RECYCLING

BACKGROUND OF THE INVENTION

[0001] The conversion of biomass, such as corn, sugarcane or other energy crops, as well as simple sugars, to ethanol is routinely completed through the use of yeast fermentation. However, during yeast metabolism a major by-product of fermentation is glycerol.

[0002] Glycerol is a required metabolic end-product of native yeast ethanol fermentation allowing the yeast to balance its redox state and regenerate NAD ⁺ used as a cofactor during glycolysis. During anaerobic growth on carbohydrates, production of ethanol and carbon dioxide is redox neutral, while the reactions that create cell biomass and associated carbon dioxide are more oxidized relative to carbohydrates. The production of glycerol, which is more reduced relative to carbohydrates, functions as an electron sink to off-set cell biomass formation, so that overall redox neutrality is conserved. This is essential from a theoretical consideration of conservation of mass, and in practice strains unable to produce glycerol are unable to grow under anaerobic conditions.

[0003] As glycerol is a byproduct with low value, it can be an undesirable by-product of fermentation. There is a strong commercial incentive to reduce glycerol as a by-product during the production of fuels and chemicals, as reduction typically results in an increased yield of the desired compound. Thus, it would be beneficial to reduce or eliminate the endogenous production of this by-product and further direct more carbon towards desired end-products, such as ethanol and other fuels and chemicals, including but not limited to isopropanol.

[0004] Several strategies are available in the art for the conversion of glycerol to higher value products though biochemical or other means. In addition, various strategies have been employed to reduce glycerol production, which may lead to an improvement of overall sugar yield to ethanol or other desired end-products of metabolism. See Nielsen, J., et al. "Metabolic engineering of yeast for production of fuels and chemicals," Curr. Opin. Biotechnol. 24: 1-1 (2013). Through engineering of alternate pathways, with the simultaneous reduction or deletion of the glycerol pathway, alternate or replacement electron acceptors for the regeneration of NAD ⁺ can be used during yeast metabolism. Examples of such alternate or replacement electron acceptors include molecules such as formate or hydrogen.

[0005] The elimination of glycerol synthesis genes has been demonstrated but removal of this pathway completely blocked anaerobic growth of the yeast, preventing useful application during an industrial process. Ansell, R., et al, EMBO J. 7(5:2179-87 (1997); Pahlman, A-K., et al, J. Biol. Chem. 27(5:3555-63 (2001); Guo, ZP., et al, Metab. Eng. 13:49-59 (2011). Other methods to bypass glycerol formation require the co-utilization of additional carbon sources, such as xylose or acetate, to serve as electron acceptors. Liden, G., et al, Appl. Env. Microbiol. (52:3894-96 (1996); Medina, V.G., et al, Appl. Env. Microbiol. 7(5: 190-195 (2010). The engineering of a pyruvate formate lyase from E. coli, which is capable of converting pyruvate to formate, was performed previously to increase formate production. Waks, Z., and Silver, P.A., Appl. Env. Microbiol. 75: 1867- 1875 (2009). As demonstrated in International Application No. WO 2012/138942, which is incorporated by reference herein in its entirety, incorporation of a formate pathway as an alternate electron acceptor allows for glycerol formation to be bypassed and ethanol yield to be increased.

[0006] In addition to its known role during anaerobic growth, glycerol is also synthesized by S. cerevisiae in response to osmotic stress. The formation of glycerol is mediated in part by the activity of two glycerol-3-phosphate dehydrogenases: GPD1 and GPD2. Glycerol formed in response to osmotic stress is mediated primarily through the action of GPD1, whereas glycerol formed as an electron sink for excess electrons generated during production of biomass during anaerobic growth is mediated primarily through the action of GPD2. See Ansell, et al, "The two isoenzymes for yeast NAD ⁺ -dependent glycerol 3- phosphate dehydrogenase encoded by GPD1 and GPD2 have distinct roles in osmoadaptation and redox regulation," The EMBO Journal 7(5:2179-87 (1997). Glycerol is exported from the yeast cell through an aquaporin channel known as FPS1. This channel is closed in response to osmotic stress in order to reduce glycerol efflux from the cell, thereby enabling accumulation of higher levels of intracellular glycerol. See Remize, F., et al, "Glycerol Export and Glycerol-3 -phosphate Dehydrogenase, but Not Glycerol Phosphatase, Are Rate Limiting for Glycerol Production in Saccharomyces cerevisiae," Metabol. Engineering 5:301-12 (2001). In addition, the yeast cell can increase intracellular glycerol levels through uptake of glycerol from the extracellular environment through the action of another glycerol transporter known as STL1. The expression of STL1, however, is limited by transcriptional repression of the gene in the presence of glucose. See Ferreira, C, et al., "A Member of the Sugar Transporter Family, Stllp Is the Glycerol/H ⁺ Symporter in Saccharomyces cerevisiae " Mol. Biol. Cell 76:2068-76 (2005) and Tulha, J., et al., "Saccharomyces cerevisiae glycerol/H ⁺ symporter Stllp is essential for cold, near- freeze, and freeze stress adaptation. A simple recipe with high biotechnological potential is given," Microb. Cell Factories :82 (2010).

[0007] The production of glycerol in response to osmotic stress has been identified and reviewed. See Petrovska, B. et al., "Glycerol production by yeasts under osmotic and sulfite stress," Can J Microbiol 45:695-699 (1999) and Hohmann, et al, "Yeast Osmoregulation," Methods in Enzymology 428:29-45 (2007). Anaerobic glycerol production in response to osmotic stress, however, cannot occur in the absence of an accompanying oxidation reaction. Under anaerobic conditions, a yeast strain in stationary phase needs to generate reducing power to make glycerol in response to osmotic stress. The net result is that in addition to making glycerol in response to osmotic stress, the organism must also make an oxidized end product which further reduces the yield of the desired product.

[0008] It has been shown that an increase in acetate, pyruvate and succinate production accompanies anaerobic glycerol production in response to osmotic stress. See Modig, T., et al., "Anaerobic glycerol production by Saccharomyces cerevisiae strains under hyperosmotic stress," Appl Microbiol Biotechnol 75:289-96 (2007). The concentration of these metabolites, however, was only sufficient to produce approximately half of the necessary NADH needed to balance the increase in glycerol. In a separate study, elevated levels of pyruvate, succinate, acetaldehyde, acetoin and 2,3-butanediol were observed in wine strains engineered to produce more glycerol. See Remize, D.F., et al., "Glycerol Overproduction by Engineered Saccharomyces cerevisiae Wine yeast Strains Leads to Substantial Changes in By -Product Formation and to a Stimulation of Fermentation Rate in Stationary Phase," Appl. Environ. Microbiol. 65(1):143 (1999). The production of these compounds was reflected in the redox and carbon balance although the relationship was not elaborated upon.

[0009] The importance of reducing glycerol production is exemplified in the process of corn mash fermentation. About 16 billion gallons of corn-based ethanol are produced annually, so even small increases in ethanol yield, such as 5-10%, can translate into an extra billion or so gallons of ethanol over current yields. Industrial corn mash fermentation by S. cerevisiae typically results in approximately 5 g/L cells and glycerol yields ranging from 10-12 g/L. See Yang, R.D., et ah, "Pilot plant studies of ethanol production from whole ground corn, corn flour, and starch," Fuel Alcohol U.S.A., February 13-16, 1982 (reported glycerol levels to be as high as 7.2% w/w of initial sugar consumed in normal corn mash fermentations or approximately 1.4 g/100 mL using 20% sugar). During anaerobic growth, it has been empirically determined in the literature that about 9-11 mM glycerol are formed per gram of dry cell weight ("DCW"), which is approximately a 1 :1 mass ratio of glycerol to DCW (1 gram of glycerol is produced per gram of cells). The reducing power needed to make glycerol is available from the pool of surplus NADH generated from biosynthetic reactions. Based on the biomass and glycerol assumptions above, a minimum of 5 g/L glycerol is formed independent of anaerobic growth, presumably as part of the organisms osmotic stress response. By reducing or eliminating the glycerol yield in the production of ethanol from corn mash, for example, fermentation and re-engineering metabolic processes, increased ethanol yields can be achieved.

[0010] Additional benefits may be gained in the production of ethanol from corn. Corn mash is a nutrient rich medium, in some cases containing lipid and protein content that can be >3% of the total fermentation volume. As a result of the energy contained in these components, even higher ethanol yields may be achieved than what is predicted using, for example, pure sugar. The additional increases can come from the metabolism of lipids or amino acids in the corn mash medium. The recombinant cells and methods of the invention enable increasing ethanol yields from biomass fermentation by reducing or modulating glycerol production and regulation.

BRIEF SUMMARY OF THE INVENTION

[0011] The invention is generally directed to the reduction or modulation of glycerol production in a host cell through engineering of the host cell to take up extracellular glycerol in the presence of glucose. The recombinant cells and methods of the invention enable cells to accumulate higher intracellular concentrations of glycerol to improve robustness and decrease the requirement to produce it as part of the stress response pathway. In contrast to other efforts to reduce or eliminate cellular glycerol production or to use glycerol as a fermentative substrate, the present invention uses existing glycerol present in fermentation medium to lower cellular glycerol production through glycerol uptake. Engineering of an alternate electron acceptor in the host cell for the regeneration of NAD ⁺ may also be performed.

[0012] An aspect of the invention relates to a recombinant microorganism comprising: (a) one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism, wherein said one or more native and/or heterologous proteins is activated, upregulated, or overexpressed; and (b) one or more native and/or heterologous enzymes that function in one or more engineered metabolic pathways to convert a carbohydrate source to an alcohol, wherein said one or more native and/or heterologous enzymes is activated, upregulated, overexpressed, or downregulated.

[0013] In certain embodiments, the recombinant microorganism produces less glycerol than a control recombinant microorganism without activation, upregulation, or overexpression of said one or more native and/or heterologous proteins that function to import glycerol.

[0014] In some embodiments, the one or more native and/or heterologous proteins that function to import glycerol is STL1. In certain embodiments, the STL1 is derived from S. cerevisiae. In some embodiments, the carbohydrate source is biomass.

[0015] In some aspects of the invention, the recombinant microorganism further comprises one or more native and/or heterologous proteins that function to export glycerol from the microorganism, wherein said one or more native and/or heterologous enzymes that function to export glycerol is activated, upregulated, or downregulated. In certain embodiments, the heterologous proteins that function to export glycerol from the microorganism are deleted. In some embodiments, the one or more native and/or heterologous proteins that function to export glycerol from the microorganism is FPS1. In certain embodiments, the activated or upregulated native and/or heterologous protein that functions to export glycerol from the microorganism is a constitutive ly active FPS1 (fpsl-1).

