CA2663711A1 - Acetolactate synthase (als) selectable marker from trichoderma reesei - Google Patents

Abstract

A nucleic acid encoding an acetolactate synthase (ALS) protein that provides resistance to ALS inhibitors, e.g., sulphonylurea and imidazolinone compounds, is provided. The nucleic acid may be used as a selectable marker for expression of a protein of interest in host cells.

Description

ACETOLACTATE SYNTHASE (ALS) SELECTABLE MARKER FROM
TRICHODERMA REESEI

s CROSS-REFERENCE TO RELATED APPLICATIONS
[01] This application claims priority to United States provisional applications US 60/846,804, filed September 22, 2006, and US 60/846,656, filed on September 22, 2006, both of which are herein incorporated by reference in entirety.

BACKGROUND

[02] Plants, fungi and bacteria synthesize the amino acids valine, leucine and isoleucine via a common pathway. One of the enzymes in this pathway is acetolactate synthase (ALS) (otherwise known as acetohydroxyacid synthase or AHAS), which converts pyruvate into 2-acetolactate as the first step in the synthesis of valine and leucine, and also converts pyruvate and is 2-ketobutyrate into 2-aceto-2-hydroxybutyrate, the precursor of isoleucine.
The activity of wild-type acetolactate synthase is sensitive to the action of several known classes of toxic compounds, including sulphonylurea and imidazolinone compounds. As such, such toxic compounds may be employed to kill cells containing acetolactate synthase proteins that are sensitive to those compounds.

[03] This disclosure relates to acetolactate synthase enzymes that provide resistance to toxic compounds, and hence are useful selectable markers for recombinant cells.

SUMMARY OF THE INVENTION

[04] An acetolactate synthase protein that provides resistance to ALS
inhibitors, e.g., sulphonylurea and imidazolinone compounds, is provided, as well as a polynucleotide encoding the same. In certain embodiments, the amino acid sequence of the acetolactate protein is at least 80% identical to SEQ ID NO: 1, the wild-type acetolactate protein of Trichoderma reesei. In particular embodiments, the ALS protein may contain an acidic amino acid at position 190, an acidic amino acid at position 241, or a histidine at position 372. In some embodiments, the ALS
gene or polypeptide may be employed as a selectable marker in a wide variety of species. In certain cases, the protein may be non-naturally occurring.

[05] In certain embodiments, a polynucleotide encoding ALS may be operably linked to a promoter and a terminator to provide for expression of the ALS inhibitor resistance-conferring protein in a host cell. The promoter and terminator may be endogenous to the host cell in which the polynucleotide is to be employed, and, in certain cases, the promoter and terminator may be the promoter and terminator of an ALS gene of the cell. The polynucleotide may, in certain embodiments, contain a single open reading frame encoding the acetolactate synthase protein, in which case the polynucleotide may be at least 70% identical to or may hybridize with SEQ ID
s NO:2. In other embodiments, the polynucleotide may comprise introns, in which case the polynucleotide may have a nucleotide sequence which is at least 70% identical to or may hybridize with SEQ ID NO:4. In other embodiments, the polynucleotide may be codon-optimized for expression of the acetolactate synthase protein in a particular host cell.

[06] A vector comprising the polynucleotide is also provided. In addition to the to polynucleotide, the subject vector may contain an expression cassette for expression of a recombinant protein, e.g., an enzyme or therapeutic protein, in the cell.

[07] A host cell comprising the subject polynucleotide is also provided. In certain embodiments, the host cell is resistant to an ALS inhibitor, e.g., a toxic sulphonylurea or imidazolinone compound. The host cell may be any cell that is sensitive to the ALS inhibitor in is the absence of the polynucleotide. In certain embodiments, the host cell may be a plant cell, e.g., a corn, soybean or Arabidopsis cell, a ftmgal cell, e.g., a filamentous fungal cell such as a Trichoderma sp. or Aspergillus sp. cell or a bacterial cell, e.g. a Bacillus sp. In particular embodiments, the host cell is a filamentous fungal. The cell may be present in vitro, or in a multicellular organism (e.g., a plant). The polynucleotide may be present in a genome of the host 20 cell, or may be present in a vector that autonomously replicates in the host cell.
1081 Also provided is a method of selecting a cell. In certain embodiments, the method includes: introducing a subject polynucleotide which encodes an ALS into a plurality of cells, contacting the plurality of cells with an ALS inhibitor, and culturing the cells to provide for selection of the cell. In certain embodiments, the cell is a fungal cell. The cell may be cultured in 25 a liquid medium containing the ALS inhibitor, or on a solid medium containing the ALS
inhibitor. These methods may also include introducing a second polynucleotide into the host cell, where the second polynucleotide encodes a polypeptide that is to be produced by the host cell. The subject polynucleotide and the second polynucleotide may be present on the same or different nucleic acid, e.g., the same vector or different vectors. If different vectors are 30 employed, they may be co-transformed into the same cells.
[09] Also provided are embodiments relating to relating to the 1818A and 1818B
promoters BRIEF DESCRIPTION OF THE FIGURES

[10] FIG. I shows the amino acid sequence of the wild type acetolactate synthase protein s from T. reesei (SEQ ID NO:1).
[11] FIG. 2 shows the nucleotide sequence of a T. reesei deduced cDNA (SEQ ID
NO:2) encoding the wild type acetolactate protein of Fig. 1.
1121 FIG. 3 shows the nucleotide sequence of a T. reesei gene (SEQ ID NO:3) encoding the wild type acetolactate synthase protein of Fig. 1, wherein the promoter is in italics, the sequence to encoding ALS is underlined (SEQ ID NO:4), and the terminator sequence is in italics and underlined.
[13] FIG. 4 is a general diagram of a vector that may be used to test the ALS
marker, wherein the vector includes two genes. The first gene corresponds to a polynucleotide encoding a protein of interest (e.g. a glucoamylase enzyme) and the second gene corresponds to a polynucleotide 1s coding for the ALS marker.
[14] FIGS. 5A and 5B show the nucleotide sequence of the promoters 1818A (SEQ
ID NO:7) and 1818B (SEQ ID NO:8), respectively.
1151 FIG. 6 shows the nucleotide sequence (SEQ ID NO:9) of the pTrex-glucoamylase vector used to test the ALS marker which comprises the Trichoderma reesei cbhl promoter, attB 1, a :o polynucleotide encoding a Trichoderma reesei glucoamylase, attB2, the Trichoderma reesei cbh 1 terminator and an ALS marker (A I 90D) in the E. col i vector pSL 1180.
[16] FIG. 7 illustrates an SDS-PAGE gel of supematant samples from shake flask grown transformant. Lane 1 depicts the untransformed control. Expression of the T.
reesei glucoamylase is shown in lanes 3 and 4 as highlighted by the arrow.
25 [17] FIG. 8 is a diagram of the vector used to test the 1818A and 1818B
promoters.
[18] FIG. 9 shows the nucleotide sequence of a construct used to test the 1818A and 1818B
promoters (SEQ ID NO: 10).

DETAILED DESCRIPTION
30 Definitions [19] Unless defined otherwise herein, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Singleton, et al., DICTIONARY OF MICROBIOLOGY AND MOLECULAR

