# Patent

## Title
L-arabinose fermenting yeast

## Abstract

An L-arabinose utilizing yeast strain is provided for the production of ethanol by introducing and expressing bacterial araA, araB and araD genes. L-arabinose transporters are also introduced into the yeast to enhance the uptake of arabinose. The yeast carries additional genomic mutations enabling it to consume L-arabinose, even as the only carbon source, and to produce ethanol. Methods of producing ethanol include utilizing these modified yeast strains.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a national stage entry of International Application No. PCT/US07/64330, filed Mar. 19, 2007, which claims priority to U.S. Provisional Application No. 60/810,562, filed Jun. 1, 2006. The contents of each application listed above are incorporated by reference in their entirety.


CONTRACTUAL ORIGIN
The United States Government has rights in this invention under Contract No. DE-AC36-99GO10337 between the United States Department of Energy and the National Renewable Energy Laboratory, a Division of the Midwest Research Institute.


BACKGROUND
Fuel ethanol is a suitable alternative to fossil fuels. Ethanol may be produced from plant biomass, which is an economical and renewable resource that is available in large amounts. Examples of biomass include agricultural feedstocks, paper wastes, wood chips and so on. The sources of biomass vary from region to region based on the abundance of natural or agricultural biomass that is available in a particular region. For example, while sugar cane is the primary source of biomass used to produce ethanol in Brazil, corn-derived biomass, corn starch is a large source of biomass to produce ethanol in the United States. Other agricultural feedstocks include, by way of example: straw; grasses such as switchgrass; grains; and any other lignocellulosic or starch-bearing material.
A typical biomass substrate contains from 35-45% cellulose, 25-40% hemicellulose, and 15-30% lignin, although sources may be found that deviate from these general ranges. As is known in the art, cellulose is a polymer of glucose subunits, and hemicellulose contains mostly xylose. Arabinose is also a significant fermentable substrate that is found in biomass, such as corn fiber and many herbaceous crops in varying amounts. Other researchers have investigated the utilization of arabinose and hemicellulose, as reported by Hespell, R. B. 1998. Extraction and characterization of hemicellulose from the corn fiber produced by corn wet-milling processes. J. Agric. Food Chem. 46:2615-2619, and McMillan, J. D., and B. L. Boynton. 1994. Arabinose utilization by xylose-fermenting yeasts and fungi. Appl. Biochem. Biotechnol. 45-46:569-584. The two most abundant types of pentose that exist naturally are D-xylose and L-arabinose.
It is problematic that most of the naturally available ethanol-producing microorganisms are only capable of utilizing hexose sugar, such as glucose. This is confirmed by a review of the art, such as is reported by Barnett, J. A. 1976. The utilization of sugars by yeasts. Adv. Carbohydr. Chem. Biochem. 32:125-234. Many types of yeast, especially Saccharomyces cerevisiae and related species, are very effective in fermenting glucose-based feedstocks into ethanol through anaerobic fermentation. However, these glucose-fermenting yeasts are unable to ferment xylose or L-arabinose, and are unable to grow solely on these pentose sugars. Although other yeast species, such as Pichia stipitis and Candida shehatae, can ferment xylose to ethanol, they are not as effective as Saccharomyces for fermentation of glucose and have a relatively low level of ethanol tolerance. Thus, the present range of available yeast are not entirely suitable for large scale industrial production of ethanol from biomass.
Most bacteria, including E. coli and Bacillus subtilis, utilize L-arabinose for aerobic growth, but they do not ferment L-arabinose to ethanol. These and other microorganisms, such as Zymomonas mobilis, have also been genetically modified to produce ethanol from hexose or pentose. This has been reported, for example, in Deanda, K., M. Zhang, C. Eddy, and S. Picataggio. 1996, Development of an arabinose-fermenting Zymomonas mobilis strain by metabolic pathway engineering. Appl. Environ. Microbiol. 62:4465-4470; and Zhang, M., C. Eddy, K. Deanda, M. Finkelstein, and S. Picataggio. 1995 Metabolic engineering of a pentose metabolism pathway in ethanologenic Zymomonas mobilis. Science 267:240-243. However, it remains the case that the low alcohol tolerance of these non-yeast microorganisms limits their utility in the ethanol industry.
Much effort has been made over the last decade or so, without truly overcoming the problem of developing new strains that ferment xylose to generate ethanol. Such efforts are reported, for example, in Kotter, P., R. Amore, C. P. Hollenberg, and M. Ciriacy. 1990. Isolation and characterization of the Pichia stipitis xylitol dehydrogenase gene, XYL2, and construction of a xylose-utilizing Saccharomyces cerevisiae transformant. Curr. Genet. 18:493-500; and Wahlbom, C. F., and B. Hahn-Hagerdal. 2002 Recent studies have been conducted on yeast strains that potentially ferment arabinose. Sedlak, M., and N. W. Ho. 2001. Expression of E. coli araBAD operon encoding enzymes for metabolizing L-arabinose in Saccharomyces cerevisiae, Enzyme Microb. Technol. 28:16-24 discloses the expression of an E. coli araBAD operon encoding enzymes for metabolizing L-arabinose in Saccharomyces cerevisiae. Although this strain expresses araA, araB and araD proteins, it is incapable of producing ethanol.
U.S. patent application Ser. No. 10/983,951 by Boles and Becker discloses the creation of a yeast strain that may ferment L-arabinose. However, the overall yield is relatively low, at about 60% of theoretical value. The rate of arabinose transport into S. cerevisiae may be a limiting factor for complete utilization of the pentose substrate. Boles and Becker attempted to enhance arabinose uptake by overexpressing the GAL2-encoded galactose permease in S. cerevisiae. However, the rate of arabinose transport using galactose permease was still much lower when compared to that exhibited by non-conventional yeast such as Kluyveromyces marxianus. Another limitation that may have contributed to the low yield of ethanol in the modified strain of Becker and Boles is the poor activity of the L-arabinose isomerase encoded by the bacterial araA gene. Although Becker and Boles used an araA gene from B. subtilis instead of one from E. coli, the specific activity of the enzyme was still low. Other workers in the field have reported that low isomerase activity is a bottleneck in L-arabinose utilization by yeast.
There remains a need for new arabinose-fermenting strains that are capable of producing ethanol at high yield. There is further a need to identify novel arabinose transporters for introduction into Saccharomyces cerevisiae to boost the production of ethanol from arabinose.
The foregoing examples of the related art and limitations related therewith are intended to be illustrative and not exclusive. Other limitations of the related art will become apparent to those of skill in the art upon a reading of the specification and a study of the drawings.
SUMMARY
The following embodiments and aspects thereof are described and illustrated in conjunction with systems, tools and methods which are meant to be exemplary and illustrative, not limiting in scope. In various embodiments, one or more of the above-described problems have been reduced or eliminated, while other embodiments are directed to other improvements.
The presently disclosed instrumentalities overcome some of the problems outlined above and advance the art by providing new yeast strains that are capable of using L-arabinose to produce ethanol at a relatively high yield. Since the yeast galactose permease may facilitate uptake of arabinose, any Gal+ strain possessing endogenous galactose permease activity may be used as described below. Although S. cerevisiae is used by way of example, the scope of coverage extends to any organisms possessing endogenous pathways to generate ethanol from arabinose and to organisms into which components of such arabinose metabolic pathways or arabinose transporters may be introduced. The use of S. cerevisiae is preferred.
In a brief overview of the recombinant technique, the endogenous yeast aldose reductase (AR) gene is disrupted by replacing the AR coding sequence with the yeast LEU2 gene. Because the yeast aldose reductase is the first enzyme to metabolize arabinose in yeast, an AR− strain is used to reduce diversion of arabinose to unwanted byproducts and to prevent possible inhibition of the isomerase by arabitol. The bacterial araA, araB, and araD genes are cloned into appropriate yeast expression vectors. The expression constructs containing all three ara genes are introduced in the AR− strain and the transformants were capable of making ethanol from L-arabinose.
In another aspect of this disclosure, two novel arabinose transporter genes, termed KmLAT1 and PgLAT2, have been cloned and characterized from two non-conventional yeast species, Kluyveromyces marxianus and Pichia guilliermondii (also known as Candida guilliermondii), respectively. Both Kluyveromyces marxianus and Pichia guilliermondii are efficient utilizers of L-arabinose, which renders them ideal sources for cloning L-arabinose transporter genes.
The KmLAT1 gene may be isolated using functional complementation of an adapted S. cerevisiae strain that could not grow on L-arabinose because it lacked sufficient L-arabinose transport activity. KmLat1 protein has a predicted length of 556 amino acids encoded by a single ORF of 1668 bp. It is a transmembrane protein having high homology to sugar transporters of many different yeast species. When KmLat1 is expressed in S. cerevisiae, transport assays using labeled L-arabinose show that this transporter has the kinetic characteristics of a low affinity arabinose transporter, with Km=230 mM and Vmax=55 nmol/mg·min. Transport of L-arabinose by KmLat1 is not significantly inhibited by common uncoupling agents but is out-competed by glucose, galactose, xylose, and maltose.
The PgLAT2 gene may be isolated using the technique of differential display from Pichia guilliermondii. The PgLAT2 gene has an ORF of 1617 nucleotides encoding a protein with a predicted length of 539 amino acids. When PgLAT2 is expressed in S. cerevisiae, transport assays show that this transporter has almost identical L-arabinose transport kinetics as that of wildtype Pichia guilliermondii. The PgLat2 transporter when expressed in S. cerevisiae has a K of 0.07 mM and Vmax of 18 nmol/mg·min for L-arabinose transport. Inhibition experiments show significant inhibition of the PgLat2 transporter by protonophores (e.g., NaN3, DNP, and CCP) and H+-adenosine triphosphatase (ATPase) inhibitors (e.g., DESB and DCCD) similar to inhibition in wildtype P. guilliermondii. Competition experiments show that L-arabinose uptake by the PgLat2 transporter is inhibited by glucose, galactose, xylose and to a lesser extent by maltose.
The transport kinetics of S. cerevisiae Gal2p have been measured and compared to those of KmLat1. The S. cerevisiae GAL2 gene (SEQ ID NO 5) under control of a TDH3 promoter exhibits 28 times greater (8.9 nmol/mg·min) L-arabinose transport rate as compared to GAL2 gene under control of a ADH1 promoter. The GAL2-encoded permease (SEQ ID NO 6) shows a K of 550 mM and a Vmax of 425 nmol/mg·min for L-arabinose transport and a Km of 25 mM and a Vmax of 76 nmol/mg·min for galactose transport. Although L-arabinose transport by both KmLAT1 and GAL2 encoded permeases is out-competed by glucose or galactose, the inhibitory effects of glucose or galactose are greater on the GAL2 encoded permease than on the KmLAT1 encoded transporter.
It is further disclosed here that a S. cerevisiae strain may be transformed with different combinations of the KmLAT1 and PgLAT2 transporter genes and a plasmid carrying the GAL2 gene native to S. cerevisiae. The doubling time for the PgLat2p and Gal2p co-expressing cells grown on L-arabinose is markedly shorter than that of the cells expressing only Gal2p, suggesting that L-arabinose uptake may have been enhanced in these cells. In addition, the PgLat2p and Gal2p co-expressing cells appear to grow to a higher optical density at saturation, suggesting that this strain may be able to utilize the L-arabinose in the medium more completely. This conclusion is supported by HPLC analysis which shows significantly less residual L-arabinose in the culture of cells expressing PgLat2p and Gal2p.
In one embodiment, the transformed strains that carry the new transporter genes may be further transformed with plasmids carrying three bacterial genes, araA, araB and araC, which encode proteins that may be utilized for arabinose utilization and fermentation. In another embodiment, the bacterial genes, araA, araB and araC, may be transformed into a yeast strain that does not carry any of the new transporter genes.
In addition to the exemplary aspects and embodiments described above, further aspects and embodiments will become apparent by reference to the drawings and by study of the following descriptions.