[0016] In some aspects of the invention, the recombinant microorganism further comprises a deletion or downregulation of one or more native enzymes that function to produce glycerol and/or regulate glycerol synthesis. In certain embodiments, the one or more native enzymes that function to produce glycerol is encoded by a gpdl polynucleotide, a gpd2 polynucleotide, or both a gpdl polynucleotide and a gpd2 polynucleotide. In some embodiments, the recombinant microorganism further comprises a native and/or heterologous gpdl polynucleotide operably linked to a native gpd2 promoter polynucleotide. In certain embodiments, the one or more native enzymes that function to produce glycerol is encoded by a gppl polynucleotide, a gpp2 polynucleotide, or both a gppl polynucleotide and a gpp2 polynucleotide.

[0017] In certain aspects of the invention, the one or more engineered metabolic pathways comprise conversion of acetyl-CoA to an alcohol. In some embodiments, the acetyl-CoA is converted to acetaldehyde by an acetaldehyde dehydrogenase, and the acetaldehyde is converted to an alcohol by an alcohol dehydrogenase. In certain embodiments, the acetyl-CoA is converted to an alcohol by a bifunctional acetaldehyde/alcohol dehydrogenase. In some embodiments, the acetaldehyde dehydrogenase, alcohol dehydrogenase, or bifunctional acetaldehyde/alcohol dehydrogenase is of prokaryotic or eukaryotic origin. In certain embodiments, the acetaldehyde dehydrogenase is from C. phytofermentans . In some embodiments, the bifunctional acetaldehyde/alcohol dehydrogenase is from an Escherichia, a Clostridia, a Chlamydomonas, a Piromyces, or a Bifidobacteria species. In certain embodiments, the bifunctional acetaldehyde/alcohol dehydrogenase is from Escherichia coli, Clostridium phytofermentans, Chlamydomonas reinhardtii, Piromyces sp. E2, or Bifidobacterium adolescentis . In some embodiments, the bifunctional acetaldehyde/alcohol dehydrogenase is from a Bifidobacterium adolescentis or Piromyces sp. E2.

[0018] In some aspects of the invention, the one or more engineered metabolic pathways comprise conversion of pyruvate to acetyl-CoA and formate. In certain embodiments, the pyruvate is converted to acetyl-CoA and formate by a pyruvate formate lyase (PFL). In some embodiments, the PFL is of prokaryotic or eukaryotic origin. In certain embodiments, the PFL is from one or more of a Bifidobacteria, an Escherichia, a Thermoanaerobacter, a Clostridia, a Streptococcus, a Lactobacillus, a Chlamydomonas, a Piromyces, a Neocallimastix, or a Bacillus species. In some embodiments, the PFL is from one or more of a Bacillus licheniformis, a Streptococcus thermophilus, a Lactobacillus plantarum, a Lactobacillus casei, a Bifidobacterium adolescentis, a Clostridium cellulolyticum, an Escherichia coli, a Chlamydomonas reinhardtii PflA, a Piromyces sp. E2, or a Neocallimastix frontalis. In some embodiments, the PFL is from a Bifidobacterium adolescentis. In some embodiments, the recombinant microorganism overexpresses a PflA and/or PflB.

[0019] In certain aspects of the invention, the one or more engineered metabolic pathways is the pentose phosphate pathway (PPP). In some embodiments, the one or more engineered metabolic pathways comprises the conversion of D-xylulose 5- phosphate to D-glyceraldehyde 3-phosphate or the conversion of D-fructose 6-phosphate to D-erythrose 4-phosphate. In certain embodiments, the D-xylulose 5-phosphate is converted to D-glyceraldehyde 3-phosphate by a phosphoketolase. In some embodiments, the phosphoketolase is a single-specificity phosphokelotase. In certain embodiments, the D-fructose 6-phosphate is converted to D-erythrose 4-phosphate by a phosphoketolase. In certain embodiments, the phosphoketolase is a dual-specificity phosphokelotase.

[0020] In certain aspects of the invention, the one or more engineered metabolic pathways comprises the conversion of acetate to acetyl-CoA. In some embodiments, the acetate is converted to acetyl-P by an acetate kinase, and wherein acetyl-P is converted to acetyl-CoA by a phosphotransacetylase. In certain embodiments, the acetate is converted to acetyl-CoA by an acetyl-CoA synthetase.

[0021] In some aspects of the invention, the one or more engineered metabolic pathways comprises one or more native and/or heterologous enzymes that encodes a saccharolytic enzyme. In certain embodiments, the saccharolytic enzyme is selected from the group consisting of amylases, cellulases, hemicellulases, cellulolytic and amylolytic accessory enzymes, inulinases, levanases, and pentose sugar utilizing enzymes. In some embodiments, the cellulase is xylanase. In certain embodiments, the saccharolytic enzyme is from a microorganism selected from the group consisting of H. grisea, T. aurantiacus, T. emersonii, T. reesei, C. lacteus, C. formosanus, N. takasagoensis, C. acinaciformis, M. darwinensis, N. walkeri, S. fibuligera, C. lucknowense R. speratus, Thermobfida fusca, Clostridum thermocellum, Clostridium cellulolyticum, Clostridum josui, Bacillus pumilis, Cellulomonas fimi, Saccharophagus degradans, Piromyces equii, Neocallimastix patricarum, Arabidopsis thaliana, and S. fibuligera. In some embodiments, the saccharolytic enzyme is a glucoamylase. In certain embodiments, the glucoamylase is S. fibuligera glucoamylase (glu-0111-CO). In some embodiments, the saccharolytic enzyme is a hemicellulase. The hemicellulase can be derived from any number of organisms, including but not limited to a microorganism selected from the group consisting of Neosartorya fischeri, Pyrenophora tritici-repentis, Aspergillus niger, Aspergillus fumigatus, Aspergillus oryzae, Trichoderma reesei, and Aspergillus Aculeatus. Additional examples of hemicellulases that can be used in the present invention are described in co-owned International Application No. PCT/US2014/026499 filed March 13, 2014, which is incorporated by reference in its entirety herein.

[0022] In certain aspects of the invention, the microorganism further comprises one or more native and/or heterologous enzymes that function in one or more engineered metabolic pathways to convert xylose to xylulose-5 -phosphate and/or arabinose to xylulose-5-phosphate, wherein said one or more native and/or heterologous enzymes is activated, upregulated or downregulated. In some embodiments, the one or more native and/or heterologous enzymes that function to convert xylose to xylulose-5 -phosphate is xylose isomerase. In certain embodiments, the one or more native and/or heterologous enzymes that function to convert arabinose to xylulose-5 -phosphate is selected from the group consisting of arabinose isomerase, ribulokinase, and ribulose 5-phosphate epimerase.

[0023] In some embodiments, one or more engineered metabolic pathways comprises the conversion of trehalose to acetyl-CoA. In certain embodiments, the one or more native and/or heterologous enzymes functions to convert trehalose to glucose.

[0024] In certain aspects of the invention, the alcohol is ethanol or isopropanol. In some embodiments, the microorganism produces ethanol. In certain embodiments, the microorganism produces isopropanol.

[0025] In some aspects of the invention, the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism increases intracellular glycerol concentration. In certain embodiments, the recombinant microorganism increases intracellular glycerol by at least about 0.01 to 10 fold glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In some embodiments, the recombinant microorganism increases intracellular glycerol by at least about 0.05 to 5 fold glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In certain embodiments, the recombinant microorganism increases intracellular glycerol by at least about 0.1 to 2 fold glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol.

In some embodiments, the recombinant microorganism increases intracellular glycerol by: (a) at least about 0.01 -fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (b) at least about 0.05 -fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (c) at least about 0.1 -fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (d) at least about 0.2-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (e) at least about 0.3-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (f) at least about 0.4-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (g) at least about 0.5 -fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (h) at least about 0.6-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (i) at least about 0.7-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; j) at least about 0.8-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (k) at least about 0.9-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (1) at least about 1.0-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (m) at least about 1.1 -fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (n) at least about 1.2-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (o) at least about 1.3 -fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (p) at least about 1.4-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (q) at least about 1.5 -fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (r) at least about 1.6-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (s) at least about 1.7-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (t) at least about 1.8-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (u) at least about 1.9-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (v) at least about 2.0-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (w) at least about 3.0-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (x) at least about 4.0-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (y) at least about 5.0-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (z) at least about 6.0-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (aa) at least about 7.0-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (bb) at least about 8.0-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (cc) at least about 9.0-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; or (dd) at least about 10.0-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol.

In certain embodiments, the recombinant microorganism increases intracellular glycerol by: by: (a) at least about 0.05-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (b) at least about 0.1 -fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (c) at least about 0.5-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (d) at least about 1.0-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (e) at least about 1.5 -fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; or (f) at least about 1.7-fold more intracellular glycerol than is present in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol.

In certain embodiments, the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism reduces glycerol formation. In certain embodiments, the recombinant microorganism reduces glycerol formation by at least about 1% to 100% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In some embodiments, the recombinant microorganism reduces glycerol formation by at least about 10% to 90% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In some embodiments, the recombinant microorganism reduces glycerol formation by at least about 20% to 80% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In some embodiments, the recombinant microorganism reduces glycerol formation by at least about 30% to 60% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In some embodiments, the recombinant microorganism reduces glycerol formation by at least about 40% to 50% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In some embodiments, the recombinant microorganism reduces glycerol formation by: (a) more than about 1% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (b) more than about 5% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (c) more than about 10% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (d) more than about 15% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (e) more than about 20% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (f) more than about 25% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (g) more than about 30% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (h) more than about 35% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (i) more than about 40% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (j) more than about 45% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (k) more than about 50% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (1) more than about 55% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (m) more than about 60% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (n) more than about 65% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (o) more than about 70% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (p) more than about 75% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (q) more than about 80% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (r) more than about 85% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (s) more than about 90% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (t) more than about 95% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; or (u) more than about 100% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol.

In some embodiments, the recombinant microorganism reduces glycerol formation by: (a) more than about 5% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (b) more than about 10% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (c) more than about 15% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (d) more than about 20% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; or (e) more than about 30% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol.

[0031] In some embodiments, the one or more engineered metabolic pathways of the recombinant microorganism comprises conversion of pyruvate to acetyl-CoA and formate and the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism reduces glycerol formation.

[0032] In certain embodiments, the one or more engineered metabolic pathways comprises conversion of pyruvate to acetyl-CoA and formate and the recombinant microorganism reduces glycerol formation by at least about 1% to 100% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In some embodiments, the one or more engineered metabolic pathways comprises conversion of pyruvate to acetyl-CoA and formate and the recombinant microorganism reduces glycerol formation by at least about 10% to 90% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In some embodiments, the one or more engineered metabolic pathways comprises conversion of pyruvate to acetyl-CoA and formate and the recombinant microorganism reduces glycerol formation by at least about 20% to 80% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In some embodiments, the one or more engineered metabolic pathways comprises conversion of pyruvate to acetyl-CoA and formate and the recombinant microorganism reduces glycerol formation by at least about 30% to 60% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In some embodiments, the one or more engineered metabolic pathways comprises conversion of pyruvate to acetyl-CoA and formate and the recombinant microorganism reduces glycerol formation by at least about 40% to 50% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol.

