US20130177947A1 - Novel glycosyl hydrolase enzymes and uses thereof - Google Patents

Novel glycosyl hydrolase enzymes and uses thereof Download PDF

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US20130177947A1
US20130177947A1 US13/498,069 US201013498069A US2013177947A1 US 20130177947 A1 US20130177947 A1 US 20130177947A1 US 201013498069 A US201013498069 A US 201013498069A US 2013177947 A1 US2013177947 A1 US 2013177947A1
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seq
polypeptide
sequence identity
nucleic acid
amino acid
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Benjamin Bower
Megan Yee Hsi
Thijs Kaper
Bradley R. Keleman
Suzanne E. Lantz
Edmund A. Larenas
Colin Mitchinson
Steven Kim
William D. Hitz
Mark Emptage
Keith Dumont Wing
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Danisco US Inc
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Danisco US Inc
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Assigned to DANISCO US INC. reassignment DANISCO US INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: BOWER, BENJAMIN, KELEMEN, BRADLEY R., EMPTAGE, MARK, HSI, MEGAN YEE, KAPER, THIJS, KIM, STEVEN, LARENAS, EDMUND A., HITZ, WILLIAM D., MITCHINSON, COLIN, WING, KEITH DUMONT, LANTZ, SUZANNE E.
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    • C12N9/2405—Glucanases
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    • C12N9/2405—Glucanases
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    • C12N9/2402—Hydrolases (3) acting on glycosyl compounds (3.2) hydrolysing O- and S- glycosyl compounds (3.2.1)
    • C12N9/2477—Hemicellulases not provided in a preceding group
    • C12N9/248—Xylanases
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    • C12P19/14—Preparation of compounds containing saccharide radicals produced by the action of a carbohydrase (EC 3.2.x), e.g. by alpha-amylase, e.g. by cellulase, hemicellulase
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    • C12P7/02—Preparation of oxygen-containing organic compounds containing a hydroxy group
    • C12P7/04—Preparation of oxygen-containing organic compounds containing a hydroxy group acyclic
    • C12P7/06—Ethanol, i.e. non-beverage
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    • C12Y302/01—Glycosidases, i.e. enzymes hydrolysing O- and S-glycosyl compounds (3.2.1)
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    • Y02E50/00—Technologies for the production of fuel of non-fossil origin
    • Y02E50/30—Fuel from waste, e.g. synthetic alcohol or diesel

Definitions

  • the present disclosure generally pertains to glycosyl hydrolase enzymes, compositions comprising such enzymes, and methods of using the enzymes and compositions, for example for the saccharification or conversion of cellulosic and hemicellulosic materials into sugars.
  • Ethanol has been widely used as a 10% blend to gasoline in the USA or as a neat fuel for vehicles in Brazil in the last two decades.
  • fuel bioethanol will increase in parallel with skyrocketing prices for oil and gradual depletion of its sources.
  • fermentable sugars are increasingly used to produce plastics, polymers and other biobased products, and this industry is expected to expand substantially in the coming years.
  • the demand for abundant low cost fermentable sugars, which can be used as a feed stock in lieu of petroleum based feedstocks continues to grow.
  • cellulose and hemicellulose which can be converted into fermentable sugars.
  • xylans cellulose and hemicellulose
  • the enzymatic conversion of these polysaccharides to soluble sugars for example glucose, xylose, arabinose, galactose, mannose, and/or other hexoses and pentoses, occurs due to combined actions of various enzymes.
  • endo-1,4- ⁇ -glucanases and exo-cellobiohydrolases (CBH) catalyze the hydrolysis of insoluble cellulose to cellooligosaccharides (e.g., with cellobiose being a main product), while ⁇ -glucosidases (BGL) catalyzes the conversion of the oligosaccharides to glucose.
  • EG endo-1,4- ⁇ -glucanases
  • CBH exo-cellobiohydrolases
  • BGL ⁇ -glucosidases
  • Xylanases together with other accessory proteins (non-limiting examples of which include L- ⁇ -arabinofuranosidases, feruloyl and acetylxylan esterases, glucuronidases, and ⁇ -xylosidases) catalyze the hydrolysis of hemicelluloses.
  • the cell walls of plants are composed of a heterogeneous mixture of complex polysaccharides that interact through covalent and noncovalent means.
  • Complex polysaccharides of higher plant cell walls include, for example, cellulose ( ⁇ -1,4 glucan), which generally constitutes 35-50% of carbon found in cell wall components.
  • Cellulose polymers self associate through hydrogen bonding, van der Waals interactions and hydrophobic interactions to form semi-crystalline cellulose microfibrils. These microfibrils also include noncrystalline regions, generally known as amorphous cellulose.
  • the cellulose microfibrils are embedded in a matrix formed of hemicelluloses (including, e.g., xylans, arabinans, and mannans), pectins (e.g., galacturonans and galactans), and various other ⁇ -1,3 and ⁇ -1,4 glucans. These matrix polymers are often substituted with, for example, arabinose, galactose and/or xylose residues to yield highly complex arabinoxylans, arabinogalactans, galactomannans, and xyloglucans.
  • the hemicellulose matrix is, in turn, surrounded by polyphenolic lignin.
  • the complexity of the matrix makes it difficult to degrade by microorganisms as lignin and hemicellulose components must be broken down before enzymes can act on the core cellulose microfibrils. Ordinarily, a consortium of different enzymatic activities is required to break down cell wall polymers to release the constituent monosaccharides. For saccharification of plant cell walls, the lignin must be permeabilized and hemicellulose disrupted to allow cellulose-degrading enzymes to act on their substrate.
  • the cost and hydrolytic efficiency of enzymes are major factors that restrict the commercialization of biomass bioconversion processes.
  • the production costs of microbially produced enzymes are tightly connected with the productivity of the enzyme-producing strain and the final activity yield in the fermentation broth.
  • the hydrolytic efficiency of a multienzyme complex depends both on properties of individual enzymes, the synergies among them, and their ratio in the multienzyme blend.
  • glycosyl hydrolase polypeptides having hemicellulolytic activity including, e.g., xylanases (e.g., endoxylanases), xylosidases (e.g., ⁇ -xylosidases), arabinofuranosidases (e.g., L- ⁇ -arabinofuranosidases), nucleic acids encoding these polypeptides, and methods for making and using the polypeptides and/or nucleic acids.
  • the disclosure is based, in part, on the discovery of novel enzymes and variants having xylanase, ⁇ -xylosidase, and/or L- ⁇ -arabinofuranosidase activities.
  • an enzyme can be defined either as a polypeptide having the particular enzymatic activity or as that enzyme.
  • a xylanase can be referred to as a polypeptide having xylanase activity or as a xylanase enzyme
  • a ⁇ -xylosidase can be referred to as either a polypeptide having ⁇ -xylosidase activity or a ⁇ -xylosidase enzyme.
  • the enzymes and/or enzyme blends/compositions of the disclosure can be used to produce sugars from biomass.
  • the sugars so produced can be used by microorganisms for ethanol production or can be used to produce other bioproducts in various industrial applications. Therefore, the disclosure also provides industrial applications (e.g., saccharification processes in ethanol production) using the enzymes and/or enzyme blends/compositions described herein.
  • the enzymes and/or enzyme blends/compositions of the present disclosure can be used to decrease enzyme costs in biofuel production.
  • the invention of the disclosure pertains to enzymes (including variants thereof), or enzyme blends/compositions that are useful for hydrolyzing the major components of a lignocellulosic biomass (including, e.g., cellulose, hemicellulose, and lignin) or any material comprising cellulose and/or hemicellulose.
  • a lignocellulosic biomass including, e.g., cellulose, hemicellulose, and lignin
  • any material comprising cellulose and/or hemicellulose comprising cellulose and/or hemicellulose.
  • Such lignocellulosic biomass and/or material comprising cellulose and/or hemicellulose include, e.g., seeds, grains, tubers, plant waste or byproducts of food processing or industrial processing (e.g., stalks), corn (including, e.g., cobs, stover, and the like), grasses (e.g., Indian grass, such as Sorghastrum nutans ; or, switchgrass, e.g., Panicum species, such as Panicum virgatum ), wood (including, e.g., wood chips, processing waste), paper, pulp, recycled paper (e.g., newspaper).
  • seeds, grains, tubers, plant waste or byproducts of food processing or industrial processing e.g., stalks
  • corn including, e.g., cobs, stover, and the like
  • grasses e.g., Indian grass, such as Sorghastrum nutans ; or, switchgrass, e.g., Panicum species
  • the enzyme blends/compositions of the invention can be used to hydrolyze cellulose comprising a linear chain of ⁇ -1,4-linked glucose moieties, or hemicellulose, of a complex structure that varies from plant to plant.
  • the enzyme blends/compositions of the invention can comprise a number of different enzymes, including, e.g., cellulases and/or hemicellulases.
  • the enzymes blends/compositions of the invention can be used to hydrolyze biomass or a suitable feedstock.
  • the enzyme blends/compositions of the invention desirably comprise mixtures of enzymes, selected from, e.g., xylanases, xylosidases, cellobiohydrolases, arabinofuranosidases, and/or other enzymes that can digest hemicellulose to monomer sugars.
  • An enzyme blend/composition of the invention can comprise a mixture of two or more, three or more, or four or more enzymes selected from one or more xylanases, one or more xylosidases, one or more cellobiohydrolases, one or more arabinofuranosidases, and one or more other enzymes that are capable of converting hemicelluose to monomer sugars.
  • the other enzymes that can digest hemicellulose to monomer sugars include, without limitation, a cellulase, a hemicellulase, or a composition comprising a cellulase or a hemicellulase.
  • An enzyme blend/composition of the invention can comprise a mixture of two or more, three or more, or four or more enzymes selected from a xylanase, a xylosidase, a cellobiohydrolase, an arabinofuranosidase, and at least one other enzyme capable of converting hemicellulose to monomer sugars.
  • a non-limiting example of an enzyme blend/composition of the invention comprises a mixture of a xylanase, a xylosidase, a cellobiohydrolase, an arabinofuranosidase, and a ⁇ -glucosidase.
  • the enzyme blend/composition of the invention is suitably one that is non-naturally occurring.
  • naturally occurring composition refers to a composition produced by a naturally occurring source, which comprises one or more enzymatic components or activities, wherein each of these components or activities is found at the ratio and level produced by the naturally-occurring source as it is found in nature, untouched and unmodified by the human hand.
  • a naturally occurring composition is, for example, one that is produced by an organism unmodified with respect to the cellulolytic or hemicelluloytic enzymes such that the ratio or levels of the component enzymes are unaltered from that produced by the native organism in its native environment.
  • non-naturally occurring composition refers to a composition produced by: (1) combining component cellulolytic or hemicelluloytic enzymes either in a naturally occurring ratio or a non-naturally occurring, i.e., altered, ratio; or (2) modifying an organism to express, overexpress or underexpress one or more endogeneous or exogenous enzymes; or (3) modifying an organism such that at least one endogenous enzyme is deleted.
  • non-naturally occurring composition can also refer to a composition produced by a naturally-occurring and unmodified organism, but cultured in a man-made medium or environment that is different from the organism's native environment, such that the amounts or weight ratios of particular enzymes in the composition differ from those existing in a composition made by a native organism grown in its native habitat.
  • the enzyme blend/composition of the invention described herein is, for example, a fermentation broth.
  • the fermentation broth can be one of a filamentous fungus, including, e.g., a Trichoderma, Humicola, Fusarium, Aspergillus, Neurospora, Penicillium, Cephalosporium, Achlya, Podospora, Endothia, Mucor, Cochliobolus, Pyricularia , or Chrysosporium .
  • An exemplary fungus of Trichoderma spp. is a Trichoderma reesei .
  • An exemplary fungus of Penicillium spp. is a Penicillium funiculosum .
  • the fermentation broth can be, for example, a cell-free fermentation broth or a whole cell broth.
  • the enzyme blend/composition of the invention described herein is, in another example, a cellulase compostion.
  • the cellulase composition is a filamentous fungal cellulase composition, including, for example, a Trichoderma , such as a Trichoderma reesei , cellulase composition.
  • the cellulase composition can be produced by a filamentous fungus, for example, a Trichoderma , such as a Trichoderma reesei.
  • an enzyme blend/composition of the invention can comprise (a) one or more xylanase enzyme(s), wherein at least one of said one or more xylanase enzyme(s) is a Trichoderma reesei Xyn2, a Trichoderma reesei Xyn3, an AfuXyn2, or an AfuXyn5; (b) one or more ⁇ -xylosidase enzyme(s), wherein at least one of said one or more ⁇ -xylosidase enzyme(s) is a Group 1 ⁇ -xylosidase or a Group 2 ⁇ -xylosidase, wherein the Group 1 ⁇ -xylosidase is an Fv3A or an Fv43A, and the Group 2 ⁇ -xylosidase is a Pf43A, an Fv43D, an Fv39A, an Fv43E, an Fo43A, an Fv43B, a Pa51
  • the enzyme blend/composition is suitably one that is non-naturally occurring.
  • the one or more cellulase enzyme(s) of (d) is desirably able to achieve at least 0.00005 fraction product per mg protein per gram of phosphoric acid swollen cellulose (PASC) as determined by a calcofluor assay.
  • PASC phosphoric acid swollen cellulose
  • the combined weight of xylanase enzyme(s) in the composition can represent or constitute 5 wt. % to 45 wt. % (e.g., 5 wt. % to 25 wt. %, 5 wt. % to 15 wt. %, 10 wt. % to 15 wt.
  • the combined weight of ⁇ -xylosidase enzyme(s) can represent or constitute 2 wt. % to 50 wt. % (e.g., 2 wt. % to 30 wt. %, 5 wt. % to 25 wt. %, 5 wt. % to 10 wt. %) of the total proteins in the composition, whereas the combined weight of L- ⁇ -arabinofuranosidase enzyme(s) can represent or constitute 2 wt. % to 50 wt. % (e.g., 2 wt. % to 30 wt. %, 2 wt. % to 20 wt.
  • the enzyme blend/composition as described herein is, for example, a fermentation broth composition.
  • the fermentation broth is, for example, one of a filamentous fungus, including, without limitation, a Trichoderma, Humicola, Fusarium, Aspergillus, Neurospora, Penicillium, Cephalosporium, Achlya, Podospora, Endothia, Mucor, Cochliobolus, Pyricularia , or Chrysosporium .
  • An exemplary fungus of Trichoderma spp. is a Trichoderma reesei .
  • An exemplary fungus of Penicillium spp. is a Penicillium funiculosum .
  • the fermentation can be, for example, a cell-free fermentation broth or a whole cell broth.
  • the enzyme blend/composition as described herein can also be a cellulase composition, for example, a filamentous fungal cellulase composition.
  • the cellulase composition for example, can be produced by a filamentous fungus, such as by a Trichoderma.
  • an enzyme blend/composition of the invention can comprise (a) one or more xylanase enzyme(s) wherein at least one of said one or more xylanase enzyme(s) is a Trichoderma reesei Xyn2, a Trichoderma reesei Xyn3, an AfuXyn2, or an AfuXyn5; (b) one or both of Group 1 ⁇ -xylosidase enzymes: Fv3A and Fv43A; (c) one or more of Group 2 ⁇ -xylosidase enzyme(s) selected from Pf43A, an Fv43D, an Fv39A, an Fv43E, an Fo43A, an Fv43B, a Pa51A, a Gz43A, and/or a Trichoderma reesei Bxl1; (d) one or more cellulase enzyme(s); and optionally (e) one or more other components.
  • the one or more celluase enzyme(s) of (e) is desirably able to achieve at least 0.00005 fraction product per mg protein per gram of phosphoric acid swollen cellulose (PASC) as determined by a calcofluor assay.
  • the enzyme blend/composition is suitably one that is non-naturally occurring.
  • the combined weight of xylanase enzyme(s) in the composition can represent or constitute 5 wt. % to 45 wt. % (e.g., 5 wt. % to 25 wt. %, 5 wt. % to 15 wt. %, 10 wt. % to 15 wt.
  • the combined weight of the Group 1 ⁇ -xylosidase enzyme(s) can constitute 2 wt. % to 50 wt. % (e.g., 2 wt. % to 30 wt. %, 5 wt. % to 25 wt. %, 5 wt. % to 10 wt. %) of the total protein weight in the composition, whereas the combined weight of the Group 2 ⁇ -xylosidase enzyme(s) can constitute 2 wt. % to 50 wt. % (e.g., 2 wt. % to 30 wt. %, 5 wt. % to 25 wt.
  • the ratio of the weight of Group 1 ⁇ -xylosidase enzymes to the weight of Group 2 ⁇ -xylosidase enzymes can be, for example, 1:10 to 10:1 (e.g., 1:8 to 8:1, 1:6 to 6:1, 1:4 to 4:1, 1:2 to 2:1, or 1:1).
  • the enzyme blend/composition can further comprise additional components, which may be accessory proteins or other protein/non-protein components.
  • the additional components can constitute, for example, 1 wt. % to 50 wt. %, 1 wt. % to 10 wt. %, 2 wt. % to 5 wt. %, 5 wt. % to 10 wt. %, or 5 wt. % to 20 wt. % of the total weight of proteins in the composition.
  • the enzyme blend/composition as described herein is, for example, a fermentation broth composition.
  • the fermentation broth is, for example, one of a filamentous fungus, including, without limitation, a Trichoderma, Humicola, Fusarium, Aspergillus, Neurospora, Penicillium, Cephalosporium, Achlya, Podospora, Endothia, Mucor, Cochliobolus, Pyricularia , or Chrysosporium .
  • An exemplary fungus of Trichoderma spp. is a Trichoderma reesei .
  • An exemplary fungus of Penicillium spp. is a Penicillium funiculosum .
  • the fermentation can be, for example, a cell-free fermentation broth or a whole cell broth.
  • the enzyme blend/composition as described herein can also be a cellulase composition, for example, a filamentous fungal cellulase composition.
  • the cellulase composition for example, can be produced by a filamentous fungus, such as by a Trichoderma.
  • an enzyme blend/composition of the invention can comprise (a) one or more xylanase enzyme(s) wherein at least one of said one or more xylanase enzyme(s) is a Trichoderma reesei Xyn2, a Trichoderma reesei Xyn3, an AfuXyn2, or an AfuXyn5; (b) one or more ⁇ -xylosidase enzyme(s) wherein at least one of the one or more ⁇ -xylosidase enzyme(s) is a Group 1 ⁇ -xylosidase enzyme Fv3A or Fv43A or a Group 2 ⁇ -xylosidase enzyme Pf43A, an Fv43D, an Fv39A, an Fv43E, an Fo43A, an Fv43B, a Pa51A, a Gz43A, and/or a Trichoderma reesei Bxl1; (c) one or more
  • the enzyme blend/composition is suitably one that is non-naturally occurring.
  • the combined weight of xylanase enzyme(s) in the composition can represent or constitute 5 wt. % to 45 wt. % (e.g., 5 wt. % to 25 wt. %, 5 wt. % to 15 wt. %, 10 wt. % to 15 wt. %) of the combined or total protein weight in the composition, whereas the combined weight of the ⁇ -xylosidase enzyme(s) can constitute 2 wt. % to 50 wt. % (e.g., 2 wt. % to 30 wt. %, 5 wt.
  • the combined weight of the L- ⁇ -arabinofuranosidase enzyme(s) can constitute 2 wt. % to 50 wt. % (e.g., 2 wt. % to 30 wt. %, 5 wt. % to 25 wt. %, 5 wt. % to 10 wt. %) of the total protein weight in the composition, and wherein the combined weight of the ⁇ -glucosidase enzyme(s) can constitute 2 wt. % to 50 wt. % (e.g., up to 50 wt.
  • the enzyme blend/composition can further comprise additional components, which may be accessory proteins or other protein/non-protein components.
  • the additional components can constitute, for example, 1 wt. % to 50 wt. %, 1 wt. % to 10 wt. %, 2 wt. % to 5 wt. %, 5 wt. % to 10 wt. %, or 5 wt. % to 20 wt. % of the total weight of proteins in the composition.
  • the enzyme blend/composition as described herein is, for example, a fermentation broth composition.
  • the fermentation broth is, for example, one of a filamentous fungus, including, without limitation, a Trichoderma, Humicola, Fusarium, Aspergillus, Neurospora, Penicillium, Cephalosporium, Achlya, Podospora, Endothia, Mucor, Cochliobolus, Pyricularia , or Chrysosporium .
  • An exemplary fungus of Trichoderma spp. is a Trichoderma reesei .
  • An exemplary fungus of Penicillium spp. is a Penicillium funiculosum .
  • the fermentation can be, for example, a cell-free fermentation broth or a whole cell broth.
  • the enzyme blend/composition as described herein can also be a cellulase composition, for example, a filamentous fungal cellulase composition.
  • the cellulase composition for example, can be produced by a filamentous fungus, such as by a Trichoderma.
  • An enzyme blend/composition of the invention can also comprise, for example, (a) one or more xylanase enzyme(s) wherein at least one of said one or more xylanase enzyme(s) is a Trichoderma reesei Xyn2, a Trichoderma reesei Xyn3, an AfuXyn2, or an AfuXyn5; (b) one or both of Group 1 ⁇ -xylosidase enzymes: Fv3A and Fv43A; (c) one or more of Group 2 ⁇ -xylosidase enzyme(s) selected from Pf43A, an Fv43D, an Fv39A, an Fv43E, an Fo43A, an Fv43B, a Pa51A, a Gz43A, and/or a Trichoderma reesei Bxl1; and (d) one or more ⁇ -glucosidase enzyme(s); and optionally (e) one or
  • the enzyme blend/composition is suitably one that is non-naturally occurring.
  • the combined weight of xylanase enzyme(s) constitutes 5 wt. % to 45 wt. % (e.g., 5 wt. % to 25 wt. %, 5 wt. % to 15 wt. %, 10 wt. % to 15 wt. %) of the total weight of proteins in the composition, whereas the combined weight of Group 1 ⁇ -xylosidase enzyme(s) constitutes 2 wt. % to 50 wt. % (e.g., 2 wt. % to 30 wt. %, 5 wt.
  • the ratio of the weight of Group 1 ⁇ -xylosidase enzymes to the weight of Group 2 ⁇ -xylosidase enzymes can be, for example, 1:10 to 10:1, for example, 1:8 to 8:1, 1:6 to 6:1, 1:4 to 4:1, 1:2 to 2:1, or 1:1.
  • the enzyme blend/composition can further comprise additional components, which may be accessory proteins or other protein/non-protein components.
  • the additional components can constitute, for example, 1 wt. % to 50 wt. %, 1 wt. % to 10 wt.
  • the enzyme blend/composition as described herein is, for example, a fermentation broth composition.
  • the fermentation broth is, for example, one of a filamentous fungus, including, without limitation, a Trichoderma, Humicola, Fusarium, Aspergillus, Neurospora, Penicillium, Cephalosporium, Achlya, Podospora, Endothia, Mucor, Cochliobolus, Pyricularia , or Chrysosporium .
  • An exemplary fungus of Trichoderma spp. is a Trichoderma reesei .
  • An exemplary fungus of Penicillium spp. is a Penicillium funiculosum .
  • the fermentation can be, for example, a cell-free fermentation broth or a whole cell broth.
  • the enzyme blend/composition as described herein can also be a cellulase composition, for example, a filamentous fungal cellulase composition.
  • the cellulase composition for example, can be produced by a filamentous fungus, such as by a Trichoderma.
  • an enzyme blend/composition of the invention can comprise, for example, (a) one or more xylanase enzyme(s) wherein at least one of said one or more xylanase enzyme(s) is a Trichoderma reesei Xyn2, a Trichoderma reesei Xyn3, an AfuXyn2, or an AfuXyn5; (b) one or more ⁇ -xylosidase enzyme(s) wherein at least one of said one or more ⁇ -xylosidase enzyme(s) is a Group 1 ⁇ -xylosidase or a Group 2 ⁇ -xylosidase, wherein Group 1 ⁇ -xylosidase can be an Fv3A or an Fv43A, and a Group 2 ⁇ -xylosidase can be a Pf43A, an Fv43D, an Fv39A, an Fv43E, an Fo43A, an Fv43
  • the enzyme blend/composition is suitably one that is non-naturally occurring.
  • the combined weight of the xylanase enzyme(s) constitutes 5 wt. % to 45 wt. % (e.g., 5 wt. % to 25 wt. %, 5 wt. % to 15 wt. %, 10 wt. % to 15 wt. %) of the total protein weight in the composition, whereas the combined weight of the ⁇ -xylosidase enzyme(s) constitutes 2 wt. % to 50 wt. % (e.g., 2 wt. % to 30 wt. %, 5 wt.
  • the enzyme blend/composition can further comprise additional components, which may be accessory proteins or other protein/non-protein components.
  • the additional components can constitute, for example, 1 wt. % to 50 wt.
  • the enzyme blend/composition as described herein is, for example, a fermentation broth composition.
  • the fermentation broth is, for example, one of a filamentous fungus, including, without limitation, a Trichoderma, Humicola, Fusarium, Aspergillus, Neurospora, Penicillium, Cephalosporium, Achlya, Podospora, Endothia, Mucor, Cochliobolus, Pyricularia , or Chrysosporium .
  • An exemplary fungus of Trichoderma spp. is a Trichoderma reesei .
  • An exemplary fungus of Penicillium spp. is a Penicillium funiculosum .
  • the fermentation can be, for example, a cell-free fermentation broth or a whole cell broth.
  • the enzyme blend/composition as described herein can also be a cellulase composition, for example, a filamentous fungal cellulase composition.
  • the cellulase composition for example, can be produced by a filamentous fungus, such as by a Trichoderma.
  • An enzyme blend/composition of the invention can also be one that comprises (a) one or more xylanase enzyme(s) wherein at least one of said one or more xylanase enzyme(s) is a Trichoderma reesei Xyn2, a Trichoderma reesei Xyn3, an AfuXyn2, or an AfuXyn5; (b) one or both of Group 1 ⁇ -xylosidase enzymes: Fv3A and Fv43A; (c) one or more of Group 2 ⁇ -xylosidase enzyme(s) selected from Pf43A, an Fv43D, an Fv39A, an Fv43E, an Fo43A, an Fv43B, a Pa51A, a Gz43A, and/or a Trichoderma reesei Bxl1; and optionally (d) one or more other components.
  • the enzyme blend/composition is suitably one that is non-naturally occurring.
  • the combined weight of xylanase enzyme(s) can constitute 5 wt. % to 45 wt. % (e.g., 5 wt. % to 25 wt. %, 5 wt. % to 15 wt. %, 10 wt. % to 15 wt. %) of the total protein weight in the composition, whereas the combined weight of Group 1 ⁇ -xylosidase enzyme(s) can constitute 2 wt. % to 50 wt. % (e.g., 2 wt. % to 30 wt. %, 5 wt.
  • the combined weight of Group 2 ⁇ -xylosidase enzyme(s) can constitute 2 wt. % to 50 wt. % (e.g., 2 wt. % to 30 wt. %, 5 wt. % to 25 wt. %, 5 wt. % to 10 wt. %) of the total protein weight in the composition.
  • the ratio of the weight of Group 1 ⁇ -xylosidase enzymes to the weight of Group 2 ⁇ -xylosidase enzymes can be, for example, 1:10 to 10:1, for example, 1:8 to 8:1, 1:6 to 6:1, 1:4 to 4:1, 1:2 to 2:1, or 1:1.
  • the enzyme blend/composition can further comprise additional components, which may be accessory proteins or other protein/non-protein components.
  • the additional components can constitute, for example, 1 wt. % to 50 wt. %, 1 wt. % to 10 wt. %, 2 wt. % to 5 wt. %, 5 wt. % to 10 wt. %, or 5 wt. % to 20 wt.
  • the enzyme blend/composition as described herein is, for example, a fermentation broth composition.
  • the fermentation broth is, for example, one of a filamentous fungus, including, without limitation, a Trichoderma, Humicola, Fusarium, Aspergillus, Neurospora, Penicillium, Cephalosporium, Achlya, Podospora, Endothia, Mucor, Cochliobolus, Pyricularia , or Chrysosporium .
  • An exemplary fungus of Trichoderma spp. is a Trichoderma reesei .
  • An exemplary fungus of Penicillium spp. is a Penicillium funiculosum .
  • the fermentation can be, for example, a cell-free fermentation broth or a whole cell broth.
  • the enzyme blend/composition as described herein can also be a cellulase composition, for example, a filamentous fungal cellulase composition.
  • the cellulase composition for example, can be produced by a filamentous fungus, such as by a Trichoderma.
  • the enzymes, enzyme blends/compositions of the disclosure can be used in the food industry, e.g., for baking, for fruit and vegetable processing, in breaking down of agricultural waste, in the manufacture of animal feed, in pulp and paper production, in textile manufacture, or in household and industrial cleaning agents.
  • the enzymes, and the enzymes in the enzyme blends/compositions of the disclosure are, for example, each independently produced by a microorganism, e.g., by a fungi or a bacteria.
  • the enzymes, enzyme blends/compositions of the disclosure can also be used as commercial enzymes or compositions to digest lignocellulose from any suitable sources, including all biological sources, such as plant biomasses, e.g., corn, grains, grasses (e.g., Indian grass, such as Sorghastrum nutans ; or, switchgrass, e.g., Panicum species, such as Panicum virgatum ), or, woods or wood processing byproducts, e.g., in the wood processing, pulp and/or paper industry, in textile manufacture, in household and industrial cleaning agents, and/or in biomass waste processing.
  • plant biomasses e.g., corn, grains, grasses (e.g., Indian grass, such as Sorghastrum nutans ; or, switchgrass, e.g., Panicum species, such as Panicum virgatum )
  • woods or wood processing byproducts e.g., in the wood processing, pulp and/or paper industry,
  • the disclosure provides isolated, synthetic or recombinant nucleic acids having at least about 70%, for example, at least about 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%; 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or complete (100%) sequence identity to a nucleic acid sequence of SEQ ID NO:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 46, 47, 48, 49, or 50, over a region of at least about 10, e.g., at least about 15, 20, 25, 30, 35, 40, 45, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050
  • the disclosure provides isolated, synthetic, or recombinant nucleic acids that are capable of hybridizing, under high stringency conditions, to a complement of 97%, 98%, 99%, or complete (100%) sequence identity to a nucleic acid sequence of SEQ ID NO:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 46, 47, 48, 49, or 50, or to a fragment thereof.
  • the fragment for example, can be at least 150 contiguous residues in length, for example, at least 200, 250, or 300 contiguous residues in length.
  • the present disclosure provides nucleic acids encoding a polypeptide having hemicellulolytic activity.
  • Exemplary hemicellolytic activity includes, without limitation, xylanase, ⁇ -xylosidase, and/or L- ⁇ -arabinofuranosidase activity.
  • Exemplary polypeptides having hemicellulolytic activity include, without limitation, a xylanase, a ⁇ -xylosidase, and/or an L- ⁇ -arabinofuranosidase.
  • the disclosure further provides isolated, synthetic, or recombinant nucleic acids encoding an enzyme of the disclosure, including a polypeptide comprising the amino acid sequence of SEQ ID NO:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 43, or 44, or a subsequence thereof (e.g., a catalytic domain (“CD”) or carbohydrate binding module (“CBM”)), or a suitable variant thereof.
  • a polypeptide comprising the amino acid sequence of SEQ ID NO:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 43, or 44, or a subsequence thereof (e.g., a catalytic domain (“CD”) or carbohydrate binding module (“CBM”)), or a suitable variant thereof.
  • CD catalytic domain
  • CBM carbohydrate binding module
  • a nucleic acid of the disclosure encodes the mature portion of a protein of amino acid sequence SEQ ID NO:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 43, or 44, which is optionally operably linked to a heterologous signal sequence, e.g., the Trichoderma reesei CBHI signal sequence.
  • the nucleic acid desirably encodes a polypeptide having hemicellulolytic activity, e.g., xylanase, ⁇ -xylosidase, and/or L- ⁇ -arabinofuranosidase activity.