BIOLOGY, 2D ED., John Wiley and Sons, New York (1994), and Hale & Marham, THE
HARPER
COLLINS DICTIONARY OF BIOLOGY, Harper Perennial, NY (1991) provide one of skill with general dictionaries of many of the terms used in this invention. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of s the present invention, the preferred methods and materials are described.
[20] All patents and publications, including all sequences disclosed within such patents and publications, referred to herein are expressly incorporated by reference.
(21] Numeric ranges are inclusive of the numbers defining the range. Unless otherwise indicated, nucleic acids are written left to right in 5' to 3' orientation;
amino acid sequences are written left to right in amino to carboxy orientation, respectively.
[22] The headings provided herein are not limitations of the various aspects or embodiments of the invention which can be had by reference to the specification as a whole.
Accordingly, the terms defined immediately below are more fully defined by reference to the specification as a whole.
is [23] As used herein, the term "selectable marker" refers to a gene or polynucleotide whose expression allows identification of cells that have been transformed with a DNA construct or vector containing the gene or polynucleotide. Selectable markers may provide resistance to toxic compounds such as antibiotics, herbicides, and the like.
1241 The term "acetolactate synthase (ALS)" refers to an enzyme that has an activity defined as EC 2.2.1.6, according to IUBMB Enzyme Nomenclature. The enzyme catalyses a reaction between two pyruvate molecules to produce 2-acetolactate and CO2. The enzyme requires thiamine diphosphate, and may be referred to as acetohydroxyacid synthase (AHAS) elsewhere.
1251 The term "ALS inhibitor" refers to a compound that inhibits wild-type ALS
protein and is toxic to cells that contain wild-type ALS. Such compounds include known herbicides, and include the sulfonylurea, imidazolinone, triazolopyrimidine, pyrimidinylthiobenzoate, or sulfonylamino-carbonyl-triazolinone compounds discussed below.
[26] The term "promoter" is defined herein as a nucleic acid that directs transcription of a downstream polynucleotide in a cell. In certain cases, the polynucleotide may contain a coding sequence and the promoter may direct the transcription of the coding sequence into translatable RNA.
[27] The tenm "isolated" as defined herein means a compound, a protein, cell, nucleic acid sequence or amino acid that is removed from at least one component with which it is naturally associated.
[28] The term "coding sequence" is defined herein as a nucleic acid that, when placed under the control of appropriate control sequences including a promoter, is transcribed into mRNA
which can be translated into a polypeptide. A coding sequence may contain a single open reading frame, or several open reading frames separated by introns, for example. A coding sequence may be cDNA, genomic DNA, synthetic DNA or recombinant DNA, for example. A
s coding sequence generally starts at a start codon (e.g., ATG) and ends at a stop codon (e.g., UAA, UAG and UGA).
[29] The term "recombinant" refers to a polynucleotide or polypeptide that does not naturally occur in a host cell. A recombinant molecule may contain two or more naturally occurring sequences that are linked together in a way that does not occur naturally.
[30] The term "heterologous" refers to elements that are not normally associated with each other. For example, a heterologous protein is a protein that is not produced in a wild-type host cell, a heterologous promoter is a promoter that is not present in nucleic acid that is endogenous to a wild type host cell, and a promoter operably linked to a heterologous coding sequence is a promoter that is operably linked to a coding sequence that it is not usually operably linked to in Is a wild-type host cell.
[311 The term "operably linked" refers to an arrangement of elements that allow them to be functionally related. For example, a promoter is operably linked to a coding sequence if it controls the transcription of the sequence, and a signal sequence is operably linked to a protein if the signal sequence directs the protein through the secretion system of a host cell.
[32] The term "nucleic acid" encompasses DNA, RNA, single or doubled stranded and modification thereof. The terms "nucleic acid" and "polynucleotide" may be used interchangeability herein.
1331 The term "DNA construct" as used herein means a nucleic acid sequence that comprises at least two DNA polynucleotide fragments.
zs [34] The term "signal sequence" or "signal peptide" refers to a sequence of amino acids at the N-terminal portion of a protein, which facilitates the secretion of the mature form of the protein outside the cell. The mature form of the extracellular protein lacks the signal sequence which is cleaved off during the secretion process.
[35] The term "vector" is defined herein as a polynucleotide designed to carry nucleic acid sequences to be introduced into one or more cell types. Vectors include cloning vectors, expression vectors, shuttle vectors, plasmids, phage or virus particles, DNA
constructs, cassettes and the like. Expression vectors may include regulatory sequences such as promoters, signal sequences, a coding sequences and transcription terminators.
[36] An "expression vector" as used herein means a DNA construct comprising a coding sequence that is operably linked to suitable control sequences capable of effecting expression of a protein in a suitable host. Such control sequences may include a promoter to effect transcription, an optional operator sequence to control transcription, a sequence encoding suitable ribosome binding sites on the mRNA, enhancers and sequences which control s termination of transcription and translation.
1371 As used herein, the terms "polypeptide" and "protein" are used interchangeably and include reference to a polymer of any number of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical analog of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers. The terms also apply to polymers containing conservative amino acid substitutions such that the polypeptide remains functional. "Peptides" are polypeptides having less than 50 amino acid residues.
[38] A "host cell" is a cell which that contains a subject recombinant nucleic acid, either in the genome of the host cell or in an extrachromosomal vector that replicates autonomously is from the genome of the host cell. A host cell may be any cell type.
[39] The term "filamentous fungi" refers to all filamentous forms of the subdivision Eumycotina (See, Alexopoulos, C. J. (1962), INTRODUCTORY MYCOLOGY, Wiley, New York). These fungi are characterized by a vegetative mycelium with a cell wall composed of chitin, glucans, and other complex polysaccharides. The filamentous fungi of the present invention are morphologically, physiologically, and genetically distinct from yeasts. Vegetative growth by filamentous fungi is by hyphal elongation and carbon catabolism is obligatory aerobic.
[40] A "non-pathogenic" cell is a strain that is not pathogenic to humans.
[41] "Transformation" means introducing DNA into a cell so that the DNA is maintained in the cell either as an extrachromosomal element or chromosomal integrant.
1421 Unless otherwise indicated, all amino acid positions in an acetolactate synthase protein are relative to SEQ ID NO:l, after alignment of that protein with SEQ ID NO:1 using the BLASTP program (Altschul, Nucl. Acids Res. 1997 25:3389-3402; Schaffer, Bioinformatics 1999 15:1000-1011) under default conditions, as available from the world wide website of the so National Center of Biotechnology Information (NCBI).
Polynucleotides 1431 Provided herein is a polynucleotide that encodes an acetolactate synthase protein that provides resistance to ALS inhibitors. In certain embodiments, the acetolactate synthase protein is a non-naturally occurring protein. In general terms, the polynucleotide encodes a protein that:
a) possesses acetolactate synthase activity (i.e., can catalyze a reaction between two pyruvate molecules to produce 2-acetolactate), b) confers resistance to ALS inhibitors, e.g., s sulphonylurea and imidazolinone compounds, and c) has an amino acid sequence that is at least 85% identical (e.g., at least 90% identical, at least 93% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, at least 98.5%
identical, at least 99% identical or at least 99.5% identical) to SEQ ID NO:I, where SEQ ID NO:1 sets forth the amino acid sequence of a wild-type acetolactate synthase from Trichoderma reesei.
144] In certain embodiments, the polynucleotide may encode a protein having one or more of:
a) an acidic amino acid (e.g., Asp or Glu) at position 190, b) an acidic amino acid (e.g., Asp or Glu) at position 241, or a His at position 372. Positions 190, 241 and 372 in the wild-type T.
reesei ALS protein are underlined in Fig. 1. As noted above, positions 190, 241 and 372 in a different ALS protein (e.g., an ALS protein that is, for example, shorter, longer or contains Is deletions and/or insertions relative to the wild-type T. reesei ALS
protein), are defined herein as being the positions in that protein that correspond to (i.e., align with or lie across from) positions 190, 241 and 372 of the wild-type T. reesei ALS protein when the wild-type T. reesei ALS protein and the other protein are aligned using standard sequence alignment methods, e.g., BLASTP (Altschul, Nucl. Acids Res. 1997 25:3389-3402; Schaffer, Bioinformatics 15:1000-1011) using default parameters. ALS proteins, in general, are well characterized enzymes and have been investigated in great detail functionally and structurally. ALS proteins have been reviewed in several publications (see, e.g., Chipman, Biochim.
Biophys. Acta 1998 1385:401-19; Chipman, Curr. Opin. Chem. Biol. 2005 9:475-81), and have been crystallized (see, e.g., Pang, J. Biol. Chem. 2004 279:2242-53; Pang, J. Mol. Biol. 2002 317:249-62), as well as subjected to mutagenesis to identify essential and non-essential residues (see, e.g., Ibdah, Biochemistry 1996 35:16282-91; Mendel J. Mol. Biol. 2001 307:465-771;
Hill, Biochem. J. 1998 335:653-61). Other herbicide resistance-conferring mutations are also known (see, e.g., Jung, Biochem. J. 2004 383:53-61; Duggelby, Eur. J. Biochem. 2003 270:2895-904).
Further, the amino acid sequences of several hundred ALS proteins are known, and publicly available via NCBI's Genbank database. As such, a wide variety of amino acid changes that could be made to a subject ALS protein, some of which may confer resistance to ALS
inhibitors, without abolishing its activity would be readily apparent.
1451 In certain cases, the amino acid changes described herein may be transferred into any other ALS protein, from any species, to render that protein herbicide resistant. In other words, an amino acid at position 190, 241 or 372 (relative to SEQ ID NO: 1) of any other ALS protein may be substituted by an acidic amino acid (e.g., Asp or Glu), an acidic amino acid (e.g., Asp or Glu), or a His, respectively, to provide an ALS protein that confers resistant to an ALS
inhibitor.
s 1461 For example, the amino acid sequence of the ALS proteins of several fungal species are known and are deposited into NCBI's Genbank database. In certain embodiments, the above-described amino acid alterations can be transferred to the ALS proteins of those fungi in order to provide other ALS inhibitor-resistant proteins. In other embodiments, the amino acid sequence other fungal ALS proteins may be employed to make further changes in the subject T.
reesei-based ALS proteins that do not abolish the ALS activity of those proteins. For example, a fusion between two ALS proteins from different species, or a protein containing amino acid substitutions, deletions or insertions could be made. Exemplary ALS amino acid sequences from other fungal species, including other filamentous fungal species, are deposited at NCBI's Genbank database as GIDS: 39977967 and 2547090 (Magnaporthe grisea), GID:85108881 1s (Neurospora crassa), GID:46108408 (Gibberella zeae), GID:90302929 (Coccidioides immilis), GID: 67537572 (Aspergillus nidulans); GID: 70999742 (Aspergillus fumigatus);
GIDs:
83767597 and 83771596 (Aspergillus oryzae); GID: 111063308 (Phaeosphaeria nodorum), GID: 50547615 (Yarrowia lipolytica), GID: 49657303 (Debaryomyces hansenii), GID:
68468265 (Candida albicans), GID: 21615550 (Saccharomycopsisfibuligera), GID:

(Kluyveromyces lactis); GID: 49527687 (Candida glabrata) and GID: 817866 (Saccharomyces cerevisiae). The above-referenced Genbank accessions are incorporated by reference in their entirety, including the nucleic acid and protein sequences therein, and the annotation of those sequences,.as of the earliest filing date of this patent application.
1471 Because of the redundancy of the genetic code, a subject polynucleotide may comprise any one of a number of nucleotide sequences. In particular embodiments, the subject polynucleotide may have a nucleotide sequence that is: a) at least 70%
identical to (e.g., at least 80%, at least 90%, at least 95%, at least 98% or at least 99% identical to), or b) hybridizes with under stringent hybridization conditions to SEQ ID NO:2 or SEQ ID NO:4, which sequences set forth the nucleotide sequence of a wild-type cDNA and gene of T. reesei, respectively. As ao such, the encoding polypeptide may contain introns, or may contain a single open reading frame encoding the protein.
[48] As would be apparent, in certain embodiments, the polynucleotide may have a nucleotide sequence that encodes a protein having one or more of: a) an acidic amino acid (e.g., Asp or Glu) at position 190, b) an acidic amino acid (e.g., Asp or Glu) at position 241, or a His at position 372.
[49] The term "identity" in the context of two nucleic acid sequences refers to nucleotides residues in the two sequences that are the same when aligned for maximum correspondence, as measured using any of the following sequence comparison algorithms. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith &
Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nal'1 Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, WI), or by visual inspection.
1501 An example of an algorithm that is suitable for determining sequence similarity is the BLAST algorithm, which is described in Altschul, et al., J. Mol. Biol. 215:403-410 (1990).
~s Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information available on the world wide web (www) ncbi.nlm.nih.gov. The BLAST algorithm performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA 90:5873-5787 (1993)). A
nucleotide sequence of at least 100, at least 500, at least 1000, up to entire length of the SEQ ID NOS:2 or 4 may be employed in sequence comparisons.
[51] . As noted above, the polynucleotide may include a nucleotide sequence that hybridizes under stringent hybridization conditions to a polynucleotide having the nucleotide sequence of SEQ ID NO: 2 or 4, where stringent hybridization conditions encompass low, medium, high and very high stringency hybridization conditions.
[52] "Low-stringency" conditions refer to washing with a solution of 1X
SSC/0.1% SDS at 20 C for 15 minutes. "Medium-stringency" conditions refer to washing with a solution of 1X
SSC/0.1 % SDS at 65 C for 60 minutes. "High-stringency" conditions refer to washing with a solution of 0.2X SSC/0.1 % SDS at 65 C for 10 minutes. "Very high-stringency"
conditions refer to washing with a solution of 0.2X SSC/0.1% SDS at 65 C for 60 minutes.
ao [53] Hybridization methods are described in great detail in Sambrook et al., MOLECULAR
CLONING: A LABORATORY MANUAL (2nd Ed., 1989 Cold Spring Harbor, NY). In one exemplary hybridization assay, a DNA sample is electrophoresed through an agarose gel (for example, 0.8% agarose) so that of the DNA fragment can be visualized by ethidium bromide staining.
The gel is then briefly rinsed in distilled H20 and subsequently depurinated in an appropriate solution (such as, for example, 0.25M HCI) with gentle shaking followed by denaturation for 30 minutes (in, for example, 0.4 M NaOH) with gentle shaking. A renaturation step may be included, in which the gel is placed in 1.5 M NaCI, 1MTris, pH 7.0 with gentle shaking for 30 minutes. The DNA is then transferred onto an appropriate positively charged membrane, for s example, Maximum Strength Nytran Plus membrane (Schleicher & Schuell, Keene, N.H.), using a transfer solution (such as, for example, 6XSSC, i.e., 900 mM NaCI, 90 mM trisodium citrate). Once the transfer is complete, generally after about 2 hours, the membrane is rinsed in e.g., 2X SSC (300 mM NaCI, 30 mM trisodium citrate) and air dried at room temperature. The membrane may be prehybridized (for approximately 2 hours or more) in a suitable prehybridization solution (such as, for example, an aqueous solution containing per 100 mL:
20-50 mL formamide, 25 mL of 20X SSPE (1X SSPE = 0.18 M NaCI, 1 mM EDTA, 10 mM
NaH2PO4, pH 7.7), 2.5 mL of 20% SDS, and 1 mL of 10 mg/mL sheared herring sperm DNA).
As would be known to one of skill in the art, the amount of formamide in the prehybridization solution may be varied depending on the nature of the reaction obtained according to routine Is methods. Thus, a lower amount of formamide may result in more complete hybridization in terms of identifying hybridizing molecules than the same procedure using a larger amount of formamide. On the other hand, a strong hybridization band may be more easily visually identified by using more formamide.
1541 A DNA probe of at least 100, at least 500, at least 1000, up to entire length of the SEQ
ID NOS:2 or 4 may be employed in hybridization assays or in sequence comparisons. The DNA probe may be isolated by electrophoresis in an agarose gel, the fragment excised from the gel, and recovered from the excised agarose. This purified fragment of DNA may be labeled (using, for example, the Megaprime labeling system according to the instructions of the manufacturer) to incorporate P32 in the DNA. The labeled probe is denatured by heating to :s 95 C for 5 minutes and immediately added to the membrane and prehybridization solution. The hybridization reaction should proceed for an appropriate time and under appropriate conditions, for example, for 18 hours at 37 C with gentle shaking or rotating. The membrane is rinsed (for example, in 2X SSC/0.3% SDS) and then washed in an appropriate wash solution, as described above, with gentle agitation. Hybridization can be detected by autoradiography.
so [55] In particular embodiments, the polynucleotide may be codon optimized for expression in particular host cell. In other embodiments, the polynucleotide may have a nucleotide sequence that contains less than 10 (e.g., 9, 8, 7, 6, 5, 4, 3, 2, or 1) differences compared to the wild type ALS sequence (e.g., either the genomic or cDNA sequence) of the particular host cell in which it the polynucleotide is to be employed.

[56] In certain cases, in addition to a coding sequence, the polynucleotide may further contain other elements that are necessary for expression of the encoded protein in a host cell. For example, in one embodiment, the polynucleotide may be flanked by sequences to form an expression cassette that provides expression of the encoded protein in a host cell. In certain s embodiments, the expression cassette may contain a promoter for transcription of the coding sequence, and a transcriptional terminator, and a sequence encoding a 5' untranslated region (UTR) that allows translational initiation, each in operable linkage to the coding sequence.
Promoters, enhancers, terminators, UTRs, polyadenylation signals and other regulatory sequences for a wide variety of host cells, particularly those from plants, bacteria and fungi, are well known in the art (see, e.g., Ausubel, et al, Short Protocols in Molecular Biology, 3rd ed., Wiley & Sons, 1995; Sambrook, et al., Molecular Cloning: A Laboratory Manual, Second Edition, 1989 Cold Spring Harbor, N.Y.).
[57] In particular embodiments, the subject expression cassette may contain a promoter and terminator for expression of the subject protein in a filamentous fungal cell.
Examples of 1s suitable promoters and terminators for directing the transcription of a subject nucleic acid in a filamentous fungal host cell are promoters and terminators obtained from the genes for Aspergillus oryzae TAKA amylase, Rhizomucor miehei aspartic proteinase, Aspergillus niger neutral alpha-amylase, Aspergillus niger acid stable alpha-amylase, Aspergillus niger or Aspergillus awamori glucoamylase (glaA), Rhizomucor miehei lipase, Aspergillus oryzae alkaline protease, Aspergillus oryzae triose phosphate isomerase, Aspergillus nidulans acetamidase, Fusarium venenalum amyloglucosidase, Fusarium oxysporum trypsin-like protease (WO 96/00787), Trichoderma reesei cellobiohydrolase I, Trichoderma reesei cellobiohydrolase II, Trichoderma reesei endoglucanase I, Trichoderma reesei endoglucanase II, Trichoderma reesei endoglucanase III, Trichoderma reesei endoglucanase IV, Trichoderma 2s reesei endoglucanase V, Trichoderma reesei xylanase 1, Trichoderma reesei xylanase II, Trichoderma reesei beta-xylosidase, as well as the NA2-tpi promoter (a hybrid of the promoters from the genes for Aspergillus niger neutral alpha-amylase and Aspergillus oryzae triose phosphate isomerase); and mutant, truncated, and hybrid promoters thereof.
[58] The promoter and/or terminator may be native or non-endogenous to the host cell in which the subject ALS protein is to be expressed and, in certain embodiments, the promoter and terminator may be the ALS gene promoter and terminator from the host cell.
For example, in one embodiment, an expression cassette for use in Trichoderma reesei cells may comprise the Trichoderma reesei ALS gene promoter, the Trichoderma reesei ALS coding sequence (containing one or more of the nucleotide changes outlined above) and Trichoderma reesei ALS terminator, in operable linkage (Fig. 3). The promoter and/or tenrninator may be from an ALS gene of the host cell in which the polynucleotide is to be employed.
[59] The polynucleotide may be integrated into a genome of the host cell, or may be present on a vector that autonomously replicates in the host cell.

