WO2012027580A1 - Filamentous fungi having an altered viscosity phenotype - Google Patents

Abstract

Described are compositions and methods relating variant filamentous fungi having altered growth characteristics. Such variants are well-suited for growth in submerged cultures, e.g., for the large-scale production of enzymes and other proteins for commercial applications.

Description

FILAMENTOUS FUNGI HAVING AN ALTERED VISCOSITY PHENOTYPE

PRIORITY

[01] The present application claims priority to U.S. Provisional Application Serial No. 61/377,030, filed August 25, 2010, which is incorporated by reference in its entirety.

TECHNICAL FIELD

[02] The present strains and methods relate to genetic mutations in filamentous fungi that give rise to variants having altered growth characteristics. Such variants are well-suited for growth in submerged cultures, e.g. , for the large-scale production of enzymes and other proteins or metabolites for commercial applications.

REFERENCES

[03] The following references, and additional reference cited herein, are hereby incorporated by reference:

Caracuel, Z. et al. (2005) Molecular Plant-Microbe Interactions 18:1140-47.

Hughes, H. and Stephens, D.J. (2008) Cell Biol. 129:129-51.

Karhinen, L. et al (2005) Traffic 6:562-74.

Mouyna, I. et al. (2005) Molecular Microbiology 56: 1675-88.

Passolunghi, S. et al. (2010) Microbial Cell Factories 9:7-17.

Peng, R. et al. (2000) /. Biol. Chem. 275: 11521-28.

Roberg, K.J. et al. (1999) /. Cell. Biol. 145:659-72.

Shimoni, Y. et al. (2000) /. Cell. Biol. 151:973-84.

Turchini, A. et al. (2000) . Becteriol. 182: 1167-71.

BACKGROUND

[04] Filamentous fungi are capable of expressing native and heterologous proteins to high levels, making them well-suited for the large-scale production of enzymes and other proteins for industrial applications. Filamentous fungi are typically grown in mycelial submerged cultures in bioreactors, which are adapted to introduce and distribute oxygen and nutrients into the culture medium (i.e. , broth). The morphological characteristics of the mycelium affect the Theological properties of the broth, thereby affecting bioreactor performance. [05] Generally, the higher the viscosity of the broth, the less uniform the distribution of oxygen and nutrients, and the more energy required to agitate the culture. In some cases, the viscosity of the broth becomes sufficiently high to significantly interfere with the dissolution of oxygen and nutrients, thereby adversely affecting the growth of the fungi. Additionally, the 5 power required to mix and aerate viscous broth can significantly increase the cost of production, and incur higher capital expenditures in terms of motors and power supplies.

SUMMARY

[06] Described are strains and methods relating to filamentous fungi having genetic alterations o that give rise to altered viscosity phenotypes.

[07] In one aspect, a variant strain of filamentous fungus derived from a parental strain is provided, the variant strain comprising a genetic alteration that causes cells of the variant strain to produce an altered amount of functional Sfb3 protein compared to cells of the parental strain, wherein the cells of the variant strain produce during aerobic fermentation in submerged culture a 5 cell broth that (i) requires an altered amount of agitation to maintain a preselected dissolved oxygen content compared to the cells of the parental strain, and/or (ii) maintains an altered dissolved oxygen content at a preselected amount of agitation, compared to the cells of the parental strain.

[08] In some embodiments, the altered amount of functional Sfb3 protein is a reduced amount, and the variant strain produce during aerobic fermentation in submerged culture a cell broth that (i) o requires reduced agitation to maintain a preselected dissolved oxygen content compared to the cells of the parental strain, and/or (ii) maintains an increased dissolved oxygen content at a preselected amount of agitation, compared to the cells of the parental strain.

[09] In some embodiments, the genetic alteration comprises a disruption of the sft>3 gene present in the parental strain. In some embodiments, disruption of the sfb3 gene is the result of 5 deletion of all or part of the sfb3 gene. In some embodiments, disruption of the φ3 gene is the result of deletion of a portion of genomic D A comprising the φ3 gene. In some embodiments, disruption of the φ3 gene is the result of mutagenesis of the sfl3 gene.

[10] In some embodiments, disruption of the sfb3 gene is performed using site-specific recombination. In some embodiments, disruption of the sfl3 gene is performed in combination o with introducing a selectable marker at the genetic locus of the φ3 gene. In some embodiments, disruption of the sft>3 gene is the primary genetic determinant for conferring a reduced viscosity phenotype to the variant strain.

[11] In some embodiments, the variant strain does not produce functional Sfb3 protein. In some embodiments, the variant strain does not produce Sfb3 protein. [12] In some embodiments, the variant strain further comprises a gene encoding a protein of interest.

[13] In some embodiments, the variant strain produces substantially the same amount of protein per unit amount of biomass as the parental strain. In some embodiments, the variant strain 5 produces substantially the same amount of protein of interest per unit amount of biomass as the parental strain,

[14] In some embodiments, the Sfb3 protein comprises the amino acid sequence

IQLA QGXDGXEXXXARXLXEDRNXEAXSXVDWL (SEQ ID NO: 9, where X is any amino acid residue).

0 [15] In some embodiments, the filamentous fungus is a Pezizomycotina species. In some embodiments, the filamentous fungus is Trichoderma reesei.

[16] In another aspect, a method for producing a variant strain of filamentous fungus cells is provided, comprising: introducing a genetic alteration into a parental strain of filamentous fugal cell, which genetic alteration alters the production of functional Sfb3 protein compared to the cells5 of the parental strain, thereby producing a variant filamentous fugal cell that produces during aerobic fermentation in submerged culture a cell broth that (i) requires an altered amount of agitation to maintain a preselected dissolved oxygen content, compared to the cells of the parental strain, and/or (ii) maintains an altered dissolved oxygen content at a preselected amount of agitation, compared to the cells of the parental strain.

o [17] In some embodiments, the genetic alteration reduces or prevents the production of

functional Sfb3 protein, thereby producing a variant filamentous fugal cell that produces during aerobic fermentation in submerged culture a cell broth that (i) requires reduced agitation to maintain a preselected dissolved oxygen content, compared to the cells of the parental strain, and/or (ii) maintains an increased dissolved oxygen content at a preselected amount of agitation, 5 compared to the cells of the parental strain.

[18] In some embodiments, the genetic alteration comprises disrupting the 3 gene in a parental filamentous fugal cell using genetic manipulation.

[19] In some embodiments, the genetic alteration comprises deleting the sft>3 gene in a parental filamentous fugal cell using genetic manipulation.

o [20] In some embodiments, the genetic alteration is performed using site-specific genetic

recombination. In some embodiments, the disruption of the sfb3 gene is performed in combination with introducing a selectable marker at the genetic locus of the sfl3 gene.

[21] In some embodiments, the variant strain produces substantially the same amount of protein per unit amount of biomass as the parental strain. In some embodiments, the variant strain produces substantially the same amount of protein of interest per unit amount of biomass as the parental strain.

[22] In some embodiments, the Sfb3 protein comprises the amino acid sequence

IQLARQGXDGXEXXXARXLXEDRNXEAXSXVDWL (SEQ ID NO: 9, where X is any 5 amino acid residue).

[23] In some embodiments, the filamentous fungus is a Pezizomycotina species. In some embodiments, the filamentous fungus is Trichoderma reesei,

[24] In some embodiments, the parental strain further comprises a gene encoding a protein of interest. In some embodiments, the gene encoding the protein of interest is present in the parental o strain prior to introducing the genetic alteration that reduces or prevents the production of

functional Sfb3 protein.

[25] In another aspect, a protein of interest produced by the foregoing variant strain is provided.

[26] In another aspect, a variant strain of filamentous fungus produced by the foregoing method is provided.

5 [27] In another aspect, a variant strain of filamentous fungus derived from a parental strain is provided, the variant strain comprising: (a) a genetic alteration that results in (i) a requirement for reduced agitation in submerged culture to maintain a preselected dissolved oxygen content, compared to the cells of the parental strain, and/or (ii) maintenance of an increased dissolved oxygen content in submerged culture at a preselected amount of agitation, compared to the cells of0 the parental strain, and (b) a gene encoding a protein of interest, wherein the gene encoding the protein of interest is present in the variant strain prior to the genetic alteration in (a).

[28] In some embodiments, the genetic alteration comprises a disruption of the sft>3 gene present in the parental strain. In some embodiments, disruption of the sfb3 gene is performed in combination with introducing a selectable marker at the genetic locus of the sfl>3 gene.

5 [29] In another aspect, a method for screening variant filamentous fungus cells for an altered viscosity phenotype is provided, comprising: (a) mutagenizing the cells of a parental strain of filamentous fungi to produce variant cells; (b) screening the variant cells for altered sensitivity to a fluorochrome stain; and (c) selecting the variant cells that have altered sensitivity to the fluorochrome stain; wherein the altered sensitivity to the fluorochrome stain correlates with the o ability of the variant filamentous fungus cells to produce, during aerobic fermentation in

submerged culture, a cell broth that (i) requires an altered amount of agitation to maintain a preselected dissolved oxygen content, compared to the cells of the parental strain, and/or (ii) maintains an altered dissolved oxygen content at a preselected amount of agitation, compared to the cells of the parental strain. [30] In some embodiments, the altered sensitivity is increased sensitivity, and the variant filamentous fugal cell produces, during aerobic fermentation in submerged culture, a cell broth that (i) requires reduced agitation to maintain a preselected dissolved oxygen content, compared to the cells of the parental strain, and/or (ii) maintains an increased dissolved oxygen content at a 5 preselected amount of agitation, compared to the cells of the parental strain. In some

embodiments, the fluorochrome stain is Calcofluor White.

[31] In some embodiments, mutagenizing the cells is performed by genetic recombination. In some embodiments, mutagenizing the cells is performed in combination with introducing a selectable marker at the genetic locus of the sft>3 gene.

o [32] In another aspect, a method for identifying a Sfb3 polypeptide in Pezizomycotina species of filamentous fungus is provided, comprising: (a) obtaining an amino acid sequence from a Pezizomycotina species of filamentous fungus; and (b) screening the amino acid sequence for the presence of the contiguous amino acid sequence

IQLARQGXDGXEXXXARXLXEDRNXEAXSXVDWL (SEQ ID NO: 9, where X is any 5 amino acid residue); (c) wherein the presence of SEQ ID NO: 9 in the amino acid sequence from the Pezizomycotina species of filamentous fungus indicates that the amino acid sequence from the Pezizomycotina species of filamentous fungus is a sfb3 polypeptide.

[33] In another aspect, an isolated sfb3 polypeptide identified by the foregoing method is provided.

o [34] In yet a further aspect, a method for producing a protein of interest in filamentous fungus cells is provided, comprising introducing into parental filamentous fungus cells a gene encoding the protein of interest and a genetic alteration that reduces the amount or activity of Sfb3 protein in the cells, thereby producing a variant filamentous fugal cell that produces during aerobic fermentation in submerged culture a cell broth comprising the protein of interest, which (i) 5 requires an altered amount of agitation to maintain a preselected dissolved oxygen content compared to the cells of the parental strain, and/or (ii) maintains an altered dissolved oxygen content at a preselected amount of agitation compared to the cells of the parental strain, and wherein the protein of interest is produced at substantially the same level in the variant cells compared to the parental cells.

o [35] In some embodiments, the protein of interest is more than one protein (or one or more proteins) of interest, and each of the more than one protein of interest is produced at substantially the same relative levels in the variant cells compared to the parental cells. In a particular embodiment, each of the more than one protein of interest is selected from cellulases and hemicellulases. [36] In a related aspect, a protein of interest produced by such a method is provided. In yet another related aspect, a composition comprising more than one protein of interest produced by such method is provided. In some embodiments, the composition is a whole cellulase composition.

[37] These and other aspects and embodiments of present strains and methods will be apparent from the description, including the accompanying Figures.

BRIEF DESCRIPTION OF THE DRAWINGS

[38] Figure 1 is map of plasmid pCR-BluntII-hph-loxP#4

[39] Figure 2 is map of plasmid pCR-Blunt II-TOPO 889092.

[40] Figure 3, panels A-D are images of culture plates showing the colony morphology of T. reesei strains MorphAsfb3 and 29-9Asfb3 on Congo Red-containing medium. (A) Subset of MorphAsfb3 candidates and (B) corresponding controls. (C) Subset of 29-9Asfb3 candidates and (D) corresponding controls.

[41] Figure 4 is map of plasmid pTrex-Tel-pyrG13/pDONR221/0927853cre used to transiently express the ere gene in the Morph Asfb3 strain.

[42] Figure 5 is an image showing the loss of hygromycin B resistance and the ability to grow on acetamide in candidates following transient expression of plasmid pTrex-Tel- pyrG13/pDONR221/0927853cre. Top row (A-C): Morph and Morph Asfb3 control strains on the indicated media. Bottom row (D-F): candidates after transient expression of the plasmid on the indicated media.

[43] Figure 6 is a map of plasmid pNSP23.

[44] Figure 7 is a map of one of four plasmids used for complementation in 70H2, this plasmid containing the wild type φ3 gene with the native promoter and terminator.

[45] Figure 8 is an image showing the growth of 70H2 and 29-9 transformants on PDA with hygromycin B after four days of growth at 28°C (first transfer from transformation plates). (A- C) 70H2 + wild type sfb3 from 29-9. (D-F) 70H2 + wild type 3 with native promoter and terminator from 29-9. (G) 29-9 + vector only. (H-J) 70H2 + sft>3 from 70H2. (K-M) 70H2 + sfl>3 with native promoter and terminator from 70H2. (N) 70H2 + vector only.

[46] Figure 9 is map of plasmid pCR-BluntE-TOPO 949096.

[47] Figure 10 is an image showing (A) the growth of transformants of 70H2 transformed with pCR-Bluntll-TOPO 949096 containing the wild type sfl>3 gene obtained from strain 29-9. The strains were incubated on VMH (Vogel's minimal medium containing hygromycin B) at 28°C. Two candidates have the wild type phenotype (W), two have the 70H2 phenotype (H), and two have an intermediate phenotype (I). (B) Comparison of 70H2sfb3#24, 70H2 and 29-9 on VM (Vogel's minimal medium) after 4 days of growth at 28°C followed by 3 days of growth at room temperature.

