Processes Of Producing Ethanol Using A Fermentation Organism

Abstract

The invention relates to improved processes of producing ethanol from starch-containing material wherein saccharification and/or fermentation is done at a temperature below the initial gelatinization temperature in the presence of glucoamylase and alpha-amylase, and optionally a protease and/or a cellulolytic enzyme composition; wherein the fermenting organism is Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, and compositions comprising a Saccharomyces yeast strain of the invention and naturally occurring and/or non-naturally occurring components.

Description

TECHNICAL FIELD

[0001] The present invention relates to improved raw starch hydrolysis processes of producing ethanol from starch-containing materials using a fermenting organism. The present invention also relates to a Saccharomyces strain having improved ability to ferment sugars to ethanol, to methods for the production of Saccharomyces strains having improved ability to ferment sugars to ethanol, and the use of Saccharomyces yeast strains having improved ability to ferment sugars to ethanol in the production of ethanol. Finally the invention relates to compositions comprising a Saccharomyces yeast strain of the invention and a naturally occurring and/or a non-naturally occurring component.

REFERENCE TO A SEQUENCE LISTING

[0002] This application contains a Sequence Listing in computer readable form. The computer readable form is incorporated herein by reference.

BACKGROUND ART

[0003] Processes of producing ethanol from starch-containing material are well-known in the art and used commercially today. The production of ethanol as a bio-fuel has become a major industry, with in excess of 21 billion gallons of ethanol being produced worldwide in 2012.

[0004] When producing ethanol, starch is conventionally converted into dextrins using a liquefying enzyme (e.g., Bacillus alpha-amylase) at temperatures above the initial gelatinization temperature of starch. The generated dextrins are hydrolyzed into sugars using a saccharifying enzyme (e.g., glucoamylase) and fermented into the desired fermentation product using a fermenting organism such as a yeast strain derived from Saccharomyces cerevisiae. Typically hydrolysis and fermentation are done in a simultaneous saccharification and fermentation (SSF) step.

[0005] Another type of process is also used commercially today. Starch is converted into sugars by enzymes at temperatures below the initial gelatinization temperature of the starch in question and converted into ethanol by yeast, typically derived from Saccharomyces cerevisiae. This type of process is referred to as a raw starch hydrolysis (RSH) process, or alternatively a "one-step process" or "no cook" process.

[0006] Yeast which are used for production of ethanol for use as fuel, such as in the corn ethanol industry, require several characteristics to ensure cost effective production of the ethanol. These characteristics include ethanol tolerance, low by-product yield, rapid fermentation, and the ability to limit the amount of residual sugars remaining in the ferment. Such characteristics have a marked effect on the viability of the industrial process.

[0007] Yeast of the genus Saccharomyces exhibit many of the characteristics required for production of ethanol. In particular, strains of Saccharomyces cerevisiae are widely used for the production of ethanol in the fuel ethanol industry. Strains of Saccharomyces cerevisiae that are widely used in the fuel ethanol industry have the ability to produce high yields of ethanol under fermentation conditions found in, for example, the fermentation of corn mash. An example of such a strain is the yeast used in commercially available ethanol yeast product called Ethanol Red.TM..

[0008] Strains of Saccharomyces cerevisiae are used in the fuel ethanol industry to ferment sugars such as glucose, fructose, sucrose and maltose to produce ethanol via the glycolytic pathway. These sugars are obtained from sources such as corn and other grains, sugar juice, molasses, grape juice, fruit juices, and starchy root vegetables and may include the breakdown of cellulosic material into glucose.

[0009] Although strains of Saccharomyces cerevisiae currently used in the fuel ethanol industry are well suited to ethanol production, there is an increasing need for improvements in the efficiency of ethanol production owing to the increased demand for ethanol as a fuel, and the increased availability of starch in new strains of corn.

[0010] There is therefore a need for new strains of Saccharomyces capable of improving the efficiency of ethanol production in industrial scale fermentation.

[0011] Further, despite significant improvement of ethanol production processes over the past decade there is still a desire and need for providing further improved processes of producing ethanol from starch-containing material that, e.g., can provide a higher ethanol yield.

SUMMARY OF THE INVENTION

[0012] The invention concerns improved raw starch hydrolysis processes for producing ethanol using a fermenting organism. The invention also relates to yeast strains suitable for use in processes and methods of the invention as well as compositions comprising a yeast strain of the invention.

[0013] More specifically in a first aspect the invention relates to processes of producing ethanol from starch-containing material, such as granular starch, comprising:

[0014] (a) saccharifying a starch-containing material at a temperature below the initial gelatinization temperature; and

[0015] (b) fermenting using a fermentation organism;

[0016] wherein

[0017] saccharification and/or fermentation is done in the presence of the following enzymes: glucoamylase and alpha-amylase, and optionally protease; and

[0018] the fermenting organism is Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037.

[0019] A raw starch hydrolysis process of the invention results in one or more, such as all, of the following improvements compared to a corresponding process carried out under the same conditions using Ethanol Red.TM. ("ER") as the fermenting organism:

[0020] increased ethanol yield;

[0021] reduced glycerol level;

[0022] reduced lactic acid level;

[0023] faster fermentation kinetics.

[0024] Examples of suitable enzymes used, especially glucoamylases, alpha-amylases, proteases, cellulolytic enzyme compositions etc are described in the "Enzymes And Enzyme Blends Used In A Process Of The Invention" section below.

[0025] In a preferred embodiment the following enzymes are present and/or added in saccharification and/or fermentation: Trametes cingulata glucoamylase, preferably the one shown in SEQ ID NO: 12 herein and an alpha-amylase. In a preferred embodiment the alpha-amylase is a Rhizomucor pusillus alpha-amylase, preferably the Rhizomucor pusillus alpha-amylase with a linker and starch-binding domain, in particular the Aspergillus niger glucoamylase linker and starch-binding domain (SBD) shown in SEQ ID NO: 13 herein.

[0026] In a preferred embodiment the following enzymes are present and/or added in saccharification and/or fermentation: Gloeophyllum glucoamylase, in particular Gloeophyllum trabeum glucoamylase, preferably the one shown in SEQ ID NO: 18 herein, especially one having one or more of the following substitutions: S95P, A121P, especially S95P+A121P and an alpha-amylase. In a preferred embodiment the alpha-amylase is derived from Rhizomucor pusillus, preferably Rhizomucor pusillus alpha-amylase with a linker and starch-binding domain, in particular the Aspergillus niger glucoamylase linker and starch-binding domain (SBD), disclosed as V039 in Table 5 in WO 2006/069290 or shown as SEQ ID NO: 13 herein.

[0027] In another preferred embodiment the following enzymes are present and/or added in saccharification and/or fermentation: Gloeophyllum glucoamylase, in particular Gloeophyllum trabeum glucoamylase, preferably the one shown in SEQ ID NO: 18 herein, preferably one having one or more of the following substitutions: S95P, A121P, especially S95P+A121P, and an alpha-amylase, in particular one derived from Rhizomucor pusillus, preferably Rhizomucor pusillus alpha-amylase with a linker and starch-binding domain (SBD), in particular an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), preferably the one shown in SEQ ID NO: 13 herein, preferably one having one or more of the following substitutions: G128D, D143N, especially G128D+143N.

[0028] In another preferred embodiment the following enzymes are present and/or added in saccharification and/or fermentation: Pycnoporus glucoamylase, in particular Pycnoporus sanguineus glucoamylase, preferably the one shown in SEQ ID NO: 17 herein and an alpha-amylase. In a preferred embodiment the alpha-amylase is derived from Rhizomucor pusillus, preferably with a linker and starch-binding domain (SBD), in particular an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), preferably the one disclosed as V039 in Table 5 in WO 2006/069290 or shown as SEQ ID NO: 13 herein, preferably one having one or more of the following substitutions: G128D, D143N, especially G128D+D143N.

[0029] In an embodiment a protease is present and/or added in saccharification and/or fermentation. In a preferred embodiment the protease is a metallo protease or a serine protease. In an embodiment the metallo protease is derived from a strain of the genus Thermoascus, preferably a strain of Thermoascus aurantiacus, especially Thermoascus aurantiacus CGMCC No. 0670, such as the metallo protease disclosed as the mature part of SEQ ID NO: 2 disclosed in WO 2003/048353 or the mature polypeptide of SEQ ID NO: 3 herein.

[0030] In an embodiment a cellulolytic enzyme composition is present and/or added in saccharification and/or fermentation or simultaneous saccharification and fermentation (SSF).

[0031] In a preferred embodiment the cellulolytic enzyme composition is derived from Trichoderma reesei, preferably further comprising Thermoascus aurantiacus GH61A polypeptide having cellulolytic enhancing activity (e.g., SEQ ID NO: 2 in WO 2005/074656 or SEQ ID NO: 9 herein) and Aspergillus fumigatus beta-glucosidase (e.g., SEQ ID NO: 2 of WO 2005/047499 or SEQ ID NO: 8 herein), or a cellulolytic enzyme composition derived from Trichoderma reesei, preferably further comprising Penicillium emersonii GH61A polypeptide, e.g., the one disclosed as SEQ ID NO: 2 in WO 2011/041397 or SEQ ID NO: 10 herein, and Aspergillus fumigatus beta-glucosidase, e.g., the one disclosed as SEQ ID NO: 2 in WO 2005/047499 or SEQ ID NO: 8 herein, or a variant thereof, preferably a variant having one of, preferably all of, the following substitutions: F100D, S283G, N456E, F512Y, Aspergillus fumigatus CBH1, e.g., the one disclosed as SEQ ID NO: 6 in WO2011/057140 and SEQ ID NO: 6 herein, and Aspergillus fumigatus CBH II, e.g., the one disclosed as SEQ ID NO: 18 in WO 2011/057140 and as SEQ ID NO: 7 herein.

[0032] In a preferred embodiment the glucoamylase to alpha-amylase ratio is between 99:1 and 1:2, such as between 98:2 and 1:1, such as between 97:3 and 2:1, such as between 96:4 and 3:1, such as 97:3, 96:4, 95:5, 94:6, 93:7, 90:10, 85:15, 83:17 or 65:35 (mg EP glucoamylase: mg EP alpha-amylase).

[0033] In a preferred embodiment the total dose of glucoamylase and alpha-amylase is from 10-1,000 .mu.g/g DS, such as from 50-500 .mu.g/g DS, such as 75-250 .mu.g/g DS.

[0034] In a preferred embodiment the total dose of cellulolytic enzyme composition added is from 10-500 .mu.g/g DS, such as from 20-400 .mu.g/g DS, such as 20-300 .mu.g/g DS.

[0035] In an embodiment the dose of protease added is from 1-200 .mu.g/g DS, such as from 2-100 .mu.g/g DS, such as 3-50 .mu.g/g DS.

[0036] In a preferred embodiment saccharification step (a) and fermentation step (b) are carried out simultaneously.

[0037] A second aspect provides a Saccharomyces yeast strain deposited under the Budapest Treaty and having NMI accession no. V14/004037 (Saccharomyces cerevisiae MBG4851), or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037.

[0038] A third aspect provides a method of producing a Saccharomyces strain having defining characteristics of strain V14/004037 (Saccharomyces cerevisiae MBG4851), comprising:

(a) providing: (i) a first yeast strain; and (ii) a second yeast strain, wherein the second yeast strain is strain V14/004037 or a derivative of strain V14/004037; (b) culturing the first yeast strain and the second yeast strain under conditions which permit combining of DNA between the first yeast strain and the second yeast strain; (c) screening or selecting for a derivative of strain V14/004037; (d) optionally repeating steps (b) and (c) with the screened or selected strain from step (c) as the first and/or second strain, until a derivative is obtained which exhibits defining characteristics of strain V14/004037.

[0039] A fourth aspect provides a Saccharomyces strain produced by the method of the third aspect.

[0040] A fifth aspect provides a method of producing ethanol, comprising incubating a strain of the second or fourth aspect with a substrate comprising a fermentable sugar under conditions which promote fermentation of the fermentable sugar to produce ethanol.

[0041] A sixth aspect provides use of a strain of the second or fourth aspect in the production of ethanol.

[0042] A seventh provides a method of producing distiller's grain, comprising:

(a) incubating a Saccharomyces strain of the second or fourth aspect with a substrate comprising fermentable sugar under conditions which allow fermentation of the fermentable sugar to produce ethanol and distiller's grains; (b) isolating the distiller's grains.

[0043] An eighth aspect provides distiller's grain produced by the method of the seventh aspect.

[0044] A ninth aspect provides use of a strain of the second or fourth aspect in the production of distiller's grains.

[0045] A tenth aspect provides use of a strain of the second or fourth aspect in the production of a Saccharomyces strain which exhibits one or more defining characteristics of strain V14/004037.

[0046] An eleventh aspect provides a composition comprising a Saccharomyces strain of the second or fourth aspect.

[0047] A twelfth aspect provides processes of using a Saccharomyces strain of the second or fourth aspect in a process of the first aspect.

[0048] Finally the invention relates to compositions comprising a Saccharomyces yeast strain of the invention and naturally occurring and/or non-naturally occurring components.

BRIEF DESCRIPTION OF THE FIGURES

[0049] FIG. 1 shows the ethanol titers during RSH fermentation.

[0050] FIG. 2 shows the glycerol titers during RSH fermentation.

[0051] FIG. 3 shows the lactic acid levels during RSH Bioreactor Fermentations.

DETAILED DESCRIPTION OF THE INVENTION

[0052] The invention concerns improved raw starch hydrolysis processes of producing ethanol from starch-containing material using a fermenting organism of the invention. A process for producing ethanol according to the invention is carried out as a raw starch hydrolysis (RSH) process. A raw starch hydrolysis process is a process where starch, typically granular starch, is converted into dextrins/sugars by raw starch degrading enzymes at temperatures below the initial gelatinization temperature of the starch in question and converted into ethanol by yeast, typically Saccharomyces cerevisiae. This type of process is often alternatively referred to as a "one-step process" or "no cook" process.

[0053] Specifically, the invention relates to processes of ethanol production from starch-containing material, such as granular starch, comprising:

[0054] (a) saccharifying a starch-containing material at a temperature below the initial gelatinization temperature; and

[0055] (b) fermenting using a fermentation organism;

[0056] wherein

[0057] saccharification and/or fermentation is done in the presence of the following enzymes: glucoamylase and alpha-amylase, and optionally protease; and

[0058] the fermenting organism is Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037.

[0059] A raw starch hydrolysis process of the invention results in an increased ethanol yield compared to a corresponding process where Ethanol Red.TM. ("ER") is used under the same conditions. See for instance, Example 1, table 2; Example 2, table 6; and Example 3, table 10).

[0060] A raw starch hydrolysis process of the invention results in a reduced glycerol level compared to a corresponding process where Ethanol Red.TM. ("ER") is used under the same conditions. See for instance, Example 1, table 3; Example 2, table 7; and Example 3, table 11).

[0061] A raw starch hydrolysis process of the invention results in a reduced lactic acid level compared to a corresponding process where Ethanol Red.TM. ("ER") is used under the same conditions. See for instance, Example 1, table 4; Example 2, table 8; and Example 3, table 12).

[0062] The process conditions according to the invention may be as described in any of Examples 1-3.

[0063] In processes of the invention the starch does not gelatinize as the process is carried out at temperatures below the initial gelatinization temperature of the starch in question.

[0064] The term "initial gelatinization temperature" means the lowest temperature at which starch gelatinization commences. In general, starch heated in water begins to gelatinize between about 50.degree. C. and 75.degree. C. The exact temperature of gelatinization depends on the specific starch and depends on the degree of cross-linking of the amylopectin. The initial gelatinization temperature can readily be determined by the skilled artisan. The initial gelatinization temperature may vary according to the plant species, to the particular variety of the plant species as well as with the growth conditions. In context of this invention the initial gelatinization temperature of a given starch-containing material may be determined as the temperature at which birefringence is lost in 5% of the starch granules using the method described by Gorinstein. S. and Lii. C., Starch/Starke, Vol. 44 (12) pp. 461-466 (1992).

[0065] Therefore, according to the process of the invention ethanol is produced from un-gelatinized (i.e., uncooked), preferably milled grains, such as corn, or small grains such as wheat, oats, barley, rye, rice, or cereals such as sorghum. Examples of suitable starch-containing starting materials are listed in the section "Starch-Containing Materials"-section below.

[0066] In a preferred embodiment the enzymes may be added as one or more enzyme blends. According to the invention the fermentation product, i.e., ethanol, is produced without liquefying the starch-containing material. The process of the invention includes saccharifying (e.g., milled) starch-containing material, especially granular starch, below the initial gelatinization temperature, in the presence of at least a glucoamylase and an alpha-amylase and optionally a protease and/or a cellulolytic enzyme composition. The dextrins/sugars generated during saccharification can may according to the invention be simultaneously fermented into ethanol by a suitable fermenting organism, especially Saccharomyces cerevisiae MBG4851 or a fermenting organism having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having the defining characteristics of strain V14/004037, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037. See the "Fermenting Organisms"-section below.

[0067] In a preferred embodiment step (a) and step (b) are carried out simultaneously (i.e., one-step fermentation). However, step (a) and step (b) may also be carried our sequentially.

[0068] Before step (a) an aqueous slurry of starch-containing material, such as granular starch, having 10-55 wt.-% dry solids (DS), preferably 25-45 wt.-% dry solids, more preferably 30-40% dry solids of starch-containing material may be prepared. The slurry may include water and/or process waters, such as stillage (backset), scrubber water, evaporator condensate or distillate, side-stripper water from distillation, or process water from other fermentation product plants. Because the process of the invention is carried out below the initial gelatinization temperature and thus no significant viscosity increase takes place, high levels of stillage may be used, if desired. In an embodiment the aqueous slurry contains from about 1 to about 70 vol.-%, preferably 15-60% vol.-%, especially from about 30 to 50 vol.-% water and/or process waters, such as stillage (backset), scrubber water, evaporator condensate or distillate, side-stripper water from distillation, or process water from other fermentation product plants, or combinations thereof, or the like.

[0069] In an embodiment backset, or another recycled stream, is added to the slurry before step (a), or to the saccharification (step (a)), or to the simultaneous saccharification and fermentation steps (combined step (a) and step (b)).

[0070] After being subjected to a process of the invention at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or preferably at least 99% of the dry solids in the starch-containing material are converted into a soluble starch hydrolysate.

[0071] A process of the invention is conducted at a temperature below the initial gelatinization temperature, which means that the temperature at which a separate step (a) is carried out typically lies in the range between 25-75.degree. C., such as between 30-70.degree. C., or between 45-60.degree. C.

[0072] In a preferred embodiment the temperature during fermentation in step (b) or simultaneous saccharification and fermentation in steps (a) and (b) is between 25.degree. C. and 40.degree. C., preferably between 28.degree. C. and 36.degree. C., such as between 28.degree. C. and 35.degree. C., such as between 28.degree. C. and 34.degree. C., such as around 32.degree. C.

[0073] In an embodiment of the invention fermentation or SSF is carried out for 30 to 150 hours, preferably 48 to 96 hours.

[0074] In an embodiment fermentation or SSF is carried out so that the sugar level, such as glucose level, is kept at a low level, such as below 6 wt.-%, such as below about 3 wt.-%, such as below about 2 wt.-%, such as below about 1 wt.-%., such as below about 0.5%, or below 0.25% wt.-%, such as below about 0.1 wt.-%. Such low levels of sugar can be accomplished by simply employing adjusted quantities of enzymes and fermenting organism. A skilled person in the art can easily determine which doses/quantities of enzyme and fermenting organism to use. The employed quantities of enzyme and fermenting organism may also be selected to maintain low concentrations of maltose in the fermentation broth. For instance, the maltose level may be kept below about 0.5 wt.-%, such as below about 0.2 wt.-%.

[0075] The process of the invention may be carried out at a pH from 3 and 7, preferably from 3 to 6, or more preferably from 3.5 to 5.0.

[0076] The term "granular starch" means raw uncooked starch, i.e., starch in its natural form found in, e.g., cereal, tubers or grains. Starch is formed within plant cells as tiny granules insoluble in water. When put in cold water, the starch granules may absorb a small amount of the liquid and swell. At temperatures up to around 50.degree. C. to 75.degree. C. the swelling may be reversible. However, at higher temperatures an irreversible swelling called "gelatinization" begins. The granular starch may be a highly refined starch, preferably at least 90%, at least 95%, at least 97% or at least 99.5% pure, or it may be a more crude starch-containing materials comprising (e.g., milled) whole grains including non-starch fractions such as germ residues and fibers.

[0077] The raw material, such as whole grains, may be reduced in particle size, e.g., by milling, in order to open up the structure and allowing for further processing. Examples of suitable particle sizes are disclosed in U.S. Pat. No. 4,514,496 and WO2004/081193 (incorporated by reference). Two processes are preferred according to the invention: wet and dry milling. In dry milling whole kernels are milled and used. Wet milling gives a good separation of germ and meal (starch granules and protein) and is often applied at locations where the starch hydrolysate is used in production of, e.g., syrups. Both dry and wet milling is well known in the art of starch processing.

[0078] In an embodiment the particle size is reduced to between 0.05 to 3.0 mm, preferably 0.1-0.5 mm, or so that at least 30%, preferably at least 50%, more preferably at least 70%, even more preferably at least 90% of the starch-containing material fit through a sieve with a 0.05 to 3.0 mm screen, preferably 0.1-0.5 mm screen. In a preferred embodiment starch-containing material is prepared by reducing the particle size of the starch-containing material, preferably by milling, such that at least 50% of the starch-containing material has a particle size of 0.1-0.5 mm.

[0079] According to the invention the enzymes are added so that the glucoamylase is present in an amount of 0.001 to 10 AGU/g DS, preferably from 0.01 to 5 AGU/g DS, especially 0.1 to 0.5 AGU/g DS.

[0080] According to the invention the enzymes are added so that the alpha-amylase is present or added in an amount of 0.001 to 10 AFAU/g DS, preferably from 0.01 to 5 AFAU/g DS, especially 0.3 to 2 AFAU/g DS or 0.001 to 1 FAU-F/g DS, preferably 0.01 to 1 FAU-F/g DS.

[0081] According to the invention the enzymes are added so that the cellulolytic enzyme composition is present or added in an amount 1-10,000 micro grams EP/g DS, such as 2-5,000, such as 3 and 1,000, such as 4 and 500 micro grams EP/g DS.

[0082] According to the invention the enzymes are added so that the cellulolytic enzyme composition is present or added in an amount in the range from 0.1-100 FPU per gram total solids (TS), preferably 0.5-50 FPU per gram TS, especially 1-20 FPU per gram TS.

[0083] In an embodiment of the invention the enzymes are added so that the protease is present in an amount of 0.0001-1 mg enzyme protein per g DS, preferably 0.001 to 0.1 mg enzyme protein per g DS. Alternatively, the protease is present and/or added in an amount of 0.0001 to 1 LAPU/g DS, preferably 0.001 to 0.1 LAPU/g DS and/or 0.0001 to 1 mAU-RH/g DS, preferably 0.001 to 0.1 mAU-RH/g DS.

[0084] In an embodiment of the invention the enzymes are added so that the protease is present or added in an amount in the range 1-1,000 .mu.g EP/g DS, such as 2-500 .mu.g EP/g DS, such as 3-250 .mu.g EP/g DS.

[0085] In a preferred embodiment ratio between glucoamylase and alpha-amylase is between 99:1 and 1:2, such as between 98:2 and 1:1, such as between 97:3 and 2:1, such as between 96:4 and 3:1, such as 97:3, 96:4, 95:5, 94:6, 93:7, 90:10, 85:15, 83:17 or 65:35 (mg EP glucoamylase: mg EP alpha-amylase).

[0086] In a preferred embodiment the total dose of glucoamylase and alpha-amylase is according to the invention from 10-1,000 .mu.g/g DS, such as from 50-500 .mu.g/g DS, such as 75-250 .mu.g/g DS.

[0087] In a preferred embodiment the total dose of cellulolytic enzyme composition added is from 10-500 .mu.g/g DS, such as from 20-400 .mu.g/g DS, such as 20-300 .mu.g/g DS.

[0088] In an embodiment the dose of protease added is from 1-200 .mu.g/g DS, such as from 2-100 .mu.g/g DS, such as 3-50 .mu.g/g DS.

Starch-Containing Materials

[0089] According to the process of the invention any suitable starch-containing starting material, including granular starch (raw uncooked starch), may be used. The starting material is generally selected based on the desired fermentation product. Examples of starch-containing starting materials, suitable for use in processes of the present invention, include cereal, tubers or grains. Specifically the starch-containing material may be corn, wheat, barley, rye, milo, sago, cassava, tapioca, sorghum, oats, rice, peas, beans, or sweet potatoes, or mixtures thereof. Contemplated are also waxy and non-waxy types of corn and barley.

[0090] In a preferred embodiment the starch-containing starting material is corn.

[0091] In a preferred embodiment the starch-containing starting material is wheat.

[0092] In a preferred embodiment the starch-containing starting material is barley.

[0093] In a preferred embodiment the starch-containing starting material is rye.

[0094] In a preferred embodiment the starch-containing starting material is milo.

[0095] In a preferred embodiment the starch-containing starting material is sago.

[0096] In a preferred embodiment the starch-containing starting material is cassava.

[0097] In a preferred embodiment the starch-containing starting material is tapioca.

[0098] In a preferred embodiment the starch-containing starting material is sorghum.

[0099] In a preferred embodiment the starch-containing starting material is rice,

[0100] In a preferred embodiment the starch-containing starting material is peas.

[0101] In a preferred embodiment the starch-containing starting material is beans.

[0102] In a preferred embodiment the starch-containing starting material is sweet potatoes.

[0103] In a preferred embodiment the starch-containing starting material is oats.

Fermenting Organisms

[0104] According to the process of the invention Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, is used for converting saccharified starch-containing material, such as granular starch, into ethanol.

[0105] In an embodiment the fermenting organism strain has properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, as it provides an increase in ethanol yield compared to Ethanol Red.TM. ("ER") under the same process conditions.

[0106] In an embodiment the fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, produces reduced levels of lactic acid compared to Ethanol Red.TM. ("ER") under the same process conditions.

[0107] In an embodiment the fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, produces reduced levels of glycerol compared to Ethanol Red.TM. ("ER") under the same process conditions.

[0108] In an embodiment the fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, has faster fermentation kinetics compared to Ethanol Red.TM. ("ER") under the same process conditions.

[0109] In an embodiment the fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, has one or more, such as all, of the following properties and defining characteristics:

[0110] increases ethanol yield compared to Ethanol Red.TM. ("ER") under the same process conditions;

[0111] reduces the level of lactic acid compared to Ethanol Red.TM. ("ER") under the same process conditions;

[0112] reduces the level of glycerol compared to Ethanol Red.TM. under the same process conditions;

[0113] has faster fermentation kinetics compared to Ethanol Red.TM. ("ER") under the same process conditions.

[0114] The process conditions according to the invention may be as described in any of Examples 1-3.

[0115] In an embodiment of the invention the fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, provides an ethanol yield boost/increase over Ethanol Red.TM. ("ER") of more than 0.5% (after 72 hours fermentation) determined using the process set-up and conditions used in Example 1.

[0116] In an embodiment of the invention the fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, provides an ethanol yield boost/increase over Ethanol Red.TM. ("ER") of more than 1.0% (after 88 hours fermentation) determined using the process set-up and conditions used in Example 1.

[0117] In an embodiment of the invention the fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, provides an ethanol yield boost/increase of more than 1.0%, such as more than 2.0%, such as more than 3.0%, such as more than 4.0% over Ethanol Red.TM. ("ER") when determined using the process set-up and conditions used in Example 2 (i.e., 95 hours fermentation).

[0118] In an embodiment of the invention the fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, provides a reduction in lactic acid of more than 50%, such as more than 60% (after 72 hours fermentation) over Ethanol Red.TM. ("ER") when determined using the process set-up and conditions used in Example 1.

[0119] In an embodiment of the invention the fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, provides a reduction in lactic acid of more than 20%, such as more than 30% (after 95 hours fermentation) over Ethanol Red.TM. ("ER") when determined using the process set-up and conditions used in Example 2.

[0120] In an embodiment of the invention the fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, provides a reduction in lactic acid of more than 30%, such as more than 40% (after 72 hours fermentation using PsAMG) over Ethanol Red.TM. ("ER") when determined using the process set-up and conditions used in Example 3.

[0121] In an embodiment of the invention the fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, provides a reduction in lactic acid of more than 20%, such as more than 25%, such as more than 30% (after 95 hours fermentation) over Ethanol Red.TM. ("ER") when determined using the process set-up and conditions used in Example 2.

[0122] In an embodiment of the invention the fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, provides a reduction in glycerol levels of more than 10.0%, such as more than 15.0%, such as more than 20.0% over Ethanol Red.TM. ("ER") when determined using the process set-up and conditions used in Example 1 (i.e., after 72 hours fermentation).

[0123] In an embodiment of the invention the fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, provides a reduction in glycerol levels of more than 5.0%, such as more than 10.0%, such as more than 12.0%, such as more than 14.0% over Ethanol Red.TM. ("ER") when determined using the process set-up and conditions used in Example 2 (i.e., after 95 hours fermentation).

Fermentation Medium

[0124] The term "fermentation medium" refers to the environment in which fermentation is carried out and which includes the fermentable substrate, that is, a carbohydrate source (e.g., glucose) that can be metabolized by the fermenting organism(s).

[0125] The fermentation medium may comprise nutrients and/or growth stimulator(s) for the fermenting organism(s). Nutrient and growth stimulators are widely used in the art of fermentation and include nitrogen sources, such as ammonia; urea, vitamins; and minerals, or combinations thereof.

Recovery

[0126] Subsequent to fermentation, the fermentation product (i.e., ethanol) may be separated from the fermentation medium. The slurry may be distilled to extract the desired fermentation product (i.e., ethanol). Alternatively the desired fermentation product (i.e., ethanol) may be extracted from the fermentation medium by micro or membrane filtration techniques. The fermentation product (i.e., ethanol) may also be recovered by stripping or other method well known in the art.

Enzymes and Enzyme Blends Used in a Process of the Invention

[0127] According to the invention a glucoamylase and an alpha-amylase are present and/or added in saccharification step (a) and/or fermentation step (b) (e.g., simultaneous saccharification and fermentation). Optionally a protease and/or a cellulolytic enzyme composition is(are) also present and/or added. Other enzymes such as pullulanases, pectinases, and/or trehalases may also be present and/or added.

[0128] Suitable and specifically contemplated enzymes and enzyme combinations (e.g., blends) are described below.

[0129] In an embodiment the following enzymes are present and/or added during saccharification and/or fermentation: Trametes glucoamylase, in particular Trametes cingulata glucoamylase, preferably the one shown in SEQ ID NO: 12 herein and an alpha-amylase.

[0130] In an embodiment the glucoamylase is derived from Trametes cingulata, such as the one shown in SEQ ID NO: 12 herein, or a glucoamylase selected from the group consisting of:

(i) a glucoamylase comprising the mature polypeptide of SEQ ID NO: 12 herein; (ii) a glucoamylase comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 12 herein.

[0131] In an embodiment the following enzymes are present and/or added during saccharification and/or fermentation: Gloeophyllum glucoamylase, preferably Gloeophyllum trabeum glucoamylase, especially the Gloeophyllum trabeum glucoamylase shown in SEQ ID NO: 18 herein and an alpha-amylase.