s Recombinant nucleic acid [60] A recombinant nucleic acid comprising a subject polynucleotide is also provided. A
subject recombinant nucleic acid may comprise a subject polynucleotide, e.g., an expression cassette for production of a resistance-conferring ALS protein in a host cell, as well as a second expression cassette for expression of a protein of interest in the host cell.
In a particular embodiment, the subject polynucleotide is employed as a marker for selection of host cells that contain the recombinant nucleic acid over other cells that do not contain the recombinant nucleic acid (i.e., the subject polynucleotide is employed as a "selectable marker" for cells that is contain the subject polynucleotide).
[61] The protein of interest encoded by the second expression cassette may be for example an enzyme, a therapeutic protein, a reporter protein, a food additive or a foodstuff or the like.
[62] In one embodiment, the protein of interest encoded by the second expression cassette may be an enzyme such as a carbohydrase, such as an a-amylase, an alkaline a-amylase, a(3-zo amylase, a cellulase; a dextranase, an a-glucosidase, an a-galactosidase, a glucoamylase, a hemicellulase, a pentosanase, a xylanase, an invertase, a lactase, a naringanase, a pectinase or a pullulanase; a protease such as an acid protease, an alkali protease, bromelain, ficin, a neutral protease, papain, pepsin, a peptidase, rennet, rennin, chymosin, subtilisin, thermolysin, an aspartic proteinase, or trypsin; a lipase or esterase, such as a triglyceridase, a phospholipase, a 25 pregastric esterase, a phosphatase, a phytase, an amidase, an iminoacylase, a glutaminase, a lysozyme, or a penicillin acylase; an isomerase such as glucose isomerase; an oxidoreductases, e.g., an amino acid oxidase, a catalase, a chloroperoxidase, a glucose oxidase, a hydroxysteroid dehydrogenase or a peroxidase; a lyase such as a acetolactate decarboxylase, an aspartic 0-decarboxylase, a fumarese or a histadase; a transferase such as cyclodextrin glycosyltranferase;
30 or a ligase, for example. In particular embodiments, the protein may be an aminopeptidase, a carboxypeptidase, a chitinase, a cutinase, a deoxyribonuclease, an a-galactosidase, a[3-galactosidase, a(3-glucosidase, a laccase, a mannosidase, a mutanase, a pectinolytic enzyme, a polyphenoloxidase, ribonuclease or transglutaminase, for example. The enzyme may be a wild-type enzyme or a variant of a wild-type enzyme. In addition the enzyme may be a hybrid enzyme that includes fragments of different enzymes.
[63) In other embodiment, the protein of interest encoded by the second expression cassette may be a therapeutic protein (i.e., a protein having a therapeutic biological activity). Examples of suitable therapeutic proteins include: erythropoietin, cytokines such as interferon-a, s interferon-(3, interferon-y, interferon-o, and granulocyte-CSF, GM-CSF, coagulation factors such as factor VIII, factor IX, and human protein C, antithrombin III, thrombin, soluble IgE
receptor a-chain, IgG, IgG fragments, IgG fusions, IgM, IgA, interleukins, urokinase, chymase, and urea trypsin inhibitor, IGF-binding protein, epidermal growth factor, growth hormone-releasing factor, annexin V fusion protein, angiostatin, vascular endothelial growth factor-2, myeloid progenitor inhibitory factor-1, osteoprotegerin, a-l-antitrypsin, a-feto proteins, DNase II, kringle 3 of human plasminogen, glucocerebrosidase, TNF binding protein 1, follicle stimulating hormone, cytotoxic T lymphocyte associated antigen 4-Ig, transmembrane activator and calcium modulator and cyclophilin ligand, soluble TNF receptor Fc fusion, glucagon like protein 1 and IL-2 receptor agonist. Antibody proteins, e.g., monoclonal antibodies that may be is humanized, are of particular interest.
[64] In a further embodiment, the protein encoded by the second expression cassette may be a reporter protein. Such reporter proteins may be optically detectable or colorigenic, for example.
In this embodiment, the protein may be a[i-galactosidase (lacZ), [i-glucuronidase (GUS), luciferase, alkaline phosphatase, nopaline synthase (NOS), chloramphenicol acetyltransferase (CAT), horseradish peroxidase (HR.P) or a fluorescent protein green, e.g., green fluorescent protein (GFP), or a derivative thereof.
[65] In certain embodiments, particularly those in which the host cell is a filamentous fungal host cell, the coding sequence of the second expression cassette may encode a fusion protein. In some of these embodiments, the fusion protein may provide for secretion of the protein from zs the host cell in which it is expressed and, as such, may contain a signal sequence operably linked to the N-terminus of the protein, where the signal sequence contains a sequence of amino acids that directs the protein to the secretory system of the host cell, resulting in secretion of the protein from the host cell into the medium in which the host cell is growing.
The signal sequence is cleaved from the fusion protein prior to secretion of the protein.
The signal sequence employed may be endogenous or non-endogenous to the host cell and, in certain embodiments, may be signal sequence of a protein that is known to be highly secreted from a host cell. In particular embodiments, the signal sequence protein may be any signal sequence that facilitates protein secretion from a filamentous fungal (e.g., Trichoderma or Aspergillus) host cell. Such signal sequence include, but are not limited to: the signal sequence of cellobiohydrolase I, cellobiohydrolase II, endoglucanases I, endoglucanases II, endoglucanases III, a-amylase, aspartyl proteases, glucoamylase, mannanase, glycosidase and barley endopeptidase B (see Saarelainen, Appl. Environ. Microbiol. 1997 63: 4938-4940), for example. Other of signal sequences are those originating from the fungal amyloglucosidase (AG) gene (glaA), the a factor gene (yeasts e.g. Saccharomyces, Kluyveromyces and Hansenula) or the a amylase gene (Bacillus). In certain embodiments, therefore, the subject recombinant nucleic acid may comprise: a signal sequence-encoding nucleic acid operably linked to a protein-encoding nucleic acid, where translation of the nucleic acid in a host cell produces a fusion protein comprising a protein having an N-terminal signal sequence for secretion of the protein from the host cell.
[661 In particular embodiments, the fusion protein may further contain a "carrier protein", which is a portion of a protein that is endogenous to and highly secreted by the host cell.
Suitable carrier proteins include those of T. reesei mannanase I (Man5A, or MANI), T. reesei cellobiohydrolase II (Ce16A, or CBHII) (see, e.g., Paloheimo et al Appi.
Environ. Microbiol.
is 2003 December; 69(12): 7073-7082 ) or T. reesei cellobiohydrolase I (CBHI).
In one embodiment, the carrier protein is a truncated T. reesei CBH I protein that includes the CBH 1 core region and part of the CBH I linker region. A fusion protein containing, from amino-terminus to carboxy-terminus, a signal sequence, a carrier protein and a subject protein in operable linkage is therefore provided, as well as a nucleic acid encoding the same.
zo [67] In certain embodiments, the polynucleotide may be codon optimized for expression of the protein in a particular host cell. Since codon usage tables listing the usage of each codon in many cells are known in the art (see, e.g., Nakamura et al, Nucl. Acids Res.
2000 28: 292) or readily derivable, such nucleic acids can be readily designed giving the amino acid sequence of a protein to be expressed.
zs [68] A subject recombinant nucleic acid may be present, e.g., integrated, into a genome (i.e., the nuclear genome) of a host cell, or may be present in a vector, e.g., a phage, plasmid, viral, or retroviral vector, that autonomously replicates in the host cell. In certain embodiments, the vector may be an expression vector for expressing a protein in a host cell and, as such, may further contain the second expression cassette discussed above. In certain embodiments, the 30 vector may be an expression vector for expressing a recombinant polypeptide in a filamentous fungal cell.
1691 Vectors for expression of recombinant proteins are well known in the art (Ausubel, et al, Short Protocols in Molecular Biology, 3rd ed., Wiley & Sons, 1995; Sambrook, et al., Molecular Cloning: A Laboratory Manual, Second Edition, (1989) Cold Spring Harbor, N.Y.).