  • the nucleic acid of the disclosure encodes a hemicellulase, for example, a xylanase, a ⁇ -xylosidase, and/or an L- ⁇ -arabinofuranosidase, or a suitable variant thereof. Further nucleic acids of the disclosure are described in Section 6.2 below.
  • the disclosure additionally provides expression cassettes comprising a nucleic acid of the disclosure or a subsequence thereof.
  • the nucleic acid comprises at least about 70%, e.g., at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to a nucleic acid sequence of SEQ ID NO:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 46, 47, 48, 49, or 50, over a region of at least about 10 residues, e.g., at least about 10, 20, 30, 40, 50, 75, 90, 100, 150, 200, 250, 300, 350, 400, or 500 residues.
  • the nucleic acid encodes a polypeptide of SEQ ID NO:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 43, or 44, wherein the nucleic acid is optionally operably linked to a promoter.
  • the promoter can be, e.g., a fungal, viral, bacterial, mammalian, or plant promoter.
  • the promoter can be a constitutive promoter or an inducible promoter.
  • An exemplary suitable promoter is expressable in filamentous fungi, e.g., Trichoderma reesei .
  • a suitable promoter can be derived from a filamentous fungus, e.g., Trichoderma reesei , e.g., a cellobiohydrolase I (“cbh1”) gene promoter from Trichoderma reesei.
  • a filamentous fungus e.g., Trichoderma reesei
  • cbh1 cellobiohydrolase I
  • the disclosure further provides a recombinant cell engineered to express a nucleic acid of the disclosure or an expression cassette of the disclosure.
  • the nucleic acid comprises at least about 70%, e.g., at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to a nucleic acid sequence of SEQ ID NO:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 46, 47, 48, 49, or 50, over a region of at least about 10, e.g., at least about 15, 20, 25, 50, 75, 100, 150, 200, 250, 300, 400, or 500 nucleotide residues.
  • the nucleic acid can encode a polypeptide of SEQ ID NO:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 43, or 44, wherein the nucleic acid is optionally operably linked to a promoter.
  • the expression cassette can comprise the nucleic acid having at least about 70% (e.g., at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) sequence identity to SEQ ID NO:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 46, 47, 48, 49, or 50, over a region of at least about 10 nucleotide residues.
  • 70% e.g., at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%
  • the expression cassette can comprise the nucleic acid encoding a polypeptide of SEQ ID NO:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 43, or 44, wherein the nucleic acid is optionally operably linked to a promoter.
  • the recombinant cell is desirably a recombinant bacterial cell, a recombinant mammalian cell, a recombinant fungal cell, a recombinant yeast cell, a recombinant insect cell, a recombinant algal cell, or a recombinant plant cell.
  • the recombinant cell is a recombinant filamentous fungal cell, such as a Trichoderma, Humicola, Fusarium, Aspergillus, Neurospora, Penicillium, Cephalosporium, Achlya, Podospora, Endothia, Mucor, Cochliobolus, Pyricularia , or Chrysosporium cell.
  • a recombinant filamentous fungal cell such as a Trichoderma, Humicola, Fusarium, Aspergillus, Neurospora, Penicillium, Cephalosporium, Achlya, Podospora, Endothia, Mucor, Cochliobolus, Pyricularia , or Chrysosporium cell.
  • the disclosure provides transgenic plants comprising a nucleic acid of the disclosure or an expression cassette of the disclosure.
  • the disclosure provides isolated, synthetic or recombinant polypeptides comprising an amino acid sequence having at least about 80%, e.g., at least about 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%, or complete (100%) sequence identity to a polypeptide of SEQ ID NO:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 43, or 44, over a region of at least about 10, e.g., at least about 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, or 350 residues, or over the full length immature polypeptide, the full length mature polypeptide, the full length CD, or the full length CBM
  • Exemplary polypeptides include fragments of at least about 10, for example, at least about 15, 20, 25, 30, 35, 40, 45, 50, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600 residues in length.
  • the fragments comprise a CD and/or a CBM.
  • the fragment optionally includes a linker separating the CD and the CBM.
  • the linker can be a native linker or a heterologous linker.
  • the polypeptides of the disclosure have one or more hemicellulase activities.
  • Polypeptides or peptide sequences of the disclosure include sequences encoded by the nucleic acids of the disclosure. Exemplary polypeptides are described in Section 6.1.
  • the disclosure additionally provides a chimeric or fusion protein comprising at least one domain of a polypeptide of the disclosure (e.g., the CD, the CBM, or both).
  • the at least one domain can be operably linked to a second amino acid sequence, e.g., a signal peptide sequence.
  • the disclosure provides a chimeric or fusion protein comprising a signal sequence of a polypeptide of the disclosure operably linked to a second sequence, e.g., encoding the amino acid sequence of a heterologous polypeptide that is not naturally associated with the signal sequence.
  • the disclosure provides a recombinant polypeptide comprising residues 1 to 13, 1 to 14, 1 to 15, 1 to 16, 1 to 17, 1 to 18, 1 to 19, 1 to 20, 1 to 21, 1 to 22, 1 to 23, 1 to 24, 1 to 25, 1 to 26, 1 to 27, 1 to 28, 1 to 28, 1 to 30, 1 to 31, 1 to 32, 1 to 33, 1 to 34, 1 to 35, 1 to 36, 1 to 37, 1 to 38, or 1 to 40 of a polypeptide of, e.g., SEQ ID NO:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 43, or 44.
  • Further exemplary chimeric or fusion polypeptides are described in Section 6.1.1.
  • the disclosure also provides methods of producing a recombinant polypeptide comprising: (a) culturing a host cell engineered to express a polypeptide of the disclosure; and (b) recovering the polypeptide.
  • the recovery of the polypeptide includes, e.g., recovery of the fermentation broth comprising the polypeptide.
  • recovery of the polypeptide can include further purification step(s).
  • the disclosure provides methods for hydrolyzing, breaking up, or disrupting a cellooligosaccharide, an arabinoxylan oligomer, or a glucan- or cellulose-comprising composition
  • methods for hydrolyzing, breaking up, or disrupting a cellooligosaccharide, an arabinoxylan oligomer, or a glucan- or cellulose-comprising composition comprising contacting the composition with an enzyme, enzyme blend/composition of the disclosure under suitable conditions, wherein the enzyme, or enzyme blend/composition hydrolyzes, breaks up, or disrupts the cellooligosaccharide, arabinoxylan oligomer, or glucan- or cellulose-comprising composition.
  • the disclosure provides enzyme “blends” or compositions (also termed “enzyme blend/composition” herein), comprising a polypeptide of the disclosure, or a polypeptide encoded by a nucleic acid of the disclosure.
  • the polypeptide of the disclosure has one or more activities selected from xylanase, ⁇ -xylosidase, and L- ⁇ -arabinofuranosidase activities.
  • the enzyme blends/compositions are used or are useful for depolymerization of cellulosic and hemicellulosic polymers to metabolizable carbon moieties.
  • the enzyme blends of the disclosure can be in the form of a composition e.g., as a product of manufacture.
  • an enzyme blend/composition of the disclosure includes a cellulase comprising at least three different enzyme types selected from (1) an endoglucanase, (2) a cellobiohydrolase, and (3) a ⁇ -glucosidase; or at least three different enzymatic activities selected from (1) an endoglucanase activity catalyzing the cleavage of internal ⁇ -1,4 linkages of cellulosic or hemicellulosic materials, resulting in shorter glucooligosaccharides, (2) a cellobiohydrolase activity catalyzing the cleavage and release, in an “exo” manner, of cellobiose units (e.g., ⁇ -1,4 glucose-glucose disaccharide), and (3) a ⁇ -glucosidase activity catalyzing the release of
  • the disclosure provides methods for processing a biomass material comprising lignocellulose comprising contacting a composition comprising a cellulose and/or a fermentable sugar with a polypeptide of the disclosure, or a polypeptide encoded by a nucleic acid of the disclosure, or an enzyme blend/composition (e.g., a product of manufacture) of the disclosure.
  • Suitable biomass material comprising lignocellulose can be derived from an agricultural crop, a byproduct of a food or feed production, a lignocellulosic waste product, a plant residue, or a waste paper or waste paper product.
  • the polypeptides of the disclosure can have one or more enzymatic activities selected from cellulase, endoglucanase, cellobiohydrolase, ⁇ -glucosidase, xylanase, mannanase, ⁇ -xylosidase, arabinofuranosidase, and other hemicellulase activities.
  • Suitable plant residue can comprise grain, seeds, stems, leaves, hulls, husks, corncobs, corn stover, straw, grasses, wood, wood chips, wood pulp and sawdust.
  • the grasses can be, e.g., Indian grass, or switchgrass.
  • the grasses can also be, for example, Miscanthus .
  • the paper waste can be, e.g., discarded or used photocopy paper, computer printer paper, notebook paper, notepad paper, typewriter paper, newspapers, magazines, cardboard, and various paper-based packaging materials.
  • the paper waste can also be, for example,
  • compositions comprising a mixture of hemicellulose- and cellulose-hydrolyzing enzymes, and at least one biomass material.
  • the biomass material comprises a lignocellulosic material derived from an agricultural crop.
  • the biomass material is a byproduct of a food or feed production.
  • Suitable biomass material can also be a lignocellulosic waste product, a plant residue, a waste paper or waste paper product, or comprises a plant residue.
  • the plant residue can, e.g., be one comprising grains, seeds, stems, leaves, hulls, husks, corncobs, corn stover, grasses, straw, wood, wood chips, wood pulp, or sawdust.
  • Exemplary grasses include, without limitation, Indian grass or switchgrass.
  • Exemplary grasses can also include Miscanthus .
  • Exemplary paper waste include, without limitation, discarded or used photocopy paper, computer printer paper, notebook paper, notepad paper, typewriter paper, newspapers, magazines, cardboard and paper-based packaging materials.
  • Exemplary paper waste can also include, e.g., pulp.
  • Tables 1A-1B Table 1A provides a summary of the sequence identifiers used in the present disclosure for glycosyl hydrolase enzymes; Table 1B provides accession numbers for additional glycosyl hydrolase enzymes referred to in the Examples.
  • Table 2 Activity of expressed proteins on synthetic substrates pNPA and pNPX (as defined in Section 7.1.6. below) in terms relative to the Trichoderma reesei Quad delete host background activity.
  • the Quad delete host background (or “XQuad”) is defined as the activity of the expressed protein(s) in the Quad delete strain divided by the activity of the Quad delete background strain without the expressed protein(s). For example, a value of >1 indicates that the expressed protein have an activity greater than that of the background.
  • Table 3 Xylanase activity of purified candidate endo-xylanases with birchwood xylan, incubated at 50° C., pH 5.
  • Table 4 Percent conversion of cob arabinoxylan oligomers to monomer products based on total sugar available as determined by acid hydrolysis. See, Example 4.
  • Table 5 Experiment results (as described in Example 7) defining the level of hemicellulase activity for hydrolyzing treated corncob to monomer sugars.
  • the column entitled “run #” indicates the randomized experimental order.
  • the column entitled “trial #” indicates the standard experimental design order.
  • the column entitled “Quad” indicates fraction of the total protein that is from the culture supernatant for a growth of the Quad deleted T. reesei strain.
  • the column entitled “Xyn3” indicates fraction of the total protein that is Trichoderma reesei Xyn3.
  • the column entitled “Fv43D” indicates fraction of the total protein that is Fv43D.
  • the column entitled “Fv51A” indicates fraction of the total protein that is Fv51A.
  • the column entitled “Fv43A” indicates fraction of the total protein that is Fv43A.
  • the column entitled “Fv43B” indicates fraction of the total protein that is Fv43B.
  • the column entitled “loading (ug/mg carbo)” indicates the protein loaded into the saccharification reaction in units of micrograms of protein per milligram of carbohydrate.
  • the columns entitled “Xyl mg/mL, Glu mg/mL, Arab mg/mL, and G+X+A mg/mL” indicate the concentration of xylose, glucose, arabinose, and the combination of those three sugar products that is detected at the end of the saccharification reaction.
  • the columns entitled “Xyl % theor, Glu % theor, and Arab % theor” indicate the percent of theoretical yield of xylose, glucose, and arabinose reached at the end of the saccharification reaction.
  • Table 6 Calculated ratios of the seven enzymatic components for predicted maximal yield of glucose, xylose and arabinose from hydrolysis of corncob.
  • the column “loading total mg/gr carb” indicates the total enzyme dose at which the predictions are calculated.
  • the rows entitled “Total mg/ml G+X+A, % Yield Glucose, % Yield Xylose, and % Yield Arabinose” indicate the response for which the optimum has been calculated.
  • the column entitled “r2 data fit to model (includes both loadings)” indicates the r-squared statistical parameter for the model fit to data presented in Table 5.
  • the columns entitled “fraction Accellerase, fraction Quad del sup, fraction purified Trichoderma reesei Xyn3, fraction purified Fv43D, fraction purified Fv51A, fraction purified Fv43A, and fraction purified Fv43B” indicate the fraction of that component that is calculated to be optimal by the model fitted to the data in Table 5.
  • Table 7 Refinement of enzyme loadings for maximal hydrolytic conversion of corncob using blends including Fv3A and Fv43D enzymes in 1.06 g, 14% dry solids pretreated cob reactions.
  • the conditions for saccharification were as described in Example 7.
  • Columns marked with enzyme names indicate the mg of each of the listed enzyme per gram of glucan or xylan used.
  • Table 8 Refinement of enzyme loadings for maximal conversion of corncob using blends containing Fv51A as the only L- ⁇ -arabinofuranosidase in 1.06 gr, 14% dry solids pretreated cob reactions.
  • the conditions used for saccharification were as described in Example 7.
  • Columns marked with enzyme names indicate the mg of each of the listed enzymes per gram of glucan or xylan used.
  • Columns marked with carbohydrates indicate the mg per mL of each carbohydrate product produced based on measurements made with size exclusion chromatography.
  • the >dp2 column includes all oligomers larger than a disaccharide.
  • Table 9 Sugar yields obtained from mixes A, B, C of purified hemicellulases tested in 1.06 g, 14% dry solids pretreated cob reactions. The conditions used for saccharification were as described in Example 7.
  • Mix A 6 mg Trichoderma reesei Xyn3, 4 mg Fv3A, 1 mg Fv51A per gram xylan.
  • Mix B 6 mg Trichoderma reesei Xyn3, 1 mg Fv43D, 3 mg Fv43A, 3 mg Fv43B per gram xylan.
  • Mix C 6 mg Trichoderma reesei Xyn3, 3 mg Fv3A, 1 mg Fv43D, 1 mg Fv51A per gram xylan. Columns marked with monomer sugars indicate the % yield of each of the listed monomer.
  • Table 10 Sugar yields from treatment of hemicellulose preparations made from corncob, sorghum, switchgrass and sugar cane bagasse by hemicellulase mixes A, B, C. The reactions were run at 100- ⁇ L scale in 50 mM pH 5.0 Sodium Acetate buffer for 6 h at 48° C. as described in Example 8. The % yield for each monomer sugar is shown.
  • Table 11 Concentration of the majority enzymes expressed by various T. reesei integrated expression strains (designated H3A, 39A, 69A, A10A, G6A, 102, 44A, 11A, G9A) as determined by percent of the integrated HPLC area.
  • Table 12 List of switchgrass pretreatment parameters and saccharification results from the various pretreatments.
  • Table 13 Saccharification results of a hardwood pulp with the enzyme composition produced by a T. reesei integrated strain, H3A, in reactions with different amounts of solids, enzymes, and incubation time.
  • Table 14 Saccharification of a hardwood pulp with the enzyme composition produced by an integrated strain H3A over a temperature range and a pH range.
  • FIGS. 1A-1B FIG. 1A : Fv3A nucleotide sequence (SEQ ID NO:1).
  • FIG. 1B Fv3A amino acid sequence (SEQ ID NO:2).
  • SEQ ID NO:2 is the sequence of the immature Fv3A.
  • Fv3A has a predicted signal sequence corresponding to positions 1 to 23 of SEQ ID NO:2 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 24 to 766 of SEQ ID NO:2. The predicted conserved domain is in boldface type.
  • FIGS. 2A-2B FIG. 2A : Pf43A nucleotide sequence (SEQ ID NO:3).
  • FIG. 2B Pf43A amino acid sequence (SEQ ID NO:4).
  • SEQ ID NO:4 is the sequence of the immature Pf43A.
  • Pf43A has a predicted signal sequence corresponding to positions 1 to 20 of SEQ ID NO:4 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 21 to 445 of SEQ ID NO:4.
  • the predicted conserved domain is in boldface type, the predicted carbohydrate binding module (“CBM”) is in uppercase type, and the predicted linker separating the CD and CBM is in italics.
  • CBM carbohydrate binding module
  • FIGS. 3A-3B FIG. 3A : Fv43E nucleotide sequence (SEQ ID NO:5).
  • FIG. 3B Fv43E amino acid sequence (SEQ ID NO:6).
  • SEQ ID NO:6 is the sequence of the immature Fv43E.
  • Fv43E has a predicted signal sequence corresponding to positions 1 to 18 of SEQ ID NO:6 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 19 to 530 of SEQ ID NO:6.
  • the predicted conserved domain is in boldface type.
  • FIGS. 4A-4B FIG. 4A : Fv39A nucleotide sequence (SEQ ID NO:7).
  • FIG. 4B Fv39A amino acid sequence (SEQ ID NO:8).
  • SEQ ID NO:8 is the sequence of the immature Fv39A.
  • Fv39A has a predicted signal sequence corresponding to positions 1 to 19 of SEQ ID NO:8 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 20 to 439 of SEQ ID NO:8.
  • the predicted conserved domain is in boldface type.
  • FIGS. 5A-5B FIG. 5A : Fv43A nucleotide sequence (SEQ ID NO:9).
  • FIG. 5B Fv43A amino acid sequence (SEQ ID NO:10).
  • SEQ ID NO:10 is the sequence of the immature Fv43A.
  • Fv43A has a predicted signal sequence corresponding to positions 1 to 22 of SEQ ID NO:10 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 23 to 449 of SEQ ID NO:10.
  • the predicted conserved domain is in boldface type, the predicted CBM is in uppercase type, and the predicted linker separating the conserved domain and CBM is in italics.
  • FIGS. 6A-6B FIG. 6A : Fv43B nucleotide sequence (SEQ ID NO:11).
  • FIG. 6B Fv43B amino acid sequence (SEQ ID NO:12).
  • SEQ ID NO:12 is the sequence of the immature Fv43B.
  • Fv43B has a predicted signal sequence corresponding to positions 1 to 16 of SEQ ID NO:12 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 17 to 574 of SEQ ID NO:12. The predicted conserved domain is in boldface type.
  • FIGS. 7A-7B FIG. 7A : Pa51A nucleotide sequence (SEQ ID NO:13).
  • FIG. 7B Pa51A amino acid sequence (SEQ ID NO:14).
  • SEQ ID NO:14 is the sequence of the immature Pa51A.
  • Pa51A has a predicted signal sequence corresponding to positions 1 to 20 of SEQ ID NO:14 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 21 to 676 of SEQ ID NO:14.
  • the predicted L- ⁇ -arabinofuranosidase conserved domain is in boldface type.
  • the genomic DNA was codon optimized for expression in T. reesei (see FIG. 60B ).
  • FIGS. 8A-8B FIG. 8A : Gz43A nucleotide sequence (SEQ ID NO:15).
  • FIG. 8B Gz43A amino acid sequence (SEQ ID NO:16).
  • SEQ ID NO:16 is the sequence of the immature Gz43A.
  • Gz43A has a predicted signal sequence corresponding to positions 1 to 18 of SEQ ID NO:16 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 19 to 340 of SEQ ID NO:16. The predicted conserved domain is in boldface type.
  • the Gz43A predicted signal sequence was replaced by the T. reesei CBH1 signal sequence (myrklavisaflatara (SEQ ID NO: 51)) in T. reesei (see FIG. 61 ).
  • FIGS. 9A-9B FIG. 9A : Fo43A nucleotide sequence (SEQ ID NO:17).
  • FIG. 9B Fo43A amino acid sequence (SEQ ID NO:18).
  • SEQ ID NO:18 is the sequence of the immature Fo43A.
  • Fo43A has a predicted signal sequence corresponding to positions 1 to 20 of SEQ ID NO:18 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 21 to 348 of SEQ ID NO:18. The predicted conserved domain is in boldface type.
  • the Fo43A predicted signal sequence was replaced by the T. reesei CBH 1 signal sequence (myrklavisaflatara (SEQ ID NO:51)) (see FIG. 62 ).
  • FIGS. 10A-10B FIG. 10A : Af43A nucleotide sequence (SEQ ID NO:19).
  • FIG. 10B Af43A amino acid sequence (SEQ ID NO:20).
  • SEQ ID NO:20 is the sequence of the immature Af43A. The predicted conserved domain is in boldface type.
  • FIGS. 11A-11B FIG. 11A : Pf51A nucleotide sequence (SEQ ID NO:21).
  • FIG. 11B Pf51A amino acid sequence (SEQ ID NO:22).
  • SEQ ID NO:22 is the sequence of the immature Pf51A.
  • Pf51A has a predicted signal sequence corresponding to positions 1 to 20 of SEQ ID NO:22 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 21 to 642 of SEQ ID NO:22.
  • the predicted L- ⁇ -arabinofuranosidase conserved domain is in boldface type.
  • the predicted Pf51A signal sequence was replaced by a codon optimized the T.
  • FIGS. 12A-12B FIG. 12A : AfuXyn2 nucleotide sequence (SEQ ID NO:23).
  • FIG. 12B AfuXyn2 amino acid sequence (SEQ ID NO:24).
  • SEQ ID NO:24 is the sequence of the immature AfuXyn2.
  • AfuXyn2 has a predicted signal sequence corresponding to positions 1 to 18 of SEQ ID NO:24 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 19 to 228 of SEQ ID NO:24.
  • the predicted GH11 conserved domain is in boldface type.
  • FIGS. 13A-13B FIG. 13A : AfuXyn5 nucleotide sequence (SEQ ID NO:25).
  • FIG. 13B AfuXyn5 amino acid sequence (SEQ ID NO:26).
  • SEQ ID NO:26 is the sequence of the immature AfuXyn5.
  • AfuXyn5 has a predicted signal sequence corresponding to positions 1 to 19 of SEQ ID NO:26 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 20 to 313 of SEQ ID NO:26.
  • the predicted GH11 conserved domain is in boldface type.
  • FIGS. 14A-14B FIG. 14A : Fv43D nucleotide sequence (SEQ ID NO:27).
  • FIG. 14B Fv43D amino acid sequence (SEQ ID NO:28).
  • SEQ ID NO:28 is the sequence of the immature Fv43D.
  • Fv43D has a predicted signal sequence corresponding to positions 1 to 20 of SEQ ID NO:28 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 21 to 350 of SEQ ID NO:28.
  • the predicted conserved domain is in boldface type.
  • FIGS. 15A-15B FIG. 15A : Pf43B nucleotide sequence (SEQ ID NO:29).
  • FIG. 15B Pf43B amino acid sequence (SEQ ID NO:30).
  • SEQ ID NO:30 is the sequence of the immature Pf43B.
  • Pf43B has a predicted signal sequence corresponding to positions 1 to 20 of SEQ ID NO:30 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 21 to 321 of SEQ ID NO:30. The predicted conserved domain is in boldface type.
  • FIGS. 16A-16B FIG. 16A : Fv51A nucleotide sequence (SEQ ID NO:31).
  • FIG. 16B Fv51A amino acid sequence (SEQ ID NO:32).
  • SEQ ID NO:32 is the sequence of the immature Fv51A.
  • Fv51A has a predicted signal sequence corresponding to positions 1 to 19 of SEQ ID NO:32 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 20 to 660 of SEQ ID NO:32.
  • the predicted L- ⁇ -arabinofuranosidase conserved domain is in boldface type.
  • FIGS. 17A-17B FIG. 17A : Cg51B nucleotide sequence (SEQ ID NO:33).
  • FIG. 17B Cg51B amino acid sequence (SEQ ID NO:34).
  • SEQ ID NO:34 is the sequence of the immature Cg51B.
  • Cg51B has a predicted signal sequence corresponding to positions 1 to 20 of SEQ ID NO:34 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 21 to 670 of SEQ ID NO:34.
  • the predicted conserved domain is in boldface type.
  • FIGS. 18A-18B FIG. 18A : Fv43C nucleotide sequence (SEQ ID NO:35).
  • FIG. 18B Fv43C amino acid sequence (SEQ ID NO:36).
  • SEQ ID NO:36 is the sequence of the immature Fv43C.
  • Fv43C has a predicted signal sequence corresponding to positions 1 to 22 of SEQ ID NO:36 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 23 to 333 of SEQ ID NO:36. The predicted conserved domain is in boldface type.
  • FIGS. 19A-19B FIG. 19A : Fv30A nucleotide sequence (SEQ ID NO:37).
  • FIG. 19B Fv30A amino acid sequence (SEQ ID NO:38).
  • SEQ ID NO:38 is the sequence of the immature Fv30A.
  • Fv30A has a predicted signal sequence corresponding to positions 1 to 19 of SEQ ID NO:38 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 20 to 537 of SEQ ID NO:38.
  • FIGS. 20A-20B FIG. 20A : Fv43F nucleotide sequence (SEQ ID NO:39).
  • FIG. 20B Fv43F amino acid sequence (SEQ ID NO:40).
  • SEQ ID NO:40 is the sequence of the immature Fv43F.
  • Fv43F has a predicted signal sequence corresponding to positions 1 to 20 of SEQ ID NO:40 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 21 to 315 of SEQ ID NO:40.
  • FIGS. 21A-21B FIG. 21A : Trichoderma reesei Xyn3 nucleotide sequence (SEQ ID NO:41).
  • FIG. 21B Trichoderma reesei Xyn3 amino acid sequence (SEQ ID NO:42).
  • SEQ ID NO:42 is the sequence of the immature Trichoderma reesei Xyn3.
  • Trichoderma reesei Xyn3 has a predicted signal sequence corresponding to positions 1 to 16 of SEQ ID NO:42 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to positions 17 to 347 of SEQ ID NO:42.
  • the predicted conserved domain is in bold face type.
  • FIG. 22 Amino acid sequence of Trichoderma reesei Xyn2 (SEQ ID NO:43). The signal sequence is underlined. The predicted conserved domain is in bold face type. The coding sequence can be found in Törrönen et al. Biotechnology, 1992, 10:1461-65.
  • FIG. 23 Amino acid sequence of Trichoderma reesei Bxl1 (SEQ ID NO:44). The signal sequence is underlined. The predicted conserved domain is in bold face type. The coding sequence can be found in Margolles-Clark et al. Appl. Environ. Microbiol. 1996, 62(10):3840-46.
  • FIG. 24 Amino acid sequence of Trichoderma reesei Bgl1 (SEQ ID NO:45). The signal sequence is underlined. The predicted conserved domain is in bold face type. The coding sequence can be found in Barnett et al. Bio-Technology, 1991, 9(6):562-567.
  • FIG. 25 Cellulase activity assay using PASC hydrolysis with calcofluor detection.
  • FIG. 26 Xylanase elution profile.
  • FIG. 27 SDS-PAGE detection of the two step separation of AfuXyn 5.
  • Lane 1 Crude sample;
  • Lane 2 Eluate from Phenyl column;
  • Lane 3 Eluate from GF column.
  • FIG. 28 pENTR/D-TOPO plasmid.
  • FIG. 29 pTrex3gM.
  • FIGS. 30A-30B Performance of different enzymes on corncob substrate. Error bars represent the experimental errors associated with triplicate cob assays. The numbers in parenthesis along the x-axis represent the enzyme doses in mg of protein per g of cellulose.
  • FIG. 31 Performance of different enzyme blends/compositions on corncob substrate. Error bars represent the experimental errors associated with triplicate cob assays. The numbers in parentheses along the x-axis represent the enzyme doses in mg of protein per g cellulose.
  • FIG. 32 Performance of different enzyme blends/compositions on corncob substrate. Error bars represent the experimental errors associated with triplicate cob assays. The numbers in parentheses along the x-axis represent the enzyme doses in mg of protein per g cellulose.
  • FIG. 33 Performance of different enzyme blends/compositions on corncob substrate. Error bars represent the experimental errors associated with triplicate cob assays. The numbers in parentheses along the x-axis represent the enzyme doses in mg of protein per g cellulose.
  • FIG. 34 Performance of different enzyme blends/compositions on corncob substrate. Error bars represent the experimental errors associated with triplicate cob assays. The numbers in parentheses along the x-axis represent the enzyme doses in mg of protein per g cellulose.
  • FIGS. 35A-35C Performance of different enzyme blends/compositions on corncob substrate. Error bars represent the experimental errors associated with triplicate cob assays. The numbers along the x-axis represent the enzyme doses in mg of protein per g cellulose.
  • FIG. 36 Anomeric proton NMR region of short arabinoxylan oligomers shows cleavage by Fv43A plus Fv43B.
  • FIG. 37 Anomeric proton NMR region of short arabinoxylan oligomers shows cleavage of ⁇ -1,2-linked xylose from arabinose by Fv3A.
  • FIG. 38 Alignment between the amino acid sequences of Trichoderma reesei ⁇ -xylosidase and Fv3A.
  • FIG. 39 pENTR-TOPO-Bgl1 (943/942) plasmid.
  • FIG. 40 pTrex3g 943/942 Bgl1 expression vector.
  • FIG. 41 pENTR- Trichoderma reesei Xyn3 plasmid.
  • FIG. 42 pTrex3g/ Trichoderma reesei Xyn3 expression vector.
  • FIG. 43 pENTR-Fv3A plasmid.
  • FIG. 44 pTrex6g/Fv3A expression vector.
  • FIG. 45 TOPO Blunt/Pegl1-Fv43D plasmid.
  • FIG. 46 TOPO Blunt/Pegl1-Fv51A plasmid.
  • FIGS. 47A-47D Glucan ( FIG. 47A ) and xylan ( FIG. 47B ) conversions to monomer sugars by secreted enzyme fermentation broths from T. reesei integrated expression strains.
  • the 3-day sample was analyzed for the extent of conversion of glucan and xylan to both monomer and soluble oligomer products ( FIG. 47C ).
  • FIG. 47D shows a chromatographic comparison of enzyme product from three T. reesei integrated expression strains.
  • the experimental conditions are described in Example 1. Protein ratios differ across transformants and can be quantified as a percentage of the total integrated peak area.
  • the “EGLs” marks the summed area of endoglucanase peaks. EndoH was added to the protein sample in small amounts as a reagent for HPLC analysis.
  • FIGS. 48A-48B Saccharification increased in xylose monomer yield in response to hemicellulase addition to the enzyme composition produced by an integrated strain at 7 mg total protein per gram glucan+xylan in ammonia pretreated cob.
  • FIG. 48A Constituent Fusarium verticillioides hemicellulases in the enzyme composition produced by the integrated strain.
  • FIG. 48B Hemicellulases from other fungi.
  • FIGS. 49A-49B Saccharification increased in glucose monomer yield in response to hemicellulase addition to the enzyme composition produced by an integrated strain at 7 mg total protein per gram glucan+xylan in ammonia pretreated cob.
  • FIG. 49A Constituent Fusarium verticillioides hemicellulases in the enzyme composition produced by the integrated strain.
  • FIG. 49B Hemicellulases from other fungi.
  • FIGS. 50A-50B Saccharification increased in arabinose monomer yield in response to hemicellulase addition to the enzyme composition produced by an integrated strain at 7 mg total protein per gram glucan+xylan in ammonia pretreated cob.
  • FIG. 50A Constituent Fusarium verticillioides hemicellulases in the enzyme composition produced by an integrated strain.
  • FIG. 50B Hemicellulases from other fungi.
  • FIG. 51 A graphical presentation of the saccharification performance across pretreatment conditions.
  • the X-axis corresponds to the experimental results listed in Table 12. Yields are calculated based on the theoretical amounts of glucan or xylan available in the raw switchgrass. All yields are based on monomeric sugars released after 3 days of saccharification with the enzyme cocktail.
