# Patent

## Title
Metabolic engineering of arabinose-fermenting yeast cells

## Abstract

The invention relates to an eukaryotic cell expressing nucleotide sequences encoding the ara A, ara B and ara D enzymes whereby the expression of these nucleotide sequences confers on the cell the ability to use L-arabinose and/or convert L-arabinose into L-ribulose, and/or xylulose 5-phosphate and/or into a desired fermentation product such as ethanol. Optionally, the eukaryotic cell is also able to convert xylose into ethanol.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application is a continuation of U.S. application Ser. No. 12/442,013, filed Jun. 12, 2009, which is a U.S. national phase of Int'l Appln. No. PCT/NL2007/00246, filed Oct. 1, 2007, which designated the U.S. and claims priority to Appln. No. EP 06121633.9 filed Oct. 2, 2006, and Appln. No. U.S. 60/848,357, filed Oct. 2, 2006; the entire contents of each of which are hereby incorporated by reference.


FIELD OF THE INVENTION
The invention relates to an eukaryotic cell having the ability to use L-arabinose and/or to convert L-arabinose into L-ribulose, and/or xylulose 5-phosphate and/or into a desired fermentation product and to a process for producing a fermentation product wherein this cell is used.
BACKGROUND OF THE INVENTION
Fuel ethanol is acknowledged as a valuable alternative to fossil fuels. Economically viable ethanol production from the hemicellulose fraction of plant biomass requires the simultaneous fermentative conversion of both pentoses and hexoses at comparable rates and with high yields. Yeasts, in particular Saccharomyces spp., are the most appropriate candidates for this process since they can grow and ferment fast on hexoses, both aerobically and anaerobically. Furthermore they are much more resistant to the toxic environment of lignocellulose hydrolysates than (genetically modified) bacteria.
EP 1 499 708 describes a process for making S. cerevisiae strains able to produce ethanol from L-arabinose. These strains were modified by introducing the araA (L-arabinose isomerase) gene from Bacillus subtilis, the araB (L-ribulokinase) and araD (L-ribulose-5-P4-epimerase) genes from Escherichia coli. Furthermore, these strains were either carrying additional mutations in their genome or overexpressing a TAL1 (transaldolase) gene. However, these strains have several drawbacks. They ferment arabinose in oxygen limited conditions. In addition, they have a low ethanol production rate of 0.05 g·g−1·h−1 (Becker and Boles, 2003). Furthermore, these strains are not able to use L-arabinose under anaerobic conditions. Finally, these S. cerevisiae strains have a wild type background, therefore they can not be used to co-ferment several C5 sugars.
WO 03/062430 and WO 06/009434 disclose yeast strains able to convert xylose into ethanol. These yeast strains are able to directly isomerise xylose into xylulose.
Still, there is a need for alternative strains for producing ethanol, which perform better and are more robust and resistant to relatively harsh production conditions.



DESCRIPTION OF THE FIGURES
FIG. 1. Plasmid maps of pRW231 and pRW243.
FIG. 2. Growth pattern of shake flask cultivations of strain RWB219 (◯) and IMS0001 (●) in synthetic medium containing 0.5% galactose (A) and 0.1% galactose+2% L-arabinose (B). Cultures were grown for 72 hours in synthetic medium with galactose (A) and then transferred to synthetic medium with galactose and arabinose (B). Growth was determined by measuring the OD660.
FIG. 3. Growth rate during serial transfers of S. cerevisiae IMS0001 in shake flask cultures containing synthetic medium with 2% (w/v) L-arabinose. Each datapoint represents the growth rate estimated from the OD660 measured during (exponential) growth. The closed and open circles represent duplicate serial transfer experiments.
FIG. 4. Growth rate during an anaerobic SBR fermentation of S. cerevisiae IMS0001 in synthetic medium with 2% (w/v) L-arabinose. Each datapoint represents the growth rate estimated from the CO2 profile (solid line) during exponential growth.
FIG. 5. Sugar consumption and product formation during anaerobic batch fermentations of strain IMS0002. The fermentations were performed in 1 synthetic medium supplemented with: 20 gl−1 arabinose (A); 20 gl−1 glucose and 20 gl−1 arabinose (B); 30 gl−1 glucose, 15 gl−1 xylose, and 15 gl−1 arabinose (C); Sugar consumption and product formation during anaerobic batch fermentations with a mixture of strains IMS0002 and RWB218. The fermentations were performed in 1 liter of synthetic medium supplemented with 30 gl−1 glucose, 15 gl−1 xylose, and 15 gl−1 arabinose (D). Symbols: glucose (●); xylose (◯); arabinose (▪); ethanol calculated from cumulative CO2 production (□); ethanol measured by HPLC (▴); cumulative CO2 production (Δ); xylitol (▾)
FIG. 6. Sugar consumption and product formation during an anaerobic batch fermentation of strain IMS0002 cells selected for anaerobic growth on xylose. The fermentation was performed in 1 liter of synthetic medium supplemented with 20 gl−1 xylose and 20 gl−1 arabinose. Symbols: xylose (◯); arabinose (▪); ethanol measured by HPLC (▴); cumulative CO2 production (Δ); xylitol (▾).
FIG. 7. Sugar consumption and product formation during an anaerobic batch fermentation of strain IMS0003. The fermentation was performed in 1 liter of synthetic medium supplemented with: 30 gl−1 glucose, 15 gl−1 xylose, and 15 gl−1 arabinose. Symbols: glucose (●); xylose (◯); arabinose (▪); ethanol calculated from cumulative CO2 production (□); ethanol measured by HPLC (▴); cumulative CO2 production (Δ);



DESCRIPTION OF THE INVENTION
Eukaryotic Cell
In a first aspect, the invention relates to a eukaryotic cell capable of expressing the following nucleotide sequences, whereby the expression of these nucleotide sequences confers on the cell the ability to use L-arabinose and/or to convert L-arabinose into L-ribulose, and/or xylulose 5-phosphate and/or into a desired fermentation product such as ethanol:

    
    
        (a) a nucleotide sequence encoding an arabinose isomerase (araA), wherein said nucleotide sequence is selected from the group consisting of:
        
            (i) nucleotide sequences encoding an araA, said araA comprising an amino acid sequence that has at least 55% sequence identity with the amino acid sequence of SEQ ID NO:1.
            (ii) nucleotide sequences comprising a nucleotide sequence that has at least 60% sequence identity with the nucleotide sequence of SEQ ID NO:2.
            (iii) nucleotide sequences the complementary strand of which hybridizes to a nucleic acid molecule of sequence of (i) or (ii);
            (iv) nucleotide sequences the sequences of which differ from the sequence of a nucleic acid molecule of (iii) due to the degeneracy of the genetic code,
        
        
        (b) a nucleotide sequence encoding a L-ribulokinase (araB), wherein said nucleotide sequence is selected from the group consisting of:
        
            (i) nucleotide sequences encoding an araB, said araB comprising an amino acid sequence that has at least 20% sequence identity with the amino acid sequence of SEQ ID NO:3.
            (ii) nucleotide sequences comprising a nucleotide sequence that has at least 50% sequence identity with the nucleotide sequence of SEQ ID NO:4.
            (iii) nucleotide sequences the complementary strand of which hybridizes to a nucleic acid molecule of sequence of (i) or (ii);
            (iv) nucleotide sequences the sequences of which differ from the sequence of a nucleic acid molecule of (iii) due to the degeneracy of the genetic code,
        
        
        (c) a nucleotide sequence encoding an L-ribulose-5-P-4-epimerase (araD), wherein said nucleotide sequence is selected from the group consisting of:
        
            (i) nucleotide sequences encoding an araD, said araD comprising an amino acid sequence that has at least 60% sequence identity with the amino acid sequence of SEQ ID NO:5.
            (ii) nucleotide sequences comprising a nucleotide sequence that has at least 60% sequence identity with the nucleotide sequence of SEQ ID NO:6.
            (iii) nucleotide sequences the complementary strand of which hybridizes to a nucleic acid molecule of sequence of (i) or (ii);
            (iv) nucleotide sequences the sequences of which differ from the sequence of a nucleic acid molecule of (iii) due to the degeneracy of the genetic code.

A preferred embodiment relates to an eukaryotic cell capable of expressing the following nucleotide sequences, whereby the expression of these nucleotide sequences confers on the cell the ability to use L-arabinose and/or to convert L-arabinose into L-ribulose, and/or xylulose 5-phosphate and/or into a desired fermentation product such as ethanol:

        
        
        (a) a nucleotide sequence encoding an arabinose isomerase (araA), wherein said nucleotide sequence is selected from the group consisting of:
        
            (i) nucleotide sequences comprising a nucleotide sequence that has at least 60% sequence identity with the nucleotide sequence of SEQ ID NO:2,
            (ii) nucleotide sequences the complementary strand of which hybridizes to a nucleic acid molecule of sequence of (i);
            (iii) nucleotide sequences the sequences of which differ from the sequence of a nucleic acid molecule of (ii) due to the degeneracy of the genetic code,
        
        
        (b) a nucleotide sequence encoding a L-ribulokinase (araB), wherein said nucleotide sequence is selected from the group consisting of:
        
            (i) nucleotide sequences encoding an araB, said araB comprising an amino acid sequence that has at least 20% sequence identity with the amino acid sequence of SEQ ID NO:3.
            (ii) nucleotide sequences comprising a nucleotide sequence that has at least 50% sequence identity with the nucleotide sequence of SEQ ID NO:4.
            (iii) nucleotide sequences the complementary strand of which hybridizes to a nucleic acid molecule of sequence of (i) or (ii);
            (iv) nucleotide sequences the sequences of which differ from the sequence of a nucleic acid molecule of (iii) due to the degeneracy of the genetic code,
        
        
        (c) a nucleotide sequence encoding an L-ribulose-5-P-4-epimerase (araD), wherein said nucleotide sequence is selected from the group consisting of:
        
            (i) nucleotide sequences encoding an araD, said araD comprising an amino acid sequence that has at least 60% sequence identity with the amino acid sequence of SEQ ID NO:5.
            (ii) nucleotide sequences comprising a nucleotide sequence that has at least 60% sequence identity with the nucleotide sequence of SEQ ID NO:6.
            (iii) nucleotide sequences the complementary strand of which hybridizes to a nucleic acid molecule of sequence of (i) or (ii);
            (iv) nucleotide sequences the sequences of which differ from the sequence of a nucleic acid molecule of (iii) due to the degeneracy of the genetic code.

Sequence Identity and Similarity

        
        
    
    