Selection methods 1701 A method for selecting host cells that contain a subject polynucleotide is also s provided. In certain embodiments, the method includes introducing a subject polynucleotide into a plurality of cells, contacting the plurality of cells with an ALS
inhibitor, e.g., a toxic sulphonylurea or imidazolinone compound, and culturing the cells to provide for selection of the cell. The cell may be selected on solid medium, e.g., by plating the plurality of cells onto an agar plate containing the ALS inhibitor, or in liquid medium, e.g., by culturing the plurality of in a liquid medium containing the ALS inhibitor.
1711 In certain embodiments, the subject selection methods may be employed to select for cells containing a second expression cassette that encodes a protein of interest. The second expression cassette may be present in a recombinant nucleic acid that also contains the instant ALS protein-encoding polynucleotide (i.e., in a single recombinant nucleic acid molecule). In Is these embodiments, the instant selection methods may be employed to select for cells that contain the recombinant nucleic acid. Since the recombinant nucleic acid also contains the second expression cassette, cells that contain the second expression cassette are selected using the ALS inhibitor. In alternative embodiments, the second expression cassette may be present on a recombinant nucleic acid that does not contain the instant ALS protein-encoding polynucleotide (e.g., a different vector). In these embodiments, a subject polynucleotide may be co-transformed with (i.e., transformed at the same time as) a separate and distinct polynucleotide molecule (e.g., a different nucleic acid molecule or vector) that contains the expression cassette. As such, the instant selection methods may be employed to select for cells that contain the second expression cassette, even though the second expression cassette is on a 2s different nucleic acid molecule to the polynucleotide.
[72] As such, the subject selection methods may be employed to select for host cells that express the protein of interest. The protein of interest may be native or non-native to the host cells used.
1731 The exact concentration of ALS inhibitor employed may vary according to the particular ALS inhibitor used and the type of host cell to be selected. In general terms, the ALS inhibitor is used at a concentration that provides selection of the host cell containing the polynucleotide.
In certain embodiments, the ALS inhibitor may be employed at a concentration of 0.5 ppm to 10,000 ppm, for example 1 ppm to 10,000 ppm or 10 ppm to 1,000 ppm. For example, in certain cases, the ALS inhibitor may be employed at a concentration in the range of 25 ppm to 100 ppm, e.g., 50 ppm or 100 ppm, or at a concentration in the range of 100 ppm to 500 ppm, e.g., 200 ppm or 500 ppm. For example, in one embodiment, the ALS inhibitor may be employed at a concentration in the range of I g/m1 to I mg/mi, e.g., 10 g/ml to 500 g/ml.
1741 ALS inhibitors include any compounds that: a) kill cells that do not have resistance to the s compounds via inhibiting an ALS enzyme and b) do not kill cells having a subject polynucleotide. ALS inhibitors of particular interest include sulfonylurea (SU), imidazolinone (IMI), triazolopyrimidine (TP), pyrimidinylthiobenzoate (PTB), and sulfonylamino-carbonyl-triazolinone (SCT) compounds that are known ALS inhibitors and, in certain cases, may be commonly employed has herbicides. Examples of sulfonylurea compounds that may be employed in the subject methods include: I) phenylsulfonylureas, including a) chlorimuron ethyl (see Agricultural Chemicals Book II "Herbicides" by W. T. Thompson, Thompson Publications, Fresno Calif., U.S.A. 1990, page 152); b) primisulfuron (CGA
136,872, see Brighton Crop Prot. Conf. "Weeds" 1989, p. 41-48), c) 3-(4-ethyl-6-methoxy-1,3,5-triazin-2-yl)-1-(2,3-dihydro-l,l-dioxo-2-methyl benzo[b]thiophen-7-sulfonyl)-urea (see, e.g., EP-A-~s 79,683), d) 3-(4-ethoxy-6-ethyl-1,3,5-triazin-2-yl)-1-(2,3-dihydro-l,l-dioxo-2-methylb enzo[b]thiophen-7-sulfonyl)urea (see, e.g., EP-A-79,683), e) tribenuron-methyl (see "The Pesticide Manual", British Crop Protection Council 9th Edition (1990/9 1), page 840), f) metsulfuron-methyl (see Proc. Int. Congr. Plant Prot., 10th, 1983, Vol. 1, 324), g) chlorsulfuron (see U.S. Pat. No. 4,127,405; Weeds Weed Control, 1980, 21 st, 24), h) triasulfuron (see "The Pesticide Manual" 9th Ed., p. 837) and i) sulfometuron-methyl (see "The Pesticide Manual" 9th Ed., p. 774); II) thienylsulfonylureas, for example thifensulfuron-methyl (see Agricultural Chemicals Book II "Herbicides" by W. T. Thompson, Thompson Publications, Fresno Calif., U.S.A. 1990, page 155); III) pyrazolylsulfonylureas, for example: a) pyrazosulfuron-ethyl (NC
311, see "The Pesticide Manual" 9th Ed., p. 735) and b) methyl 3-chloro-5-(4,6-dimethoxypyrimidin-2-ylcarbamoylsulfamoyl)-1-methyl-pyrazo le-4-carboxylate (see EP
282,613); IV) Sulfonediamide derivatives, for example amidosulfuron and structural analogs (see EP-A-0,131,258 and Z. Pfl.Krankh. Pfl.Schutz, Special Issue XII, 489-497 (1990); V) pyridylsulfonylureas, for example: a) nicosulfuron (SL-950, see Kimura et al., Brighton Crop Protection Conference "Weeds" 1989, p. 29-34); b) DPX-E 9636 (see Brighton Crop Prot.
Conf.--Weeds--1989, p. 23 et seq.) and c) pyridylsulfonylureas as are described in German Patent Applications P 4000503.8 (WO-91/10660) and P 4030577.5 and VI) Phenoxysulfonylureas such as those described in, for example, EP-A-0,342,569, EP-A-4,163, EP-A-113,956, U.S. Pat.No. 4,678,500 and U.S. Pat. No. 4,581,059. Examples of imidazolinone compounds that may be employed in the subject methods include:
a) imazethapyr (see Ch. R. Worthing's "The Pesticide Manual" 8th Edition 1987, by British Crop Protection Council, page 473), b) imazaquin (see Ch. R. Worthing's "The Pesticide Manual" 8th Edition 1987, by British Crop Protection Council, page 474), and c) imazethamethapyr (chemical name: rac-2-[4,5-dihydro4-methyl-4-(1-methylethyl)-5-oxo-1 H-imidazol-2-yl]-5-met s hyl-3-pyridine-carboxylic acid; see Weed Techn. 1991 (5), 430-433 and 434-438) and other related compounds.

Host cells [75] A host cell comprising a subject recombinant nucleic acid is also provided. The host cell may be any cell type, e.g., bacterial (such as E. coli, Bacillus sp. or Streptomyces sp.), fungal (such as a non-filamentous or filamentous fungal), or plant (such as an Arabidopsis, com or soybean plant) host cells. In some embodiments, the host cell may be a cell of a species that has a history of use for production of proteins that has GRAS status, i.e., a Generally is Recognized as Safe, by the FDA.
[76] In particular embodiments, the subject host cell may be a fungal cell of the following species: Trichoderma, (e.g., Trichoderma reesei (previously classified as T.
longibrachiatum and currently also known as Hypocreajecorina), Trichoderma viride, Trichoderma koningii, and Trichoderma harzianum)); Penicillium sp., Humicola sp. (e.g., Humicola insolens and Humicola grisea); Chrysosporium sp. (e.g., C. lucknowense), Gliocladium sp., Aspergillus sp.
(e.g., Aspergillus oryzae, Aspergillus niger, Aspergillus nidulans, Aspergillus kawachi, Aspergillus aculeatus, Aspergillus japonicus, Aspergillus sojae, and Aspergillus awamori), Fusarium sp., Mucor sp., Neurospora sp., Hypocrea sp., or Emericella sp. (See also, Innis et al., (1985) Sci. 228:21-26), among others.
zs [77] Exemplary bacterial host cells include Bacillus sp., including, but not limited to B.
subtilis, B. licheniformis, B. lentus, B. brevis, B. stearothermophilus, B.
alkalophilus, B.
amyloliquefaciens, B. clausii, B. halodurans, B. megaterium, B. coagulans, B.
circulans, B.
lautus, and B. thuringiensis, and Streptomyces sp., including, but not limited to: S. lividans, S.
carbophilus and S. helvaticus.
1781 Exemplary plant host cells include monocot and dicot plant cells, including, but not limited to corn (Zea mays), Brassica sp., rice (Oryza sativa), wheat (Triticum aestivum), soybean (Glycine max), tobacco (Nicotiana tabacum) and Arabidopsis thaliana and tomato (Lycopersicon esculentum) host cells. A host cell may be a host cell cultured in vitro, or a host cell of a multicellular organism, i.e., a plant. Methods of transferring exogenous nucleic acids into such host cells are well known in the art.
1791 In particular embodiments, a subject fungal cell may be a strain of Trichoderma and particularly T. reesei which include functional equivalents of RL-P37 (Sheir-Neiss et al. (1984) s Appi. Microbiol. Biotechnology 20:46 -53). Other useful host strains include; NRRL 15709, ATCC 13631, ATCC 26921 (QM 9414) ATCC 32098, ATCC 32086, and ATCC 56765 (RUT-30). In other embodiments, subject fungal host cell may be of a strain of Aspergillus sp., including ATCC 22342, ATCC 44733, ATCC 14331, ATCC 11490, NRRL 3112, and strains derived therefrom.
[80] In some embodiments, a host cell may be one wherein native genes have been deleted or inactivated. For example genes corresponding to protease genes (e.g. aspartyl protease) (Berka et al. (1990) Gene 86:153-162 and USP 6,509,171) or genes corresponding to cellulase genes may be deleted or inactivated, (e.g. cbhl, cbh2 and egll, and egl2) such as the quad deleted strain of T. reesei disclosed in WO 05/001036 and derivatives thereof.
Is [81] Introduction of a nucleic acid into a host cell includes techniques such as transformation;
electroporation; nuclear microinjection; transduction; transfection, (e.g., lipofection mediated and DEAE-Dextrin mediated transfection); incubation with calcium phosphate DNA
precipitate; high velocity bombardment with DNA-coated microprojectiles; and protoplast fusion. General transformation techniques are known in the art (See, e.g., Ausubel et al., (1987), supra, chapter 9; and Sambrook (1989) supra, and Campbell et al., (1989) Curr. Genet.
16:53-56). Reference is also made to WO 05/001036; USP 6,022,725; USP
6,103,490; USP
6,268,328; and published U.S. patent applications 20060041113, 20060040353, and 20050208623, which publications are incorporated herein by reference.
[82] Transformation and protein expression in Aspergillus and Trichoderma is further described in, for example U.S. Pat. No. 5,364,770; U.S. Pat. No. 6,022,725;
and Nevalainen et al., 1992, The Molecular Biology of Trichodenma and its Application to the Expression of Both Homologous and Heterologous Genes, in MOLECULAR INDUSTRIAL MYCOLOGY, Eds. Leon and Berka, Marcel Dekker, Inc. pp. 129 - 148.
[83] As noted above, a subject host cell may further contain a recombinant nucleic acid for expression of a protein of interest in the host cell, in addition to the ALS-encoding nucleic acid.
The subject recombinant nucleic acid and the ALS-encoding nucleic acid may be closely linked in cis, either in the genome or in a plasmid, such that the ALS inhibitor selects for the recombinant nucleic, and thereby selects for cells that produce the protein.