BRIEF DESCRIPTION OF THE DRAWINGS
Exemplary embodiments are illustrated in referenced figures of the drawings. It is intended that the embodiments and figures disclosed herein are to be considered illustrative rather than limiting.
FIG. 1 shows the relationship between KmLAT1 and other transporters based on the neighbor-joining method (Saitou and Nei 1987).
FIG. 2 shows the DNA (SEQ ID NO. 1) sequence of Kluyveromyces marxianus KmLAT1, and the predicted protein sequence (SEQ ID NO. 2).
FIG. 3 is a schematic presentation of the arabinose metabolic pathway in recombinant yeast containing proteins encoded by three bacterial genes araB, araA, and araD.
FIG. 4 shows the library insert from genomic K. marxianus DNA complements adapted S. cerevisiae for growth on L-arabinose. Cloning into the library expression vector is at the indicated BamHI restriction sites. The black block arrow is the L-arabinose transporter ORF responsible for complementation (KmLAT1). The block arrow with vertical stripes is the interrupted transporter ORF. The block arrow with the horizontal stripes is an un-related ORF ligated in place gratuitously during library construction. The Sau3A1 restriction site where the transporter ORF was interrupted is shown. The primer used for PCR based genomic walking in K. marxianus is shown.
FIG. 5 shows the growth curve of S. cerevisiae expressing KmLAT1 (Δ), GAL2 (▪) or a control vector (♦) on 2% L-arabinose.
FIG. 6. (A): Eadie-Hofstee plot of L-arabinose uptake by KmLat1 (♦) or Gal2 (▪) expressed in S. cerevisiae grown on 2% L-arabinose. (B): Comparison of Eadie-Hofstee plots of KmLat1 expressed in S. cerevisiae (♦) and wild type transport; activity of K. marxianus (Δ) both grown on 2% L-arabinose.
FIG. 7 shows the DNA (SEQ ID NO, 3) sequence of Pichia guilliermondii PgLAT1, and the predicted protein sequence (SEQ ID NO. 4).
FIG. 8 shows the induction of L-arabinose transport in P. guilliermondii. Uptake of 13 mM labeled sugar was assayed for cells grown in minimal media containing 2% L-arabinose, D-galactose or D-xylose. White bars indicate labeled L-arabinose transport. Black bars indicate labeled galactose transport. Bars with vertical stripes indicate labeled xylose transport.
FIG. 9 shows the sugar transport competition analysis in P. guilliermondii grown in minimal L-arabinose medium.
FIG. 10 shows the transport kinetics of L-arabinose by the PgLAT2 transporter expressed in S. cerevisiae. Open triangles indicate transport for wild type. P. guilliermondii grown on L-arabinose. Black, diamonds indicate transport for PgLAT2 expressed in S. cerevisiae grown on L-arabinose.
FIG. 11 shows comparison of the growth curves in 0.2% L-arabinose for S. cerevisiae cells expressing either Gal2p alone or both Gal2p and PgLat2. The maximum growth density and growth rate are significantly enhanced in the strain expressing both Gal2p and PgLat2.
FIG. 12 shows the growth curves of BFY001 (parent) (black square) and BFY002 (ΔAR) (black triangle) on glucose and xylulose.
FIG. 13 shows the diagrams of the expression plasmids with araB, araA, and araD genes carrying the His3 selectable marker.
FIG. 14 shows the diagrams of the expression plasmids with araB, araA, and araD genes carrying the Ura3 selectable marker.
FIG. 15 shows histogram with the result of ethanol production in whole-cell fermentation using yeast cells expressing the three bacterial genes araB, araA, and araD.
FIG. 16 shows histogram with the result of ethanol production in cell-free fermentation using yeast cells expressing the three bacterial genes araB, araA, and araD.
FIG. 17 plots ethanol production using yeast cells expressing the three bacterial genes araB, araA, and araD, as a function of the incubation time in a cell-free fermentation system.
FIG. 18 shows histogram with the result of ethanol production in cell-free fermentation using yeast cells expressing the three bacterial genes araB, araA, and araD.
FIG. 19 plots ethanol production using yeast cells expressing the three bacterial genes araB, araA, and araD, under single- and mixed-sugar fermentations.



DETAILED DESCRIPTION
There will now be shown and described methods for producing transgenic yeast that are capable of metabolizing arabinose and producing ethanol. In the discussion below, parenthetical mention is made to publications from the references section for a discussion of related procedures that may be found useful from a perspective of one skilled in the art. This is done to demonstrate what is disclosed by way of nonlimiting example.
The following definitions are provided to facilitate understanding, of certain terms used frequently herein and are not meant to limit, the scope of the present disclosure:
“Amino acid” refers to any of the twenty naturally occurring amino acids as well as any modified amino acid sequences. Modifications may include natural processes such as posttranslational processing, or may include chemical modifications which are known in the art. Modifications include but are not limited to: phosphorylation, ubiquitination, acetylation, amidation, glycosylation, covalent attachment of flavin, ADP-ribosylation, cross linking, iodination, methylation, and the like.
“Antibody” refers to a generally Y-shaped molecule having a pair of antigen binding sites, a hinge region and a constant region. Fragments of antibodies, for example an antigen binding fragment (Fab), chimeric antibodies, antibodies having a human constant region coupled to a murine antigen binding region, and fragments thereof, as well as other well known recombinant antibodies are included in this definition.
“Antisense” refers to polynucleotide sequences that are complementary to target “sense” polynucleotide sequence.
“Biomass” refers collectively to organic non-fossil material, “Biomass” in the present disclosure refers particularly to plant material that is used to generate fuel, such as ethanol. Examples of biomass includes but are not limited to corn fiber, dried distiller's grain, jatropha, manure, meat and bone meal, miscanthus, peat, plate waste, landscaping waste, maize, rice hulls, silage, stover, maiden grass, switchgrass, whey, and bagasse from sugarcane.
“Complementary” or “complementarity” refers to the ability of a polynucleotide in a polynucleotide molecule to form a base pair with another polynucleotide in a second polynucleotide molecule. For example, the sequence A-G-T is complementary to the sequence T-C-A. Complementarity may be partial, in which only some of the polynucleotides match according to base pairing, or complete, where all the polynucleotides match according to base pairing.
The term “derivative” refers to compounds that are derived from, a predecessor compound by way of chemical or physical modification. For example, a compound is a sugar derivatives if it is formed by oxidization of one or more terminal groups to carboxylic acids, by reduction of a carbonyl group, by substitution of hydrogen(s), amino group(s), thiol group(s), etc, for one or more hydroxyl groups on a sugar, or if it is formed by phosphorylation on a sugar molecule.
“Expression” refers to transcription and translation occurring within a host cell. The level of expression, of a DNA molecule in a host cell may be determined on the basis of either the amount of corresponding mRNA that is present within the cell or the amount of DNA molecule encoded protein produced by the host cell (Sambrook et al., 1989, Molecular cloning: A laboratory Manual, 18.1-18.88).
“Fusion protein” refers to a first protein attached to a second, heterologous protein. Preferably, the heterologous protein is fused via recombinant DNA techniques, such that the first and second proteins are expressed in frame. The heterologous protein may confer a desired characteristic to the fusion protein, for example, a detection signal, enhanced stability or stabilization of the protein, facilitated oligomerization of the protein, or facilitated purification of the fusion, protein. Examples of heterologous proteins useful as fusion proteins include molecules having full-length or partial protein sequence of KmLat1 or PgLat2. Further examples include peptide tags such as histidine tag (6-His), leucine zipper, substrate targeting moieties, signal peptides, and the like. Fusion proteins are also meant to encompass variants and derivatives of KmLat1 or PgLat2 polypeptides that are generated by conventional site-directed mutagenesis and more modern techniques such as directed evolution, discussed infra.
“Genetically engineered” refers to any recombinant DNA or RNA method used to create a prokaryotic or eukaryotic host cell that, expresses a protein at elevated levels, at lowered levels, or in a mutated form; in other words, the host, cell has been transfected, transformed, or transduced with a recombinant polynucleotide molecule, and thereby been altered so as to cause the cell to alter expression of the desired protein. Methods and vectors for genetically engineering host cells are well known in the art; for example various techniques are illustrated in Current Protocols in Molecular Biology, Ausubel et al., eds. (Wiley & Sons, New York, 1988, and quarterly updates). Genetic engineering techniques include but are not limited to expression vectors, targeted homologous recombination and gene activation (see, for example, U.S. Pat. No. 5,272,071 to Chappel) and trans activation by engineered transcription factors (see, for example, Segal et al., 1999, Proc Natl Acad Sci USA 96(6):2758-63). Genetic engineering also encompasses any mutagenesis techniques wherein a cell is exposed to chemicals to induce errors in DNA replication or to accelerate gene recombination. The term “spontaneous mutation” refers to mutations that occurs at a much lower rate as a result of genetic recombination or DNA replication errors that occur naturally from generation to generation.
“Heterologous” refers to DNA, RNA and/or polypeptides derived from different organisms or species, for example a bacterial polypeptide is heterologous to yeast.
“Homology” refers to a degree of similarity between polynucleotides, having significant effect on the efficiency and strength of hybridization between polynucleotide molecules. The term also refers to a degree of similarity between polypeptides. Two polypeptides having greater than, or equal to about 60% similarity are presumptively homologous.
“Host,” “Host cell” or “host cells” refers to cells expressing a heterologous polynucleotide molecule. The term “heterologous” means non-native. For instance, when a gene that is not normally expressed in an organism is introduced and expressed in that host organism, such an expression is heterologous. Host cells of the present disclosure express polynucleotides encoding KmLAT1 or PgLAT2 or a fragment thereof. Examples of suitable host cells useful in the present disclosure include, but are not limited to, prokaryotic and eukaryotic cells. Specific examples of such cells include bacteria of the genera Escherichia, Bacillus, and Salmonella, as well as members of the genera Pseudomonas, Streptomyces, and Staphylococcus; fungi, particularly filamentous fungi such as Trichoderma and Aspergillus, Phanerochaete chrysosporium and other white rot fungi; also other fungi including Fusaria, molds, and yeast including Saccharomyces sp., Pichia sp., and Candida sp. and the like; plants e.g. Arabidopsis, cotton, barley, tobacco, potato, and aquatic plants and the like; SF9 insect cells (Summers and Smith, 1987, Texas Agriculture Experiment Station Bulletin, 1555), and the like. Other specific examples include mammalian cells such as human embryonic kidney cells (293 cells). Chinese hamster ovary (CHO) cells (Puck et al., 1958, Proc. Natl. Acad. Sci. USA 60, 1275-1281), human cervical carcinoma cells (HELA) (ATCC CCL 2), human liver cells (Hep G2) (ATCC HB8065), human breast cancer cells (MCF-7) (ATCC HTB22), human color carcinoma cells (DLD-1) (ATCC CCL, 221). Daudi cells (ATCC CRL-213), murine myeloma cells such as P3/NST/1-Ag4-1 (ATCC TIB-18), P3X63Ag8 (ATCC TIB-9), SP2/0-Ag14 (ATCC CRL-1581) and the like. The most preferred host is Saccharomyces  cerevisiae. 
“Hybridization” refers to the pairing of complementary polynucleotides during an annealing period. The strength of hybridization between two polynucleotide molecules is impacted by the homology between the two molecules, stringency of the conditions involved, the melting temperature of the formed hybrid and the G:C ratio within the polynucleotides.
“Identity” refers to a comparison of two different DNA or protein sequences by comparing pairs of nucleic acid or amino acids within the two sequences. Methods for determining sequence identity are known. See, for example, computer programs commonly employed for this purpose, such as the Gap program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, Madison Wis.), that uses the algorithm of Smith and Waterman, 1981, Adv. Appl. Math., 2: 482-489.
“Isolated” refers to a polynucleotide or polypeptide that has been separated from at least, one contaminant (polynucleotide or polypeptide) with which it is normally associated. For example, an isolated polynucleotide or polypeptide is in a context or in a form that is different from that in which it is found in nature.
“Nucleic acid sequence” refers to the order or sequence of deoxyribonucleotides along a strand of deoxyribonucleic acid. The order of these deoxyribonucleotides determines the order of amino acids along a polypeptide chain. The deoxyribonucleotide sequence thus codes for the amino acid sequence.
“Polynucleotide” refers to a linear sequence of nucleotides. The nucleotides may be ribonucleotides, or deoxyribonucleotides, or a mixture of both. Examples, of polynucleotides in this context include single and double stranded DNA, single and double stranded RNA, and hybrid molecules having mixtures of single and double stranded DNA and RNA. The polynucleotides may contain one or more modified nucleotides.
“Protein,” “peptide,” and “polypeptide” are used interchangeably to denote an amino acid polymer or a set of two or more interacting or bound amino acid polymers.
“Purify,” or “purified” refers to a target protein makes up for at least about 90% of a composition, in other words, it refers to a target protein that is free from at least 5-10% of contaminating proteins. Purification of a protein from contaminating proteins may be accomplished using known techniques, including ammonium sulfate or ethanol precipitation, acid precipitation, heat precipitation, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography, size-exclusion chromatography, and lectin chromatography. Various protein purification techniques are illustrated in Current Protocols in Molecular Biology, Ausubel et al., eds. (Wiley & Sons, New York, 1988, and quarterly updates).
“Selectable marker” refers to a marker that identities a cell as having undergone a recombinant DNA or RNA event. Selectable markers include, for example, genes that encode antimetabolite resistance such as the DHFR protein that confers resistance to methotrexate (Wigler et al, 1980, Proc Natl Acad Sci USA 77:3567; O'Hare et al., 1981, Proc Natl Acad Sci USA, 78:1527), the GPT protein that confers resistance to mycophenolic acid (Mulligan & Berg, 1981, PNAS USA, 78:2072), the neomycin resistance marker that confers resistance to the aminoglycoside G-418 (Calberre-Garapin et al., 1981, J Mol Biol, 150:1), the Hygro protein that confers resistance to hygromycin B (Santerre et al., 1984, Gene 30:147), and the ZeocinTM resistance marker (Invitrogen). In addition, the herpes simplex virus thymidine kinase, hypoxanthine-guanine phosphoribosyltransferase and adenine phosphoribosyltransferase genes may be employed in tk−, bgprt− and aprt− cells, respectively.
“Transform” means the process of introducing a gene into a host cell. The gene may be foreign in origin, but the gene may also derive from the host. A transformed host cell is termed a “transformant.” The introduced gene may be integrated onto the chromosome of the host, or the gene may remain on a stand-alone vector independent of the host chromosomes.
“Variant”, as used herein, means a polynucleotide or polypeptide molecule that differs front a reference molecule. Variants may include nucleotide changes that result in amino acid substitutions, deletions, fusions, or truncations in the resulting variant polypeptide when compared to the reference polypeptide.
“Vector,” “extra-chromosomal vector” or “expression vector” refers to a first polynucleotide molecule, usually double-stranded, which may have inserted into it a second polynucleotide molecule, for example a foreign or heterologous polynucleotide. The heterologous polynucleotide molecule may or may not be naturally found in the host cell, and may be, for example, one or more additional copy of the heterologous polynucleotide naturally present in the host genome. The vector is adapted for transporting the foreign polynucleotide molecule into a suitable host cell. Once in the host cell, the vector may be capable, of integrating into the host cell chromosomes. The vector may optionally contain additional elements for selecting cells containing the integrated polynucleotide molecule as well as elements to promote transcription of mRNA from transfected DNA. Examples of vectors useful in the methods disclosed herein include, but are not limited to, plasmids, bacteriophages, cosmids, retroviruses, and artificial chromosomes.
For purpose of this disclosure, unless otherwise stated, the techniques used may be found in any of several well-known references, such as: Molecular Cloning: A Laboratory Manual (Sambrook et al. (1989) Molecular cloning; A. Laboratory Manual), Gene Expression Technology (Methods in Enzymology, Vol. 185, edited by D. Goeddel, 1991 Academic Press, San Diego, Calif.), “Guide to Protein Purification” in Methods in Enzymology (M. P. Deutshcer, 3d., (1990) Academic Press, Inc.), PCR Protocols: A Guide to Methods and Applications (Innis et al. (1990) Academic Press, San Diego, Calif.), Culture of Animal Cells: A Manual of Basic Technique, 2nd ed. (R. I. Freshney (1987) Liss, Inc., New York, N.Y.), and Gene Transfer and Expression Protocols, pp 109-128, ed. E. J. Murray, The Humana Press Inc., Clifton, N.J.).
Unless otherwise indicated, the term “yeast,” “yeas strain” or “yeast cell” refers to baker's yeast, Saccharomyces cerevisiae. Other yeast species, such, as Kluyveromyces marxianus or Pichia guilliermondii are referred to as non-conventional yeast in this disclosure. Strains of S. cerevisiae, depository information, and plasmids used for this disclosure are listed in Table 1, 2 and Table 3, respectively. The yeast Kluyveromyces marxianus CBS-1089 is obtained from the Centraalbureau voor Schiomelcultures (CBS) collection. Pichia guilliermondii NRRL Y-2075 is obtained from the Agricultural Research Service Culture Collection (NRRL).







