PRODUCTION OF ISOPRENOIDS UNDER NEUTRAL pH CONDITIONS

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of US Provisional Application No. 61/515,830, filed August 5, 2011, the disclosures of which are incorporated herein by reference in their entirety.

FIELD OF THE INVENTION

[0002] Glucoamylases capable of effectively hydrolyzing a starch substrate at a pH in the range of 5.0 to 8.0 are useful in simultaneous saccharification and fermentation (SSF) to produce a product, such as isoprenoid precursors and isoprenoids.

BACKGROUND

[0003] Industrial fermentations predominately use glucose as a feedstock for the production of a multitude of proteins, enzymes, alcohols, and other chemical end products. Typically, glucose is the product of starch processing, which is conventionally a two-step, enzymatic process that catalyzes the breakdown of starch, involving liquefaction and saccharification. During liquefaction, insoluble granular starch is slurried in water, gelatinized with heat, and hydrolyzed by a thermostable alpha-amylase. During saccharification, the soluble dextrins produced in liquefaction are further hydrolyzed by glucoamylases.

[0004] Glucoamylases are exo-acting carbohydrases, capable of hydrolyzing both the linear and branched glucosidic linkages of starch (e.g. , amylose and amylopectin). Commercially, glucoamylases are typically used in the acidic pH ranges (pH less than 5.0) to produce fermentable sugars from the enzyme liquefied starch substrate. The fermentable sugars, e.g. , low molecular weight sugars, such as glucose, may then be converted to fructose by other enzymes (e.g. , glucose isomerases); crystallized; or used in fermentations to produce numerous end products (e.g. , alcohols, monosodium glutamate, succinic acid, vitamins, amino acids, 1,3-propanediol, and lactic acid).

[0005] A system that combines (1) saccharification and (2) fermentation is known as simultaneous saccharification and fermentation (SSF). SSF replaces the classical double- step fermentation, i.e., production of fermentable sugars first and then conducting the

fermentation process for producing the end product. In SSF, an inoculum can be added along with the starch hydrolyzing enzymes to concurrently saccharify a starch substrate and convert the saccharification products (i.e., fermentable sugars) to the desired end product. The inoculum is typically a microorganism capable of producing the end product. In addition to its various advantages, SSF is particularly promising where a high concentration substrate is present in a low reactor volume.

[0006] Isoprenoids are compounds derived from the isoprenoid precursor molecules

IPP and DMAPP. Over 29,000 isoprenoid compounds have been identified and new isoprenoids are being discovered each year. Isoprenoids can be isolated from natural products, such as microorganisms and species of plants that use isoprenoid precursor molecules as a basic building block to form the relatively complex structures of isoprenoids. Isoprenoids are vital to most living organisms and cells, providing a means to maintain cellular membrane fluidity and electron transport. In nature, isoprenoids function in roles as diverse as natural pesticides in plants to contributing to the scents associated with cinnamon, cloves, and ginger. Moreover, the pharmaceutical and chemical communities use isoprenoids as pharmaceuticals, nutraceuticals, flavoring agents, and agricultural pest control agents. Given their importance in biological systems and usefulness in a broad range of applications, isoprenoids have been the focus of much attention by scientists.

[0007] What is needed is a simple, efficient method of producing isoprenoids in commercial quantities.

[0008] Throughout this specification, references are made to publications (e.g., scientific articles), patent applications, patents, etc., all of which are herein incorporated by reference in their entirety.

BRIEF SUMMARY OF THE INVENTION

[0009] The invention provides, inter alia, for methods, compositions and systems for production of isoprenoid precursors and/or isoprenoids by a simultaneous saccharification and fermentation (SSF) process. The method takes advantage of the unique properties of certain glucoamylases. Glucoamylases such as Humicola grisea glucoamylase (HgGA), Trichoderma reesei glucoamylase (TrGA), and Rhizopus sp. glucoamylase (RhGA) display different pH profiles from other known glucoamylases, such as glucoamylases (GAs) from Aspergillus niger (AnGA) and Talaromyces emersonii (TeGA). At a pH of 6.0 or above, both HgGA and TrGA retain at least 50% of the activity relative to the maximum activity at pH 4.25 or pH 3.75, respectively. These glucoamylases are capable of saccharifying a starch substrate effectively at a pH in the range of 5.0 to 8.0, where cells (e.g., bacterial cells) can efficiently ferment the saccharified starch to isoprenoids. This property enables HgGA and TrGA to be used in SSF to produce isoprenoids compositions from a starch substrate in commercial quantities.

[0010] Accordingly, in one aspect of the invention, the invention provides for method for producing an isoprenoid precursor or isoprenoid comprising culturing a host cell, which comprises a heterologous nucleic acid encoding an polyprenyl pyrophosphate synthase polypeptide, and saccharifying and fermenting a starch substrate under simultaneous saccharification and fermentation (SSF) conditions in the presence of a glucoamylase, wherein the saccharification and fermentation are performed at pH 5.0 to 8.0, wherein the glucoamylase possesses at least 50% activity at pH 6.0 or above relative to its maximum activity, wherein the glucoamylase is selected from the group consisting of a parent Humicola grisea glucoamylase (HgGA) comprising SEQ ID NO: 3, a parent Trichoderma reesei glucoamylase (TrGA) comprising SEQ ID NO: 6, a parent Rhizopus sp. glucoamylase (RhGA) comprising SEQ ID NO: 9, and a variant thereof, and wherein the variant has at least 99% sequence identity to the parent glucoamylase.

[0011] In any of the aspects herein, the isoprenoid is selected from group consisting of monoterpenes, diterpenes, triterpenes, tetraterpenes, sequiterpene, and polyterpene. In one aspect, the isoprenoid is a sesquiterpene. In another aspect, the isoprenoid is selected from the group consisting of abietadiene, amorphadiene, carene,farnesene, a-farnesene, β- farnesene, farnesol, geraniol, geranylgeraniol, linalool, limonene, myrcene, nerolidol, ocimene, patchoulol, β-pinene, sabinene, γ-terpinene, terpindene and valencene.

[0012] In one embodiment, the variant has one amino acid modification compared to the parent glucoamylase. In another embodiment, the HgGA is SEQ ID NO: 3. In another embodiment, the HgGA is produced from a Trichoderma reesei host cell. In another embodiment, the TrGA is SEQ ID No: 6. In another embodiment, the RhGA is SEQ ID NO: 9. In another embodiment, the SSF is carried out at pH 6.0 to 7.5. In another embodiment, the SSF process is carried out at pH 7.0 to 7.5. In another embodiment, the SSF is performed at a temperature in a range of about 30°C to about 60°C. In another embodiment, the SSF is performed at a temperature in a range of about 40°C to about 60°C. In another embodiment, the starch substrate is about 15% to 50% dry solid (DS). In another embodiment, the starch substrate is about 15% to 30% dry solid (DS). In another embodiment, the starch substrate is about 15% to 25% dry solid (DS). In another embodiment, the starch substrate is granular starch or liquefied starch. In another embodiment, the glucoamylase is dosed at a range of about 0.1 to about 2.0 GAU per gram of dry substance starch. In another embodiment, the glucoamylase is dosed at a range of about 0.2 to about 1.0 GAU per gram of dry substance starch. In another embodiment, the glucoamylase is dosed at a range of about 0.5 to 1.0 GAU per gram of dry substance starch. In another embodiment, alpha-amylase is further added to any of the embodiments herein. In another embodiment, the alpha-amylase is from a Bacillus species, or a variant thereof. In another embodiment, the alpha-amylase is a Bacillus subtilis alpha-amylase (AmyE), a Bacillus amyloliquefaciens alpha-amylase, a Bacillus licheniformis alpha-amylase, a Bacillus stearothermophilus alpha-amylase, or a variant thereof. In another embodiment, the starch substrate is from corn, wheat, rye, barley, sorghum, cassava, tapioca, and any combination thereof.

[0013] In another embodiment, the heterologous nucleic acid is operably linked to a promoter and wherein the production of isoprenoids by the cells is greater than about 5 g/L. . In another embodiment, the host cells further comprise (i) one or more non-modified nucleic acids encoding feedback-resistant mevalonate kinase polypeptides or (ii) one or more additional copies of an endogenous nucleic acid encoding a feedback-resistant mevalonate kinase polypeptide. In another embodiment, the feedback-resistant mevalonate kinase is archaeal mevalonate kinase. In another embodiment, the mevalonate kinase polypeptide is selected from the group consisting of M. mazei, Lactobacillus mevalonate kinase polypeptide, Lactobacillus sakei mevalonate kinase polypeptide, yeast mevalonate kinase polypeptide, Streptococcus mevalonate kinase polypeptide, Streptococcus pneumoniae mevalonate kinase polypeptide, Streptomyces mevalonate kinase polypeptide, Streptomyces CL190 mevalonate kinase polypeptide, and M. Burtonii mevalonate kinase polypeptide. In another embodiment, the host cells further comprise one or more heterologous nucleic acid encoding a mevalonate (MVA) pathway polypeptide and/or a DXP pathway polypeptide. In another embodiment, the host cell is selected from the group of bacterial cells, fungal cells, algal cells, plant cells, or cyanobacterial cells. In another embodiment, the bacterial cells are selected from the group consisting of gram-positive bacterial cells, gram-negative bacterial cells, E. coli, P. citrea, B. subtilis, B. licheniformis, B. lentus, B. brevis, B. stearothermophilus, B.

alkalophilus, B. amyloliquefaciens, B. clausii, B. halodurans, B. megaterium, B. coagulans, B. circulans, B. lautus, B. thuringiensis, S. albus, S. lividans, S. coelicolor, S. griseus, Pseudomonas sp., P. alcaligenes, and C. glutanicum cells. In another embodiment, the fungal cells are selected from the group consisting of Aspergillus, yeast, Trichoderma, or Yarrowia cells. In another embodiment, the yeast is Saccharomyces sp.,

Schizosaccharomyces sp. , Pichia sp., Candida sp.or Y. lipolytica cells. In another embodiment, the fungal cells are selected from the group consisting of A. oryzae, A. niger, S. cerevisiae, S. pombe, T. reesei, H. insolens, H. lanuginose, H. grisea, C. lucknowense, A. oryzae, A. niger, A sojae, A. japonicus, A. nidulans, A. aculeatus, A. awamori, F. roseum, F. graminum F. cerealis, F. oxysporuim, F. venenatum, N. crassa, M. miehei, T. viride, F. oxysporum, and F. solan cells. In another embodiment, the plant cells are selected from the group consisting of: the family Fabaceae, the Faboideae subfamily, kudzu, poplar, Popul s alba x tremula, Populus alba, aspen, Populus tremuloides, and Quercus robur cells. In another embodiment, the algal cells are selected from the group consisting of: green algae, red algae, glaucophytes, chlorarachniophytes, euglenids, chromista, and dinoflagellates.

[0014] In another embodiment, the invention provides for methods of processing starch comprising saccharifying a starch substrate to fermentable sugars at pH 5.0 to 8.0 in the presence of glucoamylase and at least one other enzyme, wherein the glucoamylase possesses at least 50% activity at pH 6.0 or above relative to its maximum activity, wherein the glucoamylase is selected from the group consisting of Humicola grisea glucoamylase (HgGA) comprising SEQ ID NO: 3, Trichoderma reesei glucoamylase (TrGA) comprising SEQ ID NO: 6, Rhizopus sp. glucoamylase (RhGA) comprising SEQ ID NO: 9, and a variant thereof, and wherein the variant has at least 99% sequence identity to a parent glucoamylase, and wherein the other enzyme is selected from the group consisting of proteases, pullulanases, isoamylases, cellulases, hemicellulases, xylanases, cyclodextrin

glycotransferases, lipases, phytases, laccases, oxidases, esterases, cutinases, xylanases, and alpha- gluco sidases .

[0015] In another embodiment, the invention provides for methods of processing starch comprising saccharifying a starch substrate to fermentable sugars at pH 5.0 to 8.0 in the presence of glucoamylase and at least one other non-starch polysaccharide hydrolyzing enzymes, wherein the glucoamylase possesses at least 50% activity at pH 6.0 or above relative to its maximum activity, wherein the glucoamylase is selected from the group consisting of Humicola grisea glucoamylase (HgGA) comprising SEQ ID NO: 3,

Trichoderma reesei glucoamylase (TrGA) comprising SEQ ID NO: 6, Rhizopus sp.

glucoamylase (RhGA) comprising SEQ ID NO: 9, and a variant thereof, and wherein the variant has at least 99% sequence identity to a parent glucoamylase, and wherein the non- starch polysaccharide hydrolyzing enzymes is selected from the group consisting of cellulases, hemicellulases and pectinases.

[0016] In another aspect, the invention provide for systems for producing an isoprenoid comprising (i) a bioreactor within which saccharification and fermentation are performed at pH 5.0 to 8.0; (ii) a host cell comprising a heterologous nucleic acid encoding an polyprenyl pyrophosphate synthase polypeptide; (iii) a glucoamylase that possesses at least 50% activity at pH 6.0 or above relative to its maximum activity, wherein the glucoamylase is selected from the group consisting of a parent Humicola grisea glucoamylase (HgGA) comprising SEQ ID NO: 3, a parent Trichoderma reesei glucoamylase (TrGA) comprising SEQ ID NO: 6, a parent Rhizopus p. glucoamylase (RhGA) comprising SEQ ID NO: 9, and a variant thereof, and wherein the variant has at least 99% sequence identity to the parent

glucoamylase.

[0017] In another aspect, the invention provides for methods for producing an isoprenoid comprising culturing a host cell, which comprises a heterologous nucleic acid encoding an polyprenyl pyrophosphate synthase polypeptide, and saccharifying and fermenting a starch substrate under simultaneous saccharification and fermentation (SSF) conditions in the presence of a glucoamylase and at least one other enzyme, wherein the glucoamylase possesses at least 50% activity at pH 6.0 or above relative to its maximum activity, wherein the glucoamylase is selected from the group consisting of Humicola grisea glucoamylase (HgGA) comprising SEQ ID NO: 3, Trichoderma reesei glucoamylase (TrGA) comprising SEQ ID NO: 6, Rhizopus sp. glucoamylase (RhGA) comprising SEQ ID NO: 9, and a variant thereof, and wherein the variant has at least 99% sequence identity to a parent glucoamylase, and wherein the other enzyme is selected from the group consisting of proteases, pullulanases, isoamylases, cellulases, hemicellulases, xylanases, cyclodextrin

glycotransferases, lipases, phytases, laccases, oxidases, esterases, cutinases, xylanases, and alpha- gluco sidases .

[0018] In another aspect, the invention provides for methods for producing an isoprenoid comprising culturing a host cell, which comprises a heterologous nucleic acid encoding an polyprenyl pyrophosphate synthase polypeptide, and saccharifying and fermenting a starch substrate under simultaneous saccharification and fermentation (SSF) conditions in the presence of a glucoamylase and at least one other non-starch polysaccharide hydrolyzing enzymes, wherein the glucoamylase possesses at least 50% activity at pH 6.0 or above relative to its maximum activity, wherein the glucoamylase is selected from the group consisting of Humicola grisea glucoamylase (HgGA) comprising SEQ ID NO: 3,

Trichoderma reesei glucoamylase (TrGA) comprising SEQ ID NO: 6, Rhizop s sp.

glucoamylase (RhGA) comprising SEQ ID NO: 9, and a variant thereof, and wherein the variant has at least 99% sequence identity to a parent glucoamylase, and wherein the non- starch polysaccharide hydrolyzing enzymes is selected from the group consisting of cellulases, hemicellulases and pectinases.

[0019] In another aspect, the invention provides for compositions of isoprenoids produced by the methods and/or systems described herein.

BRIEF DESCRIPTION OF THE DRAWINGS

[0020] The accompanying drawings are incorporated into the specification and provide non-limiting illustrations of various embodiments. In the drawings:

[0021] FIG. 1 depicts the pH profiles of HgGA, TrGA, AnGA, and TeGA, at 32°C. The pH profiles are presented as the percentage of the maximum activity under the

saccharification conditions described in Example 1.

[0022] FIG. 2 depicts the presence of higher sugars after 48-hour saccharification reactions catalyzed by HgGA, TrGA, and AnGA. The saccharification reactions are described in Example 4.

[0023] FIG. 3 depicts scanning electron micrographs of corn, wheat, and cassava starch treated with HgGA and an alpha-amylase at pH 6.4. Starch samples are hydrolyzed by HgGA and an alpha-amylase under the conditions as described in Example 7.

[0024] FIG. 4 depicts the time course of accumulated glucose levels during isoprene production. The simultaneous saccharification and fermentation process was carried with TrGA and an alpha-amylase as described in Example 8.2.

[0025] FIG. 5 depicts the time course of isoprene titer. Isoprene production was achieved by the simultaneous saccharification and fermentation process with TrGA and an alpha- amylase as described in Example 8.2. The titer is defined as the amount of isoprene produced per liter of fermentation broth. The equation for calculating isoprene titer:

isoprene titer = {(Instantaneous isoprene production rate, g/L/hr)dt from t = 0 to 20 hrs [=] g/L broth (total isoprene produced over the time course per liter broth, g/L broth) [0026] FIG. 6 depicts the time course of the carbon dioxide evolution rate (CER) or metabolic activity profile. Isoprene production was achieved by the simultaneous sacchanfication and fermentation process with TrGA and an alpha-amylase as described in Example 8.2.

[0027] FIG. 7 depicts the time course of the isoprene to carbon dioxide ratio in the gas stream exiting the bioreactor. The isoprene to carbon dioxide ratio is an indicator of product yield. Isoprene production was achieved by the simultaneous saccharification and fermentation process with TrGA and an alpha-amylase as described in Example 8.2.

[0028] FIG. 8 depicts the time course of accumulated glucose levels during isoprene production. The simultaneous saccharification and fermentation process was carried with HgGA as described in Example 8.3.

[0029] FIG. 9 depicts the time course of isoprene titer. Isoprene production was achieved by the simultaneous saccharification and fermentation process with HgGA as described in Example 8.3. The titer is defined as the amount of isoprene produced per liter of fermentation broth. The equation for calculating isoprene titer:

isoprene titer = {(Instantaneous isoprene production rate, g/L/hr)dt from t = 0 to 20 hrs [=] g/L broth.

[0030] FIG. 10 depicts the time course of the carbon dioxide evolution rate (CER) or metabolic activity profile. Isoprene production was achieved by the simultaneous saccharification and fermentation process with HgGA as described in Example 8.3.

[0031] FIG. 11 depicts the time course of the isoprene to carbon dioxide ratio in the gas stream exiting the bioreactor. The isoprene to carbon dioxide ratio is an indicator of product yield. Isoprene production was achieved by the simultaneous saccharification and fermentation process with HgGA as described in Example 8.3.

DETAILED DESCRIPTION

[0032] The invention provides for methods and systems of producing isoprenoid precursor molecules and/or isoprenoids using simultaneous saccharification and fermentation process and glucoamylases at neutral pH.

[0033] In one aspect, the present disclosure relates to the use of glucoamylases capable of effectively saccharifying a starch substrate at a neutral pH, for example, between pH 5.0 and 8.0, to provide an energy source for the biological production of isoprenoid precursor molecules and/or isoprenoids. At a pH of 6.0 or above, the glucoamylases of the disclosed method retains at least about 50% activity relative to the maximum activity. The glucoamylases having these properties include, for example, HgGA, TrGA, and RhGA.

[0034] In some aspects, the embodiments of the present disclosure rely on routine techniques and methods used in the field of genetic engineering and molecular biology. The following resources include descriptions of general methodology useful in accordance with the invention: Sambrook et al, MOLECULAR CLONING: A LABORATORY MANUAL (2nd Ed., 1989); Kreigler, GENE TRANSFER AND EXPRESSION; A LABORATORY MANUAL (1990) and Ausubel et al., Eds. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (1994). Unless defined otherwise herein, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Singleton, et al., DICTIONARY OF MICROBIOLOGY AND MOLECULAR BIOLOGY, 2D ED., John Wiley and Sons, New York (1994), and Hale & Markham, THE HARPER COLLINS

DICTIONARY OF BIOLOGY, Harper Perennial, N.Y. ( 1991) provide one of skill with a general dictionary of many of the terms used in this invention. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the representative methods and materials are described. Numeric ranges are inclusive of the numbers defining the range. The headings provided herein are not limitations of the various aspects or embodiments, which can be had by reference to the specification as a whole.

Definitions and Abbreviations

[0035] In accordance with this detailed description, the following abbreviations and definitions apply. It should be noted that as used herein, the singular forms "a," "an," and "the" include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to "an enzyme" includes a plurality of such enzymes.

[0036] As used herein, the term "isoprenoid" refers to a large and diverse class of naturally- occurring class of organic compounds composed of two or more units of hydrocarbons, with each unit consisting of five carbon atoms arranged in a specific pattern. As used herein, "isoprene" is expressly excluded from the definition of "isoprenoid."

[0037] As used herein, the term "terpenoid" refers to a large and diverse class of organic molecules derived from five-carbon isoprenoid units assembled and modified in a variety of ways and classified in groups based on the number of isoprenoid units used in group members. Hemiterpenoids have one isoprenoid unit. Monoterpenoids have two isoprenoid units. Sesquiterpenoids have three isoprenoid units. Diterpenoids have four isoprene units. Sesterterpenoids have five isoprenoid units. Triterpenoids have six isoprenoid units.

Tetraterpenoids have eight isoprenoid units. Polyterpenoids have more than eight isoprenoid units.

[0038] As used herein, "isoprenoid precursor" refers to any molecule that is used by organisms in the biosynthesis of terpenoids or isoprenoids. Non-limiting examples of isoprenoid precursor molecules include, e.g., mevalonate (mevolonic acid (MVA), isopentenyl pyrophosphate (IPP) and dimethylallyl diphosphate (DMAPP).

[0039] By "heterologous nucleic acid" is meant a nucleic acid whose nucleic acid sequence is not identical to that of another nucleic acid naturally found in the same host cell.

[0040] As used herein, "nucleotide sequence" or "nucleic acid sequence" refers to a sequence of genomic, synthetic, or recombinant origin and may be double- stranded or single- stranded, whether representing the sense or anti- sense strand. As used herein, the term "nucleic acid" may refer to genomic DNA, cDNA, synthetic DNA, or RNA. The residues of a nucleic acid may contain any of the chemically modifications commonly known and used in the art.

[0041] As used herein, "polypeptides" includes polypeptides, proteins, peptides, fragments of polypeptides, and fusion polypeptides. In some embodiments, the fusion polypeptide includes part or all of a first polypeptide (e.g., an polyprenyl pyrophosphate synthase, DXS, IDI, or MVA pathway polypeptide or catalytically active fragment thereof) and may optionally include part or all of a second polypeptide (e.g. , a peptide that facilitates purification or detection of the fusion polypeptide, such as a His-tag).

[0042] In some embodiments, the polypeptide is a heterologous polypeptide. By

"heterologous polypeptide" is meant a polypeptide whose amino acid sequence is not identical to that of another polypeptide naturally expressed in the same host cell. In particular, a heterologous polypeptide is not identical to a wild-type nucleic acid that is found in the same host cell in nature.

[0043] "Isolated" means that the material is at least substantially free from at least one other component that the material is naturally associated and found in nature.

[0044] "Purified" means that the material is in a relatively pure state, e.g. , at least about 90% pure, at least about 95% pure, at least about 98% pure, or at least about 99% pure. [0045] "Oligosaccharide" means a carbohydrate molecule composed of 3-20

monosaccharides.

[0046] As used herein, "transformed cell" includes cells that have been transformed by use of recombinant DNA techniques. Transformation typically occurs by insertion of one or more nucleotide sequences into a cell. The inserted nucleotide sequence may be a heterologous nucleotide sequence, i. e. , is a sequence that may not be natural to the cell that is to be transformed, such as a fusion protein.

[0047] As used herein, "starch" refers to any material comprised of the complex polysaccharide carbohydrates of plants, comprised of amylose and amylopectin with the formula (C ₆ HioOs) _x , wherein "X" can be any number. In particular, the term refers to any plant-based material including but not limited to grains, grasses, tubers and roots and more specifically wheat, barley, corn, rye, rice, sorghum, brans, cassava, millet, potato, sweet potato, and tapioca.

[0048] As used herein, "granular starch" refers to uncooked (raw) starch, which has not been subject to gelatinization.

[0049] As used herein, "starch gelatinization" means solubilization of a starch molecule to form a viscous suspension.

[0050] As used herein, "gelatinization temperature" refers to the lowest temperature at which gelatinization of a starch substrate occurs. The exact temperature depends upon the specific starch substrate and further may depend on the particular variety and the growth conditions of plant species from which the starch is obtained.

[0051] "DE" or "dextrose equivalent" is an industry standard for measuring the concentration of total reducing sugars, calculated as the percentage of the total solids that have been converted to reducing sugars. The granular starch that has not been hydrolyzed has a DE that is about zero (0), and D-glucose has a DE of about 100.

[0052] As used herein, "starch substrate" refers to granular starch or liquefied starch using refined starch, whole ground grains, or fractionated grains.

[0053] As used herein, "liquefied starch" refers to starch that has gone through

solubilization process, for example, the conventional starch liquefaction process.

[0054] "Degree of polymerization (DP)" refers to the number (n) of anhydroglucopyranose units in a given saccharide. Examples of DPI are the monosaccharides, such as glucose and fructose. Examples of DP2 are the disaccharides, such as maltose and sucrose. A DP4+

(>DP4) denotes polymers with a degree of polymerization of greater than four. [0055] As used herein, "fermentable sugars" refer to saccharides that are capable of being metabolized under fermentation conditions. These sugars typically refer to glucose, maltose, and maltotriose (DPI, DP2 and DP3).

[0056] As used herein, "total sugar content" refers to the total sugar content present in a starch composition.

[0057] As used herein, "ds" refers to dissolved solids in a solution. The term "dry solids content (DS)" refers to the total solids of a slurry in % on a dry weight basis. The term "slurry" refers to an aqueous mixture containing insoluble solids.