[48] Figure 11 shows the colony morphologies of H3A and H3 A Asfb3 #1009 on the indicated media after 4 days of growth at 28°C.

[49] Figure 12 show images of H3A and H3A Asfb3 #1009 hyphae in liquid culture after the indicated periods of time at 28°C.

[50] Figure 13 shows an alignment of the amino acid sequences of the Sfb3proteins from S. cerevisiae (SEQ ID NO: 1) and T. reesei (SEQ ID NO: 2).

[51] Figure 14 shows an alignment of the amino acid sequences of the Sfb3proteins from S. cerevisiae (SEQ ID NO: 1), T. reesei (SEQ ID NO: 2), and A. oryzae (SEQ ID NO: 3).

DETAILED DESCRIPTION

I. Overview

[52] The present strains and methods relate to variant filamentous fungus cells having genetic modifications that affect their morphology and growth characteristics. When the variant cells are grown in submerged culture, they produce a cell broth that has different rheological properties compared to a cell broth comprising cells of the parental strain. Some of these variant strains are well-suited for the large-scale production of enzymes and other commercially important proteins.

II. Definitions

[53] Prior to describing the present strains and methods in detail, the following terms are defined for clarity. Terms not defined should be accorded their ordinary meanings as used in the relevant art.

[54] As used herein, "Trichoderma reesei' refers to a filamentous fungus of the phylum

Ascomycota, subylum Pezizomycotina. This organism was previously classified as Trichoderma longibrachiatum, and also as Hypocrea jecorina.

[55] As used herein, the phrase "variant strain of filamentous fungus cells," or similar phrases, refer to strains of filamentous fungus cells that are derived (i.e. , obtained from or obtainable from) from a parental (or reference) strain belonging to the Pezizomycotina, e.g. , by genetic manipulation.

[56] As used herein, the term "protein of interest" refers to a polypeptide that is desired to be expressed in a filamentous fungus, optionally at high levels and for the purpose of commercialization. Such a protein may be an enzyme, a substrate-binding protein, a surface- active protein, a structural protein, or the like.

[57] As used herein, the phrase "substantially free of an activity," or similar phrases, means that a specified activity is either undetectable in an admixture or present in an amount that would 5 not interfere with the intended purpose of the admixture.

[58] As used herein, the terms "polypeptide" and "protein" are used interchangeably to refer to polymers of any length comprising amino acid residues linked by peptide bonds. The conventional one-letter or three-letter codes for amino acid residues are used herein. The polymer may be linear or branched, it may comprise modified amino acids, and it may be o interrupted by non-amino acids. The terms also encompass an amino acid polymer that has been modified naturally or by intervention; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation or modification, such as conjugation with a labeling component, Also included within the definition are, for example, polypeptides containing one or more analogs of an amino acid (including, for example, unnatural5 amino acids, etc.), as well as other modifications known in the art.

[59] As used herein, functionally and/or structurally similar proteins are considered to be "related proteins." Such proteins may be derived from organisms of different genera and/or species, or even different classes of organisms (e.g., bacteria and fungus). Related proteins also encompass homologs determined by primary sequence analysis, determined by secondary or o tertiary structure analysis, or determined by immunological cross-reactivity.

[60] As used herein, the term "derivative polypeptide/protein" refers to a protein which is derived or derivable from a protein by addition of one or more amino acids to either or both the N- and C-terminal end(s), substitution of one or more amino acids at one or a number of different sites in the amino acid sequence, deletion of one or more amino acids at either or both 5 ends of the protein or at one or more sites in the amino acid sequence, and/or insertion of one or more amino acids at one or more sites in the amino acid sequence. The preparation of a protein derivative may be achieved by modifying a DNA sequence which encodes for the native protein, transformation of that DNA sequence into a suitable host, and expression of the modified DNA sequence to form the derivative protein.

0 [61] Related (and derivative) proteins include "variant proteins." Variant proteins differ from a reference/parental protein (e.g. , a wild-type protein) by substitutions, deletions, and/or insertions at small number of amino acid residues. The number of differing amino acid residues between the variant and parental protein may be one or more, for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, or more amino acid residues. Variant proteins may share at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or even at least about 99%, or more, amino acid sequence identity with a reference protein. A variant protein may also differ from a reference protein in selected motifs, domains, epitopes, conserved regions, and the like.

[62] As used herein, the term "analogous sequence" refers to a sequence within a protein that provides similar function, tertiary structure, and/or conserved residues as the protein of interest (i.e. , typically the original protein of interest). For example, in epitope regions that contain an a- helix or a β-sheet structure, the replacement amino acids in the analogous sequence preferably maintain the same specific structure. The term also refers to nucleotide sequences, as well as amino acid sequences. In some embodiments, analogous sequences are developed such that the replacement amino acids result in a variant enzyme showing a similar or improved function. In some embodiments, the tertiary structure and/or conserved residues of the amino acids in the protein of interest are located at or near the segment or fragment of interest. Thus, where the segment or fragment of interest contains, for example, an a-helix or a β-sheet structure, the replacement amino acids preferably maintain that specific structure.

[63] As used herein, the term "homologous protein" refers to a protein that has similar activity and/or structure to a reference protein. It is not intended that homologs necessarily be evolutionarily related. Thus, it is intended that the term encompass the same, similar, or corresponding enzyme(s) (i.e., in terms of structure and function) obtained from different organisms. In some embodiments, it is desirable to identify a homolog that has a quaternary, tertiary and/or primary structure similar to the reference protein. In some embodiments, homologous proteins induce similar immunological response(s) as a reference protein. In some embodiments, homologous proteins are engineered to produce enzymes with desired activity(ies).

[64] The degree of homology between sequences may be determined using any suitable method known in the art (see, e.g., Smith and Waterman (1981) Adv. Appl. Math. 2:482;

Needleman and Wunsch (1970) J. Mol. Biol., 48:443; Pearson and Lipman (1988) Proc. Natl. Acad. Sci. USA 85:2444; programs such as GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package (Genetics Computer Group, Madison, WI); and Devereux et al. (1984) Nucleic Acids Res. 12:387-95).

[65] For example, PILEUP is a useful program to determine sequence homology levels. PILEUP creates a multiple sequence alignment from a group of related sequences using progressive, pair-wise alignments. It can also plot a tree showing the clustering relationships used to create the alignment. PILEUP uses a simplification of the progressive alignment method of Feng and Doolittle, (Feng and Doolittle (1987) . Mol. Evol. 35:351-60). The method is similar to that described by Higgins and Sharp ((1989) CABIOS 5: 151-53). Useful PILEUP parameters including a default gap weight of 3.00, a default gap length weight of 0.10, and 5 weighted end gaps. Another example of a useful algorithm is the BLAST algorithm, described by Altschul et al. ((1990) /. Mol. Biol. 215:403-10) and Karlin et al. ((1993) Pro Natl. Acad. Sci. USA 90:5873-87). One particularly useful BLAST program is the WU-BLAST-2 program (see, e.g., Altschul et al. (1996) Meth. Enzymol. 266:460-80). Parameters "W," "T," and "X" determine the sensitivity and speed of the alignment. The BLAST program uses as defaults a0 word-length (W) of 11, the BLOSUM62 scoring matrix (see, e.g. , Henikoff and Henikoff (1989) Proc. Natl. Acad. Sci. USA 89: 10915) alignments (B) of 50, expectation (E) of 10, M'5, N'-4, and a comparison of both strands,

[66] As used herein, the phrases "substantially similar" and "substantially identical," in the context of at least two nucleic acids or polypeptides, typically means that a polynucleotide or5 polypeptide comprises a sequence that has at least about 70% identity, at least about 75%

identity, at least about 80% identity, at least about 85% identity, at least about 90% identity, at least about 91 % identity, at least about 92% identity, at least about 93% identity, at least about 94% identity, at least about 95% identity, at least about 96% identity, at least about 97% identity, at least about 98% identity, or even at least about 99% identity, or more, compared to the o reference (i.e. , wild-type) sequence. Sequence identity may be determined using known

programs such as BLAST, ALIGN, and CLUSTAL using standard parameters. (See, e.g. , Altschul, et al. (1990) /. Mol. Biol. 215:403-410; Henikoff et al. (1989) Proc. Natl. Acad. Sci. USA 89: 10915 ; Karin et al. (1993) Proc. Natl. Acad. Sci USA 90:5873; and Higgins et al. (1988) Gene 73:237-244). Software for performing BLAST analyses is publicly available through the 5 National Center for Biotechnology Information. Also, databases may be searched using FASTA

(Pearson et al. (1988) Proc. Natl. Acad. Sci, USA 85:2444-48). One indication that two polypeptides are substantially identical is that the first polypeptide is immunologically cross- reactive with the second polypeptide. Typically, polypeptides that differ by conservative amino acid substitutions are immunologically cross-reactive. Thus, a polypeptide is substantially o identical to a second polypeptide, for example, where the two peptides differ only by a

conservative substitution. Another indication that two nucleic acid sequences are substantially identical is that the two molecules hybridize to each other under stringent conditions (e.g. , within a range of medium to high stringency). [67] As used herein, the term "gene" is synonymous with the term "allele" in referring to a nucleic acid that encodes and directs the expression of a protein or RNA. Vegetative forms of filamentous fungi are generally haploid, therefore a single copy of a specified gene (i.e. , a single allele) is sufficient to confer a specified phenotype.

5 [68] As used herein, "wild-type" and "native" genes, proteins, or strains, are those found in nature,

[69] As used herein, "deletion of a gene," refers to its removal from the genome of a host cell. Where a gene includes control elements (e.g. , enhancer elements) that are not located immediately adjacent to the coding sequence of a gene, deletion of a gene refers to the deletion0 of the coding sequence, and optionally adjacent promoter and/or terminator sequences.

[70] As used herein, "disruption of a gene" refers broadly to any genetic or chemical manipulation that substantially prevents a cell from producing a function gene product, e.g. , a protein, in a host cell. Exemplar)' methods of disruption include complete or partial deletion of any portion of a gene, including a polypeptide-coding sequence, a promoter, an enhancer, or 5 another regulatory element, or mutagenesis of the same, where mutagenesis encompasses

substitutions, insertions, deletions, inversions, and combinations and variations, thereof, any of which mutations substantially prevent the production of a function gene product.

[71] As used herein, "genetic manipulation" refers to the alteration of a preselected nucleic acid target sequence, e.g. , using macromolecules (i.e. , enzymes and/or nucleic acids) that o preferentially act on the preselected nucleic acid sequence. In this manner genetic manipulation is distinct from chemical manipulation, in which small molecules are used to randomly affect changes to a nucleic acid sequence that is not preselected.

[72] As used herein, a "genetic alteration" is a change in the DNA of a cell that results from genetic manipulation, and is distinct from a change in the DNA of a cell that results from5 chemical manipulation.

[73] As used herein, "aerobic fermentation" refers to growth in the presence of oxygen,

[74] As used herein, the term "cell broth" refers collectively to medium and cells in a liquid/submerged culture.

[75] As used herein, the term "cell mass" refers to the cell component (including intact and o lysed cells) present in a liquid/submerged culture. Cell mass may be expressed in dry or wet weight.

[76] As used herein, the term "rheology" refers to a branch of physics dealing with the deformation and flow of matter, [77] As used herein, "viscosity" is a measure of the resistance of a fluid to deformation by mechanical stress, such as shear stress or tensile stress. In the present context, viscosity refers to the resistance of a cell broth comprising filamentous fungus cells to mechanical stress, e.g. , as provided by a rotor/impeller, Because the viscosity of a cell broth can be difficult to measure 5 directly, indirect measurements of viscosity may be used, such as the dissolved oxygen content of the culture broth at a preselected amount of agitation, the amount of agitation required to maintain a preselected dissolved oxygen content, the amount of power required to agitate a cell broth to maintain a preselected dissolved oxygen content, or even colony morphology on solid medium.

o [78] As used herein, an "altered- viscosity" variant strain of filamentous fungus cells is a variant strain that produces a cell broth that has a reduced or increased viscosity (i.e. , reduced or increased resistance to shear or tensile stress) compared to an equivalent cell broth produced by a parental strain. Generally, equivalent cell broths have comparable cell masses. Preferably, the difference between a variant, altered viscosity strain and a parental strain, with respect to any5 direct or indirect measure of viscosity, is at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or even at least 50%, or more. Methods for comparing the viscosity of filamentous fungus cells broth are described, herein. Generally, comparable (or equivalent) cell broths have comparable cell masses.

[79] As used herein, a "reduced-viscosity" variant strain of filamentous fungus cells is a o variant strain that produces a cell broth that has reduced viscosity (i.e. , reduced resistance to shear or tensile stress) compared to an equivalent cell broth produced by a parental strain.

Preferably, the difference between a variant, altered viscosity strain and a parental strain, with respect to any direct or indirect measure of viscosity, is at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or even at least 50%, or 5 more,

[80] As used herein, a "primarily genetic determinant" refers to a gene, or genetic manipulation thereof, that is necessary and sufficient to confer a specified phenotype in the absence of other genes, or genetic manipulations, thereof.

[81] As used herein, a "functional polypeptide/protein" is a protein that posses an activity, o such as an enzymatic activity, a binding activity, a surface-active property, or the like, and which has not been mutagenized, truncated, or otherwise modified to abolish or reduce that activity, Functional polypeptides may be thermostable or thermolabile, as specified.

[82] As used herein, "a functional gene" is a gene capable of being used by cellular components to produce an active gene product, typically a protein. Functional genes are the antithesis of disrupted genes, which are modified such that they cannot be used by cellular components to produce an active gene product.

[83] As used herein, variant cells (or a variant strain) "maintain or retain a high level of protein expression and/or secretion" compared to parental cells (or a parental strain) if the difference in 5 protein expression between the variant cells and a parental cells is less than about 20%, less than about 15%, less than about 10%, less than about 7%, less than about 5%, or even less than about 3%.