Sequence identity is herein defined as a relationship between two or more amino acid (polypeptide or protein) sequences or two or more nucleic acid (polynucleotide) sequences, as determined by comparing the sequences. Usually, sequence identities or similarities are compared over the whole length of the sequences compared. In the art, “identity” also means the degree of sequence relatedness between amino acid or nucleic acid sequences, as the case may be, as determined by the match between strings of such sequences. “Similarity” between two amino acid sequences is determined by comparing the amino acid sequence and its conserved amino acid substitutes of one polypeptide to the sequence of a second polypeptide. “Identity” and “similarity” can be readily calculated by various methods, known to those skilled in the art.
Preferred methods to determine identity are designed to give the largest match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. Preferred computer program methods to determine identity and similarity between two sequences include e.g. the BestFit, BLASTP, BLASTN, and FASTA (Altschul, S. F. et al., J. Mol. Biol. 215:403-410 (1990), publicly available from NCBI and other sources (BLAST Manual, Altschul, S., et al., NCBI NLM NIH Bethesda, Md. 20894). A most preferred algorithm used is EMBOSS (http://www.ebi.ac.uk/emboss/align). Preferred parameters for amino acid sequences comparison using EMBOSS are gap open 10.0, gap extend 0.5, Blosum 62 matrix. Preferred parameters for nucleic acid sequences comparison using EMBOSS are gap open 10.0, gap extend 0.5, DNA full matrix (DNA identity matrix).
Optionally, in determining the degree of amino acid similarity, the skilled person may also take into account so-called “conservative” amino acid substitutions, as will be clear to the skilled person. Conservative amino acid substitutions refer to the interchangeability of residues having similar side chains. For example, a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; and a group of amino acids having sulphur-containing side chains is cysteine and methionine. Preferred conservative amino acids substitution groups are: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, and asparagine-glutamine. Substitutional variants of the amino acid sequence disclosed herein are those in which at least one residue in the disclosed sequences has been removed and a different residue inserted in its place. Preferably, the amino acid change is conservative. Preferred conservative substitutions for each of the naturally occurring amino acids are as follows: Ala to ser; Arg to lys; Asn to gln or his; Asp to glu; Cys to ser or ala; Gln to asn; Glu to asp; Gly to pro; His to asn or gln; Ile to leu or val; Leu to ile or val; Lys to arg; gln or glu; Met to leu or ile; Phe to met, leu or tyr; Ser to thr; Thr to ser; Trp to tyr; Tyr to trp or phe; and, Val to ile or leu.
Hybridising Nucleic Acid Sequences
Nucleotide sequences encoding the enzymes expressed in the cell of the invention may also be defined by their capability to hybridise with the nucleotide sequences of SEQ ID NO.'s 2, 4, 6, 8, 16, 18, 20, 22, 24, 26, 28, 30 respectively, under moderate, or preferably under stringent hybridisation conditions. Stringent hybridisation conditions are herein defined as conditions that allow a nucleic acid sequence of at least about 25, preferably about 50 nucleotides, 75 or 100 and most preferably of about 200 or more nucleotides, to hybridise at a temperature of about 65° C. in a solution comprising about 1 M salt, preferably 6×SSC or any other solution having a comparable ionic strength, and washing at 65° C. in a solution comprising about 0.1 M salt, or less, preferably 0.2×SSC or any other solution having a comparable ionic strength. Preferably, the hybridisation is performed overnight, i.e. at least for 10 hours and preferably washing is performed for at least one hour with at least two changes of the washing solution. These conditions will usually allow the specific hybridisation of sequences having about 90% or more sequence identity.
Moderate conditions are herein defined as conditions that allow a nucleic acid sequences of at least 50 nucleotides, preferably of about 200 or more nucleotides, to hybridise at a temperature of about 45° C. in a solution comprising about 1 M salt, preferably 6×SSC or any other solution having a comparable ionic strength, and washing at room temperature in a solution comprising about 1 M salt, preferably 6×SSC or any other solution having a comparable ionic strength. Preferably, the hybridisation is performed overnight, i.e. at least for 10 hours, and preferably washing is performed for at least one hour with at least two changes of the washing solution. These conditions will usually allow the specific hybridisation of sequences having up to 50% sequence identity. The person skilled in the art will be able to modify these hybridisation conditions in order to specifically identify sequences varying in identity between 50% and 90%.
AraA
A preferred nucleotide sequence encoding a arabinose isomerase (araA) expressed in the cell of the invention is selected from the group consisting of:


    (a) nucleotide sequences encoding an araA polypeptide said araA comprising an amino acid sequence that has at least 55, 60, 65, 70, 75, 80, 85, 90, 95, 97, 98, or 99% sequence identity with the amino acid sequence of SEQ ID NO. 1;
    (b) nucleotide sequences comprising a nucleotide sequence that has at least 60, 70, 80, 90, 95, 97, 98, or 99% sequence identity with the nucleotide sequence of SEQ ID NO. 2;
    (c) nucleotide sequences the complementary strand of which hybridises to a nucleic acid molecule sequence of (a) or (b);
    (d) nucleotide sequences the sequence of which differ from the sequence of a nucleic acid molecule of (c) due to the degeneracy of the genetic code.

The nucleotide sequence encoding an araA may encode either a prokaryotic or an eukaryotic araA, i.e. an araA with an amino acid sequence that is identical to that of an araA that naturally occurs in the prokaryotic or eukaryotic organism. The present inventors have found that the ability of a particular araA to confer to a eukaryotic host cell the ability to use arabinose and/or to convert arabinose into L-ribulose, and/or xylulose 5-phosphate and/or into a desired fermentation product such as ethanol when co-expressed with araB and araD does not depend so much on whether the araA is of prokaryotic or eukaryotic origin. Rather this depends on the relatedness of the araA's amino acid sequence to that of the sequence SEQ ID NO. 1.

AraB

A preferred nucleotide sequence encoding a L-ribulokinase (AraB) expressed in the cell of the invention is selected from the group consisting of:
    
        (a) nucleotide sequences encoding a polypeptide comprising an amino acid sequence that has at least 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 97, 98, or 99% sequence identity with the amino acid sequence of SEQ ID NO. 3;
        (b) nucleotide sequences comprising a nucleotide sequence that has at least 50, 60, 70, 80, 90, 95, 97, 98, or 99% sequence identity with the nucleotide sequence of SEQ ID NO.4;
        (c) nucleotide sequences the complementary strand of which hybridises to a nucleic acid molecule sequence of (a) or (b);
        (d) nucleotide sequences the sequence of which differ from the sequence of a nucleic acid molecule of (c) due to the degeneracy of the genetic code.

The nucleotide sequence encoding an araB may encode either a prokaryotic or an eukaryotic araB, i.e. an araB with an amino acid sequence that is identical to that of a araB that naturally occurs in the prokaryotic or eukaryotic organism. The present inventors have found that the ability of a particular araB to confer to a eukaryotic host cell the ability to use arabinose and/or to convert arabinose into L-ribulose, and/or xylulose 5-phosphate and/or into a desired fermentation product when co-expressed with araA and araD does not depend so much on whether the araB is of prokaryotic or eukaryotic origin. Rather this depends on the relatedness of the araB's amino acid sequence to that of the sequence SEQ ID NO. 3.

AraD

A preferred nucleotide sequence encoding a L-ribulose-5-P-4-epimerase (araD) expressed in the cell of the invention is selected from the group consisting of:

        (e) nucleotide sequences encoding a polypeptide comprising an amino acid sequence that has at least 60, 65, 70, 75, 80, 85, 90, 95, 97, 98, or 99% sequence identity with the amino acid sequence of SEQ ID NO. 5;
        (f) nucleotide sequences comprising a nucleotide sequence that has at least 60, 65, 70, 75, 80, 85, 90, 95, 97, 98, or 99% sequence identity with the nucleotide sequence of SEQ ID NO.6;
        (g) nucleotide sequences the complementary strand of which hybridises to a nucleic acid molecule sequence of (a) or (b);
        (h) nucleotide sequences the sequence of which differs from the sequence of a nucleic acid molecule of (c) due to the degeneracy of the genetic code.

The nucleotide sequence encoding an araD may encode either a prokaryotic or an eukaryotic araD, i.e. an araD with an amino acid sequence that is identical to that of a araD that naturally occurs in the prokaryotic or eukaryotic organism. The present inventors have found that the ability of a particular araD to confer to a eukaryotic host cell the ability to use arabinose and/or to convert arabinose into L-ribulose, and/or xylulose 5-phosphate and/or into a desired fermentation product when co-expressed with araA and araB does not depend so much on whether the araD is of prokaryotic or eukaryotic origin. Rather this depends on the relatedness of the araD's amino acid sequence to that of the sequence SEQ ID NO. 5.

    
    


Surprisingly, the codon bias index indicated that expression of the Lactobacillus plantarum araA, araB and araD genes were more favorable for expression in yeast than the prokaryolic araA, araB and araD genes described in EP 1 499 708.
It is to be noted that L. plantarum is a Generally Regarded As Safe (GRAS) organism, which is recognized as safe by food registration authorities. Therefore, a preferred nucleotide sequence encodes an araA, araB or araD respectively having an amino acid sequence that is related to the sequences SEQ ID NO: 1, 3, or 5 respectively as defined above. A preferred nucleotide sequence encodes a fungal araA, araB or araD respectively (e.g. from a Basidiomycete), more preferably an araA, araB or araD respectively from an anaerobic fungus, e.g. an anaerobic fungus that belongs to the families Neocallimastix, Caecomyces, Piromyces, Orpinomyces, or Ruminomyces. Alternatively, a preferred nucleotide sequence encodes a bacterial araA, araB or araD respectively, preferably from a Gram-positive bacterium, more preferably from the genus Lactobacillus, most preferably from Lactobacillus plantarum species. Preferably, one, two or three or the araA, araB and araD nucleotide sequences originate from a Lactobacillus genus, more preferably a Lactobacillus plantarum species. The bacterial araA expressed in the cell of the invention is not the Bacillus subtilis araA disclosed in EP 1 499 708 and given as SEQ ID NO:9. SEQ ID NO:10 represents the nucleotide acid sequence coding for SEQ ID NO:9. The bacterial araB and araD expressed in the cell of the invention are not the ones of Escherichia coli (E. coli) as disclosed in EP 1 499 708 and given as SEQ ID NO: 11 and SEQ ID NO:13. SEQ ID NO: 12 represents the nucleotide acid sequence coding for SEQ ID NO:11. SEQ ID NO:14 represents the nucleotide acid sequence coding for SEQ ID NO:13.
To increase the likelihood that the (bacterial) araA, araB and araD enzymes respectively are expressed in active form in a eukaryotic host cell of the invention such as yeast, the corresponding encoding nucleotide sequence may be adapted to optimise its codon usage to that of the chosen eukaryotic host cell. The adaptiveness of a nucleotide sequence encoding the araA, araB, and araD enzymes (or other enzymes of the invention, see below) to the codon usage of the chosen host cell may be expressed as codon adaptation index (CAI). The codon adaptation index is herein defined as a measurement of the relative adaptiveness of the codon usage of a gene towards the codon usage of highly expressed genes. The relative adaptiveness (w) of each codon is the ratio of the usage of each codon, to that of the most abundant codon for the same amino acid. The CAI index is defined as the geometric mean of these relative adaptiveness values. Non-synonymous codons and termination codons (dependent on genetic code) are excluded. CAI values range from 0 to 1, with higher values indicating a higher proportion of the most abundant codons (see Sharp and Li, 1987, Nucleic Acids Research 15: 1281-1295; also see: Jansen et al., 2003, Nucleic Acids Res. 31(8):2242-51). An adapted nucleotide sequence preferably has a CAI of at least 0.2, 0.3, 0.4, 0.5, 0.6 or 0.7.
In a preferred embodiment, expression of the nucleotide sequences encoding an ara A, an ara B and an ara D as defined earlier herein confers to the cell the ability to use L-arabinose and/or to convert it into L-ribulose, and/or xylulose 5-phosphate. Without wishing to be bound by any theory, L-arabinose is expected to be first converted into L-ribulose, which is subsequently converted into xylulose 5-phosphate which is the main molecule entering the pentose phosphate pathway. In the context of the invention, “using L-arabinose” preferably means that the optical density measured at 660 nm (OD660) of transformed cells cultured under aerobic or anaerobic conditions in the presence of at least 0.5% L-arabinose during at least 20 days is increased from approximately 0.5 till 1.0 or more. More preferably, the OD660 is increased from 0.5 till 1.5 or more. More preferably, the cells are cultured in the presence of at least 1%, at least 1.5%, at least 2% L-arabinose. Most preferably, the cells are cultured in the presence of approximately 2% L-arabinose.

In the context of the invention, a cell is able “to convert L-arabinose into L-ribulose” when detectable amounts of L-ribulose are detected in cells cultured under aerobic or anaerobic conditions in the presence of L-arabinose (same preferred concentrations as in previous paragraph) during at least 20 days using a suitable assay. Preferably the assay is HPLC for L-ribulose.

In the context of the invention, a cell is able “to convert L-arabinose into xylulose 5-phosphate” when an increase of at least 2% of xylulose 5-phosphate is detected in cells cultured under aerobic or anaerobic conditions in the presence of L-arabinose (same preferred concentrations as in previous paragraph) during at least 20 days using a suitable assay. Preferably, an HPCL-based assay for xylulose 5-phosphate has been described in Zaldivar J., et al ((2002), Appl. Microbiol. Biotechnol., 59:436-442). This assay is briefly described in the experimental part. More preferably, the increase is of at least 5%, 10%, 15%, 20%, 25% or more.

In another preferred embodiment, expression of the nucleotide sequences encoding an ara A, ara B and ara D as defined earlier herein confers to the cell the ability to convert L-arabinose into a desired fermentation product when cultured under aerobic or anaerobic conditions in the presence of L-arabinose (same preferred concentrations as in previous paragraph) during at least one month till one year. More preferably, a cell is able to convert L-arabinose into a desired fermentation product when detectable amounts of a desired fermentation product are detected using a suitable assay and when the cells are cultured under the conditions given in previous sentence. Even more preferably, the assay is HPLC. Even more preferably, the fermentation product is ethanol.