[0058] As used herein, "starch-liquefying enzyme" refers to an enzyme that catalyzes the hydrolysis or breakdown of granular starch. Exemplary starch liquefying enzymes include alpha-amylases (EC 3.2.1.1).

[0059] "Amylase" means an enzyme that is, among other things, capable of catalyzing the degradation of starch. For example, β-Amylases, a-glucosidases (EC 3.2.1.20; a -D- glucoside glucohydrolase), glucoamylase (EC 3.2.1.3; a -D-(l->4)-glucan glucohydrolase), and product- specific amylases can produce malto-oligosaccharides of a specific length from starch.

[0060] "Alpha-amylases (EC 3.2.1.1)" refer to endo-acting enzymes that cleave a-D- (1→4) O-glycosidic linkages within the starch molecule in a random fashion. In contrast, the exo-acting amylolytic enzymes, such as beta-amylases (EC 3.2.1.2; a-D-(l→4)-glucan maltohydrolase) and some product- specific amylases like maltogenic alpha-amylase (EC 3.2.1.133) cleave the starch molecule from the non-reducing end of the substrate. These enzymes have also been described as those effecting the exo- or endohydro lysis of 1,4-a-D- glucosidic linkages in polysaccharides containing 1, 4-oc- linked D-glucose units. Another term used to describe these enzymes is glycogenase. Exemplary enzymes include alpha- 1, 4- glucan 4-glucanohydrolase.

[0061] As used herein, "glucoamylases" refer to the amyloglucosidase class of enzymes (EC 3.2.1.3, glucoamylase, a-1, 4-D-glucan glucohydrolase). These are exo-acting enzymes that release glucosyl residues from the non-reducing ends of amylose and/or amylopectin molecules. The enzymes are also capably of hydrolyzing a-1, 6 and a- 1,3 linkages, however, at much slower rates than the hydrolysis of a-1, 4 linkages.

[0062] As used herein, the term "non-starch polysaccharide hydrolyzing enzymes" are enzymes capable of hydrolyzing complex carbohydrate polymers such as cellulose, hemicellulose, and pectin. For example, cellulases (endo and exo-glucanases, beta glucosidase) hemicellulases (xylanases) and pectinases are non-starch polysaccharide hydrolyzing enzymes.

[0063] As used herein, "maximum activity" refers to the enzyme activity measured under the most favorable conditions, for example, at an optimum pH. As used herein, "optimum pH" refers to a pH value, under which the enzyme displays the highest activity with other conditions being equal. The "optimum pH" of HgGA and TrGA is shown in FIG. 1.

[0064] The phrase "mature form" of a protein or polypeptide refers to the final functional form of the protein or polypeptide. A mature form of a glucoamylase may lack a signal peptide and/or initiator methionine, for example. A mature form of a glucoamylase may be produced from its native host, for example, by endogenous expression. Alternatively, a mature form of a glucoamylase may be produced from a non-native host, for example, by exogenous expression. An exogenously expressed glucoamylase may have a varied glycosylation pattern compared to the endogenous expressed counterpart.

[0065] The term "parent" or "parent sequence" refers to a sequence that is native or naturally occurring.

[0066] As used herein, the terms "variant" is used in reference to glucoamylases that have some degree of amino acid sequence identity to a parent glucoamylase sequence. A variant is similar to a parent sequence, but has at least one substitution, deletion or insertion in their amino acid sequence that makes them different in sequence from a parent glucoamylase. In some cases, variants have been manipulated and/or engineered to include at least one substitution, deletion, or insertion in their amino acid sequence that makes them different in sequence from a parent. Additionally, a glucoamylase variant may retain the functional characteristics of the parent glucoamylase, e.g. , maintaining a glucoamylase activity that is at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, or 99% of that of the parent glucoamylase.

[0067] As used herein, "hydrolysis of starch" refers to the cleavage of glucosidic bonds with the addition of water molecules.

[0068] As used herein, "end product" or "desired end product" refers to a molecule or compound to which a starch substrate is converted into, by an enzyme and/or a

microorganism.

[0069] As used herein, "contacting" or "admixing" refers to the placing of the respective enzyme(s) in sufficiently close proximity to the respective substrate to enable the enzyme(s) to convert the substrate to the end product. Those skilled in the art will recognize that mixing solutions of the enzyme with the respective substrates can affect contacting or admixing.

Abbreviations

[0070] The following abbreviations apply unless indicated otherwise:

AkAA Aspergillus kawachii alpha-amylase

AmyE Bacillus subtilis alpha-amylase

AmyL Bacillus licheniformis alpha-amylase

AmyR SPEZYME® XTRA amylase

AmyS Geobacillus stearothermophilus alpha-amylase

AnGA Aspergillus niger glucoamylase

BAA bacterial alpha-amylase

cDNA complementary DNA

CER carbon dioxide evolution rate

DE Dextrose Equivalent

DI distilled, deionized

DMAPP 3,3-dimethylallyl pyrophosphate

DNA deoxyribonucleic acid

DP3 degree of polymerization with three subunits

DPn degree of polymerization with n subunits

DS or ds dry solid

dss dry solid starch

DXS l-deoxy-D-xylulose-5-phosphate synthase

EC enzyme commission for enzyme classification

g gram

gpm gallon per minute

GAU glucoamylase units

HGA Humicola grisea glucoamylase

HgGA Humicola grisea glucoamylase

HPLC high pressure liquid chromatography

IPTG isopropyl-beta-D- 1 -thiogalactopyranoside

kg kilogram

MEP methylerythritol phosphate MOPS 3-(N-morpholino)propanesulfonic acid

MT metric ton

MVA mevalonate

MW molecular weight

NCBI National Center for Biotechnology Information

nm nanometer

OD optical density

PCR polymerase chain reaction

PEG polyethylene glycol

pi isoelectric point

ppm parts per million

q.s. as much as suffices (quantum satis or quantum sufficit)

RhGA Rhizopus sp. glucoamylase

RNA ribonucleic acid

RO reverse osmosis

rpm revolutions per minute

slpm standard liters per minute

SSF simultaneous saccharification and fermentation

TeGA Talaromyces emersonii glucoamylase

TrGA Trichoderma reesei glucoamylase

w/v weight/volume

w/w weight/weight

wt wild-type

microliter

Enzymes in Starch Processing

Glucoamylase having the desired pH profile

[0071] Glucoamylases are produced by numerous strains of bacteria, fungi, yeast and plants. Many fungal glucoamylases are fungal enzymes that are extracellularly produced, for example from strains of Aspergillus (Svensson et al., Carlsberg Res. Commun. 48: 529-544 (1983); Boel et al, EMBO J. 3: 1097-1102 (1984); Hayashida et al., Agric. Biol. Chem. 53: 923-929 (1989); U.S. Patent No. 5,024,941; U.S. Patent No. 4,794,175 and WO 88/09795); Talaromyces (U.S. Patent No. 4,247,637; U.S. Patent No. 6,255,084; and U.S. Patent No. 6,620,924); Rhizopus (Ashikari et al., Agric. Biol. Chem. 50: 957-964 (1986); Ashikari et al., App. Microbio. Biotech. 32: 129-133 (1989) and U.S. Patent No. 4,863,864); Humicola (WO 05/052148 and U.S. Patent No. 4,618,579); and Mucor (Houghton-Larsen et al., Appl.

Microbiol. Biotechnol. 62: 210-217 (2003)). Many of the genes that code for these enzymes have been cloned and expressed in yeast, fungal and/or bacterial cells.

[0072] Commercially, glucoamylases are very important enzymes and have been used in a wide variety of applications that require the hydrolysis of starch (e.g., for producing glucose and other monosaccharides from starch). Glucoamylases are used to produce high fructose corn sweeteners, which comprise over 50% of the sweetener market in the United States. In general, glucoamylases may be, and commonly are, used with alpha-amylases in starch hydrolyzing processes to hydrolyze starch to dextrins and then glucose. The glucose may then be converted to fructose by other enzymes (e.g. , glucose isomerases); crystallized; or used in fermentations to produce numerous end products (e.g., ethanol, citric acid, succinic acid, ascorbic acid intermediates, glutamic acid, glycerol, 1,3 -propanediol and lactic acid).

[0073] The embodiments of the present disclosure utilize a glucoamylase capable of effectively saccharifying a starch substrate at a neutral pH, for example, between pH 5.0 and 8.0, 5.5 and 7.5, 6.0 and 7.5, 6.5 and 7.5, or 7.0 and 7.5. At a pH of 6.0 or above, the glucoamylase retains at least about 50%, about 51%, about 52%, about 53%, about 54%, or about 55% of the activity relative to the maximum activity. The glucoamylases having the desired pH profile include, but are not limited to, Humicola grisea glucoamylase (HgGA), Trichoderma reesei glucoamylase (TrGA), and Rhizopus sp. glucoamylase (RhGA).

[0074] HgGA may be the glucoamylase comprising the amino acid sequence of SEQ ID NO: 3, which is described in detail in U.S. Patent Nos. 4,618,579 and 7,262,041. This HgGA is also described as a granular starch hydrolyzing enzyme (GSHE), because it is capable of hydrolyzing starch in granular form. The genomic sequence coding the HgGA from

Humicola grisea var. thermoidea is presented as SEQ ID NO: 1, which contains three putative introns (positions 233-307, 752-817, and 950-1006). The native HgGA from Humicola grisea var. thermoidea has the amino acid sequence of SEQ ID NO: 2, which includes a signal peptide containing 30 amino acid residues (positions 1 to 30 of SEQ ID NO: 2). Cleavage of the signal peptide results in the mature HgGA having the amino acid sequence of SEQ ID NO: 3. The embodiments of the present disclosure also include a HgGA produced from a Trichoderma host cell, e.g., a Trichoderma reesei cell. See U.S. Patent No 7,262,041. [0075] A typical TrGA is the glucoamylase from Trichoderma reesei QM6a (ATCC, Accession No. 13631). This TrGA comprising the amino acid sequence of SEQ ID NO: 6, which is described in U.S. Patent No. 7,413,879, for example. The cDNA sequence coding the TrGA from Trichoderma reesei QM6a is presented as SEQ ID NO: 4. The native TrGA has the amino acid sequence of SEQ ID NO: 5, which includes a signal peptide containing 33 amino acid residues (positions 1 to 33 of SEQ ID NO: 4). See id. Cleavage of the signal peptide results in the mature TrGA having the amino acid sequence of SEQ ID NO: 6. See id. The catalytic domain of TrGA is presented as SEQ ID NO: 7. See id. The embodiments of the present disclosure also include an endogenously expressed TrGA. See id.

[0076] RhGA may be the glucoamylase from Rhizopus niveus or Rhizopus oryzae. See U.S. Patent Nos. 4,514,496 and 4,092,434. The native RhGA from R. oryzae has the amino acid sequence of SEQ ID NO: 8, which includes a signal peptide containing 25 amino acid residues (positions 1 to 25 of SEQ ID NO: 8). Cleavage of the signal peptide results in the mature RhGA having the amino acid sequence of SEQ ID NO: 9. A typical RhGA may be the glucoamylase having trade names CU.CONC (Shin Nihon Chemicals, lapan) or Ml (Biocon India, Bangalore, India).

Structure and Function

[0077] The glucoamylase of the embodiment of the present disclosure may also be a variant of HgGA, TrGA, or RhGA. The variant has at least 99% sequence identity to the parent glucoamylase. In some embodiments, the variant has at least 98%, at least 97%, at least 96%, at least 95%, at least 94%, at least 93%, at least 92%, at least 91%, or at least 90% sequence identity to the parent glucoamylase. Optionally, the variant has one, two, three, four, five, or six amino acids modification compared to the mature form of the parent glucoamylase. In other embodiments, the variant has at least 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% sequence identity to the parent glucoamylase. Optionally, the variant has more than six amino acids (e.g., 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 55, or 60) modification compared to the mature form of the parent glucoamylase. The variant possesses the desired pH profile and capability of saccharifying a starch substrate at a pH in the range of 5.0 to 8.0. In some embodiments, the variants may possess other improved properties, such as improved thermostability and improved specificity.

[0078] Glucoamylases consist of as many as three distinct structural domains, a catalytic domain of approximately 450 residues that is structurally conserved in all glucoamylases, generally followed by a linker region consisting of between 30 and 80 residues that are connected to a starch binding domain of approximately 100 residues. For example, TrGA has a catalytic domain having the amino acid sequence of SEQ ID NO: 7. The structure of the Trichoderma reesei glucoamylase (TrGA) with all three regions intact was determined to 1.8 Angstrom resolution. See WO 2009/048488 and WO 2009/048487. Using the determined coordinates, the structure was aligned with the coordinates of the catalytic domain of the glucoamylase from Aspergillus awamori strain X100 that was determined previously (Aleshin, A.E., Hoffman, C, Firsov, L.M., and Honzatko, R.B. Refined crystal structures of glucoamylase from Aspergillus awamori var. X100. /. Mol. Biol. 238: 575-591 (1994)). See id. The structure of the catalytic domains of TrGA and Aspergillus awamori glucoamylase overlap very closely, and it is possible to identify equivalent residues based on this structural superposition. See id. It is further believed that all glucoamylases share the basic structure. See id.

[0079] Given the well-known structure and function relationship of glucoamylases, glucoamylase variants having altered properties have been successfully created and characterized. The variants may display improved properties as compared to the parent glucoamylases. The improved properties may include, and are not limited to, increased thermostability and increased specific activity. For example, methods for making and characterizing TrGA variants with altered properties have been described in WO

2009/067218. Functional TrGA variants have been identified having one or more specific sequence modifications. Some TrGA variants, for example, have multiple sequence modifications. WO 2009/067218 discloses TrGA variants with six or more amino acid modifications, for example. These TrGA variants show at least as much activity as the parent TrGA, and in many cases show improved properties. It is expected that corresponding residue changes in HgGA and RhGA, for example, will yield variants with glucoamylase activity. The glucoamylase variants useful in the present methods have, at a pH of 6.0 or above, at least about 50% activity relative to the maximum activity.

Production of Glucoamylase

[0080] Glucoamylases suitable for the embodiments of the present disclosure may be produced with recombinant DNA technology in various host cells.

[0081] In some embodiments, the host cells are selected from bacterial, fungal, plant and yeast cells. The term host cell includes both the cells, progeny of the cells and protoplasts created from the cells that are used to produce a variant glucoamylase according to the disclosure. In some embodiments, the host cells are fungal cells and typically filamentous fungal host cells. The term "filamentous fungi" refers to all filamentous forms of the subdivision Eumycotina (See, Alexopoulos, C. J. (1962), INTRODUCTORY MYCOLOGY, Wiley, New York). These fungi are characterized by a vegetative mycelium with a cell wall composed of chitin, cellulose, and other complex polysaccharides. The filamentous fungi of the present disclosure are morphologically, physiologically, and genetically distinct from yeasts. Vegetative growth by filamentous fungi is by hyphal elongation and carbon catabolism is obligatory aerobic. In the embodiments of the present disclosure, the filamentous fungal parent cell may be a cell of a species of, but not limited to, Trichoderma, (e.g., Trichoderma reesei, the asexual morph of Hypocrea jecorina, previously classified as T. longibrachiatum, Trichoderma viride, Trichoderma koningii, Trichoderma harzianum) (Sheir-Neirs et al., (1984) Appl. Microbiol. Biotechnol 20:46-53; ATCC No. 56765 and ATCC No. 26921); Penicillium sp., Humicola sp. (e.g., H. insolens, H. lanuginosa and H. grisea); Chrysosporium sp. (e.g., C. lucknowense), Gliocladium sp., Aspergillus sp. (e.g., A. oryzae, A. niger, A sojae, A. japonicus, A. nidulans, and A. awamori) (Ward et al., (1993) Appl. Microbiol. Biotechnol. 39:738-743 and Goedegebuur et al, (2002) Genet 41:89-98), Fusarium sp.,(e.g., F. roseum, F. graminum F. cerealis, F. oxysporuim and / ⁷ , venenatum), Neurospora sp., (N. crassa), Hypocrea sp., Mucor sp.,( . miehei),, Rhizopus sp. and Emericella sp. (see also, Innis et al., (1985) Sci. 228:21-26). The term "Trichoderma" or "Trichoderma sp." or "Trichoderma spp." refers to any fungal genus previously or currently classified as Trichoderma. In other embodiments, the host cell will be a genetically engineered host cell wherein native genes have been inactivated, for example by deletion in fungal cells. Where it is desired to obtain a fungal host cell having one or more inactivated genes known methods may be used (e.g. methods disclosed in U.S. Patent Nos. 5,246,853 and 5,475,101, and WO 92/06209). Gene inactivation may be accomplished by complete or partial deletion, by insertional inactivation or by any other means that renders a gene nonfunctional for its intended purpose (such that the gene is prevented from expression of a functional protein). In some embodiments, when the host cell is a Trichoderma cell and particularly a T. reesei host cell, the cbh\, cbKl, egll and eg/2 genes will be inactivated and/or typically deleted. Typically, Trichoderma reesei host cells having quad-deleted proteins are set forth and described in U.S. Patent No. 5,847,276 and WO 05/001036. In other embodiments, the host cell is a protease deficient or protease minus strain.

[0082] To produce the glucoamylase of the embodiments of the present disclosure with the recombinant DNA technology, a DNA construct comprising nucleic acid encoding the amino acid sequence of the designated glucoamylase can be constructed and transferred into, for example, a Trichoderma reesei host cell. The vector may be any vector which when introduced into a Trichoderma reesei host cell can be integrated into the host cell genome and can be replicated. Reference is made to the Fungal Genetics Stock Center Catalogue of Strains (FGSC, <www.fgsc.net>) for a list of vectors. Additional examples of suitable expression and/or integration vectors are provided in Sambrook et al., (1989) supra, and Ausubel (1987) supra, and van den Hondel et al. (1991) in Bennett and Lasure (Eds.) MORE GENE MANIPULATIONS IN FUNGI, Academic Press pp. 396-428 and U.S. Patent No.

5,874,276. The nucleic acid encoding the glucoamylase can be operably linked to a suitable promoter, which shows transcriptional activity in Trichoderma reesei host cell. The promoter may be derived from genes encoding proteins either homologous or heterologous to the host cell. Suitable non-limiting examples of promoters include cbhl, cbh2, egll, egl2. In one embodiment, the promoter may be a native T. reesei promoter. Typically, the promoter can be T. reesei cbhl, which is an inducible promoter and has been deposited in GenBank under Accession No. D86235. An "inducible promoter" may refer to a promoter that is active under environmental or developmental regulation. In another embodiment, the promoter can be one that is heterologous to T. reesei host cell. Other examples of useful promoters include promoters from A. awamori and A. niger glucoamylase genes {see, e.g., Nunberg et al., (1984) Mol. Cell Biol. 4:2306-2315 and Boel et al., (1984) EMBO J. 3:1581-1585). Also, the promoters of the T. reesei xlnl gene and the cellobiohydrolase 1 gene may be useful (EPA 13f280Al).

[0083] In some embodiments, the glucoamylase coding sequence can be operably linked to a signal sequence. The signal sequence may be the native signal peptide of the glucoamylase (residues 1-20 of SEQ ID NO: 2 for HgGA, or residues 1-33 of SEQ ID NO: 5 for TrGA, for example). Alternatively, the signal sequence may have at least 90% or at least 95% sequence identity to the native signal sequence. In additional embodiments, a signal sequence and a promoter sequence comprising a DNA construct or vector to be introduced into the T reesei host cell are derived from the same source. For example, in some embodiments, the signal sequence can be the cdhl signal sequence that is operably linked to a cdhl promoter.

[0084] In some embodiments, the expression vector may also include a termination sequence. In one embodiment, the termination sequence and the promoter sequence can be derived from the same source. In another embodiment, the termination sequence can be homologous to the host cell. A particularly suitable terminator sequence can be cbhl derived from T. reesei. Other exemplary fungal terminators include the terminator from A. niger or A. awamori glucoamylase gene.

[0085] In some embodiments, an expression vector may include a selectable marker. Examples of representative selectable markers include ones that confer antimicrobial resistance (e.g., hygromycin and phleomycin). Nutritional selective markers also find use in the present invention including those markers known in the art as amdS, argB, and pyr4. Markers useful in vector systems for transformation of Trichoderma are known in the art (see, e.g., Finkelstein, chapter 6 in BIOTECHNOLOGY OF FILAMENTOUS FUNGI, Finkelstein et al. Eds. Butterworth-Heinemann, Boston, Mass. (1992), Chap. 6.; and Kinghorn et al. (1992) APPLIED MOLECULAR GENETICS OF FILAMENTOUS FUNGI, Blackie Academic and Professional, Chapman and Hall, London). In a representative embodiment, the selective marker may be the amdS gene, which encodes the enzyme acetamidase, allowing transformed cells to grow on acetamide as a nitrogen source. The use of A. nidulans amdS gene as a selective marker is described for example in elley et al., (1985) EMBO J. 4:475-479 and Penttila et al, (1987) Gene 61: 155-164.

[0086] An expression vector comprising a DNA construct with a polynucleotide encoding the glucoamylase may be any vector which is capable of replicating autonomously in a given fungal host organism or of integrating into the DNA of the host. In some embodiments, the expression vector can be a plasmid. In typical embodiments, two types of expression vectors for obtaining expression of genes are contemplated.

[0087] The first expression vector may comprise DNA sequences in which the promoter, glucoamylase-coding region, and terminator all originate from the gene to be expressed. In some embodiments, gene truncation can be obtained by deleting undesired DNA sequences (e.g., DNA encoding unwanted domains) to leave the domain to be expressed under control of its own transcriptional and translational regulatory sequences.

[0088] The second type of expression vector may be preassembled and contains sequences needed for high-level transcription and a selectable marker. In some embodiments, the coding region for the glucoamylase gene or part thereof can be inserted into this general- purpose expression vector such that it is under the transcriptional control of the expression construct promoter and terminator sequences. In some embodiments, genes or part thereof may be inserted downstream of a strong promoter, such as the strong cbhl promoter.

[0089] Methods used to ligate the DNA construct comprising a polynucleotide encoding the glucoamylase, a promoter, a terminator and other sequences and to insert them into a suitable vector are well known in the art. Linking can be generally accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide linkers are used in accordance with conventional practice, (see, Sambrook (1989) supra, and Bennett and Lasure, MORE GENE MANIPULATIONS IN FUNGI, Academic Press, San Diego (1991) pp 70-76.). Additionally, vectors can be constructed using known recombination techniques (e.g., Invitrogen Life Technologies, Gateway Technology).

[0090] Introduction of a DNA construct or vector into a host cell includes techniques such as transformation; electroporation; nuclear microinjection; transduction; transfection, (e.g., lipofection mediated and DEAE-Dextrin mediated transfection); incubation with calcium phosphate DNA precipitate; high velocity bombardment with DNA-coated microprojectiles; and protoplast fusion. General transformation techniques are known in the art (see, e.g., Ausubel et al., (1987), supra, chapter 9; and Sambrook (1989) supra, and Campbell et al., (1989) Curr. Genet. 16:53-56). The expression of heterologous protein in Trichoderma is described in U.S. Pat. Nos. 6,022,725; 6,268,328; Harkki et al. (1991); Enzyme Microb. Technol. 13:227-233; Harkki et al., ( 1989) Bio Technol. 7:596-603; EP 244,234; EP 215,594; and Nevalainen et al., "The Molecular Biology of Trichoderma and its Application to the Expression of Both Homologous and Heterologous Genes," in MOLECULAR INDUSTRIAL MYCOLOGY, Eds. Leong and Berka, Marcel Dekker Inc., NY ( 1992) pp. 129- 148).

[0091] In some embodiments, genetically stable transformants can be constructed with vector systems whereby the nucleic acid encoding glucoamylase is stably integrated into a host strain chromosome. Transformants are then purified by known techniques.

[0092] In one non-limiting example, stable transformants including an amdS marker are distinguished from unstable transformants by their faster growth rate and the formation of circular colonies with a smooth, rather than ragged outline on solid culture medium containing acetamide. Additionally, in some cases a further test of stability can be conducted by growing the transformants on solid non-selective medium (i.e., medium that lacks acetamide), harvesting spores from this culture medium and determining the percentage of these spores which subsequently germinate and grow on selective medium containing acetamide. Alternatively, other methods known in the art may be used to select

transformants.

[0093] Uptake of DNA into the host Trichoderma sp. strain is dependent upon the calcium ion concentration. Generally, between about 10 mM CaC and 50 mM CaCl ₂ may be used in an uptake solution. Besides the need for the calcium ion in the uptake solution, other compounds generally included are a buffering system such as TE buffer (10 mM Tris, pH 7.4; 1 mM EDTA) or 10 mM MOPS, pH 6.0 buffer (morpholinepropanesulfonic acid) and polyethylene glycol (PEG). It is believed that the polyethylene glycol acts to fuse the cell membranes, thus permitting the contents of the medium to be delivered into the cytoplasm of the Trichoderma sp. strain and the plasmid DNA is transferred to the nucleus. This fusion frequently leaves multiple copies of the plasmid DNA integrated into the host chromosome.

[0094] Usually a suspension containing the Trichoderma sp. protoplasts or cells that have been subjected to a permeability treatment at a density of 10 ⁵ to 10 ⁷ /mL, typically, 2 x 10 ⁶ /mL are used in transformation. A volume of 100 μΕ of these protoplasts or cells in an appropriate solution (e.g., 1.2 M sorbitol; 50 mM CaCl ₂ ) are mixed with the desired DNA. Generally, a high concentration of PEG may be added to the uptake solution. From 0.1 to 1 volume of 25% PEG 4000 can be added to the protoplast suspension. It is also typical to add about 0.25 volumes to the protoplast suspension. Additives such as dimethyl sulfoxide, heparin, spermidine, potassium chloride and the like may also be added to the uptake solution and aid in transformation. Similar procedures are available for other fungal host cells. See, e.g., U.S. Patent Nos. 6,022,725 and 6,268,328.