In some embodiments, the one or more engineered metabolic pathways comprises conversion of pyruvate to acetyl-CoA and formate and the recombinant microorganism reduces glycerol formation by: (a) more than about 1% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (b) more than about 5% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (c) more than about 10% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (d) more than about 15% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (e) more than about 20% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (f) more than about 25% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (g) more than about 30%> of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (h) more than about 35% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (i) more than about 40% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; j) more than about 45% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (k) more than about 50%> of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (1) more than about 55% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (m) more than about 60% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (n) more than about 65% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (o) more than about 70% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (p) more than about 75% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (q) more than about 80%> of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (r) more than about 85% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (s) more than about 90%> of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (t) more than about 95% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; or (u) more than about 100% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol.

In some embodiments, the one or more engineered metabolic pathways comprises conversion of pyruvate to acetyl-CoA and formate and the recombinant microorganism reduces glycerol formation by: (a) more than about 5% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (b) more than about 10% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (c) more than about 15% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (d) more than about 20% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (e) more than about 25% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; or (f) more than about 30% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol.

[0035] In certain embodiments, the one or more engineered metabolic pathways of the recombinant microorganism comprises one or more native and/or heterologous enzymes that encodes a saccharolytic enzyme and the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism reduces glycerol formation.

[0036] In certain embodiments, the one or more engineered metabolic pathways of the recombinant microorganism comprises one or more native and/or heterologous enzymes that encodes a saccharolytic enzyme and the recombinant microorganism reduces glycerol formation by at least about 1% to 100% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In some embodiments, the one or more engineered metabolic pathways of the recombinant microorganism comprises one or more native and/or heterologous enzymes that encodes a saccharolytic enzyme and the recombinant microorganism reduces glycerol formation by at least about 10% to 90% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In some embodiments, the one or more engineered metabolic pathways of the recombinant microorganism comprises one or more native and/or heterologous enzymes that encodes a saccharolytic enzyme and the recombinant microorganism reduces glycerol formation by at least about 20% to 80% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In some embodiments, the one or more engineered metabolic pathways of the recombinant microorganism comprises one or more native and/or heterologous enzymes that encodes a saccharolytic enzyme and the recombinant microorganism reduces glycerol formation by at least about 30% to 60% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In some embodiments, the one or more engineered metabolic pathways of the recombinant microorganism comprises one or more native and/or heterologous enzymes that encodes a saccharolytic enzyme and the recombinant microorganism reduces glycerol formation by at least about 40% to 50% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol.

In some embodiments, the one or more engineered metabolic pathways of the recombinant microorganism comprises one or more native and/or heterologous enzymes that encodes a saccharolytic enzyme and the recombinant microorganism reduces glycerol formation by: (a) more than about 1% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (b) more than about 5% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (c) more than about 10% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (d) more than about 15% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (e) more than about 20% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (f) more than about 25% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (g) more than about 30% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (h) more than about 35% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (i) more than about 40% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (j) more than about 45% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (k) more than about 50% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (1) more than about 55% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (m) more than about 60% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (n) more than about 65% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (o) more than about 70% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (p) more than about 75% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (q) more than about 80% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (r) more than about 85% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (s) more than about 90% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (t) more than about 95% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; or (u) more than about 100% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol.

[0038] In some embodiments, the one or more engineered metabolic pathways of the recombinant microorganism comprises one or more native and/or heterologous enzymes that encodes a saccharolytic enzyme and the recombinant microorganism reduces glycerol formation by: (a) more than about 5% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (b) more than about 10% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (c) more than about 15% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (d) more than about 20% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (e) more than about 25% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; or (f) more than about 30% of the glycerol produced by a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol.

[0039] In some aspects of the invention, the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism increases ethanol yield.

[0040] In some embodiments, the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism increases ethanol yield by at least about 0.001 -fold to 10-fold than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In certain embodiments, the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism increases ethanol yield by at least about 0.005 -fold to 1.10- fold than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In certain embodiments, the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism increases ethanol yield by at least about 0.01 -fold to 1.05 -fold than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In some embodiments, the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism increases ethanol yield by at least about 0.05-fold to 1.0-fold than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In some embodiments, the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism increases ethanol yield by at least about 0.1- fold to 0.5-fold than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol.

In certain embodiments, the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism increases ethanol yield by: (a) at least about 0.005-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (b) at least about 0.01 -fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (c) at least about 0.05-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (d) at least about 0.1 -fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (e) at least about 0.2-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (f) at least about 0.3 -fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (g) at least about 0.4-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (h) at least about 0.5 -fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (i) at least about 0.6-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; j) at least about 0.7-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (k) at least about 0.8-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (1) at least about 0.9-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (m) at least about 1.0-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (n) at least about 1.05-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (o) at least about 1.10-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (p) at least about 2-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (q) at least about 5-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; or r) at least about 10-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol.

[0042] In certain embodiments, the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism increases ethanol yield by: (a) at least about 0.005-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (b) at least about 0.01 -fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (c) at least about 0.05-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (d) at least about 0.1 -fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (e) at least about 0.5-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (f) at least about 1.0-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (g) at least about 1.05-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; or (h) at least about 1.10-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol.

[0043] In certain embodiments, the one or more engineered metabolic pathways of the recombinant microorganism comprises conversion of pyruvate to acetyl-CoA and formate and the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism increases ethanol yield.

In some embodiments, the one or more engineered metabolic pathways of the recombinant microorganism comprises conversion of pyruvate to acetyl-CoA and formate and the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism increases ethanol yield by at least about 0.001 -fold to 10-fold than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In certain embodiments, the one or more engineered metabolic pathways of the recombinant microorganism comprises conversion of pyruvate to acetyl-CoA and formate and the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism increases ethanol yield by at least about 0.005-fold to 1.10-fold than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In certain embodiments, the one or more engineered metabolic pathways of the recombinant microorganism comprises conversion of pyruvate to acetyl-CoA and formate and the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism increases ethanol yield by at least about 0.01 -fold to 1.05-fold than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In some embodiments, the one or more engineered metabolic pathways of the recombinant microorganism comprises conversion of pyruvate to acetyl-CoA and formate and the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism increases ethanol yield by at least about 0.05-fold to 1.0-fold than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol. In some embodiments, the one or more engineered metabolic pathways of the recombinant microorganism comprises conversion of pyruvate to acetyl-CoA and formate and the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism increases ethanol yield by at least about 0.1 -fold to 0.5-fold than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol.

In certain embodiments, the one or more engineered metabolic pathways of the recombinant microorganism comprises conversion of pyruvate to acetyl-CoA and formate and the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism increases ethanol yield by: (a) at least about 0.005-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (b) at least about 0.01 -fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (c) at least about 0.05-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (d) at least about 0.1 -fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (e) at least about 0.2-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (f) at least about 0.3 -fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (g) at least about 0.4-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (h) at least about 0.5 -fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (i) at least about 0.6-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; j) at least about 0.7-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (k) at least about 0.8-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (1) at least about 0.9-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (m) at least about 1.0-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (n) at least about 1.05-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (o) at least about 1.10-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (p) at least about 2-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (q) at least about 5-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; or r) at least about 10-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol.

In certain embodiments, the one or more engineered metabolic pathways of the recombinant microorganism comprises conversion of pyruvate to acetyl-CoA and formate and the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism increases ethanol yield by: (a) at least about 0.005-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (b) at least about 0.01 -fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (c) at least about 0.05-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; at least about 0.1 -fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (d) at least about 0.5-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (e) at least about 1.0-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; or (f) at least about 1.02- fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol.

In certain embodiments, the activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol into the recombinant microorganism increases ethanol yield by: (a) at least about 0.005-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (b) at least about 0.01 -fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (c) at least about 0.05-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (d) at least about 0.1 -fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (e) at least about 0.5-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; (f) at least about 1.0-fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol; or (g) at least about 1.02- fold more than is produced in a recombinant microorganism without activation, upregulation, or overexpression of one or more native and/or heterologous proteins that function to import glycerol.

[0048] In certain aspects, the recombinant microorganism further comprises one or more native and/or heterologous proteins that function to export glycerol from the microorganism, wherein said one or more native proteins that function to export glycerol is downregulated or deleted and is encoded by fpsl.

[0049] In some embodiments, the recombinant microorganism further comprises one or more native and/or heterologous proteins that function to export glycerol from the microorganism, wherein said one or more native proteins that function to export glycerol is activated or upregulated and is encoded by a constitutively active FPS 1 (fpsl-1).

[0050] In certain embodiments, the recombinant microorganism further comprises one or more native enzymes that function to produce glycerol, wherein said one or more native enzymes that function to produce glycerol is downregulated or deleted and is encoded by a gpdl polynucleotide, a gpd2 polynucleotide, or both a gpdl polynucleotide and a gpd2 polynucleotide. Eukaryotic GPD sequences include: S. cerevisiae gpdl (SEQ ID NOs: 206 and 207) and S. cerevisiae gpd2 (SEQ ID NOs: 204 and 205).

[0051] In some embodiments, the recombinant microorganism further comprises one or more native enzymes that function to catabolize glycerol. In certain embodiments, the recombinant microorganism overexpresses a glycerol dehydrogenase gene. In certain embodiments, the glycerol dehydrogenase gene encodes a protein having glycerol dehydrogenase activity. Glycerol dehydrogenase includes those enzymes that correspond to Enzyme Commission Number 1.1.1.6. In one embodiment, the glycerol dehydrogenase gene is GCY1 (SEQ ID NOs: 214 and 215).

[0052] In some aspects of the invention, the one or more engineered metabolic pathways comprises conversion of acetyl-CoA to an alcohol, and wherein said acetyl-CoA is converted to an alcohol by a bifunctional acetaldehyde/alcohol dehydrogenase. In some embodiments, the one or more engineered metabolic pathways comprises conversion of pyruvate to acetyl-CoA and formate, and wherein said pyruvate is converted to acetyl- CoA and formate by a pyruvate formate lyase (PFL). [0053] In certain embodiments, the one or more engineered metabolic pathway comprises the conversion of D-xylulose 5-phosphate to D-glyceraldehyde 3-phosphate or the conversion of D-fructose 6-phosphate to D-erythrose 4-phosphate, and wherein said conversion of D-xylulose 5-phosphate to D-glyceraldehyde 3-phosphate or the conversion of D-fructose 6-phosphate to D-erythrose 4-phosphate is performed by phosphokelotase. In some embodiments, the one or more engineered metabolic pathways comprises the conversion of acetate to acetyl-CoA, wherein said acetate is converted to acetyl-P by an acetate kinase, and wherein acetyl-P is converted to acetyl-CoA by a phosphotransacetylase. In certain embodiments, the one or more engineered metabolic pathways comprises the conversion of acetate to acetyl-CoA, wherein said acetate is converted to acetyl-CoA by an acetyl-CoA synthetase.