[0132] In an embodiment the glucoamylase is derived from Gloeophyllum trabeum, such as the one shown in SEQ ID NO: 18 herein, or a glucoamylase selected from the group consisting of:

(i) a glucoamylase comprising the mature polypeptide of SEQ ID NO: 18 herein; (ii) a glucoamylase comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 18 herein.

[0133] In a preferred embodiment the Gloeophyllum trabeum glucoamylase, such as the one shown in SEQ ID NO: 18, has one of the following substitutions: V59A; S95P; A121P; T119W; S95P+A121P; V59A+S95P; S95P+T119W; V59A+S95P+A121P; or S95P+T119W+A121P, especially S95P+A121P (using SEQ ID NO: 18 for numbering).

[0134] The alpha-amylase used in a process of the invention is typically a fungal alpha-amylase, such as an acid fungal alpha-amylase. In a preferred embodiment the alpha-amylase is derived from Rhizomucor pusillus, preferably Rhizomucor pusillus alpha-amylase with a linker and starch-binding domain (SBD), in particular an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), preferably the one disclosed as V039 in Table 5 in WO 2006/069290 or SEQ ID NO: 13 herein.

[0135] In an embodiment the alpha-amylase is a Rhizomucor pusillus alpha-amylase or the Rhizomucor pusillus alpha-amylase with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD) shown in SEQ ID NO: 13 herein, especially one having at least one of the following substitutions or combinations of substitutions: D165M; Y141W; Y141R; K136F; K192R; P224A; P224R; S123H+Y141W; G20S+Y141W; A76G+Y141W; G128D+Y141W; G128D+D143N; P219C+Y141W; N142D+D143N; Y141W+K192R; Y141W+D143N; Y141W+N383R; Y141W+P219C+A265C; Y141W+N142D+D143N; Y141W+K192R V410A; G128D+Y141W+D143N; Y141W+D143N+P219C; Y141W+D143N+K192R; G128D+D143N+K192R; Y141W+D143N+K192R+P219C; G128D+Y141W+D143N+K192R; or G128D+Y141W+D143N+K192R+P219C, especially G128D+D143N (using SEQ ID NO: 13 for numbering).

[0136] In an embodiment the alpha-amylase is selected from the group consisting of:

(i) an alpha-amylase comprising the mature polypeptide of SEQ ID NO: 13 herein; (ii) an alpha-amylase comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 13 herein.

[0137] In an embodiment the following enzymes are present and/or added in saccharification and/or fermentation: Trametes glucoamylase, in particular Trametes cingulata glucoamylase, especially the Trametes cingulata glucoamylase shown in SEQ ID NO: 12 herein and an alpha-amylase derived from Rhizomucor pusillus, preferably with a linker and starch-binding domain (SBD), in particular an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), especially the one disclosed as V039 in Table 5 in WO 2006/069290 or SEQ ID NO: 13 herein.

[0138] In an embodiment the following enzymes are present and/or added in saccharification and/or fermentation: Gloeophyllum glucoamylase, in particular Gloeophyllum trabeum glucoamylase, preferably the one shown in SEQ ID NO: 18 and an alpha-amylase derived from Rhizomucor pusillus, preferably with a linker and starch-binding domain (SBD), in particular an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), such as the one disclosed as V039 in Table 5 in WO 2006/069290 or SEQ ID NO: 13 herein.

[0139] In another preferred embodiment the enzymes present and/or added comprises the Gloeophyllum trabeum glucoamylase shown in SEQ ID NO: 18 herein having one or more of the following substitutions: S95P, A121P, especially S95P+A121P (using SEQ ID NO: 13 herein for numbering) and the alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), preferably one shown in SEQ ID NO: 13 herein, preferably one having one or more of the following substitutions: G128D, D143N, especially G128D+D143N (using SEQ ID NO: 13 for numbering).

[0140] In an embodiment the following enzymes are present and/or added in saccharification and/or fermentation: the Pycnoporus sanguineus glucoamylase shown in SEQ ID NO: 17 and the Rhizomucor pusillus alpha-amylase with a linker and starch-binding domain (SBD), in particular an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), especially the one shown in SEQ ID NO: 13 herein.

[0141] In an especially preferred embodiment the enzymes present and/or added in saccharification and or fermentation comprises a Pycnoporus sanguineus glucoamylase, such as the one shown in SEQ ID NO: 17 herein and the alpha-amylase derived from Rhizomucor pusillus with a linker and starch-binding domain (SBD), in particular an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), preferably the one shown in SEQ ID NO: 13 herein, especially one having one or more of the following substitutions: G128D, D143N, especially G128D+D143N.

[0142] The enzymes present and/or added in saccharification and/or fermentation in a process of the invention comprise i) glucoamylase and ii) alpha-amylase; and may optionally further comprise iii) a cellulolytic enzyme composition and/or iv) a protease.

[0143] In an embodiment the protease is a metallo protease, preferably derived from a strain of the genus Thermoascus, preferably a strain of Thermoascus aurantiacus, especially Thermoascus aurantiacus CGMCC No. 0670, such as the metallo protease disclosed as the mature part of SEQ ID NO: 2 disclosed in WO 2003/048353 or the mature polypeptide of SEQ ID NO: 3 herein.

[0144] In an embodiment the protease is selected from the group consisting of:

(i) a protease comprising the mature polypeptide of SEQ ID NO: 3 herein; (ii) a protease comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 3 herein.

[0145] In an especially preferred embodiment the enzymes present and/or added in saccharification and/or fermentation comprises a Trametes glucoamylase, in particular Trametes cingulata glucoamylase, especially the one shown in SEQ ID NO: 12 herein and the alpha-amylase, in particular one derived from Rhizomucor pusillus with a linker and starch-binding domain (SBD), in particular an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), preferably the one shown in SEQ ID NO: 13 herein, preferably having one or more of the following substitutions: G128D, D143N, especially G128D+D143N, and further a cellulolytic enzyme composition, in particular one derived from Trichoderma reesei, preferably further comprising Thermoascus aurantiacus GH61A polypeptide having cellulolytic enhancing activity (SEQ ID NO: 2 in WO 2005/074656 or SEQ ID NO: 9 herein) and Aspergillus fumigatus beta-glucosidase (SEQ ID NO: 2 of WO 2005/047499 or SEQ ID NO: 8 herein); or a cellulolytic enzyme composition, in particular one derived from Trichoderma reesei, preferably further comprising Penicillium emersonii GH61A polypeptide disclosed as SEQ ID NO: 2 in WO 2011/041397 or SEQ ID NO: 10 herein and Aspergillus fumigatus beta-glucosidase disclosed as SEQ ID NO: 2 in WO 2005/047499 or SEQ ID NO: 8 herein, or a variant thereof, preferably a variant having one of, preferably all of, the following substitutions: F100D, S283G, N456E, F512Y, Aspergillus fumigatus Cel7A CBH1 disclosed as SEQ ID NO: 6 in WO2011/057140 and SEQ ID NO: 6 herein and Aspergillus fumigatus CBH II disclosed as SEQ ID NO: 18 in WO 2011/057140 and as SEQ ID NO: 7 herein.

[0146] In an especially preferred embodiment the enzymes present and/or added in saccharification and/or fermentation comprises Gloeophyllum glucoamylase, in particular Gloeophyllum trabeum glucoamylase, preferably the one shown in SEQ ID NO: 18 herein, preferably having one or more of the following substitutions: S95P, A121P, especially S95P+A121P and the alpha-amylase, in particular one derived from Rhizomucor pusillus with a linker and starch-binding domain (SBD), in particular an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), preferably the one shown in SEQ ID NO: 13 herein, preferably having one or more of the following substitutions: G128D, D143N, especially G128D+D143N, and further a cellulolytic enzyme composition derived from Trichoderma reesei, preferably further comprising Thermoascus aurantiacus GH61A polypeptide having cellulolytic enhancing activity (SEQ ID NO: 2 in WO 2005/074656 or SEQ ID NO: 9 herein) and Aspergillus fumigatus beta-glucosidase (SEQ ID NO: 2 of WO 2005/047499 or SEQ ID NO: 8 herein); or a cellulolytic enzyme composition, in particular one derived from Trichoderma reesei, preferably further comprising Penicillium emersonii GH61A polypeptide disclosed as SEQ ID NO: 2 in WO 2011/041397 or SEQ ID NO: 10 herein and Aspergillus fumigatus beta-glucosidase disclosed as SEQ ID NO: 2 in WO 2005/047499 or SEQ ID NO: 8 herein, or a variant thereof, preferably a variant having one of, preferably all of, the following substitutions: F100D, S283G, N456E, F512Y, Aspergillus fumigatus Cel7A CBH1 disclosed as SEQ ID NO: 6 in WO2011/057140 and SEQ ID NO: 6 herein and Aspergillus fumigatus CBH II disclosed as SEQ ID NO: 18 in WO 2011/057140 and as SEQ ID NO: 7 herein.

[0147] In an especially preferred embodiment the enzymes present and/or added in saccharification and/or fermentation according to the invention comprises a Pycnoporus glucoamylase, in particular a Pycnoporus sanguineus glucoamylase, preferably the one shown in SEQ ID NO: 17 herein and the alpha-amylase, in particular one derived from Rhizomucor pusillus with a linker and starch-binding domain (SBD), in particular an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), preferably the one shown in SEQ ID NO: 13 herein, preferably having one or more of the following substitutions: G128D, D143N, especially G128D+D143N, and further a cellulolytic enzyme composition, in particular one derived from Trichoderma reesei, preferably further comprising Thermoascus aurantiacus GH61A polypeptide having cellulolytic enhancing activity (SEQ ID NO: 2 in WO 2005/074656 or SEQ ID NO: 9 herein) and Aspergillus fumigatus beta-glucosidase (SEQ ID NO: 2 of WO 2005/047499 or SEQ ID NO: 8 herein); or a cellulolytic enzyme composition, in particular one derived from Trichoderma reesei, preferably further comprising Penicillium emersonii GH61A polypeptide disclosed as SEQ ID NO: 2 in WO 2011/041397 or SEQ ID NO: 10 herein and Aspergillus fumigatus beta-glucosidase disclosed as SEQ ID NO: 2 in WO 2005/047499 or SEQ ID NO: 8 herein, or a variant thereof, preferably a variant having one of, preferably all of, the following substitutions: F100D, S283G, N456E, F512Y, Aspergillus fumigatus Cel7A CBH1 disclosed as SEQ ID NO: 6 in WO2011/057140 and SEQ ID NO: 6 herein and Aspergillus fumigatus CBH II disclosed as SEQ ID NO: 18 in WO 2011/057140 and as SEQ ID NO: 7 herein.

[0148] In a preferred embodiment a cellulolytic enzyme composition is one described below in the "Cellulolytic Enzyme Compositions"-section.

[0149] The cellulolytic enzyme composition may be added in the process of the invention at the same time as the glucoamylase and alpha-amylase. According to the invention the enzymes, e.g., in the form of an enzyme composition, are added to the saccharification and/or fermentation, preferably simultaneous saccharification and fermentation (i.e., one-step process). It should be understood that the enzymes may also be added individually or as two, three, four or more enzyme compositions. In an embodiment the glucoamylase and alpha-amylase are added as one blend composition and the optional cellulolytic enzyme composition and optional protease are added separately. In another embodiment the glucoamylase, the alpha-amylase, and the cellulolytic enzyme composition are added as one enzyme composition and the optional protease is added separately. All enzymes may also in one embodiment be added as one enzyme composition comprising a glucoamylase, an alpha-amylase, a cellulolytic enzyme composition and/or a protease, and optionally other enzymes including pullulanase, trehalase and/or pectinase, such as pectin lyase or polygalacturonase.

[0150] Other enzymes may also be present. Specifically contemplated enzymes are described further below.

Glucoamylase

[0151] The glucoamylase used in a process of the invention may be of any origin, such as of bacterial or fungal origin. Fungal glucoamylases are preferred.

[0152] In an embodiment the glucoamylase may be one derived from a strain of Trametes, such as a strain of Trametes cingulata (SEQ ID NO: 12 herein); or a strain of Pachykytospora, such as a strain of Pachykytospora papyracea; or a strain of Leucopaxillus, such as a strain of Leucopaxillus giganteus (all disclosed in WO 2006/069289).

[0153] In an embodiment the glucoamylase is derived from a strain of Tramates, such as a strain of Trametes cingulata.

[0154] In a preferred embodiment the glucoamylase, such as one derived from a strain of Trametes cingulata, is selected from the group consisting of:

(i) a glucoamylase comprising the mature polypeptide of SEQ ID NO: 12 herein; (ii) a glucoamylase comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 12 herein.

[0155] In an embodiment the glucoamylase is from a strain of Aspergillus, preferably Aspergillus niger, Aspergillus awamori, or Aspergillus oryzae; or a strain of Trichoderma, preferably Trichoderma reesei; or a strain of Talaromyces, preferably Talaromyces emersonii (SEQ ID NO: 11 herein).

[0156] In an embodiment the glucoamylase is derived from a strain of Talaromyces, such as a strain of Talaromyces emersonii.

[0157] In an embodiment the glucoamylase, such as one derived from a strain of Talaromyces emersonii, is selected from the group consisting of:

(i) a glucoamylase comprising the mature polypeptide of SEQ ID NO: 11 herein; (ii) a glucoamylase comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 11 herein.

[0158] In another embodiment the glucoamylase is derived from a strain of Penicillium, such as a strain of Penicillium oxalicum.

[0159] In an embodiment the glucoamylase, such as one derived from a strain of Penicillium oxalicum, is selected from the group consisting of:

(i) a glucoamylase comprising the mature polypeptide of SEQ ID NO: 16 herein; (ii) a glucoamylase comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 16 herein.

[0160] In an embodiment the glucoamylase is derived from a strain of Gloeophyllum, such as a strain of Gloeophyllum sepiarium or Gloeophyllum trabeum, such as one disclosed in WO 2011/068803 as any of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14 or 16. In a preferred embodiment the glucoamylase is SEQ ID NO: 2 in WO 2011/068803 or SEQ ID NO: 4 herein. In another embodiment the glucoamylase is SEQ ID NO: 18 in WO 2011/068803 (i.e., Gloeophyllum trabeum glucoamylase) or the mature part of the glucoamylase shown as SEQ ID NO: 3 in WO2014/177546 (hereby incorporated by reference) and SEQ ID NO: 18 herein.

[0161] In a preferred embodiment the glucoamylase, such as one derived from a strain of Gloeophyllum sepiarium, is selected from the group consisting of:

(i) a glucoamylase comprising the mature polypeptide of SEQ ID NO: 4 herein; (ii) a glucoamylase comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 4 herein.

[0162] In a further embodiment the glucoamylase is derived from a strain of the genus Pycnoporus, in particular a strain of Pycnoporus sanguineus, such as a strain described in WO 2011/066576 (SEQ ID NOs 2, 4 or 6). In a preferred embodiment the glucoamylase is the one shown in SEQ ID NO: 4 in WO 2011/066576 or SEQ ID NO: 17 herein.

[0163] In a preferred embodiment the glucoamylase, such as one derived from a strain of Pycnoporus sanguineus, is selected from the group consisting of:

(i) a glucoamylase comprising the mature polypeptide of SEQ ID NO: 17 herein; (ii) a glucoamylase comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 17 herein.

[0164] Contemplated are also glucoamylases which exhibit a high identity to any of the above-mentioned glucoamylases, i.e., at least 60%, such as at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, such as 100% identity to any one of the mature parts of the enzyme sequences mentioned above.

[0165] In a preferred embodiment the glucoamylase, such as one derived from a strain of Gloeophyllum trabeum, is selected from the group consisting of:

(i) a glucoamylase comprising the mature polypeptide of SEQ ID NO: 18 herein; (ii) a glucoamylase comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 18 herein.

[0166] In a preferred embodiment the Gloeophyllum trabeum glucoamylase shown in SEQ ID NO: 18 has one of the following substitutions: V59A; S95P; A121P; T119W; S95P+A121P; V59A+S95P; S95P+T119W; V59A+S95P+A121P; or S95P+T119W+A121P, especially S95P+A121P. In a preferred embodiment the Gloeophyllum trabeum glucoamylase shown in SEQ ID NO: 18 has one of the following substitutions: V59A; S95P; A121P; T119W; S95P+A121P; V59A+S95P; S95P+T119W; V59A+S95P+A121P; or S95P+T119W+A121P, especially S95P+A121P (using SEQ ID NO: 18 herein for numbering). All Gloeophyllum trabeum glucoamylase variants disclosed in co-pending PCT application # PCT/EP2014/058692 is hereby incorporated by reference.

[0167] A glucoamylase variant may comprise an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%, but less than 100% sequence identity to the mature polypeptide of SEQ ID NO: 18.

Alpha-Amylase

[0168] The alpha-amylase used in a process of the invention may be of any origin, such as of fungal or bacterial origin. In a preferred embodiment the alpha-amylase is an acid alpha-amylase, such as an acid fungal alpha-amylase, i.e., having a pH optimum below pH 7.

[0169] In an embodiment the alpha-amylase may be derived from a strain of the genus Rhizomucor, preferably a strain the Rhizomucor pusillus, such as the one shown in SEQ ID NO: 3 in WO 2013/006756 (see e.g., Table 1 in Example 1 hereby incorporated by reference), or the genus Meripilus, preferably a strain of Meripilus giganteus.

[0170] In a preferred embodiment the alpha-amylase is derived from a Rhizomucor pusillus, such as one with a linker and starch-binding domain (SBD), preferably Aspergillus niger glucoamylase linker and starch-binding domain (SBD), disclosed as V039 in Table 5 in WO 2006/069290 (incorporated by reference) or SEQ ID NO: 13 herein.

[0171] In a preferred embodiment the alpha-amylase is derived from a Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), disclosed in WO 2013/006756 (incorporated by reference) or SEQ ID NO: 13 herein.

[0172] In an embodiment the Rhizomucor pusillus alpha-amylase or the Rhizomucor pusillus alpha-amylase with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD) has at least one of the following substitutions or combinations of substitutions: D165M; Y141W; Y141R; K136F; K192R; P224A; P224R; S123H+Y141W; G20S+Y141W; A76G+Y141W; G128D+Y141W; G128D+D143N; P219C+Y141W; N142D+D143N; Y141W+K192R; Y141W+D143N; Y141W+N383R; Y141W+P219C+A265C; Y141W+N142D+D143N; Y141W+K192R V410A; G128D+Y141W+D143N; Y141W+D143N+P219C; Y141W+D143N+K192R; G128D+D143N+K192R; Y141W+D143N+K192R+P219C; G128D+Y141W+D143N+K192R; or G128D+Y141W+D143N+K192R+P219C, especially G128D+D143N (using SEQ ID NO: 13 herein for numbering).

[0173] In an embodiment the Rhizomucor pusillus alpha-amylase with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), is selected from the group consisting of:

(i) an alpha-amylase comprising the mature polypeptide of SEQ ID NO: 13 herein; (ii) a glucoamylase comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 13 herein.

[0174] In a preferred embodiment the alpha-amylase is a variant of the Rhizomucor pusillus alpha-amylase with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), wherein the alpha-amylase variant comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity, but less than 100% to the mature polypeptide of SEQ ID NO: 13 herein.

[0175] In a preferred embodiment the alpha-amylase variant has one of the above mentioned substitutions, such as: G128D, Y141W, D143W or K192R.

[0176] In a preferred embodiment the alpha-amylase (using SEQ ID NO: 13 herein for numbering) has the following substitutions: Y141W+D143N.

[0177] In a preferred embodiment the alpha-amylase has the following substitutions: G128D+Y141W+D143N.

[0178] In a preferred embodiment the alpha-amylase has the following substitutions: G128D+Y141W+D143N+K192R;

[0179] In a preferred embodiment the alpha-amylase has the following substitutions: G128D+D143N (using SEQ ID NO: 13 for numbering).

[0180] A variant may comprise an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%, but less than 100% sequence identity to the mature polypeptide of SEQ ID NO: 13.

Protease

[0181] The enzymes present and/or added to saccharification and/or fermentation may optionally further include a protease. The protease may be of any origin, such as fungal or bacterial origin.

[0182] In an embodiment the protease is of fungal origin.

[0183] In an embodiment the protease is a metallo protease derived from a strain of the genus Thermoascus, preferably a strain of Thermoascus aurantiacus, especially Thermoascus aurantiacus CGMCC No. 0670, such as the metallo protease disclosed as the mature part of SEQ ID NO: 2 disclosed in WO 2003/048353 or the mature polypeptide of SEQ ID NO: 3 herein.

[0184] In an embodiment the protease, such as one derived from a strain of Thermoascus aurantiacus, is selected from the group consisting of:

(i) a protease comprising the mature polypeptide of SEQ ID NO: 3 herein; (ii) a protease comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 3 herein.

[0185] In an embodiment the protease is of bacterial origin.

[0186] In an embodiment the protease is derived from a strain of Pyrococcus, such as a strain of Pyrococcus furiosus, such as the protease shown in SEQ ID NO: 1 in U.S. Pat. No. 6,358,726 or SEQ ID NO: 5 herein.

[0187] In an embodiment the protease, such as one derived from Pyrococcus furiosus, is selected from the group consisting of:

(i) a protease comprising the mature polypeptide of SEQ ID NO: 5 herein; (ii) a protease comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 5 herein.

Cellulolytic Enzyme Compositions

[0188] The enzymes present and/or added to saccharification and/or fermentation may optionally further include a cellulolytic enzyme composition. The cellulolytic enzyme composition may consist of or comprise one or more cellulolytic enzymes. The cellulolytic enzyme composition may be of any origin. In a preferred embodiment the cellulolytic enzyme composition comprises cellulolytic enzymes of fungal origin.

[0189] In an embodiment the cellulolytic enzyme composition is derived from a strain of Trichoderma, such as Trichoderma reesei; or a strain of Humicola, such as Humicola insolens; or a strain of Chrysosporium, such as Chrysosporium lucknowense; or a strain of Penicillium, such as Penicillium decumbens. In a preferred embodiment the cellulolytic enzyme composition is derived from a strain of Trichoderma reesei.

[0190] The cellulolytic enzyme composition may comprise a beta-glucosidase, a cellobiohydrolase, and an endoglucanase.

[0191] In an embodiment the cellulolytic enzyme composition comprising one or more polypeptides selected from the group consisting of:

[0192] beta-glucosidase;

[0193] cellobiohydrolase I;

[0194] cellobiohydrolase II;

[0195] or a mixture thereof.

[0196] In a preferred embodiment the cellulolytic enzyme composition further comprises a GH61 polypeptide having cellulolytic enhancing activity. Cellulolytic enhancing activity is defined and determined as described in WO 2011/041397 (incorporated by reference).

[0197] The term "GH61 polypeptide having cellulolytic enhancing activity" means a GH61 polypeptide that enhances the hydrolysis of a cellulosic material by enzymes having cellulolytic activity. For purposes of the present invention, cellulolytic enhancing activity is determined by measuring the increase in reducing sugars or the increase of the total of cellobiose and glucose from hydrolysis of a cellulosic material by cellulolytic enzyme under the following conditions: 1-50 mg of total protein/g of cellulose in PCS (Pretreated Corn Stover), wherein total protein is comprised of 50-99.5% w/w cellulolytic enzyme protein and 0.5-50% w/w protein of a GH61 polypeptide having cellulolytic enhancing activity for 1-7 days at 50.degree. C. compared to a control hydrolysis with equal total protein loading without cellulolytic enhancing activity (1-50 mg of cellulolytic protein/g of cellulose in PCS). In a preferred aspect, a mixture of CELLUCLAST.TM.1.5 L (Novozymes A/S, Bagsv.ae butted.rd, Denmark) in the presence of 2-3% of total protein weight Aspergillus oryzae beta-glucosidase (recombinantly produced in Aspergillus oryzae according to WO 02/095014) or 2-3% of total protein weight Aspergillus fumigatus beta-glucosidase (recombinantly produced in Aspergillus oryzae as described in WO 2002/095014) of cellulase protein loading is used as the source of the cellulolytic activity.

[0198] The cellulolytic enzyme composition comprises a beta-glucosidase, preferably one derived from a strain of the genus Aspergillus, such as Aspergillus oryzae, such as the one disclosed in WO 2002/095014 or the fusion protein having beta-glucosidase activity disclosed in WO 2008/057637 (see SEQ ID NOs: 74 or 76), or Aspergillus fumigatus, such as one disclosed in SEQ ID NO: 2 in WO 2005/047499 or SEQ ID NO: 8 herein; or an Aspergillus fumigatus beta-glucosidase variant disclosed in WO 2012/044915; or a strain of the genus a strain Penicillium, such as a strain of the Penicillium brasilianum disclosed in WO 2007/019442, or a strain of the genus Trichoderma, such as a strain of Trichoderma reesei. In an embodiment the beta-glucosidase is from a strain of Aspergillus, such as a strain of Aspergillus fumigatus, such as Aspergillus fumigatus beta-glucosidase (SEQ ID NO: 8 herein), or a variant thereof, which variant comprises one or more substitutions selected from the group consisting of L89M, G91L, F100D, I140V, I186V, S283G, N456E, and F512Y; such as a variant thereof with the following substitutions:

[0199] F100D+S283G+N456E+F512Y;

[0200] L89M+G91L+I186V+I140V;

[0201] I186V+L89M+G91L+I140V+F100D+S283G+N456E+F512Y.

[0202] In an embodiment the parent beta-glucosidase has at least 60% identity, such as at least 70%, such as at least 80%, such as at least 90%, such as at least 95%, such as at least 96%, such as at least 97%, such as at least 98%, such as at least 99% identity to the mature polypeptide of SEQ ID NO: 8 herein.

[0203] In case the beta-glucosidase is a beta-glucosidase variant it has at least 60% identity, such as at least 70%, such as at least 80%, such as at least 90%, such as at least 95%, such as at least 96%, such as at least 97%, such as at least 98%, such as at least 99%, but less than 100% identity to the mature polypeptide of SEQ ID NO: 8 herein.

[0204] In case the cellulolytic enzyme composition comprises a GH61 polypeptide, it may be one derived from the genus Thermoascus, such as a strain of Thermoascus aurantiacus, such as the one described in WO 2005/074656 as SEQ ID NO: 2 or SEQ ID NO: 9 herein; or one derived from the genus Thielavia, such as a strain of Thielavia terrestris, such as the one described in WO 2005/074647 as SEQ ID NO: 7 and SEQ ID NO: 8 (hereby incorporated by reference); or one derived from a strain of Aspergillus, such as a strain of Aspergillus fumigatus, such as the one described in WO 2010/138754 as SEQ ID NO: 1 and SEQ ID NO: 2 (hereby incorporated by reference); or one derived from a strain from Penicillium, such as a strain of Penicillium emersonii, such as the one disclosed in WO 2011/041397 as SEQ ID NO: 2 or SEQ ID NO: 10 herein.

[0205] In a preferred embodiment the GH61 polypeptide, such as one derived from a strain of Thermoascus, is selected from the group consisting of:

(i) a GH61 polypeptide comprising the mature polypeptide of SEQ ID NO: 9 herein; (ii) a GH61 polypeptide comprising an amino acid sequence having at least 60%, such as at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 9 herein.

[0206] In a preferred embodiment the GH61 polypeptide, such as one derived from a strain of Penicillium sp., is selected from the group consisting of:

(i) a GH61 polypeptide comprising the mature polypeptide of SEQ ID NO: 10 herein; (ii) a GH61 polypeptide comprising an amino acid sequence having at least 60%, such as at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 10 herein.

[0207] In an embodiment the cellulolytic enzyme composition comprises a cellobiohydrolase I (CBH I), such as one derived from a strain of the genus Aspergillus, such as a strain of Aspergillus fumigatus, such as the Cel7a CBHI disclosed in SEQ ID NO: 6 in WO 2011/057140 or SEQ ID NO: 6 herein, or a strain of the genus Trichoderma, such as a strain of Trichoderma reesei.

[0208] In a preferred embodiment the cellobiohydrolase I, such as one derived from a strain of Aspergillus fumigatus, is selected from the group consisting of:

(i) a cellobiohydrolase I comprising the mature polypeptide of SEQ ID NO: 6 herein; (ii) a cellobiohydrolase I comprising an amino acid sequence having at least 60%, such as at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 6 herein.

[0209] In an embodiment the cellulolytic enzyme composition, comprised in an enzyme composition of the invention, comprises a cellobiohydrolase II (CBH II), such as one derived from a strain of the genus Aspergillus, such as a strain of Aspergillus fumigatus; such as the one disclosed as SEQ ID NO: 7 herein or a strain of the genus Trichoderma, such as Trichoderma reesei, or a strain of the genus Thielavia, such as a strain of Thielavia terrestris, such as cellobiohydrolase II CEL6A from Thielavia terrestris.

[0210] In a preferred embodiment cellobiohydrolase II, such as one derived from a strain of Aspergillus fumigatus, is selected from the group consisting of:

(i) a cellobiohydrolase II comprising the mature polypeptide of SEQ ID NO: 7 herein; (ii) a cellobiohydrolase II comprising an amino acid sequence having at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 7 herein.

[0211] In an embodiment the cellulolytic enzyme composition comprises a GH61 polypeptide having cellulolytic enhancing activity and a beta-glucosidase.

[0212] In an embodiment the cellulolytic enzyme composition comprises a GH61 polypeptide having cellulolytic enhancing activity derived from a strain of Penicillium, such as a strain of Penicillium emersonii, such as the one disclosed as SEQ ID NO: 2 in WO 2011/041397 or SEQ ID NO: 10 herein, and a beta-glucosidase.

[0213] In an embodiment the cellulolytic enzyme composition comprises a GH61 polypeptide having cellulolytic enhancing activity, a beta-glucosidase, and a CBHI.

[0214] In an embodiment the cellulolytic enzyme composition comprises a GH61 polypeptide having cellulolytic enhancing activity derived from a strain of Penicillium, such as a strain of Penicillium emersonii, such as the one disclosed as SEQ ID NO: 2 in WO 2011/041397 or SEQ ID NO: 10 herein, a beta-glucosidase, and a CBHII.

[0215] In an embodiment the cellulolytic enzyme composition, comprised in an enzyme composition of the invention, comprises a GH61 polypeptide having cellulolytic enhancing activity, a beta-glucosidase, a CBHI, and a CBHII.

[0216] In an embodiment the cellulolytic enzyme composition comprises a GH61 polypeptide having cellulolytic enhancing activity derived from a strain of Penicillium, such as a strain of Penicillium emersonii, such as the one disclosed as SEQ ID NO: 2 in WO 2011/041397 or SEQ ID NO: 10 herein, a beta-glucosidase, a CBHI, and a CBHII.

[0217] In an embodiment the cellulolytic enzyme composition is a Trichoderma reesei cellulolytic composition further comprising Thermoascus aurantiacus GH61A polypeptide (SEQ ID NO: 2 in WO 2005/074656 or SEQ ID NO: 9 herein), and Aspergillus oryzae beta-glucosidase fusion protein (WO 2008/057637).