TABLE 1







S. cerevisiae Strains Used in this Disclosure









Strain
Genotype
Plasmids





BFY001
MATa ura3-52 trp1-Δ63 his3-Δ200 leu2-Δ1



BFY002
MATa ura3-52 trp1-Δ63 his3-Δ200 leu2-Δ1




yhr104w::LEU2



BFY507
MATa ura3-52 trp1-Δ63 his3-Δ200 leu2-Δ1
p138, p42



yhr104w::LEU2




adapted for growth on L-arabinose



BFY518
same as BFY507
p138


BFY566
same as BFY518
p138, p171


BFY590
same as BFY518 gal2Δ::HIS3
p138


BFY597
same as BFY590
p138, p42


BFY598
same as BFY590
p138, p187


BFY012
same as BFY002
pBFY004, pBFY013, pBFY012


BFY013
same as BFY002
pBFY007, pBFY016, pBFY014


BFY014
same as BFY002
pBFY007, pBFY015, pBFY017


BFY015
same as BFY002
pBFY005, pBFY016, pBFY019


BFY016
same as BFY002
pBFY005, pBFY018, pBFY017


BFY017
same as BFY002
pBFY009, pBFY018, pBFY014


BFY018
same as BFY002
pBFY009, pBFY015, pBFY019


BFY057
MATa his3D1 leu2D0 ura3D0 met15D0




gal80D::G418 yhr104w::LEU2



BFY534
same as BFY057
p144, p165


BFY535
same as BFY057
p144, pBFY13


BFY605
same as BFY590
p244


BFY625
MATa his3Δ1 leu2Δ0 ura3Δ0 trp1Δ
pBFY12, pBFY13, p138



met15Δ0 gal80Δ::G418




adapted for growth on L-arabinose



BFY626
Same as BFY625
pBFY12, p138, p204









Yeast strains may be grown on liquid or solid media with 2% agar for solid media. Where appropriate, some amino acids or nucleic acids are purposely left out from the media for plasmid maintenance. Growth conditions are typically 30° C. unless otherwise indicated, with shaking in liquid cultures. Anaerobic conditions are generally more favorable to metabolize the various sugars to ethanol.
A number of the yeast strains listed in Table 1 have been deposited at the American Type Culture Collection (ATCC) in accordance with the provisions of the Budapest Treatey on the International Recognition of the Deposit of Microorganisms Air the Purposes of Patent Procedures. In each instance, the yeast strain was deposited by the inventors listed herein-on Mar. 16, 2007 at American Type Culture. Collection, 10801 University Boulevard, Manassas, Va. 20110 U.S.A.







TABLE 2





Depository Information


Yeast Strain/Accession Number

















BFY013/PTA-8258



BFY534/PTA-8257



BFY598/PTA-8256



BFY626/PTA-8255
















TABLE 3







Plasmids Used in this Disclosure










Plasmid
Marker and expressed genes






p42
URA3, GAL2 over-expression



p138
TRP1, B. subtilis araA, E. coli araB, E. coli araD



p144
E. coli araB, D; B. subtilis araA in pBFY012



p165
HIS3, GAL2 over-expression



p171
HIS3, 8.8 kb K. marxianus genomic DNA fragment



p187
URA3, KmLAT1 over-expression plasmid



p204
HIS3, PgLAT2 over-expression plasmid



p244
URA3, PgLAT2 over-expression plasmid



pBFY004
control 2μ vector with PGK promoter,




GAL10 terminator and Trp1 marker



pBFY005
E. coli araB in pBFY004



pBFY007
E. coli araA in pBFY004



pBFY009
E. coli araD in pBFY004



pBFY012
control 2μ vector with PGK promoter,




GAL10 terminator and Ura3 marker



pBFY013
control 2μ vector with PGK promoter,




GAL10 terminator and His3 marker



pBFY014
E. coli araB in pBFY012



pBFY015
E. coli araB in pBFY013



pBFY016
E. coli araD in pBFY013



pBFY017
E. coli araD in pBFY012



pBFY018
E. coli araA in pBFY013



pBFY019
E. coli araA in pBFY012









Yeast cells may be grown in rich media. YPD or minimum media conventionally used in the field. YPD medium contains about 1% yeast extract, 2% peptone and 2% dextrose. Yeast minimum media typically contains 0.67% of yeast nitrogen base (“YNB”) without amino acids supplemented with appropriate amino acids or purine or pyrimidine bases. An amount of sugar, typically 2% unless otherwise indicated, may be used as carbon source, including glucose (dextrose), galactose, maltose or L-arabinose among others. Adaptation for growth on L-arabinose is performed as described in, for example, Becker and Boles (2003) with modifications as detailed in Example 3.
Over-expression plasmids are constructed by cloning the gene for over-expression downstream of the S. cerevisiae PGK1 or TDH3 promoter in a 2μ-based vector. Construction of a DNA library is detailed in the Examples. Note that other like S. cerevisiae promoters can also be used for overexpression, including ADH2, PDC1, PGI1, etc.
E. coli cells may be grown in LB liquid media or on LB agar plates supplemented with ampicillin at 100 μg/ml as needed. Transformation of E. coli DH5α is by electrotransformation according to a protocol by Invitrogen (Invitrogen 11319-019). After transformation, the bacterial cells are plated tin LB plates containing 100 μg/ml ampicillin for selection. Transformation of S. cerevisiae was performed using a DMSO-enhanced lithium-acetate procedure as described with the following modifications (Hill et al., 1991). Cells are harvested and initially washed in water. 600 μl of PEG4000 solution is added and 70 μl DMSO is added just prior to heat shocking. Cells are heat-shocked for 15 min. at 42° C. and the last wash step is skipped. Cells are resuspended in 10 mM TE solution and plated.
Yeast DNA is isolated using the Easy DNA kit according to manufacturers protocol (Invitrogen, K1800-01). DNA manipulations and library construction are performed as described in Molecular Cloning: A Laboratory Manual (1989), except otherwise specifically indicated in this disclosure. Plasmids are cured from yeast by growing the strain in rich non-selective media overnight followed by plating on non-selective media, isolated colonies are replica plated to screen for loss of selective markers. Plasmid rescue is performed by transforming isolated yeast DNA into E. coli followed by isolation and characterization. E. coli plasmid isolation is accomplished using plasmid spin mini-prep kit according to the manufacturer's manual (Qiagen, 27106). PCR-based chromosomal walking is performed using the Universal GenomeWalker. Kit as described (BP Biosciences, K1807-1).
For the transport assays, cells may be grown in minimal media supplemented with 20 g/L of L-arabinose. Cells are collected in mid-growth and washed twice before suspension in water at 30 mg/ml. Uptake of L-(1-14C) arabinose (54 mCi/mmol, Moravek Biochemical Inc.) or D-(1-14C) galactose-(57 mCi/mmol, Amersham Biosciences) is measured as previously described by Stambuk et al. (2003). Assays are performed in 30 seconds to maintain initial rates after appropriate experiments to ensure uptake is linear for at least 1 minute. Transport activity is described as nano-moles of labeled sugar transported per mg cell dry weight per minute, inhibition and competition assays are performed as previously described by Stambuk et al. (2003).
Sequencing results showed that the KmLAT1 gene contains an ORF of 1668 bp in length. The predicted amino acid; sequence of KmLAT1 shares homology with high-affinity glucose transporters, in particular, with HGT1 from K. lactis (Table 4). KmLAT1 transporter shows a much higher sequence similarity with high-affinity glucose transporters from non-conventional yeast than with transporter proteins encoded by the bacterial araE gene or hexose transporters from S. cerevisiae (FIG. 1).