  • FIG. 52 Amino acid sequence alignment of a number of GH39 ⁇ -xylosidases. Underlined residues in bold face are the predicted catalytic general acid-base residue (marked with “A” above the alignment) and catalytic nucleophile residue (marked with “N” above the alignment). Underlined residues in normal face in the bottom two sequences are within 4 angstroms of the substrate in the active sites of the respective 3D structures (pdb: 1uhv and 2bs9, respectively). Underlined residues in the Fv39A sequence are predicted to be within 4 angstroms of a bound substrate in the active site.
  • FIG. 53 Amino acid sequence alignment of a number of GH43 family hydrolases. Amino acid residues highly conserved among members of the family are shown underlined and in bold face.
  • FIG. 54 Amino acid sequence alignment of a number of GH51 family enzymes. Amino acid residues highly conserved among members of the family are shown underlined and in bold type.
  • FIGS. 55A-55B Amino acid sequence alignments of a number of GH10 and GH11 family endoxylanases.
  • FIG. 55A Alignment of GH10 family xylanases. Underlined residues in bold face are the catalytic nucleophile residues (marked with “N” above the alignment).
  • FIG. 55B Alignment of GH11 family xylanases. Underlined residues in bold face are the catalytic nucleophile residues and general acid base residues (marked with “N” and “A”, respectively, above the alignment).
  • FIGS. 56A-56B Saccharification of dilute ammonia pretreated switchgrass with various enzyme blends/compositions; FIG. 56A : glucan conversion; FIG. 56B : xylan conversion.
  • the numbers below the figures on the x-axis refer to the amount of total mg of each protein in a given blend/composition per g of glucan or xylan, as described in Example 13.
  • FIGS. 57A-57B Saccharification of dilute ammonia pretreated switchgrass with an enzyme composition produced by integrated strain H3A; FIG. 57A : glucan conversion; FIG. 57B : xylan conversion. Experimental conditions are described in Example 14.
  • FIGS. 58A-58C Saccharification of steam-expanded sugarcane bagasse with an enzyme composition produced by integrated strain H3A at different enzyme doses; FIG. 58A : glucan conversion; FIG. 58B : xylan conversion; FIG. 58C : 3-day glucan and xylan conversions. Experimental conditions are described in Example 17.
  • FIGS. 59A-59C Saccharification of dilute-acid pretreated corn fiber with various enzymes or enzyme blends; FIG. 59A : glucan conversion; FIG. 59B : xylan conversion: FIG. 59C : 5-day glucan and xylan conversions.
  • the adjusted sugar glucose or xylose
  • Ratios shown along the x-axis represent the enzyme dose in mg of total protein per gram of cellulose. Experimental conditions are described in Example 18.
  • FIGS. 60A-60B FIG. 60A : Deduced cDNA for Pa51A (SEQ ID NO:46).
  • FIG. 60B Codon optimized cDNA for Pa51A (SEQ ID NO:47).
  • FIG. 61 Coding sequence for a construct comprising a CBH1 signal sequence (underlined) upstream of genomic DNA encoding mature Gz43A (SEQ ID NO:48).
  • FIG. 62 Coding sequence for a construct comprising a CBH1 signal sequence (underlined) upstream of genomic DNA encoding mature Fo43A (SEQ ID NO:49).
  • FIG. 63 Codon optimized coding sequence for a construct comprising a CBH1 signal sequence (underlined) upstream of codon optimized DNA encoding mature Pf51A (SEQ ID NO:50).
  • FIG. 64 Amino acid sequence alignment of a number of GH3 family hydrolases. Amino acid residues highly conserved among members of the family are shown underlined and in bold face type. The box marks the predicted catalytic residue with flanking residues predicted to be involved in substrate binding.
  • FIG. 65 Amino acid sequence alignment of two representative Fusarium GH30 family hydrolases. Amino acid residues that are conserved among members of the family are shown underlined and in bold face type.
  • Enzymes have traditionally been classified by substrate specificity and reaction products. In the pre-genomic era, function was regarded as the most amenable (and perhaps most useful) basis for comparing enzymes and assays for various enzymatic activities have been well-developed for many years, resulting in the familiar EC classification scheme.
  • Cellulases and other glycosyl hydrolases which act upon glycosidic bonds between two carbohydrate moieties (or a carbohydrate and non-carbohydrate moiety—as occurs in nitrophenol-glycoside derivatives) are, under this classification scheme, designated as EC 3.2.1.-, with the final number indicating the exact type of bond cleaved. For example, according to this scheme an endo-acting cellulase (1,4- ⁇ -endoglucanase) is designated EC 3.2.1.4.
  • CAZy defines four major classes of carbohydrases distinguishable by the type of reaction catalyzed: Glycosyl Hydrolases (GH's), Glycosyltransferases (GT's), Polysaccharide Lyases (PL's), and Carbohydrate Esterases (CE's).
  • the enzymes of the disclosure are glycosyl hydrolases.
  • GH's are a group of enzymes that hydrolyze the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety.
  • a classification system for glycosyl hydrolases, grouped by sequence similarity, has led to the definition of over 85 different families. This classification is available on the CAZy web site.
  • the enzymes of the disclosure belong, inter alia, to the glycosyl hydrolase families 3, 10, 11, 30, 39, 43, and/or 51.
  • Glycoside hydrolase family 3 (“GH3”) enzymes include, e.g., ⁇ -glucosidase (EC:3.2.1.21); ⁇ -xylosidase (EC:3.2.1.37); N-acetyl ⁇ -glucosaminidase (EC:3.2.1.52); glucan ⁇ -1,3-glucosidase (EC:3.2.1.58); cellodextrinase (EC:3.2.1.74); exo-1,3-1,4-glucanase (EC:3.2.1); and ⁇ -galactosidase (EC 3.2.1.23).
  • ⁇ -glucosidase EC:3.2.1.21
  • ⁇ -xylosidase EC:3.2.1.37
  • N-acetyl ⁇ -glucosaminidase EC:3.2.1.52
  • glucan ⁇ -1,3-glucosidase EC:3.2.1.58
  • cellodextrinase
  • GH3 enzymes can be those that have ⁇ -glucosidase, ⁇ -xylosidase, N-acetyl ⁇ -glucosaminidase, glucan ⁇ -1,3-glucosidase, cellodextrinase, exo-1,3-1,4-glucanase, and/or ⁇ -galactosidase activity.
  • GH3 enzymes are globular proteins and can consist of two or more subdomains.
  • a catalytic residue has been identified as an aspartate residue that, in ⁇ -glucosidases, located in the N-terminal third of the peptide and sits within the amino acid fragment SDW (Li et al.
  • the corresponding sequence in Bgl1 from T. reesei is T266D267W268 (counting from the methionine at the starting position), with the catalytic residue aspartate being the D267.
  • the hydroxyl/aspartate sequence is also conserved in the GH3 ⁇ -xylosidases tested.
  • the corresponding sequence in T. reesei Bxl1 is S310D311 and the corresponding sequence in Fv3A is S290D291.
  • Glycoside hydrolase family 39 (“GH39”) enzymes have ⁇ -L-iduronidase (EC:3.2.1.76) or ⁇ -xylosidase (EC:3.2.1.37) activity.
  • Fv39A residues E168 and E272 are predicted to function as catalytic acid-base and nucleophile, respectively, based on a sequence alignment of the abovementioned GH39 ⁇ -xylosidases from Thermoanaerobacterium saccharolyticum and Geobacillus stearothermophilus with Fv39A.
  • Glycoside hydrolase family 43 (“GH43”) enzymes include, e.g., L- ⁇ -arabinofuranosidase (EC 3.2.1.55); ⁇ -xylosidase (EC 3.2.1.37); endo-arabinanase (EC 3.2.1.99); and/or galactan 1,3- ⁇ -galactosidase (EC 3.2.1.145).
  • GH43 enzymes can have L- ⁇ -arabinofuranosidase activity, ⁇ -xylosidase activity, endo-arabinanase activity, and/or galactan 1,3- ⁇ -galactosidase activity.
  • GH43 family enzymes display a five-bladed- ⁇ -propeller-like structure.
  • the propeller-like structure is based upon a five-fold repeat of blades composed of four-stranded ⁇ -sheets.
  • the catalytic general base, an aspartate, the catalytic general acid, a glutamate, and an aspartate that modulates the pKa of the general base were identified through the crystal structure of Cellvibrio japonicus CjAbn43A, and confirmed by site-directed mutagenesis (see Nurizzo et al. Nat. Struct. Biol. 2002, 9(9) 665-8).
  • the catalytic residues are arranged in three conserved blocks spread widely through the amino acid sequence (Pons et al. Proteins: Structure, Function and Bioinformatics, 2004, 54:424-432).
  • Glycoside hydrolase family 51 (“GH51”) enzymes have L- ⁇ -arabinofuranosidase (EC 3.2.1.55) and/or endoglucanase (EC 3.2.1.4) activity.
  • High-resolution crystal structure of a GH51 L- ⁇ -arabinofuranosidase from Geobacillus stearothermophilus T-6 shows that the enzyme is a hexamer, with each monomer organized into two domains: an 8-barrel ( ⁇ / ⁇ ) and a 12-stranded ⁇ sandwich with jelly-roll topology (see Hovel et al. EMBO J. 2003, 22(19):4922-4932).
  • catalytic residues will be acidic and conserved across enzyme sequences in the family.
  • amino acid sequences of Fv51A, Pf51A, and Pa51A are aligned with GH51 enzymes of more diverse sequence, 8 acidic residues remain conserved. Those are shown bold and underlined in FIG. 54 .
  • Glycoside hydrolase family 10 (“GH10”) enzymes also have an 8-barrel ( ⁇ / ⁇ ) structure. They hydrolyze in an endo fashion with a retaining mechanism that uses at least one acidic catalytic residue in a generally acid/base catalysis process (Pell et al., J. Biol. Chem., 2004, 279(10): 9597-9605). Crystal structures of the GH10 xylanases of Penicillium simplicissimum (Uniprot P56588) and Thermoascus aurantiacus (Uniprot P23360) complexed with substrates in the active sites have been solved (see Schmidt et al.
  • Trichoderma reesei Xyn3 residues that are important for substrate binding and catalysis can be derived from an alignment with the sequences of abovementioned GH10 xylanases from Penicillium simplicissimum and Thermoascus aurantiacus ( FIG. 55A ).
  • Trichoderma reesei Xyn3 residue E282 is predicted to be the catalytic nucleophilic residue, whereas residues E91, N92, K95, Q97, S98, H128, W132, Q135, N175, E176, Y219, Q252, H254, W312, and/or W320 are predicted to be involved in substrate binding and/or catalysis.
  • Glycoside hydrolase family 11 (“GH11”) enzymes have a ⁇ -jelly roll structure. They hydrolyze in an endo fashion with a retaining mechanism that uses at least one acidic catalytic residue in a generally acid/base catalysis process. Several other residues spread throughout their structure may contribute to stabilizing the xylose units in the substrate neighboring the pair of xylose monomers that are cleaved by hydrolysis. Three GH11 family endoxylanases were tested and their sequences are aligned in FIG. 55B . E118 (or E86 in mature T. reesei Xyn2) and E209 (or E177 in mature T.
  • Glycoside hydrolase family 30 (“GH30”) enzymes are retaining enzymes having glucosylceramidase (EC 3.2.1.45); ⁇ -1,6-glucanase (EC 3.2.1.75); ⁇ -xylosidase (EC 3.2.1.37); ⁇ -glucosidase (3.2.1.21) activity.
  • the first GH30 crystal structure was the Gaucher disease-related human ⁇ -glucocerebrosidase solved by Grabowski, Gatt and Horowitz (Crit. Rev Biochem Mol Biol 1990; 25(6) 385-414).
  • GH30 have an ( ⁇ / ⁇ ) 8 TIM barrel fold with the two key active site glutamic acids located at the C-terminal ends of ⁇ -strands 4 (acid/base) and 7 (nucleophile) (Henrissat B, et al. Proc Natl Acad Sci USA, 92(15):7090-4, 1995; Jordan et al., Applied Microbiol Biotechnol, 86:1647, 2010).
  • Glutamate 162 of Fv30A is conserved in 14 of 14 aligned GH30 proteins (13 bacterial proteins and one endo-b-xylanase from the fungi Biospora accession no. ADG62369) and glutamate 250 of Fv30A is conserved in 10 of the same 14, is an aspartate in another three and non-acidic in one. There are other moderately conserved acidic residues but no others are as widely conserved.
  • the disclosure provides isolated, synthetic or recombinant polypeptides comprising an amino acid sequence having at least about 80%, e.g., at least about 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or complete (100%) sequence identity to a polypeptide of SEQ ID NO:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 43, 44, or 45, over a region of at least about 10, e.g., at least about 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, or 350 residues, or over the full length of the immature polypeptide, the full length mature polypeptide, the full length of the conserved domain
  • the conserved domain can be a predicted catalytic domain (“CD”).
  • Exemplary polypeptides also include fragments of at least about 10, e.g., at least about 15, 20, 25, 30, 35, 40, 45, 50, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, or 600 residues in length.
  • the fragments can comprise a conserved domain and/or a CBM. Where a fragment comprises a conserved domain and a CBM of an enzyme, the fragment optionally includes a linker separating the two.
  • the linker can be a native linker or a heterologous linker It is contemplated that the polypeptides of the disclosure can be encoded by a nucleic acid sequence having at least about 85%, about 86%, about 87%, about 88%, about 89%, or about 90% sequence identity to SEQ ID NO:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, or 41, or by a nucleic acid sequence capable of hybridizing under high stringency conditions to a complement of SEQ ID NO:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, or 41, or to a fragment thereof. Exemplary nucleic acids of the disclosure are described in Section 6.2 below.
  • polypeptides of the disclosure include proteins having an amino acid sequence with at least 85%, e.g., at least 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to at least 50 contiguous amino acid residues of the glycosyl hydrolase sequences of SEQ ID NO:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 43, 44, or 45.
  • a polypeptide of the disclosure can include amino acid sequences having at least 85%, e.g., at least 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to at least 10, e.g., at least 11, 12, 13, 14, 15, 20, 25, 30, 40, 50, 75, 100, 125, 150, 175, 200, 250, 300, or 350 contiguous amino acid residues of the glycosyl hydrolase sequences of SEQ ID NO:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 43, 44, or 45.
  • the contiguous amino acid sequence corresponds to the conserved domain and/or the CBM and/or the signal sequence.
  • amino acid sequences described herein can be produced together or in conjunction with at least 1, e.g., at least 2, 3, 5, 10, or 20 heterologous amino acids flanking each of the C- and/or N-terminal ends of the specified amino acid sequence, and or deletions of at least 1, e.g., at least 2, 3, 5, 10, or 20 amino acids from the C- and/or N-terminal ends of an enzyme of the disclosure.
  • one or more amino acid residues can be modified to increase or decrease the pI of an enzyme.
  • the change of pI value can be achieved by removing a glutamate residue or substituting it with another amino acid residue.
  • the disclosure specifically provides an Fv3A, a Pf43A, an Fv43E, an Fv39A, an Fv43A, an Fv43B, a Pa51A, a Gz43A, an Fo43A, an Af43A, a Pf51A, an AfuXyn2, an AfuXyn5, a Fv43D, a Pf43B, Fv43B, a Fv51A, a Trichoderma reesei Xyn3, a Trichoderma reesei Xyn2, a Trichoderma reesei Bxl1, and/or a Trichoderma reesei Bgl1 polypeptide.
  • a combination of one or more of these enzymes is suitably present in the enzyme blend/composition of the invention, for example, one that is non-naturally occurring.
  • Fv3A The amino acid sequence of Fv3A (SEQ ID NO:2) is shown in FIGS. 1B , 38 , and 64 .
  • SEQ ID NO:2 is the sequence of the immature Fv3A.
  • Fv3A has a predicted signal sequence corresponding to residues 1 to 23 of SEQ ID NO:2 (underlined); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to residues 24 to 766 of SEQ ID NO:2.
  • the predicted conserved domains are in boldface type in FIG. 1B .
  • Fv3A was shown to have ⁇ -xylosidase activity, for example, in an enzymatic assay using p-nitrophenyl- ⁇ -xylopyranoside, xylobiose, mixed linear xylo-oligomers, branched arabinoxylan oligomers from hemicellulose, or dilute ammonia pretreated corncob as substrates.
  • the predicted catalytic residue is D291, while the flanking residues, S290 and C292, are predicted to be involved in substrate binding ( FIG. 64 ).
  • E175 and E213 are conserved across other GH3 enzymes and are predicted to have catalytic functions.
  • an Fv3A polypeptide refers to a polypeptide and/or to a variant thereof comprising a sequence having at least 85%, e.g., at least 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, e.g., at least 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, or 700 contiguous amino acid residues among residues 24 to 766 of SEQ ID NO:2.
  • An Fv3A polypeptide preferably is unaltered as compared to native Fv3A in residues D291, S290, C292, E175, and E213.
  • An Fv3A polypeptide is preferably unaltered in at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% of the amino acid residues that are conserved among Fv3A, Trichoderma reesei Bxl1 and/or Trichoderma reesei Bgl1, as shown in the alignment of FIG. 64 .
  • An Fv3A polypeptide suitably comprises the entire predicted conserved domain of native Fv3A as shown in FIG. 1B .
  • An exemplary Fv3A polypeptide of the invention comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the mature Fv3A sequence as shown in FIG. 1B .
  • the Fv3A polypeptide of the invention preferably has ⁇ -xylosidase activity.
  • an Fv3A polypeptide of the invention suitably comprises an amino acid sequence with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the amino acid sequence of SEQ ID NO:2, or to residues (i) 24-766, (ii) 73-321, (iii) 73-394, (iv) 395-622, (v) 24-622, or (vi) 73-622 of SEQ ID NO:2.
  • the polypeptide suitably has ⁇ -xylosidase activity.
  • SEQ ID NO:4 is the sequence of the immature Pf43A.
  • Pf43A has a predicted signal sequence corresponding to residues 1 to 20 of SEQ ID NO:4 (underlined in FIG. 2B ); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to residues 21 to 445 of SEQ ID NO:4.
  • the predicted conserved domain is in boldface type, the predicted CBM is in uppercase type, and the predicted linker separating the CD and CBM is in italics in FIG. 2B .
  • Pf43A has been shown to have ⁇ -xylosidase activity, in, for example, an enzymatic assay using p-nitophenyl- ⁇ -xylopyranoside, xylobiose, mixed linear xylo-oligomers, or ammonia pretreated corncob as substrates.
  • the predicted catalytic residues include either D32 or D60, D145, and E206.
  • the C-terminal region underlined in FIG. 53 is the predicted CBM.
  • a Pf43A polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, or 400 contiguous amino acid residues among residues 21 to 445 of SEQ ID NO:4.
  • a Pf43A polypeptide preferably is unaltered as compared to the native Pf43A in residues D32 or D60, D145, and E206.
  • a Pf43A is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are found conserved across a family of proteins including Pf43A and 1, 2, 3, 4, 5, 6, 7, or all 8 of other amino acid sequences in the alignment of FIG. 53 .
  • a Pf43A polypeptide of the invention suitably comprises two or more or all of the following domains: (1) the predicted CBM, (2) the predicted conserved domain, and (3) the linker of Pf43A as shown in FIG. 2B .
  • An exemplary Pf43A polypeptide of the invention comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the mature Pf43A sequence as shown in FIG. 2B .
  • the Pf43A polypeptide of the invention preferably has ⁇ -xylosidase activity.
  • a Pf43A polypeptide of the invention suitably comprises an amino acid sequence with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the amino acid sequence of SEQ ID NO:4, or to residues (i) 21-445, (ii) 21-301, (iii) 21-323, (iv) 21-444, (v) 302-444, (vi) 302-445, (vii) 324-444, or (viii) 324-445 of SEQ ID NO:4.
  • the polypeptide suitably has ⁇ -xylosidase activity.
  • SEQ ID NO:6 is the sequence of the immature Fv43E.
  • Fv43E has a predicted signal sequence corresponding to residues 1 to 18 of SEQ ID NO:6 (underlined in FIG. 3B ); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to residues 19 to 530 of SEQ ID NO:6.
  • the predicted conserved domain is marked in boldface type in FIG. 3B .
  • Fv43E was shown to have ⁇ -xylosidase activity, in, for example, enzymatic assay using 4-nitophenyl- ⁇ -D-xylopyranoside, xylobiose, and mixed, linear xylo-oligomers, or ammonia pretreated corncob as substrates.
  • the predicted catalytic residues include either D40 or D71, D155, and E241.
  • an Fv43E polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, or 500 contiguous amino acid residues among residues 19 to 530 of SEQ ID NO:6.
  • An Fv43E polypeptide preferably is unaltered as compared to the native Fv43E in residues D40 or D71, D155, and E241.
  • An Fv43E polypeptide is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are found to be conserved among a family of enzymes including Fv43E, and 1, 2, 3, 4, 5, 6, 7, or all other 8 amino acid sequences in the alignment of FIG. 53 .
  • An Fv43E polypeptide suitably comprises the entire predicted conserved domain of native Fv43E as shown in FIG. 3B .
  • An exemplary Fv43E polypeptide comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to mature Fv43E sequence as shown in FIG. 3B .
  • the Fv43E polypeptide of the invention preferably has ⁇ -xylosidase activity.
  • an Fv43E polypeptide of the invention suitably comprises an amino acid sequence with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO:6, or to residues (i) 19-530, (ii) 29-530, (iii) 19-300, or (iv) 29-300 of SEQ ID NO:6.
  • the polypeptide suitably has ⁇ -xylosidase activity.
  • Fv39A The amino acid sequence of Fv39A (SEQ ID NO:8) is shown in FIGS. 4B and 52 .
  • SEQ ID NO:8 is the sequence of the immature Fv39A.
  • Fv39A has a predicted signal sequence corresponding to residues 1 to 19 of SEQ ID NO:8 (underlined in FIG. 4B ); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to residues 20 to 439 of SEQ ID NO:8.
  • the predicted conserved domain is shown in boldface type in FIG. 4B .
  • Fv39A was shown to have ⁇ -xylosidase activity in, for example, an enzymatic assay using p-nitophenyl- ⁇ -xylopyranoside, xylobiose or mixed, linear xylo-oligomers as substrates.
  • Fv39A residues E168 and E272 are predicted to function as catalytic acid-base and nucleophile, respectively, based on a sequence alignment of the above-mentioned GH39 xylosidases from Thermoanaerobacterium saccharolyticum (Uniprot Accession No. P36906) and Geobacillus stearothermophilus (Uniprot Accession No.
  • an Fv39A polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, or 400 contiguous amino acid residues among residues 20 to 439 of SEQ ID NO:8.
  • An Fv39A polypeptide preferably is unaltered as compared to native Fv39A in residues E168 and E272.
  • An Fv39A polypeptide is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are conserved among a family or enzymes including Fv39A and xylosidases from Thermoanaerobacterium saccharolyticum and Geobacillus stearothermophilus (see above).
  • An Fv39A polypeptide suitably comprises the entire predicted conserved domain of native Fv39A as shown in FIG. 4B .
  • An exemplary Fv39A polypeptide comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the mature Fv39A sequence as shown in FIG. 4B .
  • the Fv39A polypeptide of the invention preferably has ⁇ -xylosidase activity.
  • an Fv39A polypeptide of the invention suitably comprises an amino acid sequence with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO:8, or to residues (i) 20-439, (ii) 20-291, (iii) 145-291, or (iv) 145-439 of SEQ ID NO:8.
  • the polypeptide suitably has ⁇ -xylosidase activity.
  • Fv43A The amino acid sequence of Fv43A (SEQ ID NO:10) is provided in FIGS. 5B and 53 .
  • SEQ ID NO:10 is the sequence of the immature Fv43A.
  • Fv43A has a predicted signal sequence corresponding to residues 1 to 22 of SEQ ID NO:10 (underlined in FIG. 5B ); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to residues 23 to 449 of SEQ ID NO:10.
  • the predicted conserved domain is in boldface type
  • the predicted CBM is in uppercase type
  • the predicted linker separating the CD and CBM is in italics.
  • Fv43A was shown to have ⁇ -xylosidase activity in, for example, an enzymatic assay using 4-nitophenyl- ⁇ -D-xylopyranoside, xylobiose, mixed, linear xylo-oligomers, branched arabinoxylan oligomers from hemicellulose, and/or linear xylo-oligomers as substrates.
  • the predicted catalytic residues including either D34 or D62, D148, and E209.
  • an Fv43A polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, or 400 contiguous amino acid residues among residues 23 to 449 of SEQ ID NO:10.
  • An Fv43A polypeptide preferably is unaltered, as compared to native Fv43A, at residues D34 or D62, D148, and E209, An Fv43A polypeptide is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are conserved among a family of enzymes including Fv43A and 1, 2, 3, 4, 5, 6, 7, 8, or all 9 other amino acid sequences in the alignment of FIG. 53 .
  • An Fv43A polypeptide suitably comprises the entire predicted CBM of native Fv43A, and/or the entire predicted conserved domain of native Fv43A, and/or the linker of Fv43A as shown in FIG. 5B .
  • An exemplary Fv43A polypeptide comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the mature Fv43A sequence as shown in FIG. 5B .
  • the Fv45A polypeptide of the invention preferably has ⁇ -xylosidase activity.
  • an Fv43A polypeptide of the invention suitably comprises an amino acid sequence with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO:10, or to residues (i) 23-449, (ii) 23-302, (iii) 23-320, (iv) 23-448, (v) 303-448, (vi) 303-449, (vii) 321-448, or (viii) 321-449 of SEQ ID NO:10.
  • the polypeptide suitably has ⁇ -xylosidase activity.
  • Fv43B The amino acid sequence of Fv43B (SEQ ID NO:12) is shown in FIGS. 6B and 53 .
  • SEQ ID NO:12 is the sequence of the immature Fv43B.
  • Fv43B has a predicted signal sequence corresponding to residues 1 to 16 of SEQ ID NO:12 (underlined in FIG. 6B ); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to residues 17 to 574 of SEQ ID NO:12.
  • the predicted conserved domain is in boldface type in FIG. 6B .
  • Fv43B was shown to have both ⁇ -xylosidase and L- ⁇ -arabinofuranosidase activities, in, for example, a first enzymatic assay using 4-nitophenyl- ⁇ -D-xylopyranoside and p-nitrophenyl- ⁇ -L-arabinofuranoside as substrates. It was shown, in a second enzymatic assay, to catalyze the release of arabinose from branched arabino-xylooligomers and to catalyze the increased xylose release from oligomer mixtures in the presence of other xylosidase enzymes.
  • the predicted catalytic residues include either D38 or D68, D151, and E236.
  • an Fv43B polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, or 550 contiguous amino acid residues among residues 17 to 574 of SEQ ID NO:12.
  • An Fv43B polypeptide preferably is unaltered, as compared to native Fv43B, at residues D38 or D68, D151, and E236.
  • An Fv43B polypeptide is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are conserved among a family of enzymes including Fv43B and 1, 2, 3, 4, 5, 6, 7, 8, or all 9 other amino acid sequences in the alignment of FIG. 53 .
  • An Fv43B polypeptide suitably comprises the entire predicted conserved domain of native Fv43B as shown in FIGS. 6B and 53 .
  • An exemplary Fv43B polypeptide comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the mature Fv43B sequence as shown in FIG. 6B .
  • the Fv43B polypeptide of the present invention preferably has ⁇ -xylosidase activity, L- ⁇ -arabinofuranosidase activity, or both ⁇ -xylosidase and L- ⁇ -arabinofuranosidase activities.
  • an Fv43B polypeptide of the invention suitably comprises an amino acid sequence with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO:12, or to residues (i) 17-574, (ii) 27-574, (iii) 17-303, or (iv) 27-303 of SEQ ID NO:12.
  • the polypeptide suitably has ⁇ -xylosidase activity, L- ⁇ -arabinofuranosidase activity, or both ⁇ -xylosidase and L- ⁇ -arabinofuranosidase activities.
  • SEQ ID NO:14 is the sequence of the immature Pa51A.
  • Pa51A has a predicted signal sequence corresponding to residues 1 to 20 of SEQ ID NO:14 (underlined in FIG. 7B ); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to residues 21 to 676 of SEQ ID NO:14.
  • the predicted L- ⁇ -arabinofuranosidase conserved domain is in boldface type in FIG. 7B .
  • Pa51A was shown to have both ⁇ -xylosidase activity and L- ⁇ -arabinofuranosidase activity in, for example, enzymatic assays using artificial substrates p-nitrophenyl- ⁇ -xylopyranoside and p-nitophenyl- ⁇ -L-arabinofuranoside. It was shown to catalyze the release of arabinose from branched arabino-xylo oligomers and to catalyze the increased xylose release from oligomer mixtures in the presence of other xylosidase enzymes.
  • conserveed acidic residues include E43, D50, E257, E296, E340, E370, E485, and E493.
  • a Pa51A polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, 550, 600, or 650 contiguous amino acid residues among residues 21 to 676 of SEQ ID NO:14.
  • a Pa51A polypeptide preferably is unaltered, as compared to native Pa51A, at residues E43, D50, E257, E296, E340, E370, E485, and E493.
  • a Pa51A polypeptide is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are conserved among a group of enzymes including Pa51A, Fv51A, and Pf51A, as shown in the alignment of FIG. 54 .
  • a Pa51A polypeptide suitably comprises the predicted conserved domain of native Pa51A as shown in FIG. 7B .
  • An exemplary Pa51A polypeptide comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the mature Pa51A sequence as shown in FIG. 7B .
  • the Pa51A polypeptide of the invention preferably has ⁇ -xylosidase activity, L- ⁇ -arabinofuranosidase activity, or both ⁇ -xylosidase and L- ⁇ -arabinofuranosidase activities.
  • a Pa51A polypeptide of the invention suitably comprises an amino acid sequence with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO:14, or to residues (i) 21-676, (ii) 21-652, (iii) 469-652, or (iv) 469-676 of SEQ ID NO:14.
  • the polypeptide suitably has ⁇ -xylosidase activity, L- ⁇ -arabinofuranosidase activity, or both ⁇ -xylosidase and L- ⁇ -arabinofuranosidase activities.
  • SEQ ID NO:16 The amino acid sequence of Gz43A (SEQ ID NO:16) is shown in FIGS. 8B and 53 .
  • SEQ ID NO:16 is the sequence of the immature Gz43A.
  • Gz43A has a predicted signal sequence corresponding to residues 1 to 18 of SEQ ID NO:16 (underlined in FIG. 8B ); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to residues 19 to 340 of SEQ ID NO:16.
  • the predicted conserved domain is in boldface type in FIG. 8B .
  • Gz43A was shown to have ⁇ -xylosidase activity in, for example, an enzymatic assay using p-nitophenyl- ⁇ -xylopyranoside, xylobiose or mixed, and/or linear xylo-oligomers as substrates.
  • the predicted catalytic residues include either D33 or D68, D154, and E243.
  • a Gz43A polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, 175, 200, 250, or 300 contiguous amino acid residues among residues 19 to 340 of SEQ ID NO:16.
  • a Gz43A polypeptide preferably is unaltered, as compared to native Gz43A, at residues D33 or D68, D154, and E243.
  • a Gz43A polypeptide is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are conserved among a group of enzymes including Gz43A and 1, 2, 3, 4, 5, 6, 7, 8 or all 9 other amino acid sequences in the alignment of FIG. 53 .
  • a Gz43A polypeptide suitably comprises the predicted conserved domain of native Gz43A as shown in FIG. 8B .
  • An exemplary Gz43A polypeptide comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the mature Gz43A sequence as shown in FIG. 8B .
  • the Gz43A polypeptide of the invention preferably has ⁇ -xylosidase activity.
  • a Gz43A polypeptide of the invention suitably comprises an amino acid sequence with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO:16, or to residues (i) 19-340, (ii) 53-340, (iii) 19-383, or (iv) 53-383 of SEQ ID NO:16.
  • the polypeptide suitably has ⁇ -xylosidase activity.
  • the amino acid sequence of Fo43A (SEQ ID NO:18) is shown in FIGS. 9B and 53 .
  • SEQ ID NO:18 is the sequence of the immature Fo43A.