[84] As used herein, host cells have been "modified to prevent the production of a Sfb3" if they have been genetically or chemically altered to prevent the production of a functional Sfb3 o polypeptide that exhibits an activity characteristic of wild-type Sfb3 protein, particularly an activity that promotes elongation of hyphae or otherwise increases the viscosity of a filamentous fungus in liquid culture, Such modifications include, but are not limited to, deletion of the sfi3 gene, disruption of the sfb3 gene, modification of the sfb3 gene such that the encoded polypeptide lacks the aforementioned activity, modification of the sfl?3 gene to affect post- 5 translational processing or stability, and combinations, thereof.

[85] As used herein, a "protein of interest" is a protein that is desired to be produced in a submerged culture of filamentous fungus cells. Generally, proteins of interest are commercially important for industrial or pharmaceutical use, making them desirable to produce in large quantities, Proteins of interest are to be distinguished from myriad other proteins expressed by the o filamentous fungus cells, which are generally not of interest as products and are mainly considered background protein contaminants.

[86] As used herein, variant cells (or a variant strain) produce(s) "substantially the same amount" of protein per unit amount of biomass as parental cells (or a parental strain) if the amount of protein produced by the variant cells is no more than 20% reduced, no more than 15% reduced,5 no more than 10% reduced, an even no more than 5% reduced compared to the amount of protein produced by the parental cells, wherein the amount of protein is normalized to the total amount of biomass of cells from which protein production is measured, wherein biomass may be expressed in terms of either wet (e.g. , of cell pellet) or dry weight.

[87] As used herein, the amount of protein of interest expressed by variant cells and parental o cells is "substantially similar" if the difference in expression between the variant cells and the parental cells is less than about 20%, less than about 15%, less than about 10%, less than about 5%, less than about 4%, less than about 3%, less than about 2%, or even less than about 1%.

[88] As used herein, "fluorochromes" are fluorescent dyes. Preferred fluorochromes bind to cellulose and/or chitin in the cell walls of fungi. [89] As used herein, the singular articles "a," "an," and "the" encompass the plural referents unless the context clearly dictates otherwise. All references cited herein are hereby incorporated by reference in their entirety. The following abbreviations/acronyms have the following meanings unless otherwise specified:

EC enzyme commission

kDa kiloDalton

kb kilobase

MW molecular weight

w/v weight/volume

w/w weight/weight

v/v volume/volume

wt% weight percent

°C degrees Centigrade

¾0 water

H₂0₂ hydrogen peroxide

dH₂O or DI deionized water

dIH₂0 deionized water, Milli-Q filtration

g or gm gram

microgram

mg milligram

kg kilogram

lb pound

μΐ_^ and μΐ microliter

mL and ml milliliter

mm millimeter

μηι micrometer

M molar

mM millimolar

μΜ micromolar

U unit

ppm parts per million

sec and " second

min and ' minute

hr hour EtOH ethanol

eq. equivalent

N normal

PCR polymerase chain reaction

DNA deoxyribonucleic acid

FOA fluoroorotic acid

UV ultraviolet

A540 absorbance measured at a wavelength of 540 nm

CMC carboxymethyl cellulose

rpm revolutions per minute

Δ relating to a deletion

DO dissolved oxygen

III. The reduced viscosity phenotype in filamentous fungi

[90] Previous efforts to develop reduced viscosity strains of Trichoderma reesei involved chemical mutagenesis, followed by screening the resulting mutants (sometimes referred to herein as "strains") for sensitivity to Calcofluor White, a fluorochrome stain that binds to cellulose and chitin in the cell walls of fungi. Sensitivity to Calcofluor White is associated with changes in yeast morphology, although the significance of Calcofluor White sensitivity in filamentous fungi was heretofore unknown. In this manner the parental Trichoderma reesei strain Morph TrglaA (29-9) was chemically mutagenized, and one resulting strain (i.e. , 70H2) was found to exhibit reduced colonial growth rate on agar plates, reduced sporulation, altered morphology, and reduced viscosity in liquid medium, while maintaining a high level of protein expression and secretion. Comparative genomic sequence analysis revealed mutations in multiple genes in the 70H2 strain, compared to parental 29-9 strain.

[91] While the 70H2 strain demonstrated a "reduced viscosity" phenotype, it lacked a fully defined genome, and the gene or genes responsible for the reduced viscosity phenotype were unknown. Moreover, while 70H2 could be used as host strain for introducing exogenous genes for high levels of expression, it was not possible to introduce the gene or genes responsible for the reduced viscosity phenotype into other strains.

IV. Alterations in Sfb3 production affect cell viscosity in filamentous fungus [92] It has now been discovered that alterations in Sfb3 production affect cell viscosity in filamentous fungus. This discovery has significant implications for the use of filamentous fungi for the expression of commercially important proteins.

[93] The Sft>3 gene (also known as Lstl) has previously only been characterized in budding yeast (i.e. , Saccharomyc.es cerevisiae), where it encodes a protein associated with the COPII protein coat surrounding transport vesicles that carry proteins from the endoplasmic reticulum to the Golgi apparatus. Sfl>3, as well as Sfb2, are homologs of Sec24, all of which genes are involved with packaging specific cargo proteins into the vesicles.

[94] While Sec24 is an essential gene in yeast, 5β3 and Sft>2 are not, although the deletion of Sfl>3 in yeast is known to affect the transport of a plasma membrane transport protein (Pmalp) and a glucanosyltransferase (Gaslp) that is involved in cell wall synthesis.

[95] Using BLAST to search the publicly available genome sequence of Trichoderma reesei using S. cerevisiae Sec24p, Sfb3p or Sfb2p amino acid sequences as query sequences reveals that T. reesei has a single gene that is most closely homologous to yeast Sec24 and a single gene that is most closely homologous to yeast Sfb3. No other homolog was identified suggesting that T. reesei does not have a gene equivalent to Sfb2.

[96] Using BLAST to search publicly available genome sequences of Pezizomycotina species using the T. reesei Sfb3 amino acid sequence as query demonstrates a general pattern. That is, each fungus has a clear homolog of each of Sfb3 and Sec24 but an additional homolog more closely related to yeast Sfb2 is not present in the genomes of these filamentous ascomycetes.

[97] Homologs of the Sfb3 proteins are found in filamentous fungi, e.g., Trichoderma reesei and Aspergillus oryzae, although the function of these proteins was heretofore unknown. The amino acid sequences of the S. cerevisiae (SEQ ID NO: 1), T. reesei (SEQ ID NO: 2), A. oryzae (SEQ ID NO: 3), A. niger (SEQ ID NO: 4), P. funic losum (SEQ ID NO: 5), P. chrysogenum (SEQ ID NO: 6), N. Crassa (SEQ ID NO: 7), and F. oxysporum (SEQ ID NO: 8) Sfb3proteins are shown, below, as examples: SEQ ID NOs: 4-8 were obtained from publicly-accessible fungal genome databases but do not have accession numbers.

[98] Saccharomyces cerevisiae Sfb3 amino acid sequence (SEQ ID NO: 1):

MSQQNILAASVSALSLDESTVHTGGASSKKSRRPHRAYHNFSSGTVPTLGNSPYTTPQLNQQDG FQQPQAFTPKQFGGFNNGSGSVMSTPVMVSQERFGASEASSPYGQSMLDMTAPQPTSHIVPTQR FEDQAQYLQRSFETCRDSVPPLPTTQFYCVDQGSCDPHLMSLSMYNIPESEHLRAATKLPLGLT IQPFSTLTPNDAEVPTIPLPMDGTPLRCRRCRAYANPKFQFTYDSSVICNICRVKMQVPGEHFA PMGPNGQRSDLNEKSELLHGTVDFLVPSIYNAIQEKELLPLHYVFLIDVSLLANENGSSLAMVE GVRSCIEYISDFQPNCEVAIIVYDNKLRFFNLRPDLDNAQEYIVSELDDVFLPFYNGLFVKPGN SMKI INDTLIKISGYISTDKYSHVPQVCYGSALQAAKLALDTVTGGQGGKIICSLNSLPTIGNG NLSLKRDNAHIAHVKCDNGFYKKLASDFLKSYISLDLYVTNAGFIDMATVGHPVEMTSGILKYY PHFQQETDAFTLVNDMVTNVSNIVGYQALLKVRCSTGLSVEQYYCDSSDNTDHDPIIPVLTRDT TLDVLLKYDSKIKTGTDVHFQTALLYTDIDGVRKVRSINTSGAVSNNIREIFKFINQNPV RIM IKDVIKTLGDCDFVKIRRLIDDKMVEILTQYRGLVSSNSSTQLILPDSIKTLPAYMLAFEKSEL MKPNAQSTRGNERIYDLLKYDSLNSAQLCYKLYPQIVPFHVLLEETDLTFYDANDKLLQINSSS INNLSVRASHSNFINGGCYLIFQGDTIYLWFNENTNRMLLQDLLSVDESLPVSQISLFSGTLPE TGTSINQKASNVIKNWQQWNKSSLPLVLLRPNVDQYYSNVMSQLLCEDKTVNRIESYDNYLVI MHKKIQEKLQKDDFIKVSTAATHENIHQKFVQF

[99] Trichoderma reesei Sfb3 amino acid sequence (SEQ ID NO: 2):

MDYTQYHALGHGEVLDPNDPNKTSAPAAPQFQPPSSPYVPPGSPYGAPPYHGGHQAPPMA PPP STPGYGPPQGQSFPGSPMPSQDAGLAAQFGGMSLGADAGGAAARKKKKDRHAYHSVEPTGSSQA FNGLPPC-TPAEQFLNVNNPQGIPALGGQFGSPLASPMGTPHMANPGQFPAPTSPFTPSAPVSPA EFASRFGSPDAATSIGSAGPSQVSPDDMPSIPASRDAIQEHFFKNVYPTFERHVPPPATVSFVA FDQGNASPKFTRLTLNNIPTTAEGLHATGLPLGMLIQPLAPLQAGEAEIPVLDFGDAGPPRCRR CRAYINPFMMFRSGGNKFVCNLCSYPNETPPEYFCAVSPQGVRLDRDQRPELHRGTVEFVVPKE YWTREPVGLRWLFVIDVTQESYNKGFMETFCEGILAALYGGNDEENDEDGEPKRRIPKGAKVGF ITYDKDIHFYNINPHLDQAH MIMPDLEDPFLPLGEGLFVDPYESKAIITSLLTRLPEMFSTIK NPEPALLATLNAAVAALEATGGKWCSCSTLPTWGPGRLFMRDDGNHPGGELDKKLYTTEHPAW KKVSEKMASSGIGVDFFLAAPSGGYLDIATIGHVAATTGGETFYYPNFIAPRDGARLSMEITHA ITRETGFQALMKVRCSTGLQVAAYHGNFVQHTFGADLEIGVIDADKALGVSFSHDGKLDPKLDA HFQTALLYTTASGQRRVRCSNVIAS SDTSKESNTKELAIRQCLKFVDQDAVVGIFAKEASTKL ATTSANLQDVRNWLTERTIDIMAYYKKHSANQFPPSQLVMPERLKEFCMYMLGMLKCRAFKGGI ENSDRRVHELRMVRSMGPLELSLYLYPRMIALHNLQPEEGFADPETGHLKMPPSVRTSFSRVEP GGVYLVDNGQQCLLWFHAQTSPNLITDLFGEGHDSLKGLDPYTSTLPVLETHLSAQVRNIIEFL KS RGSKGMTIQLARQGIDGAEYEFARMLVEDRNNEAKSYVDWLVHIHRGVQLELSGQRKKEGD GEATAVMANFAGLRPAYW [100] Aspergillus oryzae RIB40 Sfb3 amino acid sequence (GI: 83766074; SEQ ID NO: 3):

MADQSMYNTLC-QGTSPAEDPSNPNRMAHQVPPQSQPAAGFPPGPYPPQPGAYYGNPPPNQYDAPA AAPPTQQLQSPPPRGLAPSPQLAYGTETQTHMGAPADPMAGLASQMSGLGIMGDSGARPGKKKHR HAHHEIGGATASAPQQFAG PQAGMQPSSQFLNTGLNQAPRPISPAAGVPPAGIVPQPGVPAPGS GSVPTQGKIDPEQIPSIPQSRDIPTMYYFDHIYPTMERHLPPPAAVPFVAHDQGNSSPKHARLTL NNIPTTSDFLSSTALPLGMVLQPLARLDPGEPEVPVLDFGEMGPPRCRRCRAYINPFMTFRSGGN KFVCNMCTFPNDVAPEYFAPLDMSGARVDRLQRPELMIGTVEFMVPKEYWNKEPVGLQRLFLIDV SQESVNRGFLKGVCKGITEALYGAPDASEEDAAARRVPEGSKIGIVTYDREVHFYNLSAQLDQAQ MMVMTDLEEPFVPLSEGLFVDPYESKDIITSLLHRIPKIFSHIKKPEPALLPALNAAMSALQATG GKIFASICSLPTWGPGALH RDDPKVHGTDAERKLFTTDNQAWRTTAGKMAEEGIGVDMFVAAPG GTYVDVATIGHVAEVSGGETFFYPNFHAPRDILKLSQEFAHAVTRETGYQA MKVRCSNGLQVSA YHGNFIQHALGADLEIGSIDADKAIGVMFSYDGKLDPKLDAHFQAALLYTTAEGQRRVRCINWA AVNEGGLETMKFIDQDCWSIMAKEAAAKTVDKSLKDIRASITEKTVDIFSGYRKVFSGSHPPGQ LVLPENLKEFSMYMLALIKSRAFKGGQEASDRRIHD RMLRSIGATELALYLYPRVIPIHN QPE DGFPNEQGQLQVPPSLRASFSKIEEGGAYLVDNGQICLLWLHSRVSPNLLEDLLGPGQSSLQGLN PQTSSLPVLETHLNAQVRNLLQYFSTMRGSKSVAIQLARQGLDGAEYEFARLLVEDRNNEAQSYV DWLVHIHRQINLELAGHRKREDTSAEGSLTSLAGLRAPYW

[101] Aspergillus niger Sfb3 amino acid sequence (SEQ ID NO: 4)

