombinant Saccharomyces cerevisiae. Biotechnology Advances, Vol. 14, No. 4, pp. 401-435, 1996). Strains transformed with integrative plasmids are extremely stable, even in the absence of selective pressure (Fred Sherman, Yeast Genetics, in THE ENCYCLOPEDIA OF MOLECULAR BIOLOGY AND MOLECULAR MEDICINE. 1997; 6:302-305; Sherman, “Getting Started with Yeast,” Methods Enymol. 2002; 350:3-41, and references therein).
The heterologous DNA is usually introduced into the organism in the form of extra-chromosomal plasmids (YEp, YCp and YRp). Unfortunately, it has been found with both bacteria and yeasts that the new characteristics may not be retained, especially if the selection pressure is not applied continuously. This is due to the segregational instability of the hybrid plasmid when recombinant cells grow for a long period of time. This leads to population heterogeneity and clonal variability, and eventually to a cell population in which the majority of the cells has lost the properties that were introduced by transformation. If vectors with auxotrophic markers are being used, cultivation in rich media often leads to rapid loss of the vector, since the vector is only retained in minimal media. The alternative, the use of dominant antibiotic resistance markers, is often not compatible with production processes. The use of antibiotics may not be desired from a registration point of view (the possibility that trace amounts of the antibiotic end up in the end product) or for economic reasons (costs of the use of antibiotics at industrial scale).
Loss of vectors leads to problems in large scale production situations. Alternative methods for introduction of DNA do exist for yeasts, such as the use of integrating plasmids (YIp). The DNA is integrated into the host genome by recombination, resulting in high stability. (Gaunt, P. Stability of recombinant plasmids in yeast. Journal of Biotechnology 9 (1988) 173-192). We have found that an integration method using the host transposons are a good alternative.
Transposons
According to the invention, two to fifteen xylose isomerase gene or xylose reductase gene and xylitol dehydrogenase is integrated into the mixed sugar cell genome. In an embodiment the Initial introduction (i.e. before adaptive evolution) of multiple copies be executed in any way known in the art that leads to introduction of the genes. In an embodiment, this may be accomplished using a vector with parts homologous to repeated sequences (transposons), of the host cell. When the host cell is a yeast cell, suitable repeated sequences are the long terminal repeats (LTR) of the Ty element, known as delta sequence.
Ty elements fall into two rather similar subfamilies called Ty1 and Ty2. These elements are about 6 kilobases (kb) in length and are bounded by long terminal repeats (LTR), sequences of about 335 base pairs (Boeke J D et al, The Saccharomyces cerevisiae Genome Contains Functional and Nonfunctional Copies of Transposon Ty1. Molecular and Cellular Biology, April 1988, p. 1432-1442 Vol. 8, No. 4). In the fully sequenced S. cerevisiae strain, S288c, the most abundant transposons are Ty1 (31 copies) and Ty2 (13 copies) (Gabriel A, Dapprich J, Kunkel M, Gresham D, Pratt S C, et al. (2006) Global mapping of transposon location. PLoS Genet. 2(12): e212.doi:10.1371/journal.pgen.0020212). These transposons consist of two overlapping open reading frames (ORFS), each of which encode several proteins. The coding regions are flanked by the aforementioned, nearly identical LTRs. Other, but less abundant and more distinct Ty elements in S. cereviaise comprise Ty3, Ty4 and Ty5. For each family of full-length Ty elements there are an order of magnitude more solo LTR elements dispersed through the genome. These are thought to arise by LTR-LTR recombination of full-length elements, with looping out of the internal protein encoding regions.
The retrotransposition mechanism of the Ty retrotransposon has been exploited to integrate multiple copies throughout the genome (Boeke et al., 1988; Jacobs et al., 1988). The long terminal repeats (LTR) of the Ty element, known as delta sequences, are also good targets for integration by homologous recombination as they exist in about 150-200 copies that are either Ty associated or solo sites (Boeke, 1989; Kingsman and Kingsman, 1988). (Parekh R. N. (1996). An Integrating Vector for Tunable, High Copy, Stable Integration into the Dispersed Ty DELTA Sites of Saccharomyces cerevisiae. Biotechnol. Prog. 1996, 12, 16-21). By adaptive evolution, the number of copies may change.
The Host Cell
The host cell may be any host cell suitable for production of a useful product. A host cell may be any suitable cell, such as a prokaryotic cell, such as a bacterium, or a eukaryotic cell. Typically, the cell will be a eukaryotic cell, for example a yeast or a filamentous fungus.
Yeasts are herein defined as eukaryotic microorganisms and include all species of the subdivision Eumycotina (Alexopoulos, C. J., 1962, In: Introductory Mycology, John Wiley & Sons, Inc., New York) that predominantly grow in unicellular form.
Yeasts may either grow by budding of a unicellular thallus or may grow by fission of the organism. A preferred yeast as a mixed sugar cell may belong to the genera Saccharomyces, Kluyveromyces, Candida, Pichia, Schizosaccharomyces, Hansenula, Kloeckera, Schwanniomyces or Yarrowia. Preferably the yeast is one capable of anaerobic fermentation, more preferably one capable of anaerobic alcoholic fermentation.
Filamentous fungi are herein defined as eukaryotic microorganisms that include all filamentous forms of the subdivision Eumycotina. These fungi are characterized by a vegetative mycelium composed of chitin, cellulose, and other complex polysaccharides. The filamentous fungi of the suitable for use as a cell of the present invention are morphologically, physiologically, and genetically distinct from yeasts. Filamentous fungal cells may be advantageously used since most fungi do not require sterile conditions for propagation and are insensitive to bacteriophage infections. Vegetative growth by filamentous fungi is by hyphal elongation and carbon catabolism of most filamentous fungi is obligately aerobic. Preferred filamentous fungi as a host cell may belong to the genus Aspergillus, Trichoderma, Humicola, Acremoniurra, Fusarium or Penicillium. More preferably, the filamentous fungal cell may be a Aspergillus niger, Aspergillus oryzae, a Penicillium chrysogenum, or Rhizopus oryzae cell.
In one embodiment the host cell may be yeast.
Preferably the host is an industrial host, more preferably an industrial yeast. An industrial host and industrial yeast cell may be defined as follows. The living environments of yeast cells in industrial processes are significantly different from that in the laboratory. Industrial yeast cells must be able to perform well under multiple environmental conditions which may vary during the process. Such variations include change in nutrient sources, pH, ethanol concentration, temperature, oxygen concentration, etc., which together have potential impact on the cellular growth and ethanol production of Saccharomyces cerevisiae. Under adverse industrial conditions, the environmental tolerant strains should allow robust growth and production. Industrial yeast strains are generally more robust towards these changes in environmental conditions which may occur in the applications they are used, such as in the baking industry, brewing industry, wine making and the ethanol industry. Examples of industrial yeast (S. cerevisiae) are ETHANOL RED® (S. cerevisiae. Fermentis) FERMIOL® (S. cerevisiae; DSM) and THERMOSACC® (S. cerevisiae; Lallemand).
In an embodiment the host is inhibitor tolerant. Inhibitor tolerant host cells may be selected by screening strains for growth on inhibitors containing materials, such as illustrated in Kadar et al, Appl. Biochem. Biotechnol. (2007), Vol. 136-140, 847-858, wherein an inhibitor tolerant S. cerevisiae strain ATCC 26602 was selected.
araA, araB and araD Genes
A mixed sugar cell is capable of using arabinose. A mixed sugar cell is therefore, be capable of converting L-arabinose into L-ribulose and/or xylulose 5-phosphate and/or into a desired fermentation product, for example one of those mentioned herein.
Organisms, for example S. cerevisiae strains, able to produce ethanol from L-arabinose may be produced by modifying a cell introducing the araA (L-arabinose isomerase), araB (L-ribulokinase) and araD (L-ribulose-5-P4-epimerase) genes from a suitable source. Such genes may be introduced into a mixed sugar cell is order that it is capable of using arabinose. Such an approach is given is described in WO2003/095627. araA, araB and araD genes from Lactobacillus plantanum may be used and are disclosed in WO2008/041840. The araA gene from Bacillus subtilis and the araB and araD genes from Escherichia coli may be used and are disclosed in EP1499708. In another embodiment, araA, araB and araD genes may derived from of at least one of the genus Clavibacter, Arthrobacter and/or Gramella, in particular one of Clavibacter michiganensis, Arthrobacter aurescens, and/or Gramella forsetii, as disclosed in WO 2009011591.
PPP-Genes
A mixed sugar cell may comprise one or more genetic modifications that increases the flux of the pentose phosphate pathway. In particular, the genetic modification(s) may lead to an increased flux through the non-oxidative part of the pentose phosphate pathway. A genetic modification that causes an increased flux of the non-oxidative part of the pentose phosphate pathway is herein understood to mean a modification that increases the flux by at least a factor of about 1.1, about 1.2, about 1.5, about 2, about 5, about 10 or about 20 as compared to the flux in a strain which is genetically identical except for the genetic modification causing the increased flux. The flux of the non-oxidative part of the pentose phosphate pathway may be measured by growing the modified host on xylose as sole carbon source, determining the specific xylose consumption rate and subtracting the specific xylitol production rate from the specific xylose consumption rate, if any xylitol is produced. However, the flux of the non-oxidative part of the pentose phosphate pathway is proportional with the growth rate on xylose as sole carbon source, preferably with the anaerobic growth rate on xylose as sole carbon source. There is a linear relation between the growth rate on xylose as sole carbon source (μmax) and the flux of the non-oxidative part of the pentose phosphate pathway. The specific xylose consumption rate (Qs) is equal to the growth rate (μ) divided by the yield of biomass on sugar (Yxs) because the yield of biomass on sugar is constant (under a given set of conditions: anaerobic, growth medium, pH, genetic background of the strain, etc.; i.e. Qs=μ/Yxs). Therefore the increased flux of the non-oxidative part of the pentose phosphate pathway may be deduced from the increase in maximum growth rate under these conditions unless transport (uptake is limiting).
One or more genetic modifications that increase the flux of the pentose phosphate pathway may be introduced in the host cell in various ways. These including e.g. achieving higher steady state activity levels of xylulose kinase and/or one or more of the enzymes of the non-oxidative part pentose phosphate pathway and/or a reduced steady state level of unspecific aldose reductase activity. These changes in steady state activity levels may be effected by selection of mutants (spontaneous or induced by chemicals or radiation) and/or by recombinant DNA technology e.g. by overexpression or inactivation, respectively, of genes encoding the enzymes or factors regulating these genes.