  • Fo43A has a predicted signal sequence corresponding to residues 1 to 20 of SEQ ID NO:18 (underlined in FIG. 9B ); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to residues 21 to 348 of SEQ ID NO:18.
  • the predicted conserved domain is in boldface type in FIG. 9B .
  • Fo43A was shown to have ⁇ -xylosidase activity in, for example, an enzymatic assay using p-nitophenyl- ⁇ -xylopyranoside, xylobiose and/or mixed, linear xylo-oligomers as substrates.
  • the predicted catalytic residues include either D37 or D72, D159, and E251.
  • an Fo43A polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, 175, 200, 250, or 300 contiguous amino acid residues among residues 18 to 344 of SEQ ID NO:18.
  • An Fo43A polypeptide preferably is unaltered, as compared to native Fo43A, at residues D37 or D72, D159, and E251.
  • An Fo43A polypeptide is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are conserved among a group of enzymes including Fo43A and 1, 2, 3, 4, 5, 6, 7, 8 or all 9 other amino acid sequences in the alignment of FIG. 53 .
  • An Fo43A polypeptide suitably comprises the predicted conserved domain of native Fo43A as shown in FIG. 9 B.
  • An exemplary Fo43A polypeptide comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the mature Fo43A sequence as shown in FIG. 9B .
  • the Fo43A polypeptide of the invention preferably has ⁇ -xylosidase activity.
  • an Fo43A polypeptide of the invention suitably comprises an amino acid sequence with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO:18, or to residues (i) 21-341, (ii) 107-341, (iii) 21-348, or (iv) 107-348 of SEQ ID NO:18.
  • the polypeptide suitably has ⁇ -xylosidase activity.
  • Af43A The amino acid sequence of Af43A (SEQ ID NO:20) is shown in FIGS. 10B and 53 .
  • SEQ ID NO:20 is the sequence of the immature Af43A.
  • the predicted conserved domain is in boldface type in FIG. 10B .
  • Af43A was shown to have L- ⁇ -arabinofuranosidase activity in, for example, an enzymatic assay using p-nitophenyl- ⁇ -L-arabinofuranoside as a substrate.
  • Af43A was shown to catalyze the release of arabinose from the set of oligomers released from hemicellulose via the action of endoxylanase.
  • the predicted catalytic residues include either D26 or D58, D139, and E227.
  • an Af43A polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, 175, 200, 250, or 300 contiguous amino acid residues of SEQ ID NO:20.
  • An Af43A polypeptide preferably is unaltered, as compared to native Af43A, at residues D26 or D58, D139, and E227.
  • An Af43A polypeptide is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are conserved among a group of enzymes including Af43A and 1, 2, 3, 4, 5, 6, 7, 8, or all 9 other amino acid sequences in the alignment of FIG. 53 .
  • An Af43A polypeptide suitably comprises the predicted conserved domain of native Af43A as shown in FIG. 10B .
  • An exemplary Af43A polypeptide comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO:20.
  • the Af43A polypeptide of the invention preferably has L- ⁇ -arabinofuranosidase activity.
  • an Af43A polypeptide of the invention suitably comprises an amino acid sequence with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO:20, or to residues (i) 15-558, or (ii) 15-295 of SEQ ID NO:20.
  • the polypeptide suitably has L- ⁇ -arabinofuranosidase activity.
  • SEQ ID NO:22 The amino acid sequence of Pf51A (SEQ ID NO:22) is shown in FIGS. 11B and 54 .
  • SEQ ID NO:22 is the sequence of the immature Pf51A.
  • Pf51A has a predicted signal sequence corresponding to residues 1 to 20 of SEQ ID NO:22 (underlined in FIG. 11B ); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to residues 21 to 642 of SEQ ID NO:22.
  • the predicted L- ⁇ -arabinofuranosidase conserved domain is in boldface type in FIG. 11B .
  • Pf51A was shown to have L- ⁇ -arabinofuranosidase activity in, for example, an enzymatic assay using 4-nitrophenyl- ⁇ -L-arabinofuranoside as a substrate. Pf51A was shown to catalyze the release of arabinose from the set of oligomers released from hemicellulose via the action of endoxylanase.
  • the predicted conserved acidic residues include E43, D50, E248, E287, E331, E360, E472, and E480.
  • a Pf51A polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, 550, or 600 contiguous amino acid residues among residues 21 to 642 of SEQ ID NO:22.
  • a Pf51A polypeptide preferably is unaltered, as compared to native Pf51A, at residues E43, D50, E248, E287, E331, E360, E472, and E480.
  • a Pf51A polypeptide is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are conserved among Pf51A, Pa51A, and Fv51A, as shown in in the alignment of FIG. 54 .
  • a Pf51A polypeptide suitably comprises the predicted conserved domain of native Pf51A shown in FIG. 11B .
  • An exemplary Pf51A polypeptide comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the mature Pf51A sequence shown in FIG. 11B .
  • the Pf51A polypeptide of the invention preferably has L- ⁇ -arabinofuranosidase activity.
  • a Pf51A polypeptide of the invention suitably comprises an amino acid sequence with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO:22, or to residues (i) 21-632, (ii) 461-632, (iii) 21-642, or (iv) 461-642 of SEQ ID NO:22.
  • the polypeptide has L- ⁇ -arabinofuranosidase activity.
  • SEQ ID NO:24 is the sequence of the immature AfuXyn2.
  • AfuXyn2 has a predicted signal sequence corresponding to residues 1 to 18 of SEQ ID NO:24 (underlined in FIG. 12B ); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to residues 19 to 228 of SEQ ID NO:24.
  • the predicted GH11 conserved domain is in boldface type in FIG. 12B .
  • AfuXyn2 was shown to have endoxylanase activity indirectly by observing its ability to catalyze the increased xylose monomer production in the presence of xylobiosidase when the enzymes act on pretreated biomass or on isolated hemicellulose.
  • the conserved catalytic residues include E124, E129, and E215.
  • an AfuXyn2 polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, 175, or 200 contiguous amino acid residues among residues 19 to 228 of SEQ ID NO:24.
  • An AfuXyn2 polypeptide preferably is unaltered, as compared to native AfuXyn2, at residues E124, E129 and E215.
  • An AfuXyn2 polypeptide is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are conserved among AfuXyn2, AfuXyn5, and Trichoderma reesei Xyn2, as shown in the alignment of FIG. 55B .
  • An AfuXyn2 polypeptide suitably comprises the entire predicted conserved domain of native AfuXyn2 shown in FIG. 12B .
  • An exemplary AfuXyn2 polypeptide comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the mature AfuXyn2 sequence shown in FIG. 12B .
  • the AfuXyn2 polypeptide of the invention preferably has xylanase activity.
  • SEQ ID NO:26 The amino acid sequence of AfuXyn5 (SEQ ID NO:26) is shown in FIGS. 13B and 55B .
  • SEQ ID NO:26 is the sequence of the immature AfuXyn5.
  • AfuXyn5 has a predicted signal sequence corresponding to residues 1 to 19 of SEQ ID NO:26 (underlined in FIG. 13B ); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to residues 20 to 313 of SEQ ID NO:26.
  • the predicted GH11 conserved domains are in boldface type in FIG. 13B .
  • AfuXyn5 was shown to have endoxylanase activity indirectly by observing its ability to catalyze increased xylose monomer production in the presence of xylobiosidase when the enzymes act on pretreated biomass or on isolated hemicellulose.
  • the conserved catalytic residues include E119, E124, and E210.
  • the predicted CBM is near the C-terminal end, characterized by numerous hydrophobic residues and follows the long serine-, threonine-rich series of amino acids. The region is shown underlined in FIG. 55B .
  • an AfuXyn5 polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, 175, 200, 250, or 275 contiguous amino acid residues among residues 20 to 313 of SEQ ID NO:26.
  • An AfuXyn5 polypeptide preferably is unaltered, as compared to native AfuXyn5, at residues E119, E120, and E210.
  • An AfuXyn5 polypeptide is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are conserved among AfuXyn5, AfuXyn2, and Trichoderma reesei Xyn2, as shown in the alignment of FIG. 55B .
  • An AfuXyn5 polypeptide suitably comprises the entire predicted CBM of native AfuXyn5 and/or the entire predicted conserved domain of native AfuXyn5 (underlined) shown in FIG. 13B .
  • An exemplary AfuXyn5 polypeptide comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the mature AfuXyn5 sequence shown in FIG. 13B .
  • the AfuXyn5 polypeptide of the invention preferably has xylanase activity.
  • Fv43D The amino acid sequence of Fv43D (SEQ ID NO:28) is shown in FIGS. 14B and 53 .
  • SEQ ID NO:28 is the sequence of the immature Fv43D.
  • Fv43D has a predicted signal sequence corresponding to residues 1 to 20 of SEQ ID NO:28 (underlined in FIG. 14B ); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to residues 21 to 350 of SEQ ID NO:28.
  • the predicted conserved domain is in boldface type in FIG. 14B .
  • Fv43D was shown to have ⁇ -xylosidase activity in, for example, an enzymatic assay using p-nitophenyl- ⁇ -xylopyranoside, xylobiose, and/or mixed, linear xylo-oligomers as substrates.
  • the predicted catalytic residues include either D37 or D72, D159, and E251.
  • an Fv43D polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, 175, 200, 250, 300, or 320 contiguous amino acid residues among residues 21 to 350 of SEQ ID NO:28.
  • An Fv43D polypeptide preferably is unaltered, as compared to native Fv43D, at residues D37 or D72, D159, and E251.
  • An Fv43D polypeptide is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are conserved among a group of enzymes including Fv43D and 1, 2, 3, 4, 5, 6, 7, 8, or all 9 other amino acid sequences in the alignment of FIG. 53 .
  • An Fv43D polypeptide suitably comprises the entire predicted CD of native Fv43D shown in FIG. 14B .
  • An exemplary Fv43D polypeptide comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the mature Fv43D sequence shown in FIG. 14B .
  • the Fv43D polypeptide of the invention preferably has ⁇ -xylosidase activity.
  • an Fv43D polypeptide of the invention suitably comprises an amino acid sequence with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO:28, or to residues (i) 20-341, (ii) 21-350, (iii) 107-341, or (iv) 107-350 of SEQ ID NO:28.
  • the polypeptide suitably has ⁇ -xylosidase activity.
  • SEQ ID NO:30 is the sequence of the immature Pf43B.
  • Pf43B has a predicted signal sequence corresponding to residues 1 to 20 of SEQ ID NO:30 (underlined in FIG. 15B ); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to residues 21 to 321 of SEQ ID NO:30.
  • the predicted conserved domain is in boldface type in FIG. 15B . conserveed acidic residues within the conserved domain include D32, D61, D148, and E212.
  • Pf43B was shown to have ⁇ -xylosidase activity in, for example, an enzymatic assay using p-nitrophenyl-p-xylopyranaside, xylobiose, and/or mixed, linear xylo-oligomers as substrates.
  • a Pf43B polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, 175, 200, 250, or 280 contiguous amino acid residues among residues 21 to 321 of SEQ ID NO:30.
  • a Pf43B polypeptide preferably is unaltered, as compared to native Pf43B, at residues D32, D61, D148, and E212.
  • a Pf43B polypeptide is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are conserved among a group of enzymes including Pf43B and 1, 2, 3, 4, 5, 6, 7, 8, or all 9 other amino acid sequences in the alignment of FIG. 53 .
  • a Pf43B polypeptide suitably comprises the predicted conserved domain of native Pf43B shown in FIG. 15B .
  • An exemplary Pf43B polypeptide comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the mature Pf43B sequence shown in FIG. 15B .
  • the Pf43B polypeptide of the invention preferably has ⁇ -xylosidase activity.
  • a Pf43B polypeptide of the invention suitably comprises an amino acid sequence with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO:30.
  • the polypeptide suitably has ⁇ -xylosidase activity.
  • SEQ ID NO:32 is the sequence of the immature Fv51A.
  • Fv51A has a predicted signal sequence corresponding to residues 1 to 19 of SEQ ID NO:32 (underlined in FIG. 16B ); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to residues 20 to 660 of SEQ ID NO:32.
  • the predicted L- ⁇ -arabinofuranosidase conserved domain is in boldface type in FIG. 16B .
  • Fv51A was shown to have L- ⁇ -arabinofuranosidase activity in, for example, an enzymatic assay using 4-nitrophenyl- ⁇ -L-arabinofuranoside as a substrate.
  • Fv51A was shown to catalyze the release of arabinose from the set of oligomers released from hemicellulose via the action of endoxylanase. conserveed residues include E42, D49, E247, E286, E330, E359, E479, and E487.
  • an Fv51A polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, 550, 600, or 625 contiguous amino acid residues among residues 20 to 660 of SEQ ID NO:32.
  • An Fv51A polypeptide preferably is unaltered, as compared to native Fv51A, at residues E42, D49, E247, E286, E330, E359, E479, and E487.
  • An Fv51A polypeptide is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are conserved among Fv51A, Pa51A, and Pf51A, as shown in the alignment of FIG. 54 .
  • An Fv51A polypeptide suitably comprises the predicted conserved domain of native Fv51A shown in FIG. 16B .
  • An exemplary Fv51A polypeptide comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the mature Fv51A sequence shown in FIG. 16B .
  • the Fv51A polypeptide of the invention preferably has L- ⁇ -arabinofuranosidase activity.
  • an Fv51A polypeptide of the invention suitably comprise an amino acid sequence with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO:32, or to residues (i) 21-660, (ii) 21-645, (iii) 450-645, or (iv) 450-660 of SEQ ID NO:32.
  • the polypeptide suitably has L- ⁇ -arabinofuranosidase activity.
  • Trichoderma reesei Xyn3 The amino acid sequence of Trichoderma reesei Xyn3 (SEQ ID NO:42) is shown in FIG. 21B .
  • SEQ ID NO:42 is the sequence of the immature Trichoderma reesei Xyn3.
  • Trichoderma reesei Xyn3 has a predicted signal sequence corresponding to residues 1 to 16 of SEQ ID NO:42 (underlined in FIG. 21B ); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to residues 17 to 347 of SEQ ID NO:42.
  • the predicted conserved domain is in boldface type in FIG. 21B .
  • Trichoderma reesei Xyn3 was shown to have endoxylanase activity indirectly by observation of its ability to catalyze increased xylose monomer production in the presence of xylobiosidase when the enzymes act on pretreated biomass or on isolated hemicellulose.
  • the conserved catalytic residues include E91, E176, E180, E195, and E282, as determined by alignment with another GH10 family enzyme, the Xys1 delta from Streptomyces halstedii (Canals et al., 2003, Act Crystalogr. D Biol. 59:1447-53), which has 33% sequence identity to Trichoderma reesei Xyn3.
  • a Trichoderma reesei Xyn3 polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, 175, 200, 250, or 300 contiguous amino acid residues among residues 17 to 347 of SEQ ID NO:42.
  • a Trichoderma reesei Xyn3 polypeptide preferably is unaltered, as compared to native Trichoderma reesei Xyn3, at residues E91, E176, E180, E195, and E282.
  • a Trichoderma reesei Xyn3 polypeptide is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are conserved between Trichoderma reesei Xyn3 and Xys1 delta.
  • a Trichoderma reesei Xyn3 polypeptide suitably comprises the entire predicted conserved domain of native Trichoderma reesei Xyn3 shown in FIG. 21B .
  • Trichoderma reesei Xyn3 polypeptide comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the mature Trichoderma reesei Xyn3 sequence shown in FIG. 21B .
  • the Trichoderma reesei Xyn3 polypetpide of the invention preferably has xylanase activity.
  • SEQ ID NO:43 is the sequence of the immature Trichoderma reesei Xyn2.
  • Trichoderma reesei Xyn2 has a predicted prepropeptide sequence corresponding to residues 1 to 33 of SEQ ID NO:43 (underlined in FIG. 22 ); cleavage of the predicted signal sequence between positions 16 and 17 is predicted to yield a propeptide, which is processed by a kexin-like protease between positions 32 and 33, generating the mature protein having a sequence corresponding to residues 33 to 222 of SEQ ID NO:43.
  • Trichoderma reesei Xyn2 was shown to have endoxylanase activity indirectly by observation of its ability to catalyze an increased xylose monomer production in the presence of xylobiosidase when the enzymes act on pretreated biomass or on isolated hemicellulose.
  • the conserved acidic residues include E118, E123, and E209.
  • a Trichoderma reesei Xyn2 polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, or 175 contiguous amino acid residues among residues 33 to 222 of SEQ ID NO:43.
  • a Trichoderma reesei Xyn2 polypeptide preferably is unaltered, as compared to a native Trichoderma reesei Xyn2, at residues E118, E123, and E209.
  • a Trichoderma reesei Xyn2 polypeptide is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are conserved among Trichoderma reesei Xyn2, AfuXyn2, and AfuXyn5, as shown in the alignment of FIG. 55B .
  • a Trichoderma reesei Xyn2 polypeptide suitably comprises the entire predicted conserved domain of native Trichoderma reesei Xyn2 shown in FIG. 22 .
  • An exemplary Trichoderma reesei Xyn2 polypeptide comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the mature Trichoderma reesei Xyn2 sequence shown in FIG. 22 .
  • the Trichoderma reesei Xyn2 polypeptide of the invention preferably has xylanase activity.
  • SEQ ID NO:44 is the sequence of the immature Trichoderma reesei Bxl1.
  • Trichoderma reesei Bxl1 has a predicted signal sequence corresponding to residues 1 to 18 of SEQ ID NO:44 (underlined in FIG. 23 ); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to residues 19 to 797 of SEQ ID NO:44.
  • the predicted conserved domains are in boldface type in FIG. 23 .
  • Trichoderma reesei Bxl1 was shown to have ⁇ -xylosidase activity in, for example, an enzymatic assay using p-nitophenyl- ⁇ -xylopyranoside, xylobiose and/or mixed, linear xylo-oligomers as substrates.
  • the conserved acidic residues include E193, E234, and D310.
  • a Trichoderma reesei Bxl1 polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, or 750 contiguous amino acid residues among residues 17 to 797 of SEQ ID NO:44.
  • a Trichoderma reesei Bxl1 polypeptide preferably is unaltered, as compared to a native Trichoderma reesei Bxl1, at residues E193, E234, and D310.
  • a Trichoderma reesei Bxl1 polypeptide is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are conserved among Trichoderma reesei Bxl1, Fv3A, and Trichoderma reesei Bgl1, as shown in the alignment of FIG. 64 .
  • a Trichoderma reesei Bxl1 polypeptide suitably comprises the entire predicted conserved domains of native Trichoderma reesei Bxl1 shown in FIG. 23 .
  • An exemplary Trichoderma reesei Bxl1 polypeptide comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the mature Trichoderma reesei Bxl1 sequence shown in FIG. 23 .
  • the Trichoderma reesei Bxl1 polypeptide of the invention preferably has ⁇ -xylosidase activity.
  • Trichoderma reesei Bxl1 polypeptide of the invention suitably comprises an amino acid sequence with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to the amino acid sequence of SEQ ID NO: 44.
  • the polypeptide suitably has ⁇ -xylosidase activity.
  • Trichoderma reesei Bgl1 The amino acid sequence of Trichoderma reesei Bgl1 (SEQ ID NO:45) is shown in FIGS. 24 and 64 .
  • Trichoderma reesei Bgl1 has a predicted signal sequence corresponding to residues 1 to 19 of SEQ ID NO:45 (underlined in FIG. 24 ); cleavage of the signal sequence is predicted to yield a mature protein having a sequence corresponding to residues 20 to 744 of SEQ ID NO:45.
  • the predicted conserved domain is in boldface type in FIG. 24 .
  • Trichoderma reesei Bgl1 has been shown to have ⁇ -glucosidase activity by observation of a capacity to catalyze the hydrolysis of para-nitrophenyl- ⁇ -D-glucopyranoside to produce para-nitrophenol, and a capacity to catalyze the hydrolysis of cellobiose.
  • the conserved acidic residues include D164, E197, and D267.
  • a Trichoderma reesei Bgl1 polypeptide refers to a polypeptide and/or a variant thereof comprising a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to at least 50, 75, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, or 780 contiguous amino acid residues among residues 20 to 744 of SEQ ID NO:45.
  • a Trichoderma reesei Bgl1 polypeptide preferably is unaltered, as compared to a native Bgl1, at residues D164, E197, and D267.
  • a Trichoderma reesei Bgl1 polypeptide is preferably unaltered in at least 70%, 80%, 90%, 95%, 98%, or 99% of the amino acid residues that are conserved among Trichoderma reesei Bgl1, Fv3A, and Trichoderma reesei Bxl1, as shown in the alignment of FIG. 64 .
  • a Trichoderma reesei Bgl1 polypeptide suitably comprises the entire predicted conserved domain of native Trichoderma reesei Bgl1 shown in FIG.
  • An exemplary Trichoderma reesei Bgl1 polypeptide comprises a sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the mature Trichoderma reesei Bgl1 sequence shown in FIG. 24 .
  • the Trichoderma reesei Bgl1 polypeptide of the invention preferably has 3-glucosidase activity.
  • the present disclosure provides a number of isolated, synthetic, or recombinant hemicelluloytic polypeptides or variants as described below:
  • polypeptide comprising an amino acid sequence with at least 90%, at least 95%, at least 98%, at least 99%, or 100% sequence identity to the amino acid sequence corresponding to positions (i) 24 to 766 of SEQ ID NO:2; (ii) 73 to 321 of SEQ ID NO:2; (iii) 73 to 394 of SEQ ID NO:2; (iv) 395 to 622 of SEQ ID NO:2; (v) 24 to 622 of SEQ ID NO:2; or (iv) 73 to 622 of SEQ ID NO:2; the polypeptide preferably has ⁇ -xylosidase activity; or (2) a polypeptide comprising an amino acid sequence with at least 90%, at least 95%, at least 98%, at least 99%, or 100% sequence identity to the amino acid sequence corresponding to positions (i) 21 to 445 of SEQ ID NO:4; (ii) 21 to 301 of SEQ ID NO:4; (iii) 21 to 323 of SEQ ID NO:
  • compositions e.g., cellulase compositions, or enzyme blends/compositions
  • fermentation broths enriched with one or more of the above-described polypeptides.
  • the enzyme blend/composition is thus a non-naturally-occurring composition.
  • the cellulase composition can be, for example, a filamentous fungal cellulase composition, such as a Trichoderma cellulase composition.
  • the fermentation broth can be a fermentation broth of a filamentous fungus, for example, a Trichoderma, Humicola, Fusarium, Aspergillus, Neurospora, Penicillium, Cephalosporium, Achlya, Podospora, Endothia, Mucor, Cochliobolus, Pyricularia , or Chrysosporium fermentation broth.
  • the fermentation broth can be, for example, one of Trichoderma spp. such as a Trichoderma reesei , or Penicillium spp., such as a Penicillium funiculosum .
  • the fermentation broth can also suitably be a cell-free fermentation broth.
  • the instant disclosure provides host cells that are recombiantly engineered to express a polypeptide described above.
  • the host cells can be, for example, filamentous fungal host cells, such as Trichoderma, Humicola, Fusarium, Aspergillus, Neurospora, Penicillium, Cephalosporium, Achlya, Podospora, Endothia, Mucor, cochliobolus, Pyricularia , or Chrysosporium cells.
  • the host cells can be, for example, a Trichoderma spp.
  • a Trichoderma reesei cell such as a Trichoderma reesei cell
  • a Penicillium cell such as a Penicillium funiculosum cell
  • an Aspergillus cell such as an Aspergillus oryzae or Aspergillus nidulans cell
  • a Fusarium cell such as a Fusarium verticilloides or Fusarium oxysporum cell.
  • the present disclosure also provides a fusion protein that includes a domain of a protein of the present disclosure attached to one or more fusion segments, which are typically heterologous to the protein (i.e., derived from a different source than the protein of the disclosure).
  • Suitable fusion segments include, without limitation, segments that can enhance a protein's stability, provide other desirable biological activity, and/or facilitate purification of the protein (e.g., by affinity chromatography).
  • a suitable fusion segment can be a domain of any size that has the desired function (e.g., imparts increased stability, solubility, action or biological activity; and/or simplifies purification of a protein). Fusion segments can be joined to amino and/or carboxyl termini of the domain(s) of a protein of the present disclosure.
  • the fusion segments can be susceptible to cleavage. There may be some advantage in having this susceptibility, for example, it may enable straight-forward recovery of the protein of interest.
  • Fusion proteins are preferably produced by culturing a recombinant cell transfected with a fusion nucleic acid that encodes a protein, which includes a fusion segment attached to either the carboxyl or amino terminal end, or fusion segments attached to both the carboxyl and amino terminal ends, of a protein, or a domain thereof.
  • proteins of the present disclosure also include expression products of gene fusions (e.g., an overexpressed, soluble, and active form of a recombinant protein), of mutagenized genes (e.g., genes having codon modifications to enhance gene transcription and translation), and of truncated genes (e.g., genes having signal sequences removed or substituted with a heterologous signal sequence).
  • gene fusions e.g., an overexpressed, soluble, and active form of a recombinant protein
  • mutagenized genes e.g., genes having codon modifications to enhance gene transcription and translation
  • truncated genes e.g., genes having signal sequences removed or substituted with a heterologous signal sequence
  • Glycosyl hydrolases that utilize insoluble substrates are often modular enzymes. They usually comprise catalytic modules appended to one or more non-catalytic carbohydrate-binding domains (CBMs). In nature, CBMs are thought to promote the glycosyl hydrolase's interaction with its target substrate polysaccharide. Thus, the disclosure provides chimeric enzymes having altered substrate specificity; including, for example, chimeric enzymes having multiple substrates as a result of “spliced-in” heterologous CBMs.
  • heterologous CBMs of the chimeric enzymes of the disclosure can also be designed to be modular, such that they are appended to a catalytic module or catalytic domain (a “CD”, e.g., at an active site), which can likewise be heterologous or homologous to the glycosyl hydrolase.
  • a catalytic module or catalytic domain a “CD”, e.g., at an active site
  • the disclosure provides peptides and polypeptides consisting of, or comprising, CBM/CD modules, which can be homologously paired or joined to form chimeric (heterologous) CBM/CD pairs.
  • these chimeric polypeptides/peptides can be used to improve or alter the performance of an enzyme of interest.
  • the disclosure provides chimeric enzymes comprising, e.g., at least one CBM of an enzyme of SEQ ID NO:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 43, 44, or 45.
  • a polypeptide of the disclosure includes an amino acid sequence comprising the CD and/or CBM of the glycosyl hydrolase sequence of SEQ ID NO:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 43, 44, or 45.
  • the polypeptide of the disclosure can thus suitably be a fusion protein comprising functional domains from two or more different proteins (e.g., a CBM from one protein linked to a CD from another protein).
  • polypeptides of the disclosure can suitably be obtained and/or used in “substantially pure” form.
  • a polypeptide of the disclosure constitutes at least about 80 wt. % (e.g., at least about 85 wt. %, 90 wt. %, 91 wt. %, 92 wt. %, 93 wt. %, 94 wt. %, 95 wt. %, 96 wt. %, 97 wt. %, 98 wt. %, or 99 wt. %) of the total protein in a given composition, which also includes other ingredients such as a buffer or solution.
  • the polypeptides of the disclosure can suitably be obtained and/or used in recombinant culture broths (e.g., a filamentous fungal culture broth).
  • the recombinant culture broths can be non-naturally occurring; for example, the culture broth can be produced by a recombinant host cell that is engineered to express a heterologous polypeptide of the disclosure, or by a recombinant host cell that is engineered to express an endogenous polypeptide of the disclosure in greater or lesser amounts than the endogenous expression levels (e.g., in an amount that is 1-, 2-, 3-, 4-, 5-, or more-fold greater or less than the endogenous expression levels).
  • polypeptides of the disclosure can suitably be obtained and/or used as recombinant culture broths produced by “integrated” host cell strains that have been engineered to express a plurality of polypeptides of the disclosure in desired ratios.
  • desired ratios are described herein, for example, in Section 6.3.4 below.
  • the present disclosure provides nucleic acids encoding a polypeptide of the disclosure, for example one described in Section 6.1 above.
  • nucleic acids comprising a nucleic acid sequence having at least about 70%, e.g., at least about 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%; 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%, or complete (100%) sequence identity to a nucleic acid of SEQ ID NO:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 46, 47, 48, 49, or 50, over a region of at least about 10, e.g., at least about 15, 20, 25, 30, 35, 40, 45, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900
  • the present disclosure also provides nucleic acids encoding at least one polypeptide having a hemicellulolytic activity (e.g., a xylanase, ⁇ -xylosidase, and/or L- ⁇ -arabinofuranosidase activity).
  • a hemicellulolytic activity e.g., a xylanase, ⁇ -xylosidase, and/or L- ⁇ -arabinofuranosidase activity.
  • Nucleic acids of the disclosure also include isolated, synthetic or recombinant nucleic acids encoding an enzyme having the sequence of SEQ ID NO:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 43, 44, or 45, and subsequences thereof (e.g., a conserved domain or carbohydrate binding domain (“CBM”), and variants thereof.
  • a nucleic acid of the disclosure can, for example, encode the mature portion of a protein of SEQ ID NO:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 43, 44, or 45.
  • the disclosure specifically provides a nucleic acid encoding an Fv3A, a Pf43A, an Fv43E, an Fv39A, an Fv43A, an Fv43B, a Pa51A, a Gz43A, an Fo43A, an Af43A, a Pf51A, an AfuXyn2, an AfuXyn5, a Fv43D, a Pf43B, an Fv43B, an Fv51A, a Trichoderma reesei Xyn3, a Trichoderma reesei Xyn2, a Trichoderma reesei Bxl1, or a Trichoderma reesei Bgl1 polypeptide.
  • the disclosure provides an isolated nucleic acid molecule, wherein the nucleic acid molecule encodes:
  • a polypeptide comprising an amino acid sequence with at least 90%, at least 95%, at least 98%, at least 99%, or 100% sequence identity to the amino acid sequence corresponding to positions (i) 24 to 766 of SEQ ID NO:2; (ii) 73 to 321 of SEQ ID NO:2; (iii) 73 to 394 of SEQ ID NO:2; (iv) 395 to 622 of SEQ ID NO:2; (v) 24 to 622 of SEQ ID NO:2; or (iv) 73 to 622 of SEQ ID NO:2; or (2) a polypeptide comprising an amino acid sequence with at least 90%, at least 95%, at least 98%, at least 99%, or 100% sequence identity to the amino acid sequence corresponding to positions (i) 21 to 445 of SEQ ID NO:4; (ii) 21 to 301 of SEQ ID NO:4; (iii) 21 to 323 of SEQ ID NO:4; (iv) 21 to 444 of SEQ ID NO:4;
  • the instant disclosure also provides:
  • nucleic acid having at least 90% e.g., at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO:1, or a nucleic acid that is capable of hybridizing under high stringency conditions to a complement of SEQ ID NO:1, or to a fragment thereof; or (2) a nucleic acid having at least 90% (e.g., at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more) sequence identity to SEQ ID NO:3, or a nucleic acid that is capable of hybridizing under high stringency conditions to a complement of SEQ ID NO:3, or to a fragment thereof; or (3) a nucleic acid having at least 90% (e.g., at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more) sequence identity to SEQ ID NO:5, or a nucleic acid
  • the disclosure also provides expression cassettes and/or vectors comprising the above-described nucleic acids.
  • the nucleic acid encoding an enzyme of the disclosure is operably linked to a promoter.
  • the promoter can be a filamentous fungal promoter.
  • the nucleic acids can be, for example, under the control of heterologous promoters.
  • the nucleic acids can also be expressed under the control of constitutive or inducible promoters. Examples of promoters that can be used include, but are not limited to, a cellulase promoter, a xylanase promoter, the 1818 promoter (previously identified as a highly expressed protein by EST mapping Trichoderma ).
  • the promoter can suitably be a cellobiohydrolase, endoglucanase, or ⁇ -glucosidase promoter.
  • a particularly suitable promoter can be, for example, a T. reesei cellobiohydrolase, endoglucanase, or 6-glucosidase promoter.
  • the promoter is a cellobiohydrolase I (cbh1) promoter.