TABLE 4







Properties and similarities of KmLat1 to other sugar


transporters.














Predicted








protein








(no. of

Predicted
Degree of





aa/no. of
pl of
transmembrane
identity (%)/

Putative function


gene
kDa)
protein
regions
similarity (%)
Organism
of gene product





KmLat1
556/61.3
8.22
12
—
K. marxianus1
L-arabinose








transporter


K1Hgt1
551/60.8
5.76
12
77/89
K. lactis2
high affinity








glucose








transporter


AEL042Cp
547/59.8
8.82
12
65/82
A. gossypii3
putative hexose








transporter


DEHA0E01738g
545/61.1
5.55
12
52/70
D. hansenii4
hexose








transporter


CaHgt1
545/60.7
8.05
12-13
50/71
C. albicans5
putative hexose








transporter


CaHgt2
545/60.4
8.48
12-14
51/71
C. albicans6
putative hexose








transporter





Accession numbers:


1Not yet assigned,


21346290,


3AEL042C,


4DEHA0E01738g,


5CAA76406,


6orf19.3668






Transmembrane regions predicted for KmLat1 and PgLat2 by the software Tmpred shows 12 transmembrane regions with a larger intercellular loop between regions 6 and 7 (FIG. 2) (See Hofmann et al, 1993), typical of GAL2 and other yeast sugar transporters having 10-12 transmembrane regions (See e.g., Alves-Araujo et al., 2004; Day et al., 2002; Kruckeberg et al., 1996; Pina et al., 2004; and Weierstall et al. 1999).
Like other members of the transporter family, and in particular sugar transporters, KmLat1 and PgLat2 polypeptides are useful in facilitating the uptake of various sugar molecules into the cells. It is envisioned that KmLat1 or PgLat2 polypeptides could be used for other purposes, for example, in analytical instruments or other processes where uptake of sugar is required. KmLat1 or PgLat2 polypeptides may be used alone or in combination with one or more other transporters to facilitate the movement of molecules across a membrane structure, which function may be modified by one skilled in the relevant art, all of which are within the scope of the present disclosure.
The KmLAT1 polypeptides include isolated polypeptides having an amino acid sequence as shown below in Example 2; and in SEQ ID NO:2, as well as variants and derivatives, including fragments, having substantial sequence similarity to the amino acid sequence of SEQ ID NO:2 and that retain any of the functional activities of KmLAT1. PgLAT2 polypeptides include isolated polypeptides having an amino acid sequence as shown below in Example 5; and in SEQ ID NO:4, as well as variants and derivatives, including fragments, having substantial sequence similarity to the amino acid sequence of SEQ ID NO:4 and that retain any of the functional activities of PgLAT2. The functional activities of the KmLAT1 or PgLAT2 polypeptides include but are not limited to transport of L-arabinose across cell membrane. Such activities may be determined, for example, by subjecting the variant, derivative, or fragment to a arabinose transport assay as detailed, lot example in Example 4.
Variants and derivatives of KmLAT1 or PgLAT2 include, for example, KmLAT1 or PgLAT2 polypeptides modified by covalent or aggregative conjugation with other chemical moieties, such as glycosyl groups, polyethylene glycol (PEG) groups, lipids, phosphate, acetyl groups, and the like.
The amino acid sequence of KmLAT1 or PgLAT2 polypeptides is preferably at least about 60% identical, more preferably at least about 70% identical, more preferably still at least about 80% identical, and in some embodiments at least about 90%, 95%, 96%, 97%, 98%, and 99% identical, to the KmLAT1 and PgLAT2 amino acid sequences of SEQ ID NO: 2 and SEQ ID NO: 4, respectively. The percentage sequence identity, also termed homology (see definition above) may be readily determined, for example, by comparing the two polypeptide sequences using any of the computer programs commonly employed for this purpose, such as the Gap program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, Madison Wis.), which uses the algorithm of Smith and Waterman, 1981, Adv. Appl. Math. 2:482-489.
Variants and derivatives of the KmLAT1 or PgLAT2 polypeptides may further include, for example, fusion proteins formed of a KmLAT1 or PgLAT2 polypeptide and another polypeptide. Fusion protein may be formed between a fragment of the KmLAT1 polypeptide and another polypeptide, such that the fusion protein may retain none or only part of the activities normally performed by the foil-length KmLAT1 or PgLAT2 polypeptide. Preferred polypeptides for constructing the fusion protein include those that facilitate purification or oligomerization, or those that enhance KmLAT1 or PgLAT2 stability and/or transport, capacity or transport rate for sugars, especially for arabinose. Preferred polypeptides may also include those that gain enhanced transport capability when fused with KmLAT1, PgLAT2 or fragments thereof.
KmLAT1 or PgLAT2 variants and derivatives may contain conservatively substituted amino acids, meaning that one or more amino acid may be replaced by an amino acid that does not alter the secondary and/or tertiary structure of the polypeptide. Such substitutions may include the replacement of an amino acid, by a residue having similar physicochemical properties, such, as substituting one aliphatic residue (Ile, Val, Leu, or Ala) for another, or substitutions between basic residues Lys and Arg, acidic residues Glu and Asp, amide residues GIn and Asn, hydroxyl residues Ser and Tyr, or aromatic residues Phe and Tyr. Phenotypically silent amino acid exchanges are described more fully in Bowie et al., 1990. In addition, functional KmLAT1 or PgLAT2 polypeptide variants include those having amino acid substitutions, deletions, or additions to the amino acid sequence outside functional regions of the protein. Techniques for making these substitutions and deletions are well known in the art and include, for example, site-directed mutagenesis.
The KmLAT1 or PgLAT2 polypeptides may be provided in an isolated form, or in a substantially purified form. The polypeptides may be recovered and purified from recombinant cell cultures by known methods, including, for example, ammonium sulfate or ethanol precipitation, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography, and lectin chromatography. Preferably, protein chromatography is employed for purification.
A preferred form of KmLAT1 or PgLAT2 polypeptides is that of recombinant polypeptides expressed by suitable hosts. In one preferred embodiment, when heterologous expression of KmLAT1 or PgLAT2 is desired, the coding sequences of KmLAT1 or PgLAT2 may be modified in accordance with, the codon usage of the host. Such modification may result in increase protein expression of a foreign in the host. Furthermore, the hosts may simultaneously produce other transporters such that multiple transporters are expressed in the same cell, wherein the different transporters may form oligomers to transport, the same sugar. Alternatively, the different transporters may function independently to transport different sugars. Such recombinant cells may be useful in crude fermentation processing or in other industrial processing.
KmLAT1 or PgLAT2 polypeptides may be fused to heterologous polypeptides to facilitate purification. Many available heterologous peptides (peptide tags) allow selective binding of the fusion protein to a binding partner. Non-limiting examples of peptide tags include 6-His, thioredoxin, hemaglutinin, GST, and the OmpA signal sequence tag. A binding partner that recognizes and binds to the heterologous peptide may be any molecule or compound, including metal ions (for example, metal affinity columns), antibodies, antibody fragments, or any protein or peptide that preferentially hinds the heterologous peptide to permit purification of the fusion protein.
KmLAT1 or PgLAT2 polypeptides may be modified to facilitate formation of KmLAT1 or PgLAT2 oligomers. For example, KmLAT1 polypeptides may be fused to peptide moieties that promote oligomerization, such as leucine zippers and certain antibody fragment polypeptides, for example, Fc polypeptides. Techniques for preparing these fusion proteins are known, and are described, for example, in WO 99/31241 and in Cosman et. al., 2001. Fusion to an Fc polypeptide offers the additional advantage of facilitating purification by affinity chromatography over Protein A or Protein G columns. Fusion to a leucine-zipper (LZ), for example, a repetitive heptad repeat, often with four or five leucine residues interspersed with other amino acids, is described in Landschultz et al., 1988.
it is also envisioned that an expanded set of variants and derivatives of KmLAT1 or PgLAT2 polynucleotides and/or polypeptides may be generated to select for useful molecules, where such expansion is achieved not only by conventional methods such as site-directed mutagenesis but also by more modern techniques, either independently or in combination.
Site-directed-mutagenesis is considered an informational approach to protein engineering and may rely on high-resolution crystallographic structure's of target proteins for specific amino acid changes (van den Burg et al. 1998). For example, modification of the amino acid sequence of KmLAT1 or PgLAT2 polypeptides may be accomplished as is known in the art, such as by introducing mutations at particular locations by oligonucleotide-directed mutagenesis Site-directed-mutagenesis may also take advantage of the recent advent of computational methods for identifying site-specific changes for a variety of protein engineering objectives (Hellinga, 1998).
The more modern techniques include, but are not limited to, non-informational mutagenesis techniques (referred to generically as “directed evolution”). Directed evolution, in conjunction with high-throughput screening, allows testing of statistically meaningful variations in protein conformation (Arnold, 1998). Directed evolution technology may include diversification methods similar to that described by Crameri et al. (1998), site-saturation mutagenesis, staggered extension process (StEP) (Zhao et al., 1998), and DNA synthesis/reassembly (U.S. Pat. No. 5,965,408).
Fragments of the KmLAT1 or PgLAT2 polypeptide may be used, for example, to generate specific anti-KmLAT1 antibodies. Using known selection techniques, specific epitopes may be selected and used to generate monoclonal or polyclonal antibodies. Such antibodies have utility in the assay of KmLAT1 or PgLAT2 activity as well as in purifying recombinant KmLAT1 or PgLAT2 polypeptides from genetically engineered host cells.
Tire disclosure also provides polynucleotide molecules encoding the KmLAT1 or PgLAT2 polypeptides discussed above. KmLAT1 or PgLAT2 polynucleotide molecules include polynucleotide molecules having the nucleic acid sequence shown, in SEQ ID NOT and SEQ ID NO:3, respectively; polynucleotide molecules that hybridize to the nucleic acid sequence of SEQ ID NO:1 and SEQ ID NO:3, respectively, under high stringency hybridization conditions (for example, 42°, 2.5 hr., 6×SCC, 0.1% SDS); and polynucleotide molecules having substantial nucleic acid sequence identity with the nucleic acid sequence of SEQ ID NO:1 and SEQ ID NO:3, respectively. It will be appreciated that such polynucleotide molecules also broadly encompass equivalent substitutions of codons that may be translated to produce the same amino acid sequences, truncated fragments of the polynucleotide molecules, and polynucleotide molecules with a high incidence of homology, such as 90%, 95%, 96%, 97%, 98%, or 99% or more homology with respect to what is disclosed.
The KmLAT1 or PgLAT2 polynucleotide molecules of the disclosure are preferably isolated molecules encoding the KmLAT1 or PgLAT2 polypeptide having an amino acid sequence as shown in SEQ ID NO:2 and SEQ ID NO:4, respectively, as well as derivatives, variants, and useful fragments of the KmLAT1 or PgLAT2 polynucleotide. The KmLAT1 or PgLAT2 polynucleotide sequence may include deletions, substitutions, or additions to the nucleic acid sequence of SEQ ID NO:1 and SEQ ID NO:3, respectively.
The KmLAT1 or PgLAT2 polynucleotide molecule may be cDNA, chemically synthesized DNA, DNA amplified by PCR, RNA, or combinations thereof. Due to the degeneracy of the genetic code, two DNA sequences may differ and yet encode identical amino acid sequences. The present disclosure thus provides an isolated polynucleotide molecule having a KmLAT1 or PgLAT2 nucleic acid sequence encoding KmLAT1 or PgLAT2 polypeptide, wherein the nucleic acid sequence encodes a polypeptide having the complete amino acid sequences as shown in SEQ ID NO:2 and SEQ ID NO:4, respectively, or variants, derivatives, and fragments thereof.