In a preferred host cell, the genetic modification comprises overexpression of at least one enzyme of the (non-oxidative part) pentose phosphate pathway. Preferably the enzyme is selected from the group consisting of the enzymes encoding for ribulose-5-phosphate isomerase, ribulose-5-phosphate epimerase, transketolase and transaldolase. Various combinations of enzymes of the (non-oxidative part) pentose phosphate pathway may be overexpressed. E.g. the enzymes that are overexpressed may be at least the enzymes ribulose-5-phosphate isomerase and ribulose-5-phosphate epimerase; or at least the enzymes ribulose-5-phosphate isomerase and transketolase; or at least the enzymes ribulose-5-phosphate isomerase and transaldolase; or at least the enzymes ribulose-5-phosphate epimerase and transketolase; or at least the enzymes ribulose-5-phosphate epimerase and transaldolase; or at least the enzymes transketolase and transaldolase; or at least the enzymes ribulose-5-phosphate epimerase, transketolase and transaldolase; or at least the enzymes ribulose-5-phosphate isomerase, transketolase and transaldolase; or at least the enzymes ribulose-5-phosphate isomerase, ribulose-5-phosphate epimerase, and transaldolase; or at least the enzymes ribulose-5-phosphate isomerase, ribulose-5-phosphate epimerase, and transketolase. In one embodiment of the invention each of the enzymes ribulose-5-phosphate isomerase, ribulose-5-phosphate epimerase, transketolase and transaldolase are overexpressed in the host cell. More preferred is a host cell in which the genetic modification comprises at least overexpression of both the enzymes transketolase and transaldolase as such a host cell is already capable of anaerobic growth on xylose. In fact, under some conditions host cells overexpressing only the transketolase and the transaldolase already have the same anaerobic growth rate on xylose as do host cells that overexpress all four of the enzymes, i.e. the ribulose-5-phosphate isomerase, ribulose-5-phosphate epimerase, transketolase and transaldolase. Moreover, host cells overexpressing both of the enzymes ribulose-5-phosphate isomerase and ribulose-5-phosphate epimerase are preferred over host cells overexpressing only the isomerase or only the epimerase as overexpression of only one of these enzymes may produce metabolic imbalances.
The enzyme “ribulose 5-phosphate epimerase” (EC 5.1.3.1) is herein defined as an enzyme that catalyses the epimerisation of D-xylulose 5-phosphate into D-ribulose 5-phosphate and vice versa. The enzyme is also known as phosphoribulose epimerase; erythrose-4-phosphate isomerase; phosphoketopentose 3-epimerase; xylulose phosphate 3-epimerase; phosphoketopentose epimerase; ribulose 5-phosphate 3-epimerase; D-ribulose phosphate-3-epimerase; D-ribulose 5-phosphate epimerase; D-ribulose-5-P 3-epimerase; D-xylulose-5-phosphate 3-epimerase; pentose-5-phosphate 3-epimerase; or D-ribulose-5-phosphate 3-epimerase. A ribulose 5-phosphate epimerase may be further defined by its amino acid sequence. Likewise a ribulose 5-phosphate epimerase may be defined by a nucleotide sequence encoding the enzyme as well as by a nucleotide sequence hybridising to a reference nucleotide sequence encoding a ribulose 5-phosphate epimerase. The nucleotide sequence encoding for ribulose 5-phosphate epimerase is herein designated RPE1.
The enzyme “ribulose 5-phosphate isomerase” (EC 5.3.1.6) is herein defined as an enzyme that catalyses direct isomerisation of D-ribose 5-phosphate into D-ribulose 5-phosphate and vice versa. The enzyme is also known as phosphopentosisomerase; phosphoriboisomerase; ribose phosphate isomerase; 5-phosphoribose isomerase; D-ribose 5-phosphate isomerase; D-ribose-5-phosphate ketol-isomerase; or D-ribose-5-phosphate aldose-ketose-isomerase. A ribulose 5-phosphate isomerase may be further defined by its amino acid sequence. Likewise a ribulose 5-phosphate isomerase may be defined by a nucleotide sequence encoding the enzyme as well as by a nucleotide sequence hybridising to a reference nucleotide sequence encoding a ribulose 5-phosphate isomerase. The nucleotide sequence encoding for ribulose 5-phosphate isomerase is herein designated RKI1.
The enzyme “transketolase” (EC 2.2.1.1) is herein defined as an enzyme that catalyses the reaction: D-ribose 5-phosphate+D-xylulose 5-phosphate<->sedoheptulose 7-phosphate+D-glyceraldehyde 3-phosphate and vice versa. The enzyme is also known as glycolaldehydetransferase or sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glycolaldehydetransferase. A transketolase may be further defined by its amino acid. Likewise a transketolase may be defined by a nucleotide sequence encoding the enzyme as well as by a nucleotide sequence hybridising to a reference nucleotide sequence encoding a transketolase. The nucleotide sequence encoding for transketolase is herein designated TKL1.
The enzyme “transaldolase” (EC 2.2.1.2) is herein defined as an enzyme that catalyses the reaction: sedoheptulose 7-phosphate+D-glyceraldehyde 3-phosphate<->D-erythrose 4-phosphate+D-fructose 6-phosphate and vice versa. The enzyme is also known as dihydroxyacetonetransferase; dihydroxyacetone synthase; formaldehyde transketolase; or sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glyceronetransferase. A transaldolase may be further defined by its amino acid sequence. Likewise a transaldolase may be defined by a nucleotide sequence encoding the enzyme as well as by a nucleotide sequence hybridising to a reference nucleotide sequence encoding a transaldolase. The nucleotide sequence encoding for transketolase from is herein designated TAL1.
Xylose Isomerase or Xylose Reductase Genes
According to the invention, two to fifteen copies of one or more xylose isomerase gene and/or one or more xylose reductase and xylitol dehydrogenase are introduced into the genome of the host cell. The presence of these two to fifteen genetic elements confers on the cell the ability to convert xylose by isomerisation or reduction.
In one embodiment, the two to fifteen copies of one or more xylose isomerase gene are introduced into the genome of the host cell.
A “xylose isomerase” (EC 5.3.1.5) is herein defined as an enzyme that catalyses the direct isomerisation of D-xylose into D-xylulose and/or vice versa. The enzyme is also known as a D-xylose ketoisomerase. A xylose isomerase herein may also be capable of catalysing the conversion between D-glucose and D-fructose (and accordingly may therefore be referred to as a glucose isomerase). A xylose isomerase herein may require a bivalent cation, such as magnesium, manganese or cobalt as a cofactor.
Accordingly, such a mixed sugar cell is capable of isomerizing xylose to xylulose. The ability of isomerizing xylose to xylulose is conferred on the host cell by transformation of the host cell with a nucleic acid construct comprising a nucleotide sequence encoding a defined xylose isomerase. A mixed sugar cell isomerizes xylose into xylulose by the direct isomerisation of xylose to xylulose.
A unit (U) of xylose isomerase activity may herein be defined as the amount of enzyme producing 1 nmol of xylulose per minute, under conditions as described by Kuyper et al. (2003, FEMS Yeast Res. 4: 69-78).
The Xylose isomerise gene may have various origin, such as for example Pyromyces sp. as disclosed in WO2006/009434. Other suitable origins are Bacteroides, in particular Bacteroides uniformis as described in PCT/EP2009/52623, Bacillus, in particular Bacillus stearothermophilus as described in PCT/EP2009/052625.
In another embodiment, the two to fifteen copies of one or more xylose reductase and xylitol dehydrogenase genes are introduced into the genome of the host cell. In this embodiment the conversion of xylose is conducted in a two step conversion of xylose into xylulose via a xylitol intermediate as catalysed by xylose reductase and xylitol dehydrogenase, respectively. In an embodiment thereof xylose reductase (XR), xylitol dehydrogenase (XDH), and xylokinase (XK) may be overexpressed, and optionally one or more of genes encoding NADPH producing enzymes are up-regulated and one or more of the genes encoding NADH consuming enzymes are up-regulated, as disclosed in WO 2004085627.
XKS1 Gene
A mixed sugar cell may comprise one or more genetic modifications that increase the specific xylulose kinase activity. Preferably the genetic modification or modifications causes overexpression of a xylulose kinase, e.g. by overexpression of a nucleotide sequence encoding a xylulose kinase. The gene encoding the xylulose kinase may be endogenous to the host cell or may be a xylulose kinase that is heterologous to the host cell. A nucleotide sequence used for overexpression of xylulose kinase in the host cell is a nucleotide sequence encoding a polypeptide with xylulose kinase activity.
The enzyme “xylulose kinase” (EC 2.7.1.17) is herein defined as an enzyme that catalyses the reaction ATP+D-xylulose=ADP+D-xylulose 5-phosphate. The enzyme is also known as a phosphorylating xylulokinase, D-xylulokinase or ATP:D-xylulose 5-phosphotransferase. A xylulose kinase of the invention may be further defined by its amino acid sequence. Likewise a xylulose kinase may be defined by a nucleotide sequence encoding the enzyme as well as by a nucleotide sequence hybridising to a reference nucleotide sequence encoding a xylulose kinase.
In a mixed sugar cell, a genetic modification or modifications that increase(s) the specific xylulose kinase activity may be combined with any of the modifications increasing the flux of the pentose phosphate pathway as described above. This is not, however, essential.
Thus, a host cell may comprise only a genetic modification or modifications that increase the specific xylulose kinase activity. The various means available in the art for achieving and analysing overexpression of a xylulose kinase in the host cells of the invention are the same as described above for enzymes of the pentose phosphate pathway. Preferably in the host cells of the invention, a xylulose kinase to be overexpressed is overexpressed by at least a factor of about 1.1, about 1.2, about 1.5, about 2, about 5, about 10 or about 20 as compared to a strain which is genetically identical except for the genetic modification(s) causing the overexpression. It is to be understood that these levels of overexpression may apply to the steady state level of the enzyme's activity, the steady state level of the enzyme's protein as well as to the steady state level of the transcript coding for the enzyme.
Aldose reductase (GRE3) Gene Deletion
In the embodiment, where XI is used as gene to convert xylose, it may be advantageous to reduce aldose reducatase activity. A mixed sugar cell may therefore comprise one or more genetic modifications that reduce unspecific aldose reductase activity in the host cell. Preferably, unspecific aldose reductase activity is reduced in the host cell by one or more genetic modifications that reduce the expression of or inactivates a gene encoding an unspecific aldose reductase. Preferably, the genetic modification(s) reduce or inactivate the expression of each endogenous copy of a gene encoding an unspecific aldose reductase in the host cell (herein called GRE3 deletion). Mixed sugar cells may comprise multiple copies of genes encoding unspecific aldose reductases as a result of di-, poly- or aneu-ploidy, and/or the host cell may contain several different (iso)enzymes with aldose reductase activity that differ in amino acid sequence and that are each encoded by a different gene. Also in such instances preferably the expression of each gene that encodes an unspecific aldose reductase is reduced or inactivated. Preferably, the gene is inactivated by deletion of at least part of the gene or by disruption of the gene, whereby in this context the term gene also includes any non-coding sequence up- or down-stream of the coding sequence, the (partial) deletion or inactivation of which results in a reduction of expression of unspecific aldose reductase activity in the host cell.
A nucleotide sequence encoding an aldose reductase whose activity is to be reduced in the host cell is a nucleotide sequence encoding a polypeptide with aldose reductase activity.
Thus, a host cell comprising only a genetic modification or modifications that reduce(s) unspecific aldose reductase activity in the host cell is specifically included in the invention.
The enzyme “aldose reductase” (EC 1.1.1.21) is herein defined as any enzyme that is capable of reducing xylose or xylulose to xylitol. In the context of the present invention an aldose reductase may be any unspecific aldose reductase that is native (endogenous) to a host cell of the invention and that is capable of reducing xylose or xylulose to xylitol. Unspecific aldose reductases catalyse the reaction:

aldose+NAD(P)H+H+alditol+NAD(P)+

The enzyme has a wide specificity and is also known as aldose reductase; polyol dehydrogenase (NADP+); alditol:NADP oxidoreductase; alditol:NADP+ 1-oxidoreductase; NADPH-aldopentose reductase; or NADPH-aldose reductase.
A particular example of such an unspecific aldose reductase that is endogenous to S. cerevisiae and that is encoded by the GRE3 gene (Traff et al., 2001, Appl. Environ. Microbiol. 67: 5668-74). Thus, an aldose reductase of the invention may be further defined by its amino acid sequence. Likewise an aldose reductase may be defined by the nucleotide sequences encoding the enzyme as well as by a nucleotide sequence hybridising to a reference nucleotide sequence encoding an aldose reductase.
Sequence Identity
Amino acid or nucleotide sequences are said to be homologous when exhibiting a certain level of similarity. Two sequences being homologous indicate a common evolutionary origin. Whether two homologous sequences are closely related or more distantly related is indicated by “percent identity” or “percent similarity”, which is high or low respectively. Although disputed, to indicate “percent identity” or “percent similarity”, “level of homology” or “percent homology” are frequently used interchangeably.
The terms “homology”, “percent homology”, “percent identity” or “percent similarity” are used interchangeably herein. For the purpose of this invention, it is defined here that in order to determine the percent identity of two amino acid sequences or of two nucleic acid sequences, the complete sequences are aligned for optimal comparison purposes. In order to optimize the alignment between the two sequences gaps may be introduced in any of the two sequences that are compared. Such alignment is carried out over the full length of the sequences being compared. Alternatively, the alignment may be carried out over a shorter length, for example over about 20, about 50, about 100 or more nucleic acids/based or amino acids. The identity is the percentage of identical matches between the two sequences over the reported aligned region.
A comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. The skilled person will be aware of the fact that several different computer programs are available to align two sequences and determine the homology between two sequences (Kruskal, J. B. (1983) An overview of sequence comparison In D. Sankoff and J. B. Kruskal, (ed.), Time warps, string edits and macromolecules: the theory and practice of sequence comparison, pp. 1-44 Addison Wesley). The percent identity between two amino acid sequences can be determined using the Needleman and Wunsch algorithm for the alignment of two sequences. (Needleman, S. B. and Wunsch, C. D. (1970) J. Mol. Biol. 48, 443-453). The algorithm aligns amino acid sequences as well as nucleotide sequences. The Needleman-Wunsch algorithm has been implemented in the computer program NEEDLE. For the purpose of this invention the NEEDLE program from the EMBOSS package was used (version 2.8.0 or higher, EMBOSS: The European Molecular Biology Open Software Suite (2000) Rice, P. Longden, I. and Bleasby, A. Trends in Genetics 16, (6) pp 276-277). For protein sequences, EBLOSUM62 is used for the substitution matrix. For nucleotide sequences, EDNAFULL is used. Other matrices can be specified. The optional parameters used for alignment of amino acid sequences are a gap-open penalty of 10 and a gap extension penalty of 0.5. The skilled person will appreciate that all these different parameters will yield slightly different results but that the overall percentage identity of two sequences is not significantly altered when using different algorithms.
Global Homology Definition
The homology or identity is the percentage of identical matches between the two full sequences over the total aligned region including any gaps or extensions. The homology or identity between the two aligned sequences is calculated as follows: Number of corresponding positions in the alignment showing an identical amino acid in both sequences divided by the total length of the alignment including the gaps. The identity defined as herein can be obtained from NEEDLE and is labelled in the output of the program as “IDENTITY”.
Longest Identity Definition
The homology or identity between the two aligned sequences is calculated as follows: Number of corresponding positions in the alignment showing an identical amino acid in both sequences divided by the total length of the alignment after subtraction of the total number of gaps in the alignment. The identity defined as herein can be obtained from NEEDLE by using the NOBRIEF option and is labelled in the output of the program as “longest-identity”. For purposes of the invention the level of identity (homology) between two sequences (amino acid or nucleotide) is calculated according to the definition of “longest-identity” as can be carried out by using the program NEEDLE.
The protein sequences used in the present invention can further be used as a “query sequence” to perform a search against sequence databases, for example to identify other family members or related sequences. Such searches can be performed using the BLAST programs. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (NCBI). BLASTP is used for amino acid sequences and BLASTN for nucleotide sequences. The BLAST program uses as defaults:
Cost to open gap: default=5 for nucleotides/11 for proteins
Cost to extend gap: default=2 for nucleotides/1 for proteins
Penalty for nucleotide mismatch: default=−3
Reward for nucleotide match: default=1
Expect value: default=10
Wordsize: default=11 for nucleotides/28 for megablast/3 for proteins
Furthermore the degree of local identity (homology) between the amino acid sequence query or nucleic acid sequence query and the retrieved homologous sequences is determined by the BLAST program. However only those sequence segments are compared that give a match above a certain threshold. Accordingly the program calculates the identity only for these matching segments. Therefore the identity calculated in this way is referred to as local identity.
Bioproducts Production
Over the years suggestions have been made for the introduction of various organisms for the production of bio-ethanol from crop sugars. In practice, however, all major bio-ethanol production processes have continued to use the yeasts of the genus Saccharomyces as ethanol producer. This is due to the many attractive features of Saccharomyces species for industrial processes, i.e., a high acid-, ethanol- and osmo-tolerance, capability of anaerobic growth, and of course its high alcoholic fermentative capacity. Preferred yeast species as host cells include S. cerevisiae, S. bulderi, S. barnetti, S. exiguus, S. uvarum, S. diastaticus, K. lactis, K. marxianus or K. fragilis. 
A mixed sugar cell may be a cell suitable for the production of ethanol. A mixed sugar cell may, however, be suitable for the production of fermentation products other than ethanol
Such non-ethanolic fermentation products include in principle any bulk or fine chemical that is producible by a eukaryotic microorganism such as a yeast or a filamentous fungus.
A mixed sugar cell that may be used for production of non-ethanolic fermentation products is a host cell that contains a genetic modification that results in decreased alcohol dehydrogenase activity.
In an embodiment the mixed sugar cell may be used in a process wherein sugars originating from lignocellulose are converted into ethanol.
Liqnocellulose
Lignocellulose, which may be considered as a potential renewable feedstock, generally comprises the polysaccharides cellulose (glucans) and hemicelluloses (xylans, heteroxylans and xyloglucans). In addition, some hemicellulose may be present as glucomannans, for example in wood-derived feedstocks. The enzymatic hydrolysis of these polysaccharides to soluble sugars, including both monomers and multimers, for example glucose, cellobiose, xylose, arabinose, galactose, fructose, mannose, rhamnose, ribose, galacturonic acid, glucoronic acid and other hexoses and pentoses occurs under the action of different enzymes acting in concert.
In addition, pectins and other pectic substances such as arabinans may make up considerably proportion of the dry mass of typically cell walls from non-woody plant tissues (about a quarter to half of dry mass may be pectins).
Pretreatment
Before enzymatic treatment, the lignocellulosic material may be pretreated. The pretreatment may comprise exposing the lignocellulosic material to an acid, a base, a solvent, heat, a peroxide, ozone, mechanical shredding, grinding, milling or rapid depressurization, or a combination of any two or more thereof. This chemical pretreatment is often combined with heat-pretreatment, e.g. between 150-220° C. for 1 to 30 minutes.
Enzymatic Hydrolysis
The pretreated material is commonly subjected to enzymatic hydrolysis to release sugars that may be fermented according to the invention. This may be executed with conventional methods, e.g. contacting with cellulases, for instance cellobiohydrolase(s), endoglucanase(s), beta-glucosidase(s) and optionally other enzymes. The conversion with the cellulases may be executed at ambient temperatures or at higher tempatures, at a reaction time to release sufficient amounts of sugar(s). The result of the enzymatic hydrolysis is hydrolysis product comprising C5/C6 sugars, herein designated as the sugar composition.
Fermentation
The fermentation process may be an aerobic or an anaerobic fermentation process. An anaerobic fermentation process is herein defined as a fermentation process run in the absence of oxygen or in which substantially no oxygen is consumed, preferably less than about 5, about 2.5 or about 1 mmol/L/h, more preferably 0 mmol/L/h is consumed (i.e. oxygen consumption is not detectable), and wherein organic molecules serve as both electron donor and electron acceptors. In the absence of oxygen, NADH produced in glycolysis and biomass formation, cannot be oxidised by oxidative phosphorylation. To solve this problem many microorganisms use pyruvate or one of its derivatives as an electron and hydrogen acceptor thereby regenerating NAD+.
Thus, in a preferred anaerobic fermentation process pyruvate is used as an electron (and hydrogen acceptor) and is reduced to fermentation products such as ethanol, butanol, lactic acid, 3-hydroxy-propionic acid, acrylic acid, acetic acid, succinic acid, citric acid, malic acid, fumaric acid, an amino acid, 1,3-propane-diol, ethylene, glycerol, a β-lactam antibiotic and a cephalosporin.
The fermentation process is preferably run at a temperature that is optimal for the cell. Thus, for most yeasts or fungal host cells, the fermentation process is performed at a temperature which is less than about 42° C., preferably less than about 38° C. For yeast or filamentous fungal host cells, the fermentation process is preferably performed at a temperature which is lower than about 35, about 33, about 30 or about 28° C. and at a temperature which is higher than about 20, about 22, or about 25° C.
The ethanol yield on xylose and/or glucose in the process preferably is at least about 50, about 60, about 70, about 80, about 90, about 95 or about 98%. The ethanol yield is herein defined as a percentage of the theoretical maximum yield.
The invention also relates to a process for producing a fermentation product.
The fermentation process according to the present invention may be run under aerobic and anaerobic conditions. In an embodiment, the process is carried out under micro-aerophilic or oxygen limited conditions.
An anaerobic fermentation process is herein defined as a fermentation process run in the absence of oxygen or in which substantially no oxygen is consumed, preferably less than about 5, about 2.5 or about 1 mmol/L/h, and wherein organic molecules serve as both electron donor and electron acceptors.
An oxygen-limited fermentation process is a process in which the oxygen consumption is limited by the oxygen transfer from the gas to the liquid. The degree of oxygen limitation is determined by the amount and composition of the ingoing gasflow as well as the actual mixing/mass transfer properties of the fermentation equipment used. Preferably, in a process under oxygen-limited conditions, the rate of oxygen consumption is at least about 5.5, more preferably at least about 6, such as at least 7 mmol/L/h. A process of the invention may comprise recovery of the fermentation product.
In a preferred process the cell ferments both the xylose and glucose, preferably simultaneously in which case preferably a cell is used which is insensitive to glucose repression to prevent diauxic growth. In addition to a source of xylose (and glucose) as carbon source, the fermentation medium will further comprise the appropriate ingredient required for growth of the cell. Compositions of fermentation media for growth of microorganisms such as yeasts are well known in the art
The fermentation processes may be carried out in batch, fed-batch or continuous mode. A separate hydrolysis and fermentation (SHF) process or a simultaneous saccharification and fermentation (SSF) process may also be applied. A combination of these fermentation process modes may also be possible for optimal productivity. These processes are described hereafter in more detail.
SSF Mode
For Simultaneous Saccharification and Fermentation (SSF) mode, the reaction time for liquefaction/hydrolysis or presaccharification step is dependent on the time to realize a desired yield, i.e. cellulose to glucose conversion yield. Such yield is preferably as high as possible, preferably 60% or more, 65% or more, 70% or more, 75% or more 80% or more, 85% or more, 90% or more, 95% or more, 96% or more, 97% or more, 98% or more, 99% or more, even 99.5% or more or 99.9% or more.
According to the invention very high sugar concentrations in SHF mode and very high product concentrations (e.g. ethanol) in SSF mode are realized. In SHF operation the glucose concentration is 25 g/L or more, 30 g/L or more, 35 g/L or more, 40 g/L or more, 45 g/L or more, 50 g/L or more, 55 g/L or more, 60 g/L or more, 65 g/L or more, 70 g/L or more, 75 g/L or more, 80 g/L or more, 85 g/L or more, 90 g/L or more, 95 g/L or more, 100 g/L or more, 110 g/L or more, 120 g/L or more or may e.g. be 25 g/L-250 g/L, 30 gl/L-200 g/L, 40 g/L-200 g/L, 50 g/L-200 g/L, 60 g/L-200 g/L, 70 g/L-200 g/L, 80 g/L-200 g/L, 90 g/L, 80 g/L-200 g/L.
Product Concentration in SSF mode
In SSF operation, the product concentration (g/L) is dependent on the amount of glucose produced, but this is not visible since sugars are converted to product in the SSF, and product concentrations can be related to underlying glucose concentration by multiplication with the theoretical maximum yield (Yps max in gr product per gram glucose)
The theoretical maximum yield (Yps max in gr product per gram glucose) of a fermentation product can be derived from textbook biochemistry. For ethanol, 1 mole of glucose (180 gr) yields according to normal glycolysis fermentation pathway in yeast 2 moles of ethanol (=2×46=92 gr ethanol. The theoretical maximum yield of ethanol on glucose is therefore 92/180=0.511 gr ethanol/gr glucose.
For Butanol (MW 74 gr/mole) or iso butanol, the theoretical maximum yield is 1 mole of butanol per mole of glucose. So Yps max for (iso-)butanol=74/180=0.411 gr (iso-)butanol/gr glucose.
For lactic acid the fermentation yield for homolactic fermentation is 2 moles of lactic acid (MW=90 gr/mole) per mole of glucose. According to this stoichiometry, the Yps max=1 gr lactic acid/gr glucose.
For other fermentation products a similar calculation may be made.
SSF Mode
In SSF operation the product concentration is 25 g*Yps g/L/L or more, 30*Yps g/L or more, 35 g*Yps/L or more, 40*Yps g/L or more, 45*Yps g/L or more, 50*Yps g/L or more, 55*Yps g/L or more, 60*Yps g/L or more, 65*Yps g/L or more, 70*Yps g/L or more, 75*Yps g/L or more, 80*Yps g/L or more, 85*Yps g/L or more, 90*Yps g/L or more, 95*Yps g/L or more, 100*Yps g/L or more, 110*Yps g/L or more, 120 g/L*Yps or more or may e.g. be 25*Yps g/L-250*Yps g/L, 30*Yps gl/L-200*Yps g/L, 40*Yps g/L-200*Yps g/L, 50*Yps g/L-200*Yps g/L, 60*Yps g/L-200*Yps g/L, 70*Yps g/L-200*Yps g/L, 80*Yps g/L-200*Yps g/L, 90*Yps g/L, 80*Yps g/L-200*Yps g/L
Accordingly, the invention provides a method for the preparation of a fermentation product, which method comprises:
a. degrading lignocellulose using a method as described herein; and
b. fermenting the resulting material, thereby to prepare a fermentation product.
Fermentation Product
The fermentation product of the invention may be any useful product. In one embodiment, it is a product selected from the group consisting of ethanol, n-butanol, isobutanol, lactic acid, 3-hydroxy-propionic acid, acrylic acid, acetic acid, succinic acid, fumaric acid, malic acid, itaconic acid, maleic acid, citric acid, adipic acid, an amino acid, such as lysine, methionine, tryptophan, threonine, and aspartic acid, 1,3-propane-diol, ethylene, glycerol, a β-lactam antibiotic and a cephalosporin, vitamins, pharmaceuticals, animal feed supplements, specialty chemicals, chemical feedstocks, plastics, solvents, fuels, including biofuels and biogas or organic polymers, and an industrial enzyme, such as a protease, a cellulase, an amylase, a glucanase, a lactase, a lipase, a lyase, an oxidoreductases, a transferase or a xylanase. For example the fermentation products may be produced by cells according to the invention, following prior art cell preparation methods and fermentation processes, which examples however should herein not be construed as limiting. n-butanol may be produced by cells as described in WO2008121701 or WO2008086124; lactic acid as described in US2011053231 or US2010137551; 3-hydroxy-propionic acid as described in WO2010010291; acrylic acid as described in WO2009153047 acetic acid as described in . . . , succinic acid as described in . . . cells of the fumarase-deficient mutant fermenting glucose accumulated extracellular fumaric acid (***Note still to be added.
Recovery of the Fermentation Product
For the recovery of the fermentation product existing technologies are used. For different fermentation products different recovery processes are appropriate. Existing methods of recovering ethanol from aqueous mixtures commonly use fractionation and adsorption techniques. For example, a beer still can be used to process a fermented product, which contains ethanol in an aqueous mixture, to produce an enriched ethanol-containing mixture that is then subjected to fractionation (e.g., fractional distillation or other like techniques). Next, the fractions containing the highest concentrations of ethanol can be passed through an adsorber to remove most, if not all, of the remaining water from the ethanol.
The following examples illustrate the invention:
Unless indicated otherwise, the methods described in here are standard biochemical techniques. Examples of suitable general methodology textbooks include Sambrook et al., Molecular Cloning, a Laboratory Manual (1989) and Ausubel et al., Current Protocols in Molecular Biology (1995), John Wiley & Sons, Inc.
Medium Composition
Growth experiments: Saccharomyces cerevisiae strains are grown on medium having the following composition: 0.67% (w/v) yeast nitrogen base or synthetic medium (Verduyn et al., Yeast 8:501-517, 1992) and glucose, arabinose, galactose or xylose, or a combination of these substrates, at varying concentrations (see examples for specific details; concentrations in % weight over volume (w/v)). For agar plates the medium is supplemented with 2% (w/v) bacteriological agar.
Ethanol Production
Pre-cultures were prepared by inoculating 25 ml Verduyn-medium (Verduyn et al., Yeast 8:501-517, 1992) supplemented with 2% glucose in a 100 ml shake flask with a frozen stock culture or a single colony from agar plate. After incubation at 30° C. in an orbital shaker (280 rpm) for approximately 24 hours, this culture was harvested and used for determination of CO2 evolution and ethanol production experiments.
Cultivations for ethanol production were performed at 30° C. in 100 ml synthetic model medium (Verduyn-medium (Verduyn et al., Yeast 8:501-517, 1992) with 5% glucose, 5% xylose, 3.5% arabinose and 1% galactose) in the BAM (Biological Activity Monitor, Halotec, The Netherlands). The pH of the medium was adjusted to 4.2 with 2 M NaOH/H2SO4 prior to sterilisation. The synthetic medium for anaerobic cultivation was supplemented with 0.01 g I−1 ergosterol and 0.42 g I−1 Tween 80 dissolved in ethanol (Andreasen and Stier. J. Cell Physiol. 41:23-36, 1953; and Andreasen and Stier. J. Cell Physiol. 43:271-281, 1954). The medium was inoculated at an initial OD600 of approximately 2. Cultures were stirred by a magnetic stirrer. Anaerobic conditions developed rapidly during fermentation as the cultures were not aerated. CO2 production was monitored constantly. Sugar conversion and product formation (ethanol, glycerol) was analyzed by NMR. Growth was monitored by following optical density of the culture at 600 nm on a LKB Ultrospec K spectrophotometer.
Transformation of S. cerevisiae 
Transformation of S. cerevisiae was done as described by Gietz and Woods (2002; Transformation of the yeast by the LiAc/SS carrier DNA/PEG method. Methods in Enzymology 350: 87-96).
Colony PCR
A single colony isolate was picked with a plastic toothpick and resuspended in 50 μl milliQ water. The sample was incubated for 10 minutes at 99° C. 5 μl of the incubated sample was used as a template for the PCR reaction, using PHUSION® DNA polymerase (Finnzymes) according to the instructions provided by the supplier.
PCR Reaction Conditions:


