[0054] In some aspects of the invention, the one or more engineered metabolic pathways comprises one or more native and/or heterologous enzymes that encodes a saccharolytic enzyme, and wherein said saccharolytic enzyme is glucoamylase.

[0055] In some aspects of the invention, the recombinant microorganism further comprises one or more native and/or heterologous enzymes that function in one or more engineered metabolic pathways to convert xylose to xylulose-5 -phosphate, and wherein xylose is converted to xylulose-5-phosphate by xylose isomerase. In certain embodiments, the one or more engineered metabolic pathway is the pentose phosphate pathway (PPP).

[0056] In some aspects of the invention, the recombinant microorganism further comprises one or more native and/or heterologous enzymes that function in one or more engineered metabolic pathways to convert arabinose to xylulose-5-phosphate, and wherein arabinose is converted to xylulose-5 -phosphate by arabinose isomerase, ribulokinase, or ribulose 5-phosphate epimerase.

[0057] In some embodiments, the recombinant microorganism further comprises one or more native enzymes that function to produce glycerol, wherein said one or more native enzymes that function to produce glycerol is downregulated or deleted and is encoded by a gppl polynucleotide, a gpp2 polynucleotide, or both a gppl polynucleotide and a gpp2 polynucleotide.

[0058] In certain aspects of the invention, the one or more engineered metabolic pathways comprises the conversion of trehalose to acetyl-CoA, and wherein said one or more native and/or heterologous enzymes functions to convert trehalose to glucose. In some embodiments, the one or more engineered metabolic pathways comprises one or more native and/or heterologous enzymes that encodes a saccharolytic enzyme, and wherein said saccharolytic enzyme is cellulase. In certain embodiments, the one or more engineered metabolic pathways comprises one or more native and/or heterologous enzymes that encodes a saccharolytic enzyme, and wherein said saccharolytic enzyme is xylanase.

[0059] In certain aspects of the invention, the recombinant microorganism is a thermophilic or mesophilic bacterium. In some embodiments, the thermophilic or mesophilic bacterium is a species of the genera Thermoanaerobacterium, Thermoanaerobacter, Clostridium, Geobacillus, Saccharococcus, Paenibacillus, Bacillus, Caldicellulosiruptor, Anaerocellum, or Anoxybacillus. In certain embodiments, the microorganism is a bacterium selected from the group consisting of: Thermoanaerobacterium thermo sulfur igenes, Thermoanaerobacterium aotearoense, Thermoanaerobacterium polysaccharolyticum, Thermoanaerobacterium zeae, Thermoanaerobacterium xylanolyticum, Thermoanaerobacterium saccharolyticum, Thermoanaerobium brockii, Thermoanaerobacterium thermosaccharolyticum, Thermoanaerobacter thermohydrosulfuricus, Thermoanaerobacter ethanolicus, Thermoanaerobacter brocki, Clostridium thermocellum, Clostridium cellulolyticum, Clostridium phytofermentans, Clostridium straminosolvens, Geobacillus thermoglucosidasius, Geobacillus stearothermophilus, Saccharococcus caldoxylosilyticus, Saccharoccus thermophilus, Paenibacillus campinasensis, Bacillus flavothermus, Anoxybacillus kamchatkensis, Anoxybacillus gonensis, Caldicellulosiruptor acetigenus, Caldicellulosiruptor saccharolyticus, Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor owensensis, Caldicellulosiruptor lactoaceticus, and Anaerocellum thermophilum. In certain embodiments, the microorganism is selected from the group consisting of Clostridium thermocellum, and Thermoanaerobacterium saccharolyticum.

[0060] In some embodiments, the recombinant microorganism is a yeast. In certain embodiments, the yeast is selected from the group consisting of Saccharomyces cerevisiae, Kluyveromyces lactis, Kluyveromyces marxianus, Pichia pastoris, Yarrowia lipolytica, Hansenula polymorpha, Phaffia rhodozyma, Candida utliis, Arxula adeninivorans, Pichia stipitis, Debaryomyces hansenii, Debaryomyces polymorphus, Schizosaccharomyces pombe, Candida albicans, and Schwanniomyces occidentalis . In some embodiments, the yeast is Saccharomyces cerevisiae.

[0061] Another aspect of the invention is a method for decreasing cellular-produced glycerol comprising contacting biomass with a recombinant microorganism of the invention. An aspect of the invention is a process for converting biomass to ethanol comprising contacting biomass with a recombinant microorganism of the invention.

[0062] Another aspect of the invention is a process for converting biomass to isopropanol comprising contacting biomass with a recombinant microorganism of the invention. In certain embodiments of these methods and processes, the biomass comprises lignocellulosic biomass. In some embodiments, the lignocellulosic biomass is selected from the group consisting of grass, switch grass, cord grass, rye grass, reed canary grass, mixed prairie grass, miscanthus, sugar-processing residues, sugarcane bagasse, sugarcane straw, agricultural wastes, rice straw, rice hulls, barley straw, corn cobs, cereal straw, wheat straw, canola straw, oat straw, oat hulls, corn fiber, stover, soybean stover, corn stover, forestry wastes, recycled wood pulp fiber, paper sludge, sawdust, hardwood, softwood, agave, and combinations thereof. In certain embodiments, the biomass is corn mash or corn starch.

[0063] In some embodiments of the invention, one of the engineered metabolic pathways comprises (a) conversion of acetyl-CoA to acetoacetyl-CoA; (b) conversion of acetoacetyl-CoA to acetoacetate; (c) conversion of acetoacetate to acetone; and (d) conversion of acetone to isopropanol. In some embodiments, the acetyl-CoA is converted to acetoacetyl-CoA by a thiolase. In certain embodiments, the acetoacetyl-CoA is converted to acetoacetate by a CoA transferase. In some embodiments, the acetoacetate is converted to acetone by an acetoacetate decarboxylase. In certain embodiments, the acetone is converted to isopropanol by an alcohol dehydrogenase. In some embodiments, the alcohol dehydrogenase is a bifunctional acetaldehyde/alcohol dehydrogenase. In certain embodiments, the bifunctional acetaldehyde/alcohol dehydrogenase is of prokaryotic or eukaryotic origin. In some embodiments, the bifunctional acetaldehyde/alcohol dehydrogenase is from an Escherichia, a Clostridia, a Chlamydomonas, a Piromyces, or a Bifidobacteria species. In certain embodiments, the bifunctional acetaldehyde/alcohol dehydrogenase is from Escherichia coli, Clostridium phytofermentans, Chlamydomonas reinhardtii, Piromyces sp. E2, or Bifidobacterium adolescentis. In some embodiments, the bifunctional acetaldehyde/alcohol dehydrogenase is from a Bifidobacterium adolescentis or Piromyces sp. E2. In some embodiments of the invention, the recombinant microorganism is an S. cerevisiae of strain PE-2. In certain embodiments, the PE-2 strain comprises a deletion or disruption of one or more endogenous genes selected from the group consisting of GPD1, GPD2, FDH1, FDH2, and any combination thereof. In certain embodiments, the PE-2 strain comprises a deletion or disruption of an aldose reductase gene, e.g., GRE3. In some embodiments, the PE-2 strain overexpresses one or more genes selected from the group consisting of AdhE, PflA, PlfB, STL1, GCY1, and DAK1. In some embodiments, the AdhE, PflA, and PflB are from Bifidobacterium adolescentis. In some embodiments, the PE-2 strain overexpresses a hemicellulase and/or a gene encoding a protein of the xylose fermentation pathway. In some embodiments, the gene encoding a protein of the xylose fermentation pathway is selected from the group consisting of xylose isomerase (XylA), xylulokinase (XKS1), transketolase (TKL2), transaldolase (TALI), and any combination thereof. In some embodiments, the xylose isomerase can be any protein that catalyzes the reaction of converting xylose to xylulose, including those enzymes that correspond to Enzyme Commission number 5.3.1.5, and including but not limited to a xylose isomerase from a microorganism selected from Piromyces sp. or B. thetaiotaomicron. In certain embodiments, the hemicellulase is from a microorganism selected from the group consisting of H. grisea, T. aurantiacus, T. emersonii, T. reesei, C. lacteus, C. formosanus, N. takasagoensis, C. acinaciformis, M. darwinensis, N. walkeri, S. fibuligera, C. lucknowense R. speratus, Thermobfida fiusca, Clostridum thermocellum, Clostridium cellulolyticum, Clostridum josui, Bacillus pumilis, Cellulomonas fimi, Saccharophagus degradans, Piromyces equii, Neocallimastix patricarum, Arabidopsis thaliana, and S. fibuligera. In some embodiments, the hemicellulase is from a microorganism selected from the group consisting of Neosartorya fischeri, Pyrenophora tritici-repentis, Aspergillus niger, Aspergillus fumigatus, Aspergillus oryzae, Trichoderma reesei, and Aspergillus Aculeatus.

BRIEF DESCRIPTION OF THE DRAWINGS/FIGURES Figure 1 is an overview of glycerol recycling. [0065] Figures 2A and 2B depict glycerol and ethanol concentrations, respectively, in strains of the invention following fermentation in YMD280 medium.

[0066] Figures 3A, 3B, and 3C depict ethanol, glycerol, and glucose concentrations, respectively, in strains of the invention following fermentation in YMD-300 medium.

[0067] Figure 4 depicts intracellular glycerol concentration in strains of the invention.

[0068] Figures 5A and 5B depict glycerol and ethanol titers, respectively, of strains of the invention after 72 hours of fermentation on industrial corn mash.

[0069] Figures 6A and 6B depict ethanol and glycerol titers, respectively, of the strains of the invention after 68 hours of fermentation on 33% solids corn mash.

[0070] Figures 7A and 7B depict ethanol and glycerol titers, respectively, of strains of the invention after 72 hours of fermentation on 33% solids corn mash.

[0071] Figures 8A and 8B depict ethanol and glycerol titers, respectively, of strains of the invention after 68 hours of fermentation on 33% solids corn mash.

[0072] Figure 9 shows a schematic for integration of STLl into the FCY1 locus.

[0073] Figure 10 shows a schematic for integration of STLl into the STLl locus.

[0074] Figure 11 shows a pathway for the recombinant production of ethanol.

[0075] Figure 12 shows a pathway for the recombinant production of isopropanol.

[0076] Figure 13 shows a tree depicting the relation of the PE-2-derived STLl overexpressing strains M7772, M9208, and M9725 to M7101.

[0077] Figure 14 shows a vector map of pMU228.

[0078] Figure 15 shows a schematic for integration of STLl into the FCY1 locus in creating strain M7772.

[0079] Figures 16A and B depict ethanol and glycerol titers of STLl overexpressing PE-2 strains.

[0080] Figures 17A-D depict ethanol and glycerol titers as well as cell viability and mass accumulation of wild-type parent strain M7101 and S. cerevisiae STLl overexpressing strain M7772.

DETAILED DESCRIPTION OF THE INVENTION Definitions

[0081] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Also, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. All publications, patents and other references mentioned herein are incorporated by reference in their entireties for all purposes.