The KmLAT1 or PgLAT2 polynucleotides of the disclosure have a nucleic acid sequence that is at least about 60% identical to the nucleic acid sequence shown in SEQ ID NOT and SEQ ID NO:3, respectively, in some embodiments at least about 70% identical to the nucleic acid sequence shown in SEQ ID NOT and SEQ ID NO:3, respectively, at least about 80% identical to the nucleic acid sequence shown in SEQ ID NOT and SEQ ID NO:3, respectively, and in other embodiments at least about 90%-95%, 96%, 97%, 98%, 99%% identical to the nucleic acid sequence shown in SEQ ID NO:1 and SEQ ID NO:3, respectively. Nucleic acid sequence identity is determined by known methods, for example by aligning two sequences in a software program such as the BLAST program (Altschul, S. F et al. (1990) J. Mol. Biol. 215:403-410, from the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/BLAST/).
The KmLAT1 or PgLAT2 polynucleotide molecules of the disclosure also include isolated polynucleotide molecules having a nucleic acid sequence that hybridizes under high stringency conditions (as defined above) to a the nucleic acid sequence shown in SEQ ID NO:1 and SEQ ID NO:3, respectively. Hybridization of the polynucleotide is to at least about 15 contiguous nucleotides, or at least about 20 contiguous nucleotides, and in other embodiments at least about 30 contiguous nucleotides, and in still other embodiments at least about 100 contiguous nucleotides of the nucleic acid sequence shown in SEQ ID NO:1 and SEQ ID NO:3, respectively.
Useful fragments of the KmLAT1 or PgLAT2 polynucleotide molecules described herein, include probes and primers. Such probes and primers may be used, for example, in PCR methods to amplify and detect the presence of KmLAT1 or PgLAT2 polynucleotides in vitro, as well as in Southern and Northern blots for analysis of KmLAT1 or PgLAT2. Celts expressing the KmLAT1 or PgLAT2 polynucleotide molecules may also be identified by the use of such probes. Methods for the production and use of such primers and probes are known. For PCR, 5′ and 3′ primers corresponding to a region at the termini of the KmLAT1 or PgLAT2 polynucleotide molecule may be employed to isolate and amplify the KmLAT1 or PgLAT2 polynucleotide using conventional techniques.
Other useful fragments of the KmLAT1 or PgLAT2 polynucleotides include antisense or sense oligonucleotides comprising a single-stranded nucleic acid sequence capable of binding to a target KmLAT1 or PgLAT2 mRNA (using a sense strand), or DNA (using an antisense strand) sequence.
The present disclosure also provides vectors containing the polynucleotide molecules, as well as host cells transformed with such vectors. Any of the polynucleotide molecules of the disclosure may be contained in a vector, which generally includes a selectable marker and an origin of replication, for propagation in a host. The vectors may further include suitable transcriptional or translational regulatory sequences, such as those derived from a mammalian, fungal, bacterial, viral, or insect, genes, operably linked to the KmLAT1 or PgLAT2 polynucleotide molecule. Examples of such regulatory sequences include transcriptional promoters, operators, or enhancers, mRNA ribosomal binding sites, and appropriate sequences which control transcription and translation. Nucleotide sequences are operably linked when the regulatory sequence functionally relates to the DNA encoding the target protein. Thus, a promoter nucleotide sequence is operably linked to a KmLAT1 or PgLAT2 DNA sequence if the promoter nucleotide sequence directs the transcription of the KmLAT1 or PgLAT2 sequence.
Selection of suitable vectors for the cloning of KmLAT1 or PgLAT2 polynucleotide molecules encoding the KmLAT1 or PgLAT2 polypeptides of this disclosure depends upon the host cell in which the vector will be transformed, and, where applicable, the host cell from which the target polypeptide is to be expressed. Suitable host cells for expression of KmLAT1 or PgLAT2 polypeptides include prokaryotes, yeast, and higher eukaryotic cells, each of which is discussed below. Selection of suitable combinations of vectors and host organisms is a routine matter from a perspective of skill.
The KmLAT1 or PgLAT2 polypeptides to be expressed in such host cells may also be fusion proteins that, include sequences from other proteins. As discussed above, such regions may be included to allow, for example, enhanced functionality, improved stability, or facilitated purification of the KmLAT1 or PgLAT2 polypeptide. For example, a nucleic acid sequence encoding a peptide that binds strongly to arabinose may be fused in-frame to the transmembrane sequence of the KmLAT1 or PgLAT2 polypeptides so that the resulting fusion protein binds arabinose and transports the sugar across the cell membrane at a higher rate than the KmLAT1 or PgLAT2 transporter.
Suitable host cells for expression of target polypeptides include prokaryotes, yeast, and higher eukaryotic cells. Suitable prokaryotic hosts to be used for the expression of these polypeptides include bacteria of the genera Escherichia, Bacillus, and Salmonella, as well as members of the genera Pseudomonas, Streptomyces, and Staphylococcus. 
Expression vectors for use in prokaryotic hosts generally comprise one or more phenotypic selectable marker genes. Such genes encode, for example, a protein that confers antibiotic resistance or that supplies an auxotrophic requirement. A wide variety of such vectors are readily available from commercial sources. Examples include pSPORT vectors, pGEM vectors (Promega, Madison, Wis.), pPROEX vectors (LTI, Bethesda, Md.), Bluescript vectors (Stratagene), and pQE vectors (Qiagen).
KmLAT1 or PgLAT2 may also be expressed in yeast, host cells from genera including Saccharomyces, Pichia, and Kluyveromyces. Preferred yeast host is S. cerevisiae. Yeast vectors will often contain an origin of replication sequence from a 2μ yeast plasmid for high copy vectors and a CEN sequence for a low copy number vector. Other sequences on a yeast, vector may include an autonomously replicating sequence (ARS), a promoter region, sequences for polyadenylation, sequences for transcription termination, and a selectable marker gene. Vectors replicable in both yeast and E. coli (termed shuttle vectors) are preferred. In addition to the above-mentioned features of yeast vectors, a shuttle vector will also include sequences for replication and selection in E. coli. 
Insect host cell culture systems may also be used for the expression of KmLAT1 or PgLAT2 polypeptides. The target polypeptides are preferably expressed using a baculovirus expression system, as described, for example, in the review by Luckow and Summers, 1988.
The choice of a suitable expression, vector for expression of KmLAT1 or PgLAT2 polypeptides will depend upon the host cell to be used. Examples of suitable expression vectors for E. coli Include pET, pUC, and similar vectors as is known in the art. Preferred vectors for expression of the KmLAT1 or PgLAT2 polypeptides include the shuttle plasmid pIJ702 for Streptomyces lividans, pGAPZalpha-A, B, C and pPICZalpha-A, B, C (Invitrogen) for Pichia pastoris, and pFE-1 and pFE-2 for filamentous fungi and similar vectors as is known in the art. The vectors preferred for expression in S. cerevisiae are listed in Table 2.
Modification a KmLAT1 or PgLAT2 polynucleotide molecule to facilitate insertion into a particular vector (for example, by modifying restriction sites), ease of use in a particular expression system or host (for example, using preferred host codons), and the like, are known and are contemplated for use. Genetic engineering methods for the production of KmLAT1 or PgLAT2 polypeptides include the expression of the polynucleotide molecules in cell tree expression systems, in host cells, in tissues, and in animal models, according to known methods.
This disclosure also provides reagents, compositions, and methods that are useful for analysis of KmLAT1 or PgLAT2 activity and for assessing the amount and rate of arabinose transport.
The KmLAT1 or PgLAT2 polypeptides of the present disclosure, in whole or in part, may be used to raise polyclonal and monoclonal antibodies that are useful in purifying KmLAT1 or PgLAT2, or detecting KmLAT1 or PgLAT2 polypeptide expression, as well as a reagent tool for characterizing the molecular actions of the KmLAT1 or PgLAT2 polypeptide. Preferably, a peptide containing a unique epitope of the KmLAT1 or PgLAT2 polypeptide is used in preparation of antibodies, using conventional techniques. Methods for the selection of peptide epitopes and production of antibodies are known. See, for example. Antibodies: A Laboratory Manual, Harlow and Land (eds.), 1988 Gold Spring Harbor Laboratory Press, Cold Spring Harbor. N.Y.; Monoclonal Antibodies. Hybridomas: A New Dimension in Biological Analyses, Rennet et al. (eds.), 1980 Plenum Press, New York.
Agents that modify, for example, to increase or decrease, KmLAT1 or PgLAT2 transport of arabinose or other sugar's may be identified by the transport assay described in Example 4, for example. Performing the transport assay in the presence or absence of a test agent permits screening of such agents.
The KmLAT1 or PgLAT2 transport activity is determined in the presence or absence of a test agent and then compared. For instance, a lower KmLAT1 transport activity in the presence of the test, agent, than in the absence of the test, agent, indicates that the test agent has decreased the activity of the KmLAT1. Stimulators and inhibitors of KmLAT1 or PgLAT2 may be used to augment, inhibit, or modify KmLAT1 or PgLAT2 transport activity, and therefore may have potential industrial uses as well as potential use in further elucidation of the molecular actions of KmLAT1 or PgLAT2.
The KmLAT1 or PgLAT2 polypeptide of the disclosure is an effective arabinose transporter. In the methods of the disclosure, the sugar transporting effects of KmLAT1 or PgLAT2 are achieved by mixing cells expressing KmLAT1 or PgLAT2 with pure sugar or sugar-containing biomass. KmLAT1 or PgLAT2 may also be used in a cell-free system. KmLAT1 or PgLAT2 may be used under other conditions, for example, at elevated temperatures or under acidic pH. Other methods of using KmLAT1, or PgLAT2 to transport sugar, especially arabinose, for fermentation, are envisioned to be within the scope of what is disclosed. KmLAT1 or PgLAT2 polypeptides may be used in any known application currently utilizing a sugar transporter, all of which are within the scope of this disclosure.
It is shown, in this disclosure that Gal2p is an effective L-arabinose transporter at high concentrations of arabinose, whereas KmLAT1 or PgLAT2 may be more effective at different concentrations of L-arabinose. Combination of the Gal2p and the two new transporters from non-conventional yeast may be employed to provide complementary transport into S. cerevisiae of L-arabinose down to very low residual concentration of arabinose.
It is shown here that combinatorial expression of Gal2p. KmLAT1 and PgLAT2 may enhance the overall rate and extent of arabinose utilization, by recombinant S. cerevisiae cells expressing these transporters. As shown in Example 8, the doubling time for S. cerevisiae strain expressing both PgLAT2 and Gal2p is shorter than S. cerevisiae cells expressing Gal2p alone (15 hours vs. 19 hours), suggesting that L-arabinose uptake may be enhanced by the synergistic effect of PgLAT2 and Gal2p in these cells. Moreover, the PgLAT2 expressing strain appears to grow to a higher overall optical density at saturation, suggesting that this strain was able to utilize the carbon source (L-arabinose) in the medium more completely. This hypothesis is supported by HPLC analysis of the final culture media (Table 5) which indicates that there is significantly less residual L-arabinose in the culture of cells expressing Gal2p and PgLAT2 than in the culture of those expressing Gal2p alone. Thus, heterologous expression of either or both KmLAT1 and PgLAT2 in S. cerevisiae may enhance arabinose utilization by facilitating arabinose transport when the concentration of arabinose is relatively low.