  • Non-limiting examples of promoters include a cbh1, cbh2, egl1, egl2, egl3, egl4, egl5, pki1, gpd1, xyn1, or xyn2 promoter.
  • promoters include a T. reesei cbh1, cbh2, egl1, egl2, egl3, egl4, egl5, pki1, gpd1, xyn1, or xyn2 promoter.
  • Suitable host cells include cells of any microorganism (e.g., cells of a bacterium, a protist, an alga, a fungus (e.g., a yeast or filamentous fungus), or other microbe), and are preferably cells of a bacterium, a yeast, or a filamentous fungus.
  • Suitable host cells of the bacterial genera include, but are not limited to, cells of Escherichia, Bacillus, Lactobacillus, Pseudomonas , and Streptomyces .
  • Suitable cells of bacterial species include, but are not limited to, cells of Escherichia coli, Bacillus subtilis, Bacillus licheniformis, Lactobacillus brevis, Pseudomonas aeruginosa , and Streptomyces lividans.
  • Suitable host cells of the genera of yeast include, but are not limited to, cells of Saccharomyces, Schizosaccharomyces, Candida, Hansenula, Pichia, Kluyveromyces , and Phaffia .
  • Suitable cells of yeast species include, but are not limited to, cells of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans, Hansenula polymorpha, Pichia pastoris, P. canadensis, Kluyveromyces marxianus , and Phaffia rhodozyma.
  • Suitable host cells of filamentous fungi include all filamentous forms of the subdivision Eumycotina .
  • Suitable cells of filamentous fungal genera include, but are not limited to, cells of Acremonium, Aspergillus, Aureobasidium, Bjerkandera, Ceriporiopsis, Chrysoporium, Coprinus, Coriolus, Corynascus, Chaetomium, Cryptococcus, Filobasidium, Fusarium, Gibberella, Humicola, Hypocrea, Magnaporthe, Mucor, Myceliophthora, Mucor, Neocaffimastix, Neurospora, Paecilomyces, Penicillium, Phanerochaete, Phlebia, Piromyces, Pleurotus, Scytaldium, Schizophyllum, Sporotrichum, Talaromyces, Thermoascus, Thielavia, Tolypocladium, Trametes , and Trichoderma .
  • Suitable cells of filamentous fungal species include, but are not limited to, cells of Aspergillus awamori, Aspergillus fumigatus, Aspergillus foetidus, Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae, Chrysosporium lucknowense, Fusarium bactridioides, Fusarium cerealis, Fusarium crookwellense, Fusarium culmorum, Fusarium graminearum, Fusarium graminum, Fusarium heterosporum, Fusarium negundi, Fusarium oxysporum, Fusarium reticulatum, Fusarium roseum, Fusarium sambucinum, Fusarium sarcochroum, Fusarium sporotrichioides, Fusarium sulphureum, Fusarium torulosum, Fus
  • the disclosure further provides a recombinant host cell that is engineered to express one or more, two or more, three or more, four or more, or five or more of an Fv3A, a Pf43A, an Fv43E, an Fv39A, an Fv43A, an Fv43B, a Pa51A, a Gz43A, an Fo43A, an Af43A, a Pf51A, an AfuXyn2, an AfuXyn5 an Fv43D, a Pf43B, and an Fv51A polypeptide.
  • the recombinant host cell is, for example, a recombinant Trichoderma reesei host cell.
  • the disclosure provides a recombinant fungus, such as a recombinant Trichoderma reesei , that is engineered to express one or more, two or more, three or more, four or more, or five or more of an Fv3A, a Pf43A, an Fv43E, an Fv39A, an Fv43A, an Fv43B, a Pa51A, a Gz43A, an Fo43A, an Af43A, a Pf51A, an AfuXyn2, an AfuXyn5, an Fv43D, a Pf43B, and an Fv51A polypeptide.
  • a recombinant fungus such as a recombinant Trichoderma reesei , that is engineered to express one or more, two or more, three or more, four or more, or five or more of an Fv3A, a Pf43A, an Fv43E, an Fv39A, an F
  • the disclosure provides a recombinant Trichoderma reesei host cell engineered to express 1, 2, 3, 4, 5, or more of an Fv3A, a Pf43A, an Fv43E, an Fv39A, an Fv43A, an Fv43B, a Pa51A, a Gz43A, an Fo43A, an Af43A, a Pf51A, an AfuXyn2, an AfuXyn5, an Fv43D, a Pf43B, and an Fv51A polypeptide.
  • the disclosure provides a host cell, for example, a recombinant fungal host cell or a recombinant filamentous fungus, engineered to recombinantly express at least one xylanase, at least one ⁇ -xylosidase, and one L- ⁇ -arabinofuranosidase.
  • a host cell for example, a recombinant fungal host cell or a recombinant filamentous fungus, engineered to recombinantly express at least one xylanase, at least one ⁇ -xylosidase, and one L- ⁇ -arabinofuranosidase.
  • the disclosure also provides a recombinant host cell, e.g., a recombinant fungal host cell or a recombinant filamentous fungus such as a recombinant Trichoderma reesei , that is engineered to express 1, 2, 3, 4, 5, or more of an Fv3A, a Pf43A, an Fv43E, an Fv39A, an Fv43A, an Fv43B, a Pa51A, a Gz43A, an Fo43A, an Af43A, a Pf51A, an AfuXyn2, an AfuXyn5, an Fv43D, a Pf43B, and an Fv51A polypeptide, in addition to one or more of Trichoderma reesei Xyn2, Trichoderma reesei Xyn3, Trichoderma reesei Bxl1 and/or Trichoderma reesei Bgl1.
  • the recombinant host cell is, for example, a Trichoderma reesei host cell.
  • the recombinant fungus is, for example, a recombinant Trichoderma reesei .
  • the disclosure provides a Trichoderma reesei host cell, or a recombinant Trichoderma reesei fungus, that is engineered to recombinantly express 1, 2, 3, 4, 5, or more of an Fv3A, a Pf43A, an Fv43E, an Fv39A, an Fv43A, an Fv43B, a Pa51A, a Gz43A, an Fo43A, an Af43A, a Pf51A, an AfuXyn2, an AfuXyn5, an Fv43D, a Pf43B, and an Fv51A polypeptide, in addition to recombiantly express one or more of Trichoderma reesei Xy
  • the present disclosure also provides a recombinant host cell e.g., a recombinant fungal host cell or a recombinant organism, e.g., a filamentous fungus, such as a recombinant Trichoderma reesei , that is engineered to recombinantly express Trichoderma reesei Xyn3, Trichoderma reesei Bgl1, Fv3A, Fv43D, and Fv51A polypeptides.
  • the recombinant host cell is suitably a Trichoderma reesei host cell.
  • the recombinant fungus is suitably a recombinant Trichoderma reesei .
  • the disclosure provides, for example, a Trichoderma reesei host cell engineered to recombinantly express Trichoderma reesei Xyn3, Trichoderma reesei Bgl1, Fv3A, Fv43D, and Fv51A polypeptides.
  • the disclosure provides a recombinant host cell or recombinant fungus that is engineered to express an enzyme blend comprising suitable enzymes in ratios suitable for saccharification.
  • the recombinant host cell is, for example, a fungal host cell.
  • the recombinant fungus is, for example, a recombinant Trichoderma reesei .
  • Exemplary enzyme ratios/amounts present in suitable enzyme blends are described in Section 6.3.4 below.
  • the disclosure further provides transgenic plants comprising a nucleic acid of the disclosure or an expression cassette of the disclosure.
  • the transgenic plant can be, for example, a cereal plant, a corn plant, a potato plant, a tomato plant, a wheat plant, an oilseed plant, a rapeseed plant, a soybean plant, a rice plant, a barley plant, or a tobacco plant.
  • the present disclosure provides a composition comprising an enzyme blend/composition that is capable of breaking down lignocellulose material.
  • a multi-enzyme blend/composition comprises at least one polypeptide of the present disclosure, in combination with one or more additional polypeptides of the present disclosure, or one or more enzymes from other microorganisms, plants, or organisms. Synergistic enzyme combinations and related methods are contemplated.
  • the disclosure includes methods for identifying the optimum ratios of the enzymes included in the blends/compositions for degrading a particular lignocellulosic material. These methods include, e.g., tests to identify the optimum enzyme blend/composition and ratios for efficient conversion of a given lignocellulosic substrate to its constituent sugars.
  • the Examples below include assays that may be used to identify optimum ratios and blends/compositions of enzymes with which to degrade lignocellulosic materials.
  • the cell walls of higher plants are comprised of a variety of carbohydrate polymer (CP) components. These CP interact through covalent and non-covalent means, providing the structural integrity required to form rigid cell walls and resist turgor pressure in plants.
  • the major CP found in plants is cellulose, which forms the structural backbone of the cell wall.
  • chains of poly- ⁇ -1,4-D-glucose self associate through hydrogen bonding and hydrophobic interactions to form cellulose microfibrils, which further self-associate to form larger fibrils.
  • Cellulose microfibrils are often irregular structurally and contain regions of varying crystallinity. The degree of crystallinity of cellulose fibrils depends on how tightly ordered the hydrogen bonding is between and among its component cellulose chains. Areas with less-ordered bonding, and therefore more accessible glucose chains, are referred to as amorphous regions.
  • Endoglucanases cleave cellulose chains internally to shorter chains in a process that increases the number of accessible ends, which are more susceptible to exoglucanase activity than the intact cellulose chains.
  • exoglucanases e.g., cellobiohydrolases
  • cellobiohydrolases are specific for either reducing ends or non-reducing ends, liberating, in most cases, cellobiose, the dimer of glucose.
  • the accumulating cellobiose is then subject to cleavage by cellobiases (e.g., ⁇ -1,4-glucosidases) to glucose.
  • hemicellulose contains only anhydro-glucose.
  • sugar monomers in hemicellulose can also include xylose, mannose, galactose, rhamnose, and arabinose.
  • Hemicelluloses mostly contain D-pentose sugars and occasionally small amounts of L-sugars.
  • Xylose is typically present in the largest amount, but mannuronic acid and galacturonic acid also tend to be present.
  • Hemicelluloses include xylan, glucuronoxylan, arabinoxylan, glucomannan, and xyloglucan.
  • the enzymes and multi-enzyme compositions of the disclosure are useful for saccharification of hemicellulose materials, including, e.g., xylan, arabinoxylan, and xylan- or arabinoxylan-containing substrates.
  • Arabinoxylan is a polysaccharide composed of xylose and arabinose, wherein L- ⁇ -arabinofuranose residues are attached as branch-points to a ⁇ -(1,4)-linked xylose polymeric backbone.
  • the present disclosure provides enzyme blends/compositions containing enzymes that impart a range or variety of substrate specificities when working together to degrade biomass into fermentable sugars in the most efficient manner.
  • One example of a multi-enzyme blend/composition of the present invention is a mixture of cellobiohydrolase(s), xylanase(s), endoglucanase(s), ⁇ -glucosidase(s), ⁇ -xylosidase(s), and, optionally, accessory proteins.
  • the enzyme blend/composition is suitably a non-naturally occurring composition.
  • the disclosure provides enzyme blends/compositions (including products of manufacture) comprising a mixture of xylan-hydrolyzing, hemicellulose- and/or cellulose-hydrolyzing enzymes, which include at least one, several, or all of a cellulase, including a glucanase; a cellobiohydrolase; an L- ⁇ -arabinofuranosidase; a xylanase; a ⁇ -glucosidase; and a ⁇ -xylosidase.
  • each of the enzyme blends/compositions of the disclosure comprises at least one enzyme of the disclosure.
  • the present disclosure also provides enzyme blends/compositions that are non-naturally occurring compositions.
  • the term “enzyme blends/compositions” refers to:
  • fermentation broth refers to an enzyme preparation produced by fermentation that undergoes no or minimal recovery and/or purification subsequent to fermentation.
  • microbial cultures are grown to saturation, incubated under carbon-limiting conditions to allow protein synthesis (e.g., expression of enzymes). Then, once the enzyme(s) are secreted into the cell culture media, the fermentation broths can be used.
  • the fermentation broths of the disclosure can contain unfractionated or fractionated contents of the fermentation materials derived at the end of the fermentation.
  • the fermentation broths of the invention are unfractionated and comprise the spent culture medium and cell debris present after the microbial cells (e.g., filamentous fungal cells) undergo a fermentation process.
  • the fermentation broth can suitably contain the spent cell culture media, extracellular enzymes, and live or killed microbial cells.
  • the fermentation broths can be fractionated to remove the microbial cells.
  • the fermentation broths can, for example, comprise the spent cell culture media and the extracellular enzymes.
  • Any of the enzymes described specifically herein can be combined with any one or more of the enzymes described herein or with any other available and suitable enzymes, to produce a suitable multi-enzyme blend/composition.
  • the disclosure is not restricted or limited to the specific exemplary combinations listed below.
  • biomass saccharification using enzymes, enzyme blends/compositions of the disclosure.
  • biomass refers to any composition comprising cellulose and/or hemicellulose (optionally also lignin in lignocellulosic biomass materials).
  • biomass includes, without limitation, seeds, grains, tubers, plant waste or byproducts of food processing or industrial processing (e.g., stalks), corn (including, e.g., cobs, stover, and the like), grasses (including, e.g., Indian grass, such as Sorghastrum nutans ; or, switchgrass, e.g., Panicum species, such as Panicum virgatum ), wood (including, e.g., wood chips, processing waste), paper, pulp, and recycled paper (including, e.g., newspaper, printer paper, and the like).
  • Other biomass materials include, without limitation, potatoes, soybean (e.g., rapeseed), barley, rye, oats, wheat, beets, and sugar cane bagasse.
  • the disclosure provides methods of saccharification comprising contacting a composition comprising a biomass material, for example, a material comprising xylan, hemicellulose, cellulose, and/or a fermentable sugar, with a polypeptide of the disclosure, or a polypeptide encoded by a nucleic acid of the disclosure, or any one of the enzyme blends/compositions, or products of manufacture of the disclosure.
  • a biomass material for example, a material comprising xylan, hemicellulose, cellulose, and/or a fermentable sugar
  • the saccharified biomass (e.g., lignocellulosic material processed by enzymes of the disclosure) can be made into a number of bio-based products, via processes such as, e.g., microbial fermentation and/or chemical synthesis.
  • microbial fermentation refers to a process of growing and harvesting fermenting microorganisms under suitable conditions.
  • the fermenting microorganism can be any microorganism suitable for use in a desired fermentation process for the production of bio-based products. Suitable fermenting microorganisms include, without limitation, filamentous fungi, yeast, and bacteria.
  • the saccharified biomass can, for example, be made it into a fuel (e.g., a biofuel such as a bioethanol, biobutanol, biomethanol, a biopropanol, a biodiesel, a jet fuel, or the like) via fermentation and/or chemical synthesis.
  • a fuel e.g., a biofuel such as a bioethanol, biobutanol, biomethanol, a biopropanol, a biodiesel, a jet fuel, or the like
  • the saccharified biomass can, for example, also be made into a commodity chemical (e.g., ascorbic acid, isoprene, 1,3-propanediol), lipids, amino acids, proteins, and enzymes, via fermentation and/or chemical synthesis.
  • a commodity chemical e.g., ascorbic acid, isoprene, 1,3-propanediol
  • lipids e.g., amino acids, proteins, and enzymes
  • biomass e.g., lignocellulosic material
  • pretreatment step(s) in order to render xylan, hemicellulose, cellulose and/or lignin material more accessible or susceptable to enzymes and thus more amenable to hydrolysis by the enzyme(s) and/or enzyme blends/compositions of the disclosure.
  • the pretreatment entails subjecting biomass material to a catalyst comprising a dilute solution of a strong acid and a metal salt in a reactor.
  • the biomass material can, e.g., be a raw material or a dried material.
  • This pretreatment can lower the activation energy, or the temperature, of cellulose hydrolysis, ultimately allowing higher yields of fermentable sugars. See, e.g., U.S. Pat. Nos. 6,660,506; 6,423,145.
  • Another exemplary pretreatment method entails hydrolyzing biomass by subjecting the biomass material to a first hydrolysis step in an aqueous medium at a temperature and a pressure chosen to effectuate primarily depolymerization of hemicellulose without achieving significant depolymerization of cellulose into glucose.
  • This step yields a slurry in which the liquid aqueous phase contains dissolved monosaccharides resulting from depolymerization of hemicellulose, and a solid phase containing cellulose and lignin.
  • the slurry is then subject to a second hydrolysis step under conditions that allow a major portion of the cellulose to be depolymerized, yielding a liquid aqueous phase containing dissolved/soluble depolymerization products of cellulose. See, e.g., U.S. Pat. No. 5,536,325.
  • a further exemplary method involves processing a biomass material by one or more stages of dilute acid hydrolysis using about 0.4% to about 2% of a strong acid; followed by treating the unreacted solid lignocellulosic component of the acid hydrolyzed material with alkaline delignification. See, e.g., U.S. Pat. No. 6,409,841.
  • Another exemplary pretreatment method comprises prehydrolyzing biomass (e.g., lignocellulosic materials) in a prehydrolysis reactor; adding an acidic liquid to the solid lignocellulosic material to make a mixture; heating the mixture to reaction temperature; maintaining reaction temperature for a period of time sufficient to fractionate the lignocellulosic material into a solubilized portion containing at least about 20% of the lignin from the lignocellulosic material, and a solid fraction containing cellulose; separating the solubilized portion from the solid fraction, and removing the solubilized portion while at or near reaction temperature; and recovering the solubilized portion.
  • the cellulose in the solid fraction is rendered more amenable to enzymatic digestion. See, e.g., U.S. Pat. No. 5,705,369.
  • Pretreatment can also comprise contacting a biomass material with stoichiometric amounts of sodium hydroxide and ammonium hydroxide at a very low concentration. See Teixeira et al., 1999, Appl. Biochem. and Biotech. 77-79:19-34.
  • Pretreatment can also comprise contacting a lignocellulose with a chemical (e.g., a base, such as sodium carbonate or potassium hydroxide) at a pH of about 9 to about 14 at moderate temperature, pressure, and pH.
  • a chemical e.g., a base, such as sodium carbonate or potassium hydroxide
  • Ammonia is used, for example, in a preferred pretreatment method.
  • a pretreatment method comprises subjecting a biomass material to low ammonia concentration under conditions of high solids. See, e.g., U.S. Patent Publication No. 20070031918 and PCT publication WO 06110901.
  • the present disclosure provides enzyme blends/compositions comprising one or more enzymes of the disclosure.
  • One or more enzymes of the enzyme blends/compositions can be produced by a recombinant host cell or a recombinant organism.
  • the enzyme blends/compositions are suitably non-naturally occurring compositions.
  • An enzyme blend/composition of the disclosure can suitably comprise a first polypeptide having ⁇ -xylosidase activity, and further comprises 1, 2, 3, or 4 of a second polypeptide having ⁇ -xylosidase activity, one or more polypeptides having L- ⁇ -arabinofuranosidase activity, one or more polypeptides having xylanase activity, and one or more polypeptides having cellulase activity.
  • the first polypeptide having ⁇ -xylosidase activity is, for example, an Fv3A, a Pf43A, an Fv43E, an Fv43A, an Fv43B, a Pa51A, a Gz43A, an Fo43A, or an Fv39A polypeptide.
  • the second polypeptide having R-xylosidase activity is, for example, different from the first polypeptide having ⁇ -xylosidase activity, and is suitably an Fv3A, a Pf43A, an Fv43E, an Fv43A, an Fv43B, a Pa51A, a Gz43A, an Fv43D, an Fo43A, an Fv39A, or a Trichoderma reesei Bxl1 polypeptide.
  • Each of the one or more polypeptides having L- ⁇ -arabinofuranosidase activity is, for example, an Af43A, a Pf51A, a Pa51A, an Fv43B, or an Fv51A polypeptide.
  • Each of the one or more polypeptides having xylanase activity is, for example, a Trichoderma reesei Xyn, a Trichoderma reesei Xyn2, an AfuXyn2, or an AfuXyn5.
  • Each of the one or more polypeptides having cellulase activity is, for example, an endoglucanase, for example, a Trichoderma reesei EG1 or EG2, a cellobiohydrolase, for example, a Trichoderma reesei CBH1 or CBH2, or a ⁇ -glucosidase, for example, a Trichoderma reesei Bgl1.
  • Another enzyme blend/composition of the disclosure can suitably comprise a first polypeptide having L- ⁇ -arabinofuranosidase activity, and further comprises 1, 2, 3, or 4 of a second polypeptide having L- ⁇ -arabinofuranosidase activity, one or more polypeptides having ⁇ -xylosidase activity, one or more polypeptides having xylanase activity, and/or one or more polypeptides having cellulase activity.
  • the first L- ⁇ -arabinofuranosidase is an Af43A, a Pf51A, or an Fv51A polypeptide.
  • the second L- ⁇ -arabinofuranosidase is different from the first L- ⁇ -arabinofuranosidase, and is, for example, an Af43A, a Pf51A, a Pa51A, an Fv43B, or an Fv51A polypeptide.
  • Each of the one or more ⁇ -xylosidases is, for example, an Fv3A, a Pf43A, an Fv43E, an Fv43A, an Fv43B, a Pa51A, an Fv43D, a Gz43A, an Fo43A, an Fv39A, or a Trichoderma reesei Bxl 1 polypeptide.
  • each of the one or more xylanases is a Trichoderma reesei Xyn3, a Trichoderma reesei Xyn2, an AfuXyn2, or an AfuXyn5 polypeptide.
  • each of the one or more cellulases is independently an endoglucanase, for example, a Trichoderma reesei EG1 or EG2 polypeptide, a cellobiohydrolase, for example, a Trichoderma reesei CBH1 or CBH2 polypeptide, or a ⁇ -glucosidase, for example, a Trichoderma reesei Bgl1 polypeptide.
  • the xylanase(s) suitably constitutes about 0.05 wt. % to about 75 wt. % of the enzymes in an enzyme blend/composition of the disclosure (i.e., the percentage xylanase(s) is a weight percentage relative to the weight of all proteins in the composition) or a relative weight basis (i.e., wherein the percentage xylanase(s) is a weight percentage relative to the combined weight of xylanases, ⁇ -xylosidases, cellulases, L- ⁇ -arabinofuranosidases, and accessory proteins).
  • the ratio of any pair of proteins relative to each other can be readily calculated in the enzyme blends/compositions of the disclosure.
  • Blends/compositions comprising enzymes in any weight ratio derivable from the weight percentages disclosed herein are contemplated.
  • the xylanase content can be in a range wherein the lower limit is 0.05 wt. %, 1 wt. %, 2 wt. %, 3 wt. %, 4 wt. %, 5 wt. %, 6 wt. %, 7 wt. %, 8 wt. %, 9 wt. %, 10 wt. %, 12 wt. %, 15 wt. %, 20 wt. %, 25 wt. %, 30 wt. %, 40 wt.
  • the one or more xylanases in an enzyme blend or composition can represent, for example, 5 wt.
  • the L- ⁇ -arabinofuranosidase(s) suitably constitutes about 0.05 wt. % to about 75 wt. % of the total weight of all enzymes in a given enzyme blend/composition (i.e., wherein the percentage L- ⁇ -arabinofuranosidase(s) is a weight percentage relative to the weight of all proteins in the blend/composition) or a relative weight basis (i.e., wherein the percentage L- ⁇ -arabinofuranosidase(s) is a weight percentage relative to the combined weight of xylanases, ⁇ -xylosidases, cellulases, L- ⁇ -arabinofuranosidases, and accessory proteins).
  • Blends/compositions comprising enzymes in any weight ratio derivable from the weight percentages disclosed herein are contemplated.
  • the L- ⁇ -arabinofuranosidase content can be in a range wherein the lower limit is 0.05 wt. %, 1 wt. %, 2 wt. %, 3 wt. %, 4 wt. %, 5 wt. %, 6 wt. % 7 wt. %, 8 wt. %, 9 wt. %, 10 wt. %, 12 wt. %, 15 wt. %, 20 wt.
  • the upper limit is 10 wt. %, 15 wt. %, 20 wt. %, 25 wt. %, 30 wt. %, 35 wt. %, 40 wt. %, 50 wt. %, 55 wt. %, 60 wt. %, 65 wt. %, 70 wt. % or 75 wt. % of the total weight of enzymes in the blend/composition.
  • the one or more L- ⁇ -arabinofuranosidase(s) can suitably represent 2 wt. % to 25 wt. %; 5 wt. % to 20 wt. %; or 5 wt. % to 10 wt. % of the total weight of enzymes in the blend/composition.
  • Exemplary suitable L- ⁇ -arabinofuranosidase(s) for inclusion in the enzyme blends/compositions of the disclosure are described in Section 6.3.8 below.
  • the ⁇ -xylosidase(s) suitably constitutes about 0.05 wt. % to about 75 wt. % of the total weight of enzymes in an enzyme blend/composition.
  • the ratio of any pair of proteins relative to each other can be readily calculated based on the disclosure herein.
  • Blends/compositions comprising enzymes in any weight ratio derivable from the weight percentages disclosed herein are contemplated.
  • the 6-xylosidase content can be in a range wherein the lower limit is about 0.05 wt. %, 1 wt. %, 2 wt. %, 3 wt. %, 4 wt. %, 5 wt. %, 6 wt. % 7 wt.
  • wt. % 8 wt. %, 9 wt. %, 10 wt. %, 12 wt. %, 15 wt. %, 20 wt. %, 25 wt. %, 30 wt. %, 40 wt. %, 45 wt. %, or 50 wt. % of the total weight of enzymes in the blend/composition, and the upper limit is about 10 wt. %, 15 wt. %, 20 wt. %, 25 wt. %, 30 wt. %, 35 wt. %, 40 wt. %, 50 wt. %, 55 wt. %, 60 wt.
  • the ⁇ -xylosidase(s) can represent about 0.05 wt. % to about 75 wt. % of the total weight of enzymes in the blend/composition.
  • the ⁇ -xylosidase(s) can represent 0.05 wt. % to about 70 wt. %, about 1 wt. % to about 65 wt. %, about 1 wt. % to about 60 wt. %, about 2 wt. % to about 55 wt %, about 3 wt.
  • the ⁇ -xylosidase(s) suitably represent 2 wt. % to 30 wt. %; 10 wt. % to 20 wt. %; or 5 wt. % to 10 wt. % of the total weight of enzymes in the blend/composition.
  • Exemplary suitable ⁇ -xylosidase(s) are described in Section 6.3.7 below.
  • the cellulase(s) suitably constitutes about 0.05 wt. % to about 90 wt. % of the total weight of enzymes in an enzyme blend/composition. Ratio of any pair of proteins relative to each other can be readily calculated based on the disclosure herein. Blends/compositions comprising enzymes in any weight ratio derivable from the weight percentages disclosed herein are contemplated.
  • the cellulase content can be in a range wherein the lower limit is about 0.05 wt. %, 5 wt. %, 10 wt. %, 20 wt. %, 30 wt. %, 40 wt. %, 50 wt. %, 60 wt. %, 70 wt.
  • the cellulase(s) suitably represents 30 wt. % to 80 wt. %, 50 wt. % to 70 wt. %, or 40 wt. % to 60 wt. % of the total weight of enzymes in the blend/composition.
  • Exemplary suitable cellulases are described in Section 6.3.5 below.
  • the cellulase components in an enzyme blend/composition of the disclosure are suitably capable of achieving at least about 0.005 fraction product per mg protein per gram of phosphoric acid swollen cellulose (PASC) as determined by a calcofluor assay.
  • PASC phosphoric acid swollen cellulose
  • the cellulase components in a blend/composition of the disclosure are capable of achieving a range of fraction product per mg protein per gram of PASC, wherein the lower limit of the range is about 0.005, 0.01, 0.015, 0.02, 0.03, 0.04, 0.05, 0.06, 0.075, or 0.1, and wherein the upper limit of the range is, 0.03, 0.04, 0.05, 0.06, 0.075, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, or 0.7.
  • the cellulase components in a blend/composition of the disclosure can, for example, achieve 0.00005-0.0001, 0.0005-0.001, 0.001-0.005, 0.005-0.03, 0.01-0.06, 0.02-0.04, 0.01-0.03, 0.02-0.05, 0.02-0.04, 0.01-0.05, 0.015-0.035, or 0.015-0.075 product fraction product per mg protein per gram PASC as determined by a calcofluor assay.
  • the cellulase can be, for example, a whole cellulase.
  • the cellulase can also, for example, suitably be enriched with a ⁇ -glucosidase.
  • the enzyme blend/composition may suitably further comprise one or more accessory proteins.
  • the accessory protein content of an enzyme blend/composition can range from about 0 wt. % to about 60 wt. % of the total weight of proteins in an enzyme blend/composition. Ratio of any pair of proteins relative to each other can be readily determined based on the disclosure herein. Blends/compositions comprising enzymes in any weight ratio derivable from the weight percentages disclosed herein are contemplated.
  • the accessory protein content can be in a range wherein the lower limit is 0 wt. %, 1 wt. %, 2 wt. %, 3 wt. %, 4 wt. %, 5 wt. %, 6 wt.
  • the accessory protein(s) can suitably represent 0 wt. % to 2 wt. %, 5 wt. % to 10 wt. %, 20 wt. % to 50 wt. %, or 2 wt. % to 5 wt. % in the enzyme blend/composition.
  • Exemplary suitable accessory proteins for inclusion in the enzyme blends/compositions of the disclosure are described in Section 6.3.9 below.
  • the present disclosure provides a first enzyme blend/composition for lignocellulose saccharification comprising:
  • the present disclosure provides a second enzyme blend/composition for lignocellulose saccharification comprising:
  • the present disclosure provides a third enzyme blend/composition for lignocellulose saccharification comprising:
  • the present disclosure provides a fourth enzyme blend/composition for lignocellulose saccharification comprising:
  • the present disclosure provides a fifth enzyme blend/composition for lignocellulose saccharification comprising:
  • the present disclosure provides a sixth enzyme blend/composition for lignocellulose saccharification comprising:
  • the sixth enzyme blend/composition for lignocellulose saccharification above can, for example, comprise about 2 wt. % to about 40 wt. % of at least two ⁇ -xylosidase, wherein at least one ⁇ -xylosidase is selected from Group 1 and at least one ⁇ -xylosidase is selected from Group 2; wherein:
  • the ratio of Group 1 to Group 2 ⁇ -xylosidases is preferably 1:10 to 10:1.
  • the ratio is suitably 1:2 to 2:1, 2:5 to 5:2, 3:8 to 8:3, 1:4 to 4:1, 1:5 to 5:1, 1:7 to 7:1, or any range between any pair the foregoing endpoints (e.g., 1:10 to 2:1, 4:1 to 2:5, 3:8 to 5:1, etc.).
  • a particular example of a suitable ratio is approximately 1:1.
  • an enzyme blend/composition of the disclosure contains an Fv43A as a ⁇ -xylosidase
  • the blend/composition can further contain Fv43B as an L- ⁇ -arabinofuranosidase.
  • An enzyme blend/composition of the disclosure is, for example, suitably part of a saccharification reaction mixture containing biomass in addition to the components of the enzyme blend/composition.
  • the saccharification reaction mixture can be characterized by 1, 2, 3 or all 4 of the following features:
  • the enzyme blends/compositions of the disclosure can comprise one or more cellulases.
  • Cellulases are enzymes that hydrolyze cellulose ( ⁇ -1,4-glucan or ⁇ D-glucosidic linkages) resulting in the formation of glucose, cellobiose, cellooligosaccharides, and the like.
  • Endoglucanases EC 3.2.1.4
  • CBH cellobiohydrolases
  • BG ⁇ -glucosidases
  • Cellulases for use in accordance with the methods and compositions of the disclosure can be obtained from, or produced recombinantly from, inter alia, one or more of the following organisms: Crinipellis scapella, Macrophomina phaseolina, Myceliophthora thermophila, Sordaria fimicola, Volutella colletotrichoides, Thielavia terrestris, Acremonium sp., Exidia glandulosa, Fomes fomentarius, Spongipeffis sp., Rhizophlyctis rosea, Rhizomucor pusillus, Phycomyces niteus, Chaetostylum fresenii, Diplodia gossypina, Ulospora bilgramii, Saccobolus dilutellus, Penicillium verruculosum, Penicillium chrysogenum, Thermomyces verrucosus, Diaporthe syngenesia, Colleto
  • a cellulase for use in the method and/or composition of the disclosure is a whole cellulase and/or is capable of achieving at least 0.1 (e.g. 0.1 to 0.4) fraction product as determined by the calcofluor assay described in Section 7.1.10 below.