[0095] Generally, the mixture can be then incubated at approximately 0°C for a period of between 10 to 30 minutes. Additional PEG may then be added to the mixture to further enhance the uptake of the desired gene or DNA sequence. The 25% PEG 4000 can be generally added in volumes of 5 to 15 times the volume of the transformation mixture;

however, greater and lesser volumes may be suitable. The 25% PEG 4000 may be typically about 10 times the volume of the transformation mixture. After the PEG is added, the transformation mixture can then be incubated either at room temperature or on ice before the addition of a sorbitol and CaCl ₂ solution. The protoplast suspension can then be further added to molten aliquots of a growth medium. This growth medium permits the growth of transformants only.

[0096] Generally, cells are cultured in a standard medium containing physiological salts and nutrients (see, e.g., Pourquie, J. et al, BIOCHEMISTRY AND GENETICS OF CELLULOSE DEGRADATION, eds. Aubert, J. P. et al., Academic Press, pp. 71 86, 1988 and Ilmen, M. et al, (1997) Appl. Environ. Microbiol. 63: 1298-1306). Common commercially prepared media (e.g., Yeast Malt Extract (YM) broth, Luria Bertani (LB) broth and Sabouraud Dextrose (SD) broth also find use in the present embodiments. [0097] Culture-conditions are also standard, e.g., cultures are incubated at approximately 28 °C in appropriate medium in shake cultures or fermentors until desired levels of glucoamylase expression are achieved. After fungal growth has been established, the cells are exposed to conditions effective to cause or permit the expression of the glucoamylase. In cases where the glucoamylase coding sequence is under the control of an inducible promoter, the inducing agent (e.g., a sugar, metal salt or antimicrobial), can be added to the medium at a concentration effective to induce glucoamylase expression.

[0098] In general, the glucoamylase produced in cell culture may be secreted into the medium and may be purified or isolated, e.g., by removing unwanted components from the cell culture medium. In some cases, the glucoamylase can be produced in a cellular form, necessitating recovery from a cell lysate. In such cases, the enzyme may be purified from the cells in which it was produced using techniques routinely employed by those of skill in the art. Examples of these techniques include, but are not limited to, affinity chromatography (Tilbeurgh et a., (1984) FEBS Lett. 16: 215), ion-exchange chromatographic methods (Goyal et al., (1991) Biores. Technol. 36: 37; Fliess et al., (1983) Eur. J. Appl. Microbiol. Biotechnol. 17: 314; Bhikhabhai et al, (1984) /. Appl. Biochem. 6: 336; and Ellouz et al, (1987)

Chromatography 396: 307), including ion-exchange using materials with high resolution power (Medve et al., (1998) /. Chromatography A 808: 153), hydrophobic interaction chromatography (see, Tomaz and Queiroz, (1999) /. Chromatography A 865: 123; two-phase partitioning (see, Brumbauer, et al., (1999) Bioseparation 7: 287); ethanol precipitation; reverse phase HPLC, chromatography on silica or on a cation-exchange resin such as DEAE, chromatofocusing, SDS-PAGE, ammonium sulfate precipitation, and gel filtration (e.g., Sephadex G-75).

Alpha- amylases

[0099] Alpha-amylases constitute a group of enzymes present in microorganisms and tissues from animals and plants. They are capable of hydrolyzing alpha- 1,4-glucosidic bonds of glycogen, starch, related polysaccharides, and some oligosaccharides. Although all alpha- amylases possess the same catalytic function, their amino acid sequences vary greatly. The sequence identity between different amylases can be virtually non-existent, e.g. , falling below 25%. Despite considerable amino acid sequence variation, alpha-amylases share a common overall topological scheme that has been identified after the three-dimensional structures of alpha-amylases from different species have been determined. The common three-dimensional structure reveals three domains: (1) a "TIM" barrel known as domain A, (2) a long loop region known as domain B that is inserted within domain A, and (3) a region close to the C-terminus known as domain C that contains a characteristic beta- structure with a Greek-key motif.

[0100] "Termamyl-like" alpha-amylases refer to a group of alpha-amylases widely used in the starch-processing industry. The Bacillus licheniformis alpha-amylase having an amino acid sequence of SEQ ID NO: 2 of U.S. Patent No. 6,440,716 is commercially available as Termamyl®. Termamyl-like alpha-amylases commonly refer to a group of highly homologous alpha-amylases produced by Bacillus spp. Other members of the group include the alpha-amylases from Geobacillus stearothermophilus (previously known as Bacillus stearothermophilus; both names are used interchangeably in the present disclosure) and Bacillus amyloliquefaciens, and those derived from Bacillus sp. NCIB 12289, NCIB 12512, NCIB 12513, and DSM 9375, all of which are described in detail in U.S. Patent No.

6,440,716 and WO 95/26397.

[0101] Although alpha-amylases universally contain the three domains discussed above, the three-dimensional structures of some alpha-amylases, such as AmyE from Bacillus subtilis, differ from Termamyl-like alpha-amylases. These enzymes are collectively referred as non-Termamyl-like alpha-amylases. "AmyE" for the purpose of this disclosure means a naturally occurring alpha-amylase (EC 3.2.1.1 ; 1, 4-a-D-glucan glucanohydrolase) from Bacillus subtilis. Representative AmyE enzymes and the variants thereof are disclosed in U.S. Patent Application 12/478,266 and 12/478,368, both filed June 4, 2009, and 12/479,427, filed June 5, 2009.

[0102] Other commercially available amylases can be used, e.g., TERMAMYL ^® 120-L, LC and SC SAN SUPER ^® , SUPRA ^® , and LIQUEZYME ^® SC available from Novo Nordisk A/S, FUELZYME ^® FL from Diversa, and CLARASE ^® L, SPEZYME ^® FRED, SPEZYME ^® ETHYL, GC626, and GZYME ^® G997 available from Danisco, US, Inc., Genencor Division.

Other enzymes and enzyme combinations

[0103] In embodiments of the present disclosure, other enzyme(s) may also be

supplemented in starch processing, during saccharification and/or fermentation. These supplementary enzymes may include proteases, pullulanases, isoamylases, cellulases, hemicellulases, xylanases, cyclodextrin glycotransferases, lipases, phytases, laccases, oxidases, esterases, cutinases, xylanases, pullulanases, and/or alpha-glucosidases. See e.g. , WO 2009/099783. Skilled artisans in the art are well aware of the methods using the above- listed enzymes. [0104] The glucoamylases disclosed herein can be used in combination with any other enzyme. For example, glucoamylase maybe used in combination with amylases (e.g., alpha- amylases). In one embodiment, saccharification and/or fermentation or the simultaneous saccharification and fermentation (SSF) process use glucoamylase and one or more non- starch polysaccharide hydrolyzing enzymes. These enzymes are capable of hydrolyzing complex carbohydrate polymers such as cellulose, hemicellulose, and pectin. Non-limiting examples include cellulases (e.g., endo and exo-glucanases, beta glucosidase) hemicellulases (e.g., xylanases) and pectinases. In another embodiment, saccharification and/or

fermentation or the SSF process use glucoamylase, alpha-amylase and one or more non- starch polysaccharide hydrolyzing enzymes. In another embodiment, saccharification and/or fermentation or the SSF process use glucoamylase with phytases, proteases, isoamylases and pullulanases.

[0105] In some embodiments, the saccharification and/or fermentation or the SSF process can use at least two non-starch polysaccharide hydrolyzing enzymes. In some embodiments, the saccharification and/or fermentation or the SSF process can use at least three non-starch polysaccharide hydrolyzing enzymes.

[0106] Cellulases are enzyme compositions that hydrolyze cellulose ( -l,4-D-glucan linkages) and/or derivatives thereof, such as phosphoric acid swollen cellulose. Cellulases include the classification of exo-cellobiohydrolases (CBH), endoglucanases (EG) and β- glucosidases (BG) (EC3.2.191, EC3.2.1.4 and EC3.2.1.21). Examples of cellulases include cellulases from Penicillium, Trichoderma, Humicola, Fusarium, Thermomonospora, Cellulomonas, Hypocrea, Clostridium, Thermomonospore, Bacillus, Cellulomonas and Aspergillus. Non-limiting examples of commercially available cellulases sold for feed applications are beta-glucanases such as ROVABIO ^® (Adisseo), NATUGRAIN ^® (BASF), MULTIFECT ^® BGL (Danisco Genencor) and ECONASE ^® (AB Enzymes). Some commercial cellulases includes ACCELERASE ^® . The cellulases and endoglucanases described in US20060193897 A 1 also may be used.

[0107] Beta-glucosidases (cellobiase) hydrolyzes cellobiose into individual

monosaccharides. Various beta glucanases find use in the invention in combination with phytases. Beta glucanases (endo-cellulase-enzyme classification EC 3.2.1.4) also called endoglucanase I, II, and III, are enzymes that will attack the cellulose fiber to liberate smaller fragments of cellulose which is further attacked by exo-cellulase to liberate glucose. Commercial beta-glucanases useful in the methods of the invention include OPTIMASH BG and OPTIMASH ^® TBG (Danisco, US, Inc. Genencor Division).

[0108] Hemicellulases are enzymes that break down hemicellulose. Hemicellulose categorizes a wide variety of polysaccharides that are more complex than sugars and less complex than cellulose, that are found in plant walls. In some embodiments, a xylanase find use as a secondary enzyme in the methods of the invention. Any suitable xylanase can be used in the invention. Xylanases (e.g. endo- -xylanases (E.C. 3.2.1.8), which hydrolyze the xylan backbone chain, can be from bacterial sources (e.g., Bacillus, Streptomyces,

Clostridium, Acidothermus, Micro tetrapsora or Thermonospora) or from fungal sources (Aspergillus, Trichoderma, Neurospora, Humicola, Penicillium or Fusarium (See, e.g., EP473 545; U.S. Pat. No. 5,612,055; WO 92/06209; and WO 97/20920)). Xylanases useful in the invention include commercial preparations (e.g., MULTIFECT ^® and FEEDTREAT ^® Y5 (Danisco Genencor), RONOZYME ^® WX (Novozymes A/S) and NATUGRAIN WHEAT ^® (BASF). In some embodiments the xylanase is from Trichoderma reesei or a variant xylanase from Trichoderma reesei, or the inherently thermostable xylanase described in

EP1222256B 1, as well as other xylanases from Aspergillus niger, Aspergillus kawachii, Aspergillus tubigensis, Bacillus circulans, Bacillus pumilus, Bacillus subtilis, Neocallimastix patriciarum, Penicillium species, Streptomyces lividans, Streptomyces thermoviolaceus, Thermomonospora fusca, Trichoderma harzianum, Trichoderma reesei, and Trichoderma viridae.

[0109] Phytases that can be used include those enzymes capable of liberating at least one inorganic phosphate from inositol hexaphosphate. Phytases are grouped according to their preference for a specific position of the phosphate ester group on the phytate molecule at which hydrolysis is initiated, (e.g., as 3-phytases (EC 3.1.3.8) or as 6-phytases (EC 3.1.3.26)). A typical example of phytase is myo-inositol-hexakiphosphate-3-phosphohydrolase. Phytases can be obtained from microorganisms such as fungal and bacterial organisms (e.g.

Aspergillus (e.g., A. niger, A. terreus, and A. fumigatus), Myceliophthora (M. thermophila), Talaromyces (T. thermophilus) Trichoderma spp (T. reesei). And Thermomyces (See e.g., WO 99/49740)). Also phytases are available from Penicillium species, (e.g., P. hordei (See e.g., ATCC No. 22053), P. piceum (See e.g., ATCC No. 10519), or P. brevi-compactum (See e.g., ATCC No. 48944) (See, e.g. U.S. Pat. No. 6,475,762). Additional phytases that find use in the invention are available from Peniophora, E. coli, Citrobacter, Enterbacter and Buttiauxella (see e.g., WO2006/043178, filed Oct. 17, 2005). Additional phytases useful in the invention can be obtained commercially (e.g. NATUPHOS ^® (BASF), RONOZYME ^® P (Novozymes A/S), PHZYME ^® (Danisco A/S, Diversa) and FINASE ^® (AB Enzymes).

[0110] Various acid fungal proteases (AFP) can be used as part of the combination as well. Acid fungal proteases include for example, those obtained from Aspergillus, Trichoderma, Mucor and Rhizopus, such as A. niger, A. awamori, A. oryzae and M. miehei. AFP can be derived from heterologous or endogenous protein expression of bacteria, plants and fungi sources. IAFP secreted from strains of Trichoderma can be used. Suitable AFP includes naturally occurring wild-type AFP as well as variant and genetically engineered mutant AFP. Some commercial AFP enzymes useful in the invention include FERMGEN ^® (Danisco US, Inc, Genencor Division), and FORMASE ^® 200.

[0111] Proteases can also be used with glucoamylase and any other enzyme combination. Any suitable protease can be used. Proteases can be derived from bacterial or fungal sources. Sources of bacterial proteases include proteases from Bacillus (e.g., B, amyloliquefaciens, B. lentus, B. licheniformis, and B. subtilis). Exemplary proteases include, but are not limited to, subtilisin such as a subtilisin obtainable from B. amyloliquefaciens and mutants thereof (U.S. Pat. No. 4,760,025). Suitable commercial protease includes MULTIFECT ^® P 3000 (Danisco Genencor) and SUMIZYME ^® FP (Shin Nihon). Sources of suitable fungal proteases include, but are not limited to, Trichoderma, Aspergillus, Humicola and Penicillium, for example.

[0112] Debranching enzymes, such as an isoamylase (EC 3.2.1.68) or pullulanase (EC 3.2.1.41), can also be used in combination with the glucoamylases in the saccharification and/or fermentation or SSF processes of the invention. A non-limiting example of a pullulanase that can be used is Promozyme ^® .

Starch Processing

Starch Substrates and Raw Materials

[0113] Those of skill in the art are well aware of available methods that may be used to prepare starch substrates for use in the processes disclosed herein. For example, a useful starch substrate may be obtained from tubers, roots, stems, legumes, cereals, or whole grain. More specifically, the granular starch comes from plants that produce high amounts of starch. For example, granular starch may be obtained from corn, wheat, barley, rye, milo, sago, cassava, tapioca, sorghum, rice, peas, bean, banana, or potatoes. Corn contains about 60-68% starch; barley contains about 55-65% starch; millet contains about 75-80% starch; wheat contains about 60-65% starch; and polished rice contains about 70-72% starch. Specifically contemplated starch substrates are cornstarch, wheat starch, and barley starch. The starch from a grain may be ground or whole and includes corn solids, such as kernels, bran and/or cobs. The starch may be highly refined raw starch or feedstock from starch refinery processes. Various starches also are commercially available. For example, cornstarch may be available from Cerestar, Sigma, and Katayama Chemical Industry Co. (Japan); wheat starch may be available from Sigma; sweet potato starch may be available from Wako Pure Chemical Industry Co. (Japan); and potato starch may be available from Nakaari Chemical Pharmaceutical Co. (Japan).

Milling

[0114] The starch substrate can be a crude starch from milled whole grain, which contains non-starch fractions, e.g. , germ residues and fibers. Milling may comprise either wet milling or dry milling. In wet milling, whole grain can be soaked in water or dilute acid to separate the grain into its component parts, e.g. , starch, protein, germ, oil, kernel fibers. Wet milling efficiently separates the germ and meal {i.e. , starch granules and protein) and can be especially suitable for production of syrups. In dry milling, whole kernels are ground into a fine powder and processed without fractionating the grain into its component parts. Dry milled grain thus will comprise significant amounts of non- starch carbohydrate compounds, in addition to starch. Most ethanol comes from dry milling. Alternatively, the starch to be processed may be a highly refined starch quality, for example, at least about 90%, at least about 95%, at least about 97%, or at least about 99.5% pure.

Gelatinization and Liquefaction

[0115] In some embodiments of the invention, gelatinazation and/or liquefaction may be used. As used herein, the term "liquefaction" or "liquefy" means a process by which starch is converted to less viscous and soluble shorter chain dextrins. In some embodiments, this process involves gelatinization of starch simultaneously with or followed by the addition of alpha- amylases. Additional liquefaction-inducing enzymes, e.g. , a phytase, optionally may be added. In some embodiments, gelatinization is not used. In other embodiments, a separate liquefaction step is not used. Starches can be converted to shorter chains at the same time that saccharification and/or fermentation is performed. In some embodiments, the starch is being converted directly to glucose. In other embodiments, a separate liquefaction step is used prior to saccharification. [0116] In some embodiments, the starch substrate prepared as described above may be slurried with water. The starch slurry may contain starch as a weight percent of dry solids of about 10-55%, about 20-45%, about 30-45%, about 30-40%, or about 30-35%. In some embodiments, the starch slurry is at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, or at least about 55%.

[0117] To optimize alpha- amylase stability and activity, the pH of the slurry may be adjusted to the optimal pH for the alpha-amylases. Alpha-amylases remaining in the slurry following liquefaction may be deactivated by lowering pH in a subsequent reaction step or by removing calcium from the slurry. The pH of the slurry should be adjusted to a neutral pH (e.g., pH 5.0 to 8.0 and any pH in between this range) when the glucoamylases of the invention are used.

[0118] The slurry of starch plus the alpha-amylases may be pumped continuously through a jet cooker, which may be steam heated from about 85°C to up to about 105°C. Gelatinization occurs very rapidly under these conditions, and the enzymatic activity, combined with the significant shear forces, begins the hydrolysis of the starch substrate. The residence time in the jet cooker can be very brief. The partly gelatinized starch may be passed into a series of holding tubes maintained at about 85-105°C and held for about 5 min. to complete the gelatinization process. These tanks may contain baffles to discourage back mixing. As used herein, the term "secondary liquefaction" refers the liquefaction step subsequent to primary liquefaction, when the slurry is allowed to cool to room temperature. This cooling step can be about 30 minutes to about 180 minutes, e.g. , about 90 minutes to 120 minutes. Milled and liquefied grain is also known as mash.

Saccharification

[0119] Following liquefaction, the mash can be further hydrolyzed through saccharification to produce fermentable sugars that can be readily used in the downstream applications. The saccharification of the present embodiments can be carried out at a pH in the range of 5.0 to 8.0, 5.5 to 7.5, 6.0 to 7.5, 6.5 to 7.5, or 7.0 to 7.5, by using a glucoamylase as described above. In other embodiments, the pH used can be 5.0, 5.25, 5.50, 5.75, 6.0, 6.50, 7.0, 7.50 or 8.0.

[0120] In one embodiment, at pH 6.0 or higher, the glucoamylase possesses at least about 50%, about 51%, about 52%, about 53%, about 54%, or about 55% activity relative to its maximum activity at the optimum pH. In another embodiment, for a pH range of 6.0 to 7.5, HgGA can have at least 53% activity relative to its maximum activity. In another embodiment, at pH 6.0, TrGA can have at least 50% activity relative to its maximum activity. In one embodiment, a glucoamylase (e.g. HgGA) has 67% maximal activity at pH 7.0. In another embodiment, a glucoamylase (e.g., TrGA) has 66% maximal activity at pH 5.25.

[0121] In one embodiment, the glucoamylase may be dosed at the range of about 0.2 to 2.0 GAU /g dss, about 0.5 to 1.5 GAU /g dss, or 1.0 to 1.5 GAU /g dss. In another embodiment, glucoamylase (e.g., TrGA) can be used at a dose of about 1 GAU/ gds starch, 2 GAU/ gds starch, 3 GAU/ gds starch, 4 GAU/ gds starch, or 5 GAU/ gds starch. In one embodiment, glucoamylase (e.g., HgGA) can be used at a dose of about 0.25 to 1 GAU/ gds starch. In another embodiment, glucoamylase (e.g., HgGA) can be used at a dose of about 0.25 GAU/ gds starch, 0.5 GAU/ gds starch, 0.75 GAU/ gds starch, or 1 GAU/ gds starch. The saccharification may be performed at about 30 to about 60°C, or about 40 to about 60°C. In some embodiments, the saccharification occurs at ph 7.0 at 32°C. In other embodiments, the saccharification occurs at ph 6.5 at 58°C.

[0122] A full saccharification step may typically range 24 to 96 hours, 24 to 72 hours, or 24 to 48 hours. In some embodiments, saccharification occurs after about 2, 4, 6, 7.7, 8, 110, 14, 16, 18, 20, 22, 23.5, 24, 26, 28, 30, 31.5, 34, 36, 38, 40, 42, 44, 46, or 48 hours.. In some embodiments, the saccharification step and fermentation step are combined and the process is referred to as simultaneous saccharification and fermentation (SSF).

[0123] It is understood that generally, as time elapses, the enzymes (glucoamylase with or without other enzymes, such as alpha-amylases or non-starch polysaccharide hydrolyzing enzyme) reduces the higher sugars to lower DP sugars (such as DPI). The sugar profile can be varied by using different parameters, such as, but not limited to, starting starch substrate, temperature, amount of glucoamylase, type of glucoamylase, and pH. For example, in one embodiment, at 32 degrees Celsius and pH 7.0, the sugar or oligosaccharide distribution during the saccharification process can be between about 0.36% to about 96.50% DPI, about 3.59% to about 11.80% DP2, about 0.12% to about 7.75%, and/or about 2.26% to about 88.30% for higher sugars for HgGA. In another embodiment, at 32 degrees Celsius and pH 7.0, the sugar distribution during the saccharification process can be between about 0.36% to about 79.19% DPI, between about 3.59% to about 9.92% DP2, about 0.17% to about 9.10% DP3 and/or about 17.15% to about 88.30% for higher sugars for TrGA. Thus, in one embodiment, using HgGA, the DPI content can reach more than 90% after 24 hours. After 45 hours, the DPI content can reach more than 96%, while the content of higher sugars can decrease to less than 3%. Using TrGA, more than 70% DPI can be obtained after 24 hours. After 45 hours, the DPI content can reach about 80%, while the content of higher sugars can drop to less than 20%.

[0124] In another embodiment, at 58 degrees Celsius and pH 6.5, the sugar distribution during the saccharification process can be between about 60.66% to about 93.67% DPI, between about 1.49% to about 8.87% DP2, about 0.33% to about 1.93% DP3 and/or about 4.51% to about 28.17% for higher sugars for HgGA. In other embodiments, at 58 degrees Celsius and pH 6.5, the sugar or oligosaccharide distribution during the saccharification process can be between about 37.08% to about 75.25% DPI, about 5.48% to about 10.19% DP2, about 0.46% to about 5.06%, and/or about 18.37% to about 47.47% for higher sugars for TrGA. Thus, in one embodiment, using HgGA, the DPI content can reach more than 90% after 24 hours. After 48 hours, the DPI content can reach more than 93%, while the content of higher sugars can decrease to less than 5%. Using TrGA, more than 70% DPI can be obtained after 24 hours. After 45 hours, the DPI content can reach about 75%, while the content of higher sugars can drop to about 18%.

[0125] In yet another embodiment, at 58 degrees Celsius and pH 6.5, glucoamylases disclosed herein can be used to saccharify a starch substrate where high sugars (e.g., DP4+) is reduced. In some embodiments, the sugar or oligosaccharide distribution during the saccharification process can be between about 81.10% to about 90.36% DPI, about 1.99% to about 3.96% DP2, about 0.49% to about 0.61% DP3, about 4.48% to about 16.13% DP4+ for TrGA. In other embodiments, the sugar or oligosaccharide distribution during the saccharification process can be between about 93.15% to about 95.33% DPI, about 2.10% to about 3.94% DP2, about 0.53% to about 1.00% DP3, about 0.94% to about 3.76% DP4+ for HgGA.

[0126] In yet another embodiment, at 58 degrees Celsius and pH 6.4, the sugar or oligosaccharide distribution during the saccharification process can be between about 93.79% to about 96.9% DPI, about 1.55% to about 3.02% DP2, about 0.2% to about 0.49% DP3 and about 0% to about 3.98% DP4+ for HgGA. In some cases, about 93% solubility and about 96.9% glucose yield can be achieved within 24 hours. Continuous saccharification can result in 99% solubility and about 96.8% glucose after about 48 hours.

[0127] In another embodiment, at 58 degrees Celsius and pH 6.4, the sugar or

oligosaccharide distribution during the saccharification process can be between about 75.08% to about 96.5% DPI, 1.57% to about 9.16% DP2, 0.67% to about 15.76% DP3+. In some cases, HgGA can maintain a significant amount of glucoamylase activity for about 52 hours at pH6.4 to yield continued production of DPI products, DP2 products, and increase of percentage of soluble solids. Increased amounts of HgGA can result in increased rates of percentage solubilization and DPI production.

[0128] In some embodiments, the invention can be used to produce DP2 sugars for fermentation by yeast. For example, DP2 sugars can be produced from about 3.59% to about 11.80% DP2, from about 3.59% to about 9.92% DP2, from about 1.49% to about 8.87% DP2, from about 5.48% to about 10.19% DP2, from about 1.99% to about 3.96% DP2, from about 2.10% to about 3.94% DP2, from about 1.55% to about 3.02% DP2, or from about 1.57% to about 9.16% DP2.

Fermentation

[0129] In some embodiments of the present disclosure, the fermentable sugars may be subject to batch or continuous fermentation conditions. A classical batch fermentation is a closed system, wherein the composition of the medium is set at the beginning of the fermentation and is not subject to artificial alterations during the fermentation. Thus, at the beginning of the fermentation the medium may be inoculated with the desired organism(s), e.g., a microorganism engineered to produce isoprenoids. In this method, fermentation can be permitted to occur without the addition of any components to the system. Typically, a batch fermentation qualifies as a "batch" with respect to the addition of the carbon source and attempts are often made at controlling factors such as pH and oxygen concentration. The metabolite and biomass compositions of the batch system change constantly up to the time the fermentation is stopped. Within batch cultures, cells progress through a static lag phase to a high growth log phase, and finally to a stationary phase where growth rate is diminished or halted. If untreated, cells in the stationary phase eventually die. In general, cells in log phase are responsible for the bulk of production of the end product.

[0130] A variation on the standard batch system is the "fed-batch fermentation" system, which may be used in some embodiments of the present disclosure. In this variation of a typical batch system, the substrate can be added in increments as the fermentation progresses. Fed-batch systems are particularly useful when catabolite repression is apt to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the medium. Measurement of the actual substrate concentration in fed-batch systems may be difficult and is therefore estimated on the basis of the changes of measurable factors such as H, dissolved oxygen and the partial pressure of waste gases such as C0 ₂ . Both batch and fed-batch fermentations are common and well known in the art.