[0082] The term "heterologous" when used in reference to a polynucleotide, a gene, a polypeptide, or an enzyme refers to a polynucleotide, gene, polypeptide, or an enzyme not normally found in the host organism. "Heterologous" also includes a native coding region, or portion thereof, that is reintroduced into the source organism in a form that is different from the corresponding native gene, e.g., not in its natural location in the organism's genome. The heterologous polynucleotide or gene may be introduced into the host organism by, e.g. , gene transfer. A heterologous gene may include a native coding region that is a portion of a chimeric gene including non-native regulatory regions that is reintroduced into the native host. Foreign genes can comprise native genes inserted into a non-native organism, or chimeric genes.

[0083] The term "heterologous polynucleotide" is intended to include a polynucleotide that encodes one or more polypeptides or portions or fragments of polypeptides. A heterologous polynucleotide may be derived from any source, e.g., eukaryotes, prokaryotes, viruses, or synthetic polynucleotide fragments.

[0084] The terms "promoter" or "surrogate promoter" is intended to include a polynucleotide that can transcriptionally control a gene-of-interest that it does not transcriptionally control in nature. In certain embodiments, the transcriptional control of a surrogate promoter results in an increase in expression of the gene-of-interest. In certain embodiments, a surrogate promoter is placed 5' to the gene-of-interest. A surrogate promoter may be used to replace the natural promoter, or may be used in addition to the natural promoter. A surrogate promoter may be endogenous with regard to the host cell in which it is used, or it may be a heterologous polynucleotide sequence introduced into the host cell, e.g., exogenous with regard to the host cell in which it is used.

[0085] The terms "gene(s)" or "polynucleotide" or "polynucleotide sequence(s)" are intended to include nucleic acid molecules, e.g. , polynucleotides which include an open reading frame encoding a polypeptide, and can further include non-coding regulatory sequences, and introns. In addition, the terms are intended to include one or more genes that map to a functional locus. In addition, the terms are intended to include a specific gene for a selected purpose. The gene may be endogenous to the host cell or may be recombinantly introduced into the host cell, e.g., as a plasmid maintained episomally or a plasmid (or fragment thereof) that is stably integrated into the genome. In addition to the plasmid form, a gene may, for example, be in the form of linear DNA. In certain embodiments, the gene or polynucleotide is involved in at least one step in the bioconversion of biomass to, e.g., ethanol. Accordingly, the term is intended to include any gene encoding a polypeptide, such as the enzymes acetate kinase (ACK), phosphotransacetylase (PTA), lactate dehydrogenase (LDH), pyruvate formate lyase (PFL), aldehyde dehydrogenase (ADH) and/or alcohol dehydrogenase (ADH), acetyl- CoA transferase (ACS), acetaldehyde dehydrogenase (ACDH), acetaldehyde/alcohol dehydrogenase (AADH), glycerol-3 -phosphate dehydrogenase (GPD), glycerol 3- phosphatase (GPP), acetyl-CoA synthetase, thiolase, CoA transferase, acetoacetate decarboxylase, alcohol acetyltransferase enzymes in the D-xylose pathway, such as xylose isomerase and xylulokinase, enzymes in the L-arabinose pathway, such as L- arabinose isomerase and L-ribulose-5-phosphate 4-epimerase. The term gene is also intended to cover all copies of a particular gene, e.g., all of the DNA sequences in a cell encoding a particular gene product.

[0086] The term "transcriptional control" is intended to include the ability to modulate gene expression at the level of transcription. In certain embodiments, transcription, and thus gene expression, is modulated by replacing or adding a surrogate promoter near the 5' end of the coding region of a gene-of-interest, thereby resulting in altered gene expression. In certain embodiments, the transcriptional control of one or more genes is engineered to result in the optimal expression of such genes, e.g., in a desired ratio. The term also includes inducible transcriptional control as recognized in the art.

[0087] The term "expression" is intended to include the expression of a gene at least at the level of mRNA production.

[0088] The term "expression product" is intended to include the resultant product, e.g., a polypeptide, of an expressed gene.

[0089] The term "increased expression" and "overexpression" are used interchangeably and are intended to include an alteration in gene expression at least at the level of increased mRNA production and, preferably, at the level of polypeptide expression. The term "increased production" is intended to include an increase in the amount of a polypeptide expressed, in the level of the enzymatic activity of the polypeptide, or a combination thereof, as compared to the native production of, or the enzymatic activity, of the polypeptide.

[0090] The terms "activity," "activities," "enzymatic activity," and "enzymatic activities" are used interchangeably and are intended to include any functional activity normally attributed to a selected polypeptide when produced under favorable conditions. Typically, the activity of a selected polypeptide encompasses the total enzymatic activity associated with the produced polypeptide. The polypeptide produced by a host cell and having enzymatic activity may be located in the intracellular space of the cell, cell- associated, secreted into the extracellular milieu, or a combination thereof. Techniques for determining total activity as compared to secreted activity are described herein and are known in the art.

[0091] The term "xylanolytic activity" is intended to include the ability to hydrolyze glycosidic linkages in oligopentoses and polypentoses.

[0092] The term "arabinolytic activity" is intended to include the ability to hydrolyze glycosidic linkages in oligopentoses and polypentoses.

[0093] The term "cellulolytic activity" is intended to include the ability to hydrolyze glycosidic linkages in oligohexoses and polyhexoses. Cellulolytic activity may also include the ability to depolymerize or debranch cellulose and hemicellulose.

[0094] As used herein, the term "lactate dehydrogenase" or "LDH" is intended to include the enzymes capable of converting pyruvate into lactate. It is understood that LDH can also catalyze the oxidation of hydroxybutyrate. LDH includes those enzymes that correspond to Enzyme Commission Number 1.1.1.27.

[0095] As used herein the term "alcohol dehydrogenase" or "ADH" is intended to include the enzymes capable of converting acetaldehyde into an alcohol, such as ethanol. ADH also includes the enzymes capable of converting acetone to isopropanol. ADH includes those enzymes that correspond to Enzyme Commission Number 1.1.1.1.

[0096] As used herein, the term "phosphotransacetylase" or "PTA" is intended to include the enzymes capable of converting acetyl-phosphate into acetyl-CoA. PTA includes those enzymes that correspond to Enzyme Commission Number 2.3.1.8. [0097] As used herein, the term "acetate kinase" or "ACK" is intended to include the enzymes capable of converting acetate into acetyl-phosphate. ACK includes those enzymes that correspond to Enzyme Commission Number 2.7.2.1.

[0098] As used herein, the term "pyruvate formate lyase" or "PFL" is intended to include the enzymes capable of converting pyruvate into acetyl-CoA and formate. PFL includes those enzymes that correspond to Enzyme Commission Number 2.3.1.54.

[0099] As used herein, the term "formate dehydrogenase" or "FDH" is intended to include the enzymes capable of converting formate and NAD ⁺ to NADH and C0 ₂ . FDH includes those enzymes that correspond to Enzyme Commission Number 1.2.1.2.

[0100] As used herein, the term "acetaldehyde dehydrogenase" or "ACDH" is intended to include the enzymes capable of converting acetyl-CoA to acetaldehyde. ACDH includes those enzymes that correspond to Enzyme Commission Number 1.2.1.3.

[0101] As used herein, the term "acetaldehyde/alcohol dehydrogenase" is intended to include the enzymes capable of converting acetyl-CoA to ethanol. Acetaldehyde/alcohol dehydrogenase includes those enzymes that correspond to Enzyme Commission Numbers 1.2.1.10 and 1.1.1.1.

[0102] As used herein, the term "glycerol-3-phosphate dehydrogenase" or "GPD" is intended to include the enzymes capable of converting dihydroxyacetone phosphate to glycerol-3-phosphate. GPD includes those enzymes that correspond to Enzyme Commission Number 1.1.1.8, including GPD1 and GPD2. Eukaryotic GPD sequences include: S. cerevisiae gpdl (SEQ ID NOs: 206 and 207) and S. cerevisiae gpd2 (SEQ ID NOs: 204 and 205).

[0103] As used herein, the term "glycerol 3 -phosphatase" or "GPP" is intended to include the enzymes capable of converting glycerol 3-phosphate to glycerol. GPP includes those enzymes that correspond to Enzyme Commission Number 3.1.3.21, including GPP1 and GPP2.

[0104] As used herein, the term "acetyl-CoA synthetase" or "ACS" is intended to include the enzymes capable of converting acetate to acetyl-CoA. Acetyl-CoA synthetase includes those enzymes that correspond to Enzyme Commission Number 6.2.1.1. In some embodiments, ACS is from S. cerevisiae.

[0105] S. cerevisiae ACS1 nucleotide and amino acid sequences correspond to SEQ ID

NO: 1 and SEQ ID NO: 2, respectively. S. cerevisiae ACS2 nucleotide and amino acid sequences correspond to SEQ ID NO: 3 and SEQ ID NO: 4, respectively. In some embodiments, ACS is from Zygosaccharomyces Bailii.

[0106] Zygosaccharomyces Bailii ACS nucleotide and amino acid sequences correspond to SEQ ID NO: 5 and SEQ ID NO: 6, respectively. In some embodiments, ACS is from

Salmonella enterica. Salmonella enterica ACS nucleotide and amino acid sequences correspond to SEQ ID NO: 7 and SEQ ID NO: 8, respectively.

[0107] As used herein, the term "thiolase" is intended to include the enzymes capable of converting acetyl-CoA to acetoacetyl-CoA. Thiolase includes those enzymes that correspond to Enzyme Commission Number 2.3.1.9.

[0108] As used herein, the term "CoA transferase" is intended to include the enzymes capable of converting acetate and acetoacetyl-CoA to acetoacetate and acetyl-CoA. CoA transferase includes those enzymes that correspond to Enzyme Commission Number

2.8.3.8.

[0109] As used herein, the term "acetoacetate decarboxylase" is intended to include the enzymes capable of converting acetoacetate to acetone and carbon dioxide. Acetoacetate decarboxylase includes those enzymes that correspond to Enzyme Commission Number 4.1.1.4.

[0110] As used herein, the term "alcohol acetyltransferase" is intended to include the enzymes capable of converting acetyl-CoA and ethanol to ethyl acetate. Alcohol acetyltransferase includes those enzymes that correspond to Enzyme Commission Number 2.3.1.84.

[0111] The term "pyruvate decarboxylase activity" is intended to include the ability of a polypeptide to enzymatically convert pyruvate into acetaldehyde and carbon dioxide (e.g., "pyruvate decarboxylase" or "PDC"). Typically, the activity of a selected polypeptide encompasses the total enzymatic activity associated with the produced polypeptide, comprising, e.g., the superior substrate affinity of the enzyme, thermostability, stability at different pHs, or a combination of these attributes. PDC includes those enzymes that correspond to Enzyme Commission Number 4.1.1.1.