TABLE 5







Doubling times and HPLC Measurement of Residual


Arabinose Concentration in Cultures Described in FIG. 11.















L-



Transporters
Doubling

arabinose


Flask
Expressed
Time (hours)
Final OD600
(g/L) by HPLC





1
Gal2p only
19.2
0.72
0.68


2

18.6
0.72
0.67


3
Gal2p + PgLat2
15.0
0.85
0.49


4

14.8
0.85
0.48





*starting L-arabinose concentration 1.89 g/L and media without L-arabinose had an undetectable level (<0.1 g/L).


ND = not determined.






L-arabinose metabolism in bacteria involves three enzymes: L-arabinose isomerase (araA), L-ribulokinase (araB), and L-ribulose-5-p 4-epimerase (araD), which may be collectively referred to as the “araBAD” proteins in this disclosure. The genes encoding these three enzymes may be referred to as the “araBAD” genes in this disclosure. The combined action of these three bacterial proteins convert L-arabinose to Xylulose-5-phosphate (See FIG. 3). S. cerevisiae contains the pathway to utilize and ferment the final product xylulose-5-phosphate and produce ethanol under certain conditions (see FIG. 3).
S. cerevisiae strain to be used to construct an arabinose fermenting yeast strain preferably possesses Gal+ phenotype. A Gal+ strain is likely to express galactose permease which may facilitate the uptake of arabinose by S. cerevisiae. 
S. cerevisiae typically possesses endogenous aldose reductase (“AR”) activity, which may divert arabinose to a pathway different from the one that may lead to the production of ethanol through the action of the bacterial araBAD proteins. Moreover, the arabitol generated by the AR protein may inhibit the isomerase encoded by araA. In order to increase the overall yield of ethanol from arabinose, it is preferable to use an AR-deficient strain to construct the arabinose fermenting yeast of the present disclosure. The AR-deficient strain may be obtained by screening for spontaneous mutations, or preferably by targeted gene disruption or mutation. An example of such gene disruption is detailed in Example 10.
As shown in FIG. 3, die engineered pathway utilizing bacterial araBAD converts L-arabinose to xylulose-5-P that S. cerevisiae can convert to ethanol using endogenous enzymatic activities. It is thus desirable to ensure that the arabinose metabolic pathway starting from xylulose to ethanol remains intact in the AR-deficient strain. This may be tested by comparing the growth of the AR-deficient strain with its parental strain on glucose or xylulose, if both strains proliferate at about the same rate on glucose or xylulose, it is likely that the AR gene disruption-event has not negatively impacted the catabolism of glucose or xylulose.
The present disclosure also provides a new method to measure arabinose uptake by yeast cells. Traditionally, L-arabinose transport is measured by using radio-labeled substrate. Since aldose reductase, which converts L-arabinose to arabitol, is cytosolic, it is possible to use the formation of new arabitol as an indicator of arabinose uptake. Higher levels of arabitol indicates higher uptake of L-arabinose. To confirm the validity of this method, L-arabinose transport was measured using the traditional 14C-labelled L-arabinose in various yeast strains with different levels of arabitol formation. These experiments show that the level of arabitol formation corresponds well, with, the level of L-arabinose uptake.
Using this method, several high arabitol producing strains have been isolated, including two gal80 mutants and two otherwise wildtype strains, which have 3 to 4 folds higher L-arabinose and D-galactose transport activity than the BFY001 originally used to construct the arabinose fermenting strains. Bacterial genes encoding the araBAD proteins may be introduced into these strains to achieve higher rate of arabinose uptake and thus higher overall yield. This result also validates the indirect screening method for strains with higher arabinose transport activity.
Although the present disclosure teaches the introduction of foreign genes such as E. coli araBAD genes, into yeast cells, genes from other species encoding proteins that perform the same or similar, function as the E. coli araBAD proteins, i.e., converting L-arabinose into various intermediates and eventually into ethanol, may be used in place of the E. coli araBAD genes (See e.g., Becker and Boles, 2003, using araA from Bacillus subtilis). The DNA of the foreign genes may be present in a host cell at one copy, or preferably, in more than one copy. The foreign genes may be under control of a constitutive promoter or an inducible promoter.
The foreign genes may be present as plasmids or minichromosomes in the host yeast cells, or alternatively, the plasmids carrying the foreign genes may be engineered so that the foreign genes are integrated into the chromosomes of the host through genetic recombination. In the latter case, the foreign tends to be maintained after generations, even when the host cells are grown in rich media where no selective pressure is present. By contrast, in the former case where the genes remain on a vector, the genes may be lost after a few generations. Under those circumstances, the host yeast cells are preferably grown in a minimum media supplemented with appropriate amino acids or purine or pyrimidine bases so that a selective pressure helps maintain the plasmids.
Cell-free or whole-cell fermentation may be used to convert arabinose to ethanol. In the whole cell fermentation process, the transformants may be grown on minimum media with appropriate supplementation to maintain the plasmids. The transformant cells are preferably grown on galactose to induce the expression of galactose permease. More preferably, the cells are grown on both arabinose and galactose before the fermentation assays, in addition, transformant cells can be grown on both arabinose and glucose before the fermentation assays (see FIG. 19).
In the cell-free fermentation system, cells are harvested and the cells are lysed to release enzymes for the conversion of the sugar to ethanol. One bottleneck for a whole-cell fermentation system is the uptake of arabinose by the cells, which may explain its lower overall yield of ethanol than the cell-free system. However, whole-cell fermentation is preferred because it is easier to perform. In a whole-cell fermentation system, the cells may be mixed directly with the biomass or other substrates, requiring no extra steps of cell-handling.
In a preferred embodiment, the various arabinose metabolic pathways disclosed here may be introduced into a S. cerevisiae strain that have been modified to facilitate its arabinose uptake. Such strain may include but are not limited to strains that express both the Gal2p and one or two of the novel arabinose transporters similar to the ones disclosed here. The expression levels of the array of arabinose transporters may be fine-tuned such that they are commensurate with the rate of arabinose metabolism inside the engineered yeast, cells. Most preferably, the expression levels of the transporters may be linked to the arabinose metabolic rate in each cell, such that the arabinose is taken in more rapidly by those cells that convert arabinose to ethanol more efficiently.
The examples herein illustrate the present instrumentalities by way of illustration, and not by limitation. The chemicals, biological agents and other ingredients are presented as typical components or reactants, and the procedures described herein may represent but one of the typical ways to accomplish the goal of the particular experiment, it is understood that various modification may be derived in view of the foregoing disclosure without departing from the spirit of the present disclosure.
Example 1
Cloning of the New Transporter Gene KmLAT1
K. marxianus genomic library was constructed in our yeast vector pBFY13 which contains the yeast 2μ origin of replication, a URA3 selection cassette, and a BamHI site located between the PGK1 promoter and GAL10 terminator. After partial digestion of 200 μg of genomic DNA with Sau3A1 restriction enzyme, fragments of 2-8 kb in length were gel-isolated and ligated into the BamHI site of pBFY013. This ligation reaction was then transformed into E. coli and plated for recovery. Plate counts produced  ̃3000 cfu's/10 μl of transformed cells and the plasmid DNA from 24 colonies was screened for presence of insert revealing 22 of 24 transformants had an insert ranging from 1 kb to  ̃8 kb giving an average, insert size of 3.2 kb. The transformed cells were scraped from the plates, DNA recovered, and 5 μl was transformed into competent BPY518 cells. The strain, BFY518, was cured of the GAL2 over-expression plasmid negating its ability to form colonies on agar plates containing L-arabinose as the sole carbon source enabling restoration of colony formation by complementation with a heterologous L-arabinose transporter. To count the number of transformed yeast cells, 10 μl of the yeast library transformation were plated onto minimal glucose media yet the colonies were so dense that only an estimate of  ̃5000 colonies was possible. The rest of the transformation mix ( ̃140 μl) was plated onto minimal media containing 2% L-arabinose for selection from which a small amount of background growth was noticed. The plates were then replica plated to fresh L-arabinose minimal media. The total number of cells plated for selection represented  ̃280,000 transformants representing  ̃8 fold coverage of the 10.7 mb K. marxianus genome (See Dujon et al., 2004). Two colonies grew on the replica plates and the plasmid DNA was rescued and re-transformed into BFY5.18 allowing growth once again on L-arabinose confirming that the K. marxianus genomic insert carried on these plasmids was responsible for growths. Restriction analysis suggested both plasmids harbored the same insert of approximately 8.8 kb in size.
Example 2
Sequence Analysis of the KmLAT1 Gene
Sequencing results showed that both plasmids had identical inserts of 8838 kb containing two ORFs on the 5′ end of the insert. Both of these ORFs showed strong homology to yeast sugar transporters. One transporter ORF was interrupted by a fragment of an unrelated ORF suggesting that recombination of fragments during ligation into the vector occurred in library construction (FIG. 4). Recombination of library fragments during ligation into the vector was shown, by PCR walking experiments performed on K. marxianus genomic DNA. Walking was performed out of the transporter in a 5′ direction and additional transporter sequence including the start codon was recovered rather than the additional sequence from the unrelated ORF. The uninterrupted transporter ORF, termed KmLAT1 was recovered twice more in another subsequent library screening. This ORF was 1668 bp in length, and shared homology with high-affinity glucose transporters in particular, HGT1 from K. lactis (Table 4) and showed a much closer association with high-affinity glucose transporters from non-conventional yeasts than the bacterial araE genes or S. cerevisiae hexose transporters (FIG. 1).
Transmembrane region prediction by the software Tmpred shows 12 transmembrane regions with a larger intercellular loop between regions 6 and 7 (FIG. 2) (See Hofmann et al, 1993), typical of GAL2 and other yeast sugar transporters having 10-12 transmembrane regions (See e.g., Alves-Araujo et al., 2004; Day et al., 2002; Kruckeberg et al., 1996; Pina et al., 2004; and Weierstall et al. 1999).
Example 3
KmLat1 Expressed in S. cerevisiae Enables Growth on Arabinose
The coding sequence of KmLAT1 was isolated by PCR from genomic DNA of K. marxianus and cloned into a yeast 2μ plasmid under control of the PGK1 promoter of S. cerevisiae. This construct was transformed info a GAL2 deleted strain of S. cerevisiae adapted to L-arabinose. Briefly, cells are grown in appropriate selective glucose minimal media until saturation then washed and diluted to a starting. OD600 of 0.2 in minimal media supplemented with 2% L-arabinose. Cultures are incubated until exponential growth is observed then the cultures are diluted twice into the same media for continued growth to establish the final L-arabinose utilizing adapted strain which is purified on streak plates. Control plasmids carrying the yeast GAL2 gene and an empty vector were also used to transform yeast cells.
Yeast cells with a 2μ plasmid carrying the KmLAT1 or GAL2 gene or cells with an empty 2 μl plasmid were grown with shaking in liquid minimum media containing 2% L-arabinose as the sole, carbon source. The OD600 of each culture was measured and monitored by 140 hours. Growth curve results show that KmLat1 is sufficient to support growth on L-arabinose when compared to cells harboring tire empty vector which does not show any signs of growth (FIG. 5). This result confirms that the KmLat1 gene encodes an arabinose transporter that enables yeast cells to grow on L-arabinose.
Example 4
Comparison of the Arabinose Transport Kinetics Between Gal2 and KmLat1 Expressed in S. cerevisiae 
The transport characteristics of the KmLat1 and the Gal 2 transporters expressed in S. cerevisiae were compared. Both transporters were expressed in a host background adapted for growth on L-arabinose in which the endogenous copy of GAL2 had been entirely replaced with a HIS3 selection marker. The KmLat1 transporter showed a low-affinity transporter having a Km=230 mM and a Vmax=55 nmol/mg·min (FIG. 6A). This is in contrast to the high-affinity active transport activity induced, in the wild type K. marxianus when grown on 2% L-arabinose (FIG. 6B). These results suggest there are at least 2 transporters in K. marxianus that may transport L-arabinose but just the high-affinity activity is induced in the wild type when grown on 2% L-arabinose. Inhibition experiments showed that when KmLat1 is expressed in S. cerevisiae it is not significantly inhibited by protonophores such as NaN3, DNP, and CCP. Neither is KmLat1 inhibited by H+-adenosine triphosphatase (ATPase) inhibitors such as DESB and DCCD (Table 6). This is in contrast to the transport activity in wild type K. marxianus, suggesting that KmLat1 is a facilitated diffusion permease similar to the Gal2 permease. Competition experiments showed that KmLat1 is out-competed by glucose, galactose, xylose, and maltose when expressed in S. cerevisiae (Table 6).







TABLE 6







Effect of Inhibitors or Competing Sugars on the Rate


of L-Arabinose Transport in L-Arabinose-Grown S. cerevisiae


Expressing GAL2 or KmLAT1














Relative






L-arabinose




Inhibitor or
Concentration
transport (%)













Competing Sugar
(mM)
Gal2
KmLat1






None
NA
100a
100c



NaN3
10
66
11



CCCP
5
46
61



DCCD
5
69
55



DNP
5
72
75



DESB
5
81
100 



None
NA
100b
100d



Glucose
900
10
17



Galactose
900
 3
23



Xylose
900
25
25



Maltose
450
ND
38





aUptake rate was 66.0 nmol mg−1 min−1 determined with 118 mM labeled L-arabinose.


bUptake rate was 18.9 nmol mg−1 min−1 determined with 30 mM labeled L-arabinose.


cUptake rate was 7.7 nmol mg−1 min−1 determined with 118 mM labeled L-arabinose.


dUptake rate was 3.6 nmol mg−1 min−1 determined with 30 mM labeled L-arabinose.