[0131] On the other hand, continuous fermentation is an open system where a defined fermentation medium can be added continuously to a bioreactor and an equal amount of conditioned medium can be removed simultaneously for processing. Continuous

fermentation generally maintains the cultures at a constant high density where cells are primarily in log phase growth. Continuous fermentation allows for the modulation of one factor or any number of factors that affect cell growth and/or end product concentration. For example, in one embodiment, a limiting nutrient such as the carbon source or nitrogen source can be maintained at a fixed rate while all other parameters are allowed to moderate. In other systems, a number of factors affecting growth can be altered continuously while the cell concentration, measured by media turbidity, may be kept constant. Continuous systems strive to maintain steady state growth conditions. Thus, cell loss due to medium being drawn off must be balanced against the cell growth rate in the fermentation. Methods of modulating nutrients and growth factors for continuous fermentation processes as well as techniques for maximizing the rate of product formation are well known in the art of industrial

microbiology.

[0132] In further embodiments, by use of appropriate fermenting microorganisms as known in the art, the fermentation end product may include without limitation alcohol, 1,3- propanediol, succinic acid, lactic acid, amino acids, proteins, functional oligosaccharides, and derivatives thereof. See e.g., WO 2008/086811 (methanol, ethanol, propanol, and butanol fermentation); WO 2003/066816, U.S. Patent Nos. 5,254,467 and 6,303,352 (1,3-propanediol fermentation); U.S. Patent Nos. RE 37,393, 6,265, 190, and 6,596,521 (succinic acid fermentation); U.S. Patent No. 5,464,760, WO 2003/095659, Mercier et al, /. Chem. Tech. Biotechnol. 55: 111-121, Zhang and Cheryan, Biotechnol. Lett. 13: 733-738 (1991), Linko and Javanainen, Enzyme Microb. Technol. 19: 118- 123 (1996), and Tsai and Moon, Appl. Biochem. Biotechnol. 70-72: 417-428 (1998) (lactic acid fermentation); U.S. Patent Nos. 7,320,882, 7,332,309, 7,666,634, and Zhang et al., Appl. Microbiol. Biotechnol. 77: 355-366 (2007) (fermentation of various amino acids).

Recombinant cells capable of increased production of isoprenoid precursors and/or isoprenoids

[0133] Isoprenoids can be produced in many organisms from the synthesis of the isoprenoid precursor molecules which are the end products of the MVA pathway. As stated above, isoprenoids represent an important class of compounds and include, for example, food and feed supplements, flavor and odor compounds, and anticancer, antimalarial, antifungal, and antibacterial compounds.

[0134] As a class of molecules, isoprenoids are classified based on the number of isoprene units comprised in the compound. Monoterpenes comprise ten carbons or two isoprene units, sesquiterpenes comprise 15 carbons or three isoprene units, diterpenes comprise 20 carbons or four isoprene units, sesterterpenes comprise 25 carbons or five isoprene units, and so forth. Steroids (generally comprising about 27 carbons) are the products of cleaved or rearranged isoprenoids.

[0135] Isoprenoids can be produced from the isoprenoid precursor molecules IPP and DMAPP. These diverse compounds are derived from these rather simple universal precursors and are synthesized by groups of conserved polyprenyl pyrophosphate synthases (Hsieh et al, Plant Physiol. 2011 Mar; 155(3): 1079-90). The various chain lengths of these linear prenyl pyrophosphates, reflecting their distinctive physiological functions, in general are determined by the highly developed active sites of polyprenyl pyrophosphate synthases via condensation reactions of allylic substrates (dimethylallyl diphosphate (C5-DMAPP), geranyl pyrophosphate (C1 ₀ -GPP), farnesyl pyrophosphate (C15-FPP), geranylgeranyl pyrophosphate (C20-GGPP)) with corresponding number of isopentenyl pyrophosphates (C5- IPP) (Hsieh et al, Plant Physiol. 2011 Mar;155(3): 1079-90).

[0136] Production of isoprenoid precursors and/or isoprenoid can be made by using any of the recombinant host cells disclosed herein, in particular by using the SSF methodology with the glucoamylases and/or other enzyme combinations disclosed herein. In some aspects, these cells comprise one or more heterologous nucleic acids encoding polypeptides of the MVA pathway, IDI, and/or the DXP pathway, as described above, and a heterologous nucleic acid encoding a polyprenyl pyrophosphate synthase polypeptide. Without being bound to theory, it is thought that increasing the cellular production of mevalonate in bacterial cells by any of the compositions and methods described above will similarly result in the production of higher amounts of isoprenoid precursor molecules and/or isoprenoids. Increasing the molar yield of mevalonate production from glucose translates into higher molar yields of isoprenoid precursor molecules and/or isoprenoids,produced from glucose when combined with appropriate enzymatic activity levels of mevalonate kinase, phosphomevalonate kinase, diphosphomevalonate decarboxylase, isopentenyl diphosphate isomerase and other appropriate enzymes for isoprenoid production. Types of isoprenoids

[0137] The cells of the present invention are capable of increased production of isoprenoids and the isoprenoid precursor molecules DMAPP and IPP. Examples of isoprenoids include, without limitation, hemiterpenoids, monoterpenoids, sesquiterpenoids, diterpenoids, sesterterpenoids, triterpenoids, tetraterpenoids, and higher polyterpenoids. In some aspects, the hemiterpenoid is prenol {i.e., 3-methyl-2-buten- l-ol), isoprenol {i.e. , 3-methyl-3-buten-l- ol), 2-methyl-3-buten-2-ol, or isovaleric acid. In some aspects, the monoterpenoid can be, without limitation, geranyl pyrophosphate, eucalyptol, limonene, or pinene. In some aspects, the sesquiterpenoid is farnesyl pyrophosphate, artemisinin, or bisabolol. In some aspects, the diterpenoid can be, without limitation, geranylgeranyl pyrophosphate, retinol, retinal, phytol, taxol, forskolin, or aphidicolin. In some aspects, the triterpenoid can be, without limitation, squalene or lanosterol. The isoprenoid can also be selected from the group consisting of abietadiene, amorphadiene, carene, farnesene, a-famesene, β-farnesene, farnesol, geraniol, geranylgeraniol, linalool, limonene, myrcene, nerolidol, ocimene, patchoulol, β-pinene, sabinene, γ-terpinene, terpindene and valencene.

[0138] In some aspects, the tetraterpenoid is lycopene or carotene (a carotenoid). As used herein, the term "carotenoid" refers to a group of naturally- occurring organic pigments produced in the chloroplasts and chromoplasts of plants, of some other photo synthetic organisms, such as algae, in some types of fungus, and in some bacteria. Carotenoids include the oxygen-containing xanthophylls and the non-oxygen-containing carotenes. In some aspects, the carotenoids are selected from the group consisting of xanthophylls and carotenes. In some aspects, the xanthophyll is lutein or zeaxanthin. In some aspects, the carotenoid is a- carotene, β-carotene, γ-carotene, β-cryptoxanthin or lycopene.

Heterologous nucleic acids encoding polyprenyl pyrophosphate synthases polypeptides

[0139] In some aspects of the invention, the recombinant cells described in any of the compositions or methods herein comprising acetoacetyl-CoA synthase further comprise one or more nucleic acids encoding a non-thiolase MVA pathway polypeptide(s), as described above, as well as one or more nucleic acids encoding a polyprenyl pyrophosphate synthase polypeptides(s). The polyprenyl pyrophosphate synthase polypeptide can be an endogenous polypeptide. The endogenous nucleic acid encoding a polyprenyl pyrophosphate synthase polypeptide can be operably linked to a constitutive promoter or can similarly be operably linked to an inducible promoter. The endogenous nucleic acid encoding a polyprenyl pyrophosphate synthase polypeptide can additionally be operably linked to a strong promoter. Alternatively, the endogenous nucleic acid encoding a polyprenyl pyrophosphate synthase polypeptide can be operably linked to a weak promoter. In particular, the cells can be engineered to over-express the endogenous polyprenyl pyrophosphate synthase polypeptide relative to wild-type cells.

[0140] In some aspects, the polyprenyl pyrophosphate synthase polypeptide is a heterologous polypeptide. The cells of the present invention can comprise more than one copy of a heterologous nucleic acid encoding a polyprenyl pyrophosphate synthase polypeptide. In some aspects, the heterologous nucleic acid encoding a polyprenyl pyrophosphate synthase polypeptide is operably linked to a constitutive promoter. In some aspects, the heterologous nucleic acid encoding a polyprenyl pyrophosphate synthase polypeptide is operably linked to an inducible promoter. In some aspects, the heterologous nucleic acid encoding a polyprenyl pyrophosphate synthase polypeptide is operably linked to a strong promoter. In some aspects, the heterologous nucleic acid encoding a polyprenyl pyrophosphate synthase polypeptide is operably linked to a weak promoter.

[0141] The nucleic acids encoding a polyprenyl pyrophosphate synthase polypeptide(s) can be integrated into a genome of the host cells or can be stably expressed in the cells. The nucleic acids encoding a polyprenyl pyrophosphate synthase polypeptide(s) can additionally be on a vector.

[0142] Exemplary polyprenyl pyrophosphate synthase nucleic acids include nucleic acids that encode a polypeptide, fragment of a polypeptide, peptide, or fusion polypeptide that has at least one activity of a polyprenyl pyrophosphate synthase. Polyprenyl pyrophosphate synthase polypeptides convert isoprenoid precursor molecules into more complex isoprenoid compounds. Exemplary polyprenyl pyrophosphate synthase polypeptides include

polypeptides, fragments of polypeptides, peptides, and fusions polypeptides that have at least one activity of a polyprenyl pyrophosphate synthase polypeptide. Exemplary polyprenyl pyrophosphate synthase polypeptides and nucleic acids include naturally- occurring polypeptides and nucleic acids from any of the source organisms described herein. In addition, variants of polyprenyl pyrophosphate synthase can possess improved activity such as improved enzymatic activity. In some aspects, a polyprenyl pyrophosphate synthase variant has other improved properties, such as improved stability (e.g., thermo-stability), and/or improved solubility. Exemplary polyprenyl pyrophosphate synthase nucleic acids can include nucleic acids which encode polyprenyl pyrophosphate synthase polypeptides such as, without limitation, geranyl diphosposphate (GPP) synthase, farnesyl pyrophosphate (FPP) synthase, and geranylgeranyl pyrophosphate (GGPP) synthase, or any other known polyprenyl pyrophosphate synthase polypeptide.

[0143] In some aspects of the invention, the cells described in any of the compositions or methods herein further comprise one or more nucleic acids encoding a farnesyl

pyrophosphate (FPP) synthase. The FPP synthase polypeptide can be an endogenous polypeptide encoded by an endogenous gene. In some aspects, the FPP synthase polypeptide is encoded by an endogenous ispA gene in E. coli. The endogenous nucleic acid encoding an FPP synthase polypeptide can be operably linked to a constitutive promoter or can similarly be operably linked to an inducible promoter. The endogenous nucleic acid encoding an FPP synthase polypeptide can additionally be operably linked to a strong promoter. In particular, the cells can be engineered to over-express the endogenous FPP synthase polypeptide relative to wild- type cells.

[0144] In some aspects, the FPP synthase polypeptide is a heterologous polypeptide. The cells of the present invention can comprise more than one copy of a heterologous nucleic acid encoding a FPP synthase polypeptide. In some aspects, the heterologous nucleic acid encoding a FPP synthase polypeptide is operably linked to a constitutive promoter. In some aspects, the heterologous nucleic acid encoding a FPP synthase polypeptide is operably linked to an inducible promoter. In some aspects, the heterologous nucleic acid encoding a polyprenyl pyrophosphate synthase polypeptide is operably linked to a strong promoter.

[0145] The nucleic acids encoding an FPP synthase polypeptide can be integrated into a genome of the host cells or can be stably expressed in the cells. The nucleic acids encoding an FPP synthase can additionally be on a vector.

[0146] Standard methods can be used to determine whether a polypeptide has polyprenyl pyrophosphate synthase polypeptide activity by measuring the ability of the polypeptide to convert IPP into higher order isoprenoids in vitro, in a cell extract, or in vivo. These methods are well known in the art and are described, for example, in U.S. Patent No.: 7,915,026; Hsieh et al., Plant Physiol. 2011 Mar;155(3): 1079-90; Danner et al., Phytochemistry . 2011 Apr 12 [Epub ahead of print]; Jones et al., / Biol Chem. 2011 Mar 24 [Epub ahead of print] ; Keeling et al., BMC Plant Biol. 2011 Mar 7; l l:43; Martin et al., BMC Plant Biol. 2010 Oct 21 ; 10:226; Kumeta & Ito, Plant Physiol. 2010 Dec;154(4): 1998-2007; and Kollner & Boland, J Org Chem. 2010 Aug 20;75(16):5590-600. MVA Pathway

[0147] In some aspects of the invention, the cells described in any of the compositions or methods described herein comprise a nucleic acid encoding an MVA pathway polypeptide. In some embodiments, the MVA pathway polypeptide is an endogenous polypeptide. In some embodiments, the cells comprise one or more additional copies of an endogenous nucleic acid encoding an MVA pathway polypeptide. In some embodiments, the endogenous nucleic acid encoding an MVA pathway polypeptide operably linked to a constitutive promoter. In some embodiments, the endogenous nucleic acid encoding an MVA pathway polypeptide operably linked to a constitutive promoter. In some embodiments, the endogenous nucleic acid encoding an MVA pathway polypeptide is operably linked to a strong promoter. In a particular embodiment, the cells are engineered to over-express the endogenous MVA pathway polypeptide relative to wild-type cells.

[0148] In some embodiments, the MVA pathway polypeptide is a heterologous polypeptide. In some embodiments, the cells comprise more than one copy of a heterologous nucleic acid encoding an MVA pathway polypeptide. In some embodiments, the

heterologous nucleic acid encoding an MVA pathway polypeptide is operably linked to a constitutive promoter. In some embodiments, the heterologous nucleic acid encoding an MVA pathway polypeptide is operably linked to a strong promoter.

[0149] Exemplary MVA pathway polypeptides include acetyl-CoA acetyltransferase (AA- CoA thiolase) polypeptides, 3-hydroxy-3-methylglutaryl-CoA synthase (HMG-CoA synthase) polypeptides, 3-hydroxy-3-methylglutaryl-CoA reductase (HMG-CoA reductase) polypeptides, mevalonate kinase (MVK) polypeptides, phosphomevalonate kinase (PMK) polypeptides, diphosphomevalonate decarboxylase (MVD) polypeptides, phosphomevalonate decarboxylase (PMDC) polypeptides, isopentenyl phosphate kinase (IPK) polypeptides, IDI polypeptides, and polypeptides (e.g., fusion polypeptides) having an activity of two or more MVA pathway polypeptides. In particular, MVA pathway polypeptides include

polypeptides, fragments of polypeptides, peptides, and fusions polypeptides that have at least one activity of an MVA pathway polypeptide. Exemplary MVA pathway nucleic acids include nucleic acids that encode a polypeptide, fragment of a polypeptide, peptide, or fusion polypeptide that has at least one activity of an MVA pathway polypeptide. Exemplary MVA pathway polypeptides and nucleic acids include naturally-occurring polypeptides and nucleic acids from any of the source organisms described herein. In addition, variants of MVA pathway polypeptide that confer the result of better isoprenoid production can also be used as well.

[0150] In some embodiments, feedback resistant mevalonate kinase polypeptides can be used to increase the production of isoprenoids. As such, the invention provides methods for producing isoprenoids wherein the host cells further comprise (i) one or more non-modified nucleic acids encoding feedback-resistant mevalonate kinase polypeptides or (ii) one or more additional copies of an endogenous nucleic acid encoding a feedback-resistant mevalonate kinase polypeptide. Non-limiting examples of mevalonate kinase which can be used include: archaeal mevalonate kinase (e.g., from M. mazei, Lactobacillus mevalonate kinase polypeptide, Lactobacillus sakei mevalonate kinase polypeptide, yeast mevalonate kinase polypeptide, Streptococcus mevalonate kinase polypeptide, Streptococcus pneumoniae mevalonate kinase polypeptide, Streptomyces mevalonate kinase polypeptide, Streptomyces CL190 mevalonate kinase polypeptide, and M. Burtonii mevalonate kinase polypeptide).

[0151] In another embodiment, aerobes are engineered with polyprenyl pyrophosphate synthase using standard techniques known to one of skill in the art. In another embodiment, anaerobes are engineered with polyprenyl pyrophosphate synthase and one or more MVA pathway polypeptides using standard techniques known to one of skill in the art. In yet another embodiment, either aerobes or anaerobes are engineered with polyprenyl pyrophosphate synthase, one or more MVA pathway polypeptides and/or one or more DXP pathway polypeptides using standard techniques known to one of skill in the art.

[0152] Types of MVA pathway polypeptides and/or DXP pathway polypeptides which can be used and methods of making microorganisms (e.g., facultative anaerobes such as E. coli) encoding MVA pathway polypeptides and/or DXP pathway polypeptides are also described in International Patent Application Publication No. WO2009/076676; U.S. Publ.

20100048964, US Publ. 2010/0086978, US Publ. 2010/0167370, US Publ. 2010/0113846, US Publ. 2010/0184178, and US Publ. 2010/0167371 ; U.S. Publ. 2011/0014672, U.S. Publ. 2010/0196977, and US Publ. 2011/0046422; WO 2004/033646 and WO 96/35796.

[0153] One of skill in the art can readily select and/or use suitable promoters to optimize the expression of polyprenyl pyrophosphate synthase or and one or more MVA pathway polypeptides and/or one or more DXP pathway polypeptides in anaerobes. Similarly, one of skill in the art can readily select and/or use suitable vectors (or transfer vehicle) to optimize the expression of polyprenyl pyrophosphate synthase or and one or more MVA pathway polypeptides and/or one or more DXP pathway polypeptides in anaerobes. In some embodiments, the vector contains a selective marker. Examples of selectable markers include, but are not limited to, antibiotic resistance nucleic acids (e.g. , kanamycin, ampicillin, carbenicillin, gentamicin, hygromycin, phleomycin, bleomycin, neomycin, or

chloramphenicol) and/or nucleic acids that confer a metabolic advantage, such as a nutritional advantage on the host cell. In some embodiments, an polyprenyl pyrophosphate synthase or MVA pathway nucleic acid integrates into a chromosome of the cells without a selective marker.

[0154] In some embodiments, the vector is a shuttle vector, which is capable of propagating in two or more different host species. Exemplary shuttle vectors are able to replicate in E. coli and/or Bacillus subtilis and in an obligate anaerobe, such as Clostridium. Upon insertion of an polyprenyl pyrophosphate synthase or MVA pathway nucleic acid into the shuttle vector using techniques well known in the art, the shuttle vector can be introduced into an E. coli host cell for amplification and selection of the vector. The vector can then be isolated and introduced into an obligate anaerobic cell for expression of the polyprenyl pyrophosphate synthase or MVA pathway polypeptide.

Exemplary IDI Polypeptides and Nucleic Acids

[0155] Isopentenyl diphosphate isomerase polypeptides (isopentenyl-diphosphate delta- isomerase or IDI) catalyses the interconversion of isopentenyl diphosphate (IPP) and dimethyl allyl diphosphate (DMAPP) (e.g. , converting IPP into DMAPP and/or converting DMAPP into IPP). While not intending to be bound by any particular theory, it is believed that increasing the amount of IDI polypeptide in cells increases the amount (and conversion rate) of IPP that is converted into DMAPP, which in turn is converted into an isoprenoid product. Exemplary IDI polypeptides include polypeptides, fragments of polypeptides, peptides, and fusions polypeptides that have at least one activity of an IDI polypeptide.

Standard methods can be used to determine whether a polypeptide has IDI polypeptide activity by measuring the ability of the polypeptide to interconvert IPP and DMAPP in vitro, in a cell extract, or in vivo. Exemplary IDI nucleic acids include nucleic acids that encode a polypeptide, fragment of a polypeptide, peptide, or fusion polypeptide that has at least one activity of an IDI polypeptide. Exemplary IDI polypeptides and nucleic acids include naturally- occurring polypeptides and nucleic acids from any of the source organisms described herein as well as mutant polypeptides and nucleic acids derived from any of the source organisms described herein. Exemplary DXP Pathway Polypeptides and Nucleic Acids

[0156] DXS and IDI polypeptides are part of the DXP pathway for the biosynthesis of isoprenoids. l-deoxy-D-xylulose-5-phosphate synthase (DXS) polypeptides convert pyruvate and D-glyceraldehyde-3-phosphate into l-<ieo y-D-xylulose-5-phosphate. While not intending to be bound by any particular theory, it is believed that increasing the amount of DXS polypeptide increases the flow of carbon through the DXP pathway, leading to greater production of isoprenoids.

[0157] Exemplary DXS polypeptides include polypeptides, fragments of polypeptides, peptides, and fusions polypeptides that have at least one activity of a DXS polypeptide. Standard methods known to one of skill in the art and as taught the references cited herein can be used to determine whether a polypeptide has DXS polypeptide activity by measuring the ability of the polypeptide to convert pyruvate and D-glyceraldehyde-3-phosphate into 1- deoxy-D-xylulose-5-phosphate in vitro, in a cell extract, or in vivo. Exemplary DXS nucleic acids include nucleic acids that encode a polypeptide, fragment of a polypeptide, peptide, or fusion polypeptide that has at least one activity of a DXS polypeptide. Exemplary DXS polypeptides and nucleic acids include naturally-occurring polypeptides and nucleic acids from any of the source organisms described herein as well as mutant polypeptides and nucleic acids derived from any of the source organisms described herein. Exemplary DXS polypeptides and nucleic acids and methods of measuring DXS activity are described in more detail in International Publication No. WO 2009/076676, U.S. Patent Application No.

12/335,071 (US Publ. No. 2009/0203102), WO 2010/003007, US Publ. No. 2010/0048964, WO 2009/132220, and US Publ. No. 2010/0003716.

[0158] Exemplary DXP pathways polypeptides include, but are not limited to any of the following polypeptides: DXS polypeptides, DXR polypeptides, MCT polypeptides, CMK polypeptides, MCS polypeptides, HDS polypeptides, HDR polypeptides, and polypeptides {e.g. , fusion polypeptides) having an activity of one, two, or more of the DXP pathway polypeptides. In particular, DXP pathway polypeptides include polypeptides, fragments of polypeptides, peptides, and fusions polypeptides that have at least one activity of a DXP pathway polypeptide. Exemplary DXP pathway nucleic acids include nucleic acids that encode a polypeptide, fragment of a polypeptide, peptide, or fusion polypeptide that has at least one activity of a DXP pathway polypeptide. Exemplary DXP pathway polypeptides and nucleic acids include naturally- occurring polypeptides and nucleic acids from any of the source organisms described herein as well as mutant polypeptides and nucleic acids derived from any of the source organisms described herein. Exemplary DXP pathway polypeptides and nucleic acids and methods of measuring DXP pathway polypeptide activity are described in more detail in International Publication No.: WO 2010/148150.

[0159] In particular, DXS polypeptides convert pyruvate and D-glyceraldehyde 3- phosphate into 1-deoxy-d-xylulose 5-phosphate (DXP). Standard methods can be used to determine whether a polypeptide has DXS polypeptide activity by measuring the ability of the polypeptide to convert pyruvate and D-glyceraldehyde 3 -phosphate in vitro, in a cell extract, or in vivo.

[0160] DXR polypeptides convert 1-deoxy-d-xylulose 5-phosphate (DXP) into 2-C- methyl-D-erythritol 4-phosphate (MEP). Standard methods can be used to determine whether a polypeptide has DXR polypeptides activity by measuring the ability of the polypeptide to convert DXP in vitro, in a cell extract, or in vivo.

[0161] MCT polypeptides convert 2-C-methyl-D-erythritol 4-phosphate (MEP) into 4- (cytidine 5'-diphospho)-2-methyl-D-erythritol (CDP-ME). Standard methods can be used to determine whether a polypeptide has MCT polypeptides activity by measuring the ability of the polypeptide to convert MEP in vitro, in a cell extract, or in vivo.

[0162] CMK polypeptides convert 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol (CDP-ME) into 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol (CDP-MEP). Standard methods can be used to determine whether a polypeptide has CMK polypeptides activity by measuring the ability of the polypeptide to convert CDP-ME in vitro, in a cell extract, or in vivo.

[0163] MCS polypeptides convert 2-phospho-4-(cytidine 5'-diphospho)-2-C-mefhyl-D- eryfhritol (CDP-MEP) into 2-C-methyl-D-erythritol 2, 4-cyclodiphosphate (ME-CPP or cMEPP). Standard methods can be used to determine whether a polypeptide has MCS polypeptides activity by measuring the ability of the polypeptide to convert CDP-MEP in vitro, in a cell extract, or in vivo.

[0164] HDS polypeptides convert 2-C-methyl-D-erythritol 2, 4-cyclodiphosphate into (E)- 4-hydroxy-3-methylbut-2-en-l-yl diphosphate (HMBPP or HDMAPP). Standard methods can be used to determine whether a polypeptide has HDS polypeptides activity by measuring the ability of the polypeptide to convert ME-CPP in vitro, in a cell extract, or in vivo.

[0165] HDR polypeptides convert (E)-4-hydroxy-3-mefhylbut-2-en-l-yl diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Standard methods can be used to determine whether a polypeptide has HDR polypeptides activity by measuring the ability of the polypeptide to convert HMBPP in vitro, in a cell extract, or in vivo.

[0166] In some embodiments, the DXS or DXP pathway polypeptide is an endogenous polypeptide. In some embodiments, the cells comprise one or more additional copies of an endogenous nucleic acid encoding a DXS or DXP pathway polypeptide. In other embodiments, the DXS or DXP pathway polypeptide is a heterologous polypeptide. In some embodiments, the cells comprise more than one copy of a heterologous nucleic acid encoding an DXS or DXP pathway polypeptide. In any of the embodiments herein, the nucleic acid is operably linked to a promoter (e.g., inducible or constitutive promoter).