[0112] As used herein, the term "sugar transporter-like protein," "STL1" or "Stllp" is intended to include glycerol proton symporter proteins capable of transporting glycerol across a plasma membrane. Included within the scope of this term are the S. cerevisiae glycerol active transporter, as well as those from other yeast such as C. albicans, Saccharomyces paradoxus, and Pichia sorbitophila.

[0113] As used herein, the term "arabinose isomerase" is intended to include the enzymes capable of converting L-arabinose to L-ribulose. Arabinose isomerase includes those enzymes that correspond to Enzyme Commission Number 5.3.1.4. In some embodiments, arabinose isomerase is from B. thetaiotaomicron. B. thetaiotaomicron arabinose isomerase nucleotide and amino acid sequences correspond to SEQ ID NO: 133 and SEQ ID NO: 134, respectively.

[0114] As used herein, the term "ribulokinase" is intended to include the enzymes capable of converting L- or D-ribulose to L- or D-ribulose 5 -phosphate. Ribulokinase includes those enzymes that correspond to Enzyme Commission Number 2.7.1.16. In some embodiments, ribulokinase is araB from B. thetaiotaomicron. B. thetaiotaomicron araB nucleotide and amino acid sequences correspond to SEQ ID NO: 135 and SEQ ID NO: 136, respectively.

[0115] As used herein, the term "ribulose-5 -phosphate epimerase" or "D-ribulose-5- phosphate 3-epimerase" is intended to include the enzymes capable of converting D- ribulose 5 -phosphate to D-xylulose 5 -phosphate. Ribulose-5 -phosphate epimerase or D- ribulose-5 -phosphate 3-epimerase include those enzymes that correspond to Enzyme Commission Number 5.1.3.1.

[0116] In some embodiments, ribulose-5 -phosphate epimerase is from B. thetaiotaomicron. B. thetaiotaomicron ribulose-5 -phosphate epimerase nucleotide and amino acid sequences correspond to SEQ ID NO: 137 and SEQ ID NO: 138, respectively.

[0117] As used herein, the term "xylose isomerase" or "XI" is meant to refer to an enzyme that catalyzes the chemical reaction: D-xylose ϊ D-xylulose. This enzyme belongs to the family of isomerases, specifically those intramolecular oxidoreductases interconverting aldoses and ketoses. The systematic name of this enzyme class is D- xylose aldose-ketose-isomerase. Other names in common use include D-xylose isomerase, D-xylose ketoisomerase, and D-xylose ketol-isomerase. This enzyme participates in pentose and glucuronate interconversions and fructose and mannose metabolism. The enzyme is used industrially to convert glucose to fructose in the manufacture of high-fructose corn syrup. It is sometimes referred to as "glucose isomerase". XI includes those enzymes that correspond to Enzyme Commission Number 5.3.1.5.

[0118] As used herein, the term "phosphoketolase", "single-specificity phosphoketolase" or "dual-specificity phosphoketolase" is intended to include the enzymes that catalyze the conversion of D-xylulose 5-phosphate to D-glyceraldehyde 3-phosphate. Dual specificity phosphoketolase additionally includes the enzymes that catalyze the conversion of D- fructose 6-phosphate to D-erythrose 4-phosphate. Phosphoketolase, single-specificity phosphoketolase and dual-specificity phosphoketolase are referred to collectively as "PHKs" or "phosphoketolase" (Figure 7). PHKs include those enzymes that correspond to Enzyme Commission Number (EC) 4.1.2.9 and 4.1.2.22. In some embodiments, PHK is from niger (SEQ ID NOs: 143 and 144), N. crassa (SEQ ID NOs: 145 and 146), L. casei PHK (SEQ ID NOs: 147 and 148), L. plantarum PHK1 (SEQ ID NOs: 149 and 150), L. plantarum PHK2 (SEQ ID NOs: 151 and 152), B. adolescentis (SEQ ID NOs: 153 and 154), B. bifidum (SEQ ID NOs: 155 and 156), B. gallicum (SEQ ID NOs: 157 and 158), B. animalis (SEQ ID NOs: 159 and 160), L. pentosum (SEQ ID NOs: 161 and 162), L. acidophilus (SEQ ID NOs: 163 and 164), P. chrysogenum (SEQ ID NOs: 165 and 166), A. nidulans (SEQ ID NOs: 167 and 168), A. clavatus (SEQ ID NOs: 169 and 170), L. mesenteroides (SEQ ID NOs: 171 and 172), or O. oenii (SEQ ID NOs: 173 and 174).

[0119] As used herein, the term "phosphotransacetylase" or "PTA" is intended to include the enzymes capable of converting acetyl-phosphate into acetyl-CoA. PTA includes those enzymes that correspond to Enzyme Commission Number 2.3.1.8.

[0120] As used herein, the term "acetate kinase" or "ACK" is intended to include the enzymes capable of converting acetate into acetyl-phosphate or acetyl-P. ACK includes those enzymes that correspond to Enzyme Commission Number 2.7.2.1.

[0121] The term "ethanologenic" is intended to include the ability of a microorganism to produce ethanol from a carbohydrate as a fermentation product. The term is intended to include, but is not limited to, naturally occurring ethanologenic organisms, ethanologenic organisms with naturally occurring or induced mutations, and ethanologenic organisms which have been genetically modified. [0122] The terms "fermenting" and "fermentation" are intended to include the enzymatic process (e.g., cellular or acellular, e.g., a lysate or purified polypeptide mixture) by which ethanol is produced from a carbohydrate, in particular, as a product of fermentation.

[0123] The term "secreted" is intended to include the movement of polypeptides to the periplasmic space or extracellular milieu. The term "increased secretion" is intended to include situations in which a given polypeptide is secreted at an increased level (i.e., in excess of the naturally-occurring amount of secretion). In certain embodiments, the term "increased secretion" refers to an increase in secretion of a given polypeptide that is at least about 10% or at least about 100%, 200%, 300%, 400%, 500%, 600%, 700%, 800%, 900%), 1000%), or more, as compared to the naturally-occurring level of secretion.

[0124] The term "secretory polypeptide" is intended to include any polypeptide(s), alone or in combination with other polypeptides, that facilitate the transport of another polypeptide from the intracellular space of a cell to the extracellular milieu. In certain embodiments, the secretory polypeptide(s) encompass all the necessary secretory polypeptides sufficient to impart secretory activity to a Gram-negative or Gram-positive host cell or to a yeast host cell. Typically, secretory proteins are encoded in a single region or locus that may be isolated from one host cell and transferred to another host cell using genetic engineering. In certain embodiments, the secretory polypeptide(s) are derived from any bacterial cell having secretory activity or any yeast cell having secretory activity. In certain embodiments, the secretory polypeptide(s) are derived from a host cell having Type II secretory activity. In certain embodiments, the host cell is a thermophilic bacterial cell. In certain embodiments, the host cell is a yeast cell.

[0125] The term "derived from" is intended to include the isolation (in whole or in part) of a polynucleotide segment from an indicated source or the purification of a polypeptide from an indicated source. The term is intended to include, for example, direct cloning, PCR amplification, or artificial synthesis from or based on a sequence associated with the indicated polynucleotide source.

[0126] The term "recombinant microorganism" or "recombinant host cell" is intended to include progeny or derivatives of the recombinant microorganisms of the invention. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny or derivatives may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.

[0127] By "thermophilic" is meant an organism that thrives at a temperature of about

45°C or higher.

[0128] By "mesophilic" is meant an organism that thrives at a temperature of about 20-

45°C.

[0129] The term "organic acid" is art-recognized. "Organic acid," as used herein, also includes certain organic solvents such as ethanol. The term "lactic acid" refers to the organic acid 2-hydroxypropionic acid in either the free acid or salt form. The salt form of lactic acid is referred to as "lactate" regardless of the neutralizing agent, i.e., calcium carbonate or ammonium hydroxide. The term "acetic acid" refers to the organic acid methanecarboxylic acid, also known as ethanoic acid, in either free acid or salt form. The salt form of acetic acid is referred to as "acetate."

[0130] Certain embodiments of the present invention provide for the "insertion," (e.g., the addition, integration, incorporation, or introduction) of certain genes or particular polynucleotide sequences within thermophilic or mesophilic microorganisms, which insertion of genes or particular polynucleotide sequences may be understood to encompass "genetic modification(s)" or "transformation(s)" such that the resulting strains of said thermophilic or mesophilic microorganisms may be understood to be "genetically modified" or "transformed." In certain embodiments, strains may be of bacterial, fungal, or yeast origin.

[0131] Certain embodiments of the present invention provide for the "inactivation" or

"deletion" of certain genes or particular polynucleotide sequences within thermophilic or mesophilic microorganisms, which "inactivation" or "deletion" of genes or particular polynucleotide sequences may be understood to encompass "genetic modification(s)" or "transformation(s)" such that the resulting strains of said thermophilic or mesophilic microorganisms may be understood to be "genetically modified" or "transformed." In certain embodiments, strains may be of bacterial, fungal, or yeast origin.

[0132] The term "consolidated bioprocessing" or "CBP" refers to biomass processing schemes involving enzymatic or microbial hydrolysis that commonly involve four biologically mediated transformations: (1) the production of saccharolytic enzymes (amylases, cellulases, and hemicellulases); (2) the hydrolysis of carbohydrate components present in pretreated biomass to sugars; (3) the fermentation of hexose sugars (e.g., glucose, mannose, and galactose); and (4) the fermentation of pentose sugars (e.g., xylose and arabinose). These four transformations occur in a single step in a process configuration called CBP, which is distinguished from other less highly integrated configurations in that it does not involve a dedicated process step for cellulase and/or hemicellulase production.

[0133] The term "CBP organism" is intended to include microorganisms of the invention, e.g., microorganisms that have properties suitable for CBP.

[0134] In one aspect of the invention, the genes or particular polynucleotide sequences are inserted to activate the activity for which they encode, such as the expression of an enzyme. In certain embodiments, genes encoding enzymes in the metabolic production of ethanol, e.g., enzymes that metabolize pentose and/or hexose sugars, may be added to a mesophilic or thermophilic organism. In certain embodiments of the invention, the enzyme may confer the ability to metabolize a pentose sugar and be involved, for example, in the D-xylose pathway and/or L-arabinose pathway.

[0135] In one aspect of the invention, the genes or particular polynucleotide sequences are partially, substantially, or completely deleted, silenced, inactivated, or down-regulated in order to inactivate the activity for which they encode, such as the expression of an enzyme. Deletions provide maximum stability because there is no opportunity for a reverse mutation to restore function. Alternatively, genes can be partially, substantially, or completely deleted, silenced, inactivated, or down-regulated by insertion of nucleic acid sequences that disrupt the function and/or expression of the gene (e.g., PI transduction or other methods known in the art). The terms "eliminate," "elimination," and "knockout" are used interchangeably with the terms "deletion," "partial deletion," "substantial deletion," or "complete deletion." In certain embodiments, strains of thermophilic or mesophilic microorganisms of interest may be engineered by site directed homologous recombination to knockout the production of organic acids. In still other embodiments, RNAi or antisense DNA (asDNA) may be used to partially, substantially, or completely silence, inactivate, or down-regulate a particular gene of interest.