MADPNMYHTYGQAPVPGENPSDPNQMAYQVPPQGYPAAGIPPGPSPPQPGAAYGVPAPNQQWPA YGSPPPAQQPLQQPPSQFAHQADPQAAMGAPVDPGMAGLASQMSGLGIMGGEGGAARSSKKKHR HAHHEIAGASASVAQPFAAAPQDPMQPTSQFLNTGLNQAPRPISPAASIPAPVNPAFGGGAGAV PTQGKVDPEQIPSIPRSRDLPAQYYFNHVYPTMERHLPPPAAVPFVAHDQGNSSPKYARLTLNN IPSTSDFLSSTGLPLC-MVLQPLARLDGEQPIPVLDFGDAGPPRCRRCRAYINPFMSFRSGGNKF VCNMCTFPNDVPPEYFAPLDPSGSRIDRMQRPELMMGTVEFLVPKDYWNKEPVGLQWLLLIDVS QESVNKGFLKGVCKGIMEALYSEETENPEDEAPARRIPEGAKIGIVTYDKEVHFYNLSAQLDQA QMMVMTDLEEPFVPLSEGLFVDPYESKDVITSLLQRIPSIFSHVKNPQPALLPALNAALSALRP TGGKIVGTIASLPTWC-PGALSLRDDPKVHGTDAERKLFTTEHAGWRETAGHLAEAGIGLD FIA APSGTYMDVATIGHIPEVTGGETFFYPNFHAPRDIRKLSKELAHAITRETGYQALMKVRCSNGL QVSGYHC-NFVQHTFGADLEIGAIDADKAIGVVFSYDGKLDPKLDAHFQAALLYTSANGQRRVRC INTVAAVNEGGMETMKFVDQDAVVAMVAKDAASKTLDKSLKDIRAGVSEKTVDIFSGYRKIFSG SHPPGQLVLPENLKEFSMYMLSLIKSRAIKGGQEASDRRIHDMRMLRSIGCTELSLYLYPRIIP IHNMQPTDGFPNEQGQLQVPPSLRASFSKIEEGGAYLVDNGQQCLLWLHSHVSPNLLEDLFGEG QTSLQGLSPQISTIPVLETHLNAQVRNLLQYFSTIRGSKAVTIQLARQGLDGAEYEFARMLVED RNNEAQSSVDWLVHIHRQINLELAGHRKREDTAGEGGLTSLAGLRAPYW

[102] Penici!liumfuniculosum Sfb3 amino acid sequence (SEQ ID NO: 5)

MADYSTYHSSGYAGAPGEDPNRQQPAVPAPYHSPNAPPGQAIQQPGITPYGAAQPPQFPGQPGV GYGVAPVPSPPQALGC-PDVGDLATRIGGLGIISDAGTRSHKKKHRHAYHDIGGPNAQGLNTFPS QTNLQSQFLNTGLNQPEQQPAAPAAFPGAPVGQVPANVAPGAAPEVGGVGSVPTQGKIDPEQIP SVPRSRDLPAQYYFNNVYPTMERHVPPPASIPFIAHDQGNSSPKVARLTLNNIPSSSDFLQSTG LPLGMILQPLAKLDAC-EQPVPVIDFGDIGPPRCRRCRTYINPFMTFRSGGNKFVCNMCTFPNDV PPEYFAPVDPSGVRVDRLQRPELMLGTVEFTVPKEYWVKEPAGLHQLFLIDVSQESVNRGFLKG VCDGIINALYGEEEPVEGAEPETRKVPEGSKIGIVTFDREIHFYNLLPRLDKAQMMVMTDLEEP FVPLSEC-LFVDPYESKDVITSLLEQLPSLFARVKSPESTLLPTIKAAISALQATGGKIICCLTS LPTYGPG LVMKDKSQAPDGEN LFAIDNPDYKAAATKLTEAGVGIDFFVAAPGGSFMDLTTIG YTAAISGGECFFYPNFHSPRDSLKLAQEISHTVTRETGYQAL KVRCSNGLQVSAYYGNFLQHT FGADLEIGTIDADKALGVLFSYDGKLDPKLDAHFQAALLYTAANGQRRVRCINIVAGVNEGGIE TMKCIDQDAVVAIIAKEAASKAGDKTLKDIRASITEKTVDIFSGYRKNFSGSHPPGQLVLPENL KEFSMYMLGLL SRAFKGGSETADRRVHDLRMLRSIGCLELSLYLYPRI IPIHNMSAEDGFANE QGQLQVPPALRASFSRVEEGGAYLIDNGQGILLWIHSFVSPNLLEDLFGPGITSLQALDPNTSS LPVLETHLNAQVRNLLQYLSTVRGSKAVTIQLARQGIDGAEYEFARSLVEDRNNEAQSYVDWLV HIHRQINLEL GHRKKEDS TSSGEGALSSLAGIRAPYW

[103] Penicillium chrysogenum Sfb3 amino acid sequence (SEQ ID NO: 6)

MADSSMYNTMGQGSSEDPSNPQYMAQVPPQQYPAGYPPTAAPLQPGAPYANPAPNQWPAYGSPQ QPGMASPGIAYNAPQQPMGAAVDPGMAGLASQMGGLDIAADAGARTHRKKHRHAHHDIGGGAAP PAQGFNTGMDQGGLQQPQPQQQSQFLNTGLNQHADRPVSPAVGLVSGQSVAAIPGIQSGAGSVP TSGRIDPEHIPSIPRSRDLPAQYYFNHVYPTMDQHLPPPAAIPFVAQDQGNSSPKYARLTLNNI PSASDFLTSTGLPLGMILQPLAPLDPGEQPIPVLDFGDVGPPRCRRCRTYINPFMSFRSGGSKF VCNMCTFPNDTPPEYFAPLDPSGARVDRMQRPELLMGTVEFTVPKEYWNKEPVGLQTLFLIDVS RESVHRGFLKGVCAGIKDALYGDDDKASEGTEGDGSSRKLPVGAKVGIVTYDKEVHFYNLAAAL DQAQMMVMTDLDEPFVPLSEGLFVDPYESKSVITSLLSRIPKIFSSIKNPESALLPTLNSALSA LQATGGKIVCAVASLPTCGPGHLAIREDPKVHGTDAERKLFTTENPAWKKTASKLAEAGVGLDL FMAAPGGTYLDVATIC-HVSSLTGGETFFYPNFHAPRDLLKLRKEIAEAVTRETGYQTLMKVRCS NGLQVSAYHGNFVQHTLGADLEIAGVDADKAVGVLFSYDGKLDPKLDAHFQAALLYTSADGQRR VRCINVVAAVNEGGLETMKFVDQDAVVSVIAKEAASKTLDKNLKDIRASISEKTVDIFSGYRKI FSGSHPPGQLVLPENLKEFSMYMLSLVKSRAFKAGPESSDRRIHDMRLIRSMGCTEMALYLYPR IIPVHNMQPEDGFANEHGQLQIPPTMRASYSRIEDGGVYIVDNGQAILLWIHAQVSPNLLEDLF GPGHNSLQGLNPNTSSLPVLETHLNAQVRNLLQYLSTVRGSKSVTIQLARQGLDGAEYEFARLL LEDRNNEAQSYVDWLVHIHRQINLELAGHRKKEEGGEGALASLSAMRTPYW

[104] Neurospora crassa Sfb3 amino acid sequence (SEQ ID NO: 7)

MADYTMYHALGQGETLDPNDPNRTTQPAPPQFQPPVAPNPYHPGAEYNAPGQQQQQQQQYGQQY GQQYGQQYGQQQYGQEYGHQQQQQQQQQYGAPSPYGAPPAHSPVSPMDDVGLAAQMGGMSLGAG AGAADHHGRKKKKDRHAFHTVEAPAGSSQPFNGMPPAGIPATQFLNADPSLAGRIPGPGHGQFP MPASPAFGPVPTSAADFAARDATQGVGSGVFAAGGPQGGKPSPDDTPSVPLSRDAVQPYFHTNV YPTFERLVPPPAVTSEVALDQGNSSPKFARLTMTNLPASAEGLKSTGLPLGLLLQPLAETQPGE LPIPVLDFGEQGPPRCHRCRAYMNPFMMFKAGGNKFVCNLCTYANDTPPEYFCALSPQGVRVDR DQRPELTRGTVEFVVPKEYWTKEPVGMRYLFVIDVTQESYNKGFLESFCEGILSALYGGSEEGE DQDETGEPKRKIPAGAKVGFVTFDQEIHFYNVSPALEQAQMIVMPDIEDPFLPLSDGLFVDPYE SKAVISSLLIRLPQMFSNIKNPEPALLSALNSAVAALEKTGGKVFCSLAALPTWGPGRLFMRDD GKHPGGEPDKKLFTTEHPGWRKLAEKMVSLGVGADFFMASPSGGYLDIATIGHVSSTTGGETFF YPNFVVQRDSTKLSLEIHHAVRRETGYAALMKVRCSNGLQVNAYHGNFIQHTFGADLEIGVIDA DKALAVTFGYDGKLDSKLDAHFQAALLYTTASGQRRVRCINVIAGVSDLARDCMKYIDQDAIVS ILAKEASTKLSTTSANLKEVRSSLTEKTIDILALYRKNHLAVPHPPQQLVMPERLKEFTMYVLG MLKCRAFKGGNETTDRRVHDMRLIRSMGARELSLYLYPRIIPLHSLQPEDGYPDATTGHLRMPS TMRASFARVEPGGVYLVDNGQVCLLWMHAQTAPALIQDLFGEDKTTLQSLDPYTSTIPVLETHL NAQTRNIIEYMRTVRC-SKGLTIQLARQGIDGAEFEFARMLVEDRNNEAQSYVD LVHVHKGVQL ELAGQRKREDGESHSALGSFTGLRPAYW

[105] Fusarium oxysporum Sfb3 amino acid sequence (SEQ ID NO: 8)

MADYAQYHALGQGEVIDPNDPNRTSQPSAQQFQPPIAPSPYQQQASPYGAPQYLGGQQAPPPMT GSPAPAPGYGYAPPQAQAPPGQAPPSQDATLAAQLGGMNLGDGHGTARRKKKDRHAYHTVEPTG SSQAFNGMPPQGTSATQFLDSVPGGPGFGGQFGSPQGTPQMQSQSQFSAPVNPAFGPGPVAGTP GVGEGLGTASVSTSGPKGVSPDDMPSVPASRDAIQQYYLKNVYPTFERHVPPPSTVSFVAYDQG NSSP YTRLTLNNIPTTQDALQATGLSLGLLLQPLAPLQAGEAEIPVLDFGEAGPPRCRRCRAY MNPFMMFRSGGNKFVCNLCAYPNDTPPEYFSATNPQGVRVDRDTRPELHRGTVEFVVPKEYWTR EPVGLRWLFLIDVTQESYNKGYVEAFCEGIRVALYGGEDQELDENGEPKRRIPEGAKVGFVTYD KDIHFYNV PALDQAQMMIMPDLEDPFVPLSEGLFVDPYESKDVITSLLTRLPDMFSTIKNPEP ALLAALNSALAALEATGGKVVASCSALPTWGPGRLFMRDNGNHPGGEIDKKLYTTEHPAWKKVA EKMAASGVGADFFLAAPSGGYLD IATIGHVSSTTGGETFYYPNFIAARDSRKLSLEISHAVTRE TGFQALMKVRCSNGLQVSGYHGNFIQHTFGADLEIGVIDADKAMGVSFSYDGKLDPKLDAHFQS ALLYTTASGERRVRCSNVIASVTETSKESGAREQGIRECLKFVDQDAVIGMLAKEASTKLATTS SNLKDIRHWLSEKAIDVLACYRKHAAQQHPPGQLVMPERLKEYCMYLLGLLKCRALKGGVENSD RRVHEMRMLRS GALELSLYLYPRMIPIHNLAPEEGFADPETGHLKMPPAIRTSFSRVEPGGVY LVDNGQQCLLWFHSQTSPNLISDLFGEDKDSLKSLDPYTSALPLLETHLNAQVRNIIEFLRTMR GSKGLTIQLARQGIDC-AEFDFARMLVEDRNNEAQSYVDWLVHIHKGVQLELSGQRKKEGEEHTA ASLSNFAGLRPAYW

[106] An alignment of the amino acid sequences of the Sfb3 proteins from S. cerevisiae (SEQ ID NO: 1) and T. reesei (SEQ ID NO: 2) is shown in Figure 13. These sequences have approximately 30% amino acid sequence identity. By contrast, the Sfb3 proteins from T. reesei and A. oryzae have approximately 58% amino acid sequence identity. An alignment of the amino acid sequences of the Sfb3proteins from S. cerevisiae (SEQ ID NO: 1), T. reesei (SEQ ID NO: 2), and A. oryzae (SEQ ID NO: 3) is shown in Figure 14.

[107] An alignment of the amino acid sequences of the Sfb3 proteins from approximately 40 Pezizomycotina species revealed a specific amino acid sequence, i.e. ,

IQLARQGXDGXEXXXARXLXEDRNXEAXSXVDWL (SEQ ID NO: 9, where X is any amino acid residue), which is close to the C-terminus of the Sfb3 proteins, and not found in Sec24 proteins. This consensus sequence can be used to identify Sfb3 proteins in other members of the Pezizomycotina.

[108] Separate studies have shown that mutation of the gasl gene (or the gell gene as it is known in Aspergillus fumigatus) affects fungal cell wall structure and leads to morphological changes as well as hypersensitivity to Calcofluor White, Congo Red and sodium dodecyl sulfate. [109] Without being limited to a theory, it is believed that the alteration of Sfb3 expression and/or activity in filamentous fungi interferes with the transport of proteins involved in cell wall synthesis, thereby altering cell wall structure and producing a more compact cellular morphology characterized by shorter hyphae and a more yeast-like appearance. A likely candidate for a 5 protein involved in cell wall synthesis is Gasl/Gell.

[110] Variant filamentous fungi strains that exhibit an altered viscosity phenotype in liquid medium can be well suited for the large scale production of commercially important proteins. While the present strains and methods are exemplified using the filamentous fungus T. reesei, the function of the Sfb3 protein within the Pezizomycotina is expected to be conserved. Therefore0 the present strains and methods are in no way limited to T. reesei.