step 1
 3′
98° C.




step 2
10′′
98° C.



step 3
15′′
58° C.
repeat step 2 to 4 for 30 cycles



step 4
30′′
72° C.



step 5
 4′
72° C.



step 6
30′′
20° C.










Chromosomal DNA Isolation
Yeast cells were grown in YEP-medium containing 2% glucose, in a rotary shaker (overnight, at 30° C. and 280 rpm in an orbital shaker). 1.5 ml of these cultures were transferred to an Eppendorf tube and centrifuged for 1 minute at maximum speed. The supernatant was decanted and the pellet was resuspended in 200 μl of YCPS (0.1% SB3-14 (Sigma Aldrich, the Netherlands) in 10 mM Tris.HCl pH 7.5; 1 mM EDTA) and 1 μl RNase (20 mg/ml RNase A from bovine pancreas, Sigma, the Netherlands). The cell suspension was incubated for 10 minutes at 65° C. The suspension was centrifuged in an Eppendorf centrifuge for 1 minute at 7000 rpm. The supernatant was discarded. The pellet was carefully dissolved in 200 μl CLS (25 mM EDTA, 2% SDS) and 1 μl RNase A. After incubation at 65° C. for 10 minutes, the suspension was cooled on ice. After addition of 70 μl PPS (10M ammonium acetate) the solutions were thoroughly mixed on a Vortex mixer. After centrifugation (5 minutes in Eppendorf centrifuge at maximum speed), the supernatant was mixed with 200 μl ice-cold isopropanol. The DNA readily precipitated and was pelleted by centrifugation (5 minutes, maximum speed). The pellet was washed with 400 μl ice-cold 70% ethanol. The pellet was dried at room temperature and dissolved in 50 μl TE (10 mM Tris.HCl pH7.5, 1 mM EDTA).
Transformation of Yeast Cells by Electroporation
Yeast cells were cultured by inoculating 25 ml of YEP-medium containing 2% glucose with a single yeast colony. The flask was incubated overnight at 30° C.
The optical density at 600 nm was determined and the amount needed to obtain an optical density of 0.2 was transferred to 100 ml YEP-medium with 2% glucose. The cells were grown for 4 to 5 hours, in order to reach an optical density of approximately 1.2 to 1.3, which corresponds to 2 to 3 generations. Cells were collected by centrifugation and resuspended in 28 ml TE (10 mM Tris.HCl, 1 mM EDTA, pH 7.5). 3 ml of a 1M LiAC solution (set at pH 7.5 with concentrated HAc) was added. The cells were gently shaken in a rotary incubator (150 rpm, 30° C.) for 45 minutes. After addition of 500 μl of a 1M DTT (dithiothreitol) solution, the cells were incubated once more under these conditions, for 15 minutes. The volume was made up to 100 ml with sterile, ice-cold milliQ water. The cells were collected by centrifugation.
The supernatant was discarded and the pelleted cells were washed with 50 ml of sterile, ice cold milliQ water, and collected by centrifugation. A subsequent washing treatment was done with 30 ml of an ice cold 1M sorbitol solution. After centrifugation, the supernatant was discarded and the cell pellet was resuspended in 4 ml of an ice cold 1M sorbitol solution. After centrifugation, the supernatant was discarded and the cell pellet was resuspended in 300 μl of an ice cold 1M sorbitol solution.
For each transformation, 40 μl of the cell suspension is transferred into ice cold Eppendorf tubes. The transforming DNA and 5 μg salmon sperm DNA (as carrier DNA) is added, together in a maximum volume of 20 μl. The DNA should be dissolved in TE. Carefully tap the Eppendorf tube in order to mix the content gently. Transfer the content to a pre-chilled (on ice) electroporation cuvette with a gap of 0.2 cm. Apply a pulse (using e.g. a BioRad Electroporation Device) at 1.5 kV, 200 Ohm and 25 μF. The pulse time should be around 5 ms.
Transfer the cells immediately to 200 μl 1M sorbitol. Add 4 ml of YEP 2% glucose and incubate at 30° C. for 1 hour. Collect cells by centrifugation, discard the supernatant and resuspend the pellet in 4 ml of 1M sorbitol. Collect cells by centrifugation, discard the supernatant and resuspend the pellet in 300 μl of 1M sorbitol. Dilute the cells as appropriate and spread on selective plates or use in selective media.
Yeast Application Test on Real Hydrolysates
Dilute acid pretreated samples of corn stover and wheat straw were enzymatically hydrolyzed by using an experimental broad spectrum cellulase preparation at 60° C. for 3 days (72 hours). The pH at the start of the hydrolysis was 5.0. The dry matter content at the start of the hydrolysis was 10% w/w.
The conditions for the hydrolysis of pretreated corn fiber samples was essentially the same, except that the hydrolysis temperature was 50° C. and the dry matter content at the start of the hydrolysis was 13.8%.
After hydrolysis (72 hrs), the samples were allowed to be cooled to room temperature. The pH was adjusted to 5.5 using 10% NaOH. Subsequently, 1 milliliter of a 200 gram per liter (NH4)2SO4 and 1 milliliter of 100 gram per liter KH2PO4 was added. Finally, yeast samples were added corresponding to a yeast dry matter content of 1 gram yeast per kilogram hydrolysate. The CO2 evolution in time was followed using the AFM (Alcohol Fermentation Monitor; HaloteC Instruments BV, Veenendaal, the Netherlands). Experiments were performed in at least triplicate, for 72 hours at 33° C. One of these is sampled at regular intervals in order to be able to analyze ethanol formation and residual sugar concentrations. These data can be used to calculate fermentation yields. The broth of the other two experiments is not sampled. Instead, at the end of the fermentation the broth is distilled using a Buchi K-355 distillation unit at 45% steam for 15 minutes. The alcohol produced is being determined using an Anton Paar DMA 5000 density meter (Anton Paar Benelux BVBA, Dongen, the Netherlands).
Quantitative PCR
Quantitative PCR reactions were performed to determine the copy number of the genes that were present in the genome, especially in case of the xylose isomerase genes. To this end, the Bio-Rad iCycler iQ system from Bio-Rad (Bio-Rad Laboratories, Hercules, Calif., USA) was used. The iQ SYBR Green Supermix (Bio-Rad) was used. Experiments were set up as suggested in the manual of the provider. As primers for the detection of the xylose isomerase gene, primers of SEQ ID NO: 23 and SEQ ID NO: 24 were used.
The PCR conditions were as follows:

    
    
        3 minutes incubation at 95° C.
        40 cycles: 10 seconds at 95° C.
        
            45 seconds at 58° C.
            45 seconds at 72° C.
        
        
        1 minute incubation at 95° C.
        1 minute incubation at 65° C.
    
    


The melting curve is being determined by starting to measure fluorescence at 65° C. for 10 seconds. The temperature is increased every 10 seconds with 0.5° C., until a temperature of 95° C. is reached. From the reads, the copy number of the gene of interest may be calculated and/or estimated. The method has its limitations with respect to an accurate determination of the copy number above a certain threshold, as will be appreciated by those skilled in the art.
Example 1
Construction of Strain BIE104A2P1
1.1 Construction of an Expression Vector Containing the Genes for Arabinose Pathway
Plasmid pPWT018, as set out in FIG. 2, was constructed as follows: vector pPWT006 (FIG. 1, consisting of a S/T2-locus (Gottlin-Ninfa and Kaback (1986) Molecular and Cell Biology vol. 6, no. 6, 2185-2197) and the markers allowing for selection of transformants on the antibiotic G418 and the ability to grow on acetamide was digested with the restriction enzymes BsiWI and MluI. The kanMX-marker, conferring resistance to G418, was isolated from p427TEF (Dualsystems Biotech) and a fragment containing the amdS-marker has been described in the literature (Swinkels, B. W., Noordermeer, A. C. M. and Renniers, A. C. H. M (1995) The use of the amdS cDNA of Aspergillus nidulans as a dominant, bidirectional selectable marker for yeast transformation. Yeast Volume 11, Issue 1995A, page S579; and U.S. Pat. No. 6,051,431). The genes encoding arabinose isomerase (araA), L-ribulokinase (araB) and L-ribulose-5-phosphate-4-epimerase (araD) from Lactobacillus plantarum, as disclosed in patent application WO2008/041840, were synthesized by BaseClear (Leiden, the Netherlands). One large fragment was synthesized, harbouring the three arabinose-genes mentioned above, under control of (or operable linked to) strong promoters from S. cerevisiae, i.e. the TDH3-promoter controlling the expression of the araA-gene, the ENO1-promoter controlling the araB-gene and the PGI1-promoter controlling the araD-gene. This fragment was surrounded by the unique restriction enzymes Acc65I and MluI. Cloning of this fragment into pPWT006 digested with MluI and BsiWI, resulted in plasmid pPWT018 (FIG. 2). The sequence of plasmid pPWT018 is set out in SEQ ID NO: 1.
1.2 Yeast Transformation
CEN.PK113-7D (MATa URA3 HIS3 LEU2 TRP1 MAL2-8 SUC2) was transformed with plasmid pPWT018, which was previously linearized with SfiI (New England Biolabs), according to the instructions of the supplier. A synthetic SfiI-site was designed in the 5′-flank of the SIT2-gene (see FIG. 2). Transformation mixtures were plated on YPD-agar (per liter: 10 grams of yeast extract, 20 grams per liter peptone, 20 grams per liter dextrose, 20 grams of agar) containing 100 μg G418 (Sigma Aldrich) per ml. After two to four days, colonies appeared on the plates, whereas the negative control (i.e. no addition of DNA in the transformation experiment) resulted in blank YPD/G418-plates. The integration of plasmid pPWT018 is directed to the SIT2-locus. Transformants were characterized using PCR and Southern blotting techniques.
PCR reactions, which are indicative for the correct integration of one copy of plasmid pPWT018, were performed with the primers indicated by SEQ ID NO: 2 and SEQ ID NO: 3, and SEQ ID NO: 3 and SEQ ID NO: 4. With the primer pairs of SEQ ID NO: 2 and SEQ ID NO: 3, the correct integration at the S/T2-locus was checked. If plasmid pPWT018 was integrated in multiple copies (head-to-tail integration), the primer pair of SEQ ID NO: 3 and SEQ ID NO: 4 will give a PCR-product. If the latter PCR product is absent, this is indicative for one copy integration of pPWT018. A strain in which one copy of plasmid pPWT018 was integrated in the S/T2-locus was designated BIE104R2.
1.3 Marker Rescue
In order to be able to transform the yeast strain with other constructs using the same selection markers, it is necessary to remove the selectable markers. The design of plasmid pPWT018 was such, that upon integration of pPWT018 in the chromosome, homologous sequences are in close proximity of each other. This design allows the selectable markers to be lost by spontaneous intramolecular recombination of these homologous regions.
Upon vegetative growth, intramolecular recombination will take place, although at low frequency. The frequency of this recombination depends on the length of the homology and the locus in the genome (unpublished results). Upon sequential transfer of a subfraction of the culture to fresh medium, intramolecular recombinants will accumulate in time.
To this end, strain BIE104R2 was cultured in YPD-medium (per liter: 10 grams of yeast extract, 20 grams per liter peptone, 20 grams per liter dextrose), starting from a single colony isolate. 25 μl of an overnight culture was used to inoculate fresh YPD medium. After at least five of such serial transfers, the optical density of the culture was determined and cells were diluted to a concentration of approximately 5000 per ml. 100 μl of the cell suspension was plated on Yeast Carbon Base medium (Difco) containing 30 mM KPi (pH 6.8), 0.1% (NH4)2SO4, 40 mM fluoro-acetamide (Amersham) and 1.8% agar (Difco). Cells identical to cells of strain BIE104R2, i.e. without intracellular recombination, still contain the amdS-gene. To those cells, fluoro-acetamide is toxic. These cells will not be able to grow and will not form colonies on a medium containing fluoro-acetamide. However, if intramolecular recombination has occurred, BIE104R2-variants that have lost the selectable markers will be able to grow on the fluoro-acetamide medium, since they are unable to convert fluoro-acetamide into growth inhibiting compounds. Those cells will form colonies on this agar medium.
The thus obtained fluoro-acetamide resistant colonies were subjected to PCR analysis using primers of SEQ ID NO:2 and SEQ ID NO: 3, and SEQ ID NO: 4 and SEQ ID NO: 5. Primers of SEQ ID NO: 2 and SEQ ID NO: 3 will give a band if recombination of the selectable markers has taken place as intended. As a result, the cassette with the genes araA, araB and araD under control of the strong yeast promoters have been integrated in the SIT2-locus of the genome of the host strain. In that case, a PCR reaction using primers of SEQ ID NO: 4 and SEQ ID NO: 5 should not result in a PCR product, since primer 4 primes in a region that should be lost due to the recombination. If a band is obtained with the latter primers, this is indicative for the presence of the complete plasmid pPWT018 in the genome, so no recombination has taken place.
If primers of SEQ ID NO: 2 and SEQ ID NO: 3 do not result in a PCR product, recombination has taken place, but in such a way that the complete plasmid pPWT018 has recombined out of the genome. Not only were the selectable markers lost, but also the arabinose-genes. In fact, wild-type yeast has been retrieved.
Isolates that showed PCR results in accordance with one copy integration of pPWT018 were subjected to Southern blot analysis. The chromosomal DNA of strains CEN.PK113-7D and the correct recombinants were digested with EcoRI and HindIII (double digestion). A S/T2-probe was prepared with primers of SEQ ID NO: 6 and SEQ ID NO: 7, using chromosomal DNA of strain CEN.PK113-7D as a template. The result of the hybridisation experiment is shown in FIG. 3.
In the wild-type strain, a band of 2.35 kb is observed, which is in accordance with the expected size of the wild-type gene. Upon integration and partial loss by recombination of the plasmid pPWT018, a band of 1.06 kb was expected. Indeed, this band is observed, as shown in FIG. 3 (lane 2).
One of the strains that showed the correct pattern of bands on the Southern blot (as can be deduced from FIG. 3) is the strain designated as BIE104A2.
1.4 Introduction of Four Constitutively Expressed Genes of the Non-Oxidative Pentose Phosphate Pathway
Saccharomyces cerevisiae BIE104A2, expressing the genes araA, araB and araD constitutively, was transformed with plasmid pPWT080 (FIG. 4). The sequence of plasmid pPWT080 is set out in SEQ ID NO: 8. The procedure for transformation and selection, after selecting a one copy integration transformant, are the same as described above in sections 1.1, 1.2 and 1.3. In short, BIE104A2 was transformed with SfiI-digested pPWT080. Transformation mixtures were plated on YPD-agar (per liter: 10 grams of yeast extract, 20 grams per liter peptone, 20 grams per liter dextrose, 20 grams of agar) containing 100 μg G418 (Sigma Aldrich) per ml.
After two to four days, colonies appeared on the plates, whereas the negative control (i.e. no addition of DNA in the transformation experiment) resulted in blank YPD/G418-plates.
The integration of plasmid pPWT080 is directed to the GRE3-locus. Transformants were characterized using PCR and Southern blotting techniques. The correct integration of the plasmid pPWT080 at the GRE3-locus was checked by PCR using primer pairs SEQ ID NO: 9 and SEQ ID NO: 10, and the primer pair SEQ ID NO: 9 and SEQ ID NO: 11 was used to detect single or multicopy integration of the plasmid pPWT080. For Southern analysis, a probe was prepared by PCR using SEQ ID NO: 12 and SEQ ID NO: 13, amplifying a part of the RKI1-gene of S. cerevisiae. Next to the native RKI1-gene, an extra signal was obtained resulting from the integration of the plasmid pPWT080 (data not shown)
A transformant showing correct integration of one copy of plasmid pPWT080, in accordance with the expected hybridisation pattern, was designated BIE104A2F1. In order to remove the selection markers introduced by the integration of plasmid pPWT080, strain BIE104A2F1 was cultured in YPD-medium, starting from a colony isolate. 25 μl of an overnight culture was used to inoculate fresh YPD-medium. After five serial transfers, the optical density of the culture was determined and cells were diluted to a concentration of approximately 5000 per ml. 100 μl of the cell suspension was plated on Yeast Carbon Base medium (Difco) containing 30 mM KPi (pH 6.8), 0.1% (NH4)2SO4, 40 mM fluoro-acetamide (Amersham) and 1.8% agar (Difco). Fluoro-acetamide resistant colonies were subjected to PCR analysis using the primers of SEQ ID NO: 9 and SEQ ID NO: 10. In case of correct PCR-profiles, Southern blot analysis was performed in order to verify the correct integration, again using the probe of the RKI1-gene. One of the strains that showed the correct pattern of bands on the Southern blotis the strain designated as BIE104A2P1.
Example 2
Adaptive Evolution in Shake Flask Leading to BIE104A2P1c and BIE201
2.1 Adaptive Evolution (Aerobically)
A single colony isolate of strain BIE104A2P1 was used to inoculate YNB-medium (Difco) supplemented with 2% galactose. The preculture was incubated for approximately 24 hours at 30° C. and 280 rpm in an orbital shaker. Cells were harvested and inoculated in YNB medium containing 1% galactose and 1% arabinose at a starting OD600 of 0.2 (FIG. 5). Cells were grown at 30° C. and 280 rpm in an orbital shaker. The optical density at 600 nm was monitored regularly.
When the optical density reached a value of 5, an aliquot of the culture was transferred to fresh YNB medium containing the same medium. The amount of cells added was such that the starting OD600 of the culture was 0.2. After reaching an OD600 of 5 again, an aliquot of the culture was transferred to YNB medium containing 2% arabinose as sole carbon source (event indicated by (1) in FIG. 5).
Upon transfer to YNB with 2% arabinose as sole carbon source growth could be observed after approximately two weeks. When the optical density at 600 nm reached a value at least of 1, cells were transferred to a shake flask with fresh YNB-medium supplemented with 2% arabinose at a starting OD600 of 0.2 (FIG. 5, day 28).
Sequential transfer was repeated three times, as is set out it in FIG. 5. The resulting strain which was able to grow fast on arabinose was designated BIE104A2P1c.
2.2 Adaptive Evolution (Anaerobically)
After adaptation on growth on arabinose under aerobic conditions, a single colony from strain BIE104A2P1c was inoculated in YNB medium supplemented with 2% glucose. The preculture was incubated for approximately 24 hours at 30° C. and 280 rpm in an orbital shaker. Cells were harvested and inoculated in YNB medium containing 2% arabinose, with a initial optical density OD600 of 0.2. The flasks were closed with waterlocks, ensuring anaerobic growth conditions after the oxygen was exhausted from the medium and head space. After reaching an OD600 minimum of 3, an aliquot of the culture was transferred to fresh YNB medium containing 2% arabinose (FIG. 6), each time at an initial OD600 value of 0.2. After several transfers the resulting strain was designated BIE104A2P1d (=BIE201).
Example 3
Construction of strain BIE201X9
3.1 Transformation of Strain BIE201
Strain BIE201 was transformed with plasmid pPWT042. The physical map of plasmid pPWT042 is set out in FIG. 7. Plasmid pPWT042 (SEQ ID NO: 14) contains a 4630 by insert containing a codon pair optimized xylA-gene from Bacteroides uniformis under control of the TPI1-promoter and the XKS1-gene from S. cerevisiae under control of the TDH1-promoter. Prior to the transformation of BIE201, pPWT042 was linearized using the restriction enzyme SfiI, according to the instructions provided by the supplier. Transformation mixtures were plated on YPD-agar (per liter: 10 grams of yeast extract, 20 grams per liter peptone, 20 grams per liter dextrose, 20 grams of agar) containing 100 μg G418 (Sigma Aldrich) per ml.
After two to four days, colonies appeared on the plates, whereas the negative control (i.e. no addition of DNA in the transformation experiment) resulted in blank YPD/G418-plates.
Upon digestion of plasmid pPWT042 with SfiI, its integration is directed to the SIT4-locus (Gottlin-Ninfa and Kaback (1986) Molecular and Cellular Biology Vol. 6, No. 6, 2185-2197) in the genome. Transformants were characterized using PCR and Southernblotting techniques. PCR reactions, using PHUSION® DNA polymerase (Finnzymes), which are indicative for the correct integration of one copy of plasmid pPWT042, were performed with the primers indicated by SEQ ID NO's 15 and 16 (correct integration of pPWT042 at the SIT4-locus), and SEQ ID NO's 16 and 17 (band only appears in case of multicopy integration). A strain with one copy of plasmid pPWT042 integrated into the genome was designated BIE201Y9.