[0136] In certain embodiments, the genes targeted for deletion or inactivation as described herein may be endogenous to the native strain of the microorganism, and may thus be understood to be referred to as "native gene(s)" or "endogenous gene(s)." An organism is in "a native state" if it has not been genetically engineered or otherwise manipulated by the hand of man in a manner that intentionally alters the genetic and/or phenotypic constitution of the organism. For example, wild-type organisms may be considered to be in a native state. In other embodiments, the gene(s) targeted for deletion or inactivation may be non-native to the organism.

[0137] Similarly, the enzymes of the invention as described herein can be endogenous to the native strain of the microorganism, and can thus be understood to be referred to as "native" or "endogenous."

[0138] The term "upregulated" means increased in activity, e.g., increase in enzymatic activity of the enzyme as compared to activity in a native host organism.

[0139] The term "downregulated" means decreased in activity, e.g., decrease in enzymatic activity of the enzyme as compared to activity in a native host organism.

[0140] The term "activated" means expressed or metabolically functional.

[0141] The term "adapted for growing" means selection of an organism for growth under conditions in which the organism does not otherwise grow or in which the organism grows slowly or minimally. Thus, an organism that is said to be adapted for growing under the selected condition, grows better than an organism that has not been adapted for growing under the selected conditions. Growth can be measured by any methods known in the art, including, but not limited to, measurement of optical density or specific growth rate.

[0142] The term "carbohydrate source" is intended to include any source of carbohydrate including, but not limited to, biomass or carbohydrates, such as a sugar or a sugar alcohol. "Carbohydrates" include, but are not limited to, monosaccharides (e.g., glucose, fructose, galactose, xylose, arabinose, or ribose), sugar derivatives (e.g., sorbitol, glycerol, galacturonic acid, rhamnose, xylitol), disaccharides (e.g., sucrose, cellobiose, maltose, or lactose), oligosaccharides (e.g., xylooligomers, cellodextrins, or maltodextrins), and polysaccharides (e.g., xylan, cellulose, starch, mannan, alginate, or pectin).

[0143] As used herein, an "amylolytic enzyme" can be any enzyme involved in amylase digestion, metabolism and/or hydrolysis. The term "amylase" refers to an enzyme that breaks starch down into sugar. Amylase is present in human saliva, where it begins the chemical process of digestion. Foods that contain much starch but little sugar, such as rice and potato, taste slightly sweet as they are chewed because amylase turns some of their starch into sugar in the mouth. The pancreas also makes amylase (a-amylase) to hydrolyse dietary starch into disaccharides and trisaccharides which are converted by other enzymes to glucose to supply the body with energy. Plants and some bacteria also produce amylase. All amylases are glycoside hydrolases and act on a-l,4-glycosidic bonds. Some amylases, such as γ-amylase (glucoamylase), also act on a-l,6-glycosidic bonds. Amylase enzymes include a-amylase (EC 3.2.1.1), β-amylase (EC 3.2.1.2), and y- amylase (EC 3.2.1.3). The a-amylases are calcium metalloenzymes, unable to function in the absence of calcium. By acting at random locations along the starch chain, a-amylase breaks down long-chain carbohydrates, ultimately yielding maltotriose and maltose from amylose, or maltose, glucose and "limit dextrin" from amylopectin. Because it can act anywhere on the substrate, α-amylase tends to be faster-acting than β-amylase. In animals, it is a major digestive enzyme and its optimum pH is about 6.7-7.0. Another form of amylase, β-amylase is also synthesized by bacteria, fungi, and plants. Working from the non-reducing end, β-amylase catalyzes the hydrolysis of the second a- 1,4 glycosidic bond, cleaving off two glucose units (maltose) at a time. Many microbes produce amylase to degrade extracellular starches. In addition to cleaving the last a(l- 4)glycosidic linkages at the nonreducing end of amylose and amylopectin, yielding glucose, γ-amylase will cleave a(l-6) glycosidic linkages. Another amylolytic enzyme is alpha-glucosidase that acts on maltose and other short malto-oligosaccharides produced by alpha-, beta- , and gamma-amylases, converting them to glucose. Another amylolytic enzyme is pullulanase. Pullulanase is a specific kind of glucanase, an amylolytic exoenzyme, that degrades pullulan. Pullulan is regarded as a chain of maltotriose units linked by alpha- 1,6-glycosidic bonds. Pullulanase (EC 3.2.1.41) is also known as pullulan-6-glucanohydrolase (Debranching enzyme). Another amylolytic enzyme, isopullulanase, hydrolyses pullulan to isopanose (6-alpha-maltosylglucose). Isopullulanase (EC 3.2.1.57) is also known as pullulan 4-glucanohydrolase. An "amylase" can be any enzyme involved in amylase digestion, metabolism and/or hydrolysis, including a-amylase, β-amylase, glucoamylase, pullulanase, isopullulanase, and alpha-glucosidase.

As used herein, a "saccharolytic enzyme" can be any enzyme involved in carbohydrate digestion, metabolism and/or hydrolysis, including amylases, cellulases, hemicellulases, cellulolytic and amylolytic accessory enzymes, inulinases, levanases, and pentose sugar utilizing enzymes. In certain embodiments, the saccharolytic enzyme is a hemicellulase. Various hemicellulases can be used in the present invention, including but not limited to those described in co-owned International Application No. PCT/US2014/026499 filed March 13, 2014, which is incorporated by reference in its entirety herein. Additional non-limiting hemicellulase examples include hemicellulases obtained from a microorganism selected from the group consisting of Neosartorya fischeri, Pyrenophora tritici-repentis, Aspergillus niger, Aspergillus fumigatus, Aspergillus oryzae, Trichoderma reesei, and Aspergillus Aculeatus. Table 1 lists exemplary hemicellulases that can be engineered, as indicated, in the recombinant microorganisms of the invention. The plasmids and strains presented in Table 1 are disclosed in co-owned International Application Publication Nos. WO 2014/035458, which is herein incorporated by reference in its entirety.

Table 1

* "Enzyme type" is descriptive in the field for the type of enzyme, and each enzyme is further defined in the "activity" column.

[0145] The terms "industrial corn mash," "solids corn mash," and "corn mash" are used interchangeably and are intended to include liquefied corn obtained from a commercial facility.

Biomass

[0146] Biomass can include any type of biomass known in the art or described herein.

For example, biomass can include, but is not limited to, starch, sugar, and lignocellulosic materials. Starch materials can include, but are not limited to, mashes such as corn, wheat, rye, barley, rice, or milo. Sugar materials can include, but are not limited to, sugar beets, artichoke tubers, sweet sorghum, or cane. The terms "lignocellulosic material," "lignocellulosic substrate," and "cellulosic biomass" mean any type of biomass comprising cellulose, hemicellulose, lignin, or combinations thereof, such as but not limited to woody biomass, forage grasses, herbaceous energy crops, non-woody-plant biomass, agricultural wastes and/or agricultural residues, forestry residues and/or forestry wastes, paper-production sludge and/or waste paper sludge, waste -water-treatment sludge, municipal solid waste, corn fiber from wet and dry mill corn ethanol plants, and sugar-processing residues. The terms "hemicellulosics," "hemicellulosic portions," and "hemicellulosic fractions" mean the non-lignin, non-cellulose elements of lignocellulosic material, such as but not limited to hemicellulose (i.e., comprising xyloglucan, xylan, glucuronoxylan, arabinoxylan, mannan, glucomannan, and galactoglucomannan, inter alia), pectins (e.g., homogalacturonans, rhamnogalacturonan I and II, and xylogalacturonan), and proteoglycans (e.g., arabinogalactan-protein, extensin, and pro line -rich proteins).

[0147] In a non-limiting example, the lignocellulosic material can include, but is not limited to, woody biomass, such as recycled wood pulp fiber, sawdust, hardwood, softwood, and combinations thereof; grasses, such as switch grass, cord grass, rye grass, reed canary grass, miscanthus, or a combination thereof; sugar-processing residues, such as but not limited to sugar cane bagasse; agricultural wastes, such as but not limited to rice straw, rice hulls, barley straw, corn cobs, cereal straw, wheat straw, canola straw, oat straw, oat hulls, and corn fiber; stover, such as but not limited to soybean stover, corn stover; succulents, such as but not limited to, Agave; and forestry wastes, such as but not limited to, recycled wood pulp fiber, sawdust, hardwood (e.g., poplar, oak, maple, birch, willow), softwood, or any combination thereof. Lignocellulosic material may comprise one species of fiber; alternatively, lignocellulosic material may comprise a mixture of fibers that originate from different lignocellulosic materials. Other lignocellulosic materials are agricultural wastes, such as cereal straws, including wheat straw, barley straw, canola straw and oat straw; corn fiber; stovers, such as corn stover and soybean stover; grasses, such as switch grass, reed canary grass, cord grass, and miscanthus; or combinations thereof.

[0148] Paper sludge is also a viable feedstock for lactate or acetate production. Paper sludge is solid residue arising from pulping and paper-making, and is typically removed from process wastewater in a primary clarifier. At a disposal cost of $30/wet ton, the cost of sludge disposal equates to $5/ton of paper that is produced for sale. The cost of disposing of wet sludge is a significant incentive to convert the material for other uses, such as conversion to ethanol. Processes provided by the present invention are widely applicable. Moreover, the saccharification and/or fermentation products may be used to produce ethanol or higher value added chemicals, such as organic acids, aromatics, esters, acetone and polymer intermediates.

Glycerol Reduction

[0149] Anaerobic growth conditions require the production of endogenous electron acceptors, such as the coenzyme nicotinamide adenine dinucleotide (NAD ⁺ ). In cellular redox reactions, the NAD /NADH couple plays a vital role as a reservoir and carrier of reducing equivalents. Ansell, R., et al, EMBO J. 7(5:2179-87 (1997). Cellular glycerol production, which generates an NAD ⁺ , serves as a redox valve to remove excess reducing power during anaerobic fermentation in yeast. In addition to functioning as an electron sink, yeast require intracellular glycerol as a compatible solute to balance high extracellular osmolarity.

[0150] Glycerol production is, however, an energetically wasteful process that expends

ATP and results in the loss of a reduced three-carbon compound. Ansell, R., et al, EMBO J. 76:2179-87 (1997). Furthermore, a considerable amount of the glycerol produced by the organism is excreted from the cell where it offers no advantage to the organism. To generate glycerol from a starting glucose molecule, glycerol 3-phosphate dehydrogenase (GPD) reduces dihydroxyacetone phosphate to glycerol 3-phosphate and glycerol 3 -phosphatase (GPP) dephosphorylates glycerol 3-phosphate to glycerol. Despite being energetically wasteful, glycerol production is a necessary metabolic process for anaerobic growth as deleting GPD activity completely inhibits growth under anaerobic conditions. See Ansell, R., et al, EMBO J. 7(5:2179-87 (1997).