V. Filamentous fungal strain with altered Sfb3 protein production

[111] In one aspect, a variant strain of filamentous fungus derived from a parental strain is provided, the variant strain comprising a genetic alteration that causes cells of the variant strain to 5 produce an altered amount of functional Sfb3 protein compared to cells of the parental strain. The cells of the variant strain subsequently produce, during aerobic fermentation in submerged culture, a cell broth that requires an altered amount of agitation to maintain a preselected dissolved oxygen content, or a cell mass that maintains an altered dissolved oxygen content at a preselected amount of agitation, compared to the cells of the parental strain.

o [112] In some cases, the genetic alteration causes cells of the variant strain to produce a reduced amount of functional Sfb3 protein compared to cells of the parental strain, and the resulting cell broth requires reduced agitation to maintain a preselected dissolved oxygen content, or maintains a higher dissolved oxygen content at a preselected amount of agitation, compared to the cells of the parental strain. In such cases, it is believed that the cell mass of the variant strain exhibits reduced 5 viscosity compared to a cell mass of the parental strain, which accounts for the observations

relating to dissolved oxygen content and agitation.

[113] The reduction in the amount of functional Sfb3 protein may result from disruption of the sfb3 gene present in the parental strain. Because disruption of the sft>3 gene is a primary genetic determinant for conferring a reduced viscosity phenotype to the variant strain, such variant strains o need only comprise a disrupted sfl3 gene, while all other genes may remain intact. In some cases, the variant strains may optionally include additional genetic alterations compared to the parental stain from which they are derived. Such additional genetic alterations are not necessary to confer a reduction in viscosity but may confer other advantageous to the strain. [114] Disruption of the sft>3 gene can be performed using any suitable methods that substantially prevent expression of a function sjb3 gene product, i.e., the Sfb3 protein.

Exemplary methods of disruption include complete or partial deletion of the sft>3 gene, including complete or partial deletion of, e.g., the Sfb3-coding sequence, the promoter, the terminator, an 5 enhancer, or another regulatory element. Disruption of the sfb3 gene can also be performed by the complete or partial deletion of a portion of the chromosome that includes any portion of the sfb3 gene. Particular methods of disrupting the sfb3 gene include making nucleotide substitutions or insertions in any portion of the sft>3 gene, e.g., the Sfb3-coding sequence, the promoter, the terminator, an enhancer, or another regulatory element. Preferably, deletions, o insertions, and/or substitutions (collectively referred to as mutations) are made by genetic

manipulation using sequence-specific molecular biology techniques, as opposed to by chemical mutagenesis, which is generally not targeted to specific nucleic acid sequences.

[115] Mutations in the sfb3 gene may reduce the efficiency of the 3 promoter, reduce the efficiency of a φ3 enhancer, interfere with the splicing or editing of the sft>3 mRNA, interfere 5 with the translation of the sfb3 mRNA, introduce a stop codon into the Sfb3 -coding sequence to prevent the translation of full-length Sfb3 protein, change the coding sequence of the Sfb3 protein to produce a less active or inactive protein or reduce Sfb3 interaction with other cell wall components, change the coding sequence of the Sfb3 protein to produce a less stable protein or target the protein for destruction, cause the Sfb3 protein to misfold or be incorrectly modified o (e.g. , by glycosylation), or interfere with cellular trafficking of the Sfb3 protein.

[116] Generally, the goal of these and other genetic manipulations is to reduce or prevent the expression of a functional Sfb3 protein, or reduce or prevent the normal biological activity of the Sfb3 protein, thereby producing a morphology change that results in a reduced viscosity phenotype.

5 [117] In other cases, the genetic alteration increases or restores the expression of a functional

Sfb3 protein, or increases the normal biological activity of the Sfb3 protein, thereby producing a morphology change that results in an increased or restored viscosity phenotype. Exemplary genetic alterations that increase or restore Sfb3 function are those that introduce addition copies of the sft)3 gene into a cell, increase the efficiency of the sfl>3 promoter, enhancer, or other o control element, increase the translation of the mRNA encoding the Sfb3 protein, increase the stability of mRNA encoding the Sfb3 protein, introduce changes in the sfl3 gene that increase the activity or stability of the Sfb3 protein, introduce changes in the sfl>3 gene that modulate the interaction with other proteins or cell wall components, and the like. Other genetic alterations that increase or restore Sfb3 function are those that reverse the effect of genetic alterations that reduce or prevent the expression of a functional Sfb3 protein

[118] Filamentous fungus cells for manipulation and use as described are generally from the phylum Ascomycota, subphylum Pezizomycotina, particularly fungi that have a vegetative hyphae state and include a homolog of the sfb3 gene. Such organisms include filamentous fungus cells used for the production of commercially important industrial and pharmaceutical proteins, including, but are not limited to Trichoderma spp., Aspergillus spp., Fusarium spp., Scedosporium spp., Penicillium spp., Chrysosporium spp., Cephalosporium spp., Talaromyces spp., Geosmithia spp., Myceliophthora spp., and Neurospora spp. Particular organisms include, but are not limited to, Trichoderma reesei (previously classified as Trichoderma

longibrachiatum and Hypocrea jecorina), Aspergillus niger, Aspergillus fumigatus, Aspergillus itaconicus, Aspergillus oryzae, Aspergillus nidulans, Aspergillus terreus, Aspergillus sojae, Aspergillus japonicus, Scedosporium prolificans, Neurospora crassa, Penicillium funiculosum, Penicillium chrysogenum, Talaromyces (Geosmithia) emersonii, Fusarium venenatum, Myceliophthora thermophila, and Chrysosporium lucknowense.

[119] In some embodiments, e.g. , where the filamentous fungus is T. reesei, the sfl>3 gene encodes a protein having the amino acid sequence of SEQ ID NO: 2. In other embodiments, the sfl)3 gene encodes a protein having a specified degree of overall amino acid sequence identity to the amino acid sequence of SEQ ID NO: 2, e.g. , at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or even at least about 99% identity.

[120] In some embodiments, e.g. , where the filamentous fungus is A. oryzae, the sfl)3 gene encodes a protein having the amino acid sequence of SEQ ID NO: 3. In other embodiments, the sft3 gene encodes a protein having a specified degree of overall amino acid sequence identity to the amino acid sequence of SEQ ID NO: 3, e.g. , at least about 70%, at least about 75%, at least about 80%o, at least about 85%), at least about 90%), at least about 91%o, at least about 92%o, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or even at least about 99% identity.

[121] In some embodiments, e.g. , where the filamentous fungus is T. reesei, the sfl)3 gene has the nucleotide sequence of SEQ ID NO: 10 shown, below. In other embodiments, the sfb3 gene has a nucleotide sequence with a specified degree of overall nucleotide sequence identity to the nucleotide sequence of SEQ ID NO: 10, e.g. , at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or even at least about 99% identity.

[122] Trichoderma reesei sft>3 DNA sequence (SEQ ID NO: 10; 2 introns are underlined): atggactacacgcagtatcacgccctgggccacggcgaggtcctcgaccccaacgaccccaaca agacgtccgctccagcggctccccagttccagcccccctcctcgccctacgtgccaccgggctc cccttacggcgctcccccgtaccatggcggccaccaagctcctcccatggcaatgccgcctccg tcgacgcccggctacggcccgccgcagggccagagcttccccgggtctccgatgccgtcgcagg atgctggccttgccgcgcagtttggcgggatgagcctgggtgcggatgcgggaggcgccgccgc gaggaagaagaagaaggacaggcacgcgtaccacagcgtggagccgacgggctcgtcgcaggcc ttcaatggcctgccgccggggacgcccgccgagcagttcctcaacgtcaacaacccgcagggca tcccggcgctgggagggcagtttggaagccctctggccagccccatgggcacgcctcacatggc caatccgggccagttcccggcgccaacctctcccttcaccccctcggcccctgtgtcgccggcc gagttcgcatccaggtttggctctcccgacgctgccacgtcaataggctcggctggccccagcc aggtgtcgccagacgacatgcccagcatacccgcctcgagggacgccatccaggagcacttttt taagaacgtttacccgaccttcgagcgccatgtgccccctcctgcgacggtttcctttgttgcc ttcgaccaaggcaatgcctctcccaaattcacccgactcaccctcaacaacatcccaaccacag ccgagggcctccatgcgacgggcttgcccctgggcatgctcatccagcctctggccccacttca agcgggagaggccgagattcccgttctcgactttggcgacgccggcccgcctcgatgtcgaaga tgccgggcttatatcaaccccttcatgatgttccgatcgggcggcaacaagttcgtgtgcaacc tctgctcgtaccccaacgaaacgccgcccgagtacttttgcgccgtcagcccacagggagtgcg cctagatcgagaccagcggccggagcttcaccgcggtaccgtcgagttcgtcgtccccaaggag tactggacccgagagcccgtcggcctccgctggctgtttgtcatcgacgtcacgcaggaatcct ataacaagggcttcatggagacattctgcgagggcatcctcgcggccctctacggcggcaacga cgaggagaatgatgaagatggcgagccaaagcgaaggatacccaagggagccaaggttgggttc atcacgtacgacaaggacattcacttttacaacatcaacgtgagttcacgagcactgggaacaa gaatgagatggcccgctaacattaagacagcctcatctggatcaagcgcacat atgatcatgc ccgacctcgaagacccattcctccccctcggcgagggcctctttgtcgacccgtacgagtcaaa ggccatcat cacctctctcctcacccgcctccccgagatgttctccaccatcaaaaaccccgag cccgctctgcttgccacgctcaatgccgccgtggctgcgctggaggcaacgggaggtaaagtcg tgtgctcgtgctcgaccttgcctacctggggccctggccgactgttcatgcgcgacgacggcaa ccatcccggtggcgagctggacaagaagctgtatacgacggaacaccccgcgtggaagaaggt c t cggagaagatggcttcgtccggcattggtgtcgacttcttccttgctgcgccct ccggcggct acctggacattgcgacgataggccatgtcgccgccacgactggtggagagacgttctactaccc caacttcatcgccccgcgagacggtgcccggctgtcaatggagattacgcacgccatcacgagg gaaacgggcttccaggcgctgatgaaggtccgctgctcgaccgggctgcaggtggcggcgtacc acggcaactttgtccagcacacctttggggcagacctggagattggcgtcattgacgcggacaa ggcgctcggcgtgtcgtttagccacgacggtaaactggatcccaagctggacgcccacttccag acggctctcctgtacacgaccgcgtccggacagcgacgcgtgcgatgttccaacgtgattgcca gcgtcagcgacacctccaaggagtccaacaccaaggagctggccattcggcagtgcctcaagtt tgtcgaccaggacgcggttgtgggtatctttgcaaaagaagccagcaccaagctcgccacgaca tcggccaatctccaggatgtgcgaaactggctgacggagcgaacaatcgacatcatggcctact acaagaagcactctgccaatcagttccctccgagccagctggtcatgcccgaacggctgaagga 5 gttctgcatgtacatgctaggcatgttgaaatgcagagctttcaagggcggtatcgagaactcg gatcgcagagtgcacgagctgcgcatggtccgcagcatgggcccgctggagcttagcctgtatc tgtacccccggatgattgctctgcacaacctccagcccgaagagggctttgccgaccccgaaac aggccacctcaagatgcccccgtccgtgcggacgtccttttcacgggtcgagccgggtggcgtc tacctggtggacaacggacagcagtgcttgctgtggtttcacgcccagacgtcgcccaacctca0 tcaccgacctgtttggcgagggccacgactcgctcaaggggctggatccgtacacgtccacgct gccggtgctggagacgcatctcagcgcacaggtccgcaacattattgagttcctcaaaagcatg aggggatccaagggcatgacgatacagctggcgcggcaggggattgacggcgccgagtacgagt ttgcgcggatgttggtggaggatcgcaacaatgaggcgaagagctacgttgactggcttgttca cattcacagaggagttcagctggaggtatgttcccccgcctccccccttttcccccttgcgtcg5 tcgtcaggagatgatgagaatgctaattcgtcctatagttgagcggacaacgaaagaaggaagg cgatggagaggctaccgccgtaatggccaactttgcaggactgagaccggcctattggtag

VI. Method for altering the viscosity phenotype of filamentous fungal cells

[123] In another aspect, a method for altering the morphology of filamentous fungus cells is o provided. The variant filamentous fungus cells exhibit altered growth morphology on solid

medium and produce cell masses having different viscosities when grown in submerged culture,

[124] In some cases, the method comprises disrupting the s Mgene in a parental strain using suitable genetic or chemical methods, wherein during aerobic fermentation the variant strain produces during aerobic fermentation in submerged culture a cell broth that requires reduced 5 agitation to maintain a preselected dissolved oxygen content, or maintains an increased dissolved oxygen content at a preselected amount of agitation, compared to the cells of the parental strain. Such methods may be used to disrupt the s/¾3gene in any manner described above and elsewhere. Preferably, disruption of the s/¾3gene is performed by genetic manipulation using sequence- specific molecular biology techniques, as opposed to chemical mutagenesis, which is generally o not targeted to specific nucleic acid sequences.

[125] In some embodiments, the parental strain into which the reduced viscosity phenotype is introduced already comprises a gene of interest intended to be expressed at high levels. In this manner, the present methods obviate the need to introduce a gene of interest into a pre-existing reduced viscosity strain for production. Thus, the present methods can be used to produce a 5 reduced viscosity variant strain of filamentous fungus cells from a parental strain already

comprising a gene of interest. [126] In another aspect, a method for screening filamentous fungus cells for an altered viscosity phenotype is also provided. The method involves screening a panel of filamentous fungus cells (e.g., mutagenized cells or field isolates) for altered sensitivity to a fluorochrome stain, wherein altered sensitivity to the fluorochrome stain indicates that the variant cells produce during aerobic 5 fermentation in submerged culture a cell broth that requires more or less agitation to maintain a preselected dissolved oxygen content, and/or maintain an increased or decreased dissolved oxygen content at a preselected amount of agitation, compared to the cells of the parental strain. In this manner sensitivity to the fluorochrome stain can be used to identify variant filamentous fungus cells that have an altered viscosity phenotype. In some cases, the method involves screening a i o panel of filamentous fungus cells (e.g., mutagenized cells or field isolates) for increased sensitivity to a fluorochrome stain, wherein increased sensitivity to the fluorochrome stain indicates that the variant cells produce during aerobic fermentation in submerged culture a cell broth that requires reduced agitation to maintain a preselected dissolved oxygen content, and/or maintain an increased dissolved oxygen content at a preselected amount of agitation, compared to the cells of the parental

15 strain. In this manner sensitivity to the fluorochrome stain can be used to identify variant

filamentous fungus cells that have a reduced viscosity phenotype.