3.2 Marker Rescue
In order to remove the selection markers introduced by the integration of plasmid pPWT042, the following procedure was performed. The design of plasmid pPWT042 is such, that upon integration of pPWT042 in the chromosome, homologous sequences are in close proximity of each other. This design allows the selectable markers to be lost by spontaneous intramolecular recombination of these homologous regions. Upon vegetative growth, intramolecular recombination will take place, although at low frequency. The frequency of this recombination depends on the length of the homology and the locus in the genome (unpublished results). Upon sequential transfer of a subfraction of the culture to fresh medium, intramolecular recombinants will accumulate in time.
To this end, strain BIE201Y9 was cultured in YPD-2% glucose, starting from a single colony isolate. 25 μl of an overnight culture was used to inoculate fresh YPD-2% glucose medium. After five serial transfers, the optical density of the culture was determined and cells were diluted to a concentration of approximately 5000 per ml. 100 μl of the cell suspension was plated on Yeast Carbon Base medium (Difco) containing 30 mM KPi (pH 6.8), 0.1% (NH4)2S4, 40 mM fluoro-acetamide (Amersham) and 1.8% agar (Difco). Cells identical to cells of strain BIE201Y9, i.e. without intracellular recombination, still contain the amdS-gene. To those cells, fluoro-acetamide is toxic. These cells will not be able to grow and will not form colonies on a medium containing fluoro-acetamide. However, if intramolecular recombination has occurred, BIE201Y9-variants that have lost the selectable markers will be able to grow on the fluoro-acetamide medium, since they are unable to convert fluoro-acetamide into growth inhibiting compounds. Those cells will form colonies on this agar medium.
The thus obtained fluoro-acetamide resistant colonies were subjected to PCR analysis using primers of SEQ ID NO: 15 and SEQ ID NO: 16, and SE ID NO: 17 and SEQ ID NO: 18. Primers of SEQ ID NO: 15 and SEQ ID NO: 16 will give a band if recombination of the selectable markers has taken place as intended. As a result, the genes xylA and XKS1 have been integrated into the SIT4-locus. In that case, a PCR reaction using primers of SEQ ID NO: 17 and SEQ ID NO: 18 should not result in a PCR product, since primer 17 primes in a region that should be out-recombined. If a band is obtained with these primers, this is indicative for the presence of the complete plasmid pPWT042 in the genome, so no recombination has taken place.
If primers of SEQ ID NO: 15 and SEQ ID NO: 16 do not result in a PCR product, recombination has taken place, but in such a way that the complete plasmid pPWT042 has recombined out of the genome. Not only were the selectable markers lost, but also the xylA- and XKS1-gene. In fact, wild-type yeast has been retrieved.
Isolates that exhibited the expected PCR results, were subjected to Southern blot analysis (vide supra). One of the strains that showed the correct pattern of bands on the Southern blot is the strain designated as BIE201X9.
Example 4
Construction and Selection of Strain BIE252
4.1 Amplification of the xylA-Cassette
In order to introduce extra copies of the xylA-gene into the genome, a PCR reaction was performed using PHUSION® DNA polymerase (Finnzymes) with plasmid pPWT042 as a template and the oligonucleotides with SEQ ID NO: 19 and SEQ ID NO: 20 as primers. With these primers, the xylA-cassette, comprising the TPI1-promotor, the codon-pair optimized xylA-gene and the PMA1-terminator, is being amplified. The primer design is such that the flanks of the PCR fragment are homologous to the consensus sequence of the delta-sequences of the yeast transposon Ty-1. These sequences can be obtained from NCBI ( ) and aligned using a software package allowing to do so, like e.g. Clone Manager 9 Professional Edition (Scientific & Educational Software, Cary, USA).
The xylA-cassette does not contain a selectable marker with which the integration into the genome can be selected for. In order to estimate transformation frequency, a second control transformation was done with the kanMX-marker. To this end, the kanMX-cassette from plasmid p427TEF (Dualsystems Biotech) was amplified in a PCR reaction using the primers corresponding to SEQ ID NO: 21 and SEQ ID NO: 22.
4.2 Transformation of BIE201X9
BIE201X9 was transformed according to the electroporation protocol (as described above) with the fragments comprising either 30 μg of the xylA-cassette (designated X18-Ty1) or 10 μg of the kanMX-cassette. The kanMX-transformation mixture was plated on YPD-agar (per liter: 10 grams of yeast extract, 20 grams per liter peptone, 20 grams per liter dextrose, 20 grams of agar) containing 100 μg G418 (Sigma Aldrich) per ml. After two to four days, colonies appeared on the plates, whereas the negative control (i.e. no addition of DNA in the transformation experiment) resulted in blank YPD/G418-plates. The transformation frequency appeared to be higher than 600 colonies per μg of kanMX-cassette.
The X18-Ty1 transformation mixture was used to inoculate a shake flask containing 100 ml of Verduyn medium, supplemented with 2% xylose. As a control, the negative control of the transformation (i.e. no addition of DNA in the transformation experiment) was used. The shake flasks were incubated at 30° C. and 280 rpm in an orbital shaker. Growth was followed by measuring the optical density at 600 nm on a regular basis.
The result of the growth curve is depicted in FIG. 8. As can be seen, between days 20 and 25, the optical density of the X18-Ty1 shake flask increased spectacularly, while the growth in the negative control was still absent. At day 25, a flask containing fresh Verduyn medium supplemented with 2% xylose was inoculated from the X18-Ty1 culture to a start optical density at 600 nm of 0.15. From FIG. 8 it is clear that upon re-inoculation the culture started to grow on xylose immediately and rapidly. Since it is likely that the culture consists of a mixture of subcultures, thus consisting of cells with differences in copy number of the X18-Ty1 cassette and in growth rate on xylose, cells were diluted in milliQ water and plated on YPD-agar plates in order to get single colony isolates. The single colony isolates were tested for their ability to utilize different carbon sources.
4.3 Selection of Strain BIE252
In order to select a strain which has gained improved growth on xylose as a sole carbon source without losing its ability to utilize the other important sugars (glucose, arabinose and galactose), ten single colony isolates of the adaptive evolution culture were restreaked on YPD-agar. Subsequently, a preculture was done on YPD-medium supplemented with 2% glucose. The ten cultures were incubated overnight at 30° C. and 280° C. Aliquots of each culture were used to inoculate fresh Verduyn medium supplemented with either 2% glucose, or 2% xylose, or 2% arabinose or 2% galactose, at an initial optical density of 0.15. As controls, strains BIE201, BIE201X9 and the mixed population (from which the ten single colony isolates were retrieved) were included in the experiment. Cells were grown at 30° C. and 280 rpm in an orbital shaker. Growth was assessed on basis of optical density measurements at 600 nm. The results of the optical density at 600 nm after 19 hours of incubation are presented in FIG. 9.
The results of FIG. 9 show that both the mixed culture and the ten single colony isolates exhibit a higher final optical density at 600 nm on xylose. Although these strains grew on arabinose as sole carbon source, the final optical density at 600 nm was less as compared to the parent strains, BIE201 and BIE201×9, at 19 hours after inoculation. After prolonged growth, for several days, colony 3 was selected because it had reached the highest optical density as compared to the other single colony isolate cultures (data not shown). Growth on xylose was not different in all colonies tested.
The colony 3 culture was diluted and plated on YPD-agar. Eleven single colony isolates were tested for their ability to grow on Verduyn medium, supplemented with either 2% arabinose or 2% xylose. To this end, a preculture was done on Verduyn 2% glucose. Cells were grown overnight at 30° C. and 280 rpm in an orbital shaker. An aliquot was transferred to Verduyn medium, supplemented with either 2% arabinose or 2% xylose at an initial optical density of 0.15. The culture of colony 3 was included as a control in this test. Cells were grown overnight at 30° C. and 280 rpm in a orbital shaker. Growth was assessed on basis of optical density measurements at 600 nm. The results of the optical density at 600 nm after 4 days of incubation are presented in FIG. 10.
The results show that colony 3.7 has reached an optical density similar to the culture of the control, colony 3, on xylose. In addition, its ability to grow on arabinose as sole carbon source has largely improved as compared to the culture of colony 3. The other single colony isolates also show an improved growth on arabinose, apparently at the expense of the ability to grow on xylose. The culture of single colony isolate 3.7 was designated strain BIE252. SNP's and amplification in BIE252 were determined following the same procedures as described in the co-pending PCT application, filed on 19 Apr. 2011, claiming priority from EP10160647.3. These test showed that BIE252 has the SNP's: G1363T in the SSY1 gene, A512T in YJR154w gene, A1186G in CEP3 gene, and A436C in GAL80 gene. These are the same as in BIE201. Also amplification in chromosome VII that exists in BIE201 is present in BIE252. This is shown in FIG. 23.
Example 5
Performance Test in BAM
In order to test the performance of the selected strain BIE252, the strain was inoculated in Verduyn medium, supplemented with 2% glucose. As controls, strains BIE201 and BIE104P1Y9mc were included. The first is a strain capable of fermenting glucose, galactose and arabinose (vide supra), and the latter is a strain capable of fermenting glucose, galactose and xylose.
After overnight incubation at 30° C. and 280 rpm in a rotary shaker, cells were harvested by centrifugation and cultivations for CO2 production were performed at 33° C. in 100 ml Verduyn medium supplemented 5% glucose, 5% xylose, 3.5% arabinose and 1% galactose) in the BAM (Biological Activity Monitor). In one experiment, the batch experiment, the cells were added to the 100 ml of Verduyn medium supplemented with the sugars. In a second experiment, the fed-batch experiment, the 100 ml of Verduyn medium supplemented with the sugars was added to the cells at a rate of 3 ml per minute. The CO2 production was constantly monitored at intervals, and samples were taken for analysis (optical density at 600 nm, ethanol, residual sugars). The strains BIE201 and BIE104P1Y9mc were mixed in a 1:1 ratio, based on the optical density, just prior to the BAM experiment.
The results of the BAM experiment are shown in FIGS. 11, 12, 13, 14, 15 and 16.
The performance of the mixed strains (BIE201 and BIE104P1Y9mc) in fed-batch mode (FIG. 11) shows that despite xylose and arabinose accumulate to a certain extent in time, already before the end of the feed (at approximately 33 hr) the consumption rate is faster than the feed rate. After 72 hrs, all arabinose has been converted, while xylose is not fully consumed. Glucose and galactose are always at or near the detection level, indicating that these sugars are preferred above the pentoses arabinose and xylose.
The performance of strain BIE252, as tested in fed-batch mode in the BAM (see FIG. 12), shows essentially the same characteristics as the mixed strains culture. However, xylose and arabinose accumulate to higher concentrations, but the subsequent conversion into ethanol takes place at a higher rate, which results in the same ethanol titer and identical cumulative CO2 production after 120 hrs (FIG. 13).
In batch mode, the performance of the mixed strains (BIE201 and BIE104P1Y9mc) in batch mode shows that glucose is consumed readily after the start of the fermentation experiment (FIG. 14). Subsequently, galactose, arabinose and xylose are being co-fermented. After approximately 30 hrs, galactose was consumed. After approximately 72 hours, arabinose was also fully consumed. Both contributed significantly to the formation of CO2 and ethanol. Xylose consumption, and thus ethanol and CO2 production slowed down significantly after the exhaustion of arabinose. Strain BIE252 performed better in that respect (FIG. 15). Immediately after glucose exhaustion within 10 hours, galactose, arabinose and xylose were co-fermented rapidly and efficiently. Even after galactose exhaustion, both pentoses arabinose and xylose were co-fermented completely, both contributing to CO2-production and ethanol formation. The fermentation of all sugars was complete after approximately 72 hours, in case of strain BIE252. This resulted in a higher cumulative CO2-production of strain BIE252 compared to the mixed strains culture (BIE201 and BIE104P1Y9mc) as is set out in FIG. 16.
Example 6
Performance Test in Real Hydrolysates
The performance test in real hydrolysates was performed using strain BIE252 which was cultured overnight in shake flasks containing YEP medium supplemented with 2% glucose. The cells were harvested by centrifugation at resuspended at a concentration of 50 grams dry matter per liter.
The feed stocks that were tested consisted of batches of corn fiber, corn stover and wheat straw. The hydrolysis and fermentation were performed as described in the materials and methods section.
The results are presented in FIG. 17 (corn fiber), 18 (corn stover) and 19 (wheat straw). In case of corn stover and wheat straw, feedstocks with a relatively low amount of galactose and arabinose but mainly consisting of glucose and xylose, all sugars were converted in 72 hours into CO2 and ethanol. In case of corn fiber (FIG. 17), there is a low residual amount left of arabinose, galactose and xylose.
In the tables below the yield of the fermentation was calculated, on basis of the sugars liberated at the end of the hydrolysis and the amount of ethanol that was produced at the end of the fermentation.