ND, Not Done.






Transport kinetics of S. cerevisiae BFY597 over-expressing the Gal2 permease grown on 2% L-arabinose showed a Km of 550 mM and a Vmax of 425 nmol/mg·min for L-arabinose transport (FIG. 6A). Inhibition assays showed a reduction but not a complete inhibition of transport suggestive of facilitated diffusion transport (Table 6). Competition studies showed that glucose, galactose, and xylose significantly reduced L-arabinose transport indicating that these sugars are preferentially transported over L-arabinose (Table 6). The kinetics of galactose transport were also measured in this strain and indicate that Gal2p has a Km of 25 mM and a Vmax of 76 nmol/mg·min for galactose transport (data not shown) demonstrating a higher affinity for galactose that would out-compete L-arabinose for transport.
Example 5
Cloning of the New Transporter Gene PgLAT2
Wildlype Pichia guilliermondii NRRL, Y-2075 was obtained from the Agricultural Research Service Culture Collection (NRRL). Pichia guilliermondii cells were grown in minimal media supplemented with 2% L-arabinose, galactose, or xylose. Cells were collected it) mid-growth and washed twice in water before suspension in water at about 30 mg/ml. RNA was extracted from the cells using the acid phenol method (Ausubel, et al., Short Protocols in Molecular Biology, John Wiley and Sons, 1999). Briefly, approximately 15 mL of fresh culture was added to about 25 ml, of crushed ice and centrifuged at 4° C. for 5 min at 3840×g. Cells were washed twice with cold DEPC-treated water, and the pellets were frozen at −80° C. After the pellets were resuspended in 400 ul TES (10 mM Tris HCl, pH 7.5, 5 mM EDTA, 0.5% SDS), 400 ul of acid phenol was added. The samples were vortexed vigorously for 10 sec, followed by incubation for 30-60 min at 65° C. with occasional vortexing. The tubes with the samples were then chilled on ice and spun for 5 min at 4° C. The aqueous phase was removed and re-extracted with chloroform. The aqueous phase was then ethanol precipitated using 0.1 volume of 3 M sodium acetate (pH 5.3) and two volumes of 100% ethanol. The pellet was washed using 80% ethanol, dried, and resuspended in 50 ul DEPC H2O. Total RNA concentration was quantitated by measuring the OD260 and visualized on agarose gels.
RNA purification, synthesis of cDNA, and differential display were performed at GenHunter Corporation according to standard techniques. DNA Bands showing higher levels of expression from arabinose-grown cells relative to xylose- or galactose-grown cells were reamplified using the differential display amplification primers. Direct sequencing was performed on the PCR products using the GenHunter arbitrary primers. In cases that did not yield clean sequence, the amplification products were cloned in the TOPO-TA vector pCR2.1 (Invitrogen) and individual clones were sequenced. Sequences were then compared to the databases using BLASTX analysis and those that showed similarity to known transporters or transporter-like proteins were examined further. One of these sequences led to the identification of a novel transporter gene, PgLAT2 from Pichia guilliermondii. PgLAT2 gene has an ORF of 1617 nucleotides encoding a protein with a predicted length of 539 amino acids (FIG. 7).
Example 6
Characteristics of Sugar Transport by Pichia guilliermondii 
The induction of L-arabinose transport in wild type P. guilliermondii was examined. Wild type Pichia guilliermondii cells were grown in minimal media supplemented with 2% L-arabinose, galactose, or xylose while BFY605 cells were grown in the same media supplemented with 0.2% L-arabinose. Cells were collected in raid-growth and washed twice in water before suspension in water at about 30 mg/ml. Uptake of L-(1-14C)arabinose (54 mCi/mmol, Moravek Biochemical Inc.), D-(1-14C)galactose (57 mCi/mmol, Amersham Biosciences), or D-(1-14C)xylose (53 mCi/mmol, Moravek Biochemicals Inc.) was measured as previously described (Stambuk, Franden et al. 2003). Assays were performed in 5, 10, or 30 second periods to maintain initial rates. Appropriate experiments ensured uptake was linear for at feast 1 minute. Transport, activity was described as nmoles of labeled sugar transported per mg cell dry weight per minute. Inhibition and competition assays were performed as previously described (Stambuk, Franden et al. 2003).
Cells grown on L-arabinose were able to transport L-arabinose whereas cells grown on galactose or xylose were not able to transport L-arabinose. Additionally, xylose transport was about double in cells grown in L-arabinose media compared to cells grown in xylose media. Galactose was transported at the same rate independent of growth substrate (FIG. 8). Transport competition between L-arabinose and xylose was also examined. Uptake of labeled L-arabinose was reduced by 96% when 100× un-labeled xylose was included in the transport assay whereas-uptake of labeled xylose was only reduced by 16% when 100× un-labeled L-arabinose was included in the assay (FIG. 9). This data suggests that in P. guilliermondii, growth on L-arabinose induces expression of a specific transport system capable of transporting L-arabinose and xylose. Additionally, this system preferentially transports xylose at live expense of L-arabinose if both sugars are present and has a higher transport velocity for xylose than the transport, system induced when grown on xylose. By contrast, transport activity for L-arabinose is not induced when grown on xylose.
Example 7
Arabinose Transport Kinetics of PgLAT2 Expressed in S. cerevisiae 
The L-arabinose transport characteristics of the PgLAT2 transporter expressed in S. cerevisiae grown on 0.2% L-arabinose medium showed the same L-arabinose transport characteristics as wildtype P. guilliermondii (FIG. 10). The PgLAT2 transporter when expressed in S. cerevisiae has a Km=0.07 mM and Vmax=18 nmol/mg·min. inhibition experiments showed significant, inhibition of transport by protonophores (NaN3, DNP, and COP) and H+-adenosine triphosphatase (ATPase) inhibitors (DESB and DCCD) similar to the inhibition observed in wildtype P. guilliermondii (Table 7). Competition experiments showed that L-arabinose uptake by the PgLAT2 transporter was inhibited by glucose, galactose, xylose and to a lesser extent by maltose (Table 7).







TABLE 7







Effect of Inhibitors or Competing Sugars on the Rate of L-Arabinose


Transport in L-Arabinose-Grown P. guilliermondii Y-2075 and


S. cerevisiae BFY605









Inhibitor or

Relative L-arabinose transport










Competing
Concentration

S. cerevisiae (PgLAT2


Sugar
(mM)
P. guilliermondii
transporter)













Nonea
—
100
100


NaN3
10
1
16


DNP
5
0
4


CCCP
5
0
2


DCCD
5
22
36


DESB
5
8
1


Noneb
—
100
100


Glucose
120
ND
17


Galactose
120
ND
20


Xylose
120
4
0


Maltose
120
ND
30





aRate of L-arabinose transport was 11.2 nmol mg−1 min−1 for P. guilliermondii and 10.4 nmol mg−1 min−1 for S. cerevisiae (PgLAT2 transporter) determined with 0.33 mM labeled L-arabinose.


bRate of L-arabinose transport was 14.2 nmol mg−1 min−1 for P. guilliermondii and 14.4 nmol mg−1 min−1 for S. cerevisiae (PgLAT2 transporter) determined with 1.2 mM labeled L-arabinose.






The transport activities, inhibition profiles, and competition rates with respect to xylose of wildtype P. guilliermondii and of the PgLAT2 transporter expressed in S. cerevisiae are identical suggesting that P. guilliermondii has a single, high affinity, active transporter charged with uptake of L-arabinose. There are no L-arabinose transport activities that are unaccounted which suggests the presence of a single L-arabinose transporter in P. guilliermondii. 
Example 8
Synergistic Effect on Growth Rate and Sugar Utilization by S. cerevisiae Expressing Gal2p and the New Transporter Proteins-PgLat2 and KmLat1
To determine the complementary effects on arabinose transport by the three transporters, namely, Gal2p, PgLat2 and KmLat1, yeast strains were constructed with appropriate selection markers to allow different pathway and transporter combinations to be expressed. All possible transporter combinations were generated by introducing transporter expression plasmids for PgLat2 and KmLat1 (or empty vectors) into S. cerevisiae strains expressing the bacterial genes araA, araB and araD (See e.g., Becker and Boles). All strains expressing Gal2p (due to the gal80Δ genotype), plus or minus other transporters, were able to grow on 2% or 0.2% L-arabinose after extensive lag times (a process termed “adaptation.”). A relatively low concentration of L-arabinose (0.2%) was used in tins experiment as strain differences are more pronounced at this concentration. Once “adapted” to growth on 0.2% L-arabinose, the strains were able to grow more quickly and growth curves for each transporter combination were generated.
FIG. 11 shows a comparison of shake flask growth curves for four strains on 0.2% L-arabinose, all of which express Gal2p (via the GAL80 deletion) in the absence or presence of the novel transporter PgLat2 (also see Table 5). A significant lag time was observed due to their inoculation from stationary cultures. However, once growth initiated, the growth rate was relatively rapid. The doubling time for each culture in the exponential phase of the curve is shown in Table 5. The doubling time for the PgLat2 and Gal2p co-expressing cells was markedly shorter than in the cells expressing only Gal2p (15 hours vs. 19 hours). A second observation relates to the overall extent of growth. The PgLat2 expressing strain appeared to grow to a higher overall optical density at saturation, suggesting that this strain was able to utilize the carbon source (L-arabinose) in the medium more completely (FIG. 11).
Example 9
Co-Expression of Gal2p with PgLAT2 or KmLAT1 Enables More Complete Utilization of Arabinose by Recombinant S. cerevisiae 
Doubling times for the cultures described above in Example 8 were measured in early exponential phase for each culture. Doubling time was measured by the period of time taken for the number of cells to double in a given cell culture (See generally, Guthirie and Fink, 1991). The concentration of remaining L-arabinose at the 276 hour time point was determined by HPLC (for saturated cultures only). The concentration of L-arabinose in the starting media was about 1.89 g/L and the concentration of L-arabinose in media without-L-arabinose had an undetectable level (<0.1 g/L). As shown in Table 5, significantly less residual L-arabinose remained, in the culture of cells expressing both, Gal2p and PgLAat2 than in the culture of cells expressing Gal2p alone.
Example 10
Construction of S. cerevisiae Strain Deficient in Aldose Reductase (AR)
Based on the sequence of a presumptive AR gene, two oligonucleotide primers were designed and the AR gene along with 600 bp of flanking DNA were cloned by PCR using genomic DNA isolated from yeast as template. Using another set of primers, an AR deletion construct was made in which all the coding sequences of the AR gene were replaced with a restriction enzyme site (SalI). The yeast LEU2 gene was isolated as a SalI-XhoI fragment and cloned into the SalI site of the AR deletion construct. The DNA fragment containing the LEU2 gene and AR flanking sequences was used to transform the leu2− yeast strain BFY001. LEU+ transformants were isolated, grown and analyzed by Southern and PCR analysis to confirm that the AR gene in the genome had been deleted and replaced with the LEU2 gene by homologous recombination.
One such transformant, designated BFY002, was chosen as a host for further construction of arabinose fermenting yeast strains. Shake-flask experiments were conducted and the results showed that arabitol formation in BFY002 had been reduced to about 50% in comparison with the parental strain BFY001.
Growth of BFY002 on glucose and xylulose was compared with that of BFY001. Briefly, yeast strains BFY001 and BFY002 were grown, in rich-medium YPD. Cells were collected by centrifugation and washed with sterile water, five washed cells were suspended in water at the original density. 50 μl of this cell suspension was used to inoculate 5 ml of medium containing yeast nitrogen base (“YNB”) supplemented with leucine (“Leu”), tryptophan (“Trp”), histidine (“His”) and uracil (“Ura”), plus with 1% glucose or 1% xylulose. The growth of each strain on both media at 30° C. with shaking was monitored by measuring the OD600 for about 6 generation times. As expected, both strains had much shorter doubling time on glucose than on xylulose. No significant difference in the growth curves was observed between BFY001 and BFY002 regardless of whether glucose or xylulose was used (FIG. 12).
Example 11
Isolation of E. coli araBAD genes and B. subtilis araA and Introduction into S. cerevisiae 
Primers were designed to isolate E. coli araA gene as a BgIII fragment, and the araB and araD genes were isolated as BamHI fragments by PCR from plasmid pZB206. The fragments containing the three, genes were cloned into a yeast expression vector pBFY004, which contains PGK promoter, GAL10 terminator, and TRP1 selection marker. Each plasmid carrying individual gene was then transformed into the yeast strain BFY002 in separate experiments. Transformants carrying individual plasmid were analyzed for the expression levels of each ara protein. L-ribulokinase (araB) and L-ribulose-5-P-4-epimerase (araD) were expressed at a higher level while L-arabinose isomerase (araA) was expressed at a lower level.
In order to introduce all three ara genes into the same cell, URA3 and HIS3 expression vectors for each ara gene were constructed by re-engineering the TRP1 plasmid, pBFY-004. Briefly, the TRP1 coding sequence was removed and replaced with a SalI restriction site to generate a plasmid designated as pBFY011. Other selection markers, HIS3 or URA3, were then cloned into this plasmid. Another strategy for introducing all three ara genes into the same cell was to construct a plasmid carrying all three genes. Briefly this was done by combining each ara gene with a different promoter/terminator combination, to prevent homologus recombination and thus loop-out of the genes with corresponding loss of function. Primers were designed to clone the E. coli araD gene between the TDH3 promoter and GAL2 terminator. This expression cassette was then moved, to pBFY007 (which already has the E. coli araA gene cloned between the PGK1 promoter and GAL10 terminator) and designated pBFY051. Similarly primers were designed to clone the E. coli araB gene between the PGI1 promoter and the PDC1 terminator. This expression cassette was then moved to pBFY051 to create pBFY090 which now has all three E. coli ara genes. The B. subtilis araA gene was then isolated using PCR and cloned between the PGK1 promoter and GAL10 terminator to replace the E. coli araA. The URA3 gene was isolated as a SalI fragment and cloned into the SalI site to construct the plasmid pBFY012. Similarly, a HIS3 expression vector, pBFY013, was constructed by engineering and cloning the HIS3 gene into pBFY011.
The engineered ara genes were cloned into each of these expression vectors to generate a series of expression vectors carrying each of the araBAD genes with either Trp1, (Ura3 or His3 markers (Table 3; also see FIG. 13 and FIG. 14). Appropriate combinations of these expression vectors were introduced into the strain BFY002. Similarly, the plasmid containing all three ara genes was introduced into the strain BFY057. The transformants were characterized and assayed for growth and fermentation of arabinose.
Example 12
Determination of the Copy Numbers of Plasmids Carrying araBAD in S. cerevisiae 
The copy numbers of the three plasmids present in the strain BFY013 (Table 8) transformed as described in Example 11 were determined. On colony of BFY013 was isolated and used to inoculate a flask with yeast minimum medium. The cells were allowed to grown to exponential phase and the cells were harvested by centrifugation. Spheroplasts of the cells were prepared and DNA was extracted from these spheroplasts (See Guthrie and Fink. 1991). E. coli strain DH5α cells were then transformed with the extracted yeast DMA. Bacterial transformants were plated out and plasmid DNA in individual colonies was isolated and characterized by restriction digest followed by agarose gel electrophoresis. Assuming that the individual plasmids carrying each of the araBAD genes possessed the same capability to transform bacterial cells, the ratio between the copy numbers of each plasmids present in the original yeast cells was estimated based on the number of E. coli transformants harboring each plasmid (Table 8).