[127] Exemplary fluorochromes bind to cellulose and/or chitin in the cell walls of filamentous fungi, and include but are not limited to, Calcofluor white (CAS No. 4193-55-9), Congo red (CAS No. 573-58-0), Solophenyl Flavine (CAS No. 61725-08-4), Pontamine Fast Scarlet (CAS

20 No. 79770-29-9), and primulin (CAS No. 30113-37-2).

[128] The particular genetic technique used to disrupt the sfl)3 gene in a parental strain of filamentous fungus is generally not critical to the method, so long as the technique targets the sfi3 gene in a sequence-specific manner. Exemplary methods are site specific recombination, targeted gene insertion, the use of transposable elements, transduction by viruses, and the use of RNA-

25 mediated gene silencing (Raponi M, and Arndt, G.M. (2003) Nucleic Acids Research 31:4481-891 Nakayashiki H. and Nguyen, Q.B. (2008) Current Opinion in Microbiology 11:494-502; Kuck, U. and Hoff, B. (2010) Applied and Environmental Biotechnology 86:51-62),

[129] Where desired, disrupting the 3 gene may be accompanied by the simultaneous or sequential insertion of, e.g. , a selectable marker, a fluorescent or other distinguishable marker, a

3 o cloning site or cloning cassette, a sequence fingerprint to allow subsequent identification of the strain, or other genetic modification to add distinctiveness or functionality to the strain. In some cases, it may be desirable to introduce a gene of interest intended for high level expression in the reduced viscosity strain at the site of disruption of the sft>3gene. In such cases, introducing the reduced viscosity phenotype and introducing a gene of interest may be performed simultaneously.

35 VII. Utility

[130] The use of reduced viscosity strains of filamentous fungi is known to improve the distribution of oxygen and nutrients in a submerged culture, reduce the amount of energy required 5 to agitate a submerged culture, and increase the cell mass present in the culture, leading to

increased protein production. However, the present variant strains of filamentous fungus offer significant advantages over previously-described reduced viscosity strains.

[131] First, the present strains may have a fully defined genome, making them well-suited for subsequent genetic manipulation, complementation, mating, and the like. Second, the present o strains are not adversely affected in secreted protein production. Third, reduced viscosity strains can be produced from essentially any parental strain, including parental strains that already produce a protein intended for high level expression (i.e. , a protein of interest), already encode a selectable marker, or already include other features that are desirable in a production host. Thus, the present strain and methods eliminate the need to transfer a gene encoding a protein of interest into a 5 preexisting reduced viscosity production strain.

[132] The present strains and methods find use in the production of commercially important protein in submerged cultures of filamentous fungi. Commercially important proteins include, for example, cellulases, xylanases, pectinases, lyases, pectinases, proteases, amylases, pullulanases, lipases, esterases, perhydrolases, transferases, laccases, catalases, oxidases, reductases, o hydrophobin, and other enzymes and non-enzyme proteins capable of being expressed in

filamentous fungi. Such proteins may be for industrial or pharmaceutical use.

[133] These and other aspects and embodiments of the present strains and methods will be apparent to the skilled person in view of the present description. The following examples are5 intended to further illustrate, but not limit, the strains and methods,

EXAMPLES

[134] To assist in reading the following examples, the common names, Genencor strain collection numbers (GICC#), and selected features of the starting filamentous fungus strains are0 listed in Table 1. The same information for the filamentous fungus strains generated is listed in Table 2. The nucleic acid primers used in the examples are listed in Table 3, Sequences in small caps are nucleotides added to allow direct digestion of the PCR amplified fragment. Sequences in italics are restriction enzyme recognition sites. Sequences in bold are loxP sites, Underlined CACC sequences were added to appropriate primers to allow incorporation of the amplified DNA fragment into a GATEWAY entry vector.

Table 1. Pre-existing Trichoderma reesei strains used in the Examples.

Table 3. Primer sequences used in the Examples.

AVG114 CTCCGGCGAAGCAGAAGA 37

AVG115 TCATGCTGTGTCCTGCCG 38

AVG160 GCCTCTCCCAAATTCACC 39

AVG161 TGGTGGAGAACATCTCGG 40

[135] Media and other stock solutions used in the Examples are described, below:

VOGEL'S MINIMAL MEDIUM (ΎΜ1 1 L

50x Vogel's Solution 20 mL

50% Glucose 20 mL

Add d¾0 to final volume

Agar 20 g

Autoclave

[137] 50x VOGELS SOLUTION

Sodium Citrate.2H₂0 125 g

KH₂P0 (Anhydrous) 250 g

MgS0₄.7H₂0 10 g

CaCl₂.2H₂0 5 g

Vogel's Trace Element Solution 5 mL

Vogel's Biotin Solution 2.5 mL

Add dH₂0 to final volume

Filter sterilize

VOGEL'S TRACE ELEMENT SOLUTION

Citric Acid 50 g

ZnS0₄.7H₂0 50 g

CuS0₄.5H₂0 2.5 g

MnS0₄.4H₂0 0.5 g

H3BO3 0.5 g

Na₂Mo0₄.2H₂0 0.5 g Add d¾0 to final volume

Filter sterilize

[139] VOGEL¹ S BIOTIN SOLUTION 1 L

D-Biotin 0.1 g

Filter sterilize

[140] VM HYGROMYCIN MEDIUM (VMH) 1 L

50x Vogel' s Solution 20 mL

50% Glucose 20 mL

Add dH₂0 to final volume

Agar 20 g

Autoclave

[141] VM SORBITOL HYGROMYCIN MEDIUM (VMSH) 1 L

50x Vogel' s Solution 20 mL

50% Glucose 20 mL

Sorbitol 218.64 g

Add d¾0 to final volume

Agar 20 g

Autoclave

Hygromycin B (50 mg/mL stock) 1 mL

[142] POTATO DEXTROSE AGAR (PDA) 1 L

BD Difco Potato Dextrose Agar 39 g

Add d¾0 to final volume

Autoclave

[143] CONGO RED MEDIUM (CR) 1L

Make VM or PDA

Autoclave

1% Congo Red stock 6 mL [144] 1% CONGO RED STOCK 25 mL

Congo Red 250 mg

dH₂0 25 mL

Filter sterilize

5

[145] YEG MEDIUM 1L

Yeast Extract 5 g

Glucose 20 g

Add dH₂0 to final volume

i o Autoclave

T. reesei GLYCINE MINIMAL MEDIUM 1 L

Glycine 6 g

(NH₄)₂S0₄ 4.7 g

KH₂P0₄ 5 g

MgS0₄.7H₂0 1 g

lOOmg/mL CaCl₂*2H₂0 solution 10 mL

T. reesei Trace Elements 400X 2.5 mL

PIPPS 33 g

Adjust pH to 5.50 with 50% NaOH (about 5 mL per liter).

Add dH₂0 to final volume

Autoclave.

Add Glucose/Sophorose 25 mL

25 [147] T. reesei TRACE ELEMENTS 400x 1 L

Citric Acid (Anhydrous) 175 g

FeS0₄.7H20 200 g

ZnS0₄.7H20 16 g

CuS0₄.5H20 3.2 g

30 MnS0₄.H20 1.4 g

H3BO3 (Boric Acid) 0.8 g Example 1. Deletion of sfl3 from T. reesei strains Morph and 29-9 to obtain a reduced viscosity phenotype

1.1. Generation of a Δ 3 deletion cassette

[148] The DNA sequences flanking the 5 ^' end of the T. reesei sfb3 gene was amplified with the primer pair AVG88/AVG89. Amplification of the fragment with this primer pair introduced a Sail site at the 5 ' end of the fragment and a BglR site at the 3 ' end of the fragment. The hygromycin B resistance cassette flanked by parallel loxP sites was amplified from plasmid pCR-Blunt H-hph-loxP#4 (Figure 1) with primer pair AVG90/AVG91, introducing a BgUI site at the 5 ' end of the fragment and a Notl site at the 3' end of the fragment. The DNA sequence flanking the 3^' end of sft>3 was amplified with primer pair AVG92/AVG93, introducing a Notl site at the 5 ' end and an Xbal site at the 3' end of the fragment.

[149] The above three fragments were successively ligated into vector pCR^®-Blunt II-TOPO^® (Invitrogen Corp., Carlsbad, CA, USA), and the resulting plasmid was named pCR-Blunt II- TOPO 889092 (Figure 2). The DNA sequences at the 5 ' and 3 ' flanks of the 3 gene were amplified using Morph TrglaA (29-9) genomic DNA as the template. The Asft>3 deletion cassette containing the 5 ^r sfl)3 flank, the hygromycin B -resistance cassette surrounded by loxP sites at each end, and the 3 ^' sft3 flank, was amplified from plasmid pCRBluntll-TOPO 889092 with primer pair AVG104/AVG105. Multiple PCR reactions were pooled, purified using a PCR purification kit, and ethanol precipitated to concentrate the amplified DNA fragment. The DNA thus prepared was used in the subsequent steps.

1.2. Generation of strains 29-9 Asfb3 and Morph Asfb3 lacking the sfi3 gene

[150] Strains Morph and 29-9 were transformed with the Asft>3 deletion cassette by PEG- mediated transformation, and plated on Vogel's minimal medium containing hygromycin B and sorbitol. Trichoderma transformation is described, e.g. , in U.S. Pat. No. 5,246,853. Candidates (684 for 29-9 + Asfb3 and 348 for Morph + Asfb3) were transferred to Vogel's minimal medium containing hygromycin B to select for hygromycin B resistant candidates. Hygromycin B resistant transformants were transferred to Vogel's minimal medium or PDA containing Congo Red to assess Congo Red sensitivity. PCR analysis revealed one Congo Red-sensitive candidate from each transformation in which the sft>3 deletion cassette integrated at the φ3 locus by homologous recombination (Figure 3). Homologous integration of the Αφ3 deletion cassette at the φ3 locus in both 29-9 Asfb3 and Morph Asfb3 was verified by amplifying DNA fragments of the expected size using primer pairs AVG108/AVG109, AVG110/AVGl 11 and

AVG108/AVG111. Primer pair AVG108/AVG109 amplifies a DNA fragment starting outside the 5 ' end of the AVG88/AVG89 deletion cassette region and ending within the hygromycin B resistance cassette. Primer pair AVG110/AVGl 11 amplifies a DNA fragment starting within the hygromycin B resistance cassette and ending outside the 3 ' end of the AVG92/AVG93 deletion cassette region. Primer pair AVG108/AVG110 amplifies the whole deletion cassette integrated at the sfb3 locus. The generated strains with confirmed homologous integration of the deletion cassette were named 29-9 Asfb3 and Morph Asfb3, respectively. 1.3. Growth of strains 29-9, 70H2, and 29-9 As M in submerged culture

[151] Strains 29-9, 70H2, and 29-9 Asft3 were grown under identical conditions in submerged (liquid) culture, and their growth phenotypes were compared.

[152] Briefly, spores of each strain were added separately to 500-mL of medium in a 3-L flask with both side and bottom baffles. The medium contained 5 g/L (NH₄)₂S0₄, 4.5 g/L H2PO4, 1 g/L MgS0₄ 7H₂0, and 14.4 g/L citric acid, adjusted to pH 5.5 with 5% NaOH. After autoclaving for 30 minutes, sterile 60% glucose was added to a final concentration of 27.5 g/L, along with 2.5 mL/L of a trace element solution containing 175 g/L citric acid, 200 g/L

FeS0₄-7H20, 16 g/L ZnS0₄-7H₂0, 3.2 g/L CuS0₄-5H₂0, 1.4 g/L MnS0₄ H₂0, and 0.8 g/L H₃BO₃. The culture was grown for 48 hrs at 34°C in a shaking incubator.

[153] After 48 hrs, the contents of each flask were added separately to 15-L fermentors containing 9.5 L of medium containing 4.7 g/L KH₂P0₄, 1.0 g/L MgS0₄-7H₂0, 4.3 g/L (NH₄)₂S0₄ and 2.5 mL/L of the same trace element solution. These components were heat sterilized together at 121°C for 30 minutes. A solution of 60% glucose and 0.48% CaCl₂ 2H₂0 was separately autoclaved, cooled, and added to the fermentor to a final concentration of 75 g/L glucose and 0.6 g/L CaCl₂-2H₂0, The medium was adjusted to pH 3.5 with 28% NH₃ and the temperature was maintained at 34°C for the entire growth period.

[154] A dissolved oxygen (DO) probe was calibrated to 100% when there was no added pressure in the headspace (i.e., 0 bar gauge, 1 bar absolute). The pressure in the headspace was then set to 0.7 bar (gauge), after which the oxygen probe read 170% before the seed culture was added. The fermentor contained two, four-blade turbines that provided mixing via a variable speed motor that was initially set at 500 rpm.

[155] As the cultures grew, DO levels dropped, at least partly as a consequence of the increased viscosity of the broth due to the proliferation of filamentous fungus hyphae, When DO fell below 40%, the agitation rate was increased to maintain the dissolved oxygen at 40%. If the DO did not fall below 40%, then it was unnecessary to increase the agitation rate during the fermentation run, and the initial agitation rate was higher than necessary. When the glucose was completely consumed, the amount of biomass produced in each fermentor was measured, and found to be substantially the same for all three strains.

5 [156] The DO level in each fermentor at a given level of agitation, and the amount of agitation required to maintain a given DO level are indirect measures of the viscosity of the different broths, due to the different strain growth phenotypes. Although it would be ideal to vary only one variable {i.e., DO or agitation) and measure the other, it is desirable to prevent the DO from falling below 40% to ensure the production of sufficient biomass in each fermentor, thereby i o permitting a more meaningful comparison between the growth of the different strains.

[157] Generally, where it is necessary to increase the agitation rate to maintain a target DO level, the amount of agitation can be estimated by the amount of power supplied to the motor driving the fermentor turbine, which provides a metric that correlates with the viscosity of the broth.