[0218] In an embodiment the cellulolytic enzyme composition is a Trichoderma reesei cellulolytic composition further comprising Thermoascus aurantiacus GH61A polypeptide having cellulolytic enhancing activity (SEQ ID NO: 2 in WO 2005/074656 or SEQ ID NO: 9 herein) and Aspergillus fumigatus beta-glucosidase (SEQ ID NO: 2 of WO 2005/047499 or SEQ ID NO: 8 herein).

[0219] In an embodiment the cellulolytic enzyme composition is a Trichoderma reesei cellulolytic composition further comprising Penicillium emersonii GH61A polypeptide disclosed as SEQ ID NO: 2 in WO 2011/041397 or SEQ ID NO: 10 herein, and Aspergillus fumigatus beta-glucosidase disclosed as SEQ ID NO: 2 in WO 2005/047499 or SEQ ID NO: 8 herein, or a variant thereof, which variant has one of, preferably all of, the following substitutions: F100D, S283G, N456E, F512Y, and optionally Aspergillus fumigatus CBH1, e.g., the one disclosed as SEQ ID NO: 6 in WO2011/057140 and SEQ ID NO: 6 herein and Aspergillus fumigatus CBH II, e.g., the one disclosed as SEQ ID NO: 18 in WO 2011/057140 and as SEQ ID NO: 7 herein.

[0220] In an embodiment the cellulolytic enzyme composition comprises one or more of the following components

(i) an Aspergillus fumigatus cellobiohydrolase I; (ii) an Aspergillus fumigatus cellobiohydrolase II; (iii) an Aspergillus fumigatus beta-glucosidase or variant thereof.

[0221] In an embodiment the Aspergillus fumigatus beta-glucosidase (SEQ ID NO: 8 herein), comprises one or more substitutions selected from the group consisting of L89M, G91L, F100D, I140V, I186V, S283G, N456E, and F512Y; such as a variant thereof, with the following substitutions:

[0222] F100D+S283G+N456E+F512Y;

[0223] L89M+G91L+I186V+I140V; or

[0224] I186V+L89M+G91L+I140V+F100D+S283G+N456E+F512Y (using SEQ ID NO: 8 for numbering).

[0225] In an embodiment the cellulolytic composition further comprises the Penicillium sp. GH61 polypeptide shown in SEQ ID NO: 10 herein; or a GH61 polypeptide comprising an amino acid sequence having at least 60%, such as at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 10 herein.

Pullulanase

[0226] The enzymes present and/or added to saccharification and/or fermentation may optionally further include a pullulanase. The pullulanase may be of any origin, such as fungal or bacterial origin.

[0227] In an embodiment the pullulanase is derived from a strain of Bacillus sp. such as the one shown in SEQ ID NO: 15 herein or a strain of Bacillus deramificans.

[0228] In an embodiment the pullulanase, such as one derived from Bacillus sp, is selected from the group consisting of:

(i) a pullulanase comprising the mature polypeptide of SEQ ID NO: 15 herein; (ii) a pullulanase comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 15 herein.

Trehalase

[0229] According to the invention the enzymes present and/or added to saccharification and/or fermentation may optionally further include a trehalase.

[0230] The trehalase may be of any origin, such as fungal or bacterial origin.

[0231] In an embodiment the trehalase is of fungal origin, such as derived from a strain of Trichoderma, such as Trichoderma reesei, such as the one shown in SEQ ID NO: 14 herein.

[0232] In an embodiment the trehalase, such as one derived from Trichoderma reesei, is selected from the group consisting of:

(i) a trehalase comprising the mature polypeptide of SEQ ID NO: 14 herein; (ii) a trehalase comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 14 herein.

Pectinase

[0233] According to the invention the enzymes present and/or added to saccharification and/or fermentation may optionally further include a pectinase, such as a pectin lyase (also known as pectolyase) and/or a polygalacturonase, or a combination thereof.

[0234] The pectinase may be of any origin, such as fungal or bacterial origin.

[0235] In a preferred embodiment the pectinase is a pectin lyase (EC 4.2.2.10).

[0236] In an embodiment the pectin lyase is derived from a strain of Aspergillus, such as Aspergillus niger.

[0237] In a preferred embodiment the pectinase is a polygalacturonase (EC. 3.2.1.15). In an embodiment the polygalacacturonase is derived from a strain of Aspergillus, such as Aspergillus aculeatus.

[0238] In an embodiment the pectinase is a combination of pectin lyase and polygalacturonase. In an embodiment the pectinase is a combination of pectin lyase derived from Aspergillus niger and polygalacturonase derived from Aspergillus aculeatus.

Examples of Enzymes (e.g., Blend) Suitable for Use in a Raw Starch Hydrolysis Process of the Invention

[0239] In an embodiment enzymes (e.g., blend) for use in a process of the invention comprise a glucoamylase and an alpha-amylase, and optionally a protease and/or cellulolytic enzyme composition. Other optional enzymes may also be used.

[0240] In a preferred embodiment the enzymes (e.g., blend) used in a process of the invention comprises or consists of a glucoamylase from Trametes cingulata and an alpha-amylase from Rhizomucor pusillus with a linker and starch-binding domain (SBD), in particular an Aspergillus niger glucoamylase linker and starch-binding domain (SBD).

[0241] In a preferred embodiment the enzymes (e.g. blend) used in a process of the invention comprises the Gloeophyllum trabeum glucoamylase shown in SEQ ID NO: 18 herein having one or more of the following substitutions: S95P, A121P, preferably S95P+A121P and an alpha-amylase, preferably an alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), shown in SEQ ID NO: 13 herein, having one or more of the following substitutions: G128D, D143N, preferably G128D+D143N.

[0242] In another preferred embodiment the enzymes (e.g., blend) used in a process of the invention comprises the Pycnoporus sanguineus glucoamylase shown in SEQ ID NO: 17 herein and an alpha-amylase, preferably one derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), preferably the one shown in SEQ ID NO: 13 herein, preferably having one or more of the following substitutions: G128D, D143N, especially G128D+D143N.

[0243] In a preferred embodiment the enzymes (e.g., blend) used in a process of the invention comprises the Gloeophyllum sepiarium glucoamylase shown in SEQ ID NO: 4 herein and an alpha-amylase, preferably an alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), shown in SEQ ID NO: 13 herein, preferably having one or more of the following substitutions: G128D, D143N, preferably G128D+D143N.

[0244] In a preferred embodiment the enzymes (e.g., blend) used in a process of the invention comprises the Trametes cingulata glucoamylase shown in SEQ ID NO: 12 herein and an alpha-amylase, preferably an alpha-amylase derived from Rhizomucor pusillus with a linker and starch-binding domain (SBD), in particular an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), such as the one shown in SEQ ID NO: 13 herein, having one or more of the following substitutions: G128D, D143N, preferably G128D+D143N.

[0245] In an embodiment the enzymes (e.g., blend) used in a process of the invention comprises

[0246] i) fungal glucoamylase;

[0247] ii) fungal alpha-amylase;

[0248] iii) cellulolytic enzyme composition derived from a strain of Trichoderma reesei, further comprising a GH61 polypeptide, beta-glucosidase, CBH I and CBH II;

[0249] iv) optionally a protease.

[0250] In an embodiment the enzymes (blend) used in a process of the invention comprises

[0251] i) Trametes cingulata glucoamylase;

[0252] ii) Rhizomucor pusillus alpha-amylase, or variant thereof;

[0253] iii) cellulolytic enzyme composition derived from a strain of Trichoderma reesei, further comprising Penicillium emersonii GH61A polypeptide, Aspergillus fumigatus beta-glucosidase with the following substitutions: F100D, S283G, N456E, F512Y, and optionally Aspergillus fumigatus CBH I and Aspergillus fumigatus CBH II;

[0254] iv) optionally a protease from Thermoascus aurantiacus, or variant thereof.

[0255] In an embodiment the enzymes (e.g., blend) used in a process of the invention comprises a

[0256] i) Trametes cingulata glucoamylase;

[0257] ii) Rhizomucor pusillus alpha-amylase, or variant thereof;

[0258] iii) cellulolytic enzyme composition derived from a strain of Trichoderma reesei, further comprising Penicillium emersonii GH61A polypeptide, Aspergillus fumigatus beta-glucosidase with the following substitutions: F100D, S283G, N456E, F512Y, and optionally Aspergillus fumigatus CBH I and Aspergillus fumigatus CBH II;

[0259] iv) optionally a protease from Pyropoccus furiosus.

In an embodiment the enzymes (e.g., blend) used in a process of the invention comprises

[0260] i) glucoamylase derived from Trametes cingulata;

[0261] ii) alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), or a variant thereof;

[0262] iii) cellulolytic enzyme composition derived from a strain of Trichoderma reesei;

[0263] iv) optionally a protease from Thermoascus aurantiacus, or a variant thereof and/or Pyrococcus furiosus.

[0264] In an embodiment the enzymes (e.g., blend) used in a process of the invention comprises

[0265] i) fungal glucoamylase;

[0266] ii) fungal alpha-amylase;

[0267] iii) cellulolytic enzyme composition derived from a strain of Trichoderma reesei, further comprising a GH61 polypeptide, beta-glucosidase CBH I and CBH II;

[0268] iv) pectinase, preferably a pectin lyase or a polygalacturonase, or a combination thereof.

[0269] In an embodiment the pectinase is a combination of pectin lyase derived from Aspergillus niger and polygalacturonase derived from Aspergillus aculeatus.

[0270] In an embodiment the pectinase is a combination of pectin lyase and polygalacturonase. In an embodiment the pectinase is a combination of pectin lyase derived from Aspergillus niger and polygalacturonase derived from Aspergillus aculeatus.

[0271] In an embodiment the enzymes (e.g., blend) used in a process of the invention comprises

[0272] i) fungal glucoamylase;

[0273] ii) fungal alpha-amylase;

[0274] iii) pectinase, preferably a pectin lyase or a polygalacturonase, or a combination thereof;

[0275] iv) cellulolytic enzyme composition derived from a strain of Trichoderma reesei, further comprising a GH61 polypeptide, beta-glucosidase CBH I and CBH II;

[0276] v) protease.

[0277] In an embodiment the enzymes (e.g., blend) used in a process of the invention comprises a

[0278] i) fungal glucoamylase;

[0279] ii) fungal alpha-amylase;

[0280] iii) cellulolytic enzyme composition derived from a strain of Trichoderma reesei, further comprising a GH61 polypeptide, beta-glucosidase, CBH I and CBH II;

[0281] iv) optionally a protease.

[0282] In an embodiment the enzymes (e.g., blend) used in a process of the invention comprises

[0283] i) Trametes cingulata glucoamylase;

[0284] ii) Rhizomucor pusillus alpha-amylase, or variant thereof;

[0285] iii) cellulolytic enzyme composition derived from a strain of Trichoderma reesei, further comprising Penicillium emersonii GH61A polypeptide, Aspergillus fumigatus beta-glucosidase with the following substitutions: F100D, S283G, N456E, F512Y, and optionally Aspergillus fumigatus CBH I and Aspergillus fumigatus CBH II;

[0286] iv) pectin lyase derived from Aspergillus niger or polygalacturonase derived from Aspergillus aculeatus, or a combination thereof;

[0287] v) protease from Thermoascus aurantiacus, or a variant thereof and/or Pyrococcus furiosus.

[0288] In a preferred embodiment the enzymes (blend) used in a process of the invention comprises

[0289] i) Gloeophyllum trabeum glucoamylase shown in SEQ ID NO: 18 herein having one or more of the following substitutions: S95P, A121P, such as S95P+A121P;

[0290] ii) alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), shown in SEQ ID NO: 13 herein, having of the following substitutions: G128D+D143N;

[0291] iii) optionally a cellulolytic enzyme composition derived from a strain of Trichoderma reesei, further comprising Penicillium emersonii GH61A polypeptide, Aspergillus fumigatus beta-glucosidase with the following substitutions: F100D, S283G, N456E, F512Y, and optionally Aspergillus fumigatus CBH I and Aspergillus fumigatus CBH II;

optionally iv) protease from Thermoascus aurantiacus, or a variant thereof.

[0292] In a preferred embodiment the enzymes (e.g., blend) used in a process of the invention comprises

[0293] i) Pycnoporus sanguineus glucoamylase shown in SEQ ID NO: 17 herein;

[0294] ii) alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), shown in SEQ ID NO: 13 herein, having of the following substitutions: G128D+D143N;

[0295] iii) optionally a cellulolytic enzyme composition derived from a strain of Trichoderma reesei, further comprising Penicillium emersonii GH61A polypeptide, Aspergillus fumigatus beta-glucosidase with the following substitutions: F100D, S283G, N456E, F512Y, and optionally Aspergillus fumigatus CBH I and Aspergillus fumigatus CBH II;

optionally iv) protease from Thermoascus aurantiacus, or a variant thereof.

[0296] In a preferred embodiment the enzymes (e.g., blend) used in a process of the invention comprises

[0297] i) Gloeophyllum sepiarium glucoamylase shown in SEQ ID NO: 4 herein;

[0298] ii) alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), shown in SEQ ID NO: 13 herein, having of the following substitutions: G128D+D143N;

[0299] iii) optionally a cellulolytic enzyme composition derived from a strain of Trichoderma reesei, further comprising Penicillium emersonii GH61A polypeptide, Aspergillus fumigatus beta-glucosidase with the following substitutions: F100D, S283G, N456E, F512Y, and optionally Aspergillus fumigatus CBH I and Aspergillus fumigatus CBH II;

optionally iv) protease from Thermoascus aurantiacus, or a variant thereof.

[0300] In a preferred embodiment the enzymes (e.g., blend) used in a process of the invention comprises

[0301] i) Trametes cingulata glucoamylase shown in SEQ ID NO: 12 herein;

[0302] ii) alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), shown in SEQ ID NO: 13 herein, having of the following substitutions: G128D+D143N;

[0303] iii) optionally cellulolytic enzyme composition derived from a strain of Trichoderma reesei, further comprising Penicillium emersonii GH61A polypeptide, Aspergillus fumigatus beta-glucosidase with the following substitutions: F100D, S283G, N456E, F512Y, and optionally Aspergillus fumigatus CBH I and Aspergillus fumigatus CBH II;

optionally iv) protease from Thermoascus aurantiacus, or a variant thereof.

Examples of Processes of the Invention

[0304] A process of the invention of producing ethanol from starch-containing material comprises:

[0305] (i) saccharifying starch-containing material at a temperature below the initial gelatinization temperature; and

[0306] (ii) fermenting using a fermentation organism;

[0307] wherein

[0308] saccharification and/or fermentation is done in the presence of the following enzymes: glucoamylase and alpha-amylase, and optionally protease; and

[0309] the fermenting organism is Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, wherein using said fermenting organism results in one or more, such as all, of the following:

[0310] increased ethanol yield compared to a corresponding process where Ethanol Red.TM. ("ER") is used under the same conditions;

[0311] reduced glycerol level compared to a corresponding process where Ethanol Red.TM. ("ER") is used under the same conditions;

[0312] reduced lactic acid level compared to a corresponding process where Ethanol Red.TM. ("ER") is used under the same conditions.

[0313] A process of the invention of producing ethanol from starch-containing material comprises:

[0314] (i) saccharifying starch-containing material at a temperature below the initial gelatinization temperature; and

[0315] (ii) fermenting using a fermentation organism;

[0316] wherein

[0317] saccharification and/or fermentation is done in the presence of the following enzymes: glucoamylase and alpha-amylase, and optionally protease; and

[0318] the fermenting organism is Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, wherein using said fermenting organism results in one or more, such as all, of the following:

[0319] an ethanol yield boost/increase over Ethanol Red.TM. ("ER") of more than 0.5% (after 72 hours fermentation) determined using the process set-up and conditions used in Example 1;

[0320] an ethanol yield boost/increase over Ethanol Red.TM. ("ER") of more than 1.0% (after 88 hours fermentation) determined using the process set-up and conditions used in Example 1;

[0321] an ethanol yield boost/increase of more than 1.0%, such as more than 2.0%, such as more than 3.0%, such as more than 4.0% over Ethanol Red.TM. ("ER") when determined using the process set-up and conditions used in Example 2 (i.e., 95 hours fermentation);

[0322] a reduction in lactic acid of more than 50%, such as more than 60% (after 72 hours fermentation) over Ethanol Red.TM. ("ER") when determined using the process set-up and conditions used in Example 1;

[0323] a reduction in lactic acid of more than 20%, such as more than 25%, such as more than 30% (after 95 hours fermentation) over Ethanol Red.TM. ("ER") when determined using the process set-up and conditions used in Example 2;

[0324] a reduction in glycerol levels of more than 10.0%, such as more than 15.0%, such as more than 20.0% over Ethanol Red.TM. ("ER") when determined using the process set-up and conditions used in Example 1 (i.e., after 72 hours fermentation);

[0325] a reduction in glycerol levels of more than 5.0%, such as more than 10.0%, such as more than 12.0%, such as more than 14.0% over Ethanol Red.TM. ("ER") when determined using the process set-up and conditions used in Example 2 (i.e., after 95 hours fermentation). In a preferred embodiment the process of producing ethanol from starch-containing material of the invention comprises: (a) saccharifying a starch-containing material at a temperature below the initial gelatinization temperature; and (b) fermenting using a fermentation organism; wherein

[0326] saccharification and/or fermentation is done in the presence of the following enzymes:

[0327] i) glucoamylase derived from Trametes cingulata, Gloeophyllum trabeum, Gloeophyllum sepiarium, or Pycnoporus sanguineus;

[0328] ii) alpha-amylase;

[0329] iii) optionally cellulolytic enzyme composition, in particular derived from Trichoderma reesei;

[0330] iv) optionally a protease, in particular one derived from Thermoascus aurantiacus, or a variant thereof and/or Pyrococcus furiosus; and wherein

[0331] the fermenting organism is Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037.

[0332] In a preferred embodiment the process of producing ethanol from starch-containing material of the invention comprises:

(a) saccharifying a starch-containing material at a temperature below the initial gelatinization temperature; and (b) fermenting using a fermentation organism; wherein

[0333] saccharification and/or fermentation is done in the presence of the following enzymes:

[0334] i) glucoamylase derived from Trametes cingulata, Gloeophyllum trabeum, Gloeophyllum sepiarium, or Pycnoporus sanguineus;

[0335] ii) alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), or a variant thereof;

[0336] iii) optionally cellulolytic enzyme composition derived from Trichoderma reesei;

[0337] iv) optionally a protease from Thermoascus aurantiacus, or a variant thereof and/or Pyrococcus furiosus; and wherein

[0338] the fermenting organism is Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037.

[0339] In a preferred embodiment the process of producing ethanol from starch-containing material of the invention comprises:

(a) saccharifying a starch-containing material at a temperature below the initial gelatinization temperature; and (b) fermenting using a fermentation organism; wherein

[0340] saccharification and/or fermentation is done in the presence of the following enzymes:

[0341] i) glucoamylase derived from Gloeophyllum trabeum disclosed in SEQ ID NO: 18, with the following substitutions: S95P+A121P;

[0342] ii) alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), or a variant thereof, shown in SEQ ID NO: 13 herein, with the following substitutions: G128D+D143N;

[0343] iii) optionally cellulolytic enzyme composition derived from Trichoderma reesei;

[0344] iv) optionally a protease from Thermoascus aurantiacus, or a variant thereof; and wherein

[0345] the fermenting organism is Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851 or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037.

[0346] In a preferred embodiment the process of producing ethanol from starch containing material of the invention comprises:

(a) saccharifying a starch-containing material at a temperature below the initial gelatinization temperature; and (b) fermenting using a fermentation organism; wherein

[0347] saccharification and/or fermentation is done in the presence of the following enzymes:

[0348] i) glucoamylase derived from Pycnoporus sanguineus shown in SEQ ID NO: 17;

[0349] ii) alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), or a variant thereof, shown in SEQ ID NO: 13 herein, with the following substitutions: G128D+D143N;

[0350] iii) optionally cellulolytic enzyme composition derived from Trichoderma reesei;

[0351] iv) optionally a protease from Thermoascus aurantiacus, or a variant thereof; and wherein

[0352] the fermenting organism is Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037.

[0353] In a preferred embodiment the process of producing ethanol from starch-containing material of the invention comprises:

(a) saccharifying a starch-containing material at a temperature below the initial gelatinization temperature; and (b) fermenting using a fermentation organism; wherein

[0354] saccharification and/or fermentation is done in the presence of the following enzymes:

[0355] i) glucoamylase derived from Gloeophyllum sepiarium shown in SEQ ID NO: 4;

[0356] ii) alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), or a variant thereof, shown in SEQ ID NO: 13 herein, with the following substitutions: G128D+D143N;

[0357] iii) optionally cellulolytic enzyme composition derived from Trichoderma reesei;

[0358] iv) optionally a protease from Thermoascus aurantiacus, or a variant thereof; wherein

[0359] the fermenting organism is Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037.

[0360] In a preferred embodiment the process of producing ethanol from starch-containing material of the invention comprises:

(a) saccharifying a starch-containing material at a temperature below the initial gelatinization temperature; and (b) fermenting using a fermentation organism; wherein

[0361] saccharification and/or fermentation is done in the presence of the following enzymes:

[0362] i) glucoamylase derived from Trametes cingulata shown in SEQ ID NO: 12;

[0363] ii) alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), or a variant thereof, shown in SEQ ID NO: 13 herein, with the following substitutions: G128D+D143N;

[0364] iii) optionally cellulolytic enzyme composition derived from Trichoderma reesei;

[0365] iv) optionally a protease from Thermoascus aurantiacus, or a variant thereof; and wherein

[0366] the fermenting organism is Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037.

Yeast of the Invention

[0367] The invention relates in one embodiment to a strain of Saccharomyces cerevisiae deposited under the Budapest Treaty at the National Measurement Institute (NMI) having deposit accession no. V14/004037.

[0368] The majority of the world's fuel ethanol is produced by industrial scale fermentation of starch-based sugars, in substrates such as corn mash. During industrial scale fermentation, the yeast encounter various physiological challenges including variable concentrations of sugars, high concentrations of yeast metabolites such as ethanol, glycerol, organic acids, osmotic stress, as well as potential competition from contaminating microbes such as wild yeasts and bacteria. As a consequence, many Saccharomyces strains are not suitable for use in industrial fermentation. The most widely used commercially available industrial strain of Saccharomyces (i.e. for industrial scale fermentation) is the Saccharomyces cerevisiae strain used, for example, in the product Ethanol Red. This strain is well suited to industrial ethanol production, however improved strains of Saccharomyces cerevisiae are needed.

[0369] WO 2011/035392 describes strain NMI V09/024011, which is a strain of Saccharomyces cerevisiae which produces higher levels of ethanol from corn mash than strains of Saccharomyces cerevisiae used in the fuel ethanol industry such as Ethanol Red.TM.. However, a limitation of strain NMI V09/024011 is that its fermentation kinetics are slower than those of Ethanol Red. Also, the higher levels of ethanol that V09/024011 produces relative to Ethanol Red were only found when corn mash has been heavily supplemented with exogenous sugar sources such as dextrin. Under such conditions, mash fermentations need to be run for extended periods, beyond what are normally encountered in the industrial process. As such, high concentration sugar supplementation is not necessarily of industrial relevance and may not be encountered at scale. The inventors have now produced strain no. V14/004037 which is capable of producing even higher ethanol yields from endogenously occurring corn sugar consumed under the conditions encountered in industrial scale fermentation, such as those encountered during fermentation of corn mash, than V09/024011 or commercially available industrial Saccharomyces cerevisiae strains used in the ethanol industry. Strain no. V14/004037 also exhibits faster fermentation kinetics than strain no. V09/024011. As described herein, the levels of ethanol produced by strain no. V14/004037 under the conditions encountered during industrial fermentation of corn mash are greater than that of the commercially available industrial yeast strains such as Ethanol Red, and that of strain V09/024011. Thus, strain no. V14/004037 has the necessary characteristics for industrial production of ethanol from substrates such as corn mash.

[0370] Strain no. V14/004037 is a non-recombinant Saccharomyces cerevisiae strain developed by breeding which:

[0371] (a) produces a higher titre of ethanol at 72 hrs fermentation than strains V09/024011 and Ethanol Red, under the same conditions in a corn mash fermentation;

[0372] (b) produces less glycerol than Ethanol Red and V09/024011 under the same conditions in a corn mash fermentation.

[0373] (c) leaves less glucose remaining following fermentation than Ethanol Red and V09/024011 under the same conditions in a corn mash fermentation;

[0374] (d) leaves less maltose remaining following fermentation than Ethanol Red and V09/024011 under the same conditions in a corn mash fermentation.

[0375] As used herein, a defining characteristics of strain no. V14/004037 is any one or more of the following characteristics:

[0376] (a) produces ethanol in an amount in the range from 15.0 to 16.5% w/v at 32.degree. C. in 96 hours in a corn mash fermentation;

[0377] (b) produces glycerol in an amount in the range from 0.900 to 1.00% w/v at 32.degree. C. in 72 hours in a corn mash fermentation;

[0378] (c) produces a ratio of % w/v ethanol produced to % w/v glycerol produced following fermentation of corn mash at 32.degree. C. in the range from 15 to 18;

[0379] (d) produces a ratio of % w/v ethanol produced to % w/v glucose remaining following fermentation of corn mash at 32.degree. C. for 96 hours in the range from 100 to 900, 200 to 850, 300 to 850, 400 to 850.

[0380] Typically, the ethanol produced from fermentation of corn mash is produced from fermentation of sugars that are endogenous to the corn mash. Sugars that are endogenous to the corn mash are sugars that are derived from the corn rather than sugars that are added from an exogenous source.

[0381] Strain V14/004037 is also capable of growth in media in which xylose is the sole carbon source. In this regard, strain V14/004037 produces about a 7-fold increase in biomass when grown under the conditions specified in Test T1. As a consequence, strain V14/004037 can be readily distinguished from:

[0382] (a) naturally occurring strains of Saccharomyces;

[0383] (b) contaminating strains of Saccharomyces that do not utilize xylose; and

[0384] (c) other strains used in the ethanol industry that do not have the ethanol producing capabilities of strain V14/004037 and/or do not exhibit about a 7-fold increase in biomass in Test T1.

[0385] As current wild type and industrial strains of Saccharomyces are not capable of growth on xylose at the rate at which strain V14/004037 grows on xylose, strain V14/004037 is readily differentiated from current wild type strains of Saccharomyces and strains of Saccharomyces that are used in the ethanol industry prior to the present invention such as Ethanol Red.

[0386] The invention also relates to a derivative of Saccharomyces strain V14/004037. As used herein, a "derivative of strain V14/004037" is a strain derived from strain V14/004037, including through mutagenesis, recombinant DNA technology, mating, cell fusion, or cytoduction between yeast strains. The strain derived from strain V14/004037 may be a direct progeny (i.e. the product of a mating between strain V14/004037 and another strain or itself), or a distant progeny resulting from an initial mating between V14/004037 and another strain or itself, followed by a large number of subsequent matings.

[0387] In one embodiment, a derivative of strain V14/004037 is a hybrid strain produced by culturing a first yeast strain with strain V14/004037 under conditions which permit combining of DNA between the first yeast strain and strain V14/004037.

[0388] In one embodiment, a derivative of strain V14/004037 may be prepared by:

[0389] (a) culturing a first yeast strain with a second yeast strain, wherein the second yeast strain is strain V14/004037 or a derivative of strain V14/004037, under conditions which permit combining of DNA between the first yeast strain and the second yeast strain; and

[0390] (b) isolating hybrid strains; and

[0391] (c) optionally repeating steps (a) and (b) using a hybrid strain isolated in step (b) as the first yeast strain and/or the derivative of strain V14/004037.

[0392] In one embodiment, the derivative of strain V14/004037 exhibits one or more defining characteristic of strain V14/004037. Derivatives of Saccharomyces which exhibit one or more defining characteristics of strain V14/004037 are produced using strain V14/004037. In this regard, strain V14/004037 forms the basis for preparing other strains having the defining characteristics of strain V14/004037. For example, strains of Saccharomyces which exhibit one or more defining characteristics of strain V14/004037 can be derived from strain V14/004037 using methods such as classical mating, cell fusion, or cytoduction between yeast strains, mutagenesis or recombinant DNA technology.

[0393] In one embodiment, a derivative of strain V14/004037 which exhibits one or more defining characteristics of strain V14/004037 may be produced by:

[0394] (a) culturing a first yeast strain with a second yeast strain, wherein the second yeast strain is strain V14/004037 or a derivative of strain V14/004037, under conditions which permit combining of DNA between the first yeast strain and the second yeast strain;

[0395] (b) screening or selecting for a derivative of strain V14/004037, such as screening or selecting for a derivative with increased ethanol production in corn mash compared to the first strain, and/or screening or selecting for a hybrid which produces less glycerol in corn mash compared to the first strain;

[0396] (c) optionally repeating steps (a) and (b) with the screened or selected strain as the first yeast strain and/or the second yeast strain, until a derivative of strain V14/004037 is obtained which exhibits one or more defining characteristics of strain V14/004037.

[0397] The first yeast strain may be any strain of yeast if the DNA of the strain can be combined with the second yeast strain using methods such as classical mating, cell fusion or cytoduction. Typically, the first yeast strain is a Saccharomyces strain. More typically, the first yeast strain is a Saccharomyces cerevisiae strain. Saccharomyces cerevisiae is as defined by Kurtzman (2003) FEMS Yeast Research vol 4 pp. 233-245. The first yeast strain may have desired properties which are sought to be combined with the defining characteristics of strain V14/004037. The first yeast strain may be, for example, any Saccharomyces cerevisiae strain, such as for example Ethanol Red, V09/024011. It will also be appreciated that the first yeast strain may be strain V14/004037 or a strain which exhibits one or more defining characteristics of strain V14/004037.

[0398] The first and second yeast strains are cultured under conditions which permit combining of DNA between the yeast strains. As used herein, "combining of DNA" between yeast strains refers to combining of all or a part of the genome of the yeast strains. Combining of DNA between yeast strains may be by any method suitable for combining DNA of at least two yeast cells, and may include, for example, mating methods which comprise sporulation of the yeast strains to produce haploid cells and subsequent hybridising of compatible haploid cells; cytoduction; or cell fusion such as protoplast fusion.

[0399] In one embodiment, culturing the first yeast strain with the second yeast, under conditions which permit combining of DNA between the first yeast strain and the second yeast strain, comprises:

[0400] (i) sporulating the first yeast strain and the second yeast strain;

[0401] (ii) germinating and hybridizing spores produced by the first yeast strain with spores produced by the second yeast strain.

[0402] In one embodiment, the method of producing a derivative of strain V14/004037 which exhibits one or more defining characteristics of strain V14/004037, comprises:

[0403] (a) providing: (i) a first yeast strain; and (ii) a second yeast strain, wherein the second yeast strain is strain V14/004037 or a derivative of strain V14/004037;

[0404] (b) sporulating the first yeast strain and the second yeast strain;

[0405] (c) germinating and hybridising the spores of the first yeast strain with germinated spores of the second yeast strain;

[0406] (d) screening or selecting for a derivative of strain V14/004037, such as screening or selecting for a derivative with increased ethanol production in corn mash compared to the first strain, and/or screening or selecting for a hybrid which produces less glycerol in corn mash compared to the first strain;

[0407] (e) optionally repeating steps (b) to (d) with the screened or selected strain as the first and/or second yeast strain.