Source Organisms

[0167] Polyprenyl pyrophosphate synthase and/or MVA pathway nucleic acids (and their encoded polypeptides) and/or DXP pathway nucleic acids (and their encoded polypeptides) can be obtained from any organism that naturally contains polyprenyl pyrophosphate synthase and/or MVA pathway nucleic acids and/or DXP pathway nucleic acids. Some organisms contain the MVA pathway for producing isoprenoids. Polyprenyl pyrophosphate synthase nucleic acids can be obtained, e.g. , from any organism that contains an polyprenyl pyrophosphate synthase. MVA pathway nucleic acids can be obtained, e.g. , from any organism that contains the MVA pathway. DXP pathway nucleic acids can be obtained, e.g. , from any organism that contains the DXP pathway.

Host cells

[0168] Various types of host cells can be used to produce isoprenoids as part of a biologically produced composition. In some embodiments, the host cell is a yeast, such as Saccharomyces sp., Schizosaccharomyces sp. , Pichia sp., Candida sp. or Y. lipolytica.

[0169] In some embodiments, the host cell is a bacterium, such as strains of Bacillus such as B. lichenformis or B. subtilis, strains of Pantoea such as P. citrea, strains of Pseudomonas such as P. alcaligenes, strains of Streptomyces such as S. lividans or S. rubiginosus, strains of Escherichia such as E. coli, strains of Enterobacter, strains of Streptococcus, or strains of Archaea such as Methanosarcina mazei, and strains of Corynebacterium such as C.

glutamicum.

[0170] As used herein, "the genus Bacillus" includes all species within the genus

"Bacillus " as known to those of skill in the art, including but not limited to B. subtilis, B. licheniformis, B. lentus, B. brevis, B. stearothermophilus, B. alkalophilus, B. amyloliquefaciens, B. clausii, B. halodurans, B. megaterium, B. coagulans, B. circulans, B. lautus, and B. thuringiensis . It is recognized that the genus Bacillus continues to undergo taxonomical reorganization. Thus, it is intended that the genus include species that have been reclassified, including but not limited to such organisms as B. stearothermophilus, which is now named "Geobacillus stearothermophilus ." The production of resistant endospores in the presence of oxygen is considered the defining feature of the genus Bacillus, although this characteristic also applies to the recently named Alley clobacillus , Amphibacillu ,

Aneurinibacillus , Anoxybacillus, Brevibacillus , Filobacillus, Gracilibacillus, Halobacillus, Paenibacillus, Salibacillus, Thermobacillus, Ureibacillus, and Virgibacillus .

[0171] In some embodiments, the host cell is a gram-positive bacterium. Non-limiting examples include strains of Streptomyces (e.g. , S. lividans, S. coelicolor, or S. griseus) and Bacillus. In some embodiments, the source organism is a gram-negative bacterium, such as E. coli or Pseudomonas sp.

[0172] In some embodiments, the host cell is a plant, such as a plant from the family Fabaceae, such as the Faboideae subfamily. In some embodiments, the source organism is kudzu, poplar (such as Populus alba x tremula CAC35696), aspen (such as Populus tremuloides), or Quercus robur.

[0173] In some embodiments, the host cell is an algae, such as a green algae, red algae, glaucophytes, chlorarachniophytes, euglenids, chromista, or dinoflagellates.

[0174] In some embodiments, the host cell is a cyanobacteria, such as cyanobacteria classified into any of the following groups based on morphology: Chroococcales,

Pleurocapsales, Oscillatoriales, Nostocales, or Stigonematales .

[0175] In some embodiments, the host cell is an anaerobic organisms. An "anaerobe" is an organism that does not require oxygen for growth. An anaerobe can be an obligate anaerobe, a facultative anaerobe, or an aerotolerant organism. Such organisms can be any of the organisms listed above, bacteria, yeast, etc. An "obligate anaerobe" is an anaerobe for which atmospheric levels of oxygen can be lethal. Examples of obligate anaerobes include, but are not limited to, Clostridium, Eurobacterium, Bacteroides, Peptostreptococcus,

Butyribacterium, Veillonella, and Actinomyces . In one embodiment, the obligate anaerobes can be any one or combination selected from the group consisting of Clostridium ljungdahlii, Clostridium autoethanogenum, Eurobacterium limosum, Clostridium carboxydivorans, Peptostreptococcus productus, and Butyribacterium methylotrophicum. A "facultative anaerobe" is an anaerobe that is capable of performing aerobic respiration in the presence of oxygen and is capable of performing anaerobic fermentation under oxygen-limited or oxygen-free conditions. Examples of facultative anaerobes include, but are not limited to, Escherichia, Pantoea, yeast, and Yarrowia.

[0176] In some embodiments, the host cell is a photo synthetic cell. In other embodiments, the host cell is a non-photosynthetic cell.

Transformation methods

[0177] Nucleic acids encoding polyprenyl pyrophosphate synthase and/or MVA pathway polypeptides and/or DXP pathway polypeptides can be inserted into any host cell using standard techniques for expression of the encoded polyprenyl pyrophosphate synthase and/or MVA pathway polypeptide. General transformation techniques are known in the art {see, e.g. , Current Protocols in Molecular Biology (F. M. Ausubel et al. (eds) Chapter 9, 1987; Sambrook et al., Molecular Cloning: A Laboratory Manual, 2 ^nd ed., Cold Spring Harbor, 1989; and Campbell et al, Curr. Genet. 16:53-56, 1989 or "Handbook on Clostridia" (P. Durre, ed., 2004). For obligate anaerobic host cells, such as Clostridium, electroporation, as described by Davis et al., 2005 and in Examples III and IV, can be used as an effective technique. The introduced nucleic acids may be integrated into chromosomal DNA or maintained as extrachromosomal replicating sequences.

[0178] Additionally, isoprenoid production by cells that contain a heterologous polyprenyl pyrophosphate synthase nucleic acid can be enhanced by increasing the amount of a 1-deoxy- D-xylulose-5-phosphate synthase (DXS) polypeptide and/or an isopentenyl diphosphate isomerase (IDI) polypeptide expressed by the cells.

[0179] Iron-sulfur cluster-interacting redox polypeptide can also be used to increase the activity demonstrated by the DXP pathway polypeptides (such as HDS (GcpE or IspG) or HDR polypeptide (IspH or LytB). While not intending to be bound to a particular theory, the increased expression of one or more endogenous or heterologous iron- sulfur interacting redox nucleic acids or polypeptides improve the rate of formation and the amount of DXP pathway polypeptides containing an iron sulfur cluster (such as HDS or HDR), and/or stabilize DXP pathway polypeptides containing an iron sulfur cluster (such as HDS or HDR). This in turn increases the carbon flux to isoprenoid synthesis in cells by increasing the synthesis of HMBPP and/or DMAPP and decreasing the cMEPP and HMBPP pools in the DXP pathway. Additional Host cell Mutations [0180] The invention also contemplates additional host cell mutations that increase carbon flux through the MVA pathway. By increasing the carbon flow, more isoprenoids can be produced. The recombinant cells as described herein can also be engineered for increased carbon flux towards mevalonate production wherein the activity of one or more enzymes from the group consisting of: (a) citrate synthase, (b) phosphotransacetylase; (c) acetate kinase; (d) lactate dehydrogenase; (e) NADP-dependent malic enzyme, and; (f) pyruvate dehydrogenase is modulated.

Citrate Synthase Pathway

[0181] Citrate synthase catalyzes the condensation of oxaloacetate and acetyl-CoA to form citrate, a metabolite of the Tricarboxylic acid (TCA) cycle (Ner, S. et al. 1983. Biochemistry 22: 5243-5249; Bhayana, V. and Duckworth, H. 1984. Biochemistry 23: 2900-2905). In E. coli, this enzyme, encoded by gltA, behaves like a trimer of dimeric subunits. The hexameric form allows the enzyme to be allosterically regulated by NADH. This enzyme has been widely studied (Wiegand, G., and Remington, S. 1986. Annual Rev. Biophysics Biophys. Chem.15: 97-117; Duckworth et al. 1987. Biochem Soc Symp. 54:83-92; Stockell, D. et al. 2003. J. Biol. Chem. 278: 35435-43; Maurus, R. et al. 2003. Biochemistry. 42:5555-5565). To avoid allosteric inhibition by NADH, replacement by or supplementation with the Bacillus s btilis NADH-insensitive citrate synthase has been considered (Underwood et al. 2002. Appl. Environ. Microbiol. 68: 1071-1081; Sanchez et al. 2005. Met. Eng. 7:229-239).

[0182] The reaction catalyzed by citrate synthase is directly competing with the thiolase catalyzing the first step of the mevalonate pathway, as they both have acetyl-CoA as a substrate (Hedl et al. 2002. 1. Bact. 184:2116-2122). Therefore, one of skill in the art can modulate citrate synthase expression (e.g., decrease enzyme activity) to allow more carbon to flux into the mevalonate pathway, thereby increasing the eventual production of mevalonate or isoprenoids. Decrease of citrate synthase activity can be any amount of reduction of specific activity or total activity as compared to when no manipulation has been effectuated. In some instances, the decrease of enzyme activity is decreased by at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%. In some aspects, the activity of citrate synthase is modulated by decreasing the activity of an endogenous citrate synthase gene. This can be accomplished by chromosomal replacement of an endogenous citrate synthase gene with a transgene encoding an NADH-insensitive citrate synthase or by using a transgene encoding an NADH-insensitive citrate synthase that is derived from Bacillus subtilis. The activity of citrate synthase can also be modulated (e.g., decreased) by replacing the endogenous citrate synthase gene promoter with a synthetic constitutively low expressing promoter. The decrease of the activity of citrate synthase can result in more carbon flux into the mevalonate dependent biosynthetic pathway in comparison to microorganisms that do not have decreased expression of citrate synthase.

Pathways involving Phosphotransacetylase and/or Acetate Kinase

[0183] Phosphotransacetylase (pta) (Shimizu et al. 1969. Biochim. Biophys. Acta 191 : 550-558) catalyzes the reversible conversion between acetyl-CoA and acetylphosphate (acetyl-P), while acetate kinase (ackA) (Kakuda, H. et al. 1994. J. Biochem. 11:916-922) uses acetyl-P to form acetate. These genes can be transcribed as an operon in E. coli. Together, they catalyze the dissimilation of acetate, with the release of ATP. Thus, one of skill in the art can increase the amount of available acetyl Co-A by attenuating the activity of

phosphotransacetylase gene (e.g., the endogenous phosphotransacetylase gene) and/or an acetate kinase gene (e.g., the endogenous acetate kinase gene). One way of achieving attenuation is by deleting phosphotransacetylase (pta) and/or acetate kinase (ackA). This can be accomplished by replacing one or both genes with a chloramphenicol cassette followed by looping out of the cassette. Acetate is produced by E. coli for a variety of reasons (Wolfe, A. 2005. Microb. Mol. Biol. Rev. 69: 12-50). Without being bound by theory, since ackA-pta use acetyl-CoA, deleting those genes might allow carbon not to be diverted into acetate and to increase the yield of mevalonate or isoprenoids.

[0184] In some aspects, the recombinant microorganism produces decreased amounts of acetate in comparison to microorganisms that do not have attenuated endogenous

phosphotransacetylase gene and/or endogenous acetate kinase gene expression. Decrease in the amount of acetate produced can be measured by routine assays known to one of skill in the art. The amount of acetate reduction is at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% as compared when no molecular

manipulations are done.

[0185] The activity of phosphotransacetylase (pta) and/or acetate kinase (ackA) can also be decreased by other molecular manipulation of the enzymes. The decrease of enzyme activity can be any amount of reduction of specific activity or total activity as compared to when no manipulation has been effectuated. In some instances, the decrease of enzyme activity is decreased by at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%.

[0186] In some cases, attenuating the activity of the endogenous phosphotransacetylase gene and/or the endogenous acetate kinase gene results in more carbon flux into the mevalonate dependent biosynthetic pathway in comparison to microorganisms that do not have attenuated endogenous phosphotransacetylase gene and/or endogenous acetate kinase gene expression.

Pathways Involving Lactate Dehydrogenase

[0187] In E. coli, D-Lactate is produced from pyruvate through the enzyme lactate dehydrogenase (IdhA) (Bunch, P. et al. 1997. Microbiol. 143: 187-195). Production of lactate is accompanied with oxidation of NADH, hence lactate is produced when oxygen is limited and cannot accommodate all the reducing equivalents. Thus, production of lactate could be a source for carbon consumption. As such, to improve carbon flow through to mevalonate production and isoprenoids production, one of skill in the art can modulate the activity of lactate dehydrogenase, such as by decreasing the activity of the enzyme.

[0188] Accordingly, in one aspect, the activity of lactate dehydrogenase can be modulated by attenuating the activity of an endogenous lactate dehydrogenase gene. Such attenuation can be achieved by deletion of the endogenous lactate dehydrogenase gene. Other ways of attenuating the activity of lactate dehydrogenase gene known to one of skill in the art may also be used. By manipulating the pathway that involves lactate dehydrogenase, the recombinant microorganism produces decreased amounts of lactate in comparison to microorganisms that do not have attenuated endogenous lactate dehydrogenase gene expression. Decrease in the amount of lactate produced can be measured by routine assays known to one of skill in the art. The amount of lactate reduction is at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% as compared when no molecular manipulations are done.

[0189] The activity of lactate dehydrogenase can also be decreased by other molecular manipulations of the enzyme. The decrease of enzyme activity can be any amount of reduction of specific activity or total activity as compared to when no manipulation has been effectuated. In some instances, the decrease of enzyme activity is decreased by at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%.

[0190] Accordingly, in some cases, attenuation of the activity of the endogenous lactate dehydrogenase gene results in more carbon flux into the mevalonate dependent biosynthetic pathway in comparison to microorganisms that do not have attenuated endogenous lactate dehydrogenase gene expression.

Pathways Involving Malic enzyme

[0191] Malic enzyme (in E. coli sfcA and maeB) is an anaplerotic enzyme that catalyzes the conversion of malate into pyruvate (using NAD+ or NADP+) by the equation below:

[0192] (S)-malate + NAD(P) ⁺ ^pyruvate + C0 ₂ + NAD(P)H

[0193] Thus, the two substrates of this enzyme are (S)-malate and NAD(P) ⁺ , whereas its 3 products are pyruvate, CO ₂ , and NADPH.

[0194] Expression of the NADP-dependent malic enzyme (maeB) (Iwikura, M. et al. 1979. J. Biochem. 85: 1355-1365) can help increase mevalonate and isoprenoid yield by 1) bringing carbon from the TCA cycle back to pyruvate, direct precursor of acetyl-CoA, itself direct precursor of the mevalonate pathway and 2) producing extra NADPH which could be used in the HMG-CoA reductase reaction (Oh, MK et al. (2002) J. Biol. Chem. 277: 13175- 13183; Bologna, F. et al. (2007) J. Bact. 189:5937-5946).

[0195] As such, more starting substrate (pyruvate or acetyl-CoA) for the downstream production of mevalonate and isoprenoids can be achieved by modulating, such as increasing, the activity and/or expression of malic enzyme. The NADP-dependent malic enzyme gene can be an endogenous gene. One non-limiting way to accomplish this is by replacing the endogenous NADP-dependent malic enzyme gene promoter with a synthetic constitutively expressing promoter. Another non-limiting way to increase enzyme activity is by using one or more heterologous nucleic acids encoding an NADP-dependent malic enzyme polypeptide. One of skill in the art can monitor the expression of maeB RNA during fermentation or culturing using readily available molecular biology techniques.

[0196] Accordingly, in some embodiments, the recombinant microorganism produces increased amounts of pyruvate in comparison to microorganisms that do not have increased expression of an NADP-dependent malic enzyme gene. In some aspects, increasing the activity of an NADP-dependent malic enzyme gene results in more carbon flux into the mevalonate dependent biosynthetic pathway in comparison to microorganisms that do not have increased NADP-dependent malic enzyme gene expression.

[0197] Increase in the amount of pyruvate produced can be measured by routine assays known to one of skill in the art. The amount of pyruvate increase can be at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% as compared when no molecular manipulations are done.

[0198] The activity of malic enzyme can also be increased by other molecular

manipulations of the enzyme. The increase of enzyme activity can be any amount of increase of specific activity or total activity as compared to when no manipulation has been effectuated. In some instances, the increase of enzyme activity is at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%.

Pathways Involving Pyruvate Dehydrogenase Complex

[0199] The pyruvate dehydrogenase complex, which catalyzes the decarboxylation of pyruvate into acetyl-CoA, is composed of the proteins encoded by the genes aceE, aceF and IpdA. Transcription of those genes is regulated by several regulators. Thus, one of skill in the art can increase acetyl-CoA by modulating the activity of the pyruvate dehydrogenase complex. Modulation can be to increase the activity and/or expression (e.g., constant expression) of the pyruvate dehydrogenase complex. This can be accomplished by different ways, for example, by placing a strong constitutive promoter, like PL.6

(aattcatataaaaaacatacagataaccatctgcggtgataaattatctctggcgg tgttgacataaataccactggcggtgatactgag cacatcagcaggacgcactgaccaccatgaaggtg - lambda promoter, GenBank NC_001416), in front of the operon or using one or more synthetic constitutively expressing promoters.

[0200] Accordingly, in one aspect, the activity of pyruvate dehydrogenase is modulated by increasing the activity of one or more genes of the pyruvate dehydrogenase complex consisting of (a) pyruvate dehydrogenase (El), (b) dihydrolipoyl transacetylase, and (c) dihydrolipoyl dehydrogenase. It is understood that any one, two or three of these genes can be manipulated for increasing activity of pyruvate dehydrogenase. In another aspect, the activity of the pyruvate dehydrogenase complex can be modulated by attenuating the activity of an endogenous pyruvate dehydrogenase complex repressor gene, further detailed below. The activity of an endogenous pyruvate dehydrogenase complex repressor can be attenuated by deletion of the endogenous pyruvate dehydrogenase complex repressor gene.

[0201] In some cases, one or more genes of the pyruvate dehydrogenase complex are endogenous genes. Another way to increase the activity of the pyruvate dehydrogenase complex is by introducing into the microorganism one or more heterologous nucleic acids encoding one or more polypeptides from the group consisting of (a) pyruvate dehydrogenase (El), (b) dihydrolipoyl transacetylase, and (c) dihydrolipoyl dehydrogenase.

[0202] By using any of these methods, the recombinant microorganism can produce increased amounts of acetyl Co-A in comparison to microorganisms wherein the activity of pyruvate dehydrogenase is not modulated. Modulating the activity of pyruvate

dehydrogenase can result in more carbon flux into the mevalonate dependent biosynthetic pathway in comparison to microorganisms that do not have modulated pyruvate

dehydrogenase expression.

Combinations of Mutations

[0203] It is understood that for any of the enzymes and/or enzyme pathways described herein, molecular manipulations that modulate any combination (two, three, four, five or six) of the enzymes and/or enzyme pathways described herein is expressly contemplated. For ease of the recitation of the combinations, citrate synthase (gltA) is designated as A, phosphotransacetylase (ptaB) is designated as B, acetate kinase (ackA) is designated as C, lactate dehydrogenase (IdhA) is designated as D, malic enzyme (sfcA or maeB) is designated as E, and pyruvate decarboxylase (aceE, aceF, and/or lpdA) is designated as F. As discussed above, aceE, aceF, and/or lpdA enzymes of the pyruvate decarboxylase complex can be used singly, or two of three enzymes, or three of three enzymes for increasing pyruvate decarboxylase activity.

[0204] Accordingly, for combinations of any two of the enzymes A-F, non-limiting combinations that can be used are: AB, AC, AD, AE, AF, BC, BD, BE, BF, CD, CE, CF, DE, DF and EF. For combinations of any three of the enzymes A-F, non-limiting combinations that can be used are: ABC, ABD, ABE, ABF, BCD, BCE, BCF, CDE, CDF, DEF, ACD, ACE, ACF, ADE, ADF, AEF, BDE, BDF, BEF, and CEF. For combinations of any four of the enzymes A-F, non-limiting combinations that can be used are: ABCD, ABCE, ABCF, ABDE, ABDF, ABEF, BCDE, BCDF, CDEF, ACDE, ACDF, ACEF, BCEF, BDEF, and ADEF. For combinations of any five of the enzymes A-F, non-limiting combinations that can be used are: ABCDE, ABCDF, ABDEF, BCDEF, ACDEF, and ABCEF. In another aspect, all six enzyme combinations are used: ABCDEF.

[0205] Accordingly, the recombinant microorganism as described herein can achieve increased mevalonate production that is increased compared to microorganisms that are not grown under conditions of tri-carboxylic acid (TCA) cycle activity, wherein metabolic carbon flux in the recombinant microorganism is directed towards mevalonate production by modulating the activity of one or more enzymes from the group consisting of (a) citrate synthase, (b) phosphotransacetylase and/or acetate kinase, (c) lactate dehydrogenase, (d) malic enzyme, and (e) pyruvate decarboxylase complex.

Other Regulators and Factors for Increased Production

[0206] Other molecular manipulations can be used to increase the flow of carbon towards mevalonate production. One method is to reduce, decrease or eliminate the effects of negative regulators for pathways that feed into the mevalonate pathway. For example, in some cases, the genes aceEF-lpdA are in an operon, with a fourth gene upstream pdhR. pdhR is a negative regulator of the transcription of its operon. In the absence of pyruvate, it binds its target promoter and represses transcription. It also regulates ndh and cyoABCD in the same way (Ogasawara, H. et al. 2007. J. Bact. 189:5534-5541). In one aspect, deletion of pdhR regulator can improve the supply of pyruvate, and hence the production of mevalonate and isoprenoids.

[0207] In other aspects, the introduction of 6-phosphogluconolactonase (PGL) into microorganisms (such as various E. coli strains) which lack PGL can be used to improve production of mevalonate and isoprenoids. PGL may be introduced using chromosomal integration or extra-chromosomal vehicles, such as plasmids. In other embodiments, PGL may be deleted from the genome of microorganisms (such as various E. coli strains) which express an endogenous PGL to improve production of isoprenoid precursors and/or isoprenoids.

Production of Isoprenoids Using SSF

[0208] Simultaneous saccharification and fermentation can be used to produce isoprenoids by using cells, which have been engineered to produce isoprenoids, as an inoculum.

Generally, the cells are engineered such they produce a level and/or rate of isoprenoids at an amount that is commercially desirable, which is detailed below. [0209] Simultaneous saccharification system allows for the production of isoprenoids more efficiently, measured by total amount of isoprenoids produced per added amount of starch, by utilizing starch under limited glucose conditions, further detailed below. Isoprenoids produced by simultaneous saccharification and fermentation at limited glucose conditions also can reduce the volatiles produced under excess glucose conditions and thus has higher purity.

Growth conditions

[0210] The cells (e.g., aerobic or anaerobic) of any of the compositions or methods should be grown under conditions that are conducive to optimal production of isoprenoids.

Considerations for optimization include cell culture media, oxygen levels, and conditions favorable for decoupling such that isoprenoids production is favored over cell growth. For aerobic cells, the cell culture conditions should be used that provide optimal oxygenation for cells to be able to produce isoprenoids.

[0211] For anaerobic cells, these cells are capable of replicating and/or producing isoprenoids in a fermentation system that is substantially free of oxygen. Thus, in one embodiment, anaerobic cells engineered to produce isoprenoids can use SSF for initial growth. In some embodiments, the fermentation system contains syngas as the carbon and/or energy source. In some embodiments, the anaerobic cells are initially grown in a medium comprising a carbon source other than syngas and then switched to syngas as the carbon source. For the cells that use syngas as a source or energy and/or carbon, the syngas includes at least carbon monoxide and hydrogen. In some embodiments, the syngas further additionally includes one or more of carbon dioxide, water, or nitrogen.

[0212] In one aspect, the amount and rate of glucose used for isoprenoids production can be controlled to maximize the production of isoprenoids. One of skill in the art should take care to monitor the amount of glucose input since too much glucose can result acetate being produced instead of isoprenoids. Accordingly, in some embodiments, limited glucose conditions are used. One of skill in the art can control the amount of glucose and

glucoamylases' role in regulation of the amount of glucose. The amount of glucoamylase can be optimized to produce glucose at a rate that would keep fermentation glucose limited. Glucoamylase to starch ratio determines that rate of glucose release is more than or equal to rate of glucose utilization by isoprenoids producing cells, resulting in low or non-detectable glucose conditions. Limited glucose conditions depend on the glucose utilizing microorganism for which glucose concentration range can be 0.2 to 10 g/L. In some embodiments, the glucose concentration range can be at least about 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5 or 10 g/L. In other embodiments, the glucose concentration range can be at most about 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5 or 10 g/L.

[0213] Renewable resources are used for production of isoprenoids. Renewable resources refer to resources that are not fossil fuels. Generally, renewable resources are derived from living organisms or recently living organisms that can be replenished as they are consumed. Renewable resources can be replaced by natural ecological cycles or sound management practices. Non-limiting examples include biomass (e.g., switchgrass, hemp, corn, poplar, willow, sorghum, sugarcane), trees, and other plants. Non-limiting examples of renewable resources (or renewable carbon sources) include cheese whey permeate, cornsteep liquor, sugar beet molasses, barley malt, and components from any of the foregoing. Exemplary renewable carbon sources also include glucose, hexose, pentose and xylose present in biomass, such as corn, switchgrass, sugar cane, cell waste of fermentation processes, and protein by-product from the milling of soy, corn, or wheat. In some embodiments, the biomass carbon source is a lignocellulosic, hemicellulosic, or cellulosic material such as, but are not limited to, a grass, wheat, wheat straw, bagasse, sugar cane bagasse, soft wood pulp, corn, corn cob or husk, corn kernel, fiber from corn kernels, corn stover, switch grass, rice hull product, or a by-product from wet or dry milling of grains (e.g. , corn, sorghum, rye, triticate, barley, wheat, and/or distillers grains). Exemplary cellulosic materials include wood, paper and pulp waste, herbaceous plants, and fruit pulp. In some embodiments, the carbon source includes any plant part, such as stems, grains, roots, or tubers. In some embodiments, all or part of any of the following plants are used as a carbon source: corn, wheat, rye, sorghum, triticate, rice, millet, barley, cassava, legumes, such as beans and peas, potatoes, sweet potatoes, bananas, sugarcane, and/or tapioca. In some embodiments, the carbon source is a biomass hydrolysate, such as a biomass hydrolysate that includes both xylose and glucose or that includes both sucrose and glucose. As discussed above, the use of simultaneous saccharification and fermentation of any renewable resources can be used for the production of isoprenoids.