15 [158] In particular, the extra power required to agitate the suspended culture is proportional to the agitation rate raised to the 3rd power. Table 4 shows the highest agitation rate required to maintain the dissolved oxygen at 40% at the end of the growth phase.

Table 4. Agitation rate required to maintain a DO of 40% at the end of the growth phase

[159] Under these growth conditions, the original strain, 29-9, required 2.6 times more power than either the 70H2 or 29-9 Asft>3 strains in order to maintain a DO of 40% and produce the amount of biomass. Strains 70H2 and 29-9 Asfl>3 had similar viscosity properties, and produced similar levels of a protein of interest (TrGA) in suspended culture, demonstrating that a reduced viscosity growth phenotype can be imparted to a filamentous fungus by disrupting the sfb3 gene. 1.4. Elimination of the fo -flanked hygrom cin B resistance cassette from Morph Asfb3

[160] The oxP-flanked hygromycin B resistance cassette was eliminated from strain Morph 5 Asfb3 by transiently expressing the ere gene which induced recombination between loxP sites.

The Morph Asfb3 strain was transformed with the cre-containing telomeric plasmid pTrex-Tel- pyrG13/pDONR221/0927853cre (Figure 4) to induce recombination between loxP sites and eliminate the hygromycin B resistance cassette, This vector contains the amdS marker cassette allowing growth on medium containing acetamide. Transformants were transferred once to o acetamide-containing medium, followed by three transfers to PDA medium to allow loss of the cre-containing telomeric plasmid. The transformants were then transferred in parallel to Vogel' s medium containing hygromycin B to assess if the hygromycin B cassette was lost and acetamide- containing medium to assess if the cre-containing plasmid was lost (Figure 5; PDA = Potato Dextrose Agar, VMH = Vogel' s minimal medium with hygromycin B, amdS = minimal medium5 with acetamide, hph^" = sensitive to hygromycin B, ere^" = sensitive to presence of acetamide in medium). 91.8 % of the transformants lost the hygromycin B cassette and 92.5 % of the transformants lost the erg-containing plasmid. This demonstrated that it is possible to eliminate the hygromycin B cassette from the integrated AsfbS deletion cassette. o 1.5. Expression of a gene of interest is not impaired by disruption of the 3 gene

[161] An expression cassette encoding a glucoamylase enzyme served as an exemplary gene of interest and provided a convenient way to measure the amount of protein secreted from the variant filamentous fungus strains. The glucoamylase expression cassette (i.e., TrglaA expression cassette), containing the cbhl promoter, the T. reesei glucoamylase gene TrglaA, and 5 the cbhl terminator, fused to the amdS marker cassette, was PCR amplified from plasmid

pNSP23 (Figure 6) using primer pair SK745/SK746. Multiple PCR reactions were pooled, purified using a PCR purification kit, and ethanol precipitated to concentrate the amplified DNA fragment. The Morph Asfb3 strain was transformed with the TrglaA expression cassette by PEG-mediated transformation, and then plated on acetamide minimal medium with sorbitol, o Stable candidates were selected on acetamide minimal medium and transferred to induction medium in a microtiter plate format. The strains were grown in microtiter plates and the activity of glucoamylase in the supernatant was assayed using PNPG as the substrate.

[162] The best Morph Asfb3 + TrglaA candidates had glucoamylase activity higher than the 29- 9 strain (which also includes the TrglaA expression cassette). The supernatant glucoamylase activity of the top candidate was verified after growth in shake flasks, and confirmed the results obtained in microtiter plates. The results show that deletion of the sft>3 does not impair the expression or secretion of a protein of interest.

5 Example 2. Complementation of the70H2 strain with the wild type φ3 gene

2.1. Generation of constructs containing the sfb3 gene

[163] Four constructs containing the sfb3 gene were made. Primer pair AVG82/AVG83 was used to amplify the wild type sfb3 gene with its native promoter and terminator from 29-9 o genomic DNA and the mutated sfb 3 gene with its native promoter and terminator from 70H2 genomic DNA. Primer pair AVG84/AVG85 was used to amplify the wild type sft>3 gene from the start codon to the stop codon using 29-9 genomic DNA the mutated sfb3 gene from the start codon to the stop codon using 70H2 genomic DNA. The result was four PCR-amplified fragments containing the wild type or mutated sfl3 gene, with or without the native 3 5 promoter and terminator. Each of these four fragments was independently cloned into the

pENTR/D-TOPO vector (Invitrogen, Carlsbad, CA, USA).

[164] In the next step the four pENTR/D-TOPO constructs were transferred to the destination vector pTrex2g HygB using the LR clonase reaction. Each of the four constructs was amplified in E. coli, and obtained minipreps for each construct were vacuum concentrated. DNA prepared o this way was used in the subsequent step. An exemplary destination construct is shown in

Figure 7.

2.2. Complementation of the 70H2 phenotype with the sfb3 gene

[165] Each of the four destination vector constructs were separately transformed into 70H2 by 5 PEG-mediated transformation, followed by plating on Vogel' s minimal medium with

hygromycin B. Thirty candidates from each of the four transformations were transferred to PDA with hygromycin B, and their phenotype compared to 70H2 and 29-9 transformed with the pTrex2g/HygB vector alone (as controls). All candidates transformed with the wild type sft>3 genes had a wild type phenotype similar to 29-9 on PDA medium with hygromycin B. All o candidates transformed with the mutated sfl>3 gene derived from 70H2 retained the 70H2

phenotype (Figure 8). These results indicated that the wild type sft)3 gene derived from 29-9, but not the mutated sfo3 gene derived from 70H2, could impart a wild type phenotype to the 70H2 strain. [166] To confirm that the phenotype reversion was caused by the presence of the wild type sfl3 gene and not by a change in the chromosomal DNA, candidates were transferred four times on PDA medium (non-selective conditions) to look for candidates that lost the vector, and then back to selective medium with hygromycin B, For all candidates that were unstable and lost the plasmid (based on the loss of hygromycin B resistance), the loss of the plasmid correlated with the reappearance of the 70H2 phenotype. These results confirm that the wild type φ3 was responsible for the restoring the wild type phenotype to 70H2.

2.3. Generation of a sfl3 gene replacement cassette containing the wild type 3 gene

[167] A DNA sequence containing about 2/3 of the 3' end of the wild type sft>3 gene was amplified with primer pair AVG94 /AVG95, which introduced a Spel site at the 5' end of the fragment and a Bglll site at the 3' end of the fragment. The hygromycin B resistance cassette flanked by loxP sites was amplified from plasmid pCR-Blunt E-hph-loxP#4 (Figure 1) with primer pair AVG90/AVG91, which introduced a Bglll site at the 5' end of the fragment and a Notl site at the 3' end of the fragment. A DNA sequence containing the 3' DNA sequence downstream of the 3 terminator region was amplified with primer pair AVG96/AVG97, which introduced a Notl site at the 5' end of the fragment and an Xbal site at the 3' end of the fragment.

[168] These three fragments were successively ligated into vector pCR^®-Blunt Π-ΤΟΡΟ^® (Invitrogen Corp., Carlsbad, CA, USA), and the resulting plasmid was named pCR-Blunt II- TOPO 949096 (Figure 9). The two DNA sequences surrounding the hygromycin B resistance cassette were amplified using 29-9 genomic DNA as the template. The sfb3 gene replacement cassette, containing part of the φ3 gene, the hygromycin B-resistance cassette surrounded by loxP sites at each end, and the 3' sequence downstream of sft>3, was amplified from plasmid pCR-Blunt II-TOPO 889092 with primers pair AVG102/AVG103. Multiple PCR reactions were pooled, purified using a PCR purification kit, and ethanol precipitated to concentrate the amplified DNA fragment. DNA prepared this way was used in the subsequent step.

2.4. Complementation of the 70H2 phenotype by expression of the sft>3 wild type gene from the native sfl3 locus

[169] Strain 70H2 was transformed with the sfb3 gene replacement cassette (described in section 2.3) by PEG-mediated transformation, followed by plating on Vogel's minimal medium containing hygromycin B and sorbitol. Fifteen candidates that had a wild type colony phenotype were transferred to Vogel's minimal medium containing hygromycin B to select for hygromycin B resistant candidates with a wild type colony phenotype. Stable candidates resistant to hygromycin B were selected on minimal medium containing hygromycin B and assessed for wild type colony phenotype (Figure 10).

[170] Homologous integration of the sfl)3 gene replacement cassette at the sfl?3 locus of 70H2 was verified by amplifying DNA fragments of the expected size using primer pairs

AVG112/AVG113 and AVG114/AVG115. Primer pair AVG112/AVG113 amplified a DNA fragment starting outside the 5' end of the AVG94/AVG95 sft>3 gene replacement cassette region and ending within the hygromycin B resistance cassette. Primer pair AVG114/AVG115 amplified a DNA fragment starting within the hygromycin B resistance cassette and ending outside the 3' end of the AVG96/AVG97 sfb3 gene replacement cassette region.

[171] The generated strain with confirmed homologous integration of the sfo3 gene replacement cassette was named 70H2 + wild type sfb3. This strain had a phenotype similar to 29-9. Thus, replacement of the mutated sfb3 gene in 70H2 with the wild type sfl>3 gene, at the native sft>3 locus, restored the wild type phenotype to 70H2, providing further evidence that disruption of the sfl3 gene is responsible for the reduced- viscosity phenotype in 70H2.

Example 3. Growth of strains 29-9, 70H2, and 29-9 &sfb3 in submerged culture.

[172] Strains 29-9, 70H2, and 29-9 Asfl)3 were grown under identical conditions in submerged (liquid) culture, and their growth phenotypes were compared. Briefly, spores of each strain were added separately to 500 mL of medium in a 3-L flask with both side and bottom baffles. The medium contained 5 g/L (NH₄)₂S0₄, 4.5 g/L KH₂P0₄, 1 g/L MgS0₄-7H₂0, and 14.4 g/L citric acid, adjusted to pH 5.5 with 5% NaOH. After autoclaving for 30 minutes, sterile 60% glucose was added to a final concentration of 27,5 g/L, along with 2.5 mL/L of a trace element solution containing 175 g/L citric acid, 200 g/L FeS0₄-7H20, 16 g/L ZnS0₄-7H₂0, 3.2 g/L CuS0₄-5H₂0, 1.4 g/L MnS0₄-H₂0, and 0.8 g/L H₃B0₃. The culture was grown for 48 hrs at 34°C in a shaking incubator. [173] After 48 hrs, the contents of each flask were added separately to 15-L fermentors containing 9.5 L of medium containing 4.7 g/L KH₂P0₄, 1.0 g/L MgS0₄-7H₂0, 4.3 g/L (NH 2SO4 and 2.5 mL/L of the same trace element solution. These components were heat sterilized together at 121°C for 30 minutes. A solution of 60% glucose and 0,48% CaCl₂-2H₂0 was separately autoclaved, cooled, and added to the fermentor to a final concentration of 75 g/L glucose and 0.6 g/L CaCi₂-2H₂0. The medium was adjusted to pH 3.5 with 28% NH₃ and the temperature was maintained at 34°C for the entire growth period.

[174] A dissolved oxygen (DO) probe was calibrated to 100% when there was no added pressure in the headspace (i.e., 0 bar gauge, 1 bar absolute). The pressure in the headspace was then set to 0.7 bar (gauge), after which the oxygen probe read 170% before the seed culture was added, The fermentor contained two, four-blade turbines that provided mixing via a variable speed motor that was initially set at 500 rpm,

[175] As the cultures grew, DO levels dropped, at least partly as a consequence of the increased viscosity of the broth due to the proliferation of filamentous fungus hyphae. When DO fell below 40%, the agitation rate was increased to maintain the dissolved oxygen at 40%. If the DO did not fall below 40%, then it was unnecessary to increase the agitation rate during the fermentation run, and the initial agitation rate was higher than necessary. When the glucose was completely consumed, the amount of biomass produced in each fermentor was measured, and found to be substantially the same for all three strains.

[176] The DO level in each fermentor at a given level of agitation, and the amount of agitation required to maintain a given DO level are indirect measures of the viscosity of the different broths, due to the different strain growth phenotypes. Although it would be ideal to vary only one variable (i.e., DO or agitation) and measure the other, it is desirable to prevent the DO from falling below 40% to ensure the production of sufficient biomass in each fermentor, thereby permitting a more meaningful comparison between the growth of the different strains.

[177] Generally, where it is necessary to increase the agitation rate to maintain a target DO level, the amount of agitation can be estimated by the amount of power supplied to the motor driving the fermentor turbine, which provides a metric that correlates with the viscosity of the broth.

[178] In particular, the extra power required to agitate the suspended culture is proportional to the agitation rate raised to the 3rd power. Table 4 shows the highest agitation rate required to maintain the dissolved oxygen at 40%o at the end of the growth phase. Table 4. Agitation rate required to maintain a DO of 40% at the end of the growth phase

[179] Under these growth conditions, the original strain, 29-9, required 2.6 times more power 5 than either the 70H2 or 29-9 Asfo3 strains in order to maintain a DO of 40% and produce the amount of biomass. Importantly, the 70H2 and 29-9 Asft>3 strains had similar viscosity properties in suspended culture, demonstrating that a reduced viscosity growth phenotype can be imparted to a filamentous fungus by disrupting the sfl?3 gene. o Example 4. Generating a

H3A strain for producing a whole cellulase composition

4.1 Generation of a As 3 deletion cassette

[180] The DNA sequences flanking the 5 ' end of the T. reesei 3 gene was amplified with the primer pair AVG88/AVG89. Amplification of the fragment with this primer pair introduced a 5 Sail site at the 5 ' end of the fragment and a Bglll site at the 3 ' end of the fragment. The

hygromycin B resistance cassette flanked by parallel loxP sites was amplified from plasmid pCR-Blunt n-hph-loxP#4 (Figure 1) with primer pair AVG90/AVG91, introducing a Bglll site at the 5 ' end of the fragment and a Notl site at the 3' end of the fragment. The DNA sequence flanking the 3^' end of φ3 was amplified with primer pair AVG92/AVG93, introducing a Notl o site at the 5 ' end and an Xbal site at the 3 ' end of the fragment.