[0408] Methods for sporulating, germinating and hybridising yeast strains, and in particular, Saccharomyces strains, are known in the art and are described in, for example, Ausubel, F. M. et al., (1997) Current Protocols in Molecular Biology, Volume 2, pages 13.2.1 to 13.2.5 (John Willey & Sons Inc); Chapter 7, "Sporulation and Hybridisation of yeast" by R. R. Fowell, in "The Yeasts" vol 1, A. H. Rose and J. S. Harrison (Eds), 1969, Academic Press.

[0409] In one embodiment, the yeast strains may be cultured under conditions which permit cell fusion. Methods for the generation of intraspecific or interspecific hybrids using cell fusion techniques are described in, for example, Spencer et al. (1990) in, Yeast Technology, Spencer JFT and Spencer DM (Eds), Springer Verlag, New York.

[0410] In another embodiment, the yeast strains may be cultured under conditions which permit cytoduction. Methods for cytoduction are described in, for example, Inge-Vechymov et al. (1986) Genetika 22: 2625-2636; Johnston (1990) in, Yeast technology, Spencer JFT and Spencer DM (Eds), Springer Verlag, New York.

[0411] In one embodiment, screening or selecting for derivatives of strain V14/004037 comprises screening or selecting for a derivative with increased ethanol production in corn mash compared to the first strain, and/or screening or selecting for a hybrid which produces less glycerol in corn mash compared to the first strain.

[0412] In another embodiment, the yeast cells may be screened or selected for strains which have one or more of the following characteristics:

[0413] (a) produces an amount of ethanol that is in the range from an amount higher than that produced by strain Ethanol Red to the amount produced by strain V14/004037, under the same conditions in a corn mash fermentation;

[0414] (b) produces an amount of glycerol that is in the range from an amount that is less than the amount produced by Ethanol Red to the amount produced by strain V14/004037, under the same conditions in a corn mash fermentation

[0415] (c) produces a ratio of ethanol to glycerol that is in the range from a ratio higher than the ratio of ethanol to glycerol of Ethanol Red to a ratio that is about the same as the ratio of ethanol to glycerol of strain V14/004037, under the same conditions in a corm mash fermentation.

[0416] (d) produces a ratio of ethanol to glucose that is in the range from a ratio higher than the ratio of ethanol to glucose of Ethanol Red to a ratio that is about the same as the ratio of ethanol to glucose of strain V14/004037 under the same conditions in a corn mash fermentation;

[0417] (e) produces a ratio of ethanol to maltose that is in the range from a ratio higher than the ratio of ethanol to maltose of Ethanol Red to a ratio that is about the same as the ratio of ethanol to maltose of strain V14/004037 under the same conditions in a corn mash fermentation.

[0418] Methods for determining the amount of ethanol and glycerol produced by a strain are known in the art. For example, methods for testing for determining the amount of ethanol and glycerol produced by a strain during fermentation of corn mash are described in, for example, WO 2011/035392. Once the amount of ethanol and glycerol produced are known, the ratio of ethanol/glycerol can be readily determined. Accordingly, strains can be readily screened for production levels of ethanol and/or glycerol using known methods.

[0419] In one embodiment, a derivative of strain V14/004037 which exhibits one or more defining characteristics of strain V14/004037 may be a mutant of strain V14/004037. Methods for producing mutants of Saccharomyces yeast, and specifically mutants of Saccharomyces cerevisiae, are known in the art and described in, for example, Lawrence C. W. (1991) Methods in Enzymology, 194: 273-281.

[0420] In another embodiment, a derivative of strain V14/004037 which exhibits one or more defining characteristics of strain V14/004037 may be a recombinant derivative of strain V14/004037. A recombinant derivative of strain V14/004037 is a strain produced by introducing into strain V14/004037 a nucleic acid using recombinant DNA technology. Methods for the introduction of nucleic acid into Saccharomyces yeast cells, and in particular strains of Saccharomyces, are known in the art and are described in, for example, Ausubel, F. M. et al. (1997), Current Protocols in Molecular Biology, Volume 2, pages 13.7.1 to 13.7.7, published by John Wiley & Sons Inc.

[0421] The invention also relates to methods for the production of ethanol using the strain described herein. In one form, strain V14/004037 or a derivative strain which exhibits the defining characteristics of strain V14/004037 is incubated with a substrate comprising fermentable sugars under conditions that allow fermentation of the fermentable sugars. The fermentable sugars may be one or more of glucose, galactose, maltose, fructose and sucrose. Typically, the fermentable sugar is glucose. While strain V14/004037 is well suited to fermentation in corn mash, it is envisaged the strain may also be suitable for other fermentation processes. Accordingly, the source of the fermentable sugar in the substrate may be, for example, hydrolysed starch, hydrolysed cellulose, molasses, cane juice, grape juice, fruit juice, glucose, maltodextrins, raw sugar juice, galactose, sucrose, or any other forms of fermentable sugars. In one form, the source of fermentable sugar in the substrate is hydrolysed starch. Typically, the starch is obtained from a substrate such as corn mash. In preparing the substrate, the grain is typically ground and mixed with water and hydrolytic enzyme(s) under conditions which result in hydrolysis of the starch and release of fermentable sugars such as glucose. Typical enzymes for hydrolysis of the starch include alpha-amylase, amyloglucosidase (glucoamylase), pullulanase, beta-amylase, glucoamylase, protease, cellulose or mixtures thereof. Enzymes suitable for hydrolysis are available from, for example, Novozymes or Genencor Inc. In one form, substrate is provided in the form of corn mash. Corn mash is typically produced by: (a) grinding corn to form a meal; (b) mixing the meal with water; and (c) hydrolyzing the starch in the corn meal. Methods for preparation of corn mash are known in the art and described in, for example, Thomas, K. C. et al., (2001) Journal of Applied Microbiology, volume 90, pages 819-828. Methods for the preparation of other starch-based substrates including sorghum, starch streams and combinations thereof are also known in the art and described in, for example, Kwiatkowski J. R. et al. (2003) Industrial Crops and Products 23: 288-296 and Bothast R. J. and Schlicher M. A. (2005) Applied Microbial Biotechnology 67: 19-25

[0422] The fermentation is carried out at a temperature which permits fermentation of the fermentable sugars. Typically, the temperature at which the fermentation is carried out is from 25-34.degree. C.

[0423] The fermentation results in an alcoholic mash comprising ethanol and residual sugars in solution, and a particulate portion comprising residual solids including yeast. Ethanol is isolated from the mash using methods know in the art such as distillation or filtration.

[0424] Methods for fermentation and distillation are known in the art and are described in, for example, Kwiatkowski J. R. et al. (2003) Industrial Crops and Products 23: 288-296 and Bothast R. J. and Schlicher M. A. (2005) Applied Microbial Biotechnology 67: 19-25

[0425] The invention further relates to a method of producing distiller's grain. Distiller's grains may be produced from the residual solids produced in the fermentation using methods known in the art and described in, for example, U.S. Pat. No. 7,572,353. Because Saccharomyces strain V14/004037 reduces the level of residual sugars remaining following fermentation, the distiller's grain which results from fermentation using strain V14/004037 has a lowered glucose content and is therefore more stable and less prone to charring, caramelisation or contamination with unwanted microorganisms.

[0426] Furthermore, lower glycerol content in distillers grains is a process advantage because less time is required for drying the distiller's grains. In addition, less glycerol in the distiller's grains results in improved flowability, and further results in distiller's grains which has a higher nutrient content (e.g. higher protein).

[0427] As used herein, the singular forms "a", "an" and "the" include plural reference unless the context clearly indicates otherwise. Thus, for example, a reference to "a cell" includes a plurality of such cells. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art.

[0428] As used herein, except where the context requires otherwise due to express language or necessary implication, the word "comprise" or variations such as "comprises" or "comprising" is used in an inclusive sense, i.e. to specify the presence of the stated features but not to preclude the presence or addition of further features in various embodiments of the invention.

Test T1

[0429] Step 1: Yeast strains are streaked onto 2% w/v D-glucose 1% bacteriological peptone and 0.5% yeast extract medium solidified with 2% agar using standard microbiological techniques. Step 2: After incubation for 72 hours at 30.degree. C., yeast cells are taken from plates using a sterile microbiological loop and inoculated to an OD.sub.600 (Optical Density at 600 nm) of between 0.1 and 0.2 units (OD.sub.600 at T.sub.0) in 50 ml of broth containing xylose (5% w/v), Difco Yeast Nitrogen Base w/o amino acids (0.67%), citric acid (0.3%) and trisodium citrate (0.7%) in distilled water in a 250 ml Erlenmeyer flask. An OD.sub.600 of 0.1 unit is equal to approximately 9.times.10.sup.5 yeast cells/mL. D-(+)-Xylose, minimum 99% can be obtained from Sigma-Aldrich. Step 3: Cultures are incubated at 30 deg Celsius with shaking at 220 rpm (10 cm orbital diameter) for 48 hours. Step 4: After 48 hours incubation, OD.sub.600 of culture is measured (OD.sub.600 at T.sub.48). Step 5: The fold increase in biomass is determined by the equation:

OD.sub.600 at T.sub.48/OD.sub.600 at T.sub.0.

Composition of the Invention

[0430] In this aspect the invention relates to a formulated Saccharomyces yeast composition comprising a yeast strain of the invention and naturally occurring and/or nonenaturally occurring components.

[0431] As mentioned above a Saccharomyces yeast strain, in particular Saccharomyces cerevisiae yeast strain, of the invention, may according to the invention may be in any viable form, including crumbled, dry, including active dry and instant, compressed, cream form etc. In a preferred embodiment the Saccharomyces cerevisiae yeast strain of the invention is dry yeast, such as active dry yeast or instant yeast. In a preferred embodiment the Saccharomyces cerevisiae yeast strain of the invention is crumbled yeast. In a preferred embodiment the Saccharomyces cerevisiae yeast strain is compressed yeast. In an embodiment the Saccharomyces cerevisiae yeast strain of the invention is cream yeast.

[0432] In an embodiment the invention relates to a composition comprising a Saccharomyces yeast of the invention, in particular Saccharmyces MBG4851 and one or more of the component selected from the group consisting of: surfactants, emulsifiers, gums, swelling agent, and antioxidants and other processing aids.

Surfactant

[0433] According to the invention the composition may comprise a Saccharomyces yeast of the invention, in particular Saccharmyces MBG4851 and any suitable surfactants. In an embodiment the surfactant(s) is/are an anionic surfactant, cationic surfactant, and/or nonionic surfactant.

Emulsifier

[0434] According to the invention the composition may comprise a Saccharomyces yeast of the invention, in particular Saccharmyces MBG4851 and any suitable emulsifier. In an embodiment the emulsifier is a fatty-acid ester of sorbitan. In an embodiment the emulsifier is selected from the group of sorbitan monostearate (SMS), citric acid esters of monodiglycerides, polyglycerolester, fatty acid esters of propylene glycol.

[0435] In an embodiment the composition of the invention comprises a Saccharomyces yeast of the invention, in particular Saccharmyces MBG4851, and Olindronal SMS, Olindronal SK, or Olindronal SPL including composition concerned in European Patent No. 1,724,336 (hereby incorporated by reference). These products are commercially available from Bussetti, Austria, for active dry yeast.

Gum

[0436] According to the invention the composition may comprise a Saccharomyces yeast of the invention, in particular Saccharmyces MBG4851 and any suitable gum. In an embodiment the gum is acacia gum, in particular for cream, compressed and dry yeast.

Swelling Agents

[0437] According to the invention the composition may comprise a Saccharomyces yeast of the invention, in particular Saccharmyces MBG4851 and any suitable swelling agent. In an embodiment the swelling agent is methyl cellulose or carboxymethyl cellulose.

Antioxidant

[0438] According to the invention the composition may comprise a Saccharomyces yeast of the invention, in particular Saccharmyces MBG4851 and any suitable anti-oxidant. In an embodiment the antioxidant is butylated hydroxyanisol (BHA) and/or butylated hydroxytoluene (BHT), or ascorbic acid (vitamin C), particular for active dry yeast.

[0439] As used herein, the singular forms "a", "an" and "the" include plural reference unless the context clearly indicates otherwise. Thus, for example, a reference to "a cell" includes a plurality of such cells. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art.

[0440] As used herein, except where the context requires otherwise due to express language or necessary implication, the word "comprise" or variations such as "comprises" or "comprising" is used in an inclusive sense, i.e. to specify the presence of the stated features but not to preclude the presence or addition of further features in various embodiments of the invention.

[0441] The invention described and claimed herein is not to be limited in scope by the specific embodiments herein disclosed, since these embodiments are intended as illustrations of several aspects of the invention. Any equivalent embodiments are intended to be within the scope of this invention. Indeed, various modifications of the invention in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims. In the case of conflict, the present disclosure, including definitions will be controlling.

[0442] Various references are cited herein, the disclosures of which are incorporated by reference in their entireties.

Materials & Methods

Materials:

[0443] GtAMG: Glucoamylase derived from Gloeophyllum trabeum disclosed in SEQ ID NO: 18 herein, with the following substitutions: S95P+A121P. PsAMG: Glucoamylase derived from Pycnoporus sanguineus disclosed as shown in SEQ ID NO: 4 in WO 2011/066576 and in SEQ ID NO: 17 herein. TcAMG: Glucoamylase derived from Trametes cingulata shown in SEQ ID NO: 12 herein or SEQ ID NO: 2 in WO 2006/69289. JA126: Alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD) shown in SEQ ID NO: 13 herein. AAPE096: Alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD) shown in SEQ ID NO: 13 herein, with the following substitutions: G128D+D143N. RSH Blend P: Blend of TcAMG and JA126 with a ratio between AGU (from TcAMG) and FAU-F (JA126) of about 10:1. Cellulase VD: Cellulolytic composition derived from Trichoderma reesei further comprising Penicillium emersonii GH61A polypeptide disclosed as SEQ ID NO: 2 in WO 2011/041397 or SEQ ID NO: 10 herein, and Aspergillus fumigatus beta-glucosidase disclosed as SEQ ID NO: 2 in WO 2005/047499 or SEQ ID NO: 8 herein, or a variant thereof, preferably a variant having one of, preferably all of, the following substitutions: F100D, S283G, N456E, F512Y and Aspergillus fumigatus Cel7A CBH1 disclosed as SEQ ID NO: 6 in WO2011/057140 and SEQ ID NO: 6 herein and Aspergillus fumigatus CBH II disclosed as SEQ ID NO: 18 in WO 2011/057140 and as SEQ ID NO: 7 herein.

Yeast:

[0444] ETHANOL RED.TM. ("ER"): Saccharomyces cerevisiae yeast available from Fermentis/Lesaffre, USA. MBG4851: Saccharomyces cerevisiae yeast (non-recombinant) deposited by Microbiogen Pty Ltd, Unit E2, Lane Cove Business Park, 16 Mars Road, Lane Cove, NSW 2066, Australia under the terms of the Budapest Treaty with the National Measurement Institute, Victoria, Australia) and given the following accession number:

TABLE-US-00001 Deposit Accession Number Date of Deposit MBG4851 V14/004037 Feb. 17, 2014 ETHANOL RED .TM. V14/007039 Mar. 19, 2014

[0445] The strains have been deposited under conditions that assure that access to the culture will be available during the pendency of this patent application to one determined by the Commissioner of Patents and Trademarks to be entitled thereto under 37 C.F.R. .sctn.1.14 and 35 U.S.C. .sctn.122. The deposits represent substantially pure cultures of the deposited strains. The deposits are available as required by foreign patent laws in countries wherein counterparts of the subject application, or its progeny are filed. However, it should be understood that the availability of deposits do not constitute a license to practice the subject invention in derogation of patent rights granted by governmental action.

Methods:

Identity

[0446] The relatedness between two amino acid sequences or between two polynucleotide sequences is described by the parameter "identity".

[0447] For purposes of the present invention, the degree of identity between two amino acid sequences is determined by the Clustal method (Higgins, 1989, CABIOS 5: 151-153) using the LASERGENE.TM. MEGALIGN.TM. software (DNASTAR, Inc., Madison, Wis.) with an identity table and the following multiple alignment parameters: Gap penalty of 10 and gap length penalty of 10. Pairwise alignment parameters are Ktuple=1, gap penalty=3, windows=5, and diagonals=5.

[0448] For purposes of the present invention, the degree of identity between two polynucleotide sequences is determined by the Wilbur-Lipman method (Wilbur and Lipman, 1983, Proceedings of the National Academy of Science USA 80: 726-730) using the LASERGENE.TM. MEGALIGN.TM. software (DNASTAR, Inc., Madison, Wis.) with an identity table and the following multiple alignment parameters: Gap penalty of 10 and gap length penalty of 10. Pairwise alignment parameters are Ktuple=3, gap penalty=3, and windows=20.

SIGMA Enzymatic Assay for Trehalase

[0449] One SIGMA unit will convert 1.0 micro mol of trehalose to 2.0 micro mol of glucose per minutes at pH 5.7 at 37.degree. C. (liberated glucose determined at pH 7.5).

Glucoamylase Activity

[0450] Glucoamylase activity may be measured in Glucoamylase Units (AGU).

Glucoamylase Activity (AGU)

[0451] The Novo Glucoamylase Unit (AGU) is defined as the amount of enzyme, which hydrolyzes 1 micromole maltose per minute under the standard conditions 37.degree. C., pH 4.3, substrate: maltose 23.2 mM, buffer: acetate 0.1 M, reaction time 5 minutes.

[0452] An autoanalyzer system may be used. Mutarotase is added to the glucose dehydrogenase reagent so that any alpha-D-glucose present is turned into beta-D-glucose. Glucose dehydrogenase reacts specifically with beta-D-glucose in the reaction mentioned above, forming NADH which is determined using a photometer at 340 nm as a measure of the original glucose concentration.

TABLE-US-00002 AMG incubation: Substrate: maltose 23.2 mM Buffer: acetate 0.1M pH: 4.30 .+-. 0.05 Incubation temperature: 37.degree. C. .+-. 1 Reaction time: 5 minutes Enzyme working range: 0.5-4.0 AGU/mL

TABLE-US-00003 Color reaction: GlucDH: 430 U/L Mutarotase: 9 U/L NAD: 0.21 mM Buffer: phosphate 0.12M; 0.15M NaCl pH: 7.60 .+-. 0.05 Incubation temperature: 37.degree. C. .+-. 1 Reaction time: 5 minutes Wavelength: 340 nm

[0453] A folder (EB-SM-0131.02/01) describing this analytical method in more detail is available on request from Novozymes A/S, Denmark, which folder is hereby included by reference.

Alpha-Amylase Activity (KNU)

[0454] The alpha-amylase activity may be determined using potato starch as substrate. This method is based on the break-down of modified potato starch by the enzyme, and the reaction is followed by mixing samples of the starch/enzyme solution with an iodine solution. Initially, a blackish-blue color is formed, but during the break-down of the starch the blue color gets weaker and gradually turns into a reddish-brown, which is compared to a colored glass standard.

[0455] One Kilo Novo alpha amylase Unit (KNU) is defined as the amount of enzyme which, under standard conditions (i.e., at 37.degree. C.+/-0.05; 0.0003 M Ca.sup.2+; and pH 5.6) dextrinizes 5260 mg starch dry substance Merck Amylum solubile.

[0456] A folder EB-SM-0009.02/01 describing this analytical method in more detail is available upon request to Novozymes A/S, Denmark, which folder is hereby included by reference.

Acid Alpha-Amylase Activity

[0457] When used according to the present invention the activity of an acid alpha-amylase may be measured in AFAU (Acid Fungal Alpha-amylase Units) or FAU-F.

Acid Alpha-Amylase Activity (AFAU)

[0458] Acid alpha-amylase activity may be measured in AFAU (Acid Fungal Alpha-amylase Units), which are determined relative to an enzyme standard. 1 AFAU is defined as the amount of enzyme which degrades 5.260 mg starch dry matter per hour under the below mentioned standard conditions.

[0459] Acid alpha-amylase, an endo-alpha-amylase (1,4-alpha-D-glucan-glucanohydrolase, E.C. 3.2.1.1) hydrolyzes alpha-1,4-glucosidic bonds in the inner regions of the starch molecule to form dextrins and oligosaccharides with different chain lengths. The intensity of color formed with iodine is directly proportional to the concentration of starch. Amylase activity is determined using reverse colorimetry as a reduction in the concentration of starch under the specified analytical conditions.

##STR00001##

[0460] blue/violet t=23 sec. decoloration

[0461] Standard Conditions/Reaction Conditions:

[0462] Substrate: Soluble starch, approx. 0.17 g/L

[0463] Buffer: Citrate, approx. 0.03 M

[0464] Iodine (12): 0.03 g/L

[0465] CaCl.sub.2: 1.85 mM

[0466] pH: 2.50.+-.0.05

[0467] Incubation temperature: 40.degree. C.

[0468] Reaction time: 23 seconds

[0469] Wavelength: 590 nm

[0470] Enzyme concentration: 0.025 AFAU/mL

[0471] Enzyme working range: 0.01-0.04 AFAU/mL

[0472] A folder EB-SM-0259.02/01 describing this analytical method in more detail is available upon request to Novozymes A/S, Denmark, which folder is hereby included by reference.

Determination of FAU-F

[0473] FAU-F Fungal Alpha-Amylase Units (Fungamyl) is measured relative to an enzyme standard of a declared strength.

TABLE-US-00004 Reaction conditions Temperature 37.degree. C. pH 7.15 Wavelength 405 nm Reaction time 5 min Measuring time 2 min

[0474] A folder (EB-SM-0216.02) describing this standard method in more detail is available on request from Novozymes A/S, Denmark, which folder is hereby included by reference.

Measurement of Cellulase Activity Using Filter Paper Assay (FPU Assay)

1. Source of Method

[0475] 1.1 The method is disclosed in a document entitled "Measurement of Cellulase Activities" by Adney, B. and Baker, J. 1996. Laboratory Analytical Procedure, LAP-006, National Renewable Energy Laboratory (NREL). It is based on the IUPAC method for measuring cellulase activity (Ghose, T. K., Measurement of Cellulse Activities, Pure & Appl. Chem. 59, pp. 257-268, 1987.

2. Procedure

[0476] 2.1 The method is carried out as described by Adney and Baker, 1996, supra, except for the use of a 96 well plates to read the absorbance values after color development, as described below.

2.2 Enzyme Assay Tubes:



[0477] 2.2.1 A rolled filter paper strip (#1 Whatman; 1.times.6 cm; 50 mg) is added to the bottom of a test tube (13.times.100 mm).

[0478] 2.2.2 To the tube is added 1.0 mL of 0.05 M Na-citrate buffer (pH 4.80).

[0479] 2.2.3 The tubes containing filter paper and buffer are incubated 5 min. at 50.degree. C. (.+-.0.1.degree. C.) in a circulating water bath.

[0480] 2.2.4 Following incubation, 0.5 mL of enzyme dilution in citrate buffer is added to the tube. Enzyme dilutions are designed to produce values slightly above and below the target value of 2.0 mg glucose.

[0481] 2.2.5 The tube contents are mixed by gently vortexing for 3 seconds.

[0482] 2.2.6 After vortexing, the tubes are incubated for 60 mins. at 50.degree. C. (.+-.0.1.degree. C.) in a circulating water bath.

[0483] 2.2.7 Immediately following the 60 min. incubation, the tubes are removed from the water bath, and 3.0 mL of DNS reagent is added to each tube to stop the reaction. The tubes are vortexed 3 seconds to mix.

2.3 Blank and Controls

[0483]

[0484] 2.3.1 A reagent blank is prepared by adding 1.5 mL of citrate buffer to a test tube.

[0485] 2.3.2 A substrate control is prepared by placing a rolled filter paper strip into the bottom of a test tube, and adding 1.5 mL of citrate buffer.

[0486] 2.3.3 Enzyme controls are prepared for each enzyme dilution by mixing 1.0 mL of citrate buffer with 0.5 mL of the appropriate enzyme dilution.

[0487] 2.3.4 The reagent blank, substrate control, and enzyme controls are assayed in the same manner as the enzyme assay tubes, and done along with them.

2.4 Glucose Standards

[0487]

[0488] 2.4.1 A 100 mL stock solution of glucose (10.0 mg/mL) is prepared, and 5 mL aliquots are frozen. Prior to use, aliquots are thawed and vortexed to mix.

[0489] 2.4.2 Dilutions of the stock solution are made in citrate buffer as follows: G1=1.0 mL stock+0.5 mL buffer=6.7 mg/mL=3.3 mg/0.5 mL G2=0.75 mL stock+0.75 mL buffer=5.0 mg/mL=2.5 mg/0.5 mL G3=0.5 mL stock+1.0 mL buffer=3.3 mg/mL=1.7 mg/0.5 mL G4=0.2 mL stock+0.8 mL buffer=2.0 mg/mL=1.0 mg/0.5 mL

[0490] 2.4.3 Glucose standard tubes are prepared by adding 0.5 mL of each dilution to 1.0 mL of citrate buffer.

[0491] 2.4.4 The glucose standard tubes are assayed in the same manner as the enzyme assay tubes, and done along with them.

2.5 Color Development

[0491]

[0492] 2.5.1 Following the 60 min. incubation and addition of DA/S, the tubes are all boiled together for 5 mins. in a water bath.

[0493] 2.5.2 After boiling, they are immediately cooled in an ice/water bath.

[0494] 2.5.3 When cool, the tubes are briefly vortexed, and the pulp is allowed to settle. Then each tube is diluted by adding 50 microL from the tube to 200 microL of ddH2O in a 96-well plate. Each well is mixed, and the absorbance is read at 540 nm.

2.6 Calculations (Examples are Given in the NREL Document)

[0494]

[0495] 2.6.1 A glucose standard curve is prepared by graphing glucose concentration (mg/0.5 mL) for the four standards (G1-G4) vs. A.sub.540. This is fitted using a linear regression (Prism Software), and the equation for the line is used to determine the glucose produced for each of the enzyme assay tubes.

[0496] 2.6.2 A plot of glucose produced (mg/0.5 mL) vs. total enzyme dilution is prepared, with the Y-axis (enzyme dilution) being on a log scale.

[0497] 2.6.3 A line is drawn between the enzyme dilution that produced just above 2.0 mg glucose and the dilution that produced just below that. From this line, it is determined the enzyme dilution that would have produced exactly 2.0 mg of glucose.

[0498] 2.6.4 The Filter Paper Units/mL (FPU/mL) are calculated as follows:

[0498] FPU/mL=0.37/enzyme dilution producing 2.0 mg glucose

Protease Assay Method--AU(RH)

[0499] The proteolytic activity may be determined with denatured hemoglobin as substrate. In the Anson-Hemoglobin method for the determination of proteolytic activity denatured hemoglobin is digested, and the undigested hemoglobin is precipitated with trichloroacetic acid (TCA). The amount of TCA soluble product is determined with phenol reagent, which gives a blue color with tyrosine and tryptophan.

[0500] One Anson Unit (AU-RH) is defined as the amount of enzyme which under standard conditions (i.e. 25.degree. C., pH 5.5 and 10 min. reaction time) digests hemoglobin at an initial rate such that there is liberated per minute an amount of TCA soluble product which gives the same color with phenol reagent as one milliequivalent of tyrosine.

[0501] The AU(RH) method is described in EAL-SM-0350 and is available from Novozymes A/S Denmark on request.

Protease Assay Method (LAPU)

[0502] 1 Leucine Amino Peptidase Unit (LAPU) is the amount of enzyme which decomposes 1 microM substrate per minute at the following conditions: 26 mM of L-leucine-p-nitroanilide as substrate, 0.1 M Tris buffer (pH 8.0), 37.degree. C., 10 minutes reaction time.

[0503] LAPU is described in EB-SM-0298.02/01 available from Novozymes A/S Denmark on request.

EXAMPLES

Example 1

Tube Scale RSH Fermentations Using MBG4851 and ER

[0504] Mash Preparation

[0505] Yellow dent corn (obtained from Lincolnway on 19 Sep. 2013; ground in-house) was mixed with tap water and the dry solids (DS) level was determined to be 33.78% by moisture balance. This mixture was supplemented with 3 ppm penicillin and 500 ppm urea. The slurry was adjusted to pH 4.5 with 40% H.sub.2SO.sub.4.

Yeast Strains and Preparation

[0506] The two yeast strains tested in these experiments were Ethanol Red.TM. ("ER") (Fermentis) and MBG4851. Yeast were propagated in filter sterilized liquid media (2% w/v D-glucose, 1% peptone, and 0.5% yeast extract). Using a sterile loop under a UV hood, cells from a lawn were transferred into 25 mL of the liquid media in 50 mL sterile centrifuge tubes with a hole drilled in the top and incubated at 150 rpm in a 30.degree. C. air shaker. Tubes were angled at approximately 30 degrees to increase aeration. Cells were harvested at 18 hours by spinning at 3000 rpm for 10 minutes and decanting the supernatant. Cells were washed once in 25 ml of water and the resulting cell pellet was resuspended in 1.5 ml tap water. Total yeast concentration was determined using the YC-100 in duplicate.

Simultaneous Saccharification and Fermentation (SSF)

[0507] Approximately 5 grams of mash was transferred to test tubes having a 1/64 hole drilled in the top to allow CO.sub.2 release. PsAMG/AAPE096 (ratio of PsAMG to AAPE096 was 33.5) was dosed to each tube of mash at 0.85 AGU/gDS. Yeast was dosed at 10e6 cells/g mash. Milli-Q water was added to each tube so that a total volume of liquid added (enzyme+MQ water) to each tube would be equally proportionate to the mash weight. Fermentations took place in a 32.degree. C. water bath for 88 hours. Samples were vortexed periodically (in the morning and in the evening) throughout the fermentation.

HPLC Analysis

[0508] Fermentation sampling took place after 72 and 88 hours of fermentation by sacrificing 3 tubes per treatment. Each tube was processed for HPLC analysis by deactivation with 50 .mu.L of 40% v/v H2SO4, vortexing, centrifuging at 1460.times.g for 10 minutes, and filtering through a 0.45 .mu.m Whatman PP filter. All samples were processed without further dilution. Samples were stored at 4.degree. C. prior to and during HPLC analysis.

TABLE-US-00005 TABLE 1 HPLC System HPLC Agilent's 1100/1200 series with Chem station software System Degasser, Quaternary Pump, Auto-Sampler, Column Compartment/w Heater Refractive Index Detector (RI) Column Bio-Rad HPX-87H Ion Exclusion Column 300 mm .times. 7.8 mm part# 125-0140 Bio-Rad guard cartridge Cation H part# 125-0129, Holder part# 125-0131 Method 0.005M H2SO4 mobile phase Flow rate: 0.6 ml/min Column temperature: 65.degree. C. RI detector temperature: 55.degree. C.

[0509] Samples were analyzed for sugars (DP4+, DP3, DP2, glucose, and fructose), organic acids (lactic and acetic), glycerol, and ethanol.

Increased Ethanol Results

[0510] Ethanol titers at 72 and 88 hours are shown in Table 2 below.

TABLE-US-00006 TABLE 2 72 and 88 hour ethanol titers % MBG4851 increase ER (g/L (g/L with Ethanol) Ethanol) MBG4851 72 155.390 156.406 0.65 Hours 88 154.898 157.210 1.49 Hours

[0511] Reduced Glycerol Results

[0512] Glycerol titers at 72 and 88 hours are shown in Table 3 below.