A cell for transformation with the nucleotide sequences encoding the araA, araB, and araD enzymes respectively as described above, preferably is a host cell capable of active or passive xylose transport into and xylose isomerisation within the cell. The cell preferably is capable of active glycolysis. The cell may further contain an endogenous pentose phosphate pathway and may contain endogenous xylulose kinase activity so that xylulose isomerised from xylose may be metabolised to pyruvate. The cell further preferably contains enzymes for conversion of pyruvate to a desired fermentation product such as ethanol, 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, butanol, a β-lactam antibiotic or a cephalosporin. The cell may be made capable of producing butanol by introduction of one or more genes of the butanol pathway as disclosed in WO2007/041269.
A preferred cell is naturally capable of alcoholic fermentation, preferably, anaerobic alcoholic fermentation. The host cell further preferably has a high tolerance to ethanol, a high tolerance to low pH (i.e. capable of growth at a pH lower than 5, 4, 3, or 2,5) and towards organic acids like lactic acid, acetic acid or formic acid and sugar degradation products such as furfural and hydroxy-methylfurfural, and a high tolerance to elevated temperatures. Any of these characteristics or activities of the host cell may be naturally present in the host cell or may be introduced or modified through genetic selection or by genetic modification. A suitable host cell is a eukaryotic microorganism like e.g. a fungus, however, most suitable as host cell are yeasts or filamentous fungi.
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. Preferred yeasts as host cells belong to one of the genera Saccharomyces, Kluyveromyces, Candida, Pichia, Schizosaccharomyces, Hansenula, Kloeckera, Schwanniomyces, or Yarrowia. Preferably the yeast is capable of anaerobic fermentation, more preferably 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 present invention are morphologically, physiologically, and genetically distinct from yeasts. Vegetative growth by filamentous fungi is by hyphal elongation and carbon catabolism of most filamentous fungi is obligately aerobic. Preferred filamentous fungi as host cells belong to one of the genera Aspergillus, Trichoderma, Humicola, Acremonium, Fusarium, or Penicillium. 
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, K. fragilis. 
In a preferred embodiment, the host cell of the invention is a host cell that has been transformed with a nucleic acid construct comprising the nucleotide sequence encoding the araA, araB, and araD enzymes as defined above. In one more preferred embodiment, the host cell is co-transformed with three nucleic acid constructs, each nucleic acid construct comprising the nucleotide sequence encoding araA, araB or araD. The nucleic acid construct comprising the araA, araB, and/or araD coding sequence is capable of expression of the araA, araB, and/or araD enzymes in the host cell. To this end the nucleic acid construct may be constructed as described in e.g. WO 03/0624430. The host cell may comprise a single but preferably comprises multiple copies of each nucleic acid construct. The nucleic acid construct may be maintained episomally and thus comprise a sequence for autonomous replication, such as an ARS sequence. Suitable episomal nucleic acid constructs may e.g. be based on the yeast 2μ or pKD1 (Fleer et al., 1991, Biotechnology 9:968-975) plasmids. Preferably, however, each nucleic acid construct is integrated in one or more copies into the genome of the host cell. Integration into the host cell's genome may occur at random by illegitimate recombination but preferably nucleic acid construct is integrated into the host cell's genome by homologous recombination as is well known in the art of fungal molecular genetics (see e.g. WO 90/14423, EP-A-0 481 008, EP-A-0 635 574 and U.S. Pat. No. 6,265,186). Accordingly, in a more preferred embodiment, the cell of the invention comprises a nucleic acid construct comprising the araA, araB, and/or araD coding sequence and is capable of expression of the araA, araB, and/or araD enzymes. In an even more preferred embodiment, the araA, araB, and/or araD coding sequences are each operably linked to a promoter that causes sufficient expression of the corresponding nucleotide sequences in a cell to confer to the cell the ability to use L-arabinose, and/or to convert L-arabinose into L-ribulose, and/or xylulose 5-phosphate. Preferably the cell is a yeast cell. Accordingly, in a further aspect, the invention also encompasses a nucleic acid construct as earlier outlined herein. Preferably, a nucleic acid construct comprises a nucleic acid sequence encoding an araA, araB and/or araD. Nucleic acid sequences encoding an araA, araB, or araD have been all earlier defined herein. Even more preferably, the expression of the corresponding nucleotide sequences in a cell confer to the cell the ability to convert L-arabinose into a desired fermentation product as defined later herein. In an even more preferred embodiment, the fermentation product is ethanol. Even more preferably, the cell is a yeast cell.
As used herein, the term “operably linked” refers to a linkage of polynucleotide elements (or coding sequences or nucleic acid sequence) in a functional relationship. A nucleic acid sequence is “operably linked” when it is placed into a functional relationship with another nucleic acid sequence. For instance, a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the coding sequence. Operably linked means that the nucleic acid sequences being linked are typically contiguous and, where necessary to join two protein coding regions, contiguous and in reading frame.
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, including, but not limited to transcription factor binding sites, repressor and activator protein binding sites, and any other sequences of nucleotides known to one of skill in the art to act directly or indirectly to regulate the amount of transcription from the promoter. 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 the nucleotide sequences coding for araA, araB and/or araD 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. 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 (to the nucleotide sequence) 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, preferably under conditions where arabinose, or arabinose and glucose, or xylose and arabinose or xylose and arabinose and glucose are available as carbon sources, more preferably as major carbon sources (i.e. more than 50% of the available carbon source consists of arabinose, or arabinose and glucose, or xylose and arabinose or xylose and arabinose and glucose), most preferably as sole carbon sources. Suitable promoters in this context include both constitutive and inducible natural promoters as well as engineered promoters. A preferred promoter for use in the present invention will in addition be insensitive to catabolite (glucose) repression and/or will preferably not require arabinose and/or xylose for induction.
Promotors having these characteristics 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 (PPK), 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), the enolase promoter (ENO), the glucose-6-phosphate isomerase promoter (PGI1, Hauf et al, 2000) or the hexose(glucose) transporter promoter (HXT7) or the glyceraldehyde-3-phosphate dehydrogenase (TDH3). The sequence of the PGI1 promoter is given in SEQ ID NO:51. The sequence of the HXT7 promoter is given in SEQ ID NO:52. The sequence of the TDH3 promoter is given in SEQ ID NO:49. 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. A preferred cell of the invention is a eukaryotic cell transformed with the araA, araB and araD genes of L. plantarum. More preferably, the eukaryotic cell is a yeast cell, even more preferably a S. cerevisiae strain transformed with the araA, araB and araD genes of L. plantarum. Most preferably, the cell is either CBS120327 or CBS120328 both deposited at the CBS Institute (The Netherlands) on Sep. 27, 2006.
The term “homologous” when used to indicate the relation between a given (recombinant) nucleic acid or polypeptide molecule and a given host organism or host cell, is understood to mean that in nature the nucleic acid or polypeptide molecule is produced by a host cell or organisms of the same species, preferably of the same variety or strain. If homologous to a host cell, a nucleic acid sequence encoding a polypeptide will typically be operably linked to another promoter sequence or, if applicable, another secretory signal sequence and/or terminator sequence than in its natural environment. When used to indicate the relatedness of two nucleic acid sequences the term “homologous” means that one single-stranded nucleic acid sequence may hybridize to a complementary single-stranded nucleic acid sequence. The degree of hybridization may depend on a number of factors including the amount of identity between the sequences and the hybridization conditions such as temperature and salt concentration as earlier presented. Preferably the region of identity is greater than about 5 bp, more preferably the region of identity is greater than 10 bp.
The term “heterologous” when used with respect to a nucleic acid (DNA or RNA) or protein refers to a nucleic acid or protein that does not occur naturally as part of the organism, cell, genome or DNA or RNA sequence in which it is present, or that is found in a cell or location or locations in the genome or DNA or RNA sequence that differ from that in which it is found in nature. Heterologous nucleic acids or proteins are not endogenous to the cell into which it is introduced, but has been obtained from another cell or synthetically or recombinantly produced. Generally, though not necessarily, such nucleic acids encode proteins that are not normally produced by the cell in which the DNA is transcribed or expressed. Similarly exogenous RNA encodes for proteins not normally expressed in the cell in which the exogenous RNA is present. Heterologous nucleic acids and proteins may also be referred to as foreign nucleic acids or proteins. Any nucleic acid or protein that one of skill in the art would recognize as heterologous or foreign to the cell in which it is expressed is herein encompassed by the term heterologous nucleic acid or protein. The term heterologous also applies to non-natural combinations of nucleic acid or amino acid sequences, i.e. combinations where at least two of the combined sequences are foreign with respect to each other.
Preferred Eukaryotic Cell Able to Use and/or Convert L-Arabinose and Xylose
In a more preferred embodiment, the cell of the invention that expresses araA, araB and araD is able to use L-arabinose and/or to convert it into L-ribulose, and/or xylulose 5-phosphate and/or a desired fermentation product as earlier defined herein and additionally exhibits the ability to use xylose and/or convert xylose into xylulose. The conversion of xylose into xylulose is preferably a one step isomerisation step (direct isomerisation of xylose into xylulose). This type of cell is therefore able to use both L-arabinose and xylose. “Using” xylose has preferably the same meaning as “using” L-arabinose as earlier defined herein.

Enzyme definitions are as used in WO 06/009434, for xylose isomerase (EC 5.3.1.5), xylulose kinase (EC 2.7.1.17), ribulose 5-phosphate epimerase (5.1.3.1), ribulose 5-phosphate isomerase (EC 5.3.1.6), transketolase (EC 2.2.1.1), transaldolase (EC 2.2.1.2), and aldose reductase” (EC 1.1.1.21).

In a preferred embodiment, the eukaryotic cell of the invention expressing araA, araB and araD as earlier defined herein has the ability of isomerising xylose to xylulose as e.g. described in WO 03/0624430 or in WO 06/009434. The ability of isomerising xylose to xylulose is conferred to the host cell by transformation of the host cell with a nucleic acid construct comprising a nucleotide sequence encoding a xylose isomerase. The transformed host cell's ability to isomerise xylose into xylulose is the direct isomerisation of xylose to xylulose. This is understood to mean that xylose isomerised into xylulose in a single reaction catalysed by a xylose isomerase, as opposed to the two step conversion of xylose into xylulose via a xylitol intermediate as catalysed by xylose reductase and xylitol dehydrogenase, respectively.

The nucleotide sequence encodes a xylose isomerase that is preferably expressed in active form in the transformed host cell of the invention. Thus, expression of the nucleotide sequence in the host cell produces a xylose isomerase with a specific activity of at least 10 U xylose isomerase activity per mg protein at 30° C., preferably at least 20, 25, 30, 50, 100, 200, 300 or 500 Upper mg at 30° C. The specific activity of the xylose isomerase expressed in the transformed host cell is herein defined as the amount of xylose isomerase activity units per mg protein of cell free lysate of the host cell, e.g. a yeast cell free lysate. Determination of the xylose isomerase activity has already been described earlier herein.
Preferably, expression of the nucleotide sequence encoding the xylose isomerase in the host cell produces a xylose isomerase with a Km for xylose that is less than 50, 40, 30 or 25 mM, more preferably, the Km for xylose is about 20 mM or less.
A preferred nucleotide sequence encoding the xylose isomerase may be selected from the group consisting of:

    (e) nucleotide sequences encoding a polypeptide comprising an amino acid sequence that has at least 60, 65, 70, 75, 80, 85, 90, 95, 97, 98, or 99% sequence identity with the amino acid sequence of SEQ ID NO. 7 or SEQ ID NO:15;
    (f) nucleotide sequences comprising a nucleotide sequence that has at least 40, 50, 60, 70, 80, 90, 95, 97, 98, or 99% sequence identity with the nucleotide sequence of SEQ ID NO. 8 or SEQ ID NO:16;
    (g) nucleotide sequences the complementary strand of which hybridises to a nucleic acid molecule sequence of (a) or (b);
    (h) nucleotide sequences the sequence of which differs from the sequence of a nucleic acid molecule of (c) due to the degeneracy of the genetic code.