[0214] Examples of other fermentation systems and culture conditions which can be used are described in International Patent Application Publication No. WO2009/076676; U.S. Publ. 20100048964, US Publ. 2010/0086978, US Publ. 2010/0167370, US Publ. 2010/0113846, US Publ. 2010/0184178, and US Publ. 2010/0167371 ; U.S. Publ.

2011/0014672, U.S. Publ. 2010/0196977, and US Publ. 2011/0046422; WO 2004/033646 and WO 96/35796.

Bioreactors

[0215] A variety of different types of reactors can be used for production of isoprenoids from any renewable resource. There are a large number of different types of fermentation processes that are used commercially. The bioreactor can be designed to optimize the retention time of the cells, the residence time of liquid, and the sparging rate of any gas (e.g., syngas).

[0216] In various embodiments, the cells are grown using any known mode of

fermentation, such as batch, fed-batch, continuous, or continuous with recycle processes. In some embodiments, a batch method of fermentation is used. Classical batch fermentation is a closed system where the composition of the media is set at the beginning of the fermentation and is not subject to artificial alterations during the fermentation. Thus, at the beginning of the fermentation the cell medium is inoculated with the desired host cells and fermentation is permitted to occur adding nothing to the system. Typically, however, "batch" fermentation is batch with respect to the addition of carbon source and attempts are often made at controlling factors such as pH and oxygen concentration. In batch systems, the metabolite and biomass compositions of the system change constantly until the time the fermentation is stopped. Within batch cultures, cells moderate through a static lag phase to a high growth log phase and finally to a stationary phase where growth rate is diminished or halted. In some embodiments, cells in log phase are responsible for the bulk of the isoprenoids production. In some embodiments, cells in stationary phase produce isoprenoids.

[0217] In some embodiments, a variation on the standard batch system is used, such as the Fed-Batch system. Fed-Batch fermentation processes comprise a typical batch system with the exception that the carbon source (e.g. syngas, glucose) is added in increments as the fermentation progresses. Fed-Batch systems are useful when catabolite repression is apt to inhibit the metabolism of the cells and where it is desirable to have limited amounts of carbon source in the cell medium. Fed-batch fermentations may be performed with the carbon source {e.g. , syngas, glucose, fructose) in a limited or excess amount. Measurement of the actual carbon source concentration in Fed-Batch systems is difficult and is therefore estimated on the basis of the changes of measurable factors such as pH, dissolved oxygen, and the partial pressure of waste gases such as CO ₂ . Batch and Fed-Batch fermentations are common and well known in the art and examples may be found in Brock, Biotechnology: A Textbook of Industrial Microbiology, Second Edition (1989) Sinauer Associates, Inc.

[0218] In some embodiments, continuous fermentation methods are used. Continuous fermentation is an open system where a defined fermentation medium is added continuously to a bioreactor and an equal amount of conditioned medium is removed simultaneously for processing. Continuous fermentation generally maintains the cultures at a constant high density where cells are primarily in log phase growth.

[0219] Continuous fermentation allows for the modulation of one factor or any number of factors that affect cell growth or isoprenoids production. For example, one method maintains a limiting nutrient such as the carbon source or nitrogen level at a fixed rate and allows all other parameters to moderate. In other systems, a number of factors affecting growth can be altered continuously while the cell concentration (e.g., the concentration measured by media turbidity) is kept constant. Continuous systems strive to maintain steady state growth conditions. Thus, the cell loss due to media being drawn off is balanced against the cell growth rate in the fermentation. Methods of modulating nutrients and growth factors for continuous fermentation processes as well as techniques for maximizing the rate of product formation are well known in the art of industrial microbiology and a variety of methods are detailed by Brock, Biotechnology: A Textbook of Industrial Microbiology, Second Edition (1989) Sinauer Associates, Inc., which is hereby incorporated by reference in its entirety, particularly with respect to cell culture and fermentation conditions.

Exemplary Production oflsoprenoids Composition

[0220] In some embodiments, the cells are cultured in a culture medium under conditions permitting the production of isoprenoidsby the cells in the SSF system with glucoamylase under neutral pH conditions. In some embodiments, the isoprenoid can be monoterpenes, diterpenes, triterpenes, tetraterpenes, sequiterpenes, or polyterpenes. In other embodiments, the isoprenoid can be abietadiene, amorphadiene, carene, farnesene, a-farnesene, β- farnesene, farnesol, geraniol, geranylgeraniol, linalool, limonene, myrcene, nerolidol, ocimene, patchoulol, β-pinene, sabinene, γ-terpinene, terpindene and valencene.

[0221] By "peak absolute productivity" is meant the maximum absolute amount of isoprenoids produced during the culturing of cells for a particular period of time (e.g., the culturing of cells during a particular fermentation run). By "peak absolute productivity time point" is meant the time point during a fermentation run when the absolute amount of isoprenoids produced is at a maximum during the culturing of cells for a particular period of time (e.g. , the culturing of cells during a particular fermentation run). In some embodiments, the isoprenoids amount is measured at the peak absolute productivity time point. In some embodiments, the peak absolute productivity for the cells is about any of the isoprenoids amounts disclosed herein.

[0222] By "peak specific productivity" is meant the maximum amount of isoprenoids produced per cell during the culturing of cells for a particular period of time (e.g. , the culturing of cells during a particular fermentation run). By "peak specific productivity time point" is meant the time point during the culturing of cells for a particular period of time (e.g. , the culturing of cells during a particular fermentation run) when the amount of isoprenoids produced per cell is at a maximum. The peak specific productivity is determined by dividing the total productivity by the amount of cells, as determined by optical density at 600nm (ΟΌβοο). In some embodiments, the isoprenoids amount is measured at the peak specific productivity time point. In some embodiments, the peak specific productivity for the cells is about any of the isoprenoids amounts per cell disclosed herein.

[0223] By "peak volumetric productivity" is meant the maximum amount of isoprenoids produced per volume of broth (including the volume of the cells and the cell medium) during the culturing of cells for a particular period of time (e.g. , the culturing of cells during a particular fermentation run). By "peak specific volumetric productivity time point" is meant the time point during the culturing of cells for a particular period of time (e.g. , the culturing of cells during a particular fermentation run) when the amount of isoprenoids produced per volume of broth is at a maximum. The peak specific volumetric productivity is determined by dividing the total productivity by the volume of broth and amount of time. In some embodiments, the isoprenoids amount is measured at the peak specific volumetric productivity time point. In some embodiments, the peak specific volumetric productivity for the cells is about any of the isoprenoids amounts per volume per time disclosed herein.

[0224] By "peak concentration" is meant the maximum amount of isoprenoids produced during the culturing of cells for a particular period of time (e.g., the culturing of cells during a particular fermentation run). By "peak concentration time point" is meant the time point during the culturing of cells for a particular period of time (e.g., the culturing of cells during a particular fermentation run) when the amount of isoprenoids produced per cell is at a maximum. In some embodiments, the isoprenoids amount is measured at the peak concentration time point. In some embodiments, the peak concentration for the cells is about any of the isoprenoids amounts disclosed herein.

[0225] By "average volumetric productivity" is meant the average amount of isoprenoids produced per volume of broth (including the volume of the cells and the cell medium) during the culturing of cells for a particular period of time (e.g. , the culturing of cells during a particular fermentation run). The average volumetric productivity is determined by dividing the total productivity by the volume of broth and amount of time. In some embodiments, the average specific volumetric productivity for the cells is about any of the isoprenoids amounts per volume per time disclosed herein.

[0226] By "cumulative total productivity" is meant the cumulative, total amount of isoprenoids produced during the culturing of cells for a particular period of time (e.g., the culturing of cells during a particular fermentation run). In some embodiments, the cumulative, total amount of isoprenoids is measured. In some embodiments, the cumulative total productivity for the cells is about any of the isoprenoids amounts disclosed herein.

[0227] As used herein, "relative detector response" refers to the ratio between the detector response (such as the GC/MS area) for one compound (such as isoprenoids) to the detector response (such as the GC/MS area) of one or more compounds (such as all CIO or >C10 hydrocarbons) The detector response may be measured as described herein, such as the GC/MS analysis performed with an Agilent 6890 GC/MS system fitted with an Agilent HP- 5MS GC/MS column (30 m x 250 μιη; 0.25 μιη film thickness). If desired, the relative detector response can be converted to a weight percentage using the response factors for each of the compounds. This response factor is a measure of how much signal is generated for a given amount of a particular compound (that is, how sensitive the detector is to a particular compound). This response factor can be used as a correction factor to convert the relative detector response to a weight percentage when the detector has different sensitivities to the compounds being compared. Alternatively, the weight percentage can be approximated by assuming that the response factors are the same for the compounds being compared. Thus, the weight percentage can be assumed to be approximately the same as the relative detector response.

[0228] In some embodiments, the cells in culture produce isoprenoids at greater than or about 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, or 20 g/L (g isoprenoids/L broth). [0229] In some embodiments, the cells in culture produce isoprenoids at greater than or about 1, 10, 25, 50, 100, 150, 200, 250, 300, 400, 500, 600, 700, 800, 900, 1,000, 1,250, 1,500, 1,750, 2,000, 2,500, 3,000, 4,000, 5,000, 10,000, 12,500, 20,000, 30,000, 40,000, 50,000, 75,000, 100,000, 125,000, 150,000, 188,000, or more nmole of isoprenoids/gram of cells for the wet weight of the cells/hour (nmole/g _wcm /hr). In some embodiments, the amount of isoprenoids is between about 2 to about 200,000 nmole/g _wcm /hr, such as between about 2 to about 100 nmole/g _wcm /hr, about 100 to about 500 nmole/g _wcm /hr, about 150 to about 500 nmole/g _wcm /hr, about 500 to about 1,000 nmole/g _wcm /hr, about 1,000 to about 2,000 nmole/g _wcm /hr, or about 2,000 to about 5,000 nmole/g _wcm /hr, about 5,000 to about 10,000 nmole/g _wcm /hr, about 10,000 to about 50,000 nmole/g _wcm hr, about 50,000 to about 100,000 nmole/g _wcm /hr, about 100,000 to about 150,000 nmole/g _wcm /hr, or about 150,000 to about 200,000 nmole/g _wcm /hr. In some embodiments, the amount of isoprenoids is between about 20 to about 5,000 nmole/g _wcm /hr, about 100 to about 5,000 nmole/g _wcm /hr, about 200 to about 2,000 nmole/g _wcm /hr, about 200 to about 1,000 nmole/g _wcm hr, about 300 to about 1,000 nmole/g _wcm /hr, or about 400 to about 1,000 nmole/g _wcm /hr, about 1,000 to about 5,000 nmole/g _wcm /hr, about 2,000 to about 20,000 nmole/g _wcm /hr, about 5,000 to about 50,000 nmole/g _wcm /hr, about 10,000 to about 100,000 nmole/g _wcm /hr, about 20,000 to about 150,000 nmole/g _wcm /hr, or about 20,000 to about 200,000 nmole/g _wcm /hr.

[0230] The amount of isoprenoids in units of nmole/g _wcm /hr can be measured as disclosed in U.S. Patent No. 5,849,970, which is hereby incorporated by reference in its entirety, particularly with respect to the measurement of isoprenoids production. For example, two mL of headspace (e.g., headspace from a culture such as 2 mL of culture cultured in sealed vials at 32 °C with shaking at 200 rpm for approximately 3 hours) are analyzed for isoprenoids using a standard gas chromatography system, such as a system operated isothermally (85 °C) with an n-octane/porasil C column (Alltech Associates, Inc., Deerfield, 111.) and coupled to a RGD2 mercuric oxide reduction gas detector (Trace Analytical, Menlo Park, CA) (see, for example, Greenberg et al, Atmos. Environ. 27 : 2689-2692, 1993; Silver et ah, Plant Physiol. 97: 1588-1591, 1991, which are each hereby incorporated by reference in their entireties, particularly with respect to the measurement of isoprenoids production). The gas chromatography area units are converted to nmol isoprenoids via a standard isoprenoids concentration calibration curve. In some embodiments, the value for the grams of cells for the wet weight of the cells is calculated by obtaining the heoo value for a sample of the cell culture, and then converting the Α _ό οο value to grams of cells based on a calibration curve of wet weights for cell cultures with a known Ae ₀₀ value. In some embodiments, the grams of the cells is estimated by assuming that one liter of broth (including cell medium and cells) with an A ₆ oo value of 1 has a wet cell weight of 1 gram. The value is also divided by the number of hours the culture has been incubating for, such as three hours.

Systems for Producing Isoprenoids

[0231] The invention also provides systems for producing isoprenoids. In one aspect, the system includes (i) a bioreactor within which saccharification and fermentation are performed at about pH 5.0 to 8.0; (ii) a host cell comprising a heterologous nucleic acid encoding an polyprenyl pyrophosphate synthase polypeptide; (iii) a glucoamylase that possesses at least 50% activity at pH 6.0 or above relative to its maximum activity, wherein the glucoamylase is selected from the group consisting of a parent Humicola grisea glucoamylase (HgGA) comprising SEQ ID NO: 3, a parent Trichoderma reesei glucoamylase (TrGA) comprising SEQ ID NO: 6, a parent Rhizopus p. glucoamylase (RhGA) comprising SEQ ID NO: 9, and a variant thereof, and wherein the variant has at least 99% sequence identity to the parent glucoamylase.

[0232] Components of the system are described herein. Various combinations of these system components are expressly contemplated within the scope of the invention.

Recovery

[0233] The isoprenoids produced by the genetically modified cells described herein can be recovered from the fermentation system using any suitable separation and purification methods known in the art, see for example US 2010/0311065, US 2007/0254354, the contents of which are expressly incorporated herein by reference.

[0234] In certain embodiments, an organic phase comprising the isoprenoid is recovered from the fermentation broth by centrifugation. In other embodiments, an organic phase comprising the isoprenoid separates from the fermentation broth spontaneously. In yet other embodiments, an organic phase comprising the isoprenoid is actively recovered from the fermentation broth by adding a deemulsifier and/or a nucleating agent into the fermentation reaction. Illustrative examples of deemulsifiers include flocculants and coagulants.

Illustrative examples of nucleating agents include droplets of the isoprenoid compound itself and organic solvents such as dodecane, isopropyl myristrate, and methyl oleate. [0235] In other embodiments, the isoprenoid can be recovered from other products that may be present in the organic phase. In certain embodiments, separation is achieved using adsorption, distillation, gas phase extraction (stripping), gas phase-liquid phase extraction (stripping), liquid phase -liquid phase extraction (solvent extraction), ultrafiltration, and standard chromatographic techniques.

[0236] The above enumerated list are only examples and one skilled in the art will be aware of a number of recovery techniques that may be appropriately used to obtain a desired end product.

Methods of using the recombinant cells to produce isoprenoids and/or isoprenoid precursor molecules

[0237] Also provided herein are methods of producing isoprenoid precursor molecules and/or isoprenoids comprising culturing recombinant microorganisms (e.g., recombinant bacterial cells) that comprise a polyprenyl pyrophosphate synthase polypeptide, and one or more nucleic acids encoding a MVA pathway polypeptide including, but not limited to, AACT, HMG-CoA reductase, 3-hydroxy-3-methylglutaryl-CoA synthase (HMG-CoA synthase) polypeptides, 3-hydroxy-3-mefhylglutaryl-CoA reductase (HMG-CoA reductase) polypeptides, mevalonate kinase (MVK) polypeptides, phosphomevalonate kinase (PMK) polypeptides, diphosphomevalonte decarboxylase (MVD) polypeptides, phosphomevalonate decarboxylase (PMDC) polypeptides, isopentenyl phosphate kinase (IPK) polypeptides, IPP isomerase polypeptides, IDI polypeptides, and polypeptides (e.g., fusion polypeptides) having an activity of two or more MVA pathway polypeptides.

[0238] The isoprenoid precursor molecules and/or isoprenoids can be produced from any of the cells described herein and according to any of the methods described herein. Any of the cells can be used for the purpose of producing isoprenoid precursor molecules and/or isoprenoids from carbohydrates, including six carbon sugars such as glucose.

[0239] Thus, provided herein are methods of making isoprenoid precursor molecules and/or isoprenoids comprising culturing recombinant cells (e.g., bacterial cell) comprising a polyprenyl pyrophosphate synthase polypeptide, and one or more heterologous nucleic acids encoding a AACT, HMG-CoA reductase and HMG-CoA synthase, in a suitable condition for producing isoprenoids and producing isoprenoid precursor molecules and/or isoprenoids. The cells can further comprise one or more nucleic acid molecules encoding the lower MVA pathway polypeptide(s) described above (e.g., MVK, PMK, MVD, and/or IDI) and any of the polyprenyl pyrophosphate synthase polypeptide(s) described above. In some aspects, the bacterial cells can be any of the cells described herein. Any of the polyprenyl pyrophosphate synthase or variants thereof described herein, any of the bacterial strains described herein, any of the promoters described herein, and/or any of the vectors described herein can also be used to produce isoprenoid precursor molecules and/or isoprenoids using any of the energy sources (e.g. glucose or any other six carbon sugar) described herein. In some aspects, the method of producing isoprenoid precursor molecules and/or isoprenoids further comprises a step of recovering the isoprenoid precursor molecules and/or isoprenoids.

[0240] The instant methods for the production of isoprenoid precursor molecules and/or isoprenoids can produce at least 5% greater amounts of isoprenoid precursors and/or isoprenoids when compared to isoprenoids and/or isoprenoid precursor -producing recombinant cells (e.g., bacterial cells) that have not been engineered for increased carbon flux to mevalonate production. Alternatively, the bacterial cells can produce greater than about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, or 15% of isoprenoid precursors and/or isoprenoids , inclusive. In some aspects, the method of producing isoprenoid precursor molecules and/or isoprenoids further comprises a step of recovering the isoprenoid precursor molecules and/or isoprenoids.

[0241] Provided herein are methods of using any of the cells described above for enhanced isoprenoid and/or isoprenoid precursor molecule production. The production of isoprenoid precursor molecules and/or isoprenoids by the cells can be enhanced by the any of the methods disclosed herein for increasing carbon flow through the MVA and/or DXP pathway, and one or more heterologous nucleic acids encoding a polyprenyl pyrophosphate synthase polypeptide. As used herein, "enhanced" isoprenoid precursor and/or isoprenoid production refers to an increased cell productivity index (CPI) for isoprenoid precursor and/or isoprenoid production, an increased titer of isoprenoid precursors and/or isoprenoids, an increased mass yield of isoprenoid precursors and/or isoprenoids, and/or an increased specific productivity of isoprenoid precursors and/or isoprenoids by the cells described by any of the compositions and methods described herein compared to cells which do not have have not been engineered. The production of isoprenoid precursor molecules and/or isoprenoids can be enhanced by about 5% to about 1,000,000 folds. The production of isoprenoid precursor molecules and/or isoprenoids can be enhanced by about 10% to about 1,000,000 folds (e.g. , about 1 to about 500,000 folds, about 1 to about 50,000 folds, about 1 to about 5,000 folds, about 1 to about 1,000 folds, about 1 to about 500 folds, about 1 to about 100 folds, about 1 to about 50 folds, about 5 to about 100,000 folds, about 5 to about 10,000 folds, about 5 to about 1,000 folds, about 5 to about 500 folds, about 5 to about 100 folds, about 10 to about 50,000 folds, about 50 to about 10,000 folds, about 100 to about 5,000 folds, about 200 to about 1,000 folds, about 50 to about 500 folds, or about 50 to about 200 folds) compared to the production of isoprenoid precursor molecules and/or isoprenoids by cells which have not been engineered for increased carbon flux to mevalonate production.

[0242] The production of isoprenoid precursor molecules and/or isoprenoids can also enhanced by at least about any of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 1 fold, 2 folds, 5 folds, 10 folds, 20 folds, 50 folds, 100 folds, 200 folds, 500 folds, 1000 folds, 2000 folds, 5000 folds, 10,000 folds, 20,000 folds, 50,000 folds, 100,000 folds, 200,000 folds, 500,000 folds, or 1,000,000 folds compared to the production of isoprenoid precursor molecules and/or isoprenoids by cells which have not been engineered for increased carbon flux to mevalonate production.

[0243] In addition, more specific cell culture conditions (e.g., SSF) can be used to culture the cells in the methods described herein. In some aspects, the method of producing mevalonate further comprises a step of recovering the isoprenoid precursor molecules and/or isoprenoids.

Simultaneous saccharification and fermentation (SSF)

[0244] During SSF, the hydrolyzing enzymes are added along with the end product producer, commonly a microorganism. Enzymes release lower molecule sugars, i.e. , fermentable sugars DPl-3, from the starch substrate, while the microorganism simultaneously uses the fermentable sugars for growth and production of the end product. Typically, fermentation conditions are selected that provide an optimal pH and temperature for promoting the best growth kinetics of the producer host cell strain and catalytic conditions for the enzymes produced by the culture. See e.g. , Doran et al., Biotechnol. Progress 9: 533-538 (1993). Table 1 presents exemplary fermentation microorganism and their optimal pH for fermentation. Because the glucoamylases disclosed herein possess significant activity at a neutral pH and an elevated temperature, they would be useful in the SSF for those microorganisms having an optimal fermenting pH in the range of 5.5 to 7.5.

Table 1. Exemplary fermentation organisms and their optimal pH. thereof Bacillus lacterosprous 7.0-7.2

Methylophilotrophus 7

Lactobacillus amylophilus 6.0-6.5

Bacillus coagulans 6.4-6.6

Lactic Acid Bacillus thermoamylovorans 5.0-6.5

Bacillus smithii 5.0-6.5

Geobacillus stearothermophilus 5.0-6.5

Corynebacterium pekinense 7

Corynebacterium crenatum 7

Monosodium Brevibacterium tianjinese 7

Glutamate (MSG) Corynebacterium glutamicum

7.0-7.2

HU7251

Arthrobacter sp 7

Succinic acid Escherichia coli 6.0-7.5

1,3-Propanediol Escherichia coli 6.5-7.5

2-Keto-gulonic acid Escherichia coli 5.0-6.0

Isoprene Escherichia coli 6-8

EXAMPLES

Methods used in the Examples

[0245] The following materials, assays, and methods were used in the examples provided below:

HPLC method to measure saccharide composition

[0246] The composition of the reaction products of oligosaccharides was measured by a HPLC system (Beckman System Gold 32 Karat Fullerton, CA). The system, maintained at 50°C, was equipped with a Rezex 8 u8% H Monosaccharides column and a refractive index (RI) detector (ERC-7515A, Anspec Company, Inc.). Diluted sulfuric acid (0.01 N) was applied as the mobile phase at a flow rate of 0.6 ml/min. 20 μΐ of 4.0% solution of the reaction mixture was injected onto the column. The column separates saccharides based on their molecular weights. The distribution of saccharides and the amount of each saccharide were determined from previously run standards. Determination of glucoamylase activity units (GAU)

[0247] Glucoamylase activity units (GAU) were determined based on the activity of a glucoamylase enzyme to catalyze the hydrolysis of p-nitrophenyl-alpha-D-glucopyranoside (PNPG) to glucose and p-nitrophenol. At an alkaline pH, /?-nitrophenol forms a yellow color that is measured spectrophotometrically at 405 nm. The amount of p-nitrophenol released correlates with the glucoamylase activity.

Protein concentration determination

[0248] The protein concentration in a sample was determined using the Bradford

QuickStart™ Dye Reagent (Bio-Rad, California, USA). For example, a 10 μΐ. sample of the enzyme was combined with 200 μυ Bradford QuickStart™ Dye Reagent. After thorough mixing, the reaction mixture was incubated for at least 10 minutes at room temperature. Air bubbles were removed and the optical density (OD) was measured at 595 nm. The protein concentration was then calculated using a standard curve generated from known amounts of bovine serum albumin.

Purification of HgGA for characterization studies

[0249] The material concentrated by ultrafiltration (UFC) was desalted / buffer-exchanged using a BioRad DP-10 desalting column and 25 mM Tris pH 8.0. 100 mg of total protein was applied to a Pharmacia Hi Prep 16/10 S Sepharose FF column, which was equilibrated with the above buffer at 5 ml/min. Glucoamylase was eluted with a 4-column volume (CV) gradient buffer containing 0-200 mM NaCl. Multiple runs were performed and the purest fractions, as determined via SDS-PAGE/coomassie blue staining analysis, were pooled and concentrated using VivaSpin 10K MWCO 25 ml spin tubes. The final material was passed over a Novagen HisBind 900 chromatography cartridge that had been washed with 250 mM EDTA and rinsed with above buffer. 2 ml of final material was obtained, having a protein concentration of 103.6 mg/ml, and a glucoamylase activity of 166.1 GAU/ml (determined by a PNPG based assay). Specific activities were determined using a standardized method using p-nitrophenyl-alpha-D-glucopyranoside (PNPG) as a substrate and reported in GAU units.

Determination of glucose concentration

[0250] Glucose concentration in a saccharification reaction mixture was determined with the ABTS assay. Samples or glucose standards in 5 μΤ were placed in wells of a 96-well microliter plate (MTP). Reactions were initiated with the addition of 95 μΙ_, of the reactant containing 2.74 mg/ml 2,2'-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) (Sigma PI 888), 0.1 U/ml horseradish peroxidase type VI (Sigma P8375), and 1 U/ml glucose oxidase (Sigma G7141). OD ₄₀ s _nm was immediately monitored at a 9-second interval for 300 seconds using a Spectramax plate reader. Because the rate of OD ₄ o5 _nm increase is proportional to the glucose concentration, the sample's glucose concentration was determined by comparing with the glucose standard, and was reported as mg/ml.