  • the enzyme blends/compositions of the disclosure can optionally comprise one or more ⁇ -glucosidases.
  • ⁇ -glucosidase refers to a ⁇ -D-glucoside glucohydrolase classified as EC 3.2.1.21, and/or members of certain GH families, including, without limitation, members of GH families 1, 3, 9 or 48, which catalyze the hydrolysis of cellobiose to release ⁇ -D-glucose.
  • Suitable ⁇ -glucosidase can be obtained from a number of microorganisms, by recombinant means, or be purchased from commercial sources.
  • ⁇ -glucosidases from microorganisms include, without limitation, ones from bacteria and fungi.
  • a ⁇ -glucosidase of the present disclosure is suitably obtained from a filamentous fungus.
  • the ⁇ -glucosidases can be obtained, or produced recombinantly, from, inter alia, Aspergillus aculeatus (Kawaguchi et al. Gene 1996, 173: 287-288), Aspergillus kawachi (Iwashita et al. Appl. Environ. Microbiol. 1999, 65: 5546-5553), Aspergillus oryzae (WO 2002/095014), Cellulomonas biazotea (Wong et al. Gene, 1998, 207:79-86), Penicillium funiculosum (WO 2004/078919), Saccharomycopsis fibuligera (Machida et al. Appl. Environ.
  • Trichoderma reesei e.g., ⁇ -glucosidase 1 (U.S. Pat. No. 6,022,725), ⁇ -glucosidase 3 (U.S. Pat. No. 6,982,159), ⁇ -glucosidase 4 (U.S. Pat. No. 7,045,332), ⁇ -glucosidase 5 (U.S. Pat. No. 7,005,289), ⁇ -glucosidase 6 (U.S. Publication No. 20060258554), ⁇ -glucosidase 7 (U.S. Publication No. 20060258554)).
  • ⁇ -glucosidase 1 U.S. Pat. No. 6,022,725
  • ⁇ -glucosidase 3 U.S. Pat. No. 6,982,159
  • ⁇ -glucosidase 4 U.S. Pat. No. 7,045,332
  • ⁇ -glucosidase 5 U.
  • the ⁇ -glucosidase can be produced by expressing an endogenous or exogenous gene encoding a ⁇ -glucosidase.
  • ⁇ -glucosidase can be secreted into the extracellular space e.g., by Gram-positive organisms (e.g., Bacillus or Actinomycetes ), or eukaryotic hosts (e.g., Trichoderma, Aspergillus, Saccharomyces , or Pichia ).
  • the ⁇ -glucosidase can be, in some circumstances, overexpressed or underexpressed.
  • the ⁇ -glucosidase can also be obtained from commercial sources.
  • commercial ⁇ -glucosidase preparation suitable for use in the present disclosure include, for example, Trichoderma reesei ⁇ -glucosidase in Accellerase® BG (Danisco US Inc., Genencor); NOVOZYMTM 188 (a ⁇ -glucosidase from Aspergillus niger ); Agrobacterium sp. ⁇ -glucosidase, and Thermatoga maritima ⁇ -glucosidase from Megazyme (Megazyme International Ireland Ltd., Ireland.).
  • the ⁇ -glucosidase can be a component of a whole cellulase, as described in Section 6.3.5.4 below.
  • ⁇ -glucosidase activity can be determined by a number of suitable means known in the art, such as the assay described by Chen et al., in Biochimica et Biophysica Acta 1992, 121:54-60, wherein 1 pNPG denotes 1 ⁇ mol. of Nitrophenol liberated from 4-nitrophenyl- ⁇ -D-glucopyranoside in 10 min at 50° C. (122° F.) and pH 4.8.
  • the enzyme blends/compositions of the disclosure optionally comprise one or more endoglucanase.
  • Any endoglucanase (EC 3.2.1.4) can be used in the methods and compositions of the present disclosure.
  • An endoglucanse can be produced by expressing an endogenous or exogenous endoglucanase gene. The endoglucanase can be, in some circumstances, overexpressed or underexpressed.
  • Trichoderma reesei EG1 (Penttila et al., Gene 1986, 63:103-112) and/or EG2 (Saloheimo et al., Gene 1988, 63:11-21) are suitably used in the methods and compositions of the present disclosure.
  • thermostable Thielavia terrestris endoglucanase (Kvesitadaze et al., Applied Biochem. Biotech. 1995, 50:137-143) is, in another example, used in the methods and compositions of the present disclosure.
  • a Trichoderma reesei EG3 (Okada et al. Appl. Environ. Microbiol. 1988, 64:555-563), EG4 (Saloheimo et al. Eur. J. Biochem. 1997, 249:584-591), EG5 (Saloheimo et al. Molecular Microbiology 1994, 13:219-228), EG6 (U.S. Patent Publication No.
  • CBH cellobiohydrolase
  • the cellobiohydrolase can be produced by expressing an endogeneous or exogeneous cellobiohydrolase gene.
  • the cellobiohydrolase can be, in some circumstances, overexpressed or under expressed.
  • Trichoderma reesei CBHI (Shoemaker et al. Bio/Technology 1983, 1:691-696) and/or GBHII (Teeri et al. Bio/Technology 1983, 1:696-699) can be suitably used in the methods and blends/compositions of the present disclosure.
  • Suitable CBHs can be selected from an Agaricus bisporus CBH1 (Swiss Prot Accession No. Q92400), an Aspergillus aculeatus CBH1 (Swiss Prot Accession No. O59843), an Aspergillus nidulans CBHA (GenBank Accession No. AF420019) or CBHB (GenBank Accession No. AF420020), an Aspergillus niger CBHA (GenBank Accession No. AF156268) or CBHB (GenBank Accession No. AF156269), a Claviceps purpurea CBH1 (Swiss Prot Accession No.
  • An enzyme blend/composition of the disclosure can further comprise a whole cellulase.
  • a “whole cellulase” refers to either a naturally occurring or a non-naturally occurring cellulase-containing composition comprising at least 3 different enzyme types: (1) an endoglucanase, (2) a cellobiohydrolase, and (3) a ⁇ -glucosidase, or comprising at least 3 different enzymatic activities: (1) an endoglucanase activity, which catalyzes the cleavage of internal ⁇ -1,4 linkages, resulting in shorter glucooligosaccharides, (2) a cellobiohydrolase activity, which catalyzes an “exo”-type release of cellobiose units ⁇ -1,4 glucose-glucose disaccharide), and (3) a ⁇ -glucosidase activity, which catalyzes the release of glucose monomer from short cellooligosaccharides (e.g., cell
  • a “naturally occurring cellulase-containing” composition is one produced by a naturally occurring source, which comprises one or more cellobiohydrolase-type, one or more endoglucanase-type, and one or more ⁇ -glucosidase-type components or activities, wherein each of these components or activities is found at the ratio and level produced in nature, untouched by the human hand.
  • a naturally occurring cellulase-containing composition is, for example, one that is produced by an organism unmodified with respect to the cellulolytic enzymes such that the ratio or levels of the component enzymes are unaltered from that produced by the native organism in nature.
  • non-naturally occurring cellulase-containing composition refers to a composition produced by: (1) combining component cellulolytic enzymes either in a naturally occurring ratio or a non-naturally occurring, i.e., altered, ratio; or (2) modifying an organism to overexpress or underexpress one or more cellulolytic enzymes; or (3) modifying an organism such that at least one cellulolytic enzyme is deleted.
  • a “non-naturally occurring cellulase containing” composition can also refer to a composition resulting from adjusting the culture conditions for a naturally-occurring organism, such that the naturally-occurring organism grows under a non-native condition, and produces an altered level or ratio of enzymes. Accordingly, in some embodiments, the whole cellulase preparation of the present disclosure can have one or more EGs and/or CBHs and/or ⁇ -glucosidases deleted and/or overexpressed.
  • a whole cellulase preparation can be from any microorganism that is capable of hydrolyzing a cellulosic material.
  • the whole cellulase preparation is a filamentous fungal whole cellulase.
  • the whole cellulase preparation can be from an Acremonium, Aspergillus, Emericella, Fusarium, Humicola, Mucor, Myceliophthora, Neurospora, Penicillium, Scytalidium, Thielavia, Tolypocladium , or Trichoderma species.
  • the whole cellulase preparation is, for example, an Aspergillus aculeatus, Aspergillus awamori, Aspergillus foetidus, Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger , or Aspergillus oryzae whole cellulase.
  • the whole cellulase preparation can be a Fusarium bactridioides, Fusarium cerealis, Fusarium crookwellense, Fusarium culmorum, Fusarium graminearum, Fusarium graminum, Fusarium heterosporum, Fusarium negundi, Fusarium oxysporum, Fusarium reticulatum, Fusarium roseum, Fusarium sambucinum, Fusarium sarcochroum, Fusarium sporotrichioides, Fusarium sulphureum, Fusarium torulosum, Fusarium trichothecioides , or Fusarium venenatum whole cellulase preparation.
  • Fusarium bactridioides Fusarium cerealis, Fusarium crookwellense, Fusarium culmorum, Fusarium graminearum, Fusarium graminum, Fusa
  • the whole cellulase preparation can also be a Humicola insolens, Humicola lanuginosa, Mucor miehei, Myceliophthora thermophila, Neurospora crassa, Penicillium purpurogenum, Penicillium funiculosum, Scytalidium thermophilum , or Thielavia terrestris whole cellulase preparation.
  • the whole cellulase preparation can be a Trichoderma harzianum, Trichoderma koningii, Trichoderma longibrachiatum, Trichoderma reesei (e.g., RL-P37 (Sheir-Neiss G et al. Appl. Microbiol.
  • Trichoderma viride e.g., ATCC 32098 and 32086 whole cellulase preparation.
  • the whole cellulase preparation can, in particular, suitably be a Trichoderma reesei RutC30 whole cellulase preparation, which is available from the American Type Culture Collection as Trichoderma reesei ATCC 56765.
  • the whole cellulase preparation can also suitably be a whole cellulase of Penicillium funiculosum , which is available from the American Type Culture Collection as Penicillium funiculosum ATCC Number: 10446.
  • the whole cellulase preparation can also be obtained from commercial sources.
  • commercial cellulase preparations suitable for use in the methods and compositions of the present disclosure include, for example, CELLUCLASTTM and CellicTM (Novozymes A/S) and LAMINEXTM BG, IndiAgeTM 44L, PrimafastTM 100, PrimafastTM 200, SpezymeTM CP, Accellerase® 1000 and Accellerase® 1500 (Danisco US. Inc., Genencor).
  • Suitable whole cellulase preparations can be made using any microorganism cultivation methods known in the art, especially fermentation, resulting in the expression of enzymes capable of hydrolyzing a cellulosic material.
  • “fermentation” refers to shake flask cultivation, small- or large-scale fermentation, such as continuous, batch, fed-batch, or solid state fermentations in laboratory or industrial fermenters performed in a suitable medium and under conditions that allow the cellulase and/or enzymes of interest to be expressed and/or isolated.
  • the microorganism is cultivated in a cell culture medium suitable for production of enzymes capable of hydrolyzing a cellulosic material.
  • the cultivation takes place in a suitable nutrient medium comprising carbon and nitrogen sources and inorganic salts, using procedures and variations known in the art.
  • suitable culture media, temperature ranges and other conditions for growth and cellulase production are known in the art.
  • a typical temperature range for the production of cellulases by Trichoderma reesei is 24° C. to 28° C.
  • the whole cellulase preparation can be used as it is produced by fermentation with no or minimal recovery and/or purification.
  • the cell culture medium containing the cellulases can be used directly.
  • the whole cellulase preparation can comprise the unfractionated contents of fermentation material, including the spent cell culture medium, extracellular enzymes and cells.
  • the whole cellulase preparation can also be subject to further processing in a number of routine steps, e.g., precipitation, centrifugation, affinity chromatography, filtration, or the like.
  • the whole cellulase preparation can be concentrated, and then used without further purification.
  • the whole cellulase preparation can, for example, be formulated to comprise certain chemical agents that decrease cell viability or kills the cells after fermentation.
  • the cells can, for example, be lysed or permeabilized using methods known in the art.
  • the endoglucanase activity of the whole cellulase preparation can be determined using carboxymethyl cellulose (CMC) as a substrate.
  • CMC carboxymethyl cellulose
  • a suitable assay measures the production of reducing ends created by the enzyme mixture acting on CMC wherein 1 unit is the amount of enzyme that liberates 1 ⁇ mol. of product/min (Ghose, T. K., Pure & Appl. Chem. 1987, 59, pp. 257-268).
  • the whole cellulase can be a ⁇ -glucosidase-enriched cellulase.
  • the ⁇ -glucosidase-enriched whole cellulase generally comprises a ⁇ -glucosidase and a whole cellulase preparation.
  • the ⁇ -glucosidase-enriched whole cellulase compositions can be produced by recombinant means.
  • such a whole cellulase preparation can be achieved by expressing a ⁇ -glucosidase in a microorganism capable of producing a whole cellulase
  • the ⁇ -glucosidase-enriched whole cellulase composition can also, for example, comprise a whole cellulase preparation and a ⁇ -glucosidase.
  • the ⁇ -glucosidase-enriched whole cellulase composition can suitably comprise at least 5 wt. %, 7 wt. %, 10 wt. %, 15 wt. % or 20 wt. %, and up to 25 wt. %, 30 wt. %, 35 wt. %, 40 wt. %, or 50 wt. % ⁇ -glucosidase based on the total weight of proteins in that blend/composition.
  • the enzyme blends/compositions of the disclosure can, comprise one or more Group A xylanases, which may be a Trichoderma reesei Xyn2, a Trichoderma reesei Xyn3, an AfuXyn2, or an AfuXyn5.
  • Group A xylanases which may be a Trichoderma reesei Xyn2, a Trichoderma reesei Xyn3, an AfuXyn2, or an AfuXyn5.
  • Suitable Trichoderma reesei Xyn2, Trichoderma reesei Xyn3, AfuXyn2, or AfuXyn5 polypeptides are described in Section 6.1 above.
  • the enzyme blends/compositions of the disclosure optionally comprise one or more xylanases in addition to or in place of the one or more Group A xylanases.
  • Any xylanase (EC 3.2.1.8) can be used as the additional one or more xylanases.
  • Suitable xylanases include, e.g., a Caldocellum saccharolyticum xylanase (Luthi et al. 1990, Appl. Environ. Microbiol. 56(9):2677-2683), a Thermatoga maritima xylanase (Winterhalter & Liebel, 1995, Appl. Environ. Microbiol.
  • the xylanase can be produced by expressing an endogenous or exogenous gene encoding a xylanase.
  • the xylanase can be, in some circumstances, overexpressed or underexpressed.
  • the enzyme blends/compositions of the disclosure can suitablycomprise one or more ⁇ -xylosidases.
  • the ⁇ -xylosidase is a Group 1 ⁇ -xylosidase enzyme (e.g., an Fv3A or an Fv43A) or a Group 2 ⁇ -xylosidase enzyme (e.g., a Pf43A, an Fv43D, an Fv39A, an Fv43E, an Fo43A, an Fv43B, a Pa51A, a Gz43A, or a Trichoderma reesei Bxl1).
  • an enzyme blend/composition of the disclosure can suitably comprise one or more Group 1 ⁇ -xylosidases and one or more Group 2 ⁇ -xylosidases.
  • the enzyme blends/compositions of the disclosure can optionally comprise one or more ⁇ -xylosidases, in addition to or in place of the Group 1 and/or Group 2 ⁇ -xylosidases above.
  • Any ⁇ -xylosidase (EC 3.2.1.37) can be used as the additional ⁇ -xylosidases.
  • Suitable ⁇ -xylosidases include, for example, a Talaromyces emersonii Bxl1 (Reen et al. 2003, Biochem Biophys Res Commun. 305(3):579-85), a Geobacillus stearothermophilus ⁇ -xylosidases (Shallom et al.
  • the ⁇ -xylosidase can be produced by expressing an endogenous or exogenous gene encoding a ⁇ -xylosidase.
  • the ⁇ -xylosidase can be, in some circumstances, overexpressed or underexpressed.
  • the enzyme blends/compositions of the disclosure can, for example, suitably comprise one or more L- ⁇ -arabinofuranosidases.
  • the L- ⁇ -arabinofuranosidase is, for example, an Af43A, an Fv43B, a Pf51A, a Pa51A, or an Fv51A.
  • Af43A, Fv43B, Pf51A, Pa51A, and Fv51A polypeptides are described in Section 6.1 above.
  • the enzyme blends/compositions of the disclosure optionally comprise one or more L- ⁇ -arabinofuranosidases in addition to or in place of the foregoing L- ⁇ -arabinofuranosidases.
  • L- ⁇ -arabinofuranosidases (EC 3.2.1.55) from any suitable organism can be used as the additional L- ⁇ -arabinofuranosidases.
  • Suitable L- ⁇ -arabinofuranosidases include, e.g., an L- ⁇ -arabinofuranosidases of Aspergillus oryzae (Numan & Bhosle, J. Ind. Microbiol. Biotechnol.
  • the L- ⁇ -arabinofuranosidase can be produced by expressing an endogenous or exogenous gene encoding an L- ⁇ -arabinofuranosidase.
  • the L- ⁇ -arabinofuranosidase can be, in some circumstances, overexpressed or underexpressed.
  • the enzyme blends/compositions of the disclosure can, for example, suitably further comprise one or more accessory proteins.
  • accessory proteins include, without limitation, mannanases (e.g., endomannanases, exomannanases, and ⁇ -mannosidases), galactanases (e.g., endo- and exo-galactanases), arabinases (e.g., endo-arabinases and exo-arabinases), ligninases, amylases, glucuronidases, proteases, esterases (e.g., ferulic acid esterases, acetyl xylan esterases, coumaric acid esterases or pectin methyl esterases), lipases, glycoside hydrolase Family 61 polypeptides, xyloglucanases, CIP1, CIP2, swollenin, expansins, and cellulose disrupting proteins.
  • accessory proteins can also include CIP1-
  • the enzymes and/or enzyme blends/compositions of the disclosure can be used in industrial, agricultural, food and feed, as well as food and feed supplement processing processes. Exemplary applications are described below.
  • the enzymes, enzyme blends/compositions, and methods of the disclosure can be used in wood, wood product, wood waste or by-product, paper, paper product, paper or wood pulp, Kraft pulp, or wood or paper recycling treatment or industrial process. These processes include, e.g., treatments of wood, wood pulp, paper waste, paper, or pulp, or deinking of wood or paper.
  • the enzymes, enzyme blends/compositions of the disclosure can be, for example, used to treat/pretreat paper pulp, or recycled paper or paper pulp, and the like.
  • the enzymes, enzyme blends/compositions of the disclosure can be used to increase the “brightness” of the paper when they are included in the paper, pulp, recycled paper or paper pulp treatment/pretreatment.
  • the enzymes, enzyme blends/compositions, and methods/processes can be used to make high grade, “bright” papers, including inkjet, laser and photo printing quality paper.
  • the enzymes, enzyme blends/compositions of the disclosure can be used to process or treat a number of other cellulosic material, including, e.g., fibers from wood, cotton, hemp, flax or linen.
  • the disclosure provides wood, wood pulp, paper, paper pulp, paper waste or wood or paper recycling treatment processes using an enzyme, enzyme blend/composition of the disclosure.
  • the enzymes, enzyme blends/compositions of the disclosure can be used for deinking printed wastepaper, such as newspaper, or for deinking noncontact-printed wastepaper, e.g., xerographic and laser-printed paper, and mixtures of contact and noncontact-printed wastepaper, as described in U.S. Pat. No. 6,767,728 or 6,426,200; Neo, J. Wood Chem. Tech. 1986, 6(2):147. They can also be used to produce xylose from a paper-grade hardwood pulp in a process involving extracting xylan contained in pulp into a liquid phase, subjecting the xylan contained in the obtained liquid phase to conditions sufficient to hydrolyze xylan to xylose, and recovering the xylose.
  • the extracting step can include at least one treatment of an aqueous suspension of pulp or an alkali-soluble material by an enzyme or an enzyme blend/composition (see, U.S. Pat. No. 6,512,110).
  • the enzymes, enzyme blends/compositions of the disclosure can be used to dissolve pulp from cellulosic fibers such as recycled paper products made from hardwood fiber, a mixture of hardwood fiber and softwood fiber, waste paper, e.g., from unprinted envelopes, de-inked envelopes, unprinted ledger paper, de-inked ledger paper, and the like, as described in, e.g., U.S. Pat. No. 6,254,722.
  • the disclosure provides methods of treating fibers and fabrics using one or more enzymes, enzyme blends/compositions of the disclosure.
  • the enzymes, enzyme blends/compositions can be used in any fiber- or fabric-treating method, which are known in the art. See, e.g., U.S. Pat. Nos. 6,261,828; 6,077,316; 6,024,766; 6,021,536; 6,017,751; 5,980,581; U.S. Patent Publication No. 20020142438 A1.
  • enzymes, enzyme blends/compositions of the disclosure can be used in fiber and/or fabric desizing.
  • the feel and appearance of a fabric can be, for example, improved by a method comprising contacting the fabric with an enzyme or enzyme blend/composition of the disclosure in a solution.
  • the fabric is treated with the solution under pressure.
  • the enzymes, enzyme blends/composition of the disclosure can also be used to remove stains.
  • the enzymes, enzyme blends/compositions of the disclosure can be used to treat a number of other cellulosic material, including fibers (e.g., fibers from cotton, hemp, flax or linen), sewn and unsewn fabrics, e.g., knits, wovens, denims, yarns, and toweling, made from cotton, cotton blends or natural or manmade cellulosics or blends thereof.
  • the textile treating processes can be used in conjunction with other textile treatments, e.g., scouring and/or bleaching.
  • Scouring is the removal of non-cellulosic material from the cotton fiber, e.g., the cuticle (mainly consisting of waxes) and primary cell wall (mainly consisting of pectin, protein and xyloglucan).
  • the cuticle mainly consisting of waxes
  • primary cell wall mainly consisting of pectin, protein and xyloglucan
  • the enzymes, enzyme blends/compositions of the disclosure have numerous applications in food processing industry. They can, for example, be used to improve extraction of oil from oil-rich plant material, e.g., oil-rich seeds.
  • the enzymes, enzyme blends/compositions of the disclosure can be used to extract soybean oil from soybeans, olive oil from olives, rapeseed oil from rapeseed, or sunflower oil from sunflower seeds.
  • the enzymes, enzyme blends/compositions of the disclosure can also be used to separate components of plant cell materials. For example, they can be used to separate plant cells into components.
  • the enzymes, enzyme blends/compositions of the disclosure can also be used to separate crops into protein, oil, and hull fractions. The separation process can be performed using known methods.
  • the enzymes, enzyme blends/compositions of the disclosure can, in addition to the uses above, be used to increase yield in the preparation of fruit or vegetable juices, syrups, extracts and the like. They can also be used in the enzymatic treatment of various plant cell wall-derived materials or waste materials from, e.g., cereals, grains, wine or juice production, or agricultural residues such as, e.g., vegetable hulls, bean hulls, sugar beet pulp, olive pulp, potato pulp, and the like. Further, they can be used to modify the consistency and/or appearance of processed fruits or vegetables. Additionally, they can be used to treat plant material so as to facilitate processing of the plant material (including foods), purification or extraction of plant components.
  • the enzymes, enzyme blends/compositions of the disclosure can be used to improve feed value, decrease the water binding capacity, improve the degradability in waste water plants and/or improve the conversion of plant material to ensilage, and the like.
  • the enzymes, enzyme blends/compositions of the disclosure can also be used in baking applications. In some embodiments, they are used to create non-sticky doughs that are not difficult to machines and to reduce biscuit sizes. They can also be used to hydrolyze arabinoxylans to prevent rapid rehydration of the baked product that can lead to loss of crispiness and reduced shelf-life. For example, they are used as additives in dough processing.
  • the disclosure provides methods for treating animal feeds and foods and food or feed additives (supplements) using enzymes, enzyme blends/compositions of the disclosure.
  • Animals including mammals (e.g., humans), birds, fish, and the like.
  • the disclosure provides animal feeds, foods, and additives (supplements) comprising enzymes, enzyme blends/compositions of the disclosure.
  • Treating animal feeds, foods and additives using enzymes of the disclosure can help in the availability of nutrients, e.g., starch, protein, and the like, in the animal feed or additive (supplements).
  • the enzymes, enzyme blends/compositions can make nutrients more accessible to other endogenous or exogenous enzymes. They can also simply cause the release of readily digestible and easily absorbed nutrients and sugars.
  • enzymes, enzyme blends/compositions of the disclosure improve the in vivo break-down of plant cell wall material partly by reducing the intestinal viscosity (see, e.g., Bedford et al., Proceedings of the 1st Symposium on Enzymes in Animal Nutrition, 1993, pp. 73-77), whereby a better utilization of the plant nutrients by the animal is achieved.
  • the growth rate and/or feed conversion ratio i.e., the weight of ingested feed relative to weight gain
  • the animal feed additive of the disclosure may be a granulated enzyme product which can be readily mixed with feed components.
  • feed additives of the disclosure can form a component of a pre-mix.
  • the granulated enzyme product of the disclosure may be coated or uncoated.
  • the particle size of the enzyme granulates can be compatible with that of the feed and/or the pre-mix components. This provides a safe and convenient mean of incorporating enzymes into feeds.
  • the animal feed additive of the disclosure can be a stabilized liquid composition. This may be an aqueous- or oil-based slurry. See, e.g., U.S. Pat. No. 6,245,546.
  • An enzyme, enzyme blend/composition of the disclosure can be supplied by expressing the enzymes directly in transgenic feed crops (e.g., as transgenic plants, seeds and the like), such as grains, cereals, corn, soy bean, rape seed, lupin and the like.
  • transgenic feed crops e.g., as transgenic plants, seeds and the like
  • the disclosure provides transgenic plants, plant parts and plant cells comprising a nucleic acid sequence encoding a polypeptide of the disclosure.
  • the nucleic acid is expressed such that the enzyme of the disclosure is produced in recoverable quantities.
  • the xylanase can be recovered from any plant or plant part.
  • the plant or plant part containing the recombinant polypeptide can be used as such for improving the quality of a food or feed, e.g., improving nutritional value, palatability, and rheological properties, or to destroy an antinutritive factor.
  • the disclosure provides methods for removing oligosaccharides from feed prior to consumption by an animal subject using an enzyme, enzyme blend/composition of the disclosure. In this process a feed is formed to have an increased metabolizable energy value.
  • enzymes enzyme blends/compositions of the disclosure, galactosidases, cellulases, and combinations thereof can be used.
  • the disclosure provides methods for utilizing an enzyme, an enzyme blend/composition of the disclosure as a nutritional supplement in the diets of animals by preparing a nutritional supplement containing a recombinant enzyme of the disclosure, and administering the nutritional supplement to an animal to increase the utilization of hemicellulase contained in food ingested by the animal.
  • the disclosure provides a solid waste digestion process using the enzymes, enzyme blends/compositions of the disclosure.
  • the methods can comprise reducing the mass and volume of substantially untreated solid waste.
  • Solid waste can be treated with an enzymatic digestive process in the presence of an enzymatic solution (including the enzymes, enzyme blends/compositions of the disclosure) at a controlled temperature. This results in a reaction without appreciable bacterial fermentation from added microorganisms.
  • the solid waste is converted into a liquefied waste and any residual solid waste.
  • the resulting liquefied waste can be separated from said any residual solidified waste. See, e.g., U.S. Pat. No. 5,709,796.
  • the disclosure provides detergent, disinfectant or cleanser (cleaning or cleansing) compositions comprising one or more enzymes, enzyme blends/compositions of the disclosure, and methods of making and using these compositions.
  • the disclosure incorporates all known methods of making and using detergent, disinfectant or cleanser compositions. See, e.g., U.S. Pat. Nos. 6,413,928; 6,399,561; 6,365,561; 6,380,147.
  • the detergent, disinfectant or cleanser compositions can be a one- and two-part aqueous composition, a non-aqueous liquid composition, a cast solid, a granular form, a particulate form, a compressed tablet, a gel and/or a paste and a slurry form.
  • the enzymes, enzyme blends/compositions of the disclosure can also be used as a detergent, disinfectant, or cleanser additive product in a solid or a liquid form. Such additive products are intended to supplement or boost the performance of conventional detergent compositions, and can be added at any stage of the cleaning process.
  • the present disclosure provides cleaning compositions including detergent compositions for cleaning hard surfaces, detergent compositions for cleaning fabrics, dishwashing compositions, oral cleaning compositions, denture cleaning compositions, and contact lens cleaning solutions.
  • the compositions can comprise, in addition to an enzyme, enzyme blend/composition of the disclosure, both a surfactant and a builder compound. They can additionally comprise one or more detergent components, e.g., organic polymeric compounds, bleaching agents, additional enzymes, suds suppressors, dispersants, lime-soap dispersants, soil suspension and anti-redeposition agents, and corrosion inhibitors.
  • detergent components e.g., organic polymeric compounds, bleaching agents, additional enzymes, suds suppressors, dispersants, lime-soap dispersants, soil suspension and anti-redeposition agents, and corrosion inhibitors.
  • Laundry compositions of the disclosure can also contain softening agents, as additional detergent components.
  • Such compositions containing carbohydrase can provide fabric cleaning, stain removal, whiteness maintenance, softening, color appearance, dye transfer inhibition and sanitization when formulated as laundry detergent compositions.
  • the disclosure thus further provides a process of saccharification a biomass material comprising hemicellulose.
  • a biomass material can optionally comprise cellulose.
  • Exemplary biomass materials include, without limitation, corcob, switchgrass, sorghum, and/or bagasse. Accordingly the disclosure provides a process of saccharification, comprising treating a biomass material herein comprising hemicelluose and optionally cellose with an enzyme blend/composition as described herein.
  • the enzyme blend/compositon used in such a process of the invention include 0.5 g to 40 g (e.g., 0.5 g to 20 g, 0.5 g to 30 g, 0.5 g to 40 g, 0.5 g to 15 g, 0.5 g to 10 g, 0.5 g to 5 g, 0.5 g to 7 g, etc) of polypeptides having xylanase activity per kg of hemicellulose in the biomass material.
  • 0.5 g to 40 g e.g., 0.5 g to 20 g, 0.5 g to 30 g, 0.5 g to 40 g, 0.5 g to 15 g, 0.5 g to 10 g, 0.5 g to 5 g, 0.5 g to 7 g, etc
  • the enzyme blend/composition used in such a process of the invention can also include 1 g to 40 g (e.g., 2 g to 20 g, 3 g to 7 g, 1 g to 5 g, or 2 g to 5 g, etc.) of polypeptides having xylanase activity per kg of hemicellulose in the biomass material.
  • 1 g to 40 g e.g., 2 g to 20 g, 3 g to 7 g, 1 g to 5 g, or 2 g to 5 g, etc.
  • the enzyme blend/composition used in such a process can include 0.5 g to 50 g (e.g., 0.5 g to 50 g, 0.5 g to 45 g, 0.5 g to 40 g, 0.5 g to 30 g, 0.5 g to 25 g, 0.5 g to 20 g, 0.5 g to 15 g, 0.5 g to 10 g, etc) of polypeptides having ⁇ -xylosidase activity per kg of hemicellulose in the biomass material.
  • 0.5 g to 50 g e.g., 0.5 g to 50 g, 0.5 g to 45 g, 0.5 g to 40 g, 0.5 g to 30 g, 0.5 g to 25 g, 0.5 g to 20 g, 0.5 g to 15 g, 0.5 g to 10 g, etc
  • the enzyme blend/composition used in such a process can also include 1 g to 50 g (e.g., 2 g to 40 g, 4 g to 20 g, 4 g to 10 g, 2 g to 10 g, 3 g to 7 g, etc.) of polypeptide having ⁇ -xylosidase activity per kg of hemicellulose in the biomass material.