Protein production 1841 Methods of using the above-described host cell are also provided. In certain embodiments, the subject methods include: culturing the cell comprising a recombinant nucleic s acid comprising a first expression cassette for producing a subject ALS
enzyme, and a second expression cassette for producing a protein, to produce the protein. In certain embodiments and as discussed above, the protein may be secreted into the culture medium. As such, certain embodiments of the method include the step of recovering the protein from the culture medium.
[85] Cells may cultured in a standard medium containing physiological salts and nutrients (See, e.g., Pourquie, J. et al., BIOCHEMISTRY AND GENETICS OF CELLULOSE
DEGRADATION, eds.
Aubert, J. P. et al., Academic Press, pp. 71-86, 1988 and Ilmen, M. et al., (1997) Appl. Environ.
Microbiol. 63:1298-1306). Common commercially prepared media (e.g., Yeast Malt Extract (YM) broth, Luria Bertani (LB) broth and Sabouraud Dextrose (SD) broth also find use in the present invention. Preferred culture conditions for a given filamentous fungus are known in the Is art and may be found in the scientific literature and/or from the source of the fungi such as the American Type Culture Collection (ATCC) and Fungal Genetics Stock Center.
1861 In some embodiments, a subject host cell may. be cultured under batch or continuous fermentation conditions. A classical batch fermentation is a closed system, wherein the composition of the medium is set at the beginning of the fermentation and is not subject to artificial alterations during the fermentation. Thus, at the beginning of the fermentation the medium is inoculated with the desired organism(s). In this method, fermentation is permitted to occur without the addition of any components to the system. Typically, a batch fermentation qualifies as a "batch" with respect to the addition of the carbon source and attempts are often made at controlling factors such as pH and oxygen concentration. The metabolite and biomass compositions of the batch system change constantly up to the time the fermentation is stopped.
Within batch cultures, cells progress through a static lag phase to a high growth log phase and finally to a stationary phase where growth rate is diminished or halted. If untreated, cells in the stationary phase eventually die. In general, cells in log phase are responsible for the bulk of production of end product.
[87] A variation on the standard batch system is the "fed-batch fermentation"
system, which also finds use with the present invention. In this variation of a typical batch system, the substrate is added in increments as the fermentation progresses. Fed-batch systems are useful when catabolite repression is apt to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the medium. Measurement of the actual substrate concentration in fed-batch systems is difficult and is therefore estimated on the basis of the changes of measurable factors such as pH, dissolved oxygen and the partial pressure of waste gases such as CO2. Batch and fed-batch fermentations are common and known in the art.
[88] Continuous fermentation is an open system where a defined fermentation medium is s added continuously to a bioreactor and an equal amount of conditioned medium is removed simultaneously for processing. Continuous fermentation generally maintains the cultures at a constant high density where cells are primarily in log phase growth.
[89] Continuous fermentation allows for the modulation of one factor or any number of factors that affect cell growth and/or end product concentration. For example, in one to embodiment, a limiting nutrient such as the carbon source or nitrogen source is maintained at a fixed rate and all other parameters are allowed to moderate. In other systems, a number of factors affecting growth can be altered continuously while the cell concentration, measured by media turbidity, is kept constant. Continuous systems strive to maintain steady state growth conditions. Thus, cell loss due to medium being drawn off must be balanced against the cell ~s growth rate in the fermentation. Methods of modulating nutrients and growth factors for continuous fermentation processes as well as techniques for maximizing the rate of product formation are known.
1901 A fungal host cell may be cultured in a standard medium containing physiological salts and nutrients (See, e.g., Pourquie, J. et al., BIOCHEMISTRY AND GENETICS OF
20 CELLULOSE DEGRADATION, eds. Aubert, J. P. et al., Academic Press, pp. 71-86, 1988 and Ilmen, M. et al., (1997) Appl. Environ. Microbiol. 63:1298-1306). Common commercially prepared media (e.g., Yeast Malt Extract (YM) broth, Luria Bertani (LB) broth and Sabouraud Dextrose (SD) broth also find use in the present methods. Preferred culture conditions for fungal host cells are known in the art and may be found in the scientific literature and/or from 25 the source of the fungi such as the American Type Culture Collection (ATCC) and Fungal Genetics Stock Center.
[91] Protein may be recovered from growth media by any convenient method, e.g., by precipitation, centrifugation, affinity, filtration or any other method known in the art. In another embodiment, a culture of cells is provided, where the culture of cells comprises: a) growth ao medium and b) the above-described host cell.
1818A and 1818B promoters 1921 A promoter that may be used to express a protein in a host cell is also provided. In one embodiment, the promoter comprises the nucleotide sequence of SEQ ID NOS:7 or 8 (shown in Figs. 5A and 5B, respectively), or a subsequence or functional equivalent thereof that has promoter activity in a host cell. Also provided are recombinant nucleic acids and vectors containing the promoter and host cells containing a recombinant nucleic acid or vector.
s Methods of producing a protein using the host cells are also provided.
[931 In certain embodiments, the promoter may comprise the nucleotide sequence of: a) SEQ
ID NO: 7 or 8; b) a subsequence of SEQ ID NO: 7 or 8 that retains promoter activity; c) a functionally equivalent sequence of SEQ ID NO: 7 or 8 that retains promoter activity or d) a nucleic acid sequence that hybridizes under stringent hybridization conditions with SEQ ID
NO: 7 or 8, or the subsequence thereof. In particular embodiments, the nucleotide sequence may be at least 80% identical to the nucleotide sequence of SEQ ID NO: 7 or 8.
[94] In particular embodiments, a subsequence of a subject promoter may contain at least about 100 nucleotides, at least about 200 nucleotides; at least about 250 nucleotides; at least about 300 nucleotides; at least about 350 nucleotides; at least about 400 nucleotides; at least Is about 450 nucleotides; least about 500 nucleotides; least about 550 nucleotides; least about 600 nucleotides; at least about 650 nucleotides; at least about 700 nucleotides;
at least about 800 nucleotides; at least about 850 nucleotides that are contiguous in SEQ ID NO:
7 or 8, the entire contiguous sequence of SEQ ID NO: 7 or 8, or a functional equivalent thereof that retains promoter activity.
[95] In certain embodiments, a functional equivalent promoter may include one or more changes (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, more than 10, up to 20 or 30 or more changes) relative to the nucleotide sequence of SEQ ID NO: 7 or 8, where a change can be a deletion, substitution or insertion, for example. In one exemplary embodiment, the nucleotide sequence of the functional equivalent promoter may include one to five nucleotide differences relative to the nucleotide sequence of the parent promoter such as SEQ ID NO: 7 or 8.
[96] In other embodiments, the promoter may include a nucleotide sequence that hybridizes under stringent hybridization conditions to a polynucleotide having the nucleotide sequence of SEQ ID NO: 7 or 8, where stringent hybridization conditions encompass low, medium, high and very high stringency hybridization conditions, where such conditions are described above.
so [97] In another embodiment, a subject promoter may contain a contiguous nucleotide sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 7 or 8, or a subsequence thereof. In one embodiment, the subject promoter may contain a contiguous nucleotide sequence that is at least 95% identical -to SEQ ID NO: 7 or 8.