[181] The above three fragments were successively ligated into vector pCR^®-Blunt II-TOPO^® (Invitrogen Corp., Carlsbad, CA, USA), and the resulting plasmid was named pCR-Blunt II- TOPO 889092 (Figure 2), The DNA sequences at the 5 ' and 3 ' flanks of the φ3 gene were amplified using Morph TrglaA (29-9) genomic DNA as the template. The Asfl>3 deletion cassette 5 containing the 5 ^' sfl3 flank, the hygromycin B-resistance cassette surrounded by loxP sites at each end, and the 3 ' sfb3 flank, was amplified from plasmid pCRBluntH-TOPO 889092 with primer pair AVG104/AVG105. Multiple PCR reactions were pooled, purified using a PCR purification kit, and ethanol precipitated to concentrate the amplified DNA fragment. The DNA thus prepared was used in the subsequent steps. 4.2 Generation of strain H3A Asfb3 #1009 lacking the s Z>3 gene

[182] An H3A integrated Trichoderma reesei expression strain was prepared in accordance with the description of PCT/US2010/049849, published as WO/2011/038019. Strain H3A was 5 transformed with the Asfl3 deletion cassette by PEG (polyethylene glycol)-mediated

transformation, and plated on Vogel's minimal medium containing hygromycin B and sorbitol. PEG-mediated transformation of Trichoderma was previously described, in e.g., U.S. Pat. No. 5,246,853.

[183] 1020 candidates were transferred to Vogel' s minimal medium plates containing o hygromycin B to select for hygromycin B-resistance. Hygromycin B-resistant candidates were then transferred to Vogel's minimal medium or a PDA medium containing Congo Red to assess Congo Red sensitivity.

[184] PCR analysis of 43 stable candidates showing mild sensitivity to Congo Red was conducted, and one candidate, #1009, showed a profile consistent with homologous integration5 of the sfb3 deletion cassette into the H3A genome coupled with the elimination of the native sft>3 gene. Homologous integration of the Asft>3 deletion cassette at the ς 3 locus in H3A Asfb3 #1009was verified by amplifying DNA fragments of the expected size using primer pairs AVG108/AVG109; AVG110/AVG111; and AVG108/AVG111. Specifically, primer pair AVG108/AVG109 amplified a DNA fragment starting outside the 5^' end of the AVG88/AVG89 o deletion cassette region and ending within the hygromycin B resistance cassette. Primer pair

AVG110/AVGl 11 amplified a DNA fragment starting within the hygromycin B resistance cassette and ending outside the 3 ' end of the AVG92/AVG93deletion cassette region. Primer pair AVG108/AVG111 amplified the whole deletion cassette integrated at the sfb3 locus.

Absence of the 3 gene was confirmed by absence of a PCR product when using primer pair5 AVG160/AVG161 designed to amplify an internal φ3 fragment.

[185] When compared to the H3A host strain, the H3A Asfb3 #1009 strain had more restricted colony morphology on Congo Red-containing medium, a slower growth rate and reduced conidiation on PDA, and was able to grow on medium containing hygromycin B (Figure 11). Liquid cultures of strains H3A and H3A Asfb3 #1009 were also compared. Shake flask cultures0 of both strains were grown in 50 mL YEG or glycine minimal medium at 28°C and 220 rpm for 1 or 6 days, respectively. In both YEG and glycine minimal medium strain H3A Asfb3 #1009 generally had shorter-length hyphae (Figure 12), suggesting improved viscosity properties. 4.3 Efficient production of a whole cellulase composition in H3A Asfb3 #1009

[186] Two fermentation runs were conducted side-by-side, one with H3A and the other with H3A Asfb3 #1009, under standard fermentation conditions, as described, for example, in PCT/US2010/049849. An agitation rate of 500 rpm was used in each fermentation tank.

Dissolved oxygen was measured at the end of the growth phase, using a Hamilton Optical Oxygen sensor (Hamilton Company, USA, Reno NV). A comparison of the DO levels is shown in Table 5, below:

Table 5. DO following growth phase

[187] The resulting whole cellulase compositions from each of the fermentation runs were characterized using an HPLC method, as described, for example, in PCT/US2010/049849. The amounts of major cellulases/hemicellulases contained therein are compared side-by-side in Table 6, below:

Table 6. Comparison of the cellulases/hemicellulases present in a whole cellulase composition

[188] Both whole cellulase compositions contained substantially the same amounts of each major component, indicating that protein expression in H3A Asfb3 #1009 was similar to that of H3A. [189] Although the foregoing compositions and methods have been described in some detail by way of illustration and examples for purposes of clarity of understanding, it will be apparent to those skilled in the art that certain changes and modifications may be made. Therefore, the description should not be construed as limiting the scope of the invention, which is delineated by the appended claims.

[190] All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entireties for all purposes and to the same extent as if each individual publication, patent, or patent application were specifically and individually indicated to be so incorporated by reference.

Claims

What is claimed is:

5 1. A variant strain of filamentous fungus derived from a parental strain, the variant strain comprising a genetic alteration that causes cells of the variant strain to produce an altered amount of functional Sfb3 protein compared to cells of the parental strain, wherein the cells of the variant strain produce during aerobic fermentation in submerged culture a cell broth that (i) requires an altered amount of agitation to maintain a preselected dissolved oxygen content compared to the i o cells of the parental strain, and/or (ii) maintains an altered dissolved oxygen content at a

preselected amount of agitation, compared to the cells of the parental strain.

2. The variant strain of claim 1, wherein the altered amount of functional Sf 3 protein is a reduced amount, and the variant strain produce during aerobic fermentation in submerged culture a

15 cell broth that (i) requires reduced agitation to maintain a preselected dissolved oxygen content compared to the cells of the parental strain, and/or (ii) maintains an increased dissolved oxygen content at a preselected amount of agitation, compared to the cells of the parental strain.

3. The variant strain of claims 1 or 2, wherein the genetic alteration comprises a disruption 20 of the sfl>3 gene present in the parental strain.

4. The variant strain of claim 3, wherein disruption of the sfb3 gene is the result of deletion of all or part of the sfb3 gene.

25 5. The variant strain of claim 3, wherein disruption of the sft>3 gene is the result of deletion of a portion of genomic DNA comprising the sfl>3 gene.

6. The variant strain of any claim 3, wherein disruption of the sft>3 gene is the result of mutagenesis of the sfb3 gene.

30

7. The variant strain of any of claims 3-6, wherein disruption of the sfb3 gene is performed using site-specific recombination.

8. The variant strain of any of claims 3-7, wherein disruption of the sfl>3 gene is performed in combination with introducing a selectable marker at the genetic locus of the sft>3 gene.

9. The variant strain of any of claims 3-8, wherein disruption of the sfl)3 gene is the

5 primary genetic determinant for conferring a reduced viscosity phenotype to the variant strain.

10. The variant strain of any of claims 1-9, wherein the variant strain does not produce functional Sfb3 protein. 0 11. The variant strain of any of claims 1-9, wherein the variant strain does not produce

Sfb3 protein.

12. The variant strain of any of claims 1-11, wherein the variant strain further comprises a gene encoding a protein of interest.

5

13. The variant strain of any of claims 1-12, wherein the variant strain produces substantially the same amount of protein per unit amount of biomass as the parental strain.

14. The variant strain of any of claims 1-13, wherein the Sfb3 protein comprises the amino o acid sequence IQLARQGXDGXEXXXARXLXEDRNXEAXSXVDWL (SEQ ID NO: 9, where

X is any amino acid residue).

15. The variant strain of any of claims 1-14 wherein the filamentous fungus is a Pezizomycotina species.

5

16. The variant strain of any of claims 1-15, wherein the filamentous fungus is Trichoderma reesei.

17. A method for producing a variant strain of filamentous fungus cells comprising: o introducing a genetic alteration into a parental strain of filamentous fugal cell, which genetic alteration alters the production of functional Sfb3 protein compared to the cells of the parental strain, thereby producing a variant filamentous fugal cell that produces during aerobic fermentation in submerged culture a cell broth that (i) requires an altered amount of agitation to maintain a preselected dissolved oxygen content, compared to the cells of the parental strain, and/or (ii) maintains an altered dissolved oxygen content at a preselected amount of agitation, compared to the cells of the parental strain.

18. The method of claim 17, wherein the genetic alteration reduces or prevents the production of functional Sfb3 protein, thereby producing a variant filamentous fugal cell that produces during aerobic fermentation in submerged culture a cell broth that (i) requires reduced agitation to maintain a preselected dissolved oxygen content, compared to the cells of the parental strain, and/or (ii) maintains an increased dissolved oxygen content at a preselected amount of agitation, compared to the cells of the parental strain.

19. The method of claim 17 or 18, wherein the genetic alteration comprises disrupting the sft3 gene in a parental filamentous fugal cell using genetic manipulation,

20. The method of claim 17 or 19, wherein the genetic alteration comprises deleting the sfl)3 gene in a parental filamentous fugal cell using genetic manipulation.

21. The method of any of claims 17-20, wherein the genetic alteration is performed using site-specific genetic recombination.

22. The method of any of claims 17-21 , wherein the disruption of the sfl>3 gene is performed in combination with introducing a selectable marker at the genetic locus of the sfb3 gene.

23. The method of any of claims 17-22, wherein the variant strain produces substantially the same amount of protein per unit amount of biomass as the parental strain.

24. The method of any of claims 17-23, wherein the Sfb3 protein comprises the amino acid sequence IQLARQGXDGXEXXXARXLXEDRNXEAXSXVDWL (SEQ ID NO: 9, where X is any amino acid residue).

25. The method of any of claims 17-24, wherein the filamentous fungus is a

Pezizomycotina species.

26. The method of any of claims 17-25, wherein the filamentous fungus is Trichoderma reesei.

27. The method of any of claims 17-26, wherein the parental strain further comprises a 5 gene encoding a protein of interest.

28. The method of claim 27, wherein the gene encoding the protein of interest is present in the parental strain prior to introducing the genetic alteration that reduces or prevents the production of functional Sfb3 protein.

0

29. A protein of interest produced by the variant strain of claim 12 or 13.

30. A variant strain of filamentous fungus produced by the method of any of claims 17-28. 5

31. A variant strain of filamentous fungus derived from a parental strain, the variant strain comprising:

(a) a genetic alteration that results in (i) a requirement for reduced agitation in submerged culture to maintain a preselected dissolved oxygen content, compared to the cells of the parental strain, and/or (ii) maintenance of an increased dissolved oxygen content in submerged culture at a o preselected amount of agitation, compared to the cells of the parental strain, and

(b) a gene encoding a protein of interest,

wherein the gene encoding the protein of interest is present in the variant strain prior to the genetic alteration in (a). 5

32. The variant strain of claim 31, wherein the genetic alteration comprises a disruption of the sfb3 gene present in the parental strain,

33. The variant strain of any of claim 31, wherein disruption of the sfb3 gene is performed in combination with introducing a selectable marker at the genetic locus of the 3 gene.

0

34. A method for screening variant filamentous fungus cells for an altered viscosity phenotype, comprising:

(a) mutagenizing the cells of a parental strain of filamentous fungi to produce variant cells;

(b) screening the variant cells for altered sensitivity to a fluorochrome stain; and (c) selecting the variant cells that have altered sensitivity to the fluorochrome stain;

wherein the altered sensitivity to the fluorochrome stain correlates with the ability of the variant filamentous fungus cells to produce, during aerobic fermentation in submerged culture, a cell broth that (i) requires an altered amount of agitation to maintain a preselected dissolved oxygen 5 content, compared to the cells of the parental strain, and/or (ii) maintains an altered dissolved oxygen content at a preselected amount of agitation, compared to the cells of the parental strain.

35. The method of claim 34, wherein the altered sensitivity is increased sensitivity, and the variant filamentous fugal cell produces, during aerobic fermentation in submerged culture, a cell o broth that (i) requires reduced agitation to maintain a preselected dissolved oxygen content,

compared to the cells of the parental strain, and/or (ii) maintains an increased dissolved oxygen content at a preselected amount of agitation, compared to the cells of the parental strain,

36. The method of claim 34 or 35, wherein the fluorochrome stain is Calcofluor White.5

37. The method of any of claims 34-36, wherein mutagenizing the cells is performed by genetic recombination.

38. The method of any of claims 34-37, wherein mutagenizing the cells is performed in o combination with introducing a selectable marker at the genetic locus of the sfl>3 gene.

39. A method for identifying a sfb3 polypeptide in Pezizomycotina species of filamentous fungus, comprising:

(a) obtaining an amino acid sequence from a Pezizomycotina species of filamentous5 fungus; and

(b) screening the amino acid sequence for the presence of the contiguous amino acid sequence IQLARQGXDGXEXXXARXLXEDRNXEAXSXVDWL (SEQ ID NO: 9, where X is any amino acid residue);

(c) wherein the presence of SEQ ID NO: 9 in the amino acid sequence from the o Pezizomycotina species of filamentous fungus indicates that the amino acid sequence from the

Pezizomycotina species of filamentous fungus is a sfb3 polypeptide.

40. An isolated sfb3 polypeptide identified by the method of claim 39.

41. A method for producing a protein of interest in filamentous fungus cells comprising: introducing into parental filamentous fungus cells a gene encoding the protein of interest and a genetic alteration that reduces the amount or activity of Sfb3 protein in the cells, thereby producing a variant filamentous fugal cell that produces during aerobic fermentation in submerged culture a cell broth comprising the protein of interest, which (i) requires an altered amount of agitation to maintain a preselected dissolved oxygen content compared to the cells of the parental strain, and/or (ii) maintains an altered dissolved oxygen content at a preselected amount of agitation compared to the cells of the parental strain, and wherein the protein of interest is produced at substantially the same level in the variant cells compared to the parental cells.

42. The method of claim 41, wherein the protein of interest is more than one protein of interest, and each of the more than one protein of interest is produced at substantially the same relative levels in the variant cells compared to the parental cells.

43. The method of claim 42, wherein the more than one protein of interest is selected from cellulases and hemicellulases.

44. A protein of interest produced by the method of any of claims 41-43.

45. A composition comprising more than one protein of interest produced by the method of any of claims 42-43.

46. The composition of claim 45, wherein the composition is a whole cellulase composition.