  • 1 g to 50 g e.g., 2 g to 40 g, 4 g to 20 g, 4 g to 10 g, 2 g to 10 g, 3 g to 7 g, etc.
  • the enzyme blend/compositon used in such a process of the invention can include 0.2 g to 20 g (e.g., 0.2 g to 18 g, 0.2 g to 15 g, 0.3 g to 10 g, 0.2 g to 8 g, 0.2 g to 5 g, etc) of polypeptides having L- ⁇ -arabinofuranosidase activity per kg of hemicellolose in the biomass material.
  • the enzyme blend/composition used in such a process of the invention can include 0.5 g to 20 g (e.g., 1 g to 10 g, 1 g to 5 g, 2 g to 6 g, 0.5 g to 4 g, or 1 g to 3 g, etc) of polypeptides having L- ⁇ -arabinofuranosidase activity per kg of hemicellolose in the biomass material.
  • the enzyme blend/composition can also include 1 g to 100 g (e.g., 1 g to 100 g, 2 g to 80 g, 3 g to 50 g, 5 g to 40 g, 2 g to 20 g, 10 g to 30 g, or 12 g to 18 g, etc) of polypeptides having cellulase activity per kg of cellulose in the biomass material.
  • the amount of polypeptides having ⁇ -glucosidase activity can constitute up to 50% of the total weight of polypeptides having cellulase activity.
  • a suitable process of the invention preferably yields 60% to 90% xylose from the hemicellulose xylan of the biomass material treated.
  • Suitable biomass materials include one or more of, for example, corncob, switchgrass, sorghum, and/or bagasse.
  • a process of the invention preferably yields at least 70% (e.g. at least 75%, at least 80%) xylose from hemicellulose xylan from one or more of these biomass materials.
  • the process yields 60% to 90% of xylose from hemicellulose xylan of a biomass material comprising hemicellulose, including, without limitation, corncob, switchgrass, sorghum, and/or bagasse.
  • the process of the invention optionally further comprises recovering monosaccharides.
  • Hemicellulose preparations were prepared using a modification of the NaOH/sonication procedure described by Erbringerova et al. (Carbohydrate Polymers 1998, 37:231). Dry plant material was ground to pass a 1 mm screen and 10 g of this material was suspended in 250 mL of 5% (wt/v) NaOH. The suspension was heated to 80° C. without stirring for 30 min then sonicated for 15 min at ambient temperature using a probe sonicator at high setting. The suspension was returned to 80° C. for an additional 30 min then allowed to cool to room temperature. Solids were removed from the suspension by centrifugation at 3000 ⁇ g for 15 min and the resulting supernatant was decanted into 1 L of ethanol which was cooled on ice.
  • the resulting precipitate was recovered by first decanting the clear liquid above the precipitate then filtration without allowing the precipitate to fully air dry.
  • the filter cake was first washed with 200 mL of cold, 80% ethanol then removed from the filter without allowing it to air dry.
  • the filter cake was re-dissolved in 200 mL of water and the pH of the solution was adjusted to 5.5 with acetic acid.
  • the extracted carbohydrate was re-precipitated by addition to 1 L of ethanol on ice and the resulting precipitate was again recovered by filtration as above.
  • the filter cake was frozen and remaining solvent and water was removed by lyophylization. Yield of recovered carbohydrate ranged from 6 to 23% of the starting plant material depending on the tissue and the preparation.
  • Crude oligomers for screening hemicellulases were prepared from corncob by the following procedure. Hammer-milled corncob ( ⁇ 1 ⁇ 4 in mean diameter) plus 6% ammonia (w/w) was heated to 145° C. with direct injection of steam into a stirred pressure reactor. After 20 min excess ammonia was flashed out of the reactor at a final vacuum of ⁇ 0.1 bar. The ammonia pretreated cob was then placed in a sterile stirred reactor for enzyme saccharification. Enough water was added to obtain a final total solids loading of 25% (w/w) after all additions are made. The pH of the reactor was maintained at pH 5.3 with 4 N sulfuric acid and the temperature controlled at 47° C.
  • the fermentation progress was followed until all of the glucose and ⁇ 95% of the xylose was consumed.
  • a 0.5 L aliquot of the fermentation broth was clarified by centrifugation (21,000 ⁇ g) for 20 min followed by filtration of the supernatant through a 0.2 micron filtering unit (Nalgene).
  • the ethanol was removed from the filtered fermentation broth on a rotovap maintained at 35° C. under house vacuum. The total volume of the final liquor was reduced by ⁇ 4 ⁇ by the latter procedure.
  • the BCA protein assay is an example of a colorimetric assay that measures protein concentration with a spectrophotometer.
  • BCA Protein Assay Kit (Pierce Chemical, Product #23227), 50 mM Sodium Acetate buffer pH 5.0, 15% trichloroacetic acid (TCA), 0.1 N NaOH, BSA stock solution, Reagent A, Reagent B (from protein assay kit)
  • Enzyme dilutions were prepared in test tubes using 50 mM Sodium Acetate buffer. Diluted enzyme solution (0.1 mL) was added to 2 mL Eppendorf centrifuge tubes containing 1 mL 15% TCA. The tubes were vortexed and placed in an ice bath for 10 min. The samples were then centrifuged at 14,000 rpm for 6 min. The supernatant was poured out, the pellet resuspended in 1 mL 0.1 N NaOH, and the tubes vortexed until the pellet dissolved.
  • BSA standard solutions were prepared from a stock solution of 2 mg/mL.
  • BCA working solution was prepared by mixing 0.5 mL Reagent B with 25 mL Reagent A.
  • the resuspended protein (0.1 mL each) was added to 3 Eppendorf centrifuge tubes. Two mL Pierce BCA working solution was added to each of the sample and serially diluted BSA standard Eppendorf tubes. All tubes were incubated in a 37° C. water bath for 30 min. The samples were then cooled to room temperature (15 min) and the absorbance measured at 562 nm in a spectrophotometer.
  • the raw concentration of the enzyme samples was calculated by substituting the absorbance for the x-value.
  • the total protein concentration was calculated by multiplying with the dilution factor.
  • the total protein of purified samples was determined by A280 (see, e.g., Pace et al., Protein Science, 1995, 4:2411).
  • Total protein content of fermentation products was also sometimes measured as total nitrogen by combustion, capture and measurement of released nitrogen, either by Kjeldahl (rtech laboratories, www.rtechlabs.com) or in-house by the DUMAS method (TruSpec CN, www.leco.com) (SADER, et al. Archives of Veterinary Science, 9(2):73-79, 2004).
  • Kjeldahl rtech laboratories, www.rtechlabs.com
  • DUMAS method TrueSpec CN, www.leco.com
  • SADER et al. Archives of Veterinary Science, 9(2):73-79, 2004.
  • total precipitable protein was measured to remove interfering non-protein nitrogen.
  • a 12.5% final TCA concentration was used and the protein-containing TCA pellet was resuspended in 0.1 M NaOH.
  • Substrate solution 100 ⁇ L was dispensed into Costar 96 well plates (Cat no. 9017). 20 ⁇ L of enzyme sample was dispensed into a microtiter plate well. The microtiter plate was incubated at 50° C. for 10 min using a Thermomixer R heating and cooling shaker (Eppendorf). 50 ⁇ L of 1 M sodium carbonate was added to each well to quench the reaction. Absorbance at 400 nm wavelength was read with SpectraMax 340C384 Microplate Spectrophotometer (Molecular Devices). Units per mL were determined by using a p-nitrophenol standard curve.
  • a Quad-delete Trichoderma host from which the cbh1, cbh2, egl1 and eg12 genes were deleted (see WO 05/001036), was analyzed with the enzyme samples as a control for the activity of enzymes expressed in this background.
  • Corncob saccharification in a microtiter plate format was performed in accordance with the following procedures.
  • the biomass substrate, dilute ammonia pretreated corncob was diluted in water and pH-adjusted with sulfuric acid to create a pH 5, 7% cellulose slurry that was used directly in the assay.
  • the enzymes tested included: commercial cellulase products, e.g. Accellerase® 1000, Accellerase® 1500 (Danisco US Inc., Genencor), T. reesei fermentation broths, and purified enzymes.
  • the enzymes were loaded based on mg total protein per gram of cellulose (as determined by compositional analysis) in the corncob substrate.
  • the enzymes were diluted in 50 mM Sodium Acetate pH 5.0 to obtain the desired loading concentration at the required volume. Forty microliters of enzyme solution was added to 70 mg of dilute-ammonia pretreated corncob at 7% cellulose per well (equivalent to 4.5% cellulose final). The assay plate was incubated at room temperature for 10 min. The assay plates were covered with aluminum plate sealers and the plates incubated at 50° C., 200 rpm, for three days. At the end of the incubation period, the saccharification reaction was quenched by adding 100 ⁇ L of 100 mM glycine buffer, pH10.0 per well and the plate was centrifuged for 5 min at 3,000 rpm. Ten microliters of the supernatant were added to 200 ⁇ L of MilliQ water in a 96-well HPLC plate and the soluble sugars were measured by HPLC.
  • corncob saccharification was measured using a modified protocol. The modifications are described with the individual examples.
  • samples from cob saccharification hydrolysis were prepared by centrifugation to clear insoluble material, filtration through a 0.22 ⁇ m nylon filter (Spin-X centrifuge tube filter, Corning Incorporated, Corning, N.Y.) and dilution to an appropriate concentration of soluble sugars with distilled water.
  • Monomer sugars were determined on a Shodex Sugar SH-G SH1011, 8 ⁇ 300 mm with a 6 ⁇ 50 mm SH-1011P guard column (www.shodex.net).
  • Solvent was 0.01 NH 2 SO 4 run at 0.6 mL/min. Column temperature was 50° C. and detection was made using a refractive index detector. External standards of glucose, xylose and arabinose were run with each sample set. Certain examples herein use a protocol to achieve the same end with a somewhat modified set of protocols. The specific modifications to the protocols are described with individual examples.
  • Oligomeric sugars were separated by size exclusion chromatography using a Tosoh Biosep G2000PW column 7.5 mm ⁇ 60 cm (www.tosohbioscience.de). The solvent was distilled water at 0.6 mL/min and the column was run at room temperature.
  • Six carbon sugar standards used for size calibration were: stachyose, raffinose, cellobiose and glucose; and 5 carbon sugars were: xylohexose, xylopentose, xylotetrose, xylotriose, xylobiose and xylose.
  • Xylo-oligomers were obtained from Megazyme (www.megazyme.com). Detection was by refractive index and when reported quantitatively results are either as peak area units or relative peak areas by percent.
  • Total soluble sugars were determined by acid hydrolysis of the centrifuged and filter clarified samples described above.
  • the clarified sample was diluted 1:1 with 0.8 N H 2 SO 4 and the resulting solution was autoclaved in a capped vial for a total cycle time of 1 h at 121° C. Results are reported without correction for loss of monomer sugar during the hydrolysis.
  • LC liquid chromatography
  • MS mass spectroscopy
  • Wild type Fusarium verticillioides source was as described in Table 1 of Fuchs et al., Fungal Genetics and Biology 2004, 41:852-863. The fungus was grown using destarched corn grain fiber using a modification of the method described in Li et al., Applied Biochemistry and Biotechnology 2005, (121-124):321-334.
  • Starch was removed from the dried corn pericarp fraction from a corn dry mill fractionation by slurrying 200 g of corn pericarp in 3 L of tap water and heating to 80° C. with 5 mL (500 mg) of high temperature amylase Liquozyme SC DS (Novozymes, Denmark). The mixture was stirred occasionally with a spatula and held at 80° C. for 30 min then allowed to cool to room temperature for about 2 h. The resulting slurry was decanted onto a 20 mesh screen to partially de-water. The solids on the screen were further washed with 4 L of tap water then air dried overnight before a final drying in an oven at 60° C. The dried material was ground to pass a 1 mm screen in a knife mill before use.
  • the F. verticillioides culture was maintained on potato dextrose agar (Sigma P6685) and a rich growth media of 24 g/L potato dextrose was inoculated with mycelia from the plate.
  • the growth culture was incubated for 3 days at 30° C. with agitation at 130 rpm. After 3 days growth the 150 mL of the resulting cell mass and spent media were used to inoculate a corn pericarp induction media.
  • the induction media was 80 g de-starched corn pericarp in 1 L base media (15 g KH 2 PO 4 , 5 g ammonium sulfate, 20 g yeast extract, 0.5 g magnesium sulfate and 1 g Tween 80 at pH4.8).
  • the culture was maintained at 30° C. with agitation at 130 rpm for 7 days.
  • Extracellular protein was separated from the spent grain and fungal cell mass by centrifugation at 2,000 ⁇ G for 20 min.
  • the partially clarified supernatant was passed first through a 0.45 ⁇ m filter and then through a 0.22 ⁇ m filter.
  • the clarified filtrate was stored at 4° C. until used.
  • the filtrate was concentrated approximately 14-fold with Amicon ultra-4 centrifugal filters with a 30 kD cutoff (Millipore).
  • L- ⁇ -arabinofuranosidase (LARF) and ⁇ -xylosidase (BXL) activities were purified from the fungal supernatant by first exchanging the proteins into 50 mM pH 6.3 (N-Morpholino) ethanesulphonic acid-NaOH (MES) buffer, then applying protein onto a GE Health Sciences Q-Sepharose Fast Flow quaternary amine anion exchange column (20 mL bed volume equilibrated with MES buffer).
  • the protein purification system used was a GH Health Sciences Akta system using Unicorn software. Proteins were eluted with a 0-0.5 M NaCl gradient in MES buffer.
  • Active enzyme fractions from the anion exchange system were collected, concentrated on Amicon Centriprep filtration, and applied to a GE Health Sciences SP-Sepharose Fast Flow sulfopropyl cation exchange column (20 mL bed equilibrated with Sodium Acetate buffer) using the same protein purification system described above. Proteins were eluted with a 0-1 M NaCl gradient in Sodium Acetate buffer, and activity in the fractions was monitored as described above. Active fractions were then collected, pooled and concentrated if necessary. Proteins in active fractions were identified by MS-MS.
  • GH54 LARF For the identification of GH54 LARF, 200 ⁇ L of 1 N HCl (EM Industries, Hawthorne, N.Y.) was added to 250 ⁇ L of “Fraction B3” (0.35 mg protein) from the purification procedure described above and the sample iced for 10 min. Next, 200 ⁇ L of 50% TCA (Sigma-Aldrich, St. Louis, Mo.) was added and samples were iced for another 10 min to precipitate protein. Samples were centrifuged for 2 min at 16,000 rcf and the supernatants were discarded. The pelleted protein was washed with 90% cold acetone (J. T. Baker, Phillipsburg, N.J.), then centrifuged for 1 min at 16,000 rcf.
  • TCA Sigma-Aldrich, St. Louis, Mo.
  • a Vydac C18 column (5 u, 300A, 0.2 ⁇ 150 mm, Michrom Bioresources, Auburn, Calif.) was run at a flow rate of 200 ⁇ L/min. The injection volumes were 50 ⁇ L, and were filtered through an on-line trapping cartridge (Peptide CapTrap, Michrom Bioresources, Auburn, Calif.) before loading onto the column. Separation of the digests was performed with a gradient as follows (Solvent A: 0.1% trifluoroacetic acid in H 2 O (J. T. Baker, Phillipsburg, N.J.), Solvent B: 0.08% trifluoroacetic acid in acetonitrile (J. T. Baker, Phillipsburg, N.J.)).
  • GH51 LARF the two GH3 ⁇ -xylosidases, and GH30 ⁇ -xylosidase
  • Chymotrypsin 7.5 ⁇ g, Sigma-Aldrich, St. Louis, Mo.
  • the TurboSequest search engine within Bioworks 3.31 was used to identify proteins from the Fusarium verticillioides protein database.
  • the protein database was downloaded from the BROAD Institute at http://www.broadinstitute.org/annotation/genome/fusarium_verticillioides/MultiDownloads.html.
  • switchgrass For induction of Fusarium verticillioides enzymes in response to dilute aqueous ammonia pretreated switchgrass, switchgrass was ground to ⁇ 1 mm diameter, then pretreated with 6% ammonia based on dry weight at 50% initial dry matter at 160° C. maximum temperature for 90 min. The resulting material was 43.3% solids and contained 0.336% residual ammonia.
  • Wild type F. verticillioides culture was maintained on potato dextrose agar (Sigma P6685) and a rich growth media of 24 g/L potato dextrose was inoculated with mycelia from the plate. The growth culture was incubated for 3 days at 24° C. with agitation at 140 rpm, during which time it became turbid with Fusarium cells.
  • the Fusarium verticillioides culture media containing the expressed enzymes from the 168-h induction described above was centrifuged at 3,500 ⁇ g to remove debris and cells. The supernatant was filtered through a 0.4 ⁇ m filter yielding a clear deep yellow liquid. The liquid was concentrated ( ⁇ 4 ⁇ ) two times in a large Amicon ultra 10K MW cutoff concentrator (UFC901024). A 1.7 mL concentrated sample was set aside for size exclusion chromatography (SEC) and assayed for protein content by BCA assay as described earlier. The concentrated protein sample was loaded onto a Superdex 16/60 SEC column equilibrated with 50 mM Sodium Acetate buffer pH 5.0.
  • SEC size exclusion chromatography
  • the column was eluted at 1 mL/min at 4° C. Absorbance of the sample at 214 nm and 280 nm were monitored. After elution of the void volume, 1 mL fractions were collected in a deep well polypropylene microtiter plate. The protein-containing fractions were aggregated into a separate deep well plate and all fractions were measured for total protein concentration by BCA assay, and p-nitrophenyl arabinosidase, p-nitrophenyl xylosidase, and p-nitrophenyl glucosidase activities as described in Example 1 (Synthetic substrate activity assays).
  • the enzyme fractions were exchanged into 50 mM pH 6.3 (N-Morpholino) ethanesulphonic acid-NaOH (MES) buffer, and then the protein sample was applied onto a GE Health Sciences Q-Sepharose Fast Flow quaternary amine anion exchange column (20 mL bed volume equilibrated with MES buffer).
  • the Akta protein purification system as described for the cation exchange step was used. Proteins were eluted with a 0-0.5 M NaCl gradient in MES buffer. The active enzymes were then exchanged into 50 mM, pH 5.0 Sodium Acetate buffer before cation exchange chromatography.
  • Hydrophobic interaction chromatography (NH 4 ) 2 SO 4 was added to fermentation supernatant to achieve a final concentration of 1 M.
  • the separation column used was a Hiprep Phenyl (highsub), 16/10, 20 mL.
  • Buffer A 20 mM sodium phosphate, pH 6.0.
  • Buffer B Buffer A+1 M (NH 4 ) 2 SO 4 . Stepwise Elution: 45% B; 0% B; water+10% glycerol.
  • FIG. 26 shows the SDS-PAGE detection of the two step separation of AfuXyn 5.
  • the Applied Biosystems BIOCAD® Vision and Amersham Pharmacia Biotech AKTA Explorer were used for protein purification of T. reesei XYN3. Approximately 150 mL of Xylanase 3, from an ultrafiltration concentrate, was loaded onto a Sephadex G-25M desalting column (total volume ⁇ 525 mL) equilibrated in 10 mM TES buffer, pH 6.8. 300-400 mL of this desalted sample was then loaded onto an anion-exchange column (high density quaternary amine resin; Applied Biosystems Inc.). The bound protein was then eluted using a salt gradient between 0-1 M sodium chloride using 8-column volumes of 25 mM TES buffer. Elution of the protein occurred between 0-250 mM sodium chloride, and was detected using 10% Bis-Tris NUPAGE® SDS-PAGE (Novex).
  • the eluted Xylanase 3-containing samples were concentrated to 10 mL with Vivaspin 5,000 MWCO (molecular weight cut-off) membrane concentrators (Vivascience; GE Healthcare). The concentrate was then loaded onto a High Load 26/60 Superdex 200 (ID no 17-1071-01; GE Healthcare). The column was equilibrated with 25 mM TES buffer, pH 6.8, containing 100 mM sodium chloride, and the bound protein was eluted over 8-column volumes of the TES buffer with sodium chloride.
  • the purity of the eluted protein was assessed using 10% Bis-Tris NUPAGE® SDS-PAGE (Novex), and determined to be greater than 95% pure.
  • the ultrafiltration concentrate (UFC) of Fusarium verticillioides 43D was buffer exchanged and dialyzed against 50 mM Sodium Acetate buffer, pH 4.0, overnight.
  • the dialyzed material was passed through a HiTrap 1 mL column prepacked with sulfopropyl sepharose fast flow resin (GE Healthcare) designed for use with a syringe.
  • the purified Fv43D was eluted with 50 mM Sodium Acetate buffer, pH 4.0, with 250 mM sodium chloride.
  • the UFC and Sodium Acetate buffer were pushed through the column using a 5 mL syringe fitted with a GE Healthcare connector.
  • the purified Fv43D was dialyzed overnight against 50 mM Sodium Acetate buffer, pH 4.0.
  • the purified protein was assayed by SDS-PAGE, HPLC, and mass spectroscopy to demonstrate homogeneity.
  • the ultrafiltration concentrate (UFC) of Fusarium verticillioides 51A was buffer exchanged and dialyzed against 50 mM Sodium Acetate buffer, pH 5.0, overnight.
  • the dialyzed material was passed through a RESOURCE 15 6 mL column prepacked with methyl sulfonate media (GE Healthcare).
  • the UFC was loaded at 1 mL/min against 50 mM Sodium Acetate buffer, pH 5.0, and eluted at 5 mL/min against 50 mM Sodium Acetate buffer, pH 5.0, using a 0 to 250 mM sodium chloride gradient.
  • the eluted fractions were collected and assayed by SDS-PAGE.
  • Fractions with purified Fv51A were concentrated using a 10,000 MWCO Vivaspin concentrator from Sartorius Stemdim Biotech.
  • the purified Fv51A was dialyzed against 50 mM Sodium Acetate buffer, pH 5.0, overnight.
  • the purified protein was assayed by SDS-PAGE, HPLC, and mass spectroscopy to demonstrate homogeneity.
  • the AKTA Explorer 100 system from GE Healthcare was used for the purification of Fv51A.
  • Fv51A The sequence for Fv51A was obtained by searching the Fusarium verticillioides genome in the Broad Institute database (http://www.broadinstitute.org/) for GH51 arabinofuranosidase homologs.
  • Fv3A The following genes from Fusarium verticillioides were expressed in Trichoderma reesei : Fv3A, Fv43A, Fv43B, Fv43D, Fv51A, Fv3B, Fv43C, Fv39A, Fv43E, Fv30A, Fv30B, and Fv43F.
  • Fv3A sequence was obtained by searching for GH3 ⁇ -xylosidase homologs in Fusarium verticillioides genome.
  • the annotated sequence lacked a signal sequence and the gene prediction program Augustus (http://augustus.gobics.de/) was used to identify upstream sequence which contained a signal sequence.
  • Sequences for Fv39A, Fv43A, Fv43B, Fv43D, Fv43E, and Fv30A were obtained by searching the Fusarium verticillioides genome for GH39, GH30, and GH43 ⁇ -xylosidase homologs.
  • Open reading frames of the hemicellulase genes of interest were amplified by PCR using purified/extracted genomic DNA from Fusarium verticillioides as the template.
  • the PCR thermocycler used was DNA Engine Tetrad 2 Peltier Thermal Cycler (BioRad Laboratories).
  • the DNA polymerase used was PfuUltra II Fusion HS DNA Polymerase (Stratagene).
  • the primers used to amplify the open reading frames were as follows:
  • Fv3A Forward primer MH124 (SEQ ID NO: 52) (5′-CACCCATGCTGCTCAATCTTCAG-3′) Reverse primer MH125 (SEQ ID NO: 53) (5′-TTACGCAGACTTGGGGTCTTGAG-3′)
  • Fv43A Forward primer MH075 (SEQ ID NO: 54) (5′-CACCATGTGGCTGACCTCCCCATT-3′) Reverse primer MH076 (SEQ ID NO: 55) (5′-TTAGCTAAACTGCCACCAGTTGAAGTTG-3′)
  • Fv43B Forward primer MH077 (SEQ ID NO: 56) (5′-CACCATGCGCTTCTCTTGGCTATTGT-3′) Reverse primer MH078 (SEQ ID NO: 57) (5′-CTACAATTCTGATTTCACAAAAACACC-3′)
  • Fv43D Forward primer MH081 (SEQ ID NO: 58) (5′-CACCATGCAGCTCAAGTTTCTG-3′) Reverse primer MH
  • the forward primers included four additional nucleotides (sequences—CACC) at the 5′-end to facilitate directional cloning into pENTR/D-TOPO (Invitrogen, Carlsbad, Calif.) ( FIG. 28 ).
  • the PCR conditions for amplifying the open reading frames were as follows (except for Fv51A): Step 1: 94° C. for 2 min. Step 2: 94° C. for 30 sec. Step 3: 57° C. for 30 sec. Step 4: 72° C. for 30-45 sec. Steps 2, 3 and 4 were repeated for an additional 29 cycles. Step 5: 72° C. for 2 min.
  • Fv51A the following conditions were used: Step 1: 94° C. for 2 min.
  • Step 2 94° C. for 30 sec.
  • Step 3 56° C. for 30 sec.
  • Step 4 72° C. for 45 sec. Steps 2, 3, 4 were repeated for an additional 25 cycles.
  • the PCR products of the corresponding hemicellulase open reading frames were purified using a Qiaquick PCR Purification Kit (Qiagen, Valencia, Calif.).
  • the purified PCR products were cloned into the pENTR/D-TOPO vector, transformed into TOP10 chemically competent E. coli cells (Invitrogen, Carlsbad, Calif.) and plated on LA plates with 50 ppm kanamycin. Plasmid DNA was obtained from the E. coli transformants using a QIAspin plasmid preparation kit (Qiagen). Sequence data for the DNA inserted in the pENTR/D-TOPO vector was obtained using M13 forward and reverse primers (Sequetech, Mountain View, Calif.).
  • a pENTR/D-TOPO vector with the correct DNA sequence of the corresponding hemicellulase open reading frame was recombined with the pTrex3gM destination vector (WO 05/001036, FIG. 29) using LR clonase reaction mixture (Invitrogen, Carlsbad, Calif.) according to the manufacturer's instructions.
  • the product of the LR clonase reaction was subsequently transformed into TOP10 chemically competent E. coli cells which were then plated on LA containing 50 ppm carbenicillin.
  • the resulting expression vectors were pTrex3gM plasmids containing the corresponding hemicellulase open reading frames that resulted from the recombination event between the attR1 and attR2 sites of pTrex3gM and the attL1 and attL2 sites of pENTR/D-TOPO; and the Aspergillus nidulans acetamidase selection marker (amdS).
  • DNA of the expression vectors containing the corresponding hemicellulase open reading frames were isolated using a Qiagen miniprep kit and used for biolistic transformation of Trichoderma reesei spores.
  • Biolistic transformation of Trichoderma reesei with the pTrex3gM expression vector containing the corresponding hemicellulase open reading frame was performed using the following protocol. Transformation of the Trichoderma reesei cellulase quad delete ( ⁇ cbh1, ⁇ cbh2, ⁇ eg1, ⁇ eg2) strain by helium-bombardment was accomplished using a Biolistic® PDS-1000/He Particle Delivery System from Bio-Rad (Hercules, Calif.) following the manufacturer's instructions (see patent publications WO 05/001036 and US 2006/0003408). Transformants were transferred to fresh acetamide selection plates (see patent publication WO 2009114380).
  • Stable transformants were inoculated into filter microtiter plates (Corning), containing 200 ⁇ L/well of Glycine Minimal media (6.0 g/L glycine; 4.7 g/L (NH 4 ) 2 SO 4 ; 5.0 g/L KH 2 PO 4 ; 1.0 g/L MgSO 4 .7H 2 O; 33.0 g/L PIPPS; pH 5.5) with post sterile addition of ⁇ 2% glucose/sophorose mixture (U.S. Pat. No. 7,713,725) as the carbon source, 10 mL/L of 100 g/L of CaCl 2 , 2.5 mL/L of T.
  • Glycine Minimal media 6.0 g/L glycine; 4.7 g/L (NH 4 ) 2 SO 4 ; 5.0 g/L KH 2 PO 4 ; 1.0 g/L MgSO 4 .7H 2 O; 33.0 g/L PIPPS; pH 5.5
  • reesei trace elements 400 ⁇ : 175 g/L Citric acid anhydrous; 200 g/L FeSO 4 .7H 2 O; 16 g/L ZnSO 4 .7H 2 O; 3.2 g/L CuSO 4 .5H 2 O; 1.4 g/L MnSO 4 .H 2 O; 0.8 g/L H 3 Bo 3 ).
  • Transformants were grown in liquid culture for 5 days in an O 2 -rich chamber housed in a 28° C. incubator. The supernatant samples from the filter microtiter plate were collected on a vacuum manifold.
  • Pf43A and Pf51A sequences were obtained by sequencing of the Penicillium funiculosum genome.
  • the queries used for the searches of the P. funiculosum genome were other fungal GH43 and GH51 homologs available in the public genomes.
  • a gene prediction program named Augustus (http://augustus.gobics.de/) was used to verify the intron sequences, along with the start codon.
  • Fv43D sequence was used to query the Gibberella zeae ( Fusarium graminearum ) and Fusarium oxysporum genomes available in the Broad Institute database and retrieve sequences for Gz43A and Fo43A respectively.
  • Gz43A and Fo43A were synthesized by GeneArt (Geneart GmbH, Regensburg, Germany) with the CBH1 signal sequence in place of the native signal sequence. Neither gene contained introns.
  • the Pf51A gene was codon-optimized and synthesized by GeneArt with the CBH1 signal sequence in place of the native signal sequence.
  • Pf43A and Pf51A were cloned and expressed in Trichoderma reesei using the following primers:
  • Pf43A MH151 (SEQ ID NO: 78) (5′-CACCATGCTTCAGCGATTTGCTTATATTTTACC-3′) Pf43A: MH152 (SEQ ID NO: 79) (5′-TTATGCGAACTGCCAATAATCAAAGTTG-3′) Pf51A: SK1168 (SEQ ID NO: 80) (5′-CACCATGTACCGGAAGCTCGCCGTG-3′) Pf51A: SK1169: (SEQ ID NO: 81) (5′-CTACTCCGTCTTCAGCACAGCCAC-3′)
  • GH11 xylanase 2 (AfuXyn2)
  • GH11 xylanase 5 (AfuXyn5)
  • GH43 Af43A The primers for AfuXyn2, AfuXyn5, and Af43A cloning primers are shown below:
  • AfuXyn2 A . fumi -Q4WG11-F: (SEQ ID NO: 82) (5′-CCGCGGCCGCACCATGGTTTCTTTCTCCTACCTGCTGCTG-3′) A . fumi -Q4WG11-R: (SEQ ID NO: 83) (5′-CCGGCGCGCCCTTACTAGTAGACAGTGATGGAAGCAGATCCG-3′) AfuXyn5: A . fumi -Q4WFZ8-F: (SEQ ID NO: 84) (5′-CCGCGGCCGCACCATGATCTCCATTTCCTCGCTCAGCT-3′) A .
  • fumi -Q4WFZ8-R (SEQ ID NO: 85) (5′-CCGGCGCGCCCTTATCACTTGGATATAACCCTGCAAGAAGGTA-3′) Af43A: SK1203: (SEQ ID NO: 86) (5′-CACCATGGCAGCTCCAAGTTTATCC-3′) SK1204- (SEQ ID NO: 87) (5′ TCAGTAGCTCGGGACCACTC-3′)
  • L- ⁇ -arabinofuranosidase candidates were evaluated in a 4-day cob saccharification assay by addition to an enzyme mixture of Accellerase® 1500/ T. reesei Xyn3/Fv3A.
  • the screen was conducted as described in the corncob Saccharification Assay (Example 1) with the following enzymes and amounts/concentrations:
  • the total protein (TP) of purified samples was determined by A280 unless otherwise noted.