TABLE-US-00007 TABLE 3 72 and 88 hour glycerol results ER MBG4851 % Reduction (g/L Glycerol) (g/L Glycerol) with MBG4851 72 Hours 9.456 7.459 21.11 88 Hours 9.676 7.601 21.45

Lactic Acid Results

[0513] Results are shown in Table 4 below.

TABLE-US-00008 TABLE 4 72 and 88 Hour Lactic Acid Results ER MBG485 % Reduction (g/L Lactic Acid) (g/L Lactic Acid) with MBG4851 72 Hours 0.597775 0.227973 61.86% 88 Hours 0.504066 0.207138 58.91%

Example 2

Reactor Scale RSH Fermentations Using MBG4851 and ER

[0514] All fermentations were done in 2 L IKA bioreactors.

Mash Preparation

[0515] Yellow dent corn (obtained from Lincolnway on 19 Sep. 2013; ground in-house) was mixed with tap water and the dry solids (DS) level was determined to be 35.5% by moisture balance. This mixture was supplemented with 3 ppm Lactrol and 200 ppm urea. The slurry was adjusted to pH 4.5 with 40% H.sub.2SO.sub.4.

Yeast Strains and Preparation

[0516] The two yeast strains tested in this experiment were Ethanol Red (Fermentis) and MBG4851. Yeasts were rehydrated by weighing 2.75 g of dried yeast into 50 ml of 36.5.degree. C. tap water in a 125 mL Erlenmeyer flask. The flasks were then covered with parafilm and allowed to incubate in a 36.5.degree. C. water bath. After 15 minutes, the flasks were swirled, but no other agitation took place. After a total of 30 minutes, the flasks were removed from the water bath.

Simultaneous Saccharification and Fermentation (SSF) PsAMG/AAPE096 (ratio of PsAMG to AAPE096 was 33.5) was dosed to each reactor at 0.85 AGU/gDS. 12.8 ml of rehydrated yeast was added to each bioreactor. Fermentations took place at 32.degree. C. for 95 hours.

HPLC Analysis

[0517] Fermentation sampling took place by sampling 5 grams of mash into 15 ml tubes at 16, 24, 40, 48, 64, 72, 88, and 95 hours of fermentation. Each tube was processed for HPLC analysis by deactivation with 150 .mu.L of 40% v/v H.sub.2SO.sub.4, vortexing, centrifuging at 1460.times.g for 10 minutes, and filtering through a 0.45 .mu.m Whatman PP filter. Samples were stored at 4.degree. C. prior to and during HPLC analysis.

TABLE-US-00009 TABLE 5 HPLC System HPLC Agilent's 1100/1200 series with Chem station software System Degasser, Quaternary Pump, Auto-Sampler, Column Compartment/w Heater Refractive Index Detector (RI) Column Bio-Rad HPX-87H Ion Exclusion Column 300 mm .times. 7.8 mm part# 125-0140 Bio-Rad guard cartridge Cation H part# 125-0129, Holder part# 125-0131 Method 0.005M H2SO4 mobile phase Flow rate: 0.6 ml/min Column temperature: 65.degree. C. RI detector temperature: 55.degree. C.

[0518] Samples were analyzed for sugars (DP4+, DP3, DP2, glucose, and fructose), organic acids (lactic and acetic), glycerol, and ethanol.

Increased Ethanol and Faster Kinetics Results

[0519] Ethanol titers are shown across the entire course of fermentation in FIG. 1 below. Levels at the end of fermentation are shown in Table 6 below.

TABLE-US-00010 TABLE 6 Ethanol Titers at 95 hours Fermentation ER MBG4851 % Increase (g/L Ethanol) (g/L Ethanol) with MBG4851 157.71 165.53 4.96%

Reduced Glycerol Results

[0520] Glycerol titers across fermentation are shown in FIG. 2 below. Levels at the end of fermentation are shown in Table 7 below.

TABLE-US-00011 TABLE 7 Glycerol Levels at 95 hours fermentation ER MBG4851 % Reduction (g/L Glycerol) (g/L Glycerol) with MBG4851 10.814 9.163 14.80%

[0521] Lactic Acid Results

[0522] Lactic Acid titers are shown across the entire course of the fermentation in FIG. 3 below. Levels at the end of fermentation are shown in Table 8 below.

TABLE-US-00012 TABLE 8 Lactic Acid Results at 95 Hours RSH Fermentation ER MBG4851 % Reduction (g/L Lactic Acid) (g/L Lactic Acid) with MBG4851 1.056 0.690 34.70%

Example 3

[0523] Tube Scale RSH Fermentations with Varying RSH Enzyme Using MBG4851 and ER

Mash Preparation

[0524] Yellow dent corn (obtained from Lincolnway on 19 Sep. 2013; ground in-house) was mixed with tap water and the dry solids (DS) level was determined to be 34.30% by moisture balance. This mixture was supplemented with 3 ppm penicillin and 500 ppm urea. The slurry was adjusted to pH 4.5 with 40% H.sub.2SO.sub.4.

Yeast Strains and Preparation

[0525] The two yeast strains tested in this experiment were Ethanol Red (Fermentis) and MBG4851. Yeasts were rehydrated by weighing 2.75 g of dried yeast into 50 ml of 36.5.degree. C. tap water in a 125 mL Erlenmeyer flask. The flasks were then covered with parafilm and allowed to incubate in a 36.5.degree. C. water bath. After 15 minutes, the flasks were swirled, but no other agitation took place. After a total of 30 minutes, the flasks were removed from the water bath.

Simultaneous Saccharification and Fermentation (SSF)

[0526] Approximately 5 grams of mash was transferred to test tubes having a 1/64 hole drilled in the top to allow CO.sub.2 release. PsAMG/AAPE096 (ratio of PsAMG to AAPE096 was 33.5) was dosed to each tube of mash at 0.85 AGU/gDS or RSH Blend P was dosed at 0.32 AGU/gDS. Yeast was dosed at 10e6 cells/g mash. Milli-Q water was added to each tube so that a total volume of liquid added (enzyme+MQ water) to each tube would be equally proportionate to the mash weight. Fermentations took place in a 32.degree. C. water bath for 88 hours. Samples were vortexed periodically (in the morning and in the evening) throughout the fermentation.

HPLC Analysis

[0527] Fermentation sampling took place after 72 and 88 hours of fermentation by sacrificing 3 tubes per treatment. Each tube was processed for HPLC analysis by deactivation with 50 .mu.L of 40% v/v H.sub.2SO.sub.4, vortexing, centrifuging at 1460.times.g for 10 minutes, and filtering through a 0.45 .mu.m Whatman PP filter. All samples were processed without further dilution. Samples were stored at 4.degree. C. prior to and during HPLC analysis.

TABLE-US-00013 TABLE 9 HPLC System HPLC Agilent's 1100/1200 series with Chem station software System Degasser, Quaternary Pump, Auto-Sampler, Column Compartment/w Heater Refractive Index Detector (RI) Column Bio-Rad HPX-87H Ion Exclusion Column 300 mm .times. 7.8 mm part# 125-0140 Bio-Rad guard cartridge Cation H part# 125-0129, Holder part# 125-0131 Method 0.005M H2SO4 mobile phase Flow rate: 0.6 ml/min Column temperature: 65.degree. C. RI detector temperature: 55.degree. C.

[0528] Samples were analyzed for sugars (DP4+, DP3, DP2, glucose, and fructose), organic acids (lactic and acetic), glycerol, and ethanol.

Increased Ethanol Results

[0529] Ethanol titers at 72 and 88 hours are shown in Table 10 below.

TABLE-US-00014 TABLE 10 72 and 88 hour ethanol titers ER (g/L MBG4851 % increase Enzyme Time Ethanol) (g/L Ethanol) with MBG4851 Ps 72 Hours 161.766 162.584 0.51 AMG 88 Hours 162.761 163.797 0.64 RSH 72 Hours 156.676 159.102 1.55 Blend P 88 Hours 160.893 164.628 2.32

Reduced Glycerol Results

[0530] Glycerol titers at 72 and 88 hours are shown in Table 11 below.

TABLE-US-00015 TABLE 11 72 and 88 hour glycerol results ER MBG4851 % Reduction Enzyme Time (g/L Glycerol) (g/L Glycerol) with MBG4851 Ps 72 Hours 10.324 7.812 24.33 AMG 88 Hours 10.439 8.364 19.88 RSH 72 Hours 9.761 7.461 23.56 Blend P 88 Hours 10.269 7.702 25.00

Lactic Acid Results

[0531] Results are shown in Table 12 below.

TABLE-US-00016 TABLE 12 72 and 88 Hour Lactic Acid Results % Reduction ER MBG4851 with Enzyme (g/L Lactic Acid) (g/L Lactic Acid) MBG4851 Ps 72 Hours 1.008 0.625 46.49 AMG 88 Hours 1.027 0.734 48.85 RSH 72 Hours 1.139 0.709 34.41 Blend P 88 Hours 1.086 0.628 48.38

Example 4

Production of Strain V14/004037 (MBG4851)

[0532] Strain V14/004037 was produced using the methods described in WO 2005/121337 and through matings with various strains of Saccharomyces cerevisiae combined with selection for characteristics including low glycerol and high ethanol production.

[0533] Strain V14/004037 was verified to be a Saccharomyces cerevisiae strain by its ability to sporulate and produce progeny when the germinated spores were mated with standard strains of Saccharomyces cerevisiae, including tester strains of Saccharomyces cerevisiae. One such haploid tester strain is W303-1A. Specifically, germinated spores of strain V14/004037 were able to produce hybrid progeny when mated with tester strain W303-1A.

[0534] In more detail, haploid strain W303-1A was obtained from the Yeast Genetic Stock Center at the ATCC, USA (ATCC #208352) Strain V14/004037 was cultured to form haploid Saccharomyces yeast as described in Ausubel, F. M. et al. (1997), Current Protocols in Molecular Biology, Volume 2, pages 13.2.1 to 13.2.5, published by John Wiley & Sons. Subsequently, the spores were germinated on a solid medium such as GYP containing 1% w/v D-glucose, 0.5% yeast extract, 1% w/v bacteriological peptone and 1.5% w/v agar and incubated at 30.degree. C. for three to five days. The isolated germinated spores from strain V14/004037 were then mated together with haploid W303-1A using the method described in, for example, Ausubel, F. M. et al. (1997), Current Protocols in molecular Biology, Volume 2, pages 13.2.1 to 13.2.5, published by John Wiley & Sons. Formation of hybrid zygotes could be observed under a microscope demonstrating that strain V14/004037 is a Saccharomyces cerevisiae strain.

[0535] Strain V14/004037 was deposited on 17 Feb. 2014 at the National Measurement Institute, 1/153 Bertie Street, Port Melbourne, Victoria 3207, Australia under the Budapest Treaty and was designated accession number V14/004037.

Example 5

Growth of Strain V14/004037 on Xylose Minimal Media

[0536] Growth of strain V14/004037 on xylose as a sole carbon source was determined using Test T1. Saccharomyces cerevisiae strain V14/004037 was streaked onto 2% w/v D-glucose 1% bacteriological peptone and 0.5% yeast extract medium (GYP) solidified with 2% agar using standard microbiological techniques. After incubation for 72 hours at 30 deg Celsius, yeast cells were taken from plates using a sterile microbiological loop and inoculated to an OD.sub.600 (Optical Density at 600 nm) of between 0.1 and 0.2 units (OD.sub.600 at T0) in 50 ml of broth. An OD.sub.600 of 0.1 unit is equal to approximately 9.times.10.sup.5 yeast cells/mL. The broth contained xylose (5% w/v), Difco Yeast Nitrogen Base w/o amino acids (0.67%), citric acid (0.3%) and trisodium citrate (0.7%) in distilled water in a 250 ml Erlenmeyer flask. Citric acid and trisodium citrate were provided as buffering agents that are not able to be used as growth substrates by Saccharomyces. D-(+)-Xylose 99% pure was obtained from Sigma-Aldrich (catalogue number X1500-500G). Cultures were incubated at 30 deg Celsius with shaking at 220 rpm (10 cm orbital diameter) for 48 hours prior to measuring OD.sub.600 (OD.sub.600 at T.sub.48 hrs). The fold increase in biomass was determined by the equation: OD.sub.600 at T.sub.48 hrs divided by OD.sub.600 at T.sub.0.

[0537] Strain V14/004037 was inoculated at an initial OD.sub.600 of 0.149 and increased more than 7-fold in 48 hours. Under the same conditions biomass of Ethanol Red yeast increased less than 2-fold.

Example 6

Raw Starch Hydrolysis Fermentation By MBG4851

[0538] Method: Whole corn was hammer-milled and sieved through a 0.85 mm filter. Raw starch mash was prepared as follows: 202.5 g sieved corn (at 85% corn solids), plus 297.5 mL water, plus 0.25 g urea was adjusted to pH4.5 with sodium hydroxide or sulphuric acid as appropriate. Suitable hydrolytic enzymes as described herein were added. Yeast were inoculated to a density equivalent of 0.5 g dry yeast weight per litre of mash. Mashes were incubated at a temperature of 32.degree. C. Samples were taken after 24, 48, 72 and 96 hrs and analysed by HPLC for glucose, fructose, glycerol and ethanol.

[0539] A representative sample of Ethanol Red (used in this example) was deposited on 19 Mar. 2014 under the Budapest Treaty at the National Measurement Institute, 1/153 Bertie Street, Port Melbourne, Victoria 3207 and designated accession no. V14/007039. Values are presented as percent weight per volume (% w/v).

Results

[0540] All figures in % w/v, except the ethanol/glycerol ratio.

TABLE-US-00017 24 hrs maltose glucose glycerol ethanol ethanol/glycerol Ethanol Red 0.112 0.825 0.78 10.267 13.2 Ethanol Red 0.086 0.871 0.781 10.332 13.2 V14/004037 0.106 0.907 0.648 10.069 15.5 V14/004037 0.137 1.017 0.641 10.063 15.7

TABLE-US-00018 48 hrs maltose glucose glycerol ethanol ethanol/glycerol Ethanol Red 0.184 1.51 0.932 13.795 14.8 Ethanol Red 0.172 1.333 0.928 13.422 14.5 V14/004037 0.111 0.778 0.806 14.116 17.5 V14/004037 0.107 0.872 0.81 14.287 17.6

TABLE-US-00019 72 hrs maltose glucose glycerol ethanol ethanol/glycerol Ethanol Red 0.307 2.418 1.052 14.045 13.4 Ethanol Red 0.255 2.001 0.979 14.305 14.6 V14/004037 0.024 0.125 0.926 15.766 17.0 V14/004037 0.036 0.165 0.906 15.648 17.3

TABLE-US-00020 96 hrs maltose glucose glycerol ethanol ethanol/glycerol Ethanol Red 0.33 2.718 1.048 14.141 13.5 Ethanol Red 0.317 2.353 1.02 14.065 13.8 V14/004037 0 0.029 0.941 16.06 17.1 V14/004037 0 0.035 0.943 16.143 17.1

The Invention is Further Described in the Following Numbered Paragraphs:

[0541] 1. A process of producing ethanol from starch-containing material comprising:

[0542] (a) saccharifying starch-containing material at a temperature below the initial gelatinization temperature; and

[0543] (b) fermenting using a fermentation organism;

[0544] wherein

[0545] saccharification and/or fermentation is done in the presence of the following enzymes: glucoamylase and alpha-amylase, and optionally protease; and

[0546] the fermenting organism is Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having the defining characteristics of strain V14/004037. 2. The process of paragraph 1, wherein the glucoamylase is a Gloeophyllum glucoamylase, preferably Gloeophyllum trabeum glucoamylase. 3. The process of any of paragraphs 1 or 2, wherein the glucoamylase is the Gloeophyllum trabeum glucoamylase shown in SEQ ID NO: 18. 4. The process of any of paragraphs 1-3, wherein the glucoamylase is the Gloeophyllum trabeum glucoamylase shown in SEQ ID NO: 18 having one of the following substitutions: V59A; S95P; A121P; T119W; S95P+A121P; V59A+S95P; S95P+T119W; V59A+S95P+A121P; or S95P+T119W+A121P, especially S95P+A121P. 5. The process of any of paragraphs 1-4, wherein the glucoamylase is a Trametes glucoamylase, preferably Trametes cingulata glucoamylase. 6. The process of any of paragraphs 1-5, wherein the glucoamylase is the Trametes cingulata glucoamylase shown in SEQ ID NO: 12. 7. The process of any of paragraphs 1-6, wherein the glucoamylase is selected from the group consisting of: (i) a glucoamylase comprising the mature polypeptide of SEQ ID NO: 12 herein; (ii) a glucoamylase comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 12 herein. 8. The process of any of paragraphs 1-7, wherein the alpha-amylase is derived from Rhizomucor pusillus, preferably with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), preferably the one disclosed as V039 in Table 5 in WO 2006/069290 or SEQ ID NO: 13 herein. 9. The process any of paragraphs 1-8, wherein the glucoamylase is the Trametes cingulata glucoamylase shown in SEQ ID NO: 12 and the alpha-amylase is Rhizomucor pusillus alpha-amylase with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD). 10. The process of any of paragraphs 1-9, wherein the alpha-amylase is derived from Rhizomucor pusillus. 11. The process of any of paragraphs 1-10, wherein the glucoamylase is selected from the group consisting of: (i) a glucoamylase comprising the mature polypeptide of SEQ ID NO: 18 herein; (ii) a glucoamylase comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 18 herein. 12. The process of any of paragraphs 1-11, wherein the alpha-amylase is Rhizomucor pusillus alpha-amylase with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), preferably one having at least one of the following substitutions or combinations of substitutions: D165M; Y141W; Y141R; K136F; K192R; P224A; P224R; S123H+Y141W; G20S+Y141W; A76G+Y141W; G128D+Y141W; G128D+D143N; P219C+Y141W; N142D+D143N; Y141W+K192R; Y141W+D143N; Y141W+N383R; Y141W+P219C+A265C; Y141W+N142D+D143N; Y141W+K192R V410A; G128D+Y141W+D143N; Y141W+D143N+P219C; Y141W+D143N+K192R; G128D+D143N+K192R; Y141W+D143N+K192R+P219C; G128D+Y141W+D143N+K192R; or G128D+Y141W+D143N+K192R+P219C, especially G128D+D143N (using SEQ ID NO: 13 for numbering). 13. The process any of paragraphs 1-12, wherein the glucoamylase is the Gloeophyllum trabeum glucoamylase shown in SEQ ID NO: 18 having one of the following substitutions: S95P+A121P and the alpha-amylase is Rhizomucor pusillus alpha-amylase with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), preferably one having the following substitutions G128D+D143N (using SEQ ID NO: 13 for numbering). 14. The process of any of paragraphs 1-13, wherein the glucoamylase is the Pycnoporus sanguineus glucoamylase shown in SEQ ID NO: 17 herein. 15. The process of any of paragraphs 1-14, wherein the glucoamylase is selected from the group consisting of: (i) a glucoamylase comprising the mature polypeptide of SEQ ID NO: 17 herein; (ii) a glucoamylase comprising an amino acid sequence having at least 60%, at least 70%, e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the mature polypeptide of SEQ ID NO: 17 herein. 16. The process of any of paragraphs 1-15, wherein the glucoamylase is the Pycnoporus sanguineus glucoamylase shown in SEQ ID NO: 17 herein, and the alpha-amylase is the Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), preferably the one disclosed as V039 in Table 5 in WO 2006/069290 or SEQ ID NO: 13 herein, preferably one having one or more of the following substitutions: G128D, D143N, especially G128D+D143N. 17. The process of any of paragraphs 1-16, wherein the ratio between glucoamylase and alpha-amylase is between 99:1 and 1:2, such as between 98:2 and 1:1, such as between 97:3 and 2:1, such as between 96:4 and 3:1, such as 97:3, 96:4, 95:5, 94:6, 93:7, 90:10, 85:15, 83:17 or 65:35 (mg EP glucoamylase: mg EP alpha-amylase). 18. The process of any of paragraphs 1-17, wherein the total dose of glucoamylase and alpha-amylase added is from 10-1,000 .mu.g/g DS, such as from 50-500 .mu.g/g DS, such as 75-250 .mu.g/g DS. 19. The process of any of paragraphs 1-18, wherein the total dose of cellulolytic enzyme composition added is from 10-500 .mu.g/g DS, such as from 20-400 .mu.g/g DS, such as 20-300 .mu.g/g DS. 20. The process of any of paragraphs 1-19, wherein the dose of protease added is from 1-200 .mu.g/g DS, such as from 2-100 .mu.g/g DS, such as 3-50 .mu.g/g DS. 21. The process of any of paragraphs 1-20, wherein the fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037, has one or more, such as all, of the following properties and defining characteristics:

[0547] increases ethanol yield compared to Ethanol Red.TM. under the same process conditions;

[0548] produces reduced levels of lactic acid compared to Ethanol Red.TM. under the same process conditions;

[0549] produces reduced levels of glycerol compared to Ethanol Red.TM. under the same process conditions;

[0550] has faster fermentation kinetics compared to Ethanol Red.TM. under the same process conditions.

22. The process of any of paragraphs 1-21, wherein the fermenting organism is a non-recombinant Saccharomyces strain, preferably non-recombinant Saccharomyces cerevisiae strain. 23. The process of any of paragraphs 1-2, wherein the fermenting organism strain is a non-recombinant Saccharomyces strain preferably non-recombinant Saccharomyces cerevisiae strain produced using the method described and concerned in U.S. Pat. No. 8,257,959-BB. 24. The process of any of paragraphs 1-23, wherein saccharification and fermentation are done separately or simultaneously.

[0551] 25. The process of any of paragraphs 1-24, wherein the ethanol (i.e., product) is recovered after fermentation.

26. The process of any of paragraphs 1-25, wherein the starch-containing material is plant material selected from the corn (maize), cobs, wheat, barley, rye, milo, sago, cassava, tapioca, sorghum, oat, rice, peas, beans, sweet potatoes, or a mixture thereof, preferably corn. 27. The process of any of paragraphs 1-26, wherein the starch-containing material is granular starch. 28. The process of any of paragraphs 1-27, wherein the process is carried out at a pH in the range between 3 and 7, preferably from 3 to 6, or more preferably from 3.5 to 5.0. 29. The process of any of paragraphs 1-28, wherein the dry solid content (DS) lies in the range from 10-55 wt.-% (DS), preferably 25-45 wt.-%, more preferably 30-40% of starch-containing material. 30. The process of any of paragraphs 1-29, wherein the sugar concentration is kept at a level below about 6 wt.-%, preferably 3 wt.-%, during saccharification and fermentation, especially below 0.25 wt.-%. 31. The process of any of paragraphs 1-30, wherein a slurry comprising starch-containing material reduced in particle size and water, is prepared before step (a). 32. The process of any of paragraphs 1-31, wherein the starch-containing material is prepared by reducing the particle size of the starch-containing material, preferably by milling, such that at least 50% of the starch-containing material has a particle size of 0.1-0.5 mm. 33. The process of any of paragraphs 1-32, wherein the starch-containing plant material is reduced in particle size, such as by dry or wet milling or using particle size emulsion technology. 34. The process of any of paragraphs 1-33, wherein the fermentation is carried out for 30 to 150 hours, preferably 48 to 96 hours. 35. The process of any of paragraphs 1-34, wherein the temperature during fermentation in step (b) or simultaneous saccharification and fermentation in steps (a) and (b) is between 25.degree. C. and 40.degree. C., preferably between 28.degree. C. and 36.degree. C., such as between 28.degree. C. and 35.degree. C., such as between 28.degree. C. and 34.degree. C., such as around 32.degree. C. 36. The process of any of paragraphs 1-35, wherein further a protease is present during saccharification and/or fermentation. 37. The process of any of paragraphs 1-36, wherein the glucoamylase is present and/or added in an amount of 0.001 to 10 AGU/g DS, preferably from 0.01 to 5 AGU/g DS, especially 0.1 to 0.5 AGU/g DS.

[0552] 38. The process of any of paragraphs 1-37, wherein the glucoamylase is present and/or added in an amount of 10-1,000 micro grams Enzyme Protein/g DS

39. The process of any of paragraphs 1-38, wherein the alpha-amylase is present and/or added in an amount of 0.001 to 10 AFAU/g DS, preferably from 0.01 to 5 AFAU/g DS, especially 0.3 to 2 AFAU/g DS or 0.001 to 1 FAU-F/g DS, preferably 0.01 to 1 FAU-F/g DS. 40. The process of any of paragraphs 1-39, wherein the alpha-amylase is present and/or added in an amount of 10-1,000 micro grams Enzyme Protein/g DS. 41. The process of any of paragraphs 1-40, wherein a cellulolytic enzyme composition is present and/or added during saccharification, fermentation or simultaneous saccharification and fermentation. 42. The process of paragraph 41, wherein the cellulolytic enzyme composition is present and/or added in an amount 1-10,000 micrograms EP/g DS, such as 2-5,000, such as 3 and 1,000, such as 4 and 500 micrograms EP/g DS. 43. The process of any of paragraphs 41-42, wherein cellulolytic enzyme composition is present and/or added in an amount in the range from 0.1-100 FPU per gram total solids (TS), preferably 0.5-50 FPU per gram TS, especially 1-20 FPU per gram TS. 44. The process of any of paragraphs 1-43, wherein protease is present and/or added in an amount in the range 1-1,000 .mu.g EP/g DS, such as 2-500 .mu.g EP/g DS, such as 3-250 .mu.g EP/g DS. 45. The process of any of paragraphs 1-44, wherein the fermenting organism, in particular yeast, is added to the fermentation, so that the count per mL of fermentation medium is in the range from 10.sup.5 to 10.sup.12, preferably from 10.sup.7 to 10.sup.10, especially about 5.times.10.sup.7. 46. The process of any of paragraphs 1-45, comprising: (a) saccharifying a starch-containing material at a temperature below the initial gelatinization temperature; and (b) fermenting using a fermentation organism; wherein saccharification and/or fermentation is done in the presence of the following enzymes:

[0553] i) glucoamylase derived from Trametes cingulata;

[0554] ii) alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), or a variant thereof;

[0555] wherein the fermenting organism is Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037.

47. The process of any of paragraphs 1-46, comprising: (a) saccharifying a starch-containing material at a temperature below the initial gelatinization temperature; and (b) fermenting using a fermentation organism; wherein saccharification and/or fermentation is done in the presence of the following enzymes:

[0556] i) glucoamylase derived from Trametes cingulata;

[0557] ii) alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), or a variant thereof;

[0558] iii) cellulolytic enzyme composition derived from a strain of Trichoderma reesei;

[0559] optionally iv) a protease from Thermoascus aurantiacus, or a variant thereof and/or Pyrococcus furiosus;

[0560] wherein the fermenting organism is Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having the defining characteristics of strain V14/004037.

48. The process of any of paragraphs 1-47, comprising: (a) saccharifying a starch-containing material at a temperature below the initial gelatinization temperature; and (b) fermenting using a fermentation organism; wherein saccharification and/or fermentation is done in the presence of the following enzymes:

[0561] i) glucoamylase derived from Gloeophyllum trabeum shown in SEQ ID NO: 18, preferably having at least one of the following substitutions: V59A; S95P; A121P; T119W; S95P+A121P; V59A+S95P; S95P+T119W; V59A+S95P+A121P; or S95P+T119W+A121P, especially S95P+A121P (using SEQ ID NO: 18 for numbering);

[0562] ii) alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), preferably one having at least one of the following substitutions or combinations of substitutions: D165M; Y141W; Y141R; K136F; K192R; P224A; P224R; S123H+Y141W; G20S+Y141W; A76G+Y141W; G128D+Y141W; G128D+D143N; P219C+Y141W; N142D+D143N; Y141W+K192R; Y141W+D143N; Y141W+N383R; Y141W+P219C+A265C; Y141W+N142D+D143N; Y141W+K192R V410A; G128D+Y141W+D143N; Y141W+D143N+P219C; Y141W+D143N+K192R; G128D+D143N+K192R; Y141W+D143N+K192R+P219C; G128D+Y141W+D143N+K192R; or G128D+Y141W+D143N+K192R+P219C, especially G128D+D143N (using SEQ ID NO: 13 for numbering);

[0563] wherein the fermenting organism is Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having the defining characteristics of strain V14/004037.

49. The process of any of paragraphs 1-48, comprising: (a) saccharifying a starch-containing material at a temperature below the initial gelatinization temperature; and (b) fermenting using a fermentation organism; wherein saccharification and/or fermentation is done in the presence of the following enzymes:

[0564] i) glucoamylase derived from Gloeophyllum trabeum shown in SEQ ID NO: 18, preferably having at least one of the following substitutions: V59A; S95P; A121P; T119W; S95P+A121P; V59A+S95P; S95P+T119W; V59A+S95P+A121P; or S95P+T119W+A121P, especially S95P+A121P (using SEQ ID NO: 18 for numbering);

[0565] ii) alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), preferably one having at least one of the following substitutions or combinations of substitutions: D165M; Y141W; Y141R; K136F; K192R; P224A; P224R; S123H+Y141W; G20S+Y141W; A76G+Y141W; G128D+Y141W; G128D+D143N; P219C+Y141W; N142D+D143N; Y141W+K192R; Y141W+D143N; Y141W+N383R; Y141W+P219C+A265C; Y141W+N142D+D143N; Y141W+K192R V410A; G128D+Y141W+D143N; Y141W+D143N+P219C; Y141W+D143N+K192R; G128D+D143N+K192R; Y141W+D143N+K192R+P219C; G128D+Y141W+D143N+K192R; or G128D+Y141W+D143N+K192R+P219C, especially G128D+D143N (using SEQ ID NO: 13 for numbering);

[0566] iii) cellulolytic enzyme composition derived from a strain of Trichoderma reesei; preferably a cellulolytic enzyme composition derived from Trichoderma reesei further comprising Penicillium emersonii GH61A polypeptide disclosed as SEQ ID NO: 2 in WO 2011/041397 or SEQ ID NO: 10 herein, and Aspergillus fumigatus beta-glucosidase disclosed as SEQ ID NO: 2 in WO 2005/047499 or SEQ ID NO: 8 herein, or a variant thereof, preferably a variant having one of, preferably all of, the following substitutions: F100D, S283G, N456E, F512Y and optionally Aspergillus fumigatus Cel7A CBH1 disclosed as SEQ ID NO: 6 in WO2011/057140 and SEQ ID NO: 6 herein and Aspergillus fumigatus CBH II disclosed as SEQ ID NO: 18 in WO 2011/057140 and as SEQ ID NO: 7 herein;

[0567] optionally iv) a protease from Thermoascus aurantiacus, or a variant thereof and/or Pyrococcus furiosus;

[0568] wherein the fermenting organism is Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having the defining characteristics of strain V14/004037.