[98] As noted in the Examples section below, the nucleic acid of SEQ ID NOS: 7 and 8 were obtained from Trichoderma reesei, a filamentous fungi. As would be readily apparent, functional equivalents of SEQ ID NO: 7 and 8 that retain promoter activity can be identified by identifying sequences that are similar to SEQ ID NO: 7 and 8 in other filamentous fungi. Since s the most or all of the genome sequences of other filamentous fungi, e.g., Aspergillus (e.g., Aspergillus fu~ rnigatus, Aspergillus oryzae (see, e.g., Machida et al, Nature 2005 438, 1157-1161), Aspergillus nidulans, Aspergillusfumigatus, Aspergillus niger, Aspergillus flavus, Aspergillus terreus), Neurospora (e.g., Neurospora crassa), and Fusarium (e.g., Fusarium graminearum) are available, functional equivalents of SEQ ID NO: 7 and 8 that have promoter activity are readily identifiable.
[99] As noted above, a subject promoter may have promoter activity in a host cell. Promoter activity may be detected using any suitable assay. In certain embodiments, a subject promoter may be operably linked to a polynucleotide, and transcription of the polynucleotide may be detected using any suitable method, e.g., Northem blotting or RT-PCR, etc. In other Is embodiments, the promoter may be operably linked to a polynucleotide that encodes a protein, e.g., a reporter protein, and the activity of the promoter can be evaluated by detecting the protein. In these embodiments, if necessary, a 5' untranslated region may be linked to the promoter such that the resultant transcript has a 5' UTR followed by a coding sequence. As would be recognized, the results obtained from such an assay may be compared to results compared to a suitable control, e.g., a negative or positive control, to determine the significance of results obtained. Any host cell, e.g., a bacterial host cell such as E.
coli, Bacillus or Streptomyces host cell, or a filamentous fungal cell, e.g., an Aspergillus ssp., Trichoderma ssp.
or Fusarium ssp. host cell may be employed. There is no requirement for a subject promoter to be contained within a particular host cell. In certain cases, the promoter may be tested for zs promoter activity in a Trichoderma reesei host cell.
[100] A recombinant nucleic acid comprising the subject promoter is also provided. In certain cases, the recombinant nucleic acid may comprise a subject promoter and a polynucleotide, where the promoter and the polynucleotide are operably linked such that the promoter causes transcription of the polynucleotide in a cell. In certain cases, the promoter and polynucleotide so are not normally linked in nature, i.e., are heterologous to each other. In certain cases, the polynucleotide may contain a coding sequence for a protein. The protein may be an enzyme, a reporter or a therapeutic protein (e.g., an antibody protein), as discussed above, for example. In certain embodiments, the protein may be a fusion protein which may, in certain cases, contain a signal sequence or carrier portion for secretion of the protein.

[101] A nucleic acid vector comprising the subject recombinant nucleic acid is also provided, as well as a host cell containing the same. In certain embodiments, the recombinant nucleic acid may be present in the genome of the host cell. In other embodiments, the recombinant nucleic acid may be present in a vector that replicates in the cell. The host cell may be any of a variety s of different host cells, including bacterial, fungal, yeast, plant and mammalian host cells. In one embodiment, the host cell may be a filamentous fungal host cell, and in another embodiment, the host cell may be a bacterial cell.
[102] A culture of cells comprising culture medium and a subject host cell is also provided.
11031 A method of producing a protein is also provided. In general terms, this method includes to maintaining a subject culture of cells under conditions suitable to produce the protein. This method may further include recovering the protein from culture medium.
[104] In order to further illustrate the present invention and advantages thereof, the following specific examples are given with the understanding that they are being offered to illustrate the present invention and should not be construed in any way as limiting its scope.

IS

Isolation of ALS genes from chlorimuron ethyl-resistant cells [105] Chlorimuron ethyl (Chem Service Inc., West Chester, PA), freshly prepared and 20 dissolved in DMF to a concentration of 20 mg/ml, was added at various concentrations to molten Vogels agar immediately prior to pouring the plates to produce media containing 25, 50, 100, 200, 300, 400 or 500 ppm chlorimuron ethyl.
11061 Approximately 25 million spores T.reesei strain QM6a (ATCC 13631) were plated onto each plate. After 10 days of growth at 28 C, five colonies were isolated, two from 50 ppm 25 plates and one each from each of the 25, 200 and 300 ppm plates. The colonies were further isolated by restreaking them onto fresh Vogels agar plates containing 200 ppm chlorimuron ethyl.
11071 Genomic DNA was prepared from each of the five chlorimuron ethyl resistant strains in order to amplify and sequence the acetolactate synthase (als) gene from those strains.
30 Herculase DNA polymerase (Stratagene, La Jolla, CA) was used for amplification following manufacturers instructions and the following primers: Forward (5'-3') GGCGCGCCTGAGACAATGGCCGGCAATGGTAAAAA (SEQ ID NO:5) and Reverse (5'-3') GCGATCGCCATCCCGTCGCGTCAAAAACACTGC (SEQ ID NO:6) 11081 Unique restriction sites were added to the 5' ends of the primers for subsequent manipulation. The resulting 4.1 kb fragments were isolated, sequenced and compared to the sequence of the native T. reesei acetolactate synthase gene (from the JGI
genome website).
11091 Three unique point mutations in the als gene that confer resistance to chlorimuron ethyl were identified.
s 11101 Compared to the sequence of the wild-type T. reesei acetolactate synthase protein (Fig.
1; SEQ ID NO: 1), the clorimuron ethyl-resistant acetolactate synthase proteins each had one of the following amino acid substitutions: A190D, K241E or R372H. The amino acids at positions 190, 241 and 372 of the wild-type T. reesei acetolactate synthase protein of SEQ ID NO:1 are underlined.
to 11111 Compared to the sequence of the wild-type T. reesei acetolactate synthase deduced cDNA (Fig. 2; SEQ ID NO:2), the clorimuron ethyl-resistant acetolactate synthase cDNAs each had one of the following nucleotide substitutions: C569A (this corresponds to the A 190D
amino acid substitution), A721 G(this corresponds to the K241 E amino acid substitution) or G1115A (this corresponds to the R372H amino acid substitution). Each of the altered codons Is (GCC, which is altered to GAC; AAG, which is altered to GAG; and CGT, which is altered to CAT) is indicated on Fig. 2.
11121 Compared to the sequence of the wild-type T. reesei acetolactate synthase gene (Fig. 3;
SEQ ID NO:3), the clorimuron ethyl-resistant acetolactate synthase genes each had one of the following nucleotide substitutions: C1023A (this corresponds to the A190D
amino acid 20 substitution), A1175G (this corresponds to the K241E amino acid substitution) or G1569A (this corresponds to the R372H amino acid substitution).
11131 Because of the degeneracy of the genetic code, other mutations in the als coding sequence can encode the A190D, K241E or R372H amino acid substitutions.

zs EXAMPLE 2' Transformation of T.reesei with A190D acetolactate synthase gene [114] The vector pTrex-glucoamylase was created to express a glucoamylase derived from Trichoderma reesei in T.reesei. Figure 4 depicts a general diagram of the vector. Three 30 different vector constructs have been made with different promoters; 1818A, 1818B and the T.
reesei cbhl promoter. Fig.5A illustrates the sequences of the promoter designated 1818A and Fig. 5B illustrates the sequences of the promoter 1818B.
[115] The entire nucleotide sequence of the pTrex-glucoamylase including the cbhl promoter is shown in Fig. 6. The pTrex-glucoamylase vector is based on vector pTrex3g as described in detail in WO 05/001036. In brief, the pTrex3g is based on the E. coli vector pSL1180 (Pharmacia, Inc., Piscataway, NJ) which is a pUC 118 phagemid based vector with an extended multiple cloning site containing 64 hexamer restriction enzyme recognition sequences. It was designed as a Gateway destination vector (Hartley, J.L. et al., (2000) Genome Research s 10:1788 - 1795) to allow insertion using Gateway Technology (Invitrogen) of any desired open reading frame between the promoter and terminator regions of the T. reesei cbhl gene.
[116] In the pTrex-glucoamylase vector, the A190D ALS gene is under control of its native promoter and terminator and is used to replace the fungal selectable marker amdS which is used in pTrex3g.
to [117] The vector was transformed into the quad deleted (Ochb1, Ocbh2, Aegll, and Deg12) T.
reesei strain (WO 05/001036) originally derived from RL-P37 (Sheir-Neiss et al., (1984) Appl.
Microbiol. Biotechnol. 20:46 - 53; USP 4,797,361) using the procedure outlined below.
[1181 A suspension of spores (approximately 5x108 spores/mi) from the Trichoderma strain was prepared. 100u1- 200u1 of spore suspension was spread onto the center of plates of Is modified Vogels medium with 200 ppm chlorimuron ethyl and allowed to dry.
[119] Modified Vogels had the following composition: 2.5 g/L Na3Citrate*2H20, 5.0 g/L
KH2PO4, 2.0 g/L NH4N03, 0.2 g/L MgSO4*7H20), 0.1 g/L CaC12*2HZ0, 5 mL/L
Modified Vogels Trace Elements Solution, 2.5 mL/L Modified Vogels Biotin Solution, 20 g/L Agar Modified Vogels trace elements solution contained 50 g/L Citric Acid, 50 g/L
ZnSO4*7H20, 20 10 g/L Fe(NH4)ZSO4*6HZO, 2.5 g/L CuSO4*5HZ0, 0.5 g/L MnSO4*4H20, 0.5 g/L
H3B03, 0.5 g/L NaMoO4*2HZ0.
[120] Modified Vogels Biotin Solution contained 0.1 g/L d-Biotin. After autoclave the following additions are made prior to pouring plates: 20 mL/L of 50% glucose, 10 mL/L of 20 mg/mL chlorimuron ethyl dissolved DMF.
25 11211 Transformation of the Trichoderma strain by the biolistic transformation method was accomplished using a Biolistic PDS-1000/he Particle Delivery System from Bio-Rad (Hercules, CA) following the manufacturers instructions (see, WO 05/001036 and US
2006/0003408).
11221 Transformants were isolated after 3 to 4 days of growth at 28 C.
Transformants were 30 serially passed twice on fresh Vogels plates with 200 ppm chlorimuron ethyl in order to isolate stable monokaryons. Transformants were cultured, and culture supernatant was tested by SDS
page electrophoresis and using an enzyme assay. An SDS PAGE gel is shown in Fig. 7 illustrating the expression of the T. reesei glucoamylase.