Example 1: Comparison of the pH and activity profiles of various glucoamylases at

32°C

[0251] The pH and activity profiles of glucoamylases (GAs) from Humicola grisea (HgGA), Trichoderma reesei (TrGA), Aspergillus niger (AnGA) and Talaromyces emersonii (TeGA) were determined at 32°C. As the substrate, 8% potato starch (Sigma Cat. No.

S2630) was solubilized by heating. A series of citrate/phosphate buffers at 0.25 or 0.5 pH increments, ranging from pH 2.0 to 8.0, were prepared. Purified enzymes were diluted to 0.1 or 0.02 GAU/ml in water (TeGA was dosed at 0.2 GAU/ml). HgGA, TrGA, AnGA, and TeGA were dosed at 0.0125, 0.0076, 0.0109, and 0.0055 mg/ml, respectively. 10 iL buffer of various pH was placed in 0.2 ml PCR tube strips (AB Gene, Cat. No. AB-0451, 800-445- 2812) with 15 μΤ of diluted enzyme. The reactions were initiated by the addition of 25 μΐ _^ soluble potato starch. The reactions were incubated on a PCR type thermocycler heating block for exactly ten minutes, then terminated by the addition of 10 μΐ _^ 0.5 M NaOH. The glucose released in the reaction was determined using the ABTS assay, and the glucoamylase activities were determined. The pH and activity profiles are presented in Table and FIG. 1 as the percentage of the maximum activity for each glucoamylase.

Table 2. pH profiles of HgGA, TrGA, AnGA, and TeGA at 32°C. The values represent % of the maximum activity for each enzyme.

H HgGA TrGA AnGA TeGA

3.75 84 100 96 79

4.00 93 84 64

4.25 100 95 78 51

4.50 84 55 34

4.75 44 46 30

5.00 40 45 29

5.25 42 66 43 27

5.50 46 41 23

5.75 48 58 39 21

6.00 53 51 35 17

6.50 62 38 27 11

7.00 67 22 17 5

7.50 58 10 7 2

8.00 39 4 3 1

[0252] As shown in Table 2 and FIG. 1 , both TeGA and AnGA exhibited significantly reduced activity in the pH range of 6.0 to 8.0. At a pH 5.0 or above, TeGA retained no more than 29% activity relative to its maximum activity. At a pH 6.0 or above, TeGA retained no more than 17% activity relative to its maximum activity. Similarly, at a pH 6.0 of 6.0 or above, AnGA displayed no more than 35% activity relative to its maximum activity. In the pH range of 6.0 to 7.5, HgGA retained at least 53% activity relative to its maximum activity. At pH 6.0, TrGA also displayed at least 50% activity relative to its maximum activity. The above observation shows that both HgGA and TrGA are suitable for producing fermentable sugars at a neutral pH range (as described herein for neutral pH glucoamylases) under fermentation conditions.

Example 2: Comparison of hydrolysis of solubilized starch at 32°C, pH 7.0

[0253] The ability of various glucoamylases to hydrolyze solubilized starch substrate (liquefact) at a neutral pH was compared. Corn starch was liquefied by following a conventional high-temperature jet cooking process using CLEARFLOW™ AA to a liquefact of DE 12-15. Saccharification of the liquefact (25% DS) was carried out using TrGA, HgGA, and AnGA at 1.0 GAU/g ds at 32°C, pH 7.0. Samples were withdrawn at different time intervals during the saccharification and subject to HPLC analysis. The composition of the oligosaccharides is presented in Table 3. Table 3. Composition of oligosaccharides in saccharification.

[0254] Using HgGA, the DPI content reached more than 90% after 24 hrs. After 45 hours, the DPI content reached more than 96%, while the content of higher sugars decreased to less than 3%. Using TrGA, more than 70% DPI was obtained after 24 hours. After 45 hours, the DPI content reaches about 80%, while the content of higher sugars dropped to less than 20%. For AnGA, less than 75% of DPI was obtained after 45 hours, while higher sugars remained more than 20%. The data in Table 3 indicate that both HgGA and TrGA are more effective than AnGA to hydrolyze solubilized starch to glucose, at a neutral pH.

Example 3: Comparison of hydrolysis of liquefied starch at 58°C, pH 6.5

[0255] Corn starch liquefact (~9. IDE) obtained by SPEZYME ^® FRED (Danisco US Inc., Genencor Division) treatment was adjusted to pH 6.5 with NaOH and equilibrated at a 58°C water bath. AnGA (OPTIDEX™ L-400, Danisco US Inc., Genencor Division), TrGA, and HgGA were added at 0.5 GAU/g ds to each flask containing corn starch liquefact.

Saccharification was carried out up to 48 hours with periodical sampling for HPLC analysis. 0.5 mL enzyme-deactivated sample was diluted with 4.5 ml of RO water. The diluted sample was then filtered through 0.45 μιη Whatman filters and subject to HPLC analysis. The HPLC analysis was conducted as described in Methods used in the Examples. The composition of the oligosaccharides is presented in Table 4.

Table 4. Composition of oligosaccharides in saccharification.

[0256] Using HgGA, the DPI content reached more than 90% after 24 hrs. After 48 hours, the DPI content reached more than 93%, while the content of higher sugars decreased to less than 5%. Using TrGA, more than 70% DPI was obtained after 24 hours. After 45 hours, the DPI content reaches about 75%, while the content of higher sugars dropped to about 18%. For AnGA, less than 65% of DPI was obtained after 45 hours, while higher sugars remained more than 25%. The data in Table 4 indicate that both HgGA and TrGA are more effective than AnGA, at a neutral pH and 58°C, to hydrolyze solubilized starch to glucose. This observation is consistent with data presented in Table 3, where saccharification was performed at 32°C.

Example 4: Comparison of high sugars (DP4+) reduction at 58°C, pH 6.5

[0257] Various concentrations of AnGA, TrGA, and HgGA were used to saccharify a starch substrate at 58°C, pH 6.5, and the reduction of high sugars (DP4+) was compared. The starch substrate was a 25% cornstarch liquefact, which was liquefied by SPEZYME ^® FRED (Danisco US Inc., Genencor Division). Glucoamylases were added as shown in Table 5, from 0.25 GAU/gds to 10.0 GAU/gds. The saccharification reaction was conducted at 58°C, pH 6.5. Samples were withdrawn at various time points and the sugar composition was determined by HPLC analysis. The composition of the oligosaccharides is presented in Table 5 and FIG. 2.

Table 5. Composition of oligosaccharides in saccharification.

GAU/gds Percent Sugar Composition at 48 hr

Glucoamylase

starch DPI DP2 DP3 DP4+

0.25 93.15 2.10 1.00 3.76

0.5 95.33 2.58 0.64 1.45

HgGA

0.75 95.08 3.36 0.53 1.02

1 94.57 3.94 0.56 0.94

[0258] The results presented in Table 5 and FIG. 2 indicated that AnGA resulted in more than 8% of higher sugars (DP4+), at 58°C, pH 6.5, even at a high dosage of glucoamylase, 10.0 GAU/gds. In contrast, lower than 5% of higher sugars (DP4+) was observed for 5 GAU/gds TrGA. HgGA resulted in the lowest levels of higher sugars (DP4+). For example, at 0.5 GAU/gds HgGA, the saccharification mixture contained less than 1.5% of higher sugars (DP4+), which is comparable to the resulted obtained under the current industrial high glucose processing conditions (pH 4.5, 60°C) using AnGA.

Example 5: Continuous production of glucose from granular Cassava starch by HgGA at a neutral pH

[0259] The capability of HgGA to convert granular unmodified cassava starch to glucose and short chain glucose polymers at a neutral pH was further characterized. A 27 % dry substance aqueous slurry of cassava starch was first adjusted to pH 6.4 with sodium carbonate. SPEZYME™ Alpha (Danisco US Inc., Genencor Division) was added at 2 AAU/g ds, and HgGA was added at 1 GAU/g ds. The reaction was carried out for 48 hours at 58 °C with continuous stirring. At selected time intervals, samples of the slurry were removed. The removed sample was added to a 2.5 ml micro-centrifuge tube and centrifuged for 4 minutes at 13,000 rpm. Refractive index (RI) of the supernatant was determined at 30°C. The remaining supernatant was filtered through a 13 mm syringe filter with a 0.45 μιη GHP membrane into a 2.5 ml micro-centrifuge tube and boiled for 10 minutes to terminate the amylase activity. 0.5 mL enzyme-deactivated sample was diluted with 4.5 ml of RO water. The diluted sample was then filtered through 0.45 μηι Whatman filters and subject to HPLC analysis. The HPLC analysis was conducted as described in Methods used in the Examples. [0260] The total dry substance was determined by taking about 1 ml of the starch slurry into a 2.5 ml spin tube, adding 1 drop of SPEZYME ^® FRED (Danisco US Inc., Genencor Division) from a micro dispo-pipette, and boiling 10 minutes. Refractive index at 30°C was determined. The dry substance of the supernatant and the whole sample (total) was determined using appropriate DE tables. The CRA 95 DE Table was used for the supernatant and corrected for consumption of water of hydrolysis. % soluble was calculated as: 100 x (the dry substance of the supernatant) / (the total dry substance). The composition of the oligosaccharides is presented in Table 6.

Table 6 Saccharide distribution for HgGA-mediated saccharification of cassava granular starch.

[0261] As shown in Table 6, the reaction achieved about 93% solubility and yielded about 96.9% glucose within 24 hours. Continuation of saccharification resulted in 99% solubility and about 96.8% glucose after 48 hours.

Example 6: Continuous production of glucose from granular cornstarch by HgGA at a neutral pH

[0262] Corn granular starch was used to characterize HgGA. The experiments were carried out using 32% ds corn granular starch. Water (64.44 g) and starch (35.56 g; at 90% ds) were mixed and the pH of the slurry was increased to 6.4. The starch slurry was placed in a water bath maintained at 58°C and enzymes were added. The enzymes included SPEZYME™ Alpha (Danisco US Inc., Genencor Division) and HgGA. The starch slurry was maintained at 58°C for 48 hrs and samples were drawn at 3, 6, 10, 24, 32, and 52 hrs to analyze the % soluble and saccharide profile. The results are presented in Table 7. Table 7. Saccharide distribution for HgGA-mediated saccharification of corn granular starch

[0263] As shown in Table 7, HgGA maintains a significant amount of glucoamylase activity for 52 hrs at pH 6.4, evidenced by the continued production of DPI and DP2, as well as the continued increase of % soluble solids. The data also suggest that the rates of DPI production and % solubilization of granular starch depend on the amount of HgGA. An increased amount of HgGA resulted in increased rates of % solubilization and DPI production.

Example 7: Characterization of granular starch hydrolysis by HgGA and SPEZYME

Alpha at a neutral pH by scanning electron microscopy [0264] Granular starch from corn, wheat, and cassava was treated with HgGA and SPEZYME™ Alpha. A 28 % dry substance aqueous slurry of granular starch was first adjusted to pH 6.4 with sodium carbonate. SPEZYME™ Alpha (Danisco US Inc., Genencor Division) was added at 2 AAU/g ds, and HgGA was added at 1 GAU/g ds. Treatment was carried out at 58 °C with continuous stirring. Samples of the slurry were removed at various time points and subject to scanning electron microscopy (SEM). Slurry samples were laid on SEM sample stubs using double-sided carbon tape. Excess sample was removed by gently dusting the mounted sample with compressed air. Mounted samples were sputter coated with gold (15 nm) for 2 min at 25 mV, using an Emitech K550 Sputter Coater (Squorum

Technologies). The scanning electron micrographs are presented in FIG. 3. Before treatment, starch surface was smooth and homogenous. Upon HgGA and SPEZYME™ Alpha treatment, the surface morphology of the granules changed over time. The enzyme blend first created small dimples (0.2-0.5 μιη in diameter) on the surface of the starch granules. Quantity and size of the dimples increased over time. At a late stage of the treatment, for example, 48 hours for cassava granular starch, empty shells were spotted. Micrographs of empty shells indicated a complete digestion of the interior of the granule. The mechanism of enzymatic action appears to be starch granule surface peeling. Once the surface has been weakened by external peeling, the amylases penetrate and hydrolyze the interior of the granule (i.e. , amylolysis) leaving hollowed out shells.

Example 8: Isoprene production by fermentation 8.1. Materials and methods

[0265] Medium Recipe (per liter fermentation medium): K ₂ HP0 ₄ 7.5 g, MgS0 ₄ · 7H ₂ 0 2 g, citric acid monohydrate 2 g, ferric ammonium citrate 0.3 g, yeast extract 0.5 g, 1000 x Modified Trace Metal Solution 1 ml. All of these components were dissolved in 60 mL DI H ₂ 0 to form "Component A." The following various starch substrates (each contained about 270 g starch) were prepared:

1) Granular cornstarch (270 g) was added to 705 ml DI H ₂ 0 and incubated at

34°C for 30 minutes with agitation. The temperature was then increased to

60°C and held for an additional 12 hours;

2) Granular endosperm 329 g (82% starch g/g) was added to 646 ml H ₂ 0 and

incubated at 34°C for 30 minutes with agitation. The temperature was then increased to 60°C and held for an additional 12 hours; 3) Granular ground corn 397 g (68% starch g/g) was added to 646 ml H ₂ 0 and incubated at 34°C for 30 minutes with agitation. The temperature was then increased to 60°C and held for an additional 12 hours;

4) 758 g liquefact corn starch (35.6% dry solids);

5) 950 g liquefact endosperm (28.4% starch g/g and 41.3% dry solids); and

6) 950 g liquefact ground corn (28.4% starch g/g, and 39.7% dry solids).

For substrates 1), 2) and 3), a slurry was treated at 60°C for 12 hours. Component A was heat sterilized (123°C for 20 minutes) and allowed to cool to 25°C. Both medium solutions were then considered sterile and combined. For substrates 4), 5), and 6), a substrate was mixed with Component A, and the mixture was heat sterilized (123°C for 20 minutes) and allowed to cool to 25°C.

[0266] Subsequently, the pH was adjusted to 7.0 with ammonium hydroxide (28%) and q.s. to volume. Mercury Vitamin Solution (8 mL) and antibiotics were added after solution had been cooled to 34°C.

[0267] 1000 x Modified Trace Metal Solution (per liter) : Citric Acid · H ₂ 0 40 g, MnS0 ₄ ^• H ₂ 0 30 g, NaCl 10 g, FeS0 ₄ · 7H ₂ 0 1 g, CoCl ₂ · 6H ₂ 0 1 g, ZnS0 ₄ · 7H ₂ 0 1 g, CuS0 ₄ · 5H ₂ 0 100 mg, H ₃ BO ₃ 100 mg, NaMo0 ₄ · 2H ₂ 0 100 mg. Each component was dissolved one at a time in DI H ₂ 0, pH was adjusted to 3.0 with HC1 or NaOH, and then the solution was q.s. to volume and filter sterilized with a 0.22 micron filter.

[0268] Mercury Vitamin Solution (per liter): Thiamine hydrochloride 1.0 g, D-(+)-biotin 1.0 g, nicotinic acid 1.0 g, D-pantothenic acid 4.8 g, pyridoxine hydrochloride 4.0 g. Each component was dissolved one at a time in DI H ₂ 0, pH was adjusted to 3.0 with HC1 or NaOH, and then the solution was q.s. to volume and filter sterilized with 0.22 micron filter.

[0269] The fermentation was performed in a 1.7-L bioreactor with E. coli BL21 cell strain MD09-317: t pgl FRT-PL.2-mKKDyI, pCLUpper (pMCM82) (Spec50),

pTrcAlba(MEA)mMVK (pDW34) (Carb50). Further information may be found in references cited herein. The experiment was carried out to monitor isoprene formation from the desired starch substrate at the desired fermentation pH 6.5 and temperature 34°C. A frozen vial of the E. coli strain was thawed and inoculated into tryptone- yeast extract medium. After the inoculum grew to optical density 1.0, measured at 550 nm (OD ₅₅₀ ), 40 mL was used to inoculate a 1.7-L bioreactor and bring the initial tank volume to 0.7 L. 8.2. Isoprene producing by simultaneous saccharification and fermentation (SSF) from various starch substrates with the combination of the Trichoderma reesei glucoamylase and an alpha-amylase

[0270] Starch hydrolysis was initiated at cell inoculation (time zero) by adding 8 GAU/L Trichoderma reesei glucoamylase (TrGA) and 404 AAU/L of SPEZYME™ Alpha (Danisco US Inc., Genencor Division). Additional enzymes were added in amounts shown in Table 8 in order to obtain a starch hydrolysis rate that roughly matched the glucose consumption rate of the cells.

Table 8. Amount of enzymes added to the bioreactor over time

[0271] At various time points of the SSF, samples were taken out and subjected to analysis. Similar results were obtained for the variety of starch substrates used. Representative data are presented in Figures 4-7.

[0272] Accumulated glucose levels in the fermentor broth over time are shown in FIG. 4. Induction was achieved by adding isopropyl-beta-D-l-thiogalactopyranoside (IPTG). The IPTG concentration was brought to 107 μΜ when the carbon dioxide evolution rate (CER) reached 25 mmol/L/hr. The IPTG concentration was raised to 202 μΜ when CER reached 175 mmol/L/hr. The isoprene level in the off gas from the bioreactor was determined using a PerkinElmer iScan mass spectrometer. The isoprene titer increased over the course of the fermentation to a maximum value of 7.6 g/L at 20 hrs (FIG. 5). The total amount of isoprene produced during the 20-hour fermentation was 6.0 g. The metabolic activity profile, as measured by the CER, is shown in FIG. 6. Carbon dioxide evolution rate (CER) = [24.851 * (airflow slpm / offgas N2%) * supply N2% * offgas C02%] / (Fermentor kgs / Broth density)

24.851 = (60 min/h * 1000 mmol/mol) / (100% * 24.14 liters/mol)

24.14 liters is how much volume an ideal gas occupies at 1 atm and 21.1 C.

8.3. Isoprene producing by simultaneous saccharification and fermentation (SSF) from granular starch with the Humicol grisea glucoamylase (HgGA)

[0273] Granular cornstarch was prepared as described in Example 8.1. to be use for isoprene production by fermentation. Starch hydrolysis was initiated at cell inoculation (time zero) by adding 2 GAU/L broth of HgGA. Additional enzyme was added by continuous feeding in amounts shown in Table 9 in order to obtain a starch hydrolysis rate that roughly matched the glucose consumption rate of the cells. HgGA was diluted in either 36% glucose or water in order to feed.

Table 9. Amount of HgGA added to the bioreactor over time.

[0274] At various time points of the SSF, samples were removed and subject to analysis. Accumulated glucose levels in the fermentor broth over time are shown in FIG. 8. Induction was achieved by adding isopropyl-beta-D-l-thiogalactopyranoside (IPTG). The IPTG concentration was brought to 117 μΜ when the carbon dioxide evolution rate (CER) reached 25 mmol/L/hr. The IPTG concentration was raised to 224 μΜ when CER reached 175 rnmol/L hr. The isoprene level in the off gas from the bioreactor was determined using a PerkinElmer iScan mass spectrometer. The isoprene titer increased over the course of the fermentation to a maximum value of 5.2 g/L at 35 hrs (FIG. 9). The total amount of isoprene produced during the 35 -hour fermentation was 3.4 g.. The metabolic activity profile, as measured by the CER, is shown in FIG. 10. The time course of the ratio of isoprene to carbon dioxide in the gas stream exiting the bioreactor, an indicator of product yield, is shown in FIG. 11. It was observed that both the TrGA+AA or H-GA fermentations reached the same peak instantaneous mol isoprene/mol carbon dioxide ratio (roughly 0.08; ratio correlates with instantaneous carbon yield) as a typical glucose fed-batch fermentation. The similarity of these values despite the different conditions indicates that cells produce isoprene in a comparable manner to the traditional process where glucose is fed to the fermentor. More experimentation was performed to elucidate any possible differences between the use of TrGA+AA or H-GA for the stated application, though it was shown that similar amounts of enzymatic activity units were added over the course of the fermentations. No significant differences between the use of TrGA+AA or H-GA were noted in the current data set.

[0275] Without being bound by theory, it appears that the TrGA+AA or H-GA activity is inactivated by some component in the fermentation broth, resulting in the need for continued addition of enzyme to the fermentation to produce glucose for cell utilization/isoprene formation. It was also noted that the fermentation broth dissolved oxygen level was lower than the glucose fed-batch fermentation as a result of the higher viscosity caused by the granular starch substrates. The low dissolved oxygen levels are not anticipated to be observed in fermentations utilizing the liquefact substrates.

Example 9 Isoprenoid Production under SSF Conditions Using MVA Pathway

Polypeptides

[0276] Host cells (e.g., bacterial cells) are engineered to contain nucleic acids encoding for one or more MVA pathway polypeptide and one or more polyprenyl pyrophosphate synthase polypeptides (e.g., geranyl diphosposphate (GPP) synthase, farnesyl pyrophosphate (FPP) synthase, and geranylgeranyl pyrophosphate (GGPP) synthase) and optionally IDI. The bacterial cells are cultured under SSF conditions where there is saccharification and fermentation of a starch substrate under simultaneous saccharification and fermentation (SSF) conditions in the presence of a glucoamylase, wherein the saccharification and fermentation are performed at pH 5.0 to 8.0, wherein the glucoamylase possesses at least 50% activity at pH 6.0 or above relative to its maximum activity, wherein the glucoamylase is selected from the group consisting of a parent Humicola grisea glucoamylase (HgGA) comprising SEQ ID NO: 3, a parent Trichoderma reesei glucoamylase (TrGA) comprising SEQ ID NO: 6, a parent Rhizopus sp. glucoamylase (RhGA) comprising SEQ ID NO: 9, and a variant thereof, and wherein the variant has at least 99% sequence identity to the parent glucoamylase.

Example 10 Isoprenoid Production under SSF Conditions Using DXP Pathway

Polypeptides

[0277] Host cells (e.g., bacterial cells) are engineered to contain nucleic acids encoding for one or more DXP pathway polypeptide and one or more polyprenyl pyrophosphate synthase polypeptides (e.g., geranyl diphosposphate (GPP) synthase, farnesyl pyrophosphate (FPP) synthase, and geranylgeranyl pyrophosphate (GGPP) synthase) and optionally IDI. The bacterial cells are cultured under SSF conditions where there is saccharification and fermentation of a starch substrate under simultaneous saccharification and fermentation (SSF) conditions in the presence of a glucoamylase, wherein the saccharification and fermentation are performed at pH 5.0 to 8.0, wherein the glucoamylase possesses at least 50% activity at pH 6.0 or above relative to its maximum activity, wherein the glucoamylase is selected from the group consisting of a parent Humicola grisea glucoamylase (HgGA) comprising SEQ ID NO: 3, a parent Trichoderma reesei glucoamylase (TrGA) comprising SEQ ID NO: 6, a parent Rhizopus sp. glucoamylase (RhGA) comprising SEQ ID NO: 9, and a variant thereof, and wherein the variant has at least 99% sequence identity to the parent glucoamylase.

Example 11 Isoprenoid Production under SSF Conditions Using MVA and DXP

Pathway Polypeptides

[0278] Host cells (e.g., bacterial cells) are engineered to contain nucleic acids encoding for one or more DXP pathway polypeptide, one or more MVA pathway polypeptides, and one or more polyprenyl pyrophosphate synthase polypeptides (e.g., geranyl diphosposphate (GPP) synthase, farnesyl pyrophosphate (FPP) synthase, and geranylgeranyl pyrophosphate (GGPP) synthase) and optionally IDI. The bacterial cells are cultured under SSF conditions where there is saccharification and fermentation of a starch substrate under simultaneous saccharification and fermentation (SSF) conditions in the presence of a glucoamylase, wherein the saccharification and fermentation are performed at pH 5.0 to 8.0, wherein the glucoamylase possesses at least 50% activity at pH 6.0 or above relative to its maximum activity, wherein the glucoamylase is selected from the group consisting of a parent Humicola grisea glucoamylase (HgGA) comprising SEQ ID NO: 3, a parent Trichoderma reesei glucoamylase (TrGA) comprising SEQ ID NO: 6, a parent Rhizopus sp. glucoamylase (RhGA) comprising SEQ ID NO: 9, and a variant thereof, and wherein the variant has at least 99% sequence identity to the parent glucoamylase.