50. The process of any of paragraphs 1-49, comprising: (a) saccharifying a starch-containing material at a temperature below the initial gelatinization temperature; and (b) fermenting using a fermentation organism; wherein saccharification and/or fermentation is done in the presence of the following enzymes:

[0569] i) glucoamylase derived from Pycnoporus sanguineus shown in SEQ ID NO: 17 herein,

[0570] ii) alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), preferably one having at least one of the following substitutions or combinations of substitutions: D165M; Y141W; Y141R; K136F; K192R; P224A; P224R; S123H+Y141W; G20S+Y141W; A76G+Y141W; G128D+Y141W; G128D+D143N; P219C+Y141W; N142D+D143N; Y141W+K192R; Y141W+D143N; Y141W+N383R; Y141W+P219C+A265C; Y141W+N142D+D143N; Y141W+K192R V410A; G128D+Y141W+D143N; Y141W+D143N+P219C; Y141W+D143N+K192R; G128D+D143N+K192R; Y141W+D143N+K192R+P219C; G128D+Y141W+D143N+K192R; or G128D+Y141W+D143N+K192R+P219C, especially G128D+D143N (using SEQ ID NO: 13 for numbering);

[0571] optionally iii) cellulolytic enzyme composition derived from a strain of Trichoderma reesei; preferably a cellulolytic composition derived from Trichoderma reesei further comprising Penicillium emersonii GH61A polypeptide disclosed as SEQ ID NO: 2 in WO 2011/041397 or SEQ ID NO: 10 herein, and Aspergillus fumigatus beta-glucosidase disclosed as SEQ ID NO: 2 in WO 2005/047499 or SEQ ID NO: 8 herein, or a variant thereof, preferably a variant having one of, preferably all of, the following substitutions: F100D, S283G, N456E, F512Y and optionally Aspergillus fumigatus Cel7A CBH1 disclosed as SEQ ID NO: 6 in WO2011/057140 and SEQ ID NO: 6 herein and Aspergillus fumigatus CBH II disclosed as SEQ ID NO: 18 in WO 2011/057140 and as SEQ ID NO: 7 herein;

[0572] optionally iv) a protease from Thermoascus aurantiacus, or a variant thereof and/or Pyrococcus furiosus;

[0573] wherein the fermenting organism is Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces strain V14/004037 having defining characteristics of strain V14/004037.

51. The process of any of paragraphs 1-50, wherein the ratio between glucoamylase and alpha-amylase is between 99:1 and 1:2, such as between 98:2 and 1:1, such as between 97:3 and 2:1, such as between 96:4 and 3:1, such as 97:3, 96:4, 95:5, 94:6, 93:7, 90:10, 85:15, 83:17 or 65:35 (mg EP glucoamylase: mg EP alpha-amylase). 52. The process of paragraphs 1-51, wherein the saccharification and fermentation are carried out simultaneously. 53. The process of any of paragraphs 1-52, wherein an enzyme composition of paragraphs 1-61 is used as the enzymes in saccharification or fermentation or simultaneous saccharification and fermentation. 54. A Saccharomyces yeast strain deposited under the Budapest Treaty and having NMI accession no. V14/004037 or a derivative of strain V14/004037 which exhibits one or more defining characteristics of strain V14/004037. 55. The strain of paragraph 54, wherein the strain is strain V14/004037. 56. A method of producing a derivative of strain V14/004037 which exhibits the defining characteristics of strain V14/004037, comprising: (a) providing: (i) a first yeast strain; and (ii) a second yeast strain, wherein the second yeast strain is strain V14/004037 or a derivative of strain V14/004037; (b) culturing the first yeast strain and the second yeast strain under conditions which permit combining of DNA between the first and second yeast strains; (c) screening or selecting for a derivative of strain V14/004037. 57. The method of paragraph 56, wherein step (c) comprises screening or selecting for a hybrid strain which exhibits one or more defining characteristic of strain V14/004037. 58. The method of paragraph 56, comprising the further step of: (d) repeating steps (b) and (c) with the screened or selected strain from step (c) as the first and/or second strain, until a derivative is obtained which exhibits defining characteristics of strain V14/004037. 59. The method of paragraph 56 or 58, wherein the culturing step (b) comprises: (i) sporulating the first yeast strain and the second yeast strain; (ii) hybridizing germinated spores produced by the first yeast strain with germinated spores produced by the second yeast strain. 60. A Saccharomyces strain produced by the method of paragraph 56. 61. A method of producing ethanol, comprising incubating a strain of paragraph 54 or 60 with a substrate comprising a fermentable sugar under conditions which permit fermentation of the fermentable sugar to produce ethanol. 62. Use of a strain of paragraph 54 or 60 in the production of ethanol. 63. A method of producing distiller's grain, comprising: (a) incubating a Saccharomyces strain of paragraph 54 or 60 with a substrate comprising fermentable sugar under conditions which allow fermentation of the fermentable sugar to produce ethanol and distiller's grains; (b) isolating the distiller's grains. 64. Distiller's grain produced by the method of paragraph 63. 65. Use of a strain of paragraph 54 or 60 in the production of distiller's grains. 66. Use of strain V14/004037 (Saccharomyces cerevisiae MBG4851) in the production of a Saccharomyces strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851 or which exhibits one or more defining characteristics of strain V14/004037. 67. Use of strain V14/004037 (Saccharomyces cerevisiae MBG4851) or a strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851 or a derivative of strain V14/004037 in a process according to any of paragraphs 1-53. 68. A composition comprising a Saccharomyces yeast strain of any of paragraphs 54 or 60 and one or more naturally occurring and/or non-naturally occurring components. 69. A composition of paragraph 68, wherein the components are selected from the group consisting of: surfactants, emulsifiers, gums, swelling agents, and antioxidants. 70. The composition of paragraph 68 or 69, wherein the Saccharomyces yeast strain is Saccharomyces MBG4851. 71. The composition of paragraphs 68-70, wherein the Saccharomyces yeast strain is in a viable form, in particular in dry, cream or compressed form.

Sequence CWU 1

1

181515PRTBacillus stearothermophilusmat_peptide(1)..(515) 1Ala Ala Pro Phe Asn Gly Thr Met Met Gln Tyr Phe Glu Trp Tyr Leu 1 5 10 15 Pro Asp Asp Gly Thr Leu Trp Thr Lys Val Ala Asn Glu Ala Asn Asn 20 25 30 Leu Ser Ser Leu Gly Ile Thr Ala Leu Trp Leu Pro Pro Ala Tyr Lys 35 40 45 Gly Thr Ser Arg Ser Asp Val Gly Tyr Gly Val Tyr Asp Leu Tyr Asp 50 55 60 Leu Gly Glu Phe Asn Gln Lys Gly Thr Val Arg Thr Lys Tyr Gly Thr 65 70 75 80 Lys Ala Gln Tyr Leu Gln Ala Ile Gln Ala Ala His Ala Ala Gly Met 85 90 95 Gln Val Tyr Ala Asp Val Val Phe Asp His Lys Gly Gly Ala Asp Gly 100 105 110 Thr Glu Trp Val Asp Ala Val Glu Val Asn Pro Ser Asp Arg Asn Gln 115 120 125 Glu Ile Ser Gly Thr Tyr Gln Ile Gln Ala Trp Thr Lys Phe Asp Phe 130 135 140 Pro Gly Arg Gly Asn Thr Tyr Ser Ser Phe Lys Trp Arg Trp Tyr His 145 150 155 160 Phe Asp Gly Val Asp Trp Asp Glu Ser Arg Lys Leu Ser Arg Ile Tyr 165 170 175 Lys Phe Arg Gly Ile Gly Lys Ala Trp Asp Trp Glu Val Asp Thr Glu 180 185 190 Asn Gly Asn Tyr Asp Tyr Leu Met Tyr Ala Asp Leu Asp Met Asp His 195 200 205 Pro Glu Val Val Thr Glu Leu Lys Asn Trp Gly Lys Trp Tyr Val Asn 210 215 220 Thr Thr Asn Ile Asp Gly Phe Arg Leu Asp Ala Val Lys His Ile Lys 225 230 235 240 Phe Ser Phe Phe Pro Asp Trp Leu Ser Tyr Val Arg Ser Gln Thr Gly 245 250 255 Lys Pro Leu Phe Thr Val Gly Glu Tyr Trp Ser Tyr Asp Ile Asn Lys 260 265 270 Leu His Asn Tyr Ile Thr Lys Thr Asn Gly Thr Met Ser Leu Phe Asp 275 280 285 Ala Pro Leu His Asn Lys Phe Tyr Thr Ala Ser Lys Ser Gly Gly Ala 290 295 300 Phe Asp Met Arg Thr Leu Met Thr Asn Thr Leu Met Lys Asp Gln Pro 305 310 315 320 Thr Leu Ala Val Thr Phe Val Asp Asn His Asp Thr Glu Pro Gly Gln 325 330 335 Ala Leu Gln Ser Trp Val Asp Pro Trp Phe Lys Pro Leu Ala Tyr Ala 340 345 350 Phe Ile Leu Thr Arg Gln Glu Gly Tyr Pro Cys Val Phe Tyr Gly Asp 355 360 365 Tyr Tyr Gly Ile Pro Gln Tyr Asn Ile Pro Ser Leu Lys Ser Lys Ile 370 375 380 Asp Pro Leu Leu Ile Ala Arg Arg Asp Tyr Ala Tyr Gly Thr Gln His 385 390 395 400 Asp Tyr Leu Asp His Ser Asp Ile Ile Gly Trp Thr Arg Glu Gly Val 405 410 415 Thr Glu Lys Pro Gly Ser Gly Leu Ala Ala Leu Ile Thr Asp Gly Pro 420 425 430 Gly Gly Ser Lys Trp Met Tyr Val Gly Lys Gln His Ala Gly Lys Val 435 440 445 Phe Tyr Asp Leu Thr Gly Asn Arg Ser Asp Thr Val Thr Ile Asn Ser 450 455 460 Asp Gly Trp Gly Glu Phe Lys Val Asn Gly Gly Ser Val Ser Val Trp 465 470 475 480 Val Pro Arg Lys Thr Thr Val Ser Thr Ile Ala Arg Pro Ile Thr Thr 485 490 495 Arg Pro Trp Thr Gly Glu Phe Val Arg Trp Thr Glu Pro Arg Leu Val 500 505 510 Ala Trp Pro 515 21068DNAThermoascus aurantiacusCDS(1)..(1065)misc_signal(1)..(57)misc_feature(58)..(534)mat_p- eptide(535)..(1068) 2atg cgg ctc gtt gct tcc cta acg gcc ttg gtg gcc ttg tcc gta 45Met Arg Leu Val Ala Ser Leu Thr Ala Leu Val Ala Leu Ser Val -175 -170 -165 cct gtc ttt ccc gct gct gtc aac gtg aag cgt gct tcg tcc tac 90Pro Val Phe Pro Ala Ala Val Asn Val Lys Arg Ala Ser Ser Tyr -160 -155 -150 ctg gag atc act ctg agc cag gtc agc aac act ctg atc aag gcc 135Leu Glu Ile Thr Leu Ser Gln Val Ser Asn Thr Leu Ile Lys Ala -145 -140 -135 gtg gtc cag aac act ggt agc gac gag ttg tcc ttc gtt cac ctg 180Val Val Gln Asn Thr Gly Ser Asp Glu Leu Ser Phe Val His Leu -130 -125 -120 aac ttc ttc aag gac ccc gct cct gtc aaa aag gta tcg gtc tat 225Asn Phe Phe Lys Asp Pro Ala Pro Val Lys Lys Val Ser Val Tyr -115 -110 -105 cgc gat ggg tct gaa gtg cag ttc gag ggc att ttg agc cgc tac aaa 273Arg Asp Gly Ser Glu Val Gln Phe Glu Gly Ile Leu Ser Arg Tyr Lys -100 -95 -90 tcg act ggc ctc tct cgt gac gcc ttt act tat ctg gct ccc gga gag 321Ser Thr Gly Leu Ser Arg Asp Ala Phe Thr Tyr Leu Ala Pro Gly Glu -85 -80 -75 tcc gtc gag gac gtt ttt gat att gct tcg act tac gat ctg acc agc 369Ser Val Glu Asp Val Phe Asp Ile Ala Ser Thr Tyr Asp Leu Thr Ser -70 -65 -60 ggc ggc cct gta act atc cgt act gag gga gtt gtt ccc tac gcc acg 417Gly Gly Pro Val Thr Ile Arg Thr Glu Gly Val Val Pro Tyr Ala Thr -55 -50 -45 -40 gct aac agc act gat att gcc ggc tac atc tca tac tcg tct aat gtg 465Ala Asn Ser Thr Asp Ile Ala Gly Tyr Ile Ser Tyr Ser Ser Asn Val -35 -30 -25 ttg acc att gat gtc gat ggc gcc gct gct gcc act gtc tcc aag gca 513Leu Thr Ile Asp Val Asp Gly Ala Ala Ala Ala Thr Val Ser Lys Ala -20 -15 -10 atc act cct ttg gac cgc cgc act agg atc agt tcc tgc tcc ggc agc 561Ile Thr Pro Leu Asp Arg Arg Thr Arg Ile Ser Ser Cys Ser Gly Ser -5 -1 1 5 aga cag agc gct ctt act acg gct ctc aga aac gct gct tct ctt gcc 609Arg Gln Ser Ala Leu Thr Thr Ala Leu Arg Asn Ala Ala Ser Leu Ala 10 15 20 25 aac gca gct gcc gac gcg gct cag tct gga tca gct tca aag ttc agc 657Asn Ala Ala Ala Asp Ala Ala Gln Ser Gly Ser Ala Ser Lys Phe Ser 30 35 40 gag tac ttc aag act act tct agc tct acc cgc cag acc gtg gct gcg 705Glu Tyr Phe Lys Thr Thr Ser Ser Ser Thr Arg Gln Thr Val Ala Ala 45 50 55 cgt ctt cgg gct gtt gcg cgg gag gca tct tcg tct tct tcg gga gcc 753Arg Leu Arg Ala Val Ala Arg Glu Ala Ser Ser Ser Ser Ser Gly Ala 60 65 70 acc acg tac tac tgc gac gat ccc tac ggc tac tgt tcc tcc aac gtc 801Thr Thr Tyr Tyr Cys Asp Asp Pro Tyr Gly Tyr Cys Ser Ser Asn Val 75 80 85 ctg gct tac acc ctg cct tca tac aac ata atc gcc aac tgt gac att 849Leu Ala Tyr Thr Leu Pro Ser Tyr Asn Ile Ile Ala Asn Cys Asp Ile 90 95 100 105 ttc tat act tac ctg ccg gct ctg acc agt acc tgt cac gct cag gat 897Phe Tyr Thr Tyr Leu Pro Ala Leu Thr Ser Thr Cys His Ala Gln Asp 110 115 120 caa gcg acc act gcc ctt cac gag ttc acc cat gcg cct ggc gtc tac 945Gln Ala Thr Thr Ala Leu His Glu Phe Thr His Ala Pro Gly Val Tyr 125 130 135 agc cct ggc acg gac gac ctg gcg tat ggc tac cag gct gcg atg ggt 993Ser Pro Gly Thr Asp Asp Leu Ala Tyr Gly Tyr Gln Ala Ala Met Gly 140 145 150 ctc agc agc agc cag gct gtc atg aac gct gac acc tac gct ctc tat 1041Leu Ser Ser Ser Gln Ala Val Met Asn Ala Asp Thr Tyr Ala Leu Tyr 155 160 165 gcg aat gcc ata tac ctt ggt tgc taa 1068Ala Asn Ala Ile Tyr Leu Gly Cys 170 175 3355PRTThermoascus aurantiacus 3Met Arg Leu Val Ala Ser Leu Thr Ala Leu Val Ala Leu Ser Val -175 -170 -165 Pro Val Phe Pro Ala Ala Val Asn Val Lys Arg Ala Ser Ser Tyr -160 -155 -150 Leu Glu Ile Thr Leu Ser Gln Val Ser Asn Thr Leu Ile Lys Ala -145 -140 -135 Val Val Gln Asn Thr Gly Ser Asp Glu Leu Ser Phe Val His Leu -130 -125 -120 Asn Phe Phe Lys Asp Pro Ala Pro Val Lys Lys Val Ser Val Tyr -115 -110 -105 Arg Asp Gly Ser Glu Val Gln Phe Glu Gly Ile Leu Ser Arg Tyr Lys -100 -95 -90 Ser Thr Gly Leu Ser Arg Asp Ala Phe Thr Tyr Leu Ala Pro Gly Glu -85 -80 -75 Ser Val Glu Asp Val Phe Asp Ile Ala Ser Thr Tyr Asp Leu Thr Ser -70 -65 -60 Gly Gly Pro Val Thr Ile Arg Thr Glu Gly Val Val Pro Tyr Ala Thr -55 -50 -45 -40 Ala Asn Ser Thr Asp Ile Ala Gly Tyr Ile Ser Tyr Ser Ser Asn Val -35 -30 -25 Leu Thr Ile Asp Val Asp Gly Ala Ala Ala Ala Thr Val Ser Lys Ala -20 -15 -10 Ile Thr Pro Leu Asp Arg Arg Thr Arg Ile Ser Ser Cys Ser Gly Ser -5 -1 1 5 Arg Gln Ser Ala Leu Thr Thr Ala Leu Arg Asn Ala Ala Ser Leu Ala 10 15 20 25 Asn Ala Ala Ala Asp Ala Ala Gln Ser Gly Ser Ala Ser Lys Phe Ser 30 35 40 Glu Tyr Phe Lys Thr Thr Ser Ser Ser Thr Arg Gln Thr Val Ala Ala 45 50 55 Arg Leu Arg Ala Val Ala Arg Glu Ala Ser Ser Ser Ser Ser Gly Ala 60 65 70 Thr Thr Tyr Tyr Cys Asp Asp Pro Tyr Gly Tyr Cys Ser Ser Asn Val 75 80 85 Leu Ala Tyr Thr Leu Pro Ser Tyr Asn Ile Ile Ala Asn Cys Asp Ile 90 95 100 105 Phe Tyr Thr Tyr Leu Pro Ala Leu Thr Ser Thr Cys His Ala Gln Asp 110 115 120 Gln Ala Thr Thr Ala Leu His Glu Phe Thr His Ala Pro Gly Val Tyr 125 130 135 Ser Pro Gly Thr Asp Asp Leu Ala Tyr Gly Tyr Gln Ala Ala Met Gly 140 145 150 Leu Ser Ser Ser Gln Ala Val Met Asn Ala Asp Thr Tyr Ala Leu Tyr 155 160 165 Ala Asn Ala Ile Tyr Leu Gly Cys 170 175 4573PRTGloeophyllum sepiarium 4Met Tyr Arg Phe Leu Val Cys Ala Leu Gly Leu Ala Ala Ser Val Leu 1 5 10 15 Ala Gln Ser Val Asp Ser Tyr Val Ser Ser Glu Gly Pro Ile Ala Lys 20 25 30 Ala Gly Val Leu Ala Asn Ile Gly Pro Asn Gly Ser Lys Ala Ser Gly 35 40 45 Ala Ser Ala Gly Val Val Val Ala Ser Pro Ser Thr Ser Asp Pro Asp 50 55 60 Tyr Trp Tyr Thr Trp Thr Arg Asp Ser Ser Leu Val Phe Lys Ser Leu 65 70 75 80 Ile Asp Gln Tyr Thr Thr Gly Ile Asp Ser Thr Ser Ser Leu Arg Thr 85 90 95 Leu Ile Asp Asp Phe Val Thr Ala Glu Ala Asn Leu Gln Gln Val Ser 100 105 110 Asn Pro Ser Gly Thr Leu Thr Thr Gly Gly Leu Gly Glu Pro Lys Phe 115 120 125 Asn Val Asp Glu Thr Ala Phe Thr Gly Ala Trp Gly Arg Pro Gln Arg 130 135 140 Asp Gly Pro Ala Leu Arg Ser Thr Ala Leu Ile Thr Tyr Gly Asn Trp 145 150 155 160 Leu Leu Ser Asn Gly Asn Thr Ser Tyr Val Thr Ser Asn Leu Trp Pro 165 170 175 Ile Ile Gln Asn Asp Leu Gly Tyr Val Val Ser Tyr Trp Asn Gln Ser 180 185 190 Thr Tyr Asp Leu Trp Glu Glu Val Asp Ser Ser Ser Phe Phe Thr Thr 195 200 205 Ala Val Gln His Arg Ala Leu Arg Glu Gly Ala Ala Phe Ala Thr Ala 210 215 220 Ile Gly Gln Thr Ser Gln Val Ser Ser Tyr Thr Thr Gln Ala Asp Asn 225 230 235 240 Leu Leu Cys Phe Leu Gln Ser Tyr Trp Asn Pro Ser Gly Gly Tyr Ile 245 250 255 Thr Ala Asn Thr Gly Gly Gly Arg Ser Gly Lys Asp Ala Asn Thr Leu 260 265 270 Leu Ala Ser Ile His Thr Tyr Asp Pro Ser Ala Gly Cys Asp Ala Ala 275 280 285 Thr Phe Gln Pro Cys Ser Asp Lys Ala Leu Ser Asn Leu Lys Val Tyr 290 295 300 Val Asp Ser Phe Arg Ser Val Tyr Ser Ile Asn Ser Gly Val Ala Ser 305 310 315 320 Asn Ala Ala Val Ala Thr Gly Arg Tyr Pro Glu Asp Ser Tyr Gln Gly 325 330 335 Gly Asn Pro Trp Tyr Leu Thr Thr Phe Ala Val Ala Glu Gln Leu Tyr 340 345 350 Asp Ala Leu Asn Val Trp Glu Ser Gln Gly Ser Leu Glu Val Thr Ser 355 360 365 Thr Ser Leu Ala Phe Phe Gln Gln Phe Ser Ser Gly Val Thr Ala Gly 370 375 380 Thr Tyr Ser Ser Ser Ser Ser Thr Tyr Ser Thr Leu Thr Ser Ala Ile 385 390 395 400 Lys Asn Phe Ala Asp Gly Phe Val Ala Ile Asn Ala Lys Tyr Thr Pro 405 410 415 Ser Asn Gly Gly Leu Ala Glu Gln Tyr Ser Lys Ser Asp Gly Ser Pro 420 425 430 Leu Ser Ala Val Asp Leu Thr Trp Ser Tyr Ala Ser Ala Leu Thr Ala 435 440 445 Phe Glu Ala Arg Asn Asn Thr Gln Phe Ala Gly Trp Gly Ala Ala Gly 450 455 460 Leu Thr Val Pro Ser Ser Cys Ser Gly Asn Ser Gly Gly Pro Thr Val 465 470 475 480 Ala Val Thr Phe Asn Val Asn Ala Glu Thr Val Trp Gly Glu Asn Ile 485 490 495 Tyr Leu Thr Gly Ser Val Asp Ala Leu Glu Asn Trp Ser Ala Asp Asn 500 505 510 Ala Leu Leu Leu Ser Ser Ala Asn Tyr Pro Thr Trp Ser Ile Thr Val 515 520 525 Asn Leu Pro Ala Ser Thr Ala Ile Glu Tyr Lys Tyr Ile Arg Lys Asn 530 535 540 Asn Gly Ala Val Thr Trp Glu Ser Asp Pro Asn Asn Ser Ile Thr Thr 545 550 555 560 Pro Ala Ser Gly Ser Thr Thr Glu Asn Asp Thr Trp Arg 565 570 5412PRTPyrococcus furiosusmat_peptide(1)..(412)Pyrococcus furiosus protease (Pfu) 5Ala Glu Leu Glu Gly Leu Asp Glu Ser Ala Ala Gln Val Met Ala Thr 1 5 10 15 Tyr Val Trp Asn Leu Gly Tyr Asp Gly Ser Gly Ile Thr Ile Gly Ile 20 25 30 Ile Asp Thr Gly Ile Asp Ala Ser His Pro Asp Leu Gln Gly Lys Val 35 40 45 Ile Gly Trp Val Asp Phe Val Asn Gly Arg Ser Tyr Pro Tyr Asp Asp 50 55 60 His Gly His Gly Thr His Val Ala Ser Ile Ala Ala Gly Thr Gly Ala 65 70 75 80 Ala Ser Asn Gly Lys Tyr Lys Gly Met Ala Pro Gly Ala Lys Leu Ala 85 90 95 Gly Ile Lys Val Leu Gly Ala Asp Gly Ser Gly Ser Ile Ser Thr Ile 100 105 110 Ile Lys Gly Val Glu Trp Ala Val Asp Asn Lys Asp Lys Tyr Gly Ile 115 120 125 Lys Val Ile Asn Leu Ser Leu Gly Ser Ser Gln Ser Ser Asp Gly Thr 130 135 140 Asp Ala Leu Ser Gln Ala Val Asn Ala Ala Trp Asp Ala Gly Leu Val 145 150 155 160 Val Val Val Ala Ala Gly Asn Ser Gly Pro Asn Lys Tyr Thr Ile Gly 165 170