The nucleotide sequence encoding the xylose isomerase may encode either a prokaryotic or an eukaryotic xylose isomerase, i.e. a xylose isomerase with an amino acid sequence that is identical to that of a xylose isomerase that naturally occurs in the prokaryotic or eukaryotic organism. The present inventors have found that the ability of a particular xylose isomerase to confer to a eukaryotic host cell the ability to isomerise xylose into xylulose does not depend so much on whether the isomerase is of prokaryotic or eukaryotic origin. Rather this depends on the relatedness of the isomerase's amino acid sequence to that of the Piromyces sequence (SEQ ID NO. 7). Surprisingly, the eukaryotic Piromyces isomerase is more related to prokaryotic isomerases than to other known eukaryotic isomerases. Therefore, a preferred nucleotide sequence encodes a xylose isomerase having an amino acid sequence that is related to the Piromyces sequence as defined above. A preferred nucleotide sequence encodes a fungal xylose isomerase (e.g. from a Basidiomycete), more preferably a xylose isomerase from an anaerobic fungus, e.g. a xylose isomerase from an anaerobic fungus that belongs to the families Neocallimastix, Caecomyces, Piromyces, Orpinomyces, or Ruminomyces. Alternatively, a preferred nucleotide sequence encodes a bacterial xylose isomerase, preferably a Gram-negative bacterium, more preferably an isomerase from the class Bacteroides, or from the genus Bacteroides, most preferably from B. thetaiotaomicron (SEQ ID NO. 15).
To increase the likelihood that the xylose isomerase is expressed in active form in a eukaryotic host cell such as yeast, the nucleotide sequence encoding the xylose isomerase may be adapted to optimise its codon usage to that of the eukaryotic host cell as earlier defined herein.
A host cell for transformation with the nucleotide sequence encoding the xylose isomerase as described above, preferably is a host capable of active or passive xylose transport into the cell. The host cell preferably contains active glycolysis. The host cell may further contain an endogenous pentose phosphate pathway and may contain endogenous xylulose kinase activity so that xylulose isomerised from xylose may be metabolised to pyruvate. The host further preferably contains enzymes for conversion of pyruvate to a desired fermentation product such as ethanol, 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, butanol, a β-lactam antibiotic or a cephalosporin. A preferred host cell is a host cell that is naturally capable of alcoholic fermentation, preferably, anaerobic alcoholic fermentation. The host cell further preferably has a high tolerance to ethanol, a high tolerance to low pH (i.e. capable of growth at a pH lower than 5, 4, 3, or 2,5) and towards organic acids like lactic acid, acetic acid or formic acid and sugar degradation products such as furfural and hydroxy-methylfurfural, and a high tolerance to elevated temperatures. Any of these characteristics or activities of the host cell may be naturally present in the host cell or may be introduced or modified by genetic modification. A suitable cell is a eukaryotic microorganism like e.g. a fungus, however, most suitable as host cell are yeasts or filamentous fungi. Preferred yeasts and filamentous fungi have already been defined herein.
As used herein the wording host cell has the same meaning as cell.
The cell of the invention is preferably transformed with a nucleic acid construct comprising the nucleotide sequence encoding the xylose isomerase. The nucleic acid construct that is preferably used is the same as the one used comprising the nucleotide sequence encoding araA, araB or araD.
In another preferred embodiment of the invention, the cell of the invention:

    
    
        expressing araA, araB and araD, and exhibiting the ability to directly isomerise xylose into xylulose, as earlier defined herein

further comprises a genetic modification that increases the flux of the pentose phosphate pathway, as described in WO 06/009434. In particular, the genetic modification causes an increased flux of the non-oxidative part 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 1.1, 1.2, 1.5, 2, 5, 10 or 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 substracting 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. In a preferred embodiment, the cell comprises a genetic modification that increases the flux of the pentose phosphate pathway and has a specific xylose consumption rate of at least 346 mg xylose/g biomass/h.

    
    


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 more 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, as described in WO 06/009434.
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 we have found that 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.
There are various means available in the art for overexpression of enzymes in the cells of the invention. 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. Suitable promoters to this end have already been defined herein.
The coding sequence used for overexpression of the enzymes preferably is homologous to the host cell of the invention. However, coding sequences that are heterologous to the host cell of the invention may likewise be applied, as mentioned in WO 06/009434.
A nucleotide sequence used for overexpression of ribulose-5-phosphate isomerase in the host cell of the invention is a nucleotide sequence encoding a polypeptide with ribulose-5-phosphate isomerase activity, whereby preferably the polypeptide has an amino acid sequence having at least 50, 60, 70, 80, 90 or 95% identity with SEQ ID NO. 17 or whereby the nucleotide sequence is capable of hybridising with the nucleotide sequence of SEQ ID NO. 18, under moderate conditions, preferably under stringent conditions.
A nucleotide sequence used for overexpression of ribulose-5-phosphate epimerase in the host cell of the invention is a nucleotide sequence encoding a polypeptide with ribulose-5-phosphate epimerase activity, whereby preferably the polypeptide has an amino acid sequence having at least 50, 60, 70, 80, 90 or 95% identity with SEQ ID NO. 19 or whereby the nucleotide sequence is capable of hybridising with the nucleotide sequence of SEQ ID NO. 20, under moderate conditions, preferably under stringent conditions.
A nucleotide sequence used for overexpression of transketolase in the host cell of the invention is a nucleotide sequence encoding a polypeptide with transketolase activity, whereby preferably the polypeptide has an amino acid sequence having at least 50, 60, 70, 80, 90 or 95% identity with SEQ ID NO. 21 or whereby the nucleotide sequence is capable of hybridising with the nucleotide sequence of SEQ ID NO. 22, under moderate conditions, preferably under stringent conditions.
A nucleotide sequence used for overexpression of transaldolase in the host cell of the invention is a nucleotide sequence encoding a polypeptide with transaldolase activity, whereby preferably the polypeptide has an amino acid sequence having at least 50, 60, 70, 80, 90 or 95% identity with SEQ ID NO. 23 or whereby the nucleotide sequence is capable of hybridising with the nucleotide sequence of SEQ ID NO. 24, under moderate conditions, preferably under stringent conditions.
Overexpression of an enzyme, when referring to the production of the enzyme in a genetically modified host 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. Overexpression of an enzyme is thus preferably determined by measuring the level of the enzyme's specific activity in the host cell using appropriate enzyme assays as described herein. Alternatively, overexpression of the enzyme may determined indirectly by quantifying the specific steady state level of enzyme protein, e.g. using antibodies specific for the enzyme, or by quantifying the specific steady level of the mRNA coding for the enzyme. The latter may particularly be suitable for enzymes of the pentose phosphate pathway for which enzymatic assays are not easily feasible as substrates for the enzymes are not commercially available. Preferably in the host cells of the invention, an enzyme to be overexpressed is overexpressed by at least a factor 1.1, 1.2, 1.5, 2, 5, 10 or 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.
In a further preferred embodiment, the host cell of the invention:

    
    
        expressing araA, araB and araD, and exhibiting the ability to directly isomerise xylose into xylulose, and optionally
        comprising a genetic modification that increase the flux of the pentose pathway as earlier defined herein

further comprises a genetic modification that increases the specific xylulose kinase activity. Preferably the genetic modification 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 of the invention is a nucleotide sequence encoding a polypeptide with xylulose kinase activity, whereby preferably the polypeptide has an amino acid sequence having at least 50, 60, 70, 80, 90 or 95% identity with SEQ ID NO. 25 or whereby the nucleotide sequence is capable of hybridising with the nucleotide sequence of SEQ ID NO. 26, under moderate conditions, preferably under stringent conditions.

    
    


A particularly preferred xylulose kinase is a xylose kinase that is related to the xylulose kinase xylB from Piromyces as mentioned in WO 03/0624430. A more preferred nucleotide sequence for use in overexpression of xylulose kinase in the host cell of the invention is a nucleotide sequence encoding a polypeptide with xylulose kinase activity, whereby preferably the polypeptide has an amino acid sequence having at least 45, 50, 55, 60, 65, 70, 80, 90 or 95% identity with SEQ ID NO. 27 or whereby the nucleotide sequence is capable of hybridising with the nucleotide sequence of SEQ ID NO. 28, under moderate conditions, preferably under stringent conditions.
In the host cells of the invention, genetic modification that increases the specific xylulose kinase activity may be combined with any of the modifications increasing the flux of the pentose phosphate pathway as described above, but this combination is not essential for the invention. Thus, a host cell of the invention comprising a genetic modification that increases the specific xylulose kinase activity in addition to the expression of the araA, araB and araD enzymes as defined herein is specifically included in the invention. 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 1.1, 1.2, 1.5, 2, 5, 10 or 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.
In a further preferred embodiment, the host cell of the invention:

    
    
        expressing araA, araB and araD, and exhibiting the ability to directly isomerise xylose into xylulose, and optionally
        comprising a genetic modification that increase the flux of the pentose pathway and/or
        further comprising a genetic modification that increases the specific xylulose kinase activity all as earlier defined herein

further comprises a genetic modification that reduces 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 inactivate a gene encoding an unspecific aldose reductase, as described in WO 06/009434. Preferably, the genetic modifications reduce or inactivate the expression of each endogenous copy of a gene encoding an unspecific aldose reductase in the host cell. Host 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 of the invention is a nucleotide sequence encoding a polypeptide with aldose reductase activity, whereby preferably the polypeptide has an amino acid sequence having at least 50, 60, 70, 80, 90 or 95% identity with SEQ ID NO. 29 or whereby the nucleotide sequence is capable of hybridising with the nucleotide sequence of SEQ ID NO. 30 under moderate conditions, preferably under stringent conditions.

    
    


In the host cells of the invention, the expression of the araA, araB and araD enzymes as defined herein is combined with genetic modification that reduces unspecific aldose reductase activity. The genetic modification leading to the reduction of unspecific aldose reductase activity may be combined with any of the modifications increasing the flux of the pentose phosphate pathway and/or with any of the modifications increasing the specific xylulose kinase activity in the host cells as described above, but these combinations are not essential for the invention. Thus, a host cell expressing araA, araB, and araD, comprising an additional genetic modification that reduces unspecific aldose reductase activity is specifically included in the invention.
In a preferred embodiment, the host cell is CBS120327 deposited at the CBS Institute (The Netherlands) on Sep. 27, 2006.
In a further preferred embodiment, the invention relates to modified host cells that are further adapted to L-arabinose (use L-arabinose and/or convert it into L-ribulose, and/or xylulose 5-phosphate and/or into a desired fermentation product and optionally xylose utilisation by selection of mutants, either spontaneous or induced (e.g. by radiation or chemicals), for growth on L-arabinose and optionally xylose, preferably on L-arabinose and optionally xylose as sole carbon source, and more preferably under anaerobic conditions. Selection of mutants may be performed by serial passaging of cultures as e.g. described by Kuyper et al. (2004, FEMS Yeast Res. 4: 655-664) and/or by cultivation under selective pressure in a chemostat culture as is described in Example 4 of WO 06/009434. This selection process may be continued as long as necessary. This selection process is preferably carried out during one week till one year. However, the selection process may be carried out for a longer period of time if necessary. During the selection process, the cells are preferably cultured in the presence of approximately 20 g/l L-arabinose and/or approximately 20 g/l xylose. The cell obtained at the end of this selection process is expected to be improved as to its capacities of using L-arabinose and/or xylose, and/or converting L-arabinose into L-ribulose and/or xylulose 5-phosphate and/or a desired fermentation product such as ethanol. In this context “improved cell” may mean that the obtained cell is able to use L-arabinose and/or xylose in a more efficient way than the cell it derives from. For example, the obtained cell is expected to better grow: increase of the specific growth rate of at least 2% than the cell it derives from under the same conditions. Preferably, the increase is of at least 4%, 6%, 8%, 10%, 15%, 20%, 25% or more. The specific growth rate may be calculated from OD660 as known to the skilled person. Therefore, by monitoring the OD660, one can deduce the specific growth rate. In this context “improved cell” may also mean that the obtained cell converts L-arabinose into L-ribulose and/or xylulose 5-phosphate and/or a desired fermentation product such as ethanol in a more efficient way than the cell it derives from. For example, the obtained cell is expected to produce higher amounts of L-ribulose and/or xylulose 5-phosphate and/or a desired fermentation product such as ethanol: increase of at least one of these compounds of at least 2% than the cell it derives from under the same conditions. Preferably, the increase is of at least 4%, 6%, 8%, 10%, 15%, 20%, 25% or more. In this context “improved cell” may also mean that the obtained cell converts xylose into xylulose and/or a desired fermentation product such as ethanol in a more efficient way than the cell it derives from. For example, the obtained cell is expected to produce higher amounts of xylulose and/or a desired fermentation product such as ethanol: increase of at least one of these compounds of at least 2% than the cell it derives from under the same conditions. Preferably, the increase is of at least 4%, 6%, 8%, 10%, 15%, 20%, 25% or more.
In a preferred host cell of the invention 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 L-arabinose and optionally xylose as carbon source, preferably as sole carbon source, and preferably under anaerobic conditions. Preferably the modified host cell produce essentially no xylitol, e.g. the xylitol produced is below the detection limit or e.g. less than 5, 2, 1, 0.5, or 0.3% of the carbon consumed on a molar basis.
Preferably the modified host cell has the ability to grow on L-arabinose and optionally xylose as sole carbon source at a rate of at least 0.001, 0.005, 0.01, 0.03, 0.05, 0.1, 0.2, 0.25 or 0.3 h−1 under aerobic conditions, or, if applicable, at a rate of at least 0.001, 0.005, 0.01, 0.03, 0.05, 0.07, 0.08, 0.09, 0.1, 0.12, 0.15 or 0.2 h−1 under anaerobic conditions Preferably the modified host cell has the ability to grow on a mixture of glucose and L-arabinose and optionally xylose (in a 1:1 weight ratio) as sole carbon source at a rate of at least 0.001, 0.005, 0.01, 0.03, 0.05, 0.1, 0.2, 0.25 or 0.3 h−1 under aerobic conditions, or, if applicable, at a rate of at least 0.001, 0.005, 0.01, 0.03, 0.05, 0.1, 0.12, 0.15, or 0.2 h−1 under anaerobic conditions.
Preferably, the modified host cell has a specific L-arabinose and optionally xylose consumption rate of at least 346, 350, 400, 500, 600, 650, 700, 750, 800, 900 or 1000 mg/g cells/h. Preferably, the modified host cell has a yield of fermentation product (such as ethanol) on L-arabinose and optionally xylose that is at least 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 80, 85, 90, 95 or 98% of the host cell's yield of fermentation product (such as ethanol) on glucose. More preferably, the modified host cell's yield of fermentation product (such as ethanol) on L-arabinose and optionally xylose is equal to the host cell's yield of fermentation product (such as ethanol) on glucose. Likewise, the modified host cell's biomass yield on L-arabinose and optionally xylose is preferably at least 55, 60, 70, 80, 85, 90, 95 or 98% of the host cell's biomass yield on glucose. More preferably, the modified host cell's biomass yield on L-arabinose and optionally xylose is equal to the host cell's biomass yield on glucose. It is understood that in the comparison of yields on glucose and L-arabinose and optionally xylose both yields are compared under aerobic conditions or both under anaerobic conditions.
In a more preferred embodiment, the host cell is CBS120328 deposited at the CBS Institute (The Netherlands) on Sep. 27, 2006 or CBS121879 deposited at the CBS Institute (The Netherlands) on Sep. 20, 2007.
In a preferred embodiment, the cell expresses one or more enzymes that confer to the cell the ability to produce at least one fermentation product selected from the group consisting of ethanol, 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, butanol, a β-lactam antibiotic and a cephalosporin. In a more preferred embodiment, the host cell of the invention is a host cell for the production of ethanol. In another preferred embodiment, the invention relates to a transformed host cell 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. Such fermentation products include e.g. 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, butanol, a β-lactam antibiotic and a cephalosporin. A preferred host cell of the invention for production of non-ethanolic fermentation products is a host cell that contains a genetic modification that results in decreased alcohol dehydrogenase activity.