  • the total protein of unpurified samples was determined by BCA according to manufacturer instructions, unless otherwise noted.
  • Accellerase® 1500 was added at 20 mg protein/g cellulose;
  • Trichoderma reesei Xyn3 was added at 5 mg protein/g cellulose;
  • Fv3A was added at 5 mg protein/g cellulose.
  • Fv51A, Mg51A, At51A, Pt51A, Ss51A, Vd51A, Cg51B, Af43A, Pf43A, or Fv43E were added at 1, 3, and 5 mg protein/g cellulose. Following 4 days incubation, 50° C., 200 rpm, the assay plate was quenched and analyzed by HPLC for soluble sugars.
  • Enzymes were found that enhanced glucose or xylose or arabinose yield, or reduced cellobiose or xylobiose concentration in this enzyme mixture. Results are shown in FIGS. 30A and 30B .
  • the saccharification performance of expressed proteins was also evaluated as additions to the enzyme mixture with an L- ⁇ -arabinofuranosidase and ⁇ -xylosidase deficiency.
  • ⁇ -xylosidase candidates were evaluated in a 3 day cob saccharification assay by addition to an enzyme mixture of Accellerase® 1500/ T. reesei Xyn3.
  • the screen was conducted as described in the corncoob saccharification assay (Example 1) with the following enzymes and amounts/concentrations:
  • Accellerase® 1500 was added at 17.9 mg protein/g cellulose; T. reesei Xyn3 was added at 5 mg protein/g cellulose.
  • Fv3A, Fv43D, Pf43A, Pf43B, Fv43E, Fv43F, or Fv30A were added at 1, 3, and 5 mg protein/g cellulose (Fv43E was only added at 1 and 3 mg/g).
  • the assay plate was quenched and analyzed by HPLC for soluble sugars. Results are shown in FIG. 31 . Enzymes were found that enhanced glucose, or xylose or arabinose yield, or reduced cellobiose or xylobiose concentration in this enzyme mixture.
  • the saccharification performance of expressed proteins was also evaluated as additions to the enzyme mix with a xylanase deficiency.
  • Trichoderma reesei integrated expression strains described in Example 9 below
  • one T. reesei strain (strain #44) was isolated that over-expressed Bgl1, Fv3A, Fv51A, Fv43D proteins but did not over-express endo-xylanase. This strain was used as the background to which candidate xylanases were added for performance screening. Endo-xylanase candidates were evaluated in a 3 day cob saccharification assay by addition to the enzyme products from strain #44. The screen was conducted as described in the corncob saccharification assay (Example 1) with the following enzymes and amounts/concentrations:
  • the enzyme composition produced by Strain #44 was added at 20 mg protein/g cellulose; candidate xylanase enzymes were added at 3 and 7 mg protein/g cellulose. Following 3 days incubation, at 50° C., 200 rpm, the assay plate was quenched and analyzed by HPLC for soluble sugars. Enzymes were found that enhanced xylose, or glucose, or arabinose yield, or reduced cellobiose or xylobiose concentration in this enzyme mixture. Results are shown in FIG. 32 .
  • Fv51A and Pa51A proteins were evaluated in a 3 day cob saccharification assay by addition to an enzyme mixture of Accellerase® 1000/ T. reesei Xyn2/Bxl1 or Fv3A.
  • the screen was conducted as described in the corncob saccharification assay (Example 1) with the following enzymes and amounts/concentrations:
  • Accellerase® 1000 was added at 20 mg protein/g cellulose; Trichoderma reesei Xyn2 was added at 5 mg protein/g cellulose; Trichoderma reesei Bxl1 or Fv3A was added at 5 mg protein/g cellulose.
  • Fv51A was added at 5 mg protein/g cellulose.
  • Pa51A was added at 1, 2, or 5 mg protein/g cellulose.
  • the assay plate was quenched and analyzed by HPLC for soluble sugars. Enzyme combinations were found that enhanced xylose, or glucose, or arabinose yield, or reduced cellobiose or xylobiose concentration in this enzyme mixture. Results are shown in FIG. 33 .
  • Fv51A and Pa51A also were evaluated in a 3 day cob saccharification assay by addition to an enzyme mixture of Accellerase® 1000/ Trichoderma reesei Xyn2.
  • Purified Fv51A 29 mg/mL TP
  • Pa51A 29 mg/mL
  • Accellerase® 1000 was added at 17.5 mg protein/g cellulose
  • Trichoderma reesei Xyn2 was added at 4.4 mg protein/g cellulose.
  • Fv51A was added at 4.4 mg protein/g cellulose.
  • Pa51A was added at 0.9, 1.8, and 4.4 mg protein/g cellulose.
  • the saccharification performance of expressed proteins was also evaluated as additions to the enzyme mix with ⁇ -xylosidase deficiency.
  • ⁇ -xylosidase candidates were evaluated in a 3 day cob saccharification assay by addition to an enzyme mixture of Accellerase® 1000/ Trichoderma reesei Xyn2/Fv51A.
  • the screen was conducted as described in the corncob saccharification assay (Example 1) with the following enzymes and amounts/concentrations:
  • Accellerase® 1000 was added at 20 mg protein/g cellulose; Trichoderma reesei Xyn2 was added at 5 mg protein/g cellulose; Fv51A was added at 5 mg protein/g cellulose. Fv39A, Fv30B, Fv3A, or Fv3B were added at 1, 2, or 5 mg protein/g cellulose. Following 3 days incubation, at 50° C., 200 rpm, the assay plate was quenched and analyzed by HPLC for soluble sugars. Enzymes and combinations were found that enhanced glucose or xylose or arabinose yield, or reduced cellobiose or xylobiose concentration in this enzyme mixture, with or without another ⁇ -xylosidase ( T. reesei Bxl1). Results are shown in FIGS. 35A-35C .
  • the activity of candidate endo-xylanases was evaluated using birchwood xylan as a substrate using the following assay.
  • Ninety microliters of a 1% (wt/vol) birchwood xylan (Sigma X0502) stock solution was added to wells in a 96-well microtiter plate and pre-incubated at 50° C. for 10 min.
  • Enzyme dilutions and xylose standards were added (10 ⁇ L) to the microtiter plate and the plates incubated at 50° C. for 10 min. Meanwhile, 100 ⁇ L of DNS solution was added to PCR tubes. Following the 10-min incubation, 60 ⁇ L of the enzyme reaction was transferred to the PCR tubes containing the DNS solution.
  • the tubes were incubated in a thermocycler at 95° C. for 5 min, and then cooled to 4° C.
  • One hundred microliters of the reaction mixture was transferred to a 96-well plate, and absorbance at 540 nm was measured.
  • a xylose standard curve was generated and used to calculate the activity.
  • One xylanase unit is defined as the amount of enzyme required to generate 1 ⁇ mole of xylose reducing sugar equivalents per minute under the conditions of the assay. Results are shown in Table 3.
  • the concentration of total sugars in the crude oligomer preparation determined by this method was 45 g/L glucose, 168 g/L xylose, and 46 g/L arabinose.
  • concentration of total sugars in the crude oligomer preparation determined by this method was 45 g/L glucose, 168 g/L xylose, and 46 g/L arabinose.
  • 86% of the glucose, 90% of the xylose, and 43% of the arabinose was present in oligomeric form.
  • Various ⁇ -xylosidases, arabinofuranosidases, and mixtures thereof were tested for increased conversion of arabinose monomer from the crude oligomers preparation.
  • the crude oligomer preparation was diluted 20-fold to 12 g/L oligomers in 50 mM Sodium Acetate buffer, pH 5.0, and maintained at 50° C.
  • the substrate range of 3 ⁇ -xylosidases and their relation to effective conversion of corncob xylooligomers to monomer sugars were determined.
  • Preparation of corncob hydrolysate containing oligomeric sugars and assay of monomer sugars was performed as described in Example 1.
  • the proton NMR spectra of oligomeric sugars with degree of polymerization (DP) greater than 2 as separated by size exclusion chromatography on Bio-Gel P2 were determined ( FIG. 36 and FIG. 37 ).
  • the spectra of oligomers before enzyme treatment is labeled “MD07 oligomers” in the bottom panel of FIG. 36 and spectra of the same oligo containing fractions after enzyme treatments are in the remaining panels of FIG. 36 and FIG. 37 labeled with the treatment enzyme.
  • Bio-gel P2 fractions containing oligomers of greater than DP2 were lyophilized then dissolved in 0.7 mL of a D 2 O solution containing 0.5 mM 2,2-dimethyl-2-silapentane-5-sulfonate (DSS) as internal standard. Aliquots of 0.55 mL were used for the NMR samples in order to optimize suppression of the residual water peak. Standard versions of the Varian 2D correlation pulse sequences were used, with optimization of the 13 C spectral width for the heteronuclear experiments. Spectra were acquired on a Varian Unity Inova using a high sensitivity cryoprobe operating at 500 MHz. Structure elucidation was done by identifying the correlations that characterize the spin-system for the individual sugar residues and then identifying the inter-glycosidic correlations.
  • DSS 2,2-dimethyl-2-silapentane-5-sulfonate
  • the arabinose containing oligomers as determined by NMR, are dominated by one or more branched structures in which arabinose is linked ⁇ -1 ⁇ 3 to a xylose residue in a polymer fragment.
  • the arabinose residue in the resulting branch is further substituted by a xylose residue linked ⁇ -1 ⁇ 2 to the arabinose. Little arabinose without this second substitution is present in the remaining xylo-oligomers.
  • T. reesei Bxl1 is not very effective at cleaving the furthest out xylose 1 ⁇ 2 to arabinose bond as evidenced by the remaining signals at 5.5 to 5.55 ppm in the spectra.
  • the combination of the Fv43A that is effective on longer chain xylose oligomers and the Fv43B L- ⁇ -arabinofuranosidase removes most but not all of the branched species with signals in the 5.5 ppm range and unlike treatment with the T. reesei Bxl1, leaves none of the signal at 5.35 that is attributable to remaining arabinose branched to xylose oligomer.
  • the anomeric proton region of the spectra of the remaining xylo-oligomers after treatment with the Fv51A alone or in combination with the Fv3A show different results.
  • the L- ⁇ -arabinofuranosidase alone is not effective at reducing the complexity of signals in the region.
  • the Fv3A ⁇ -xylosidase removes essentially all of the xylose subtending the arabinose branch leaving mostly simply linked arabinose 1 ⁇ 3 xylose oligomer structures.
  • T. reesei ⁇ -xylosidase (Bxl1) is 61% similar to the F. verticillioides ortholog (Fv3A) and shares 42% sequence identity as shown in the alignment of FIG. 38 .
  • Fv3A has much broader substrate range than Bxl1, which is likely to be attributable to the non-conserved amino acids among the two proteins.
  • Pretreated corncob as described in Example 1 was used as water slurry adjusted to about pH 5 with H 2 SO 4 in water at 18.6 g dry corncob solids/100 g of total slurry. 0.78 g of the slurry was added to 4 mL glass vials and sufficient pH 5.0, 50 mM Sodium Acetate buffer was added to give a total reaction weight of 1.06 g after the desired enzyme additions.
  • the hemicellulases were added as the purified preparations described in Example 1.
  • Supernatant from the quad deleted T. reesei strain (Quad in Tables 5 and 6) is the concentrate of background proteins expressed by the T.
  • Accellerase® 1000 is a whole cellulase mixture with high ⁇ -glucosidase activity.
  • the vials were incubated at 230 rpm in an orbital shaker at 48° C. for 72 h then 2 mL of water was added.
  • a sub-sample was taken and further diluted, centrifuged and filtered for HPLC analysis for monomer sugars as described in Example 1.
  • Experimental results defining useful amounts of defined hemicellulase activity for hydrolyzing pretreated corncob to monomer sugars is shown in Table 5.
  • a mix of 6 mg/g xylan T. reesei Xyn3, 2 mg/g Fv3A and either 1 or 2 mg/g Fv51A is a suitable loading to reduce total cob arabinoxylan to monomer sugars.
  • the addition of Fv43D to the mix aids in taking the xylobiose or other DP2 oligomers to monomer. Arabinose hydrolysis to monomer was not measured in this experiment.
  • Trichoderma reesei An integrated expression strain of Trichoderma reesei was constructed that co-expressed five genes: T. reesei ⁇ -glucosidase gene bgl1, T. reesei endoxylanase gene xyn3 , F. verticillioides ⁇ -xylosidase gene fv3A, F. verticillioides ⁇ -xylosidase gene fv43D, and F. verticillioides ⁇ -arabinofuranosidase gene fv51A.
  • the N-terminal portion of the native T. reesei ⁇ -glucosidase gene bgl1 was codon optimized by DNA 2.0 (Menlo Park, USA). This synthesized portion comprised of the first 447 bases of the coding region. This fragment was PCR amplified using primers SK943 and SK941. The remaining region of the native bgl1 gene was PCR amplified from a genomic DNA sample extracted from T. reesei strain RL-P37, using primer SK940 and SK942. These two PCR fragments of the bgl1 gene were fused together in a fusion PCR reaction, using primers SK943 and SK942:
  • Forward Primer SK943 (SEQ ID NO: 88) (5′-CACCATGAGATATAGAACAGCTGCCGCT-3′)
  • Reverse Primer SK941 (SEQ ID NO: 89))
  • Forward Primer SK940 (SEQ ID NO: 90)
  • Reverse Primer SK942 (SEQ ID NO: 91) (5′-CCTACGCTACCGACAGAGTG-3′)
  • the resulting fusion PCR fragments were cloned into the Gateway® Entry vector pENTRTTM/D-TOPO®, and transformed into E. coli One Shot® TOP10 Chemically Competent cells (Invitrogen) resulting in the intermediate vector, pENTRY-943/942 ( FIG. 39 ).
  • the nucleotide sequence of the inserted DNA was determined.
  • the pENTRY-943/942 vector with the correct bgl1 sequence was recombined with pTrex3g using a LR Clonase® reaction protocol outlined by Invitrogen. The LR clonase reaction mixture was transformed into E.
  • the vector also contains the Aspergillus nidulans amdS gene encoding acetamidase as a selectable marker for transformation of T. reesei .
  • the expression cassette was PCR amplified with primers SK745 and SK771 to generate product for transformation of the strain, using the electroporation method described in WO 08153712.
  • the native T. reesei endoxylanase gene xyn3 was PCR amplified from a genomic DNA sample extracted from T. reesei , using primers xyn3F-2 and xyn3R-2.
  • the resulting PCR fragments were cloned into the Gateway® Entry vector pENTRTM/D-TOPO®, and transformed into E. coli One Shot® TOP10 Chemically Competent cells (Invitrogen) resulting in the intermediate vector, pENTR/Xyn3 ( FIG. 41 ).
  • the nucleotide sequence of the inserted DNA was determined.
  • the pENTR/Xyn3 vector with the correct xyn3 sequence was recombined with pTrex3g using a LR Clonase® reaction protocol outlined by Invitrogen.
  • the LR clonase reaction mixture was transformed into E.
  • the vector also contains the Aspergillus nidulans amdS gene encoding acetamidase as a selectable marker for transformation of T. reesei .
  • the expression cassette was PCR amplified with primers SK745 and SK822 to generate product for transformation of the strain, using the electroporation method.
  • the F. verticilloides ⁇ -xylosidase fv3A gene was amplified from a F. verticilloides genomic DNA sample using the primers MH124 and MH125.
  • the PCR fragments were cloned into the Gateway® Entry vector pENTRTM/D-TOPO®, and transformed into E. coli One Shot® TOP10 Chemically Competent cells (Invitrogen) resulting in the intermediate vector, pENTR-Fv3A ( FIG. 43 ).
  • the nucleotide sequence of the inserted DNA was determined.
  • the pENTRY-Fv3A vector with the correct fv3A sequence was recombined with pTrex6g using a LR Clonase® reaction protocol outlined by Invitrogen.
  • the LR clonase reaction mixture was transformed into E.
  • the vector also contains a chlorimuron ethyl resistant mutant of the native T. reesei acetolactate synthase (als) gene, designated alsR, which is used together with its native promoter and terminator as a selectable marker for transformation of T. reesei (WO2008/039370 A1).
  • alsR chlorimuron ethyl resistant mutant of the native T. reesei acetolactate synthase (als) gene, designated alsR, which is used together with its native promoter and terminator as a selectable marker for transformation of T. reesei (WO2008/039370 A1).
  • the expression cassette was PCR amplified with primers SK1334, SK1335 and SK1299 to generate product for transformation of T. reesei , using the electroporation method (see, e.g., WO2008153712 A2).
  • Forward Primer SK1334 (SEQ ID NO: 100) (5′-GCTTGAGTGTATCGTGTAAG-3′)
  • Forward Primer SK1335 (SEQ ID NO: 101) (5′-GCAACGGCAAAGCCCCACTTC-3′)
  • Reverse Primer SK1299 (SEQ ID NO: 102) (5′-GTAGCGGCCGCCTCATCTCATCTCATCCATCC-3′)
  • the fv43D gene product was amplified from F. verticilloides genomic DNA using the primers SK1322 and SK1297.
  • a region of the promoter of the endoglucanase gene egl1 was PCR amplified from T. reesei genomic DNA extracted from strain RL-P37, using the primers SK1236 and SK1321. These two PCR amplified DNA fragments were subsequently fused together in a fusion PCR reaction using the primers SK1236 and SK1297.
  • the resulting fusion PCR fragment was cloned into pCR-Blunt II-TOPO vector (Invitrogen) to give the plasmid TOPO Blunt/Pegl1-Fv43D ( FIG. 45 ) and E. coli One Shot® TOP10 Chemically Competent cells (Invitrogen) were transformed using this plasmid. Plasmid DNA was extracted from several E. coli clones and confirmed by restriction digest.
  • Forward Primer SK1322 (SEQ ID NO: 103) (5′-CACCATGCAGCTCAAGTTTCTGTC-3′) Reverse Primer SK1297: (SEQ ID NO: 104) (5′-GGTTACTAGTCAACTGCCCGTTCTGTAGCGAG-3′) Forward Primer SK1236: (SEQ ID NO: 105) (5′-CATGCGATCGCGACGTTTTGGTCAGGTCG-3′) Reverse Primer SK1321: (SEQ ID NO: 106) (5′-GACAGAAACTTGAGCTGCATGGTGTGGGACAACAAGAAGG-3′)
  • the expression cassette was PCR amplified from TOPO Blunt/Pegl1-Fv43D with primers SK1236 and SK1297 to generate product for transformation of T. reesei , using the electroporation method as described in WO2008153712A2.
  • the fv51A gene product was amplified from F. verticilloides genomic DNA using the primers SK1159 and SK1289.
  • a region of the promoter of the endoglucanase gene egl1 was PCR amplified from T. reesei genomic DNA sample extracted from strain RL-P37, using the primers SK1236 and SK1262. These two PCR amplified DNA fragments were subsequently fused together in a fusion PCR reaction using the primers SK1236 and SK1289.
  • the resulting fusion PCR fragment was cloned into pCR-Blunt II-TOPO vector (Invitrogen) to give the plasmid TOPO Blunt/Pegl1-Fv51A ( FIG. 46 ) and E. coli One Shot® TOP10 Chemically Competent cells (Invitrogen) were transformed using this plasmid.
  • the expression cassette was PCR amplified with primers SK1298 and SK1289 to generate product for transformation of T. reesei using the electroporation method.
  • a Trichoderma reesei mutant strain derived from RL-P37 (Sheir-Neiss, G et al. Appl. Microbiol. Biotechnol. 1984, 20:46-53) and selected for high cellulase production was co-transformed with the ⁇ -glucosidase expression cassette (cbh1 promoter, T. reesei ⁇ -glucosidase) gene, cbh1 terminator, and amdS marker), and the endoxylanase expression cassette (cbh1 promoter, T. reesei xyn3, and cbh1 terminator) using PEG-mediated transformation (Penttila, M et al.
  • T. reesei strain #229 was used for transformation with the other expression cassettes.
  • T. reesei strain #229 was co-transformed with the 3-xylosidase fv3A expression cassette (cbh1 promoter, fv3A gene, cbh1 terminator, and alsR marker), the 3-xylosidase fv43D expression cassette (egl1 promoter, fv43D gene, native fv43D terminator), and the fv51A ⁇ -arabinofuranosidase expression cassette (egl1 promoter, fv51A gene, fv51A native terminator) using electroporation.
  • Transformants were selected on Vogels agar plates containing chlorimuron ethyl (80 ppm). Vogels agar was prepared as follows, per liter.
  • T. reesei integrated expression strains described herein are H3A, 39A, A10A, 11A, and G9A, which express all of the genes for T. reesei beta-glucosidase 1, T. reesei Xyn3, Fv3A, Fv51A, and Fv43D, at different ratios (Table 11). Examples of T.
  • reesei integrated expression strains described herein also include 44A, 69A, G6A and 102, and each includes most of the genes for T. reesei beta-glucosidase 1, T. reesei XYN3, Fv3A, Fv51A, and Fv43D, expressed at different ratios.
  • T. reesei enzyme samples were generated as either ultrafiltration concentrates (UFC) or centrate.
  • UFC ultrafiltration concentrates
  • T. reesei fermentation broths 14 L-scale were obtained after cell separation by centrifugation, concentrated using membrane-ultrafiltration through a Millipore 10 kD molecular weight cut off membrane. Then pH was adjusted to 4.8. The cell-separated broth was then polished by filtration, using FW6 Buchner filtration. Each enzyme sample was assayed for total protein concentration using the modified Biuret method.
  • the saccharification performance was evaluated in vials or in shake flasks. Each enzyme preparation was assayed for saccharification performance on 20% dry solids (DS) loading of dilute ammonia pretreated corncob (see, WO2006/110901). All saccharification reactions were then titrated with sulfuric acid to pH 5.0 and sodium azide was added to a final concentration of 0.01% (w/v), for microbial contamination control. Each saccharification reaction was then dosed with 20 mg of total protein (TP) enzyme preparation per g of substrate glucan or xylan, as appropriate. Accellerase® 1500 (Ac1500) and the integrated strain UFC's were dosed at 20 mg total protein/g glucan.
  • An enzyme blend was prepared in a ratio of 25:9:4:3:1 Accellerase® 1500:Xyn3:Fv3A:Fv51A: FV43D.
  • Accellerase® 1500 was dosed at 20 mg total protein/g glucan and the hemicellulases were dosed per g xylan (4.3 mg Xyn3/g of xylan, 1.7 mg Fv3A/g of xylan, 1.4 mg Fv51A/g of xylan, 0.5 mg Fv43D/g of xylan).
  • Each saccharification reaction was incubated at 50° C.
  • FIG. 47D A chromatographic comparison of the enzyme composition produced by three different integrated strains is shown in FIG. 47D .
  • Oligomer sugar concentration was determined by multiplying the percent retained xylose and glucose concentration of the sugar recovery standard (SRS) after acid hydrolysis, by the post acid hydrolysis HPLC sugar concentrations of each sample, then subtracting the monomeric sugar concentration determined in the “monomeric sugar HPLC Analysis” section above.
  • SRS sugar recovery standard
  • enzyme activities which limit the efficacy of enzyme compositions produced by a T. reesei integrated expression strain were identified and enzymes from different species which can compensate for those limiting activities or which could substitute for integrated strain components are exemplified.
  • T. reesei enzyme composition produced by integrated strain H3A ( FIGS. 48A , 49 A, and 50 A) was added as an ultrafiltered (i.e., cell-free) concentrate to 7 mg total protein per g of glucan and xylan combined in the feedstock to all vials.
  • candidate hemicellulases were added as the ultrafiltered preparations from 14 L fermentation cultures expressed by T. reesei Quad delete strain (described in WO 05/001036).
  • the candidate hemicellulases were added at 0, 0.5, 1.0 or 3.0 mg enzyme protein per g of glucan and xylan combined.
  • the hemicellulases included constituents of the enzyme composition produced by the integrated strain itself including:
  • FIG. 48A and FIG. 48B demonstrate that addition of ⁇ -xylosidase activities such as Fusarium verticillioides Fv43D and Fusarium oxysporum Fo43A markedly improved monomer xylose release relative to 7 mg T. reesei integrated strain total protein per g of Glucan and Xylan combined. Significant improvements were even observed at the low additions of 0.5 and 1.0 mg/g.
  • ⁇ -xylosidase activities such as Fusarium verticillioides Fv43D and Fusarium oxysporum Fo43A markedly improved monomer xylose release relative to 7 mg T. reesei integrated strain total protein per g of Glucan and Xylan combined. Significant improvements were even observed at the low additions of 0.5 and 1.0 mg/g.
  • FIG. 49A and FIG. 49B demonstrate that addition of all of the hemicellulases lead to a significant increase in monomer glucose, even >10% at hemicellulase loadings of 1-3 mg per g of Glucan and Xylan combined.
  • FIG. 50A and FIG. 50B demonstrate that addition of GH51 enzymes such as Fusarium verticillioides Fv51A, and especially Podospora anserine Pa51A and Penicillium funiculosum Pfu51A, led to an increase in monomer arabinose level.
  • GH51 enzymes such as Fusarium verticillioides Fv51A, and especially Podospora anserine Pa51A and Penicillium funiculosum Pfu51A
  • the saccharification performance of expressed cellulases and hemicellulases on pretreated raw switchgrass was evaluated.
  • a range of conditions for dilute ammonia pretreatment of switchgrass were evaluated for saccharification performance with an enzyme cocktail composed of enzymes described herein.
  • Pretreatment conditions vary and pretreatment efficacy affects enzymatic hydrolysis performance.
  • Pretreatment of raw switchgrass was performed in sealed, 6′′ ⁇ 1 ⁇ 2′′, stainless steel tubes that were immersed in a heated sand bath.
  • a slurry of raw switchgrass, water, and ammonium hydroxide ( ⁇ 28% solution) was mixed to the desired percent solids and percent ammonia and then loaded into a pretreatment tube. Tubes were then held at the desired temperature (+/ ⁇ 2° C.) for the desired time and then quenched in ice water for approximately 1 min before being brought to room temperature.
  • the pretreated slurry was removed from the tubes and allowed to dry overnight in the hood (>90% solids attainable).
  • Dried pretreated solids were then saccharified at 10% solids, pH 5, 50° C., 200 rpm using Accellerase® 1500, Xyn 3, Fv3A, Fv51A, and Fv43D (25, 9, 7, 3, 1 mg total protein/g glucan or xylan respectively).
  • Accellerase® 1500, Xyn 3, Fv3A, Fv51A, and Fv43D 25, 9, 7, 3, 1 mg total protein/g glucan or xylan respectively.
  • a 5 mL total hydrolysate volume in 20 mL scintillation vials was used.
  • Glucan and xylan yields were based on monomeric glucose and xylose released compared to the glucan or xylan available from the raw biomass. Monomeric sugar concentrations were measured by HPLC (BioRad Aminex HPX 87-H column).
  • Pretreatment time, temperature, percent solids, and percent NH 3 were varied over a wide range in order to optimize saccharification results.
  • Each pretreatment condition that had both glucan and xylan yields better than ⁇ 50% is considered a strong performer.
  • the pretreatment parameters that performed strongly are listed in Table 12 along with their respective glucan, xylan, and total percent yields.
  • Glucan and Xylan conversions are based on monomeric sugars released during saccharification as compared to glucan or xylan theoretically available in the raw switchgrass. Total conversion is glucose and xylose only ( FIG. 51 ).
  • Dilute ammonia pretreated switchgrass was prepared according to the methods and process ranges in WO06110901A: Switchgrass (38.7% glucan, 22.2% xylan, 2.5% arabinan, 23.2% lignin) was hammer-milled to pass through a 1 mm screen, then pretreated at 160° C. for 90 min with 6% NH 3 (weight/weight DM, added as NH 4 OH).
  • This pretreated substrate was treated with enzyme mixes containing Accellerase® 1500, Multifect® Xylanase (both commercial products of Danisco A/S, Genencor Division, Palo Alto, Calif.), Fv3A, Fv51A, and Fv43D in a total reaction mass of 50 g at 15% solids.
  • the total protein (TP) of the commercial products was determined by Biuret assay.
  • the other enzymes were ultra-filtration concentrates (UFCs) following expression in cellulase quad-deleted strains of T. reesei , with TP determined by Total Nitrogen analysis of TCA-precipitable protein. All reactions were dosed with Accellerase® 1500 at 25 mg TP/g Glucan and Multifect® Xylanase (MF Xyl) at 9 mg TP/g Xylan, and Fv3A, Fv51A, and Fv43D were added as indicated in FIG.
  • TP of H3A was determined by Total Nitrogen analysis of TCA-precipitable protein. Enzymes were dosed relative to the starting carbohydrate contents of the switchgrass before pretreatment.
  • the saccharification performance of an enzyme composition produced by integrated T reesei strain H3A was evaluated on industrial hardwood unbleached pulp (derived from Kraft process and oxygen delignification, Smurfit Kappa Cellulose Du Pin, Biganos, France) with the following composition: Glucan 75.1%, Xylan 19.1%, Acid soluble lignin 2.2%.
  • the enzymatic saccharification studies were carried out using NREL standard assay method LAP-009 “Enzymatic Saccharification of Lignocellulosic Biomass” (http://www.nrel.gov/biomass/pdfs/42629.pdf), except that the cellulose loading was different (varying from 9.3-20%) and a total mass of 100 g was used.
  • the experimental condition was 200 rpm and pH 5.0, 50° C. Enzyme was dosed at 20 mg TP/g glucan (based on final dry matter) at the start of the experiment. Samples were taken at timed intervals if they were liquefied, and then analyzed by HPLC for sugar concentration. Glucose, xylose, and cellobiose concentration were determined using a Waters HPLC system (Alliance system, Waters Corp., Milford, Mass.). The HPLC column used for sugar analysis was from BioRad (Aminex HPX-87H ion exclusion column (300 mm ⁇ 7.8 mm), BioRad Inc., Hercules, Calif.).
  • Results showed high levels of glucan and xylan conversion to monomers (up to 89% and 90%, respectively) with the enzyme composition produced by integrated strain H3A. Conversions increased with higher enzyme loadings and longer saccharification times. Conversion was lower when the solids were at 20% than at 15%, but this lower conversion at 20% could be partially mitigated by using a fed-batch process.
  • the saccharification performance of an enzyme composition produced by an integrated T reesei strain (H3A) on steam-expanded sugarcane bagasse was evaluated at 7% cellulose loading.
  • the bagasse was pretreated by steam injection in a StakeTech reactor at 210 psig, 200° C. with a 4 min residence time.
  • the pretreated material had the following composition: Glucan 40.9%, Xylan 20.8%, Lignin 27%.
  • the integrated strain supernatant was dosed at 10, 20, 30, 50 or 80 mg TP/g glucan (based on final dry matter and composition of the pretreated substrate). Saccharification was carried out in a 5 mL reaction volume at 50° C., pH 5 for 3 days. The results ( FIG.
  • Accellerase® 1500 (AC 1500): 20 mg TP/g glucan and 45 mg TP/g glucan; Accellerase® 1500+Multifect® Xylanase (MF): (25 mg/g glucan+9 mg TP/g xylan) and (25 mg TP/g glucan+20 mg TP/g xylan); Accellerase® 1500+Xyn 3+Fv3A+Fv51A+Fv43D: (25 mg TP/g glucan+9 mg TP/g xylan+7 mg TP/g xylan+3 mg TP/g xylan+1 mg TP/g xylan) (the full enzyme “blend”).
  • AC 1500 20 mg TP/g glucan and 45 mg TP/g glucan
  • the total protein (TP) of the commercial products (Accellerase® 1500 and Multifect® Xylanase: Danisco US Inc., Genencor) were determined by Biuret assay.
  • the other enzymes were ultra-filtration concentrates (UFCs) following expression in cellulase quad-deleted strains of T. reesei (as described earlier)—their TP were determined by Total Nitrogen analysis of TCA-precipitable protein. All enzymes were dosed relative to the starting carbohydrate contents of the corn fiber before pretreatment. Enzymatic saccharification was carried out at 200 rpm and 50° C. for 24 h, 48 h and 120 h.

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