175 Ser Pro Ala Ala Ala Ser Lys Val Ile Thr Val Gly Ala Val Asp Lys 180 185 190 Tyr Asp Val Ile Thr Ser Phe Ser Ser Arg Gly Pro Thr Ala Asp Gly 195 200 205 Arg Leu Lys Pro Glu Val Val Ala Pro Gly Asn Trp Ile Ile Ala Ala 210 215 220 Arg Ala Ser Gly Thr Ser Met Gly Gln Pro Ile Asn Asp Tyr Tyr Thr 225 230 235 240 Ala Ala Pro Gly Thr Ser Met Ala Thr Pro His Val Ala Gly Ile Ala 245 250 255 Ala Leu Leu Leu Gln Ala His Pro Ser Trp Thr Pro Asp Lys Val Lys 260 265 270 Thr Ala Leu Ile Glu Thr Ala Asp Ile Val Lys Pro Asp Glu Ile Ala 275 280 285 Asp Ile Ala Tyr Gly Ala Gly Arg Val Asn Ala Tyr Lys Ala Ile Asn 290 295 300 Tyr Asp Asn Tyr Ala Lys Leu Val Phe Thr Gly Tyr Val Ala Asn Lys 305 310 315 320 Gly Ser Gln Thr His Gln Phe Val Ile Ser Gly Ala Ser Phe Val Thr 325 330 335 Ala Thr Leu Tyr Trp Asp Asn Ala Asn Ser Asp Leu Asp Leu Tyr Leu 340 345 350 Tyr Asp Pro Asn Gly Asn Gln Val Asp Tyr Ser Tyr Thr Ala Tyr Tyr 355 360 365 Gly Phe Glu Lys Val Gly Tyr Tyr Asn Pro Thr Asp Gly Thr Trp Thr 370 375 380 Ile Lys Val Val Ser Tyr Ser Gly Ser Ala Asn Tyr Gln Val Asp Val 385 390 395 400 Val Ser Asp Gly Ser Leu Ser Gln Pro Gly Ser Ser 405 410 6532PRTAspergillus fumigatus 6Met Leu Ala Ser Thr Phe Ser Tyr Arg Met Tyr Lys Thr Ala Leu Ile 1 5 10 15 Leu Ala Ala Leu Leu Gly Ser Gly Gln Ala Gln Gln Val Gly Thr Ser 20 25 30 Gln Ala Glu Val His Pro Ser Met Thr Trp Gln Ser Cys Thr Ala Gly 35 40 45 Gly Ser Cys Thr Thr Asn Asn Gly Lys Val Val Ile Asp Ala Asn Trp 50 55 60 Arg Trp Val His Lys Val Gly Asp Tyr Thr Asn Cys Tyr Thr Gly Asn 65 70 75 80 Thr Trp Asp Thr Thr Ile Cys Pro Asp Asp Ala Thr Cys Ala Ser Asn 85 90 95 Cys Ala Leu Glu Gly Ala Asn Tyr Glu Ser Thr Tyr Gly Val Thr Ala 100 105 110 Ser Gly Asn Ser Leu Arg Leu Asn Phe Val Thr Thr Ser Gln Gln Lys 115 120 125 Asn Ile Gly Ser Arg Leu Tyr Met Met Lys Asp Asp Ser Thr Tyr Glu 130 135 140 Met Phe Lys Leu Leu Asn Gln Glu Phe Thr Phe Asp Val Asp Val Ser 145 150 155 160 Asn Leu Pro Cys Gly Leu Asn Gly Ala Leu Tyr Phe Val Ala Met Asp 165 170 175 Ala Asp Gly Gly Met Ser Lys Tyr Pro Thr Asn Lys Ala Gly Ala Lys 180 185 190 Tyr Gly Thr Gly Tyr Cys Asp Ser Gln Cys Pro Arg Asp Leu Lys Phe 195 200 205 Ile Asn Gly Gln Ala Asn Val Glu Gly Trp Gln Pro Ser Ser Asn Asp 210 215 220 Ala Asn Ala Gly Thr Gly Asn His Gly Ser Cys Cys Ala Glu Met Asp 225 230 235 240 Ile Trp Glu Ala Asn Ser Ile Ser Thr Ala Phe Thr Pro His Pro Cys 245 250 255 Asp Thr Pro Gly Gln Val Met Cys Thr Gly Asp Ala Cys Gly Gly Thr 260 265 270 Tyr Ser Ser Asp Arg Tyr Gly Gly Thr Cys Asp Pro Asp Gly Cys Asp 275 280 285 Phe Asn Ser Phe Arg Gln Gly Asn Lys Thr Phe Tyr Gly Pro Gly Met 290 295 300 Thr Val Asp Thr Lys Ser Lys Phe Thr Val Val Thr Gln Phe Ile Thr 305 310 315 320 Asp Asp Gly Thr Ser Ser Gly Thr Leu Lys Glu Ile Lys Arg Phe Tyr 325 330 335 Val Gln Asn Gly Lys Val Ile Pro Asn Ser Glu Ser Thr Trp Thr Gly 340 345 350 Val Ser Gly Asn Ser Ile Thr Thr Glu Tyr Cys Thr Ala Gln Lys Ser 355 360 365 Leu Phe Gln Asp Gln Asn Val Phe Glu Lys His Gly Gly Leu Glu Gly 370 375 380 Met Gly Ala Ala Leu Ala Gln Gly Met Val Leu Val Met Ser Leu Trp 385 390 395 400 Asp Asp His Ser Ala Asn Met Leu Trp Leu Asp Ser Asn Tyr Pro Thr 405 410 415 Thr Ala Ser Ser Thr Thr Pro Gly Val Ala Arg Gly Thr Cys Asp Ile 420 425 430 Ser Ser Gly Val Pro Ala Asp Val Glu Ala Asn His Pro Asp Ala Tyr 435 440 445 Val Val Tyr Ser Asn Ile Lys Val Gly Pro Ile Gly Ser Thr Phe Asn 450 455 460 Ser Gly Gly Ser Asn Pro Gly Gly Gly Thr Thr Thr Thr Thr Thr Thr 465 470 475 480 Gln Pro Thr Thr Thr Thr Thr Thr Ala Gly Asn Pro Gly Gly Thr Gly 485 490 495 Val Ala Gln His Tyr Gly Gln Cys Gly Gly Ile Gly Trp Thr Gly Pro 500 505 510 Thr Thr Cys Ala Ser Pro Tyr Thr Cys Gln Lys Leu Asn Asp Tyr Tyr 515 520 525 Ser Gln Cys Leu 530 7454PRTAspergillus fumigatus 7Met Lys His Leu Ala Ser Ser Ile Ala Leu Thr Leu Leu Leu Pro Ala 1 5 10 15 Val Gln Ala Gln Gln Thr Val Trp Gly Gln Cys Gly Gly Gln Gly Trp 20 25 30 Ser Gly Pro Thr Ser Cys Val Ala Gly Ala Ala Cys Ser Thr Leu Asn 35 40 45 Pro Tyr Tyr Ala Gln Cys Ile Pro Gly Ala Thr Ala Thr Ser Thr Thr 50 55 60 Leu Thr Thr Thr Thr Ala Ala Thr Thr Thr Ser Gln Thr Thr Thr Lys 65 70 75 80 Pro Thr Thr Thr Gly Pro Thr Thr Ser Ala Pro Thr Val Thr Ala Ser 85 90 95 Gly Asn Pro Phe Ser Gly Tyr Gln Leu Tyr Ala Asn Pro Tyr Tyr Ser 100 105 110 Ser Glu Val His Thr Leu Ala Met Pro Ser Leu Pro Ser Ser Leu Gln 115 120 125 Pro Lys Ala Ser Ala Val Ala Glu Val Pro Ser Phe Val Trp Leu Asp 130 135 140 Val Ala Ala Lys Val Pro Thr Met Gly Thr Tyr Leu Ala Asp Ile Gln 145 150 155 160 Ala Lys Asn Lys Ala Gly Ala Asn Pro Pro Ile Ala Gly Ile Phe Val 165 170 175 Val Tyr Asp Leu Pro Asp Arg Asp Cys Ala Ala Leu Ala Ser Asn Gly 180 185 190 Glu Tyr Ser Ile Ala Asn Asn Gly Val Ala Asn Tyr Lys Ala Tyr Ile 195 200 205 Asp Ala Ile Arg Ala Gln Leu Val Lys Tyr Ser Asp Val His Thr Ile 210 215 220 Leu Val Ile Glu Pro Asp Ser Leu Ala Asn Leu Val Thr Asn Leu Asn 225 230 235 240 Val Ala Lys Cys Ala Asn Ala Gln Ser Ala Tyr Leu Glu Cys Val Asp 245 250 255 Tyr Ala Leu Lys Gln Leu Asn Leu Pro Asn Val Ala Met Tyr Leu Asp 260 265 270 Ala Gly His Ala Gly Trp Leu Gly Trp Pro Ala Asn Leu Gly Pro Ala 275 280 285 Ala Thr Leu Phe Ala Lys Val Tyr Thr Asp Ala Gly Ser Pro Ala Ala 290 295 300 Val Arg Gly Leu Ala Thr Asn Val Ala Asn Tyr Asn Ala Trp Ser Leu 305 310 315 320 Ser Thr Cys Pro Ser Tyr Thr Gln Gly Asp Pro Asn Cys Asp Glu Lys 325 330 335 Lys Tyr Ile Asn Ala Met Ala Pro Leu Leu Lys Glu Ala Gly Phe Asp 340 345 350 Ala His Phe Ile Met Asp Thr Ser Arg Asn Gly Val Gln Pro Thr Lys 355 360 365 Gln Asn Ala Trp Gly Asp Trp Cys Asn Val Ile Gly Thr Gly Phe Gly 370 375 380 Val Arg Pro Ser Thr Asn Thr Gly Asp Pro Leu Gln Asp Ala Phe Val 385 390 395 400 Trp Ile Lys Pro Gly Gly Glu Ser Asp Gly Thr Ser Asn Ser Thr Ser 405 410 415 Pro Arg Tyr Asp Ala His Cys Gly Tyr Ser Asp Ala Leu Gln Pro Ala 420 425 430 Pro Glu Ala Gly Thr Trp Phe Gln Ala Tyr Phe Glu Gln Leu Leu Thr 435 440 445 Asn Ala Asn Pro Ser Phe 450 8863PRTAspergillus fumigatus 8Met Arg Phe Gly Trp Leu Glu Val Ala Ala Leu Thr Ala Ala Ser Val 1 5 10 15 Ala Asn Ala Gln Glu Leu Ala Phe Ser Pro Pro Phe Tyr Pro Ser Pro 20 25 30 Trp Ala Asp Gly Gln Gly Glu Trp Ala Asp Ala His Arg Arg Ala Val 35 40 45 Glu Ile Val Ser Gln Met Thr Leu Ala Glu Lys Val Asn Leu Thr Thr 50 55 60 Gly Thr Gly Trp Glu Met Asp Arg Cys Val Gly Gln Thr Gly Ser Val 65 70 75 80 Pro Arg Leu Gly Ile Asn Trp Gly Leu Cys Gly Gln Asp Ser Pro Leu 85 90 95 Gly Ile Arg Phe Ser Asp Leu Asn Ser Ala Phe Pro Ala Gly Thr Asn 100 105 110 Val Ala Ala Thr Trp Asp Lys Thr Leu Ala Tyr Leu Arg Gly Lys Ala 115 120 125 Met Gly Glu Glu Phe Asn Asp Lys Gly Val Asp Ile Leu Leu Gly Pro 130 135 140 Ala Ala Gly Pro Leu Gly Lys Tyr Pro Asp Gly Gly Arg Ile Trp Glu 145 150 155 160 Gly Phe Ser Pro Asp Pro Val Leu Thr Gly Val Leu Phe Ala Glu Thr 165 170 175 Ile Lys Gly Ile Gln Asp Ala Gly Val Ile Ala Thr Ala Lys His Tyr 180 185 190 Ile Leu Asn Glu Gln Glu His Phe Arg Gln Val Gly Glu Ala Gln Gly 195 200 205 Tyr Gly Tyr Asn Ile Thr Glu Thr Ile Ser Ser Asn Val Asp Asp Lys 210 215 220 Thr Met His Glu Leu Tyr Leu Trp Pro Phe Ala Asp Ala Val Arg Ala 225 230 235 240 Gly Val Gly Ala Val Met Cys Ser Tyr Asn Gln Ile Asn Asn Ser Tyr 245 250 255 Gly Cys Gln Asn Ser Gln Thr Leu Asn Lys Leu Leu Lys Ala Glu Leu 260 265 270 Gly Phe Gln Gly Phe Val Met Ser Asp Trp Ser Ala His His Ser Gly 275 280 285 Val Gly Ala Ala Leu Ala Gly Leu Asp Met Ser Met Pro Gly Asp Ile 290 295 300 Ser Phe Asp Asp Gly Leu Ser Phe Trp Gly Thr Asn Leu Thr Val Ser 305 310 315 320 Val Leu Asn Gly Thr Val Pro Ala Trp Arg Val Asp Asp Met Ala Val 325 330 335 Arg Ile Met Thr Ala Tyr Tyr Lys Val Gly Arg Asp Arg Leu Arg Ile 340 345 350 Pro Pro Asn Phe Ser Ser Trp Thr Arg Asp Glu Tyr Gly Trp Glu His 355 360 365 Ser Ala Val Ser Glu Gly Ala Trp Thr Lys Val Asn Asp Phe Val Asn 370 375 380 Val Gln Arg Ser His Ser Gln Ile Ile Arg Glu Ile Gly Ala Ala Ser 385 390 395 400 Thr Val Leu Leu Lys Asn Thr Gly Ala Leu Pro Leu Thr Gly Lys Glu 405 410 415 Val Lys Val Gly Val Leu Gly Glu Asp Ala Gly Ser Asn Pro Trp Gly 420 425 430 Ala Asn Gly Cys Pro Asp Arg Gly Cys Asp Asn Gly Thr Leu Ala Met 435 440 445 Ala Trp Gly Ser Gly Thr Ala Asn Phe Pro Tyr Leu Val Thr Pro Glu 450 455 460 Gln Ala Ile Gln Arg Glu Val Ile Ser Asn Gly Gly Asn Val Phe Ala 465 470 475 480 Val Thr Asp Asn Gly Ala Leu Ser Gln Met Ala Asp Val Ala Ser Gln 485 490 495 Ser Ser Val Ser Leu Val Phe Val Asn Ala Asp Ser Gly Glu Gly Phe 500 505 510 Ile Ser Val Asp Gly Asn Glu Gly Asp Arg Lys Asn Leu Thr Leu Trp 515 520 525 Lys Asn Gly Glu Ala Val Ile Asp Thr Val Val Ser His Cys Asn Asn 530 535 540 Thr Ile Val Val Ile His Ser Val Gly Pro Val Leu Ile Asp Arg Trp 545 550 555 560 Tyr Asp Asn Pro Asn Val Thr Ala Ile Ile Trp Ala Gly Leu Pro Gly 565 570 575 Gln Glu Ser Gly Asn Ser Leu Val Asp Val Leu Tyr Gly Arg Val Asn 580 585 590 Pro Ser Ala Lys Thr Pro Phe Thr Trp Gly Lys Thr Arg Glu Ser Tyr 595 600 605 Gly Ala Pro Leu Leu Thr Glu Pro Asn Asn Gly Asn Gly Ala Pro Gln 610 615 620 Asp Asp Phe Asn Glu Gly Val Phe Ile Asp Tyr Arg His Phe Asp Lys 625 630 635 640 Arg Asn Glu Thr Pro Ile Tyr Glu Phe Gly His Gly Leu Ser Tyr Thr 645 650 655 Thr Phe Gly Tyr Ser His Leu Arg Val Gln Ala Leu Asn Ser Ser Ser 660 665 670 Ser Ala Tyr Val Pro Thr Ser Gly Glu Thr Lys Pro Ala Pro Thr Tyr 675 680 685 Gly Glu Ile Gly Ser Ala Ala Asp Tyr Leu Tyr Pro Glu Gly Leu Lys 690 695 700 Arg Ile Thr Lys Phe Ile Tyr Pro Trp Leu Asn Ser Thr Asp Leu Glu 705 710 715 720 Asp Ser Ser Asp Asp Pro Asn Tyr Gly Trp Glu Asp Ser Glu Tyr Ile 725 730 735 Pro Glu Gly Ala Arg Asp Gly Ser Pro Gln Pro Leu Leu Lys Ala Gly 740 745 750 Gly Ala Pro Gly Gly Asn Pro Thr Leu Tyr Gln Asp Leu Val Arg Val 755 760 765 Ser Ala Thr Ile Thr Asn Thr Gly Asn Val Ala Gly Tyr Glu Val Pro 770 775 780 Gln Leu Tyr Val Ser Leu Gly Gly Pro Asn Glu Pro Arg Val Val Leu 785 790 795 800 Arg Lys Phe Asp Arg Ile Phe Leu Ala Pro Gly Glu Gln Lys Val Trp 805 810 815 Thr Thr Thr Leu Asn Arg Arg Asp Leu Ala Asn Trp Asp Val Glu Ala 820 825 830 Gln Asp Trp Val Ile Thr Lys Tyr Pro Lys Lys Val His Val Gly Ser 835 840 845 Ser Ser Arg Lys Leu Pro Leu Arg Ala Pro Leu Pro Arg Val Tyr 850 855 860 9250PRTThermoascus aurantiacusSIGNAL(1)..(22) 9Met Ser Phe Ser Lys Ile Ile Ala Thr Ala Gly Val Leu Ala Ser Ala 1 5 10 15 Ser Leu Val Ala Gly His Gly Phe Val Gln Asn Ile Val Ile Asp Gly 20 25 30 Lys Lys Tyr Tyr Gly Gly Tyr Leu Val Asn Gln Tyr Pro Tyr Met Ser 35 40 45 Asn Pro Pro Glu Val Ile Ala Trp Ser Thr Thr Ala Thr Asp Leu Gly 50 55 60 Phe Val Asp Gly Thr Gly Tyr Gln Thr Pro Asp Ile Ile Cys His Arg 65 70 75 80 Gly Ala Lys Pro Gly Ala Leu Thr Ala Pro Val Ser Pro Gly Gly Thr 85 90 95 Val Glu Leu Gln Trp Thr Pro Trp Pro Asp Ser His His Gly Pro Val 100 105 110 Ile Asn Tyr Leu Ala Pro Cys Asn Gly Asp Cys Ser Thr Val Asp Lys 115 120 125 Thr Gln Leu Glu Phe Phe Lys Ile Ala Glu Ser Gly Leu Ile Asn Asp 130 135 140 Asp Asn Pro Pro Gly Ile Trp Ala Ser Asp Asn Leu Ile Ala Ala Asn 145 150 155 160 Asn Ser Trp Thr Val Thr Ile Pro Thr Thr Ile Ala Pro Gly Asn Tyr 165 170 175 Val Leu Arg His Glu Ile Ile Ala Leu His Ser Ala Gln Asn Gln Asp 180 185 190 Gly Ala Gln Asn Tyr Pro Gln Cys Ile Asn Leu Gln Val Thr Gly Gly 195

200 205 Gly Ser Asp Asn Pro Ala Gly Thr Leu Gly Thr Ala Leu Tyr His Asp 210 215 220 Thr Asp Pro Gly Ile Leu Ile Asn Ile Tyr Gln Lys Leu Ser Ser Tyr 225 230 235 240 Ile Ile Pro Gly Pro Pro Leu Tyr Thr Gly 245 250 10253PRTPenicillium emersoniiSIGNAL(1)..(25) 10Met Leu Ser Ser Thr Thr Arg Thr Leu Ala Phe Thr Gly Leu Ala Gly 1 5 10 15 Leu Leu Ser Ala Pro Leu Val Lys Ala His Gly Phe Val Gln Gly Ile 20 25 30 Val Ile Gly Asp Gln Phe Tyr Ser Gly Tyr Ile Val Asn Ser Phe Pro 35 40 45 Tyr Glu Ser Asn Pro Pro Pro Val Ile Gly Trp Ala Thr Thr Ala Thr 50 55 60 Asp Leu Gly Phe Val Asp Gly Thr Gly Tyr Gln Gly Pro Asp Ile Ile 65 70 75 80 Cys His Arg Asn Ala Thr Pro Ala Pro Leu Thr Ala Pro Val Ala Ala 85 90 95 Gly Gly Thr Val Glu Leu Gln Trp Thr Pro Trp Pro Asp Ser His His 100 105 110 Gly Pro Val Ile Thr Tyr Leu Ala Pro Cys Asn Gly Asn Cys Ser Thr 115 120 125 Val Asp Lys Thr Thr Leu Glu Phe Phe Lys Ile Asp Gln Gln Gly Leu 130 135 140 Ile Asp Asp Thr Ser Pro Pro Gly Thr Trp Ala Ser Asp Asn Leu Ile 145 150 155 160 Ala Asn Asn Asn Ser Trp Thr Val Thr Ile Pro Asn Ser Val Ala Pro 165 170 175 Gly Asn Tyr Val Leu Arg His Glu Ile Ile Ala Leu His Ser Ala Asn 180 185 190 Asn Lys Asp Gly Ala Gln Asn Tyr Pro Gln Cys Ile Asn Ile Glu Val 195 200 205 Thr Gly Gly Gly Ser Asp Ala Pro Glu Gly Thr Leu Gly Glu Asp Leu 210 215 220 Tyr His Asp Thr Asp Pro Gly Ile Leu Val Asp Ile Tyr Glu Pro Ile 225 230 235 240 Ala Thr Tyr Thr Ile Pro Gly Pro Pro Glu Pro Thr Phe 245 250 11618PRTTalaromyces emersonii 11Met Ala Ser Leu Val Ala Gly Ala Leu Cys Ile Leu Gly Leu Thr Pro 1 5 10 15 Ala Ala Phe Ala Arg Ala Pro Val Ala Ala Arg Ala Thr Gly Ser Leu 20 25 30 Asp Ser Phe Leu Ala Thr Glu Thr Pro Ile Ala Leu Gln Gly Val Leu 35 40 45 Asn Asn Ile Gly Pro Asn Gly Ala Asp Val Ala Gly Ala Ser Ala Gly 50 55 60 Ile Val Val Ala Ser Pro Ser Arg Ser Asp Pro Asn Tyr Phe Tyr Ser 65 70 75 80 Trp Thr Arg Asp Ala Ala Leu Thr Ala Lys Tyr Leu Val Asp Ala Phe 85 90 95 Ile Ala Gly Asn Lys Asp Leu Glu Gln Thr Ile Gln Gln Tyr Ile Ser 100 105 110 Ala Gln Ala Lys Val Gln Thr Ile Ser Asn Pro Ser Gly Asp Leu Ser 115 120 125 Thr Gly Gly Leu Gly Glu Pro Lys Phe Asn Val Asn Glu Thr Ala Phe 130 135 140 Thr Gly Pro Trp Gly Arg Pro Gln Arg Asp Gly Pro Ala Leu Arg Ala 145 150 155 160 Thr Ala Leu Ile Ala Tyr Ala Asn Tyr Leu Ile Asp Asn Gly Glu Ala 165 170 175 Ser Thr Ala Asp Glu Ile Ile Trp Pro Ile Val Gln Asn Asp Leu Ser 180 185 190 Tyr Ile Thr Gln Tyr Trp Asn Ser Ser Thr Phe Asp Leu Trp Glu Glu 195 200 205 Val Glu Gly Ser Ser Phe Phe Thr Thr Ala Val Gln His Arg Ala Leu 210 215 220 Val Glu Gly Asn Ala Leu Ala Thr Arg Leu Asn His Thr Cys Ser Asn 225 230 235 240 Cys Val Ser Gln Ala Pro Gln Val Leu Cys Phe Leu Gln Ser Tyr Trp 245 250 255 Thr Gly Ser Tyr Val Leu Ala Asn Phe Gly Gly Ser Gly Arg Ser Gly 260 265 270 Lys Asp Val Asn Ser Ile Leu Gly Ser Ile His Thr Phe Asp Pro Ala 275 280 285 Gly Gly Cys Asp Asp Ser Thr Phe Gln Pro Cys Ser Ala Arg Ala Leu 290 295 300 Ala Asn His Lys Val Val Thr Asp Ser Phe Arg Ser Ile Tyr Ala Ile 305 310 315 320 Asn Ser Gly Ile Ala Glu Gly Ser Ala Val Ala Val Gly Arg Tyr Pro 325 330 335 Glu Asp Val Tyr Gln Gly Gly Asn Pro Trp Tyr Leu Ala Thr Ala Ala 340 345 350 Ala Ala Glu Gln Leu Tyr Asp Ala Ile Tyr Gln Trp Lys Lys Ile Gly 355 360 365 Ser Ile Ser Ile Thr Asp Val Ser Leu Pro Phe Phe Gln Asp Ile Tyr 370 375 380 Pro Ser Ala Ala Val Gly Thr Tyr Asn Ser Gly Ser Thr Thr Phe Asn 385 390 395 400 Asp Ile Ile Ser Ala Val Gln Thr Tyr Gly Asp Gly Tyr Leu Ser Ile 405 410 415 Val Glu Lys Tyr Thr Pro Ser Asp Gly Ser Leu Thr Glu Gln Phe Ser 420 425 430 Arg Thr Asp Gly Thr Pro Leu Ser Ala Ser Ala Leu Thr Trp Ser Tyr 435 440 445 Ala Ser Leu Leu Thr Ala Ser Ala Arg Arg Gln Ser Val Val Pro Ala 450 455 460 Ser Trp Gly Glu Ser Ser Ala Ser Ser Val Pro Ala Val Cys Ser Ala 465 470 475 480 Thr Ser Ala Thr Gly Pro Tyr Ser Thr Ala Thr Asn Thr Val Trp Pro 485 490 495 Ser Ser Gly Ser Gly Ser Ser Thr Thr Thr Ser Ser Ala Pro Cys Thr 500 505 510 Thr Pro Thr Ser Val Ala Val Thr Phe Asp Glu Ile Val Ser Thr Ser 515 520 525 Tyr Gly Glu Thr Ile Tyr Leu Ala Gly Ser Ile Pro Glu Leu Gly Asn 530 535 540 Trp Ser Thr Ala Ser Ala Ile Pro Leu Arg Ala Asp Ala Tyr Thr Asn 545 550 555 560 Ser Asn Pro Leu Trp Tyr Val Thr Val Asn Leu Pro Pro Gly Thr Ser 565 570 575 Phe Glu Tyr Lys Phe Phe Lys Asn Gln Thr Asp Gly Thr Ile Val Trp 580 585 590 Glu Asp Asp Pro Asn Arg Ser Tyr Thr Val Pro Ala Tyr Cys Gly Gln 595 600 605 Thr Thr Ala Ile Leu Asp Asp Ser Trp Gln 610 615 12574PRTTrametes cingulata 12Met Arg Phe Thr Leu Leu Thr Ser Leu Leu Gly Leu Ala Leu Gly Ala 1 5 10 15 Phe Ala Gln Ser Ser Ala Ala Asp Ala Tyr Val Ala Ser Glu Ser Pro 20 25 30 Ile Ala Lys Ala Gly Val Leu Ala Asn Ile Gly Pro Ser Gly Ser Lys 35 40 45 Ser Asn Gly Ala Lys Ala Gly Ile Val Ile Ala Ser Pro Ser Thr Ser 50 55 60 Asn Pro Asn Tyr Leu Tyr Thr Trp Thr Arg Asp Ser Ser Leu Val Phe 65 70 75 80 Lys Ala Leu Ile Asp Gln Phe Thr Thr Gly Glu Asp Thr Ser Leu Arg 85 90 95 Thr Leu Ile Asp Glu Phe Thr Ser Ala Glu Ala Ile Leu Gln Gln Val 100 105 110 Pro Asn Pro Ser Gly Thr Val Ser Thr Gly Gly Leu Gly Glu Pro Lys 115 120 125 Phe Asn Ile Asp Glu Thr Ala Phe Thr Asp Ala Trp Gly Arg Pro Gln 130 135 140 Arg Asp Gly Pro Ala Leu Arg Ala Thr Ala Ile Ile Thr Tyr Ala Asn 145 150 155 160 Trp Leu Leu Asp Asn Lys Asn Thr Thr Tyr Val Thr Asn Thr Leu Trp 165 170 175 Pro Ile Ile Lys Leu Asp Leu Asp Tyr Val Ala Ser Asn Trp Asn Gln 180 185 190 Ser Thr Phe Asp Leu Trp Glu Glu Ile Asn Ser Ser Ser Phe Phe Thr 195 200 205 Thr Ala Val Gln His Arg Ala Leu Arg Glu Gly Ala Thr Phe Ala Asn 210 215 220 Arg Ile Gly Gln Thr Ser Val Val Ser Gly Tyr Thr Thr Gln Ala Asn 225 230 235 240 Asn Leu Leu Cys Phe Leu Gln Ser Tyr Trp Asn Pro Thr Gly Gly Tyr 245 250 255 Ile Thr Ala Asn Thr Gly Gly Gly Arg Ser Gly Lys Asp Ala Asn Thr 260 265 270 Val Leu Thr Ser Ile His Thr Phe Asp Pro Ala Ala Gly Cys Asp Ala 275 280 285 Val Thr Phe Gln Pro Cys Ser Asp Lys Ala Leu Ser Asn Leu Lys Val 290 295 300 Tyr Val Asp Ala Phe Arg Ser Ile Tyr Ser Ile Asn Ser Gly Ile Ala 305 310 315 320 Ser Asn Ala Ala Val Ala Thr Gly Arg Tyr Pro Glu Asp Ser Tyr Met 325 330 335 Gly Gly Asn Pro Trp Tyr Leu Thr Thr Ser Ala Val Ala Glu Gln Leu 340 345 350 Tyr Asp Ala Leu Ile Val Trp Asn Lys Leu Gly Ala Leu Asn Val Thr 355 360 365 Ser Thr Ser Leu Pro Phe Phe Gln Gln Phe Ser Ser Gly Val Thr Val 370 375 380 Gly Thr Tyr Ala Ser Ser Ser Ser Thr Phe Lys Thr Leu Thr Ser Ala 385 390 395 400 Ile Lys Thr Phe Ala Asp Gly Phe Leu Ala Val Asn Ala Lys Tyr Thr 405 410 415 Pro Ser Asn Gly Gly Leu Ala Glu Gln Tyr Ser Arg Ser Asn Gly Ser 420 425 430 Pro Val Ser Ala Val Asp Leu Thr Trp Ser Tyr Ala Ala Ala Leu Thr 435 440 445 Ser Phe Ala Ala Arg Ser Gly Lys Thr Tyr Ala Ser Trp Gly Ala Ala 450 455 460 Gly Leu Thr Val Pro Thr Thr Cys Ser Gly Ser Gly Gly Ala Gly Thr 465 470 475 480 Val Ala Val Thr Phe Asn Val Gln Ala Thr Thr Val Phe Gly Glu Asn 485 490 495 Ile Tyr Ile Thr Gly Ser Val Pro Ala Leu Gln Asn Trp Ser Pro Asp 500 505 510 Asn Ala Leu Ile Leu Ser Ala Ala Asn Tyr Pro Thr Trp Ser Ile Thr 515 520 525 Val Asn Leu Pro Ala Ser Thr Thr Ile Glu Tyr Lys Tyr Ile Arg Lys 530 535 540 Phe Asn Gly Ala Val Thr Trp Glu Ser Asp Pro Asn Asn Ser Ile Thr 545 550 555 560 Thr Pro Ala Ser Gly Thr Phe Thr Gln Asn Asp Thr Trp Arg 565 570 13583PRTRhizomucor pusillus 13Ala Thr Ser Asp Asp Trp Lys Gly Lys Ala Ile Tyr Gln Leu Leu Thr 1 5 10 15 Asp Arg Phe Gly Arg Ala Asp Asp Ser Thr Ser Asn Cys Ser Asn Leu 20 25 30 Ser Asn Tyr Cys Gly Gly Thr Tyr Glu Gly Ile Thr Lys His Leu Asp 35 40 45 Tyr Ile Ser Gly Met Gly Phe Asp Ala Ile Trp Ile Ser Pro Ile Pro 50 55 60 Lys Asn Ser Asp Gly Gly Tyr His Gly Tyr Trp Ala Thr Asp Phe Tyr 65 70 75 80 Gln Leu Asn Ser Asn Phe Gly Asp Glu Ser Gln Leu Lys Ala Leu Ile 85 90 95 Gln Ala Ala His Glu Arg Asp Met Tyr Val Met Leu Asp Val Val Ala 100 105 110 Asn His Ala Gly Pro Thr Ser Asn Gly Tyr Ser Gly Tyr Thr Phe Gly 115 120 125 Asp Ala Ser Leu Tyr His Pro Lys Cys Thr Ile Asp Tyr Asn Asp Gln 130 135 140 Thr Ser Ile Glu Gln Cys Trp Val Ala Asp Glu Leu Pro Asp Ile Asp 145 150 155 160 Thr Glu Asn Ser Asp Asn Val Ala Ile Leu Asn Asp Ile Val Ser Gly 165 170 175 Trp Val Gly Asn Tyr Ser Phe Asp Gly Ile Arg Ile Asp Thr Val Lys 180 185 190 His Ile Arg Lys Asp Phe Trp Thr Gly Tyr Ala Glu Ala Ala Gly Val 195 200 205 Phe Ala Thr Gly Glu Val Phe Asn Gly Asp Pro Ala Tyr Val Gly Pro 210 215 220 Tyr Gln Lys Tyr Leu Pro Ser Leu Ile Asn Tyr Pro Met Tyr Tyr Ala 225 230 235 240 Leu Asn Asp Val Phe Val Ser Lys Ser Lys Gly Phe Ser Arg Ile Ser 245 250 255 Glu Met Leu Gly Ser Asn Arg Asn Ala Phe Glu Asp Thr Ser Val Leu 260 265 270 Thr Thr Phe Val Asp Asn His Asp Asn Pro Arg Phe Leu Asn Ser Gln 275 280 285 Ser Asp Lys Ala Leu Phe Lys Asn Ala Leu Thr Tyr Val Leu Leu Gly 290 295 300 Glu Gly Ile Pro Ile Val Tyr Tyr Gly Ser Glu Gln Gly Phe Ser Gly 305 310 315 320 Gly Ala Asp Pro Ala Asn Arg Glu Val Leu Trp Thr Thr Asn Tyr Asp 325 330 335 Thr Ser Ser Asp Leu Tyr Gln Phe Ile Lys Thr Val Asn Ser Val Arg 340 345 350 Met Lys Ser Asn Lys Ala Val Tyr Met Asp Ile Tyr Val Gly Asp Asn 355 360 365 Ala Tyr Ala Phe Lys His Gly Asp Ala Leu Val Val Leu Asn Asn Tyr 370 375 380 Gly Ser Gly Ser Thr Asn Gln Val Ser Phe Ser Val Ser Gly Lys Phe 385 390 395 400 Asp Ser Gly Ala Ser Leu Met Asp Ile Val Ser Asn Ile Thr Thr Thr 405 410 415 Val Ser Ser Asp Gly Thr Val Thr Phe Asn Leu Lys Asp Gly Leu Pro 420 425 430 Ala Ile Phe Thr Ser Ala Thr Gly Gly Thr Thr Thr Thr Ala Thr Pro 435 440 445 Thr Gly Ser Gly Ser Val Thr Ser Thr Ser Lys Thr Thr Ala Thr Ala 450 455 460 Ser Lys Thr Ser Thr Ser Thr Ser Ser Thr Ser Cys Thr Thr Pro Thr 465 470 475 480 Ala Val Ala Val Thr Phe Asp Leu Thr Ala Thr Thr Thr Tyr Gly Glu 485 490 495 Asn Ile Tyr Leu Val Gly Ser Ile Ser Gln Leu Gly Asp Trp Glu Thr 500 505 510 Ser Asp Gly Ile Ala Leu Ser Ala Asp Lys Tyr Thr Ser Ser Asp Pro 515 520 525 Leu Trp Tyr Val Thr Val Thr Leu Pro Ala Gly Glu Ser Phe Glu Tyr 530 535 540 Lys Phe Ile Arg Ile Glu Ser Asp Asp Ser Val Glu Trp Glu Ser Asp 545 550 555 560 Pro Asn Arg Glu Tyr Thr Val Pro Gln Ala Cys Gly Thr Ser Thr Ala 565 570 575 Thr Val Thr Asp Thr Trp Arg 580 14661PRTTrichoderma reesei 14Leu Tyr Ile Asn Gly Ser Val Ile Ala Pro Cys Asp Ser Pro Ile Tyr 1 5 10 15 Cys His Gly Asp Ile Leu Arg Glu Ile Glu Leu Ala His Pro Phe Ser 20 25 30 Asp Ser Lys Thr Phe Val Asp Met Pro Ala Lys Arg Pro Leu Ser Glu 35 40 45 Ile Gln Thr Ala Phe Ala Asn Leu Pro Lys Pro Leu Arg Asn Asp Ser 50 55 60 Ser Leu Gln Thr Phe Leu Ala Ser Tyr Phe Ala Asp Ala Gly Gly Glu 65 70 75 80 Leu Ile Gln Val Pro Arg Ala Asn Leu Thr Thr Asn Pro Thr Phe Leu 85 90 95 Ser Lys Ile Asn Asp Thr Val Ile Glu Gln Phe Val Thr Gln Val Ile 100 105 110 Asp Ile Trp Pro Asp Leu Thr Arg Arg Tyr Ala Gly Asp Ala Ala Val 115 120 125 Lys Asn Cys Ser Ser Cys Pro Asn Ser Phe Ile Pro Val Asn Arg Thr 130 135 140 Phe Val Val Ala Gly Gly Arg Phe Arg Glu Pro Tyr Tyr Trp Asp Ser 145 150 155 160 Tyr Trp Ile Val Glu Gly Leu Leu Arg Thr Gly Gly Ala Phe Val Gly 165 170 175 Ile Ala Arg Asn Thr Ile Asp Asn Phe Leu Asp Phe Ile Glu Arg Phe 180 185 190 Gly Phe Val Pro Asn Gly Ala Arg Leu Tyr Tyr Leu Asn Arg Ser Gln 195 200 205