Method

In a further aspect, the invention relates to fermentation processes in which a host cell of the invention is used for the fermentation of a carbon source comprising a source of L-arabinose and optionally a source of xylose. Preferably, the source of L-arabinose and the source of xylose are L-arabinose and xylose. In addition, the carbon source in the fermentation medium may also comprise a source of glucose. The source of L-arabinose, xylose or glucose may be L-arabinose, xylose or glucose as such or may be any carbohydrate oligo- or polymer comprising L-arabinose, xylose or glucose units, such as e.g. lignocellulose, xylans, cellulose, starch, arabinan and the like. For release of xylose or glucose units from such carbohydrates, appropriate carbohydrases (such as xylanases, glucanases, amylases and the like) may be added to the fermentation medium or may be produced by the modified host cell. In the latter case the modified host cell may be genetically engineered to produce and excrete such carbohydrases. An additional advantage of using oligo- or polymeric sources of glucose is that it enables to maintain a low(er) concentration of free glucose during the fermentation, e.g. by using rate-limiting amounts of the carbohydrases. This, in turn, will prevent repression of systems required for metabolism and transport of non-glucose sugars such as xylose. In a preferred process the modified host cell ferments both the L-arabinose (optionally xylose) and glucose, preferably simultaneously in which case preferably a modified host cell is used which is insensitive to glucose repression to prevent diauxic growth. In addition to a source of L-arabinose, optionally xylose (and glucose) as carbon source, the fermentation medium will further comprise the appropriate ingredient required for growth of the modified host cell. Compositions of fermentation media for growth of microorganisms such as yeasts or filamentous fungi are well known in the art.
In a preferred process, there is provided a process for producing a fermentation product selected from the group consisting of ethanol, 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, butanol, a β-lactam antibiotic and a cephalosporin whereby the process comprises the steps of:

    (a) fermenting a medium containing a source of L-arabinose and optionally xylose with a modified host cell as defined herein, whereby the host cell ferments L-arabinose and optionally xylose to the fermentation product, and optionally,
    (b) recovering the fermentation product.

The fermentation process is a process for the production of a fermentation product such as e.g. ethanol, 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, butanol, a β-lactam antibiotic, such as Penicillin G or Penicillin V and fermentative derivatives thereof, and/or a cephalosporin. 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 5, 2.5 or 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, 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, butanol, a β-lactam antibiotics and a cephalosporin. In a preferred embodiment, the fermentation process is anaerobic. An anaerobic process is advantageous since it is cheaper than aerobic processes: less special equipment is needed. Furthermore, anaerobic processes are expected to give a higher product yield than aerobic processes. Under aerobic conditions, usually the biomass yield is higher than under anaerobic conditions. As a consequence, usually under aerobic conditions, the expected product yield is lower than under anaerobic conditions. According to the inventors, the process of the invention is the first anaerobic fermentation process with a medium comprising a source of L-arabinose that has been developed so far.

In another preferred embodiment, the fermentation process is under oxygen-limited conditions. More preferably, the fermentation process is aerobic and under oxygen-limited conditions. 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 5.5, more preferably at least 6 and even more preferably at least 7 mmol/L/h.



The fermentation process is preferably run at a temperature that is optimal for the modified cell. Thus, for most yeasts or fungal cells, the fermentation process is performed at a temperature which is less than 42° C., preferably less than 38° C. For yeast or filamentous fungal host cells, the fermentation process is preferably performed at a temperature which is lower than 35, 33, 30 or 28° C. and at a temperature which is higher than 20, 22, or 25° C.
A preferred process is a process for the production of ethanol, whereby the process comprises the steps of: (a) fermenting a medium containing a source of L-arabinose and optionally xylose with a modified host cell as defined herein, whereby the host cell ferments L-arabinose and optionally xylose to ethanol; and optionally, (b) recovery of the ethanol. The fermentation medium may also comprise a source of glucose that is also fermented to ethanol. In a preferred embodiment, the fermentation process for the production of ethanol is anaerobic. Anaerobic has already been defined earlier herein. In another preferred embodiment, the fermentation process for the production of ethanol is aerobic. In another preferred embodiment, the fermentation process for the production of ethanol is under oxygen-limited conditions, more preferably aerobic and under oxygen-limited conditions. Oxygen-limited conditions have already been defined earlier herein.
In the process, the volumetric ethanol productivity is preferably at least 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 5.0 or 10.0 g ethanol per liter per hour. The ethanol yield on L-arabinose and optionally xylose and/or glucose in the process preferably is at least 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 95 or 98%. The ethanol yield is herein defined as a percentage of the theoretical maximum yield, which, for glucose and L-arabinose and optionally xylose is 0.51 g. ethanol per g. glucose or xylose. In another preferred embodiment, the invention relates to a process for producing a fermentation product selected from the group consisting of 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, butanol, a β-lactam antibiotic and a cephalosporin. The process preferably comprises the steps of (a) fermenting a medium containing a source of L-arabinose and optionally xylose with a modified host cell as defined herein above, whereby the host cell ferments L-arabinose and optionally xylose to the fermentation product, and optionally, (b) recovery of the fermentation product. In a preferred process, the medium also contains a source of glucose.
In the fermentation process of the invention leading to the production of ethanol, several advantages can be cited by comparison to known ethanol fermentations processes:


    
    
        anaerobic processes are possible.
        oxygen limited conditions are also possible.
        higher ethanol yields and ethanol production rates can be obtained.
        the strain used may be able to use L-arabinose and optionally xylose.

Alternatively to the fermentation processes described above, another fermentation process is provided as a further aspect of the invention wherein, at least two distinct cells are used for the fermentation of a carbon source comprising at least two sources of carbon selected from the group consisting of but not limited thereto: a source of L-arabinose, a source of xylose and a source of glucose. In this fermentation process, “at least two distinct cells” means this process is preferably a co-fermentation process. In one preferred embodiment, two distinct cells are used: one being the one of the invention as earlier defined able to use L-arabinose, and/or to convert it into L-ribulose, and/or xylulose 5-phosphate and/or into a desired fermentation product such as ethanol and optionally being able to use xylose, the other one being for example a strain which is able to use xylose and/or convert it into a desired fermentation product such as ethanol as defined in WO 03/062430 and/or WO 06/009434. A cell which is able to use xylose is preferably a strain which exhibits the ability of directly isomerising xylose into xylulose (in one step) as earlier defined herein. These two distinct strains are preferably cultivated in the presence of a source of L-arabinose, a source of xylose and optionally a source of glucose. Three distinct cells or more may be co-cultivated and/or three or more sources of carbon may be used, provided at least one cell is able to use at least one source of carbon present and/or to convert it into a desired fermentation product such as ethanol. The expression “use at least one source of carbon” has the same meaning as the expression “use of L-arabinose”. The expression “convert it (i.e. a source of carbon) into a desired fermentation product has the same meaning as the expression “convert L-arabinose into a desired fermentation product”.

In a preferred embodiment, the invention relates to a process for producing a fermentation product selected from the group consisting of ethanol, lactic acid, 3-hydroxy-propionic acid, acrylic acid, acetic acid, succinic acid, citric acid, malic acid, fumaric acid, amino acids, 1,3-propane-diol, ethylene, glycerol, butanol, β-lactam antibiotics and cephalosporins, whereby the process comprises the steps of:

        (a) fermenting a medium containing at least a source of L-arabinose and a source of xylose with a cell of the invention as earlier defined herein and a cell able to use xylose and/or exhibiting the ability to directly isomerise xylose into xylulose, whereby each cell ferments L-arabinose and/or xylose to the fermentation product, and optionally,
        (b) recovering the fermentation product.

All preferred embodiments of the fermentation processes as described above are also preferred embodiments of this further fermentation processes: identity of the fermentation product, identity of source of L-arabinose and source of xylose, conditions of fermentation (aerobical or anaerobical conditions, oxygen-limited conditions, temperature at which the process is being carried out, productivity of ethanol, yield of ethanol).

Genetic Modifications

    
    