TABLE 8







Ratio of the 3 plasmids in BFY013










ara gene
Number













araB
11



araA
4



araD
15









Example 13
Assays of Enzymatic Activities of araBAD Proteins Expressed in S. cerevisiae 
The activities of the three E. coli enzymes heterologously expressed in S. cerevisiae were measured in the crude extracts of die yeast transformants according to protocol described in Becker and Boles, 2003. The results of these assays are summarized in Table 9. Table 10 compares the enzymatic activities of the two strains used for subsequent fermentation. The enzymatic assays were performed in the presence of absence of 20 mM. MnCl2, but it appears that MnCl2 does not have significant, effect, on the overall results (Table 10).







TABLE 9







Enzyme activities in transformants carrying all 3 ara genes













L-ribulose 5-P4-epimerase



L-arabinose isomerase (araA)
L-ribulokinase (araB)
(araD)



Sp. act umol/min/mg
Sp. act umol/min/mg
Sp. act umol/min/mg

















Strain
Oct 20-21 (1)
Oct 20-21 (2)
Dec 20-22 (2)

Oct 20-21
Dec 20-22

Oct 20-21
Dec 20-22






BFY012
nd

nd

nd
nd

nd
nd



BFY013
0.05
0.10
0.11
trp
1.2
1.3
ura
0.5  
  1.0
his


BFY014
0.04
0.11
0.11
trp
1.2
1.9
his
nd
nd
ura


BFY015
nd

nd
ura
2.4
2.8
trp
0.39
  0.9
his


BFY016
0.03

0.06
his
2.4
2.4
trp
nd
nd
ura


BFY017
0.02

nd
his
0.9
1.1
ura
1.56
>3.5
trp


BFY018
0.01

nd
ura
1.2
1.0
his
1.12
>2.2
trp


Zymomonas
0.85



0.9


1.9 





nd = not detected


(1) = cysteine-carbozole


(2) = new method, NADH disappearance


All cultures were grown in selective medium (YNB + 2% glo-trp-his-ura)













TABLE 10







Enzyme Activities in Strains Used for Fermentation















Isomerase (araA)
Kinase (araB)
Epimerase (araD)



MnCl2
Protein
Sp. act
Sp. act
Sp. act


Strain
(20 mM)
mg/ml
umol/min/mg
umol/min/mg
umol/min/mg





BFY012
No
6.6
nd
nd
nd


BFY012
Yes
6.1
nd
nd
nd


BFY013
No
7.0
0.09
2.2
0.6


BFY013
Yes
6.7
0.09
1.9
0.5









Example 14
Whole-Cell Fermentation in S. cerevisiae 
The transformed yeast cells carrying bacterial genes araBAD were first grown in galactose or arabinose alone or in the presence of both galactose and arabinose in YNB. Cells were collected by centrifugation and washed in water. The washed cells were resuspended in liquid media containing 1% yeast extract and 2% peptone (YP). The cell suspensions were aliquoted into various tubes before appropriate sugars were added. The tubes were incubated at 30° C. and cell samples were taken at the time indicated. The samples were filtered and analyzed for ethanol concentration by gas chromatography (GC) according to Tietz, 1976 (Table 11 and FIG. 15) or by high perfoemanc liquid chromatography (HPLC). As shown in Table 11, cells that were grown in both galactose and arabinose immediately before the fermentation assay had a slightly higher overall yield of ethanol than cells grown in galactose alone dining the same period. The strains BFY534 and BFY535 were grown in arabinose alone prior to fermentation. Front a starting concentration of 19 g/L of L-arabinose. BFY534 and BFY535 used 12.7 and 11.8 g/L of L-arabinose to yield 4.7 and 4.9 g/L of ethanol in 48 hours respectively. The percentage of maximum theoretical conversion would thus be 75% and 78% respectively and a productivity of 0.012 g EtOH/g cells hr for both strains, in an additional fermentation with strain BFY534 performed in shake flasks, 19.7 g/L of L-arabinose was converted to 8.5 g/L ethanol in 96 hrs giving 85% of the theoretical maximum conversion and a productivity of 0.017 g EtOH/g cells hr.







TABLE 11







Ethanol Concentration (g/l) from Whole Cell Fermentation











Glucose
Arabinose




(66.7 g/l)
(66.7 g/l)
No sugar









Time (hrs)
















0
24
0
24
120
0
24
120


















BFY012 (Gal)
1.9
33.6
1.0
1.1
1.6
1.0
0.9
1.8


BFY013 (Gal)
1.6
33.3
0.9
1.3
2.6
0.0
0.9
0


BFY015 (Gal)
1.5
33.8
0.9
1.3
2.5
0.0
0.9
1.3


BFY012 (G + A)
2.1
34.3
1.0
1.2
1.9
1.0
1.0
1


BFY013 (G + A)
1.7
34.2
1.0
1.8
4.2
0.9
1.0
0


BFY015 (G + A)
1.5
33.8
0.9
1.5
3.2
0.0
1.0
0









Example 15
Cell-Free Fermentation in S. cerevisiae 
For fermentation of arabinose in a cell-free system, yeast transformants were grown in the presence of both galactose and arabinose in YNB. Cells were collected by centrifugation and washed in water. Cell wails were removed by enzymatic digestion and the cells were then lysed in a lysis buffer containing 20 mM potassium phosphate buffer, pH 7 and 10 mM MgCl2 and 1 mM DTT. Cells debris were removed by centrifugation, and the supernatant was transferred to a tube where various chemicals were added to the supernatant, such that the fermentation mix contained 7 mM Mg acetate, 5 mM ATP, 0.1 mM diphosphoglyceric acid, 4 mM Na arsenate and 2 mM NAD+. Fermentation was started by adding appropriate sugar to the fermentation mix in the tube. The tube; was incubated at 30° C., and samples were taken at the time indicated. The samples were boiled, centrifuged, filtered, and analyzed for ethanol concentration by gas chromatography (GC) as previously described. Results of the cell-free fermentation are shown in Table 12, FIG. 16, FIG. 17 and FIG. 18.







TABLE 12







Ethanol Concentration (g/l) from Cell-Free Fermentation











Glucose
Arabinose
No sugar









Time (hrs)























0
2
24
48
72
0
2
24
48
72
0
2
24
48
72

























BFY012
0.0
2.7
8.1
8.3
8.2
0.0
1.4
1.9
1.9
1.9
1.2
1.5
1.9
1.9
2.0


BFY013
0.0
3.1
12.6
13.2
12.8
0.0
1.7
4.5
6.0
6.8
0.0
1.5
2.1
2.1
2.0


BFY012 (20 mM MnCl2)
1.3
2.5
9.2
9.0
8.5
1.2
1.4
1.9
1.9
2.1
0.0
1.4
2.0
2.0
1.8


BFY013 (20 mM MnCl2)
1.3
3.0
12.8
13.1
—
1.3
1.8
4.6
6.1
6.8
1.3
1.6
2.0
2.0
—









Example 16
Mixed-Sugar Fermentation in S. cerevisiae 
Yeast strains adapted to contain the araB and oral) genes from E. coli, the araA isomerase gene from B. subtilis, and the GAL2 overexpression plasmid have been described previously (see for example, Example 11). Adapted strains, BFY534 for example, were tested for fermentation of glucose, arabinose, and a mixture of arabinose and glucose. In particular, 125 ml non-baffled flasks containing 50 ml of yeast-extract-peptone media (including adapted yeast) and either no sugar, glucose, L-arabinose, or both glucose and L-arabinose were prepared. The flasks were closed with Saranwrap held in place with rubber bands. The fermentations were performed at 30° C. with gentle shaking (80 rpm). In all cases, each sugar was present at a concentration of 20 g/L.
The results are illustrated in FIG. 19, where a greater than 50% increase in ethanol production was obtained in co-fermentation of glucose and L-arabinose, compared to the ethanol yield of glucose alone.
While a number of exemplary aspects and embodiments have been discussed above, those of skill in the art will recognize certain modifications, permutations, additions and sub-combinations thereof. It is therefore intended that the following appended claims and claims hereafter introduced are interpreted to include all such modifications, permutations, additions and sub-combinations as are within their true spirit and scope
This specification contains numerous citations to references such as patents, patent applications, and scientific publications. Each is hereby incorporated by reference for all purposes.
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## Claims

1. An isolated polynucleotide encoding an isolated non-conventional yeast arabinose transporter comprising the capability of adapting a conventional yeast for growth on arabinose when the arabinose transporter is included in the conventional yeast, wherein the transporter comprises an amino acid sequence at least 95% identical to SEQ ID NO:2.

2. The isolated polynucleotide of claim 1, wherein the polynucleotide comprises SEQ ID NO:1.

3. A vector comprising the polynucleotide of claim 1.

4. A yeast cell comprising the vector of claim 3.

5. The isolated polynucleotide of claim 1, wherein the transporter comprises the amino acid sequence of SEQ ID NO:2.