SEQUENCES

SEQ ID NO: 1: genomic sequence coding the full-length Humicola grisea glucoamylase; putative introns are in bold; corresponds to SEQ ID NO. 1 of U.S. Patent 7,262,041 atgcatacct tctccaagct cctcgtcctg ggctctgccg tccagtctgc cctcgggcgg 60 cctcacggct cttcgcgtct ccaggaacgc gctgccgttg ataccttcat caacaccgag 120 aagcccatcg catggaacaa gctgctcgcc aacatcggcc ctaacggcaa agccgctccc 180 ggtgccgccg ccggcgttgt gattgccagc ccttccagga cggaccctcc ttgtacgtgg 240 tggcatggaa tggacccaag agactggttt tagatgaaag agagtttctg ctaaccgcca 300 cacccagact tcttcacctg gacccgcgat gccgccctgg tcctcaccgg catcatcgag 360 tcccttggcc acaactacaa caccaccctg cagaccgtca tccagaacta cgtcgcgtcg 420 caggccaagc tgcagcaggt ctcgaacccc tcgggaacct tcgccgacgg ctcgggtctc 480 ggtgaggcca agttcaatgt cgacctcact gccttcactg gcgaatgggg tcgccctcag 540 agggacggcc cgcccctgcg cgccatcgct ctcatccagt acgccaagtg gctgatcgcc 600 aacggctaca agagcacggc caagagcgtc gtctggcccg tcgtcaagaa cgatctcgcc 660 tacacggccc agtactggaa cgagaccggc ttcgatctct gggaggaggt ccccggcagc 720 tcgttcttta ccatcgccag ctctcacagg ggtgagtcat ttattgttca gtgttttctc 780 attgaataat taccggaatg ccactgacgc caaacagctc tgactgaggg tgcttacctc 840 gccgctcagc tcgacaccga gtgccgcgcc tgcacgaccg tcgcccctca ggttctgtgc 900 ttccagcagg ccttctggaa ctccaagggc aactatgtcg tctccaacag taagatccct 960 acaccaacaa aaaaaatcga aaaggaacgb tagctgaccc ttctagtcaa cggcggcgag 1020 tatcgctccg gcaaggacgc caactcgatc ctggcgtcca tccacaactt cgaccctgag 1080 gccggctgcg acaacctgac cttccagccc tgcagcgagc gcgccctggc caaccacaag 1140 gcctatgtcg actcgttccg caacctctac gccatcaaca agggcatcgc ccagggcaag 1200 gccgttgccg tcggccgcta ctcggaggat gtctactaca acggcaaccc gtggtacctg 1260 gccaactttg ccgccgccga gcagctctac gacgccatct acgtgtggaa caagcagggc 1320 tccatcaccg tgacctcggt ctccctgccc ttcttccgcg accttgtctc gtcggtcagc 1380 accggcacct actccaagag cagctcgacc ttcaccaaca tcgtcaacgc cgtcaaggcc 1440 tacgccgacg gcttcatcga ggtggcggcc aagtacaccc cgtccaacgg cgcgctcgcc 1500 gagcagtacg accgcaacac gggcaagccc gactcggccg ccgacctgac gtggtcgtac 1560 tcggccttcc tctcggccat cgaccgccgc gcgggtctcg tccccccgag ctggcgggcc 1620 agcgtggcca agagccagct gccgtccacc tgctcgcgca tcgaggtcgc cggcacctac 1680 gtcgccgcca cgagcacctc gttcccgtcc aagcagaccc cgaacccctc cgcggcgccc 1740 tccccgtccc cctacccgac cgcctgcgcg gacgctagcg aggtgtacgt caccttcaac 1800 gagcgcgtgt cgaccgcgtg gggcgagacc atcaaggtgg tgggcaacgt gccggcgctg 1860 gggaactggg acacgtccaa ggcggtgacc ctgtcggcca gcgggtacaa gtcgaatgat 1920 cccctctgga gcatcacggt gcccatcaag gcgacgggct cggccgtgca gtacaagtat 1980 atcaaggtcg gcaccaacgg gaagattact tgggagtcgg accccaacag gagcattacc 2040 ctgcagacgg cgtcgtctgc gggcaagtgc gccgcgcaga cggtgaatga ttcgtggcgt 2100 taa 2103

SEQ ID NO: 2: amino acid sequence of full-length Humicola grisea glucoamylase; the naf ive signal sequence is in bold; corresponds to SEQ ID NO. 2 of U.S. Patent 7,262,041

1 MHTFSKLLVL GSAVQSALGR PHGSSRLQER AAVDTFINTE KPIAWNKLLA

NIGPNGKAAP

61 GAAAGVVIAS PSRTDPPYFF TWTRDAALVL TGI IESLGHN YNTTLQTVIQ

NYVASQAKLQ

121 QVSNPSGTFA DGSGLGEAKF NVDLTAFTGE WGRPQRDGPP LRAIALIQYA

KWLIANGYKS

181 TAKSVVWPW KNDLAYTAQY WNETGFDLWE EVPGSSFFTI ASSHRALTEG

AYLAAQLDTE 241 CRACTTVAPQ VLCFQQAFWN SKGNYVVSNI NGGEYRSGKD ANSILASIHN

FDPEAGCDNL

301 TFQPCSERAL ANHKAYVDSF RNLYAINKGI AQGKAVAVGR YSEDVYYNGN

PWYLANFAAA

361 EQLYDAIYVW NKQGS ITVTS VSLPFFRDLV SSVSTGTYSK SSSTFTNIVN

AVKAYADGFI

421 EVAAKYTPSN GALAEQYDRN TGKPDSAADL TWSYSAFLSA IDRRAGLVPP

SWRASVAKSQ

481 LPSTCSRIEV AGTYVAATST SFPSKQTPNP SAAPSPSPYP TACADASEVY

VTFNERVSTA

541 WGETIKVVGN VPALGNWDTS KAVTLSASGY KSNDPLWSIT VPIKATGSAV

QYKYIKVGTN

601 GKITWESDPN RSITLQTASS AGKCAAQTVN DSWR

SEQ ID NO: 3: amino acid sequence of mature Humicola grisea glucoamylase; the native signal sequence is cleaved; corresponds to SEQ ID NO. 3 of U.S. Patent 7,262,041

1 AAVDTFINTE KPIAWNKLLA NIGPNGKAAP GAAAGVVIAS PSRTDPPYFF

TWTRDAALVL

61 TGI IESLGHN YNTTLQTVIQ NYVASQAKLQ QVSNPSGTFA DGSGLGEAKF

NVDLTAFTGE

121 WGRPQRDGPP LRAIALIQYA KWLIANGYKS TAKSVVWPVV KNDLAYTAQY

WNETGFDLWE

181 EVPGSSFFTI ASSHRALTEG AYLAAQLDTE CRACTTVAPQ VLCFQQAFWN

SKGNYVVSNI

241 NGGEYRSGKD ANSILASIHN FDPEAGCDNL TFQPCSERAL ANHKAYVDSF

RNLYAINKGI

301 AQGKAVAVGR YSEDVYYNGN PWYLANFAAA EQLYDAIYVW NKQGSITVTS

VSLPFFRDLV

361 SSVSTGTYSK SSSTFTNIVN AVKAYADGFI EVAAKYTPSN GALAEQYDRN

TGKPDSAADL

421 TWSYSAFLSA IDRRAGLVPP SWRASVAKSQ LPSTCSRIEV AGTYVAATST

SFPSKQTPNP

481 SAAPSPSPYP TACADASEVY VTFNERVSTA WGETIKVVGN VPALGNWDTS

KAVTLSASGY

541 KSNDPLWSIT VPIKATGSAV QYKYIKVGTN GKITWESDPN RSITLQTASS

AGKCAAQTVN

601 DSWR

SEQ ID NO: 4: Trichoderma reesei glucoamylase cDNA

<210> 4

<211> 1899

<212> DNA

<213> Trichoderma reesei

<400> 4

atgcacgtcc tgtcgactgc ggtgctgctc ggctccgttg ccgttcaaaa ggtcctggga 60 agaccaggat caagcggtct gtccgacgtc accaagaggt ctgttgacga cttcatcagc 120 accgagacgc ctattgcact gaacaatctt ctttgcaatg ttggtcctga tggatgccgt 180 gcattcggca catcagctgg tgcggtgatt gcatctccca gcacaattga cccggactac 240 tattacatgt ggacgcgaga tagcgctctt gtcttcaaga acctcatcga ccgcttcacc 300 gaaacgtacg atgcgggcct gcagcgccgc atcgagcagt acattactgc ccaggtcact 360 ctccagggcc tctctaaccc ctcgggctcc ctcgcggacg gctctggtct cggcgagccc 420 aagtttgagt tgaccctgaa gcctttcacc ggcaactggg gtcgaccgca gcgggatggc 480 ccagctctgc gagccattgc cttgattgga tactcaaagt ggctcatcaa caacaactat 540 cagtcgactg tgtccaacgt catctggcct attgtgcgca acgacctcaa ctatgttgcc 600 cagtactgga accaaaccgg ctttgacctc tgggaagaag tcaatgggag ctcattcttt 660 actgttgcca accagcaccg agcacttgtc gagggcgcca ctcttgctgc cactcttggc 720 cagtcgggaa gcgcttattc atctgttgct ccccaggttt tgtgctttct ccaacgattc 780 tgggtgtcgt ctggtggata cgtcgactcc aacatcaaca ccaacgaggg caggactggc 840 aaggatgtca actccgtcct gacttccatc cacaccttcg atcccaacct tggctgtgac 900 gcaggcacct tccagccatg cagtgacaaa gcgctctcca acctcaaggt tgttgtcgac 960 tccttccgct ccatctacgg cgtgaacaag ggcattcctg ccggtgctgc cgtcgccatt 1020 ggccggtatg cagaggatgt gtactacaac ggcaaccctt ggtatcttgc tacatttgct 1080 gctgccgagc agctgtacga tgccatctac gtctggaaga agacgggctc catcacggtg 1140 accgccacct ccctggcctt cttccaggag cttgttcctg gcgtgacggc cgggacctac 1200 tccagcagct cttcgacctt taccaacatc atcaacgccg tctcgacata cgccgatggc 1260 ttcctcagcg aggctgccaa gtacgtcccc gccgacggtt cgctggccga gcagtttgac 1320 cgcaacagcg gcactccgct gtctgcgctt cacctgacgt ggtcgtacgc ctcgttcttg 1380 acagccacgg cccgtcgggc tggcatcgtg cccccctcgt gggccaacag cagcgctagc 1440 acgatcccct cgacgtgctc cggcgcgtcc gtggtcggat cctactcgcg tcccaccgcc 1500 acgtcattcc ctccgtcgca gacgcccaag cctggcgtgc cttccggtac tccctacacg 1560 cccctgccct gcgcgacccc aacctccgtg gccgtcacct tccacgagct cgtgtcgaca 1620 cagtttggcc agacggtcaa ggtggcgggc aacgccgcgg ccctgggcaa ctggagcacg 1680 agcgccgccg tggctctgga cgccgtcaac tatgccgata accaccccct gtggattggg 1740 acggtcaacc tcgaggctgg agacgtcgtg gagtacaagt acatcaatgt gggccaagat 1800 ggctccgtga cctgggagag tgatcccaac cacacttaca cggttcctgc ggtggcttgt 1860 gtgacgcagg ttgtcaagga ggacacctgg cagtcgtaa 1899

SEQ ID NO: 5: Trichoderma reesei glucoamylase, full length; with signal peptide

<210> 1

<211> 632

<212> PRT

<213> Trichoderma reesei

<400> 1

Met His Val Leu Ser Thr Ala Val Leu Leu Gly Ser Val Ala Val Gin

1 5 10 15

Lys Val Leu Gly Arg Pro Gly Ser Ser Gly Leu Ser Asp Val Thr Lys

20 25 30

Arg Ser Val Asp Asp Phe He Ser Thr Glu Thr Pro He Ala Leu Asn

35 40 45

Asn Leu Leu Cys Asn Val Gly Pro Asp Gly Cys Arg Ala Phe Gly Thr

50 55 60

Ser Ala Gly Ala Val He Ala Ser Pro Ser Thr He Asp Pro Asp Tyr

65 70 75 80

Tyr Tyr Met Trp Thr Arg Asp Ser Ala Leu Val Phe Lys Asn Leu He

85 90 95

Asp Arg Phe Thr Glu Thr Tyr Asp Ala Gly Leu Gin Arg Arg He Glu

100 105 110

Gin Tyr He Thr Ala Gin Val Thr Leu Gin Gly Leu Ser Asn Pro Ser

115 120 125

Gly Ser Leu Ala Asp Gly Ser Gly Leu Gly Glu Pro Lys Phe Glu Leu

130 135 140

Thr Leu Lys Pro Phe Thr Gly Asn Trp Gly Arg Pro Gin Arg Asp Gly

145 150 155 160

Pro Ala Leu Arg Ala He Ala Leu He Gly Tyr Ser Lys Trp Leu He

165 170 175

Asn Asn Asn Tyr Gin Ser Thr Val Ser Asn Val He Trp Pro He Val

180 185 190

Arg Asn Asp Leu Asn Tyr Val Ala Gin Tyr Trp Asn Gin Thr Gly Phe

195 200 205

Asp Leu Trp Glu Glu Val Asn Gly Ser Ser Phe Phe Thr Val Ala Asn 210 215 220

Gin His Arg Ala Leu Val Glu Gly Ala Thr Leu Ala Ala Thr Leu Gly

225 230 235 240

Gin Ser Gly Ser Ala Tyr Ser Ser Val Ala Pro Gin Val Leu Cys Phe

245 250 255

Leu Gin Arg Phe Trp Val Ser Ser Gly Gly Tyr Val Asp Ser Asn He

260 265 270

Asn Thr Asn Glu Gly Arg Thr Gly Lys Asp Val Asn Ser Val Leu Thr

275 280 285

Ser He His Thr Phe Asp Pro Asn Leu Gly Cys Asp Ala Gly Thr Phe

290 295 300

Gin Pro Cys Ser Asp Lys Ala Leu Ser Asn Leu Lys Val Val Val Asp

305 310 315 320

Ser Phe Arg Ser He Tyr Gly Val Asn Lys Gly He Pro Ala Gly Ala

325 330 335

Ala Val Ala He Gly Arg Tyr Ala Glu Asp Val Tyr Tyr Asn Gly Asn

340 345 350

Pro Trp Tyr Leu Ala Thr Phe Ala Ala Ala Glu Gin Leu Tyr Asp Ala

355 360 365

He Tyr Val Trp Lys Lys Thr Gly Ser He Thr Val Thr Ala Thr Ser

370 375 380

Leu Ala Phe Phe Gin Glu Leu Val Pro Gly Val Thr Ala Gly Thr Tyr

385 390 395 400

Ser Ser Ser Ser Ser Thr Phe Thr Asn He He Asn Ala Val Ser Thr

405 410 415

Tyr Ala Asp Gly Phe Leu Ser Glu Ala Ala Lys Tyr Val Pro Ala Asp

420 425 430

Gly Ser Leu Ala Glu Gin Phe Asp Arg Asn Ser Gly Thr Pro Leu Ser

435 440 445

Ala Leu His Leu Thr Trp Ser Tyr Ala Ser Phe Leu Thr Ala Thr Ala

450 455 460

Arg Arg Ala Gly He Val Pro Pro Ser Trp Ala Asn Ser Ser Ala Ser

465 470 475 480

Thr He Pro Ser Thr Cys Ser Gly Ala Ser Val Val Gly Ser Tyr Ser

485 490 495

Arg Pro Thr Ala Thr Ser Phe Pro Pro Ser Gin Thr Pro Lys Pro Gly

500 505 510

Val Pro Ser Gly Thr Pro Tyr Thr Pro Leu Pro Cys Ala Thr Pro Thr

515 520 525

Ser Val Ala Val Thr Phe His Glu Leu Val Ser Thr Gin Phe Gly Gin

530 535 540

Thr Val Lys Val Ala Gly Asn Ala Ala Ala Leu Gly Asn Trp Ser Thr

545 550 555 560

Ser Ala Ala Val Ala Leu Asp Ala Val Asn Tyr Ala Asp Asn His Pro

565 570 575

Leu Trp He Gly Thr Val Asn Leu Glu Ala Gly Asp Val Val Glu Tyr

580 585 590

Lys Tyr He Asn Val Gly Gin Asp Gly Ser Val Thr Trp Glu Ser Asp

595 600 605

Pro Asn His Thr Tyr Thr Val Pro Ala Val Ala Cys Val Thr Gin Val

610 615 620

Val Lys Glu Asp Thr Trp Gin Ser

625 630

SEQ ID NO: 6: Trichoderma reesei glucoamylase, mature protein; without signal peptide

<210> 2

<211> 599

<212> PRT

<213> Trichoderma reesei

<400> 2

Ser Val Asp Asp Phe He Ser Thr Glu Thr Pro He Ala Leu Asn Asn

1 5 10 15

Leu Leu Cys Asn Val Gly Pro Asp Gly Cys Arg Ala Phe Gly Thr Ser

20 25 30 Ala Gly Ala Val He Ala Ser Pro Ser Thr He Asp Pro Asp Tyr Tyr

35 40 45

Tyr Met Trp Thr Arg Asp Ser Ala Leu Val Phe Lys Asn Leu He Asp

50 55 60

Arg Phe Thr Glu Thr Tyr Asp Ala Gly Leu Gin Arg Arg He Glu Gin

65 70 75 80

Tyr He Thr Ala Gin Val Thr Leu Gin Gly Leu Ser Asn Pro Ser Gly

o O 90 95

Ser Leu Ala Asp Gly Ser Gly Leu Gly Glu Pro Lys Phe Glu Leu Thr

100 105 110

Leu Lys Pro Phe Thr Gly Asn Trp Gly Arg Pro Gin Arg Asp Gly Pro

115 120 125

Ala Leu Arg Ala He Ala Leu He Gly Tyr Ser Lys Trp Leu He Asn

130 135 140

Asn Asn Tyr Gin Ser Thr Val Ser Asn Val He Trp Pro He Val Arg

145 150 155 160

Asn Asp Leu Asn Tyr Val Ala Gin Tyr Trp Asn Gin Thr Gly Phe Asp

165 170 175

Leu Trp Glu Glu Val Asn Gly Ser Ser Phe Phe Thr Val Ala Asn Gin

1 1 fio nu 185 190

His Arg Ala Leu Val Glu Gly Ala Thr Leu Ala Ala Thr Leu Gly Gin

195 200 205

Ser Gly Ser Ala Tyr Ser Ser Val Ala Pro Gin Val Leu Cys Phe Leu

210 215 220

Gin Arg Phe Trp Val Ser Ser Gly Gly Tyr Val Asp Ser Asn He Asn

225 230 235 240

Thr Asn Glu Gly Arg Thr Gly Lys Asp Val Asn Ser Val Leu Thr Ser

245 250 255

He His Thr Phe Asp Pro Asn Leu Gly Cys Asp Ala Gly Thr Phe Gin

260 265 270

Pro Cys Ser Asp Lys Ala Leu Ser Asn Leu Lys Val Val Val Asp Ser

275 280 285

Phe Arg Ser He Tyr Gly Val Asn Lys Gly He Pro Ala Gly Ala Ala

290 295 300

Val Ala He Gly Arg Tyr Ala Glu Asp Val Tyr Tyr Asn Gly Asn Pro

305 310 315 320

Trp Tyr Leu Ala Thr Phe Ala Ala Ala Glu Gin Leu Tyr Asp Ala He

325 330 335

Tyr Val Trp Lys Lys Thr Gly Ser He Thr Val Thr Ala Thr Ser Leu

340 345 350

Ala Phe Phe Gin Glu Leu Val Pro Gly Val Thr Ala Gly Thr Tyr Ser

355 360 365

Ser Ser Ser Ser Thr Phe Thr Asn He He Asn Ala Val Ser Thr Tyr

370 375 380

Ala Asp Gly Phe Leu Ser Glu Ala Ala Lys Tyr Val Pro Ala Asp Gly

385 390 395 400

Ser Leu Ala Glu Gin Phe Asp Arg Asn Ser Gly Thr Pro Leu Ser Ala

405 410 415

Leu His Leu Thr Trp Ser Tyr Ala Ser Phe Leu Thr Ala Thr Ala Arg

420 425 430

Arg Ala Gly He Val Pro Pro Ser Trp Ala Asn Ser Ser Ala Ser Thr

435 440 445

He Pro Ser Thr Cys Ser Gly Ala Ser Val Val Gly Ser Tyr Ser Arg

450 455 460

Pro Thr Ala Thr Ser Phe Pro Pro Ser Gin Thr Pro Lys Pro Gly Val

465 470 475 480

Pro Ser Gly Thr Pro Tyr Thr Pro Leu Pro Cys Ala Thr Pro Thr Ser

485 490 495

Val Ala Val Thr Phe His Glu Leu Val Ser Thr Gin Phe Gly Gin Thr

500 505 510

Val Lys Val Ala Gly Asn Ala Ala Ala Leu Gly Asn Trp Ser Thr Ser

515 520 525

Ala Ala Val Ala Leu Asp Ala Val Asn Tyr Ala Asp Asn His Pro Leu

530 535 540

Trp He Gly Thr Val Asn Leu Glu Ala Gly Asp Val Val Glu Tyr Lys

545 550 555 560

Tyr He Asn Val Gly Gin Asp Gly Ser Val Thr Trp Glu Ser Asp Pro 565 570 575

Asn His Thr Tyr Thr Val Pro Ala Val Ala Cys Val Thr Gin Val Val

580 585 590

Lys Glu Asp Thr Trp Gin Ser

595

SEQ ID NO: 7: Trichoderma reesei glucoamylase catalytic domain, 1-453 of mature TrGA, catalytic domain

<210> 3

<211> 453

<212> PRT

<213> Trichoderma reesei

<400> 3

Ser Val Asp Asp Phe He Ser Thr Glu Thr Pro He Ala Leu Asn Asn

1 5 10 15

Leu Leu Cys Asn Val Gly Pro Asp Gly Cys Arg Ala Phe Gly Thr Ser

20 25 30

Ala Gly Ala Val He Ala Ser Pro Ser Thr He Asp Pro Asp Tyr Tyr

35 40 45

Tyr Met Trp Thr Arg Asp Ser Ala Leu Val Phe Lys Asn Leu He Asp

50 55 60

Arg Phe Thr Glu Thr Tyr Asp Ala Gly Leu Gin Arg Arg He Glu Gin

65 70 75 80

Tyr He Thr Ala Gin Val Thr Leu Gin Gly Leu Ser Asn Pro Ser Gly

85 90 95

Ser Leu Ala Asp Gly Ser Gly Leu Gly Glu Pro Lys Phe Glu Leu Thr

100 105 110

Leu Lys Pro Phe Thr Gly Asn Trp Gly Arg Pro Gin Arg Asp Gly Pro

115 120 125

Ala Leu Arg Ala He Ala Leu He Gly Tyr Ser Lys Trp Leu He Asn

130 135 140

Asn Asn Tyr Gin Ser Thr Val Ser Asn Val He Trp Pro He Val Arg

145 150 155 160

Asn Asp Leu Asn Tyr Val Ala Gin Tyr Trp Asn Gin Thr Gly Phe Asp

165 170 175

Leu Trp Glu Glu Val Asn Gly Ser Ser Phe Phe Thr Val Ala Asn Gin

180 185 190

His Arg Ala Leu Val Glu Gly Ala Thr Leu Ala Ala Thr Leu Gly Gin

195 200 205

Ser Gly Ser Ala Tyr Ser Ser Val Ala Pro Gin Val Leu Cys Phe Leu

210 215 220

Gin Arg Phe Trp Val Ser Ser Gly Gly Tyr Val Asp Ser Asn He Asn

225 230 235 240

Thr Asn Glu Gly Arg Thr Gly Lys Asp Val Asn Ser Val Leu Thr Ser

245 250 255

He His Thr Phe Asp Pro Asn Leu Gly Cys Asp Ala Gly Thr Phe Gin

260 265 270

Pro Cys Ser Asp Lys Ala Leu Ser Asn Leu Lys Val Val Val Asp Ser

275 280 285

Phe Arg Ser He Tyr Gly Val Asn Lys Gly He Pro Ala Gly Ala Ala

290 295 300

Val Ala He Gly Arg Tyr Ala Glu Asp Val Tyr Tyr Asn Gly Asn Pro

305 310 315 320

Trp Tyr Leu Ala Thr Phe Ala Ala Ala Glu Gin Leu Tyr Asp Ala He

325 330 335

Tyr Val Trp Lys Lys Thr Gly Ser He Thr Val Thr Ala Thr Ser Leu

340 345 350

Ala Phe Phe Gin Glu Leu Val Pro Gly Val Thr Ala Gly Thr Tyr Ser

355 360 365

Ser Ser Ser Ser Thr Phe Thr Asn He He Asn Ala Val Ser Thr Tyr

370 375 380

Ala Asp Gly Phe Leu Ser Glu Ala Ala Lys Tyr Val Pro Ala Asp Gly

385 390 395 400

Ser Leu Ala Glu Gin Phe Asp Arg Asn Ser Gly Thr Pro Leu Ser Ala 405 410 415

Leu His Leu Thr Trp Ser Tyr Ala Ser Phe Leu Thr Ala Thr Ala Arg

420 425 430

Arg Ala Gly lie Val Pro Pro Ser Trp Ala Asn Ser Ser Ala Ser Thr

435 440 445

lie Pro Ser Thr Cys

450

SEQ ID NO: 8: native R GA (P07683.2 GI: 1168453)

1 mqlfnlplkv sfflvlsyfs llvsaasips sasvqldsyn ydgstfsgki yvkniayskk

61 vtviyadgsd nwnnngntia asysapisgs nyeywtfsas ingikefyik yevsgktyyd

121 nnnsanyqvs tskpttttat attttapsts tttppsrsep atfptgnsti sswikkqegi

181 srfarnlrnin ppgsatgfia aslstagpdy yyawtrdaal tsnvivyeyn ttlsgnktil

241 nvlkdyvtfs vktqststvc nclgepkfnp dasgytgawg rpqndgpaer attfilfads

301 yltqtkdasy vtgtlkpaif kdldyvvnvw sngcfdlwee vngvhfytlm vrarkglllga

361 dfakrngdst rastysstas tiankissfw vssnnwiqvs qsvtggvskk gldvstllaa

421 nlgsvddgff tpgsekilat avavedsfas lypinknlps ylgnsigryp edtyngngns

481 qgnswflavt gyaelyyrai kewignggvt vssislpffk kfdssatsgk kytvgtsdfn

541 nlaqnialaa drflstvqlh ahnngslaee fdrttglstg ardltwshas litasyakag

601 apaa

SEQ ID NO: 9: mature RhGA (P07683.2 GI: 1168453)

1 asipssasvq ldsynydgst fsgkiyvkni ayskkvtviy adgsdnwnnn gntiaasysa

61 pisgsnyeyw tfsasingik efyikyevsg ktyydnnnsa nyqvstskpt tttatatttt

121 apststttpp srsepatfpt gnstisswik kqegisrfam Irninppgsa tgfiaaslst

181 agpdyyyawt rdaaltsnvi vyeynttlsg nktilnvlkd yvtfsvktqs tstvcnclge

241 pkfnpdasgy tgawgrpqnd gpaerattfi ifadsyltqt kdasyvtgtl kpaifkdldy

301 vvnvwsngcf dlweevngvh fytlrnvmrkg lllgadfakr ngdstrasty sstastiank

361 issfwvssnn wiqvsqsvtg gvskkgldvs tllaanlgsv ddgfftpgse kilatavave

421 dsfaslypin knlpsylgns igrypedtyn gngnsqgnsw flavtgyael yyraikewig

481 nggvtvssis lpffkkfdss atsgkkytvg tsdfnnlaqn ialaadrfIs tvqlhahnng

541 slaeefdrtt glstgardlt wshaslitas yakagapaa