For overexpression of enzymes in the host cells of the inventions as described above, as well as for additional genetic modification of host cells, preferably yeasts, host cells are transformed with the various nucleic acid constructs of the invention by methods well known in the art. Such methods are e.g. 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-0 635 574, WO 98/46772, WO 99/60102 and WO 00/37671.
Promoters for use in the nucleic acid constructs for overexpression of enzymes in the host cells of the invention have been described above. In the nucleic acid constructs for overexpression, the 3′-end of the nucleotide acid sequence encoding the enzyme(s) 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. The transcription termination sequence further preferably comprises a polyadenylation signal. Preferred terminator sequences are the alcohol dehydrogenase (ADH1) and the PGI1 terminators. More preferably, the ADH1 and the PGI1 terminators are both from S. cerevisiae (SEQ ID NO:50 and SEQ ID NO:53 respectively).
Optionally, a selectable marker may be present in the nucleic acid construct. 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. Preferably however, non-antibiotic resistance markers are used, such as auxotrophic markers (URA3, TRP1, LEU2). 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. Alternatively, a screenable marker such as Green Fluorescent Protein, lacZ, 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 of 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. Suitable episomal nucleic acid constructs may e.g. be based on the yeast 2μ or pKD1 (Fleer et al., 1991, Biotechnology 9:968-975) plasmids. Alternatively the nucleic acid construct may comprise sequences for integration, preferably by homologous recombination. Such sequences may thus be sequences homologous to the target site for integration in the host cell's genome. The nucleic acid constructs of the invention can be provided in a manner known per se, which generally involves techniques such as restricting and linking nucleic acids/nucleic acid sequences, for which reference is made to the standard handbooks, such as Sambrook and Russel (2001) “Molecular Cloning: A Laboratory Manual (3rd edition), Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press.
Methods for inactivation and gene disruption in yeast or fungi are well known in the art (see e.g. Fincham, 1989, Microbiol Rev. 53(1):148-70 and EP-A-0 635 574).
In this document and in its claims, the verb “to comprise” and its conjugations is used in its non-limiting sense to mean that items following the word are included, but items not specifically mentioned are not excluded. In addition, reference to an element by the indefinite article “a” or “an” does not exclude the possibility that more than one of the element is present, unless the context clearly requires that there be one and only one of the elements. The indefinite article “a” or “an” thus usually means “at least one”.
The invention is further described by the following examples, which should not be construed as limiting the scope of the invention.
EXAMPLES
Plasmid and Strain Construction
Strains
The L-arabinose consuming Sachharomyces cerevisiae strain described in this work is based on strain RWB220, which is itself a derivative of RWB217. RWB217 is a CEN.PK strain in which four genes coding for the expression of enzymes in the pentose phosphate pathway have been overexpressed, TAL1, TKL1, RPE1, RKI1 (Kuyper et al., 2005a). In addition the gene coding for an aldose reductase (GRE3), has been deleted. Strain RWB217 also contains two plasmids, a single copy plasmid with a LEU2 marker for overexpression of the xylulokinase (XKS1) and an episomal, multicopy plasmid with URA3 as the marker for the expression of the xylose isomerase, XylA. RWB217 was subjected to a selection procedure for improved growth on xylose which is described in Kuyper et al. (2005b). The procedure resulted in two pure strains, RWB218 (Kuyper et al., 2005b) and RWB219. The difference between RWB218 and RWB219 is that after the selection procedure, RWB218 was obtained by plating and restreaking on mineral medium with glucose as the carbon source, while for RWB219 xylose was used.
Strain RWB219 was grown non-selectively on YP with glucose (YPD) as the carbon source in order to facilitate the loss of both plasmids. After plating on YPD single colonies were tested for plasmid loss by looking at uracil and leucine auxotrophy. A strain that had lost both plasmids was transformed with pSH47, containing the cre recombinase, in order to remove a KanMX cassette (Guldener et al., 1996), still present after integrating the RKIJ overexpression construct. Colonies with the plasmid were resuspended in Yeast Peptone medium (YP) (10 g/l yeast extract and 20 g/l peptone both from BD Difco Belgium) with 1% galactose and incubated for 1 hour at 30° C. About 200 cells were plated on YPD. The resulting colonies were checked for loss of the KanMX marker (G418 resistance) and pSH47 (URA3). A strain that had lost both the KanMX marker and the pSH47 plasmid was then named RWB220. To obtain the strain tested in this patent, RWB220 was transformed with pRW231 and pRW243 (table 2), resulting in strain IMS0001.
During construction strains were maintained on complex YP: 10 gl−1 yeast extract (BD Difco), 20 gl−1 peptone (BD Difco) or synthetic medium (MY) (Verduyn et al., 1992) supplemented with glucose (2%) as carbon source (YPD or MYD) and 1.5% agar in the case of plates. After transformation with plasmids strains were plated on MYD. Transformations of yeast were done according to Gietz and Woods (2002). Plasmids were amplified in Escherichia coli strain XL-1 blue (Stratagene, La Jolla, Calif., USA). Transformation was performed according to Inoue et al. (1990). E. coli was grown on LB (Luria-Bertani) plates or in liquid TB (Terrific Broth) medium for the isolation of plasmids (Sambrook et al, 1989).
Plasmids
In order to grow on L-arabinose, yeast needs to express three different genes, an L-arabinose isomerase (AraA), a L-ribulokinase (AraB), and a L-ribulose-5-P 4-epimerase (AraD) (Becker and Boles, 2003). In this work we have chosen to express AraA, AraB, and AraD from the lactic acid bacterium Lactobacillus plantarum in S. cerevisiae. Because the eventual aim is to consume L-arabinose in combination with other sugars, like D-xylose, the genes encoding the bacterial L-arabinose pathway were combined on the same plasmid with the genes coding for D-xylose consumption.
In order to get a high level of expression, the L. plantarum AraA and AraD genes were ligated into plasmid pAKX002, the 2μ XylA bearing plasmid.
The AraA cassette was constructed by amplifying a truncated version of the TDH3 promoter with SpeI5′Ptdh3 and 5′AraAPtdh3 (SEQ ID NO: 49), the AraA gene with Ptdh5′AraA and Tadh3′AraA and the ADH1 terminator (SEQ ID NO:50) with 3′AraATadh1 and 3′Tadh1-SpeI. The three fragments were extracted from gel and mixed in roughly equimolar amounts. On this mixture a PCR was performed using the SpeI-5′Ptdh3 and 3′Tadh1SpeI oligos. The resulting PTDH3-AraA-TADH1 cassette was gel purified, cut at the 5′ and 3′ SpeI sites and then ligated into pAKX002 cut with NheI, resulting in plasmid pRW230.
The AraD construct was made by first amplifying a truncated version of the HXT7 promoter (SEQ ID NO:52) with oligos SalI5′Phxt7 and 5′AraDPhxt, the AraD gene with Phxt5′AraD and Tpgi3′AraD and the GPI1 terminator (SEQ ID NO:53) region with the 3′AraDTpgi and 3′TpgiSalI oligos. The resulting fragments were extracted from gel and mixed in roughly equimolar amounts, after which a PCR was performed using the SalI5'Phxt7 and 3′Tpgi1SalI oligos. The resulting PHXT7-AraD-TPGI1 cassette was gel purified, cut at the 5′ and 3′ SalI sites and then ligated into pRW230 cut with XhoI, resulting in plasmid pRW231 (FIG. 1).
Since too high an expression of the L-ribulokinase is detrimental to growth (Becker and Boles, 2003), the AraB gene was combined with the XKS1 gene, coding for xylulokinase, on an integration plasmid. For this, p415ADHXKS (Kuyper et al., 2005a) was first changed into pRW229, by cutting both p415ADHXKS and pRS305 with PvuI and ligating the ADHXKS-containing PvuI fragment from p415ADHXKS to the vector backbone from pRS305, resulting in pRW229.
A cassette, containing the L. plantarum AraB gene between the PGI1 promoter (SEQ ID NO:51) and ADH1 terminator (SEQ ID NO:50) was made by amplifying the PGI1 promoter with the SacIS'Ppgi1 and 5′AraBPpgi1 oligos, the AraB gene with the Ppgi5′AraB and Tadh3′AraB oligos and the ADH1 terminator with 3′AraBTadh1 and 3′Tadh1SacI oligos. The three fragments were extracted from gel and mixed in roughly equimolar amounts. On this mixture a PCR was performed using the SacI-5′Ppgi1 and 3′Tadh1SacI oligos. The resulting PPGI1-AraB-TADH1 cassette was gel purified, cut at the 5′ and 3′ SacI sites and then ligated into pRW229 cut with SacI, resulting in plasmid pRW243 (FIG. 1).
Strain RWB220 was transformed with pRW231 and pRW243 (table 2), resulting in strain IMS0001.
Restriction endonucleases (New England Biolabs, Beverly, Mass., USA and Roche, Basel, Switzerland) and DNA ligase (Roche) were used according to the manufacturers' specifications. Plasmid isolation from E. coli was performed with the Qiaprep spin miniprep kit (Qiagen, Hilden, Germany). DNA fragments were separated on a 1% agarose (Sigma, St. Louis, Mo., USA) gel in 1×TBE (Sambrook et al, 1989). Isolation of fragments from gel was carried out with the Qiaquick gel extraction kit (Quiagen). Amplification of the (elements of the) AraA, AraB and AraD cassettes was done with VentR DNA polymerase (New England Biolabs) according to the manufacturer's specification. The template was chromosomal DNA of S. cerevisiae CEN.PK113-7D for the promoters and terminators, or Lactobacillus plantarum DSM20205 for the Ara genes. The polymerase chain reaction (PCR) was performed in a Biometra TGradient Thermocycler (Biometra, Gottingen, Germany) with the following settings: 30 cycles of 1 min annealing at 55° C., 60° C. or 65° C., 1 to 3 min extension at 75° C., depending on expected fragment size, and 1 min denaturing at 94° C.
Cultivation and Media
Shake-flask cultivations were performed at 30° C. in a synthetic medium (Verduyn et al., 1992). The pH of the medium was adjusted to 6.0 with 2 M KOH prior to sterilisation. For solid synthetic medium, 1.5% of agar was added.
Pre-cultures were prepared by inoculating 100 ml medium containing the appropriate sugar in a 500-ml shake flask with a frozen stock culture. After incubation at 30° C. in an orbital shaker (200 rpm), this culture was used to inoculate either shake-flask cultures or fermenter cultures. The synthetic medium for anaerobic cultivation was supplemented with 0.01 gl−1 ergosterol and 0.42 gl−1 Tween 80 dissolved in ethanol (Andreasen and Stier, 1953; Andreasen and Stier, 1954). Anaerobic (sequencing) batch cultivation was carried out at 30° C. in 2-1 laboratory fermenters (Applikon, Schiedam, The Netherlands) with a working volume of 1 l. The culture pH was maintained at pH 5.0 by automatic addition of 2 M KOH. Cultures were stirred at 800 rpm and sparged with 0.5 l min−1 nitrogen gas (<10 ppm oxygen). To minimise diffusion of oxygen, fermenters were equipped with Norprene tubing (Cole Palmer Instrument company, Vernon Hills, USA). Dissolved oxygen was monitored with an oxygen electrode (Applisens, Schiedam, The Netherlands). Oxygen-limited conditions were achieved in the same experimental set-up by headspace aeration at approximately 0.05 l min−1.
Determination of Dry Weight
Culture samples (10.0 ml) were filtered over preweighed nitrocellulose filters (pore size 0.45 μm; Gelman laboratory, Ann Arbor, USA). After removal of medium, the filters were washed with demineralised water and dried in a microwave oven (Bosch, Stuttgart, Germany) for 20 min at 360 W and weighed. Duplicate determinations varied by less than 1%.
Gas Analysis
Exhaust gas was cooled in a condensor (2° C.) and dried with a Permapure dryer type MD-110-48P-4 (Permapure, Toms River, USA). O2 and CO2 concentrations were determined with a NGA 2000 analyser (Rosemount Analytical, Orrville, USA). Exhaust gasflow rate and specific oxygen-consumption and carbondioxide production rates were determined as described previously (Van Urk et al., 1988; Weusthuis et al., 1994). In calculating these biomass-specific rates, volume changes caused by withdrawing culture samples were taken account for.
Metabolite Analysis
Glucose, xylose, arabinose, xylitol, organic acids, glycerol and ethanol were analysed by HPLC using a Waters Alliance 2690 HPLC (Waters, Milford, USA) supplied with a BioRad HPX 87H column (BioRad, Hercules, USA), a Waters 2410 refractive-index detector and a Waters 2487 UV detector. The column was eluted at 60° C. with 0.5 gl−1 sulphuric acid at a flow rate of 0.6 ml min−1.
Assay for Xylulose 5-Phosphate (Zaldivar J., et al, Appl. Microbiol. Biotechnol., (2002), 59:436-442)
For the analysis of intracellular metabolites such as xylulose 5-phosphate, 5 ml broth was harvested in duplicate from the reactors, before glucose exhaustion (at 22 and 26 h of cultivation) and after glucose exhaustion (42, 79 and 131 h of cultivation). Procedures for metabolic arrest, solid-phase extraction of metabolites and analysis have been described in detail by Smits H. P. et al. (Anal. Biochem., 261:36-42, (1998)). However, the analysis by high-pressure ion exchange chromatography coupled to pulsed amperometric detection used to analyze cell extracts, was slightly modified. Solutions used were eluent A, 75 mM NaOH, and eluent B, 500 mM NaAc. To prevent contamination of carbonate in the eluent solutions, a 50% NaOH solution with low carbonate concentration (Baker Analysed, Deventer, The Netherlands) was used instead of NaOH pellets. The eluents were degassed with Helium (He) for 30 min and then kept under a He atmosphere. The gradient pump was programmed to generate the following gradients: 100% A and 0% B (0 min), a linear decrease of A to 70% and a linear increase of B to 30% (0-30 min), a linear decrease of A to 30% and a linear increase of B to 70% (30-70 min), a linear decrease of A to 0% and a linear increase of B to 100% (70-75 min), 0% A and 100% B (75-85 min), a linear increase of A to 100% and a linear decrease of B to 0% (85-95 min) The mobile phase was run at a flow rate of 1 ml/min. Other conditions were according to Smits et al. (1998).
Carbon Recovery
Carbon recoveries were calculated as carbon in products formed, divided by the total amount of sugar carbon consumed, and were based on a carbon content of biomass of 48%. To correct for ethanol evaporation during the fermentations, the amount of ethanol produced was assumed to be equal to the measured cumulative production of CO2 minus the CO2 production that occurred due to biomass synthesis (5.85 mmol CO2 per gram biomass (Verduyn et al., 1990)) and the CO2 associated with acetate formation.
Selection for Growth on L-Arabinose
Strain IMS0001 (CBS120327 deposited at the CBS on Sep. 27, 2006), containing the genes encoding the pathways for both xylose (XylA and XKS1) and arabinose (AraA, AraB, AraD) metabolization, was constructed according the procedure described above. Although capable of growing on xylose (data not shown), strain IMS0001 did not seem to be capable of growing on solid synthetic medium supplemented with 2% L-arabinose. Mutants of IMS0001 capable of utilizing L-arabinose as carbon source for growth were selected by serial transfer in shake flasks and by sequencing-batch cultivation in fermenters (SBR).
For the serial transfer experiments, a 500-ml shake flask containing 100 ml synthetic medium containing 0.5% galactose were inoculated with either strain IMS0001, or the reference strain RWB219. After 72 hours, at an optical density at 660 nm of 3.0, the cultures were used to inoculate a new shake flask containing 0.1% galactose and 2% arabinose. Based on HPLC determination with D-ribulose as calibration standard, it was determined that already in the first cultivations of strain IMS0001, on medium containing a galactose/arabinose mixture, part of the arabinose was converted into ribulose and subsequently excreted to the supernatant. These HPLC analyses were performed using a Waters Alliance 2690 HPLC (Waters, Milford, USA) supplied with a BioRad HPX 87H column (BioRad, Hercules, USA), a Waters 2410 refractive-index detector and a Waters 2487 UV detector. The column was eluted at 60° C. with 0.5 gl−1 sulphuric acid at a flow rate of 0.6 ml min−1. In contrast to the reference strain RWB219, the OD660 of the culture of strain IMS0001 increased after depletion of the galactose. When after approximately 850 hours growth on arabinose by strain IMS0001 was observed (FIG. 2), this culture was transferred at an OD660 of 1.7 to a shake flask containing 2% arabinose. Cultures were then sequentially transferred to fresh medium containing 2% arabinose at an OD660 of 2-3. Utilization of arabinose was confirmed by occasionally measuring arabinose concentrations by HPLC (data not shown). The growth rate of these cultures increased from 0 to 0.15 h−1 in approximately 3600 hours (FIG. 3).
A batch fermentation under oxygen limited conditions was started by inoculating 1 l of synthetic medium supplemented with 2% of arabinose with a 100 ml shake flask culture of arabinose-grown IMS0001 cells with a maximum growth rate on 2% of L-arabinose of approximately 0.12 h−1. When growth on arabinose was observed, the culture was subjected to anaerobic conditions by sparging with nitrogen gas. The sequential cycles of anaerobic batch cultivation were started by either manual or automated replacement of 90% of the culture with synthetic medium with 20 gl−1 arabinose. For each cycle during the SBR fermentation, the exponential growth rate was estimated from the CO2 profile (FIG. 4). In 13 cycles, the exponential growth rate increased from 0.025 to 0.08 h−1. After 20 cycles a sample was taken, and plated on solid synthetic medium supplemented with 2% of L-arabinose and incubated at 30° C. for several days. Separate colonies were re-streaked twice on solid synthetic medium with L-arabinose. Finally, a shake flask containing synthetic medium with 2% of L-L-arabinose was inoculated with a single colony, and incubated for 5 days at 30° C. This culture was designated as strain IMS0002 (CBS120328 deposited at the Centraal Bureau voor Schimmelculturen (CBS) on Sep. 27, 2006). Culture samples were taken, 30% of glycerol was added and samples were stored at −80° C.
Mixed Culture Fermentation
Biomass hydrolysates, a desired feedstock for industrial biotechnology, contain complex mixtures consisting of various sugars amongst which glucose, xylose and arabinose are commonly present in significant fractions. To accomplish ethanolic fermentation of not only glucose and arabinose, but also xylose, an anaerobic batch fermentation was performed with a mixed culture of the arabinose-fermenting strain IMS0002, and the xylose-fermenting strain RWB218. An anaerobic batch fermenter containing 800 ml of synthetic medium supplied with 30 gl−1 D-glucose, 15 gl−1 D-xylose, and 15 gl−1 L-arabinose was inoculated with 100 ml of pre-culture of strain IMS0002. After 10 hours, a 100 ml inoculum of RWB218 was added. In contrast to the mixed sugar fermentation with only strain IMS0002, both xylose and arabinose were consumed after glucose depletion (FIG. 5D). The mixed culture completely consumed all sugars, and within 80 hours 564.0±6 3 mmol l−1 ethanol (calculated from the CO2 production) was produced with a high overall yield of 0.42 g g−1 sugar. Xylitol was produced only in small amounts, to a concentration of 4.7 mmol l−1.
Characterization of Strain IMS0002
Growth and product formation of strain IMS0002 was determined during anaerobic batch fermentations on synthetic medium with either L-arabinose as the sole carbon source, or a mixture of glucose, xylose and L-arabinose. The pre-cultures for these anaerobic batch fermentations were prepared in shake flasks containing 100 ml of synthetic medium with 2% L-arabinose, by inoculating with −80° C. frozen stocks of strain IMS0002, and incubating for 48 hours at 30° C.
FIG. 5A shows that strain IMS0002 is capable of fermenting 20 gl−1 L-arabinose to ethanol during an anaerobic batch fermentation of approximately 70 hours. The specific growth rate under anaerobic conditions with L-arabinose as sole carbon source was 0.05±0.001 h−1. Taking into account the ethanol evaporation during the batch fermentation, the ethanol yield from 20 gl−1 arabinose was 0.43±0.003 g g−1. Without evaporation correction the ethanol yield was 0.35±0.01 g g−1 of arabinose. No formation of arabinitol was observed during anaerobic growth on arabinose. In FIG. 5B, the ethanolic fermentation of a mixture of 20 gl−1 glucose and 20 g l−1 L-arabinose by strain IMS0002 is shown. L-arabinose consumption started after glucose depletion. Within 70 hours, both the glucose and L-arabinose were completely consumed. The ethanol yield from the total of sugars was 0.42±0.003 g g−1.
In FIG. 5C, the fermentation profile of a mixture of 30 gl−1 glucose, 15 gl−1 D-xylose, and 15 gl−1 L-arabinose by strain IMS0002 is shown. Arabinose consumption started after glucose depletion. Within 80 hours, both the glucose and arabinose were completely consumed. Only 20 mM from 100 mM of xylose was consumed by strain IMS0002. In addition, the formation of 20 mM of xylitol was observed. Apparently, the xylose was converted into xylitol by strain IMS0002. Hence, the ethanol yield from the total of sugars was lower than for the above described fermentations: 0.38±0.001 g g−1. The ethanol yield from the total of glucose and arabinose was similar to the other fermentations: 0.43±0.001 g g−1.
Table 1 shows the arabinose consumption rates and the ethanol production rates observed for the anaerobic batch fermentation of strain IMS0002. Arabinose was consumed with a rate of 0.23-0.75 g h−1 g−1 biomass dry weight. The rate of ethanol produced from arabinose varied from 0.08-0.31 g h−1 g−1 biomass dry weight.
Initially, the constructed strain IMS0001 was able to ferment xylose (data not shown). In contrast to our expectations, the selected strain IMS0002 was not capable of fermenting xylose to ethanol (FIG. 5C). To regain the capability of fermenting xylose, a colony of strain IMS0002 was transferred to solid synthetic medium with 2% of D-xylose, and incubated in an anaerobic jar at 30° C. for 25 days. Subsequently, a colony was again transferred to solid synthetic medium with 2% of arabinose. After 4 days of incubation at 30° C., a colony was transferred to a shake flask containing synthetic medium with 2% arabinose. After incubation at 30° C. for 6 days, 30% of glycerol was added, samples were taken and stored at −80° C. A shake flask containing 100 ml of synthetic medium with 2% arabinose was inoculated with such a frozen stock, and was used as preculture for an anaerobic batch fermentation on synthetic medium with 20 gl−1 xylose and 20 gl1 arabinose. In FIG. 6, the fermentation profile of this batch fermentation is shown. Xylose and arabinose were consumed simultaneously. The arabinose was completed within 70 hours, whereas the xylose was completely consumed in 120 hours. At least 250 mM of ethanol was produced from the total of sugars, not taking into account the evaporation of the ethanol. Assuming an end biomass dry weight of 3.2 gl−1 (assuming a biomass yield of 0.08 g g−1 sugar), the end ethanol concentration estimated from the cumulative CO2 production (355 mmol l−1) was approximately 330 mmol l−1, corresponding to a ethanol yield of 0.41 g g−1 pentose sugar. In addition to ethanol, glycerol, and organic acids, a small amount of xylitol was produced (approximately 5 mM).
Selection of Strain IMS0003
Initially, the constructed strain IMS0001 was able to ferment xylose (data not shown). In contrast to our expectations, the selected strain IMS0002 was not capable of fermenting xylose to ethanol (FIG. 5C). To regain the capability of fermenting xylose, a colony of strain IMS0002 was transferred to solid synthetic medium with 2% of D-xylose, and incubated in an anaerobic jar at 30° C. for 25 days. Subsequently, a colony was again transferred to solid synthetic medium with 2% of arabinose. After 4 days of incubation at 30° C., a colony was transferred to a shake flask containing synthetic medium with 2% arabinose. After incubation at 30° C. for 6 days, 30% of glycerol was added, samples were taken and stored at −80° C.
From this frozen stock, samples were spread on solid synthetic medium with 2% of L-arabinose and incubated at 30° C. for several days. Separate colonies were re-streaked twice on solid synthetic medium with L-arabinose. Finally, a shake flask containing synthetic medium with 2% of L-arabinose was inoculated with a single colony, and incubated for 4 days at 30° C. This culture was designated as strain IMS0003 (CBS 121879 deposited at the CBS on Sep. 20, 2007). Culture samples were taken, 30% of glycerol was added and samples were stored at −80° C.
Characterization of Strain IMS0003
Growth and product formation of strain IMS0003 was determined during an anaerobic batch fermentation on synthetic medium with a mixture of 30 gl−1 glucose, 15 gl−1 D-xylose and 15 gl−1 L-arabinose. The pre-culture for this anaerobic batch fermentation was prepared in a shake flasks containing 100 ml of synthetic medium with 2% L-arabinose, by inoculating with a −80° C. frozen stock of strain IMS0003, and incubated for 48 hours at 30° C.
In FIG. 7, the fermentation profile of a mixture of 30 gl−1 glucose, 15 gl−1 D-xylose, and 15 gl−1 L-arabinose by strain IMS0003 is shown. Arabinose consumption started after glucose depletion. Within 70 hours, the glucose, xylose and arabinose were completely consumed. Xylose and arabinose were consumed simultaneously. At least 406 mM of ethanol was produced from the total of sugars, not taking into account the evaporation of the ethanol. The final ethanol concentration calculated from the cumulative CO2 production was 572 mmol l−1, corresponding to an ethanol yield of 0.46 g g−1 of total sugar. In contrast to the fermentation of a mixture of glucose, xylose and arabinose by strain IMS0002 (FIG. 5C) or a mixed culture of strains IMS0002 and RWB218 (FIG. 5D), strain IMS0003 did not produce detectable amounts of xylitol.
Tables