TABLE 2







Total sugar released (g/l), ethanol produced (g/l) and ethanol yield


(gethanol/gsugar) of BAM fermentation of BIE252, for different


lignocellulosic feedstock










Lignocellulosic

Produced EtOH
EtOH yield


feedstock
Total sugar* (g/l)
(g/l)
(gethanol/gsugar)













Corn Stover
45.4
22.7
0.50


Wheat Straw
42.7
20.7
0.48


Corn Fiber
58.1
27.4
0.47





*(released, monomeric sugar at start fermentation)






Based on the amount of ethanol produced at the end of the fermentation, as determined by the Anton Paar DMA 5000 density meter measurement, and the amount of pretreated feedstock that was being used, yields of the overall hydrolysis and fermentation were calculated, in duplicate. These figures are set out in table 3.







TABLE 3







Overall hydrolysis and fermentation yield (gallons of ethanol


per ton dry matter) of BAM fermentation of BIE252, for


different lignocellulosic feedstock










Overall hydrolysis and
Overall hydrolysis and



fermentation yield (gallons
fermentation yield (gallons



of ethanol per
of ethanol per


Lignocellulosic
ton dry matter)
ton dry matter)


feedstock
1st fermentation
2nd fermentation





Corn Stover
81
81


Wheat Straw
72
73


Corn Fiber
67
69









Example 7
Stability Test of Strain BIE252
7.1 Stability of Strain BIE252
In order to test the stability of the strain BIE252, a single colony isolate was used to inoculate 25 ml of YEP 2% glucose. The optical density of the culture was measured at 600 nm. The culture was incubated overnight at 30° C. and 280 rpm in a rotary shaker.
After the overnight incubation, the optical density was determined. Based on the OD600 values before and after incubation, the number of generations made during the incubations was calculated. 25 μl of the overnight culture was used to inoculate a flask containing 25 ml of fresh medium. The culture was incubated again under the same conditions as described above. This procedure was repeated until a culture was obtained in which the cells were at least one hundred generations apart from the initial single colony isolate. YEP medium supplemented with 2% glucose was chosen, because under these conditions no selection pressure is applied for maintaining the introduced genes in strain BIE252, needed for the conversion of arabinose and xylose.
The cell culture obtained after at least 100 generations was diluted and plated on YPD-agar. Two single colony isolates were inoculated in Verduyn-medium 2% glucose. As a control, the parent strain BIE252 was taken along. The cultures were incubated overnight at 30° C. and 280 rpm in a rotary shaker. An aliquot of the overnight culture was used to inoculate a flask containing 25 ml of Verduyn medium supplemented with 1% glucose, 1% xylose, 0.7% arabinose, 0.3% galactose and 0.1% mannose at a start optical density of 0.15. At regular intervals, samples were taken for analysis: optical density measurements at 600 nm, and for determination of residual sugars by NMR. The results, as depicted in FIG. 20a (BIE252 culture prior to stability test), 20b (culture from colony of BIE252 after more than 100 generations) and 20c (culture from second colony of BIE252 after more than 100 generations), show that the behavior of the three strain cultures is virtually identical under the conditions tested. In other words, the performance in this growth medium has not changed; the strain is still able to utilize five different sugars with the same rates after culturing for more than 100 generations, indicating that the strain is genetically stable.
In addition, a quantitative PCR (Q-PCR) experiment was done to assess the copy number of BIE252 prior and after 100 generations cultivation in YEP medium supplemented with 2% glucose. The Q-PCR analysis was performed using the Bio-Rad iCycler iQ system from Bio-Rad (Bio-Rad Laboratories, Hercules, Calif., USA). The iQ SYBR Green Supermix (Bio-Rad) was used. Experiments were set up as suggested in the manual of the provider.
The stability of the strain BIE252 was assessed by determining the copy number of the xylA gene encoding xylose isomerase. As a reference single copy gene, the ACT1 gene was chosen.
The primers for the detection of the genes xylA and ACT1 are:
forward primer xylA SEQ ID NO 23
reverse primer xylA SEQ ID NO 24
forward primer ACT1 SEQ ID NO 25
reverse primer ACT1 SEQ ID NO 26
The results indicated that the copy number of BIE252 is about 8 copies of the xylA gene, relative to the ACT1 gene. The copy number was determined before and after the 100 generations cultivation on YEP-medium supplemented with 2% glucose, and appeared to be essentially the same, taking into account the limitations of the quantitative PCR analysis.
The chromosomal DNA of several colonies, before and after 100 generations cultivation in YEP medium supplemented with 2% glucose, was isolated. The chromosomal DNA is cut by XbaI. A Southern blot analysis is performed using the PCR product of primer pair SEQ ID NO: 23 and SEQ ID NO: 24 as a probe. The resulting autoradiogram is showing that the pattern of bands is not changed, which indicates that the strain is genetically stable after 100 generations of growth under non-selective conditions.
Comparative Experiment A
7.2 Stability of BIE201X9 Transformed with YEP and YCp Vectors
Strain BIE201X9 was transformed with vectors pPWT148 (a YCp plasmid) and pPWT152 (a YEp plasmid). The physical map of plasmid pPWT148 is set out in FIG. 21. The physical map of plasmid pPWT152 is set out in FIG. 22. Transformation mixtures were plated on YPD-agar (per liter: 10 grams of yeast extract, 20 grams per liter peptone, 20 grams per liter dextrose, 20 grams of agar) containing 100 μg G418 (Sigma Aldrich) per ml. After two to four days, colonies appeared on the plates, whereas the negative control (i.e. no addition of DNA in the transformation experiment) resulted in blank YPD/G418-plates.
Three colonies of each transformation were used as a mixture for testing the stability. To this end, the mixed colonies were used to inoculate YEP medium, supplemented with 2% glucose and 100 μg G418/ml. Cells were incubated overnight at 30° C. and 280 rpm in a rotary shaker. The optical density was measured at 600 nm. The overnight culture was used to inoculate fresh YEP medium, supplemented with 2% glucose, and the same medium supplemented with 100 μg G418/ml, to a start optical density at 600 nm of 0.02. On basis of what is reported in the literature (vide supra), the expectation is that the cells that were cultured in the presence of G418 (i.e. selective pressure is applied), the majority of the cells will retain the plasmid inside the cell. However, in absence of G418, the cells are expected to lose their plasmid rapidly.
The cultures were incubated overnight at 30° C. and 280 rpm in a rotary shaker. The optical density was measured at 600 nm. On basis of the optical density measurements, it was calculated that the culture had made 8 generations in both media (i.e with and without G418). Dilutions were made and plated on YPD-plates with and without 100 μg G418/ml. Plates were incubated at 30° C. for approximately two days, or longer as needed to make colonies visible and countable.
In addition, 25 μl of the overnight culture was used to inoculate 25 ml of fresh YEP medium, supplemented with 2% glucose, and the same medium supplemented with 100 μg G418/ml. The cultures were incubated overnight at 30° C. and 280 rpm in a rotary shaker. The optical density was measured at 600 nm. On basis of the optical density measurements, it was calculated that the culture had made 8 extra generations in both media (i.e with and without G418). Dilutions were made and plated on YPD-plates with and without 100 μg G418/ml. Plates were incubated at 30° C. for approximately two days, or longer as needed to make colonies visible and countable.
On basis of the colonies that were counted on YDP-agar with and without G418, the stability could be calculated after 8 and 16 generations in presence or absence of G418. The results are summarized in the table 4.