Pro Pro Leu Leu Ser Arg Met Val Lys Val Tyr Ile Asp His Thr Asn 210 215 220 Asp Thr Ala Ile Leu Arg Arg Ala Leu Pro Leu Leu Val Lys Glu His 225 230 235 240 Glu Phe Trp Thr Arg Asn Arg Thr Val Asp Val Arg Val Asn Asn Lys 245 250 255 Thr Tyr Val Leu Asn Gln Tyr Ala Val Gln Asn Thr Gln Pro Arg Pro 260 265 270 Glu Ser Phe Arg Glu Asp Phe Gln Thr Ala Asn Asn Arg Ser Tyr Tyr 275 280 285 Ala Ala Ser Gly Ile Ile Tyr Pro Ala Thr Lys Pro Leu Asn Glu Ser 290 295 300 Gln Ile Glu Glu Leu Tyr Ala Asn Leu Ala Ser Gly Ala Glu Ser Gly 305 310 315 320 Asn Asp Tyr Thr Ala Arg Trp Leu Ala Asp Pro Ser Asp Ala Met Arg 325 330 335 Asp Val Tyr Phe Pro Leu Arg Ser Leu Asn Asn Lys Asp Ile Val Pro 340 345 350 Val Asp Leu Asn Ser Ile Leu Tyr Gly Asn Glu Leu Ala Ile Ala Gln 355 360 365 Phe Tyr Asn Gln Thr Gly Asn Thr Thr Ala Ala Arg Glu Trp Ser Ser 370 375 380 Leu Ala Ala Asn Arg Ser Ala Ser Ile Gln Ala Val Phe Trp Asn Glu 385 390 395 400 Thr Leu Phe Ser Tyr Phe Asp Tyr Asn Leu Thr Ser Ser Ser Gln Asn 405 410 415 Ile Tyr Val Pro Leu Asp Lys Asp Ala Val Ala Leu Asp Arg Gln Thr 420 425 430 Ala Pro Pro Gly Lys Gln Val Leu Phe His Val Gly Gln Phe Tyr Pro 435 440 445 Phe Trp Thr Gly Ala Ala Pro Glu Tyr Leu Arg Asn Asn Pro Phe Ala 450 455 460 Val Thr Arg Ile Phe Asp Arg Val Lys Ser Tyr Leu Asp Thr Arg Pro 465 470 475 480 Gly Gly Ile Pro Ala Ser Asn Val Asn Thr Gly Gln Gln Trp Asp Gln 485 490 495 Pro Asn Val Trp Pro Pro His Met His Ile Leu Met Glu Ser Leu Asn 500 505 510 Ser Val Pro Ala Thr Phe Ser Glu Ala Asp Pro Ala Tyr Gln Asp Val 515 520 525 Arg Asn Leu Ser Leu Arg Leu Gly Gln Arg Tyr Leu Asp Phe Thr Phe 530 535 540 Cys Thr Trp Arg Ala Thr Gly Gly Ser Thr Ser Glu Thr Pro Lys Leu 545 550 555 560 Gln Gly Leu Thr Asp Gln Asp Val Gly Ile Met Phe Glu Lys Tyr Asn 565 570 575 Asp Asn Ser Thr Asn Ala Ala Gly Gly Gly Gly Glu Tyr Gln Val Val 580 585 590 Glu Gly Phe Gly Trp Thr Asn Gly Val Leu Leu Trp Thr Ala Asp Thr 595 600 605 Phe Gly Ser Gln Leu Lys Arg Pro Gln Cys Gly Asn Ile Met Ala Gly 610 615 620 His Pro Ala Pro Ser Lys Arg Ser Ala Val Gln Leu Asp Met Trp Asp 625 630 635 640 Ala Ser Arg Val Lys Lys Phe Gly Arg Arg Ala Glu Gly Arg Met Gly 645 650 655 Thr Leu His Ala Trp 660 15862PRTBacillus sp.SIGNAL(1)..(33) 15Met Ser Leu Ile Arg Ser Arg Tyr Asn His Phe Val Ile Leu Phe Thr 1 5 10 15 Val Ala Ile Met Phe Leu Thr Val Cys Phe Pro Ala Tyr Lys Ala Leu 20 25 30 Ala Asp Ser Thr Ser Thr Glu Val Ile Val His Tyr His Arg Phe Asp 35 40 45 Ser Asn Tyr Ala Asn Trp Asp Leu Trp Met Trp Pro Tyr Gln Pro Val 50 55 60 Asn Gly Asn Gly Ala Ala Tyr Glu Phe Ser Gly Lys Asp Asp Phe Gly 65 70 75 80 Val Lys Ala Asp Val Gln Val Pro Gly Asp Asp Thr Gln Val Gly Leu 85 90 95 Ile Val Arg Thr Asn Asp Trp Ser Gln Lys Asn Thr Ser Asp Asp Leu 100 105 110 His Ile Asp Leu Thr Lys Gly His Glu Ile Trp Ile Val Gln Gly Asp 115 120 125 Pro Asn Ile Tyr Tyr Asn Leu Ser Asp Ala Gln Ala Ala Ala Thr Pro 130 135 140 Lys Val Ser Asn Ala Tyr Leu Asp Asn Glu Lys Thr Val Leu Ala Lys 145 150 155 160 Leu Thr Asn Pro Met Thr Leu Ser Asp Gly Ser Ser Gly Phe Thr Val 165 170 175 Thr Asp Lys Thr Thr Gly Glu Gln Ile Pro Val Thr Ala Ala Thr Asn 180 185 190 Ala Asn Ser Ala Ser Ser Ser Glu Gln Thr Asp Leu Val Gln Leu Thr 195 200 205 Leu Ala Ser Ala Pro Asp Val Ser His Thr Ile Gln Val Gly Ala Ala 210 215 220 Gly Tyr Glu Ala Val Asn Leu Ile Pro Arg Asn Val Leu Asn Leu Pro 225 230 235 240 Arg Tyr Tyr Tyr Ser Gly Asn Asp Leu Gly Asn Val Tyr Ser Asn Lys 245 250 255 Ala Thr Ala Phe Arg Val Trp Ala Pro Thr Ala Ser Asp Val Gln Leu 260 265 270 Leu Leu Tyr Asn Ser Glu Thr Gly Pro Val Thr Lys Gln Leu Glu Met 275 280 285 Gln Lys Ser Asp Asn Gly Thr Trp Lys Leu Lys Val Pro Gly Asn Leu 290 295 300 Lys Asn Trp Tyr Tyr Leu Tyr Gln Val Thr Val Asn Gly Lys Thr Gln 305 310 315 320 Thr Ala Val Asp Pro Tyr Val Arg Ala Ile Ser Val Asn Ala Thr Arg 325 330 335 Gly Met Ile Val Asp Leu Glu Asp Thr Asn Pro Pro Gly Trp Lys Glu 340 345 350 Asp His Gln Gln Thr Pro Ala Asn Pro Val Asp Glu Val Ile Tyr Glu 355 360 365 Val His Val Arg Asp Phe Ser Ile Asp Ala Asn Ser Gly Met Lys Asn 370 375 380 Lys Gly Lys Tyr Leu Ala Phe Thr Glu His Gly Thr Lys Gly Pro Asp 385 390 395 400 Asn Val Lys Thr Gly Ile Asp Ser Leu Lys Glu Leu Gly Ile Asn Ala 405 410 415 Val Gln Leu Gln Pro Ile Glu Glu Phe Asn Ser Ile Asp Glu Thr Gln 420 425 430 Pro Asn Met Tyr Asn Trp Gly Tyr Asp Pro Arg Asn Tyr Asn Val Pro 435 440 445 Glu Gly Ala Tyr Ala Thr Thr Pro Glu Gly Thr Ala Arg Ile Thr Gln 450 455 460 Leu Lys Gln Leu Ile Gln Ser Ile His Lys Asp Arg Ile Ala Ile Asn 465 470 475 480 Met Asp Val Val Tyr Asn His Thr Phe Asn Val Gly Val Ser Asp Phe 485 490 495 Asp Lys Ile Val Pro Gln Tyr Tyr Tyr Arg Thr Asp Ser Ala Gly Asn 500 505 510 Tyr Thr Asn Gly Ser Gly Val Gly Asn Glu Ile Ala Thr Glu Arg Pro 515 520 525 Met Val Gln Lys Phe Val Leu Asp Ser Val Lys Tyr Trp Val Lys Glu 530 535 540 Tyr His Ile Asp Gly Phe Arg Phe Asp Leu Met Ala Leu Leu Gly Lys 545 550 555 560 Asp Thr Met Ala Lys Ile Ser Lys Glu Leu His Ala Ile Asn Pro Gly 565 570 575 Ile Val Leu Tyr Gly Glu Pro Trp Thr Gly Gly Thr Ser Gly Leu Ser 580 585 590 Ser Asp Gln Leu Val Thr Lys Gly Gln Gln Lys Gly Leu Gly Ile Gly 595 600 605 Val Phe Asn Asp Asn Ile Arg Asn Gly Leu Asp Gly Asn Val Phe Asp 610 615 620 Lys Ser Ala Gln Gly Phe Ala Thr Gly Asp Pro Asn Gln Val Asn Val 625 630 635 640 Ile Lys Asn Gly Val Met Gly Ser Ile Ser Asp Phe Thr Ser Ala Pro 645 650 655 Ser Glu Thr Ile Asn Tyr Val Thr Ser His Asp Asn Met Thr Leu Trp 660 665 670 Asp Lys Ile Ser Ala Ser Asn Pro Asn Asp Thr Gln Ala Asp Arg Ile 675 680 685 Lys Met Asp Glu Leu Ala Gln Ala Val Val Phe Thr Ser Gln Gly Val 690 695 700 Pro Phe Met Gln Gly Gly Glu Glu Met Leu Arg Thr Lys Gly Gly Asn 705 710 715 720 Asp Asn Ser Tyr Asn Ala Gly Asp Ser Val Asn Gln Phe Asp Trp Ser 725 730 735 Arg Lys Ala Gln Phe Glu Asn Val Phe Asp Tyr Tyr Ser Trp Leu Ile 740 745 750 His Leu Arg Asp Asn His Pro Ala Phe Arg Met Thr Thr Ala Asp Gln 755 760 765 Ile Lys Gln Asn Leu Thr Phe Leu Asp Ser Pro Thr Asn Thr Val Ala 770 775 780 Phe Glu Leu Lys Asn His Ala Asn His Asp Lys Trp Lys Asn Ile Ile 785 790 795 800 Val Met Tyr Asn Pro Asn Lys Thr Ala Gln Thr Leu Thr Leu Pro Ser 805 810 815 Gly Asn Trp Thr Ile Val Gly Leu Gly Asn Gln Val Gly Glu Lys Ser 820 825 830 Leu Gly His Val Asn Gly Thr Val Glu Val Pro Ala Leu Ser Thr Ile 835 840 845 Ile Leu His Gln Gly Thr Ser Glu Asp Val Ile Asp Gln Asn 850 855 860 16616PRTPenicillium oxalicum 16Met Arg Leu Thr Leu Leu Ser Gly Val Ala Gly Val Leu Cys Ala Gly 1 5 10 15 Gln Leu Thr Ala Ala Arg Pro Asp Pro Lys Gly Gly Asn Leu Thr Pro 20 25 30 Phe Ile His Lys Glu Gly Glu Arg Ser Leu Gln Gly Ile Leu Asp Asn 35 40 45 Leu Gly Gly Arg Gly Lys Lys Thr Pro Gly Thr Ala Ala Gly Leu Phe 50 55 60 Ile Ala Ser Pro Asn Thr Glu Asn Pro Asn Tyr Tyr Tyr Thr Trp Thr 65 70 75 80 Arg Asp Ser Ala Leu Thr Ala Lys Cys Leu Ile Asp Leu Phe Glu Asp 85 90 95 Ser Arg Ala Lys Phe Pro Ile Asp Arg Lys Tyr Leu Glu Thr Gly Ile 100 105 110 Arg Asp Tyr Val Ser Ser Gln Ala Ile Leu Gln Ser Val Ser Asn Pro 115 120 125 Ser Gly Thr Leu Lys Asp Gly Ser Gly Leu Gly Glu Pro Lys Phe Glu 130 135 140 Ile Asp Leu Asn Pro Phe Ser Gly Ala Trp Gly Arg Pro Gln Arg Asp 145 150 155 160 Gly Pro Ala Leu Arg Ala Thr Ala Met Ile Thr Tyr Ala Asn Tyr Leu 165 170 175 Ile Ser His Gly Gln Lys Ser Asp Val Ser Gln Val Met Trp Pro Ile 180 185 190 Ile Ala Asn Asp Leu Ala Tyr Val Gly Gln Tyr Trp Asn Asn Thr Gly 195 200 205 Phe Asp Leu Trp Glu Glu Val Asp Gly Ser Ser Phe Phe Thr Ile Ala 210 215 220 Val Gln His Arg Ala Leu Val Glu Gly Ser Gln Leu Ala Lys Lys Leu 225 230 235 240 Gly Lys Ser Cys Asp Ala Cys Asp Ser Gln Pro Pro Gln Ile Leu Cys 245 250 255 Phe Leu Gln Ser Phe Trp Asn Gly Lys Tyr Ile Thr Ser Asn Ile Asn 260 265 270 Thr Gln Ala Ser Arg Ser Gly Ile Asp Leu Asp Ser Val Leu Gly Ser 275 280 285 Ile His Thr Phe Asp Pro Glu Ala Ala Cys Asp Asp Ala Thr Phe Gln 290 295 300 Pro Cys Ser Ala Arg Ala Leu Ala Asn His Lys Val Tyr Val Asp Ser 305 310 315 320 Phe Arg Ser Ile Tyr Lys Ile Asn Ala Gly Leu Ala Glu Gly Ser Ala 325 330 335 Ala Asn Val Gly Arg Tyr Pro Glu Asp Val Tyr Gln Gly Gly Asn Pro 340 345 350 Trp Tyr Leu Ala Thr Leu Gly Ala Ser Glu Leu Leu Tyr Asp Ala Leu 355 360 365 Tyr Gln Trp Asp Arg Leu Gly Lys Leu Glu Val Ser Glu Thr Ser Leu 370 375 380 Ser Phe Phe Lys Asp Phe Asp Ala Thr Val Lys Ile Gly Ser Tyr Ser 385 390 395 400 Arg Asn Ser Lys Thr Tyr Lys Lys Leu Thr Gln Ser Ile Lys Ser Tyr 405 410 415 Ala Asp Gly Phe Ile Gln Leu Val Gln Gln Tyr Thr Pro Ser Asn Gly 420 425 430 Ser Leu Ala Glu Gln Tyr Asp Arg Asn Thr Ala Ala Pro Leu Ser Ala 435 440 445 Asn Asp Leu Thr Trp Ser Phe Ala Ser Phe Leu Thr Ala Thr Gln Arg 450 455 460 Arg Asp Ala Val Val Pro Pro Ser Trp Gly Ala Lys Ser Ala Asn Lys 465 470 475 480 Val Pro Thr Thr Cys Ser Ala Ser Pro Val Val Gly Thr Tyr Lys Ala 485 490 495 Pro Thr Ala Thr Phe Ser Ser Lys Thr Lys Cys Val Pro Ala Lys Asp 500 505 510 Ile Val Pro Ile Thr Phe Tyr Leu Ile Glu Asn Thr Tyr Tyr Gly Glu 515 520 525 Asn Val Phe Met Ser Gly Asn Ile Thr Ala Leu Gly Asn Trp Asp Ala 530 535 540 Lys Lys Gly Phe Pro Leu Thr Ala Asn Leu Tyr Thr Gln Asp Gln Asn 545 550 555 560 Leu Trp Phe Ala Ser Val Glu Phe Ile Pro Ala Gly Thr Pro Phe Glu 565 570 575 Tyr Lys Tyr Tyr Lys Val Glu Pro Asn Gly Asp Ile Thr Trp Glu Lys 580 585 590 Gly Pro Asn Arg Val Phe Val Ala Pro Thr Gly Cys Pro Val Gln Pro 595 600 605 His Ser Asn Asp Val Trp Gln Phe 610 615 17573PRTPycnoporus sanguineusSIGNAL(1)..(18) 17Met Arg Phe Thr Leu Leu Ala Ser Leu Ile Gly Leu Ala Val Gly Ala 1 5 10 15 Phe Ala Gln Ser Ser Ala Val Asp Ala Tyr Val Ala Ser Glu Ser Pro 20 25 30 Ile Ala Lys Gln Gly Val Leu Asn Asn Ile Gly Pro Asn Gly Ser Lys 35 40 45 Ala His Gly Ala Lys Ala Gly Ile Val Val Ala Ser Pro Ser Thr Glu 50 55 60 Asn Pro Asp Tyr Leu Tyr Thr Trp Thr Arg Asp Ser Ser Leu Val Phe 65 70 75 80 Lys Leu Leu Ile Asp Gln Phe Thr Ser Gly Asp Asp Thr Ser Leu Arg 85 90 95 Gly Leu Ile Asp Asp Phe Thr Ser Ala Glu Ala Ile Leu Gln Gln Val 100 105 110 Ser Asn Pro Ser Gly Thr Val Ser Thr Gly Gly Leu Gly Glu Pro Lys 115 120 125 Phe Asn Ile Asp Glu Thr Ala Phe Thr Gly Ala Trp Gly Arg Pro Gln 130 135 140 Arg Asp Gly Pro Ala Leu Arg Ala Thr Ser Ile Ile Arg Tyr Ala Asn 145 150 155 160 Trp Leu Leu Asp Asn Gly Asn Thr Thr Tyr Val Ser Asn Thr Leu Trp 165 170 175 Pro Val Ile Gln Leu Asp Leu Asp Tyr Val Ala Asp Asn Trp Asn Gln 180 185 190 Ser Thr Phe Asp Leu Trp Glu Glu Val Asp Ser Ser Ser Phe Phe Thr 195 200 205 Thr Ala Val Gln His Arg Ala Leu Arg Glu Gly Ala Thr Phe Ala Ser 210 215 220 Arg Ile Gly Gln Ser Ser Val Val Ser Gly Tyr Thr Thr Gln Ala Asp 225 230 235 240 Asn Leu Leu Cys Phe Leu Gln Ser Tyr Trp Asn Pro Ser Gly Gly Tyr 245 250 255 Val Thr Ala Asn Thr Gly Gly Gly Arg Ser Gly Lys Asp Ser Asn Thr 260 265 270 Val Leu Thr Ser Ile His Thr Phe Asp Pro Ala Ala Gly Cys Asp Ala 275 280 285 Ala Thr Phe Gln Pro Cys Ser Asp Lys Ala Leu Ser Asn Leu Lys Val 290 295 300 Tyr Val Asp Ala Phe Arg Ser Ile Tyr Thr Ile Asn Asn Gly Ile Ala 305 310 315 320 Ser Asn Ala Ala Val Ala Thr Gly Arg Tyr Pro Glu Asp Ser Tyr Met 325 330 335 Gly Gly Asn Pro Trp Tyr Leu Thr Thr Ser Ala Val Ala Glu Gln Leu 340 345 350 Tyr Asp Ala Leu Tyr Val Trp Asp Gln Leu Gly Gly Leu Asn Val Thr 355

360 365 Ser Thr Ser Leu Ala Phe Phe Gln Gln Phe Ala Ser Gly Leu Ser Thr 370 375 380 Gly Thr Tyr Ser Ala Ser Ser Ser Thr Tyr Ala Thr Leu Thr Ser Ala 385 390 395 400 Ile Arg Ser Phe Ala Asp Gly Phe Leu Ala Ile Asn Ala Lys Tyr Thr 405 410 415 Pro Ala Asp Gly Gly Leu Ala Glu Gln Tyr Ser Arg Asn Asp Gly Thr 420 425 430 Pro Leu Ser Ala Val Asp Leu Thr Trp Ser Tyr Ala Ala Ala Leu Thr 435 440 445 Ala Phe Ala Ala Arg Glu Gly Lys Thr Tyr Gly Ser Trp Gly Ala Ala 450 455 460 Gly Leu Thr Val Pro Ala Ser Cys Ser Gly Gly Gly Gly Ala Thr Val 465 470 475 480 Ala Val Thr Phe Asn Val Gln Ala Thr Thr Val Phe Gly Glu Asn Ile 485 490 495 Tyr Ile Thr Gly Ser Val Ala Ala Leu Gln Asn Trp Ser Pro Asp Asn 500 505 510 Ala Leu Ile Leu Ser Ala Ala Asn Tyr Pro Thr Trp Ser Ile Thr Val 515 520 525 Asn Leu Pro Ala Asn Thr Val Val Gln Tyr Lys Tyr Ile Arg Lys Phe 530 535 540 Asn Gly Gln Val Thr Trp Glu Ser Asp Pro Asn Asn Gln Ile Thr Thr 545 550 555 560 Pro Ser Gly Gly Ser Phe Thr Gln Asn Asp Val Trp Arg 565 570 18559PRTGloephyllum trabeumSIGNAL(1)..(17)mat_peptide(18)..(576) 18Gln Ser Val Asp Ser Tyr Val Gly Ser Glu Gly Pro Ile Ala Lys Ala -15 -10 -5 Gly Val Leu Ala Asn Ile Gly Pro Asn Gly Ser Lys Ala Ser Gly Ala -1 1 5 10 15 Ala Ala Gly Val Val Val Ala Ser Pro Ser Lys Ser Asp Pro Asp Tyr 20 25 30 Trp Tyr Thr Trp Thr Arg Asp Ser Ser Leu Val Phe Lys Ser Leu Ile 35 40 45 Asp Gln Tyr Thr Thr Gly Ile Asp Ser Thr Ser Ser Leu Arg Ser Leu 50 55 60 Ile Asp Ser Phe Val Ile Ala Glu Ala Asn Ile Gln Gln Val Ser Asn 65 70 75 Pro Ser Gly Thr Leu Thr Thr Gly Gly Leu Gly Glu Pro Lys Phe Asn 80 85 90 95 Val Asp Glu Thr Ala Phe Thr Gly Ala Trp Gly Arg Pro Gln Arg Asp 100 105 110 Gly Pro Ala Leu Arg Ala Thr Ala Leu Ile Thr Tyr Gly Asn Trp Leu 115 120 125 Leu Ser Asn Gly Asn Thr Thr Trp Val Thr Ser Thr Leu Trp Pro Ile 130 135 140 Ile Gln Asn Asp Leu Asn Tyr Val Val Gln Tyr Trp Asn Gln Thr Thr 145 150 155 Phe Asp Leu Trp Glu Glu Val Asn Ser Ser Ser Phe Phe Thr Thr Ala 160 165 170 175 Val Gln His Arg Ala Leu Arg Glu Gly Ala Ala Phe Ala Thr Lys Ile 180 185 190 Gly Gln Thr Ser Ser Val Ser Ser Tyr Thr Thr Gln Ala Ala Asn Leu 195 200 205 Leu Cys Phe Leu Gln Ser Tyr Trp Asn Pro Thr Ser Gly Tyr Ile Thr 210 215 220 Ala Asn Thr Gly Gly Gly Arg Ser Gly Lys Asp Ala Asn Thr Leu Leu 225 230 235 Ala Ser Ile His Thr Tyr Asp Pro Ser Ala Gly Cys Asp Ala Thr Thr 240 245 250 255 Phe Gln Pro Cys Ser Asp Lys Ala Leu Ser Asn Leu Lys Val Tyr Val 260 265 270 Asp Ser Phe Arg Ser Val Tyr Ser Ile Asn Ser Gly Ile Ala Ser Asn 275 280 285 Ala Ala Val Ala Thr Gly Arg Tyr Pro Glu Asp Ser Tyr Gln Gly Gly 290 295 300 Asn Pro Trp Tyr Leu Thr Thr Phe Ala Val Ala Glu Gln Leu Tyr Asp 305 310 315 Ala Leu Asn Val Trp Ala Ala Gln Gly Ser Leu Asn Val Thr Ser Ile 320 325 330 335 Ser Leu Pro Phe Phe Gln Gln Phe Ser Ser Ser Val Thr Ala Gly Thr 340 345 350 Tyr Ala Ser Ser Ser Thr Thr Tyr Thr Thr Leu Thr Ser Ala Ile Lys 355 360 365 Ser Phe Ala Asp Gly Phe Val Ala Ile Asn Ala Gln Tyr Thr Pro Ser 370 375 380 Asn Gly Gly Leu Ala Glu Gln Phe Ser Arg Ser Asn Gly Ala Pro Val 385 390 395 Ser Ala Val Asp Leu Thr Trp Ser Tyr Ala Ser Ala Leu Thr Ala Phe 400 405 410 415 Glu Ala Arg Asn Asn Thr Gln Phe Ala Gly Trp Gly Ala Val Gly Leu 420 425 430 Thr Val Pro Thr Ser Cys Ser Ser Asn Ser Gly Gly Gly Gly Gly Ser 435 440 445 Thr Val Ala Val Thr Phe Asn Val Asn Ala Gln Thr Val Trp Gly Glu 450 455 460 Asn Ile Tyr Ile Thr Gly Ser Val Asp Ala Leu Ser Asn Trp Ser Pro 465 470 475 Asp Asn Ala Leu Leu Leu Ser Ser Ala Asn Tyr Pro Thr Trp Ser Ile 480 485 490 495 Thr Val Asn Leu Pro Ala Ser Thr Ala Ile Gln Tyr Lys Tyr Ile Arg 500 505 510 Lys Asn Asn Gly Ala Val Thr Trp Glu Ser Asp Pro Asn Asn Ser Ile 515 520 525 Thr Thr Pro Ala Ser Gly Ser Val Thr Glu Asn Asp Thr Trp Arg 530 535 540

Claims

1: A process of producing ethanol from starch-containing material comprising: (a) saccharifying starch-containing material at a temperature below the initial gelatinization temperature; and (b) fermenting using a fermentation organism; wherein saccharification and/or fermentation is done in the presence of the following enzymes: glucoamylase and alpha-amylase, and optionally protease; and the fermenting organism is Saccharomyces cerevisiae MBG4851 (deposited under Accession No. V14/004037 at National Measurement Institute, Victoria, Australia) or a fermenting organism having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces cerevisiae MBG4851 having the defining characteristics of strain V14/004037.

2: The process of claim 1, wherein the fermenting organism having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces cerevisiae MBG4851 having defining characteristics of strain V14/004037, has one or more, such as all, of the following properties and defining characteristics: increases ethanol yield compared to Ethanol Red.TM. under the same process conditions; produces reduced levels of lactic acid compared to Ethanol Red.TM. under the same process conditions; produces reduced levels of glycerol compared to Ethanol Red.TM. under the same process conditions; has faster fermentation kinetics compared to Ethanol Red.TM. under the same process conditions.

3: The process of claim 1, wherein saccharification and fermentation are done simultaneously (SSF).

4: The process of claim 1, wherein the ethanol is recovered after fermentation.

5: The process of claim 1, wherein wherein saccharification and/or fermentation is done in the presence of a protease.

6: The process of claim 1, wherein a cellulolytic enzyme composition is present and/or added during saccharification, fermentation or simultaneous saccharification and fermentation (SSF).

7: The process of claim 1, wherein saccharification and/or fermentation is done in the presence of a glucoamylase derived from Trametes cingulata.

8: (canceled)

9: The process of claim 1, wherein saccharification and/or fermentation is done in the presence of a glucoamylase derived from Gloeophyllum trabeum shown in SEQ ID NO: 18.

10: (canceled)

11: The process of claim 1, wherein saccharification and/or fermentation is done in the presence of a glucoamylase derived from Pycnoporus sanguineus shown in SEQ ID NO: 17.

12: A Saccharomyces yeast strain deposited under the Budapest Treaty and having NMI accession no. V14/004037 or a derivative of strain V14/004037 which exhibits one or more defining characteristics of strain V14/004037.

13: (canceled)

14: A method of producing ethanol, comprising incubating the Saccharomyces yeast strain of claim 12 with a substrate comprising a fermentable sugar under conditions which permit fermentation of the fermentable sugar to produce ethanol.

15: (canceled)

16: A method of producing distiller's grain, comprising: (a) incubating a Saccharomyces yeast strain of claim 12 with a substrate comprising fermentable sugar under conditions which allow fermentation of the fermentable sugar to produce ethanol and distiller's grains; (b) isolating the distiller's grains.

17: Distiller's grain produced by the method of claim 16.

18-19: (canceled)

20: A composition comprising the Saccharomyces yeast strain of claim 12 and one or more naturally occurring and/or non-naturally occurring components.

21: The Saccharomyces yeast strain of claim 12, wherein the strain having properties that are about the same as that of Saccharomyces cerevisiae MBG4851, or a derivative of Saccharomyces cerevisiae MBG4851 having defining characteristics of strain V14/004037, has one or more, such as all, of the following properties and defining characteristics: increases ethanol yield compared to Ethanol Red.TM. under the same process conditions; produces reduced levels of lactic acid compared to Ethanol Red.TM. under the same process conditions; produces reduced levels of glycerol compared to Ethanol Red.TM. under the same process conditions; reduces the level of acetaldehyde in fermentation compared to Ethanol Red.TM. under the same process condition; increases the oil recovery level compared to Ethanol Red.TM. under the same process conditions; has faster fermentation kinetics compared to Ethanol Red.TM. under the same process conditions.

22: The process of claim 9, wherein saccharification and/or fermentation is done in the presence of a glucoamylase derived from Gloeophyllum trabeum shown in SEQ ID NO: 18 having at least one of the following substitutions: V59A; S95P; A121P; T119W; S95P+A121P; V59A+S95P; S95P+T119W; V59A+S95P+A121P; or S95P+T119W+A121P (using SEQ ID NO: 18 for numbering).

23: The process of claim 1, wherein saccharification and/or fermentation is done in the presence of an alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and Aspergillus niger glucoamylase starch-binding domain (SBD).

24: The process of claim 23, wherein the alpha-amylase derived from Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and Aspergillus niger glucoamylase starch-binding domain (SBD) has at least one of the following substitutions or combinations of substitutions: D165M; Y141W; Y141R; K136F; K192R; P224A; P224R; S123H+Y141W; G20S+Y141W; A76G+Y141W; G128D+Y141W; G128D+D143N; P219C+Y141W; N142D+D143N; Y141W+K192R; Y141W+D143N; Y141W+N383R; Y141W+P219C+A265C; Y141W+N142D+D143N; Y141W+K192R V410A; G128D+Y141W+D143N; Y141W+D143N+P219C; Y141W+D143N+K192R; G128D+D143N+K192R; Y141W+D143N+K192R+P219C; G128D+Y141W+D143N+K192R; or G128D+Y141W+D143N+K192R+P219C, especially G128D+D143N (using SEQ ID NO: 13 for numbering).

25: The process of claim 5, wherein saccharification and/or fermentation is done in the presence of a protease derived from Thermoascus aurantiacus or Pyrococcus furiosus.

26: The process of claim 6, wherein the cellulolytic enzyme composition is derived from a strain of Trichoderma reesei.

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