TABLE 1







S. cerevisiae strains used.









Strain
Characteristics
Reference





RWB217
MATA ura3-52 leu2-112 loxP-PTPI::(−266, −1)TAL1 gre3::hphMXpUGPTPI-
Kuyper et al. 2005a



TKL1 pUGPTPI-RPE1 KanloxP-PTPI::(−?, −1)RKI1 {p415ADHXKS,



pAKX002}


RWB218
MATA ura3-52 leu2-112 loxP-PTPI::(−266, −1)TAL1 gre3::hphMXpUGPTPI-
Kuyper et al. 2005b



TKL1 pUGPTPI-RPE1 KanloxP-PTPI::(−?, −1)RKI1 {p415ADHXKS1,



pAKX002}


RWB219
MATA ura3-52 leu2-112 loxP-PTPI::(−266, −1)TAL1 gre3::hphMXpUGPTPI-
This work



TKL1 pUGPTPI-RPE1 KanloxP-PTPI::(−?, −1)RKI1 {p415ADHXKS1,



pAKX002}


RWB220
MATA ura3-52 leu2-112 loxP-PTPI::(−266, −1)TAL1 gre3::hphMXpUGPTPI-
This work



TKL1 pUGPTPI-RPE1 loxP-PTPI::(−?, −1)RKI1


IMS0001
MATA ura3-52 leu2-112 loxP-PTPI::(−266, −1)TAL1 gre3::hphMXpUGPTPI-
This work



TKL1 pUGPTPI-RPE1 loxP-PTPI::(−?, −1)RKI1 {pRW231, PRW243}


IMS0002
MATA ura3-52 leu2-112 loxP-PTPI::(−266, −1)TAL1 gre3::hphMXpUGPTPI-
This work



TKL1 pUGPTPI-RPE1 loxP-PTPI::(−?, −1)RKI1 {pRW231, PRW243} selected



for anaerobic growth on L-arabinose
















TABLE 2







Plasmids used









plasmid
characteristics
Reference





pRS305
Integration, LEU2
Gietz and




Sugino, 1988


pAKX002
2μ, URA3, PTPI1-Piromyces xylA
Kuyper et al.