Sequencing and cloning of the 1818A and 1818B promoters s [123] The 1818A and 1818B promoters (as shown in Figs 5A and 5B, respectively) were identified by mining the US Department of Energy Joint Genome Institute's Trichoderma reesei genome sequence database (as found at the world wide website of jgi.doe.gov) for sequences upstream of highly represented ESTs.
11241 The promoters were amplified by PCR and cloned behind a glucoamylase coding to sequence in accordance with the vector map shown in Fig. 8. The entire nucleotide sequence of this construct is shown in Fig. 9. The vector used is based on the vector pTrex3g, which is described in detail in Example 6 of WO 05/001036. In brief, the pTrex3g is based on the E. coli vector pSL 1180 (Pharmacia, Inc., Piscataway, NJ) which is a pUC 118 phagemid based vector with an extended multiple cloning site containing 64 hexamer restriction enzyme recognition Is sequences. It was designed as a Gateway destination vector (Hartley, J.L.
et al., (2000) Genome Research 10:1788 - 1795) to allow insertion using Gateway Technology (Invitrogen) of any desired open reading frame between the promoter and terminator regions of the T. reesei cbhl gene. In the vector used in this example, the cbhl promoter was replaced with either the 1818A
or the 1818B promoter, the amdS selectable marker was replaced with a Trichoderma reesei 20 acetolactate synthase marker, driven by its native promoter and terminator.

Transformation of T. reesei host cells with vectors including the 1818A and 25 promoters [1251 The vector was transformed into the quad deleted (Ochbl, Ocbh2, Deg11, and Deg12) T.
reesei strain (WO 05/001036) originally derived from RL-P37 (Sheir-Neiss et al., (1984) Appl.
Microbiol. Biotechnol. 20:46 - 53 and USP 4,797,361) using the procedure outlined below.
30 (1261 A suspension of spores (approximately 5x10g spores/ml) from the Trichoderma strain was prepared. 100ul - 200ul of spore suspension was spread onto the center of plates of modified Vogels medium with 200 ppm chlorimuron ethyl. Modified Vogels had the following composition: 2.5 g/L Na3Citrate*2H20, 5.0 g/L KH2PO4, 2.0 g/L NH4NO3, 0.2 g/L
MgSO4*7H20, ).1 g/L CaC12*2H20, 5 mL Modified Vogels Trace Elements Solution, 2.5 mL

Modified Vogels Biotin Solution, 20 g/L Agar Modified Vogels trace elements solution contained 50 g/L Citric Acid, 50 g/L ZnSO4*7HZ0, 10 g/L Fe(NH4)2SO4*6H20, 2.5 g/L
CuSO4*5Hz0, 0.5 g/L MnSO4*4Hz0, 0.5 1-13B03, 0.5 g/L NaMoO4*2H2O. Modified Vogels Biotin Solution contained 0.1 g/L d-Biotin. After autoclave the following additions are made s prior to pouring plates: 20 mL/L of 50% glucose, 10 mL/L of 20 mg/mL
chlorimuron ethyl dissolved DMF. The spore suspension was allowed to dry on the surface of the Modified Vogels plates.
[127] Transformation of the Trichoderma strain by the biolistic transformation method was accomplished using a Biolistic PDS-1000/he Particle Delivery System from Bio-Rad io (Hercules, CA) following the manufacturers instructions (see, WO 05/001036 and US
2006/0003408).
[128] Transformants were isolated.

is Screening transformants for expression of glucoamylase activity driven by 1818A and 1818B promoters [129] Stable transformants were grown on Modified Vogels Lactose Agar plates with starch (9cm diameter petri-plates). After about 4 days growth at 28 C, 10 ml of a lmg/mi solution of 20 4-methyl-umbelliferyl-a-D-glucose was poured over the grown colonies. After 30 minutes at room temperature, strains expressing glucoamylase were visualized as fluorescent blue colonies when viewed illuminated by a long wavelength UV lamp. The untransformed, parent T. reesei control strain did not show blue fluorescence.
[130] Modified Vogels Lactose Agar Plates with starch is the same recipe as Modified Vogels 2s Agar except that 25 ml/L of 20% a -lactose solution (added after autoclaving) is substituted for glucose solution and 20 g/L of Pure Food Powder cornstarch is added prior to autoclaving.
[131] The glucoamylase substrate 4-methyl-umbelliferyl-a-D-glucose was prepared as follows:
200 mg of 4-methyl-umbelliferyl-a-D-glucose (Sigma-Aldrich Co.) is dissolved in 5 ml of DMSO and 195 ml of 75 mM Potassium Phosphate Buffer pH 6.3 is added.

Shake Flask Experiments with Trichoderma reesei transformants [132] Individual fungal transformants will be grown up in shake flask culture to determine the level of glucoamylase protein expression. The experiments will be conducted essentially as described in example 1 of U.S. Patent 5,874,276 with the following modification: 16 g/L of alpha-lactose was substituted for cellulose in TSF medium.
1133] In general, the fermentation protocol as described in Foreman el al.
(Foreman et al.
s (2003) J. Biol. Chem 278:31988-31997) will be followed. Vogels minimal medium (Davis et al., (1970) Methods in Enzymology 17A, pg 79 - 143 and Davis, Rowland, NEUROSPORA, CONTRIBUTIONS OF A MODEL ORGANISM, Oxford University Press, (2000)) containing 5%
glucose will be inoculated with 1.5 ml frozen spore suspension. After about 48 hours, each culture will be transferred to 6.2L of the same medium in a 14L Biolafitte fermenter. The fermenter will be run at 25 C, 750 RPM and 8 standard liters per minute airflow. About one hour after the initial glucose is exhausted, a 25% (w/w) lactose feed will be started and fed in a carbon limiting fashion to prevent lactose accumulation. The concentrations of glucose and lactose will be monitored. Samples will be obtained at regular intervals to monitor the progress of the fermentation. Collected samples will be spun in a 50m1 centrifuge tube at 3/4 speed in an is International Equipment Company (Needham Heights, MA) clinical centrifuge.
Shake flask grown supernatant samples will be run on BIS-TRIS SDS -PAGE gels (Invitrogen), under reducing conditions with MOPS (morpholinepropanesulfonic acid) SDS running buffer and LDS sample buffer.

Claims (24)

1. An isolated polynucleotide encoding an acetolactate synthase protein that provides resistance to toxic sulphonylurea compounds, wherein the amino acid sequence of said acetolactate protein is at least 95% identical to SEQ ID NO:1.

2. The isolated polynucleotide of claim 1, wherein said protein contains an acidic amino acid at position 190.

3. The isolated polynucleotide of claim 1, wherein said protein contains a basic amino acid at position 241.

4. The isolated polynucleotide of claim 1, wherein said protein contains a basic amino acid at position 372.

5. The isolated polynucleotide of claim 1, wherein said isolated polynucleotide is operably linked to a promoter and a terminator.

6. The isolated polynucleotide of claim 1, wherein said isolated polynucleotide comprises introns.

7 The isolated polynucleotide of claim 6, wherein said isolated polynucleotide is at least 95% identical to SEQ ID NO: 1.

8. The isolated polynucleotide of claim 1, wherein said isolated polynucleotide comprises a single open reading frame.

9. The isolated polynucleotide of claim 1, wherein said isolated polynucleotide is 95%
identical to SEQ ID NO:2.

10. The isolated polynucleotide of claim 1, wherein said isolated polynucleotide is codon-optimized for expression of said acetolactate synthase protein in a particular host cell.

11. A vector comprising the isolated polynucleotide of claim 1.

12. The vector of claim 11, wherein said vector further comprises an expression cassette for expression of a recombinant protein.

13. A host cell comprising the isolated polynucleotide of claim 1, wherein said host cell is resistant to toxic sulphonylurea compounds.

14. The host-cell of claim 13, wherein said host cell is a fungal host cell.

15. The host cell of claim 14, wherein said host cell is a filamentous fungal host cell.

16. The host cell of claim 15, wherein said host cell is a Trichoderma reesei host cell.

17. The host cell of claim 13, wherein said host cell is a plant cell.

18. The host cell of claim 13, wherein isolated polynucleotide is present in a genome of said host cell.

19. The host cell of claim 13, wherein said isolated polynucleotide is present in a vector that autonomously replicates in said host cell.

20. A method of selecting a cell comprising:
introducing an isolated polynucleotide of claim 1 into a plurality of cells;
contacting said plurality of cells with a toxic sulphonylurea or imidazolinone compound;
and culturing said cells to provide for selection of said cell.

21. The method of claim 20, wherein said cell is a fungal cell.

22. The method of claim 21, wherein said cell is a Trichoderma reesei cell.

23. The method of claim 20, wherein said cell is a plant cell.

24. The method of claim 20, further comprising culturing said cell in liquid medium.