TABLE 4







Stability of the strains of comparative experiment A (% G418 resistant


clones)










BIE201X9-
BIE201X9-



pPWT148
pPWT152













% G418 resistant clones after 8 generations
4
12


of growth in YEP 2% glucose


% G418 resistant clones after 16 generations
1
5


of growth in YEP 2% glucose


% G418 resistant clones after 8 generations
9
33


of growth in YEP 2% glucose and 100 μg


G418/ml


% G418 resistant clones after 16 generations
28
40


of growth in YEP 2% glucose and 100 μg


G418/ml









From the table, it can be seen that both YCp- and YEp-plasmids (i.e. pPWT148 and pPWT152 respectively) are not stably maintained in the transformed yeast cells, even if selection pressure is being applied during cultivation, in this case by the addition of G418 to the culture medium. It must be noted however that plasmid loss is much more severe in the absence of selection pressure.
This experiment in combination with example 7, provides insight that chromosomal integration of the xylose isomerase genes into the genome is necessary to obtain stable yeast transformants.
Example 8
Deletion of GAL80 Leads to a Better Arabinose Conversion
In Example 4 it was shown that the identified SNP in the GAL80 gene has a positive additive effect on the growth on arabinose, if the amplification of a part of chromosome VII is also present.
GAL80 encodes a transcriptional repressor involved in transcriptional regulation in response to galactose (Timson D J, et al. (2002) Biochem J 363(Pt 3):515-20). In conjunction with Gal4p and Gal3p, Gal80p coordinately regulates the expression of genes containing a GAL upstream activation site in their promoter (UAS-GAL), which includes the GAL metabolic genes GAL1, GAL10, GAL2, and GAL7 (reviewed in Lohr D, et al. (1995) FASEB J 9(9):777-87). Cells null for gal80 constitutively express GAL genes, even in non-inducing media (Torchia T E, et al. (1984) Mol Cell Biol 4(8):1521-7).
The hypothesis is that the SNP that was identified in the GAL80 gene influences the interaction between Gal80p, Gal3p and Gal4p. Hence, the expression of the galactose metabolic genes, including GAL2 encoding galactose permease, will be changed as well as compared to a yeast cell with a wild type GAL80 allele. Gal2p (galactose permease) is the main sugar transporter for arabinose (Kou et al (1970) J. Bacteriol. 103(3):671-678; Becker and Boles (2003) Appl Environ Microbiol. 69(7): 4144-4150).
Apparently, the SNP in the GAL80 gene has a positive effect on the ability to convert L-arabinose. In order to investigate whether the arabinose growth phenotype could further be improved, the coding sequence of the GAL80 gene was deleted in its entirety, using a PCR-mediated gene replacement strategy.
8.1 Disruption of the GAL80 Gene
Primers of SEQ ID NO 58 and 59 (the forward and reverse primers respectively) were used for amplification of the kanMX-marker from plasmid p427-TEF (Dualsystems Biotech, Schlieren, Switzerland). The flanks of the primers are homologous to the 5′-region and 3′-region of the GAL80 gene. Upon homologous recombination, the ORF of the GAL80 gene will be replaced by the kanMX marker, similar as described by Wach (Wach et al (1994) Yeast 10, 1793-1808). The obtained fragment is designated as the GAL80::kanMX fragment.
A yeast transformation of strain BIE252 was done with the purified GAL80::kanMX fragment according to the protocol described by Gietz and Woods (2002), Methods in Enzymology 350: 87-96). The construction of strain BIE252 has been described in EP10160622.6. Strain BIE252 is a xylose and arabinose fermenting strain of S. cerevisiae, which is a derivative of BIE201. Strain BIE252 also contains the GAL80 SNP.
The transformed cells were plated on YEPD-agar containing 100 μg/ml G418 for selection. The plates were incubated at 30° C. until colonies were visible. Plasmid p427-TEF was included as a positive control and yielded many colonies. MilliQ (i.e. no DNA) was included as a negative control and yielded no colonies. The GAL80::kanMX fragment yielded many colonies. Two independent colonies were tested by Southern blotting in order to verify the correct integration (data not shown). A colony with the correct deletion of the GAL80 gene was designated BIE252ΔGAL80.
8.2 Effect of GAL80 Gene Replacement on the Performance in the BAM
A BAM (Biological Activity Monitor; Halotec B V, Veenendaal, the Netherlands) experiment was performed. Single colony isolates of strain BIE252 and strain BIE252ΔGAL80 (a transformant in which the ORF of the GAL80 gene was correctly replaced by the kanMX marker) were used to inoculate Verduyn medium (Verduyn et al., Yeast 8:501-517, 1992) supplemented with 2% glucose. The precultures were incubated for approximately 24 hours at 30° C. and 280 rpm. Cells were harvested and inoculated in a synthetic model medium (Verduyn medium supplemented with 5% glucose, 5% xylose, 3.5% arabinose, 1% galactose and 0.5% mannose, pH 4.2) at a cell density of about 1 gram dry weight per kg of medium. CO2 production was monitored constantly. Sugar conversion and product formation was analyzed by NMR. The data represent the residual amount of sugars at the indicated time points (glucose, arabinose, galactose, mannose and xylose in grams per liter) and the formation of (by-)products (ethanol, glycerol, and the like). Growth was monitored by following optical density of the culture at 600 nm. The experiment was running for approximately 72 hours.
The graphs are displayed in FIG. 23 (BIE252) and 24 (BIE252ΔGAL80).
The experiments clearly show that reference strain BIE252 converted glucose and mannose rapidly. After glucose depletion (around 10 hours), the conversion of xylose and arabinose commenced. Some galactose was already being fermented around the 10 hours time point, which might be due to the GAL80 SNP in this strain, which would allow (partial) simultaneous utilisation of glucose and galactose. At the end of the experiment, around 72 hours, almost all sugars (about 99%) were converted. An ethanol yield of 0.37 grams of ethanol per gram sugar was obtained.
Strain BIE252ΔGAL80 exhibits faster sugar conversion ability than strain BIE252. Also in case of this strain, mannose and glucose are converted in the first hours of fermentation. However, as opposed to strain BIE252, in this transformant there is some co-consumption of glucose, galactose and mannose with arabinose and especially xylose. In general, sugar consumption is faster, leading to a more complete use of all available sugars. This is also apparent from the CO2 evolution in time. In case of BIE252, a first peak is observed, which is basically the CO2 formed from glucose and mannose. After reaching a minimum of just above 10 ml/hr (FIG. 20) a second, more flat peak is observed. In case of BIE252ΔGAL80 however (FIG. 21), the second peak appears as a tail of the first peak, due to an intensified co-use of glucose, xylose, arabinose, mannose and galactose, as is apparent from the sugar analysis by NMR. In the parent strain BIE252, the use of the different sugars is more sequential. Hence, the yield of strain BIE252ΔGAL80 is higher at the end of the experiment (72 h): 0.40 grams of ethanol per gram sugar.
In conclusion, the deletion of the ORF of the GAL80 gene resulted in a further improved performance, as was tested in strain BIE252.

## Claims

1. A transformed Saccharomyces cerevisiae cell suitable for producing ethanol from a sugar composition comprising glucose, galactose, xylose, arabinose and mannose wherein said cell comprises about eight copies of at least one xylose isomerase gene, and from two to four copies of L-arabinose isomerase (araA), L-ribulokinase (araB), and L-ribulose-5-phosphate 4-epimerase (araD) genes, wherein said genes are heteroloqous and are integrated into the cell genome.

2. The yeast cell according to claim 1, wherein said cell is capable of converting at least 90% of glucose, xylose arabinose, galactose and mannose available, into ethanol.

3. The yeast cell according to claim 1, wherein said cell comprises a disruption or deletion of the GAL80 (transcriptional repressor) gene.

4. The yeast cell according claim 1, wherein said cell comprises overexpressed pentose phosphate pathway genes TAL1 (transaldolase), TKL1 (transketolase), RPE1 (ribulose-phosphate 3-epimerase), and RKI1 (ribulose-5-phosphate isomerase).

5. The yeast cell according to claim 1, wherein said cell comprises a XKS1 (xylulose kinase) gene.

6. The yeast cell according to claim 1, wherein an aldose reductase gene is deleted.

7. The yeast cell according to claim 1, wherein all genes exogenous to said cell are integrated into the genome of said cell.

8. The yeast cell according to claim 1, wherein the genes have been introduced in said cell by introduction into a host cell:
a) a cluster consisting of said genes araA, araB and araD under control of a strong constitutive promoter;
b) a cluster consisting of PPP-genes TAL1, TKL1, RPE1 and RKI1, optionally under control of strong constitutive promoter; and deletion of an aldose reductase gene;
c) a cluster consisting of a xylA (xylose isomerase) gene and a XKS1 gene under control of strong constitutive promoter;
d) a construct comprising a xylA gene under control of a strong constitutive promoter, which has the ability to integrate into the genome on multiple loci;
and adaptive evolution of the mixed sugar construct for producing said mixed sugar cell.

9. The yeast cell according to claim 8, wherein said cell is an inhibitor resistant cell.

10. The yeast cell according to claim 8, wherein said cell is an industrial cell.

11. A process for producing ethanol from a sugar composition comprising glucose, galactose, arabinose and xylose, wherein said sugar composition is fermented with a yeast cell according to claim 1.

12. The process according to claim 11, wherein said sugar composition is produced from lignocellulosic material by:
a) pretreatment of at least one lignocellulosic material to produce pretreated lignocellulosic material;
b) enzymatic treatment of the pretreated lignocellulosic material to produce said sugar composition.

13. The process according to claim 11, wherein said fermentation is conducted anaerobically.

14. The yeast cell according to claim 9, wherein said cell is an industrial cell.

15. The process according to claim 12, wherein said fermentation is conducted anaerobically.

16. The yeast cell of claim 1, wherein said at least one xylose isomerase gene is a xylA gene.