2003


p415ADHXKS1
CEN, LEU2, PADH1-S.cerXKS1
Kuyper et al.,




2005a


pRW229
integration, LEU2, PADH1-S.cerXKS1
This work


pRW230
pAKX002 with PTDH3-AraA
This work


pRW231
pAKX002 with PTDH3-AraA
This work



and PHXT7-AraD


pRW243
LEU2, integration,
This work



PADH1-ScXKS1-TCYC,



PPGI1-L. plantarumAraB-TADH1
















TABLE 3







oligos used in this work








Oligo
DNA sequence










AraA expression cassette








SpeI5′Ptdh3
5′GACTAGTCGAGTTTATCATTATCAATACTGC3′


SEQ ID NO: 31



5′AraAPtdh
5′CTCATAATCAGGTACTGATAACATTTTGTTTGTTTATGTGTGTTTATTC3′


SEQ ID NO: 32



Ptdh5′AraA
5′GAATAAACACACATAAACAAACAAAATGTTATCAGTACCTGATTATGAG3


SEQ ID NO: 33



Tadh3′AraA
5′AATCATAAATCATAAGAAATTCGCTTACTTTAAGAATGCCTTAGTCAT3′


SEQ ID NO: 34



3′AraATadh1
5′ATGACTAAGGCATTCTTAAAGTAAGCGAATTTCTTATGATTTATGATT3′


SEQ ID NO: 35



3′Tadh1SpeI
5′CACTAGTCTCGAGTGTGGAAGAACGATTACAACAGG3′


SEQ ID NO: 36



 







AraB expression cassette








SacIS′Ppgi1
5′CGAGCTCGTGGGTGTATTGGATTATAGGAAG3′


SEQ ID NO: 37



5′AraBPpgi1
5′TTGGGCTGTTTCAACTAAATTCATTTTTAGGCTGGTATCTTGATTCTA3′


SEQ ID NO: 38



Ppgi5′AraB
5′TAGAATCAAGATACCAGCCTAAAAATGAATTTAGTTGAAACAGCCCAA3′


SEQ ID NO: 39



Tadh3′AraB
5′AATCATAAATCATAAGAAATTCGCTCTAATATTTGATTGCTTGCCCAG3′


SEQ ID NO: 40



3′AraBTadh1
5′CTGGGCAAGCAATCAAATATTAGAGCGAATTTCTTATGATTTATGATT3′


SEQ ID NO: 41



3′Tadh1SacI
5′TGAGCTCGTGTGGAAGAACGATTACAACAGG3′


SEQ ID NO: 42



 







AraD expression cassette








SalI5′Phxt7
5′ACGCGTCGACTCGTAGGAACAATTTCGG3′


SEQ ID NO: 43



5′AraDPhxt
5′CTTCTTGTTTTAATGCTTCTAGCATTTTTTGATTAAAATTAAAAAAACTT3′


SEQ ID NO: 44



Phxt5′AraD
5′AAGTTTTTTTAATTTTAATCAAAAAATGCTAGAAGCATTAAAACAAGAAG3′


SEQ ID NO: 45



Tpgi3′AraD
5′GGTATATATTTAAGAGCGATTTGTTTACTTGCGAACTGCATGATCC3′


SEQ ID NO: 46



3′AraDTpgi
5′GGATCATGCAGTTCGCAAGTAAACAAATCGCTCTTAAATATATACC3′


SEQ ID NO: 47



3′TpgiSalI
5′CGCAGTCGACCTTTTAAACAGTTGATGAGAACC3′


SEQ ID NO: 48
















TABLE 4







Maximum observed specific glucose and arabinose consumption


rates and ethanol production rates during anaerobic batch


fermentations of S. cerevisiae IMS0002.












qglu
qara
qeth,glu
qeth,ara


C-source
g h−1 g−1 DW
g h−1 g−1 DW
g h−1 g−1 DW
g h−1 g−1 DW





20 g l−1
—
0.75 ± 0.04
—
0.31 ± 0.02


arabinose


20 g l−1
2.08 ± 0.09
0.41 ± 0.01
0.69 ± 0.00
0.19 ± 0.00


glucose


20 g l−1


arabinose


30 g l−1
1.84 ± 0.04
0.23 ± 0.01
0.64 ± 0.03
0.08 ± 0.01


glucose


15 g l−1


xylose


15 g l−1


arabinose





qglu: specific glucose consumption rate


qara: specific arabinose consumption rate


qeth,glu: specific ethanol production rate during growth on glucose


qeth,ara: specific ethanol production rate during growth on arabinose






REFERENCE LIST


    Andreasen A A, Stier T J (1954) Anaerobic nutrition of Saccharomyces cerevisiae. II. Unsaturated fatty acid requirement for growth in a defined medium. J Cell Physiol 43:271-281
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    Becker J, Boles E (2003) A modified Saccharomyces cerevisiae strain that consumes L-Arabinose and produces ethanol. Appl Environ Microbiol 69:4144-4150
    Gietz R. D., Sugino A. (1988). New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene 74:527-534.
    Gietz, R. D., and R. A. Woods. 2002. Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol. 350:87-96.
    Guldener U, Heck S, Fielder T, Beinhauer J, Hegemann J H. (1996) A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res. 1996 Jul. 1; 24(13):2519-24.
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    Inoue H., H. Nojima and H. Okayama, High efficiency transformation of Escherichia coli with plasmids. Gene 96 (1990), pp. 23-28
    Kuyper M, Hartog M M P, Toirkens M J, Almering M J H, Winkler A A, Van Dijken J P, Pronk J T (2005a) Metabolic engineering of a xylose-isomerase-expressing Saccharomyces cerevisiae strain for rapid anaerobic xylose fermentation. Fems Yeast Research 5:399-409
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## Claims

1. A eukaryotic cell capable of expressing the following nucleotide sequences, wherein the expression of these nucleotide sequences confers on the cell the ability to use L-arabinose and/or to convert L-arabinose into L-ribulose, and/or xylulose 5-phosphate and/or into a desired fermentation product:
(a) a nucleotide sequence encoding an arabinose isomerase (araA), wherein said nucleotide sequence is selected from the group consisting of:
i. nucleotide sequences encoding an araA, said araA comprising an amino acid sequence that has at least 90% sequence identity with the amino acid sequence of SEQ ID NO:1,
ii. nucleotide sequences comprising a nucleotide sequence that has at least 90% sequence identity with the nucleotide sequence of SEQ ID NO:2,
iii. nucleotide sequences the complementary strand of which hybridizes to a nucleic acid molecule of sequence of (i) or (ii) under moderate conditions;

(b) a nucleotide sequence encoding a L-ribulokinase (araB), wherein said nucleotide sequence is selected from the group consisting of:
i. nucleotide sequences encoding an araB, said araB comprising an amino acid sequence that has at least 90% sequence identity with the amino acid sequence of SEQ ID NO:3,
ii. nucleotide sequences comprising a nucleotide sequence that has at least 90% sequence identity with the nucleotide sequence of SEQ ID NO:4,
iii. nucleotide sequences the complementary strand of which hybridizes to a nucleic acid molecule of sequence of (i) or (ii) under moderate conditions;

(c) a nucleotide sequence encoding an L-ribulose-5-P-4-epimerase (araD), wherein said nucleotide sequence is selected from the group consisting of:
i. nucleotide sequences encoding an araD, said araD comprising an amino acid sequence that has at least 90% sequence identity with the amino acid sequence of SEQ ID NO:5,
ii. nucleotide sequences comprising a nucleotide sequence that has at least 90% sequence identity with the nucleotide sequence of SEQ ID NO:6,
iii. nucleotide sequences the complementary strand of which hybridizes to a nucleic acid molecule of sequence of (i) or (ii) under moderate conditions;

wherein moderate conditions is defined as conditions that allow a nucleic acid sequences of at least 50 nucleotides to hybridize at a temperature of about 45° C. in a solution comprising about 1 M salt and washing at room temperature in a solution comprising about 1 M salt.

2. A cell according to claim 1, wherein one, two or three of the araA, araB and araD nucleotide sequences originate from a Lactobacillus genus, optionally a Lactobacillus plantarum species.

3. A cell according to claim 1, wherein the cell is a yeast cell, optionally belonging to one of the genera: Saccharomyces, Kluyveromyces, Candida, Pichia, Schizosaccharomyces, Hansenula, Kloeckera, Schwanniomyces or Yarrowia.

4. A cell according to claim 3, wherein the yeast cell belongs to one of the species: S. cerevisiae, S. bulderi, S. barnetti, S. exiguus, S. uvarum, S. diastaticus, K. lactis, K. marxianus or K. fragilis.

5. A cell according to claim 1, wherein the nucleotide sequences encoding the araA, araB and/or araD are operably linked to a promoter that causes sufficient expression of the corresponding nucleotide sequences in the cell to confer to the cell the ability to use L-arabinose and/or to convert L-arabinose into L-ribulose, and/or xylulose 5-phosphate and/or into a desired fermentation product.

6. A cell according to claim 1, wherein the cell exhibits the ability to directly isomerise xylose into xylulose.

7. A cell according to claim 6, wherein the cell comprises a genetic modification that increases the flux of the pentose phosphate pathway.

8. A cell according to claim 6, wherein the genetic modification comprises overexpression of at least one gene of the non-oxidative part of the pentose phosphate pathway.

9. A cell according to claim 8, wherein the gene is selected from the group consisting of the genes encoding ribulose-5-phosphate isomerase, ribulose-5-phosphate epimerase, transketolase and transaldolase.

10. A cell according to claim 8, wherein the genetic modification comprises overexpression of at least the genes coding for a transketolase and a transaldolase.

11. A cell according to claim 8, wherein the cell further comprises a genetic modification that increases the specific xylulose kinase activity.

12. A cell according to claim 11, wherein the genetic modification comprises overexpression of a gene encoding a xylulose kinase.

13. A cell according to claim 8, wherein the gene that is overexpressed is endogenous to the cell.

14. A cell according to claim 5, wherein the cell comprises a genetic modification that reduces unspecific aldose reductase activity in the cell.

15. A cell according to claim 14, wherein the genetic modification reduces the expression of, or inactivates a gene encoding an unspecific aldose reductase.

16. A cell according to claim 15, wherein the gene is inactivated by deletion of at least part of the gene or by disruption of the gene.

17. A cell according to claim 14, wherein the expression of each gene in the cell that encodes an unspecific aldose reductase is reduced or inactivated.

18. A cell according to claim 1, wherein the fermentation product is selected from the group consisting of ethanol, 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, butanol, a β-lactam antibiotic and a cephalosporin.

19. A nucleic acid construct comprising a nucleic acid sequence encoding an araA, a nucleic acid sequence encoding an araB and/or a nucleic acid sequence encoding an araD all as defined in claim 1.

20. A process for producing a fermentation product selected from the group consisting of ethanol, 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, butanol, a β-lactam antibiotic and a cephalosporin, whereby the process comprises:
(a) fermenting a medium containing a source of arabinose and optionally xylose with a modified cell as defined in claim 1, whereby the cell ferments arabinose and optionally xylose to the fermentation product; and optionally,
(b) recovering the fermentation product.

21. A process for producing a fermentation product selected from the group consisting of ethanol, 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, butanol, a β-lactam antibiotic and a cephalosporin, wherein the process comprises:
(a) fermenting a medium containing at least a source of L-arabinose and a source of xylose with a cell as defined in claim 1 and a cell able to use xylose and/or exhibiting the ability to directly isomerise xylose into xylulose, whereby each cell ferments L-arabinose and/or xylose to the fermentation product; and optionally,
(b) recovering the fermentation product.

22. A process according to claim 20, wherein the medium also contains a source of glucose.

23. A process according to claim 20, wherein the fermentation product is ethanol.

24. A process according to claim 23, wherein the volumetric ethanol productivity is at least 0.5 g ethanol per liter per hour.

25. A process according to claim 23, wherein the ethanol yield is at least 30%.

26. A process according to claim 20, wherein the process is anaerobic.

27. A process according to claim 20, wherein the process is aerobic, preferably performed under oxygen limited conditions.