[0151] GPD is encoded by two isogenes, gpdl and gpd2. GPD1 encodes the major isoform in anaerobically growing cells, while GPD2 is required for glycerol production in the absence of oxygen, which stimulates its expression. Pahlman, A-K., et al, J. Biol Chem. 27(5:3555-63 (2001). The first step in the conversion of dihydroxyacetone phosphate to glycerol by GPD is rate controlling. Guo, Z.P., et al, Metab. Eng. 75:49-59 (2011). GPP is also encoded by two isogenes, gppl and gpp2. The deletion of GPP genes arrests growth when shifted to anaerobic conditions, demonstrating that GPP is important for cellular tolerance to osmotic and anaerobic stress. See Pahlman, A-K., et al., J. Biol. Chem. 276:3555-63 (2001).

[0152] In certain embodiments, one or more genes involved in dihydroxyacetone metabolism are upregulated or over expressed by the recombinant microorganism. In some embodiments the recombinant microorganism overexpresses a dihydroxyacetone kinase, such as DAK1.

[0153] Because glycerol is a major by-product of anaerobic production of ethanol, many efforts have been made to delete cellular production of glycerol. However, because of the reducing equivalents produced by glycerol synthesis, deletion of the glycerol synthesis pathway cannot be done without compensating for this valuable metabolic function. Attempts to delete glycerol production and engineer alternate electron acceptors have been made. Liden, G., et al, Appl. Env. Microbiol. (52:3894-96 (1996); Medina, V.G., et al, Appl. Env. Microbiol. 7(5: 190-195 (2010). Liden and Medina both deleted the gpdl and gpd2 genes and attempted to bypass glycerol formation using additional carbon sources. Liden engineered a xylose reductase from Pichia stipitis into an S. cerevisiae gpdl/2 deletion strain. The xylose reductase activity facilitated the anaerobic growth of the glycerol-deleted strain in the presence of xylose. See Liden, G., et al, Appl. Env. Microbiol. (52:3894-96 (1996). Medina engineered an acetylaldehyde dehydrogenase, mhpF, from E. coli into an S. cerevisiae gpdl/2 deletion strain to convert acetyl-CoA to acetaldehyde. The acetylaldehyde dehydrogenase activity facilitated the anaerobic growth of the glycerol-deletion strain in the presence of acetic acid but not in the presence of glucose as the sole source of carbon. Medina, V.G., et al, Appl. Env. Microbiol. 7(5: 190-195 (2010); see also EP 2277989. Medina noted several issues with the mhpF- containing strain that needed to be addressed before implementing industrially, including significantly reduced growth and product formation rates than yeast comprising GPD1 and GPD2.

[0154] Additional attempts to redirect flux from glycerol to ethanol have included the engineering of a non-phosphorylating NADP+-dependent glyceraldehydes-3 -phosphate dehydrogenase (GAPN) into yeast, either with or without the simultaneous knockout of GPD1. Bro, C, et al, Metab. Eng. 5:102-111 (2006); U.S. Patent Appl. Pub. No. US2006/0257983; Guo, Z.P., et al, Metab. Eng. 75:49-59 (2011). However, other cellular mechanisms exist to control the production and accumulation of glycerol, including glycerol exporters such as FPS1 and the glycerol/H ⁺ symporter STLl, that may not require the engineering of alternate NADP+/NADPH coupling or deletion of glycerol synthesis genes. Tamas, M.J., et al, Mol Microbiol 57: 1087-1004 (1999) and Ferreira, C, et al. (2005).

[0155] STLl is a protein with 12 putative transmembrane domains that functions at the cell membrane as a glycerol/H ⁺ symporter. Yeast cells lacking STLl are unable to actively uptake glycerol and heterologous expression of S. cerevisiae STLl in S. pombe results in glycerol uptake via an active mechanism. Ferreira, C, et al (2005). In addition, glycerol uptake via STLl has been shown to be repressed by the presence of glucose through transcriptional repression of the stll gene. Conversely, glycerol uptake can be induced by growth on nonfermentable carbon sources and the expression of stll is induced under gluconeogenic conditions and by osmotic shock during exponential growth on glucose-based media. Tulha, J., et al (2010) and Ferreira, C, et al (2005).

[0156] In particular embodiments of the invention that modulate STLl, the recombinant host cells are genetically modified to take up glycerol in the presence of glucose, something which cells cannot normally do. The derepression of glycerol uptake in the presence of glucose results in a three step process. First, glycerol is produced by the organism in response to osmotic or redox stress. Second, glycerol is secreted into the fermentation medium. Finally, glycerol is transported back up into the cell through the action of an active glycerol transporter, for example STLl . The net effect is creation of a futile cycle where glycerol is first excreted and then taken back up (Figure 1). Without wishing to be bound by any one theory, it is also possible that higher intracellular glycerol levels may function to reduce endogenous glycerol production through feedback inhibition of the native glycerol production machinery. Another embodiment of the invention comprises uptake of glycerol that is exogenously available in the substrate or fermentation medium.

[0157] An example STLl sequence from S. cerevisiae is provided in SEQ ID NO: 139 and SEQ ID NO: 140. In some embodiments, STLl is from C. albicans. C. albicans STLl nucleotide and amino acid sequences correspond to SEQ ID NO: 141 and SEQ ID NO: 142, respectively. In some embodiments, STLl is from Pichia sorbitophila. P. sorbitophila STLl nucleotide and amino acid sequences correspond to SEQ ID NO: 9 and SEQ ID NO: 10, respectively. In certain embodiments, STLl is from Saccharomyces paradoxus. S. paradoxus STLl nucleotide and amino acid sequences correspond to SEQ ID NO: 224 and SEQ ID NO: 225, respectively.

[0158] An additional protein that may be involved in glycerol regulation is encoded by the S. cerevisiae gene GUPl . Although the role of GUPl in glycerol regulation is unclear, overexpression of GUPl in S. cerevisiae has been shown to result in increased ethanol production. See Yu, K. O., et al., "Engineering of glycerol utilization pathway for ethanol production by Saccharomyces cerevisiae," Bioresour. Technol. 101(11): 157-61 (2010) and International Publication No. WO 2011/149353, which are incorporated by reference herein in their entireties.

[0159] S. cerevisiae GUPl nucleotide and amino acid sequences correspond to SEQ ID

NO: 11 and SEQ ID NO: 12, respectively. In some embodiments of the invention, STLl and GUPl are modulated in the same recombinant microorganism. In certain embodiments of the invention, STLl and GUPl are overexpressed in the same recombinant microorganism.

[0160] FPS1 is a channel protein located in the plasma membrane that controls the accumulation and release of glycerol in yeast osmoregulation. Null mutants of this strain accumulate large amounts of intracellular glycerol, grow much slower than wild-type, and consume the sugar substrate at a slower rate. Tamas, M.J., et al., Mol. Microbiol. 57: 1087-1004 (1999). Despite slower growth under anaerobic conditions, an fpslA strain can serve as an alternative to eliminating NAD ⁺ -dependent glycerol activity. An fpslA strain has reduced glycerol formation yet has a completely functional NAD ⁺ -dependent glycerol synthesis pathway. Alternatively, rather than deleting endogenous FPS1, constitutive ly active mutants of FPS1 (fpsl-1) or homo logs from other organisms can be used to regulate glycerol synthesis while keeping the NAD -dependent glycerol activity intact. In embodiments of the invention that modulate STLl and FPSl, the recombinant host cells can still synthesize and retain glycerol and achieve improved robustness relative to strains that are unable to make or eliminate glycerol.

[0161] An example FPSl sequence from S. cerevisiae is provided in SEQ ID NO: 13 and

SEQ ID NO: 14. Sequence for a constitutively active FPSl from S. cerevisiae is provided in SEQ ID NO:15 and SEQ ID NO: 16.

[0162] Table 2 provides exemplary genes involved in glycerol reduction that can be engineered as indicated in the recombinant microorganisms of the invention:

Table 2

Pyruvate Formate Lyase (PFL)

[0163] The conversion of the pyruvate to acetyl-CoA and formate is performed by pyruvate formate lyase (PFL). In E. coli, PFL is the primary enzyme responsible for the production of formate. PFL is a dimer of PflB that requires the activating enzyme PflAE, which is encoded by pflA, radical S-adenosylmethionine, and a single electron donor. See Waks, Z., and Silver, P.A., Appl. Env. Microbiol. 75: 1867-1875 (2009). Waks and Silver engineered strains of S. cerevisiae to secrete formate by the addition of PFL and AdhE from E. coli and deletion of endogenous formate dehydrogenases and to produce hydrogen in a two-step process using E. coli. Waks and Silver, however, did not combine formate production with the removal of glycerol formation, and the use of formate as an alternate electron acceptor for the reduction of glycerol was not proposed or evaluated.

[0164] PFL enzymes for use in the recombinant host cells of the invention can come from a bacterial or eukaryotic source. Examples of bacterial PFL include, but are not limited to, Bacillus licheniformis DSM13, Bacillus licheniformis ATCC14580, Streptococcus thermophilus CNRZ1066, Streptococcus thermophilus LMG18311, Streptococcus thermophilus LMD-9, Lactobacillus plantarum WCFS1 (Gene Accession No. lp_2598), Lactobacillus plantarum WCFS1 (Gene Accession No. lp_3313), Lactobacillus plantarum JDM1 (Gene Accession No. JDM1_2695), Lactobacillus plantarum JDM1 (Gene Accession No. JDM1_2087), Lactobacillus casei bl23, Lactobacillus casei ATCC 334, Bifidobacterium adolescentis, Bifidobacterium longum NCC2705, Bifidobacterium longum DJO10A, Bifidobacterium animalis DSM 10140, Clostridium cellulolyticum, or Escherichia coli. Additional PFL enzymes may be from the PFL1 family, the RNR pfl superfamily, or the PFL2 superfamily.

[0165] pflA sequences from bacteria include: Bacillus licheniformis DSM13 (SEQ ID

NOs: 17 and 18); Bacillus licheniformis ATCC14580 (SEQ ID NOs:19 and 20);

[0166] Streptococcus thermophilus CNRZ1066 (SEQ ID NOs:21 and 22); Streptococcus thermophilus LMG18311 (SEQ ID NOs:23 and 24); Streptococcus thermophilus LMD-9 (SEQ ID NOs:25 and 26); Lactobacillus plantarum WCFS1 (Gene Accession No: lp_2596) (SEQ ID NOs:27 and 28); Lactobacillus plantarum WCFS1 (Gene Accession No: lp_3314) (SEQ ID NOs:29 and 30); Lactobacillus plantarum JDM1 (Gene Accession No: JDM1_2660) (SEQ ID NOs:31 and 32) Lactobacillus plantarum JDM1 (Gene Accession No: JDM1_2085) (SEQ ID NOs:33 and 34); Lactobacillus casei bl23 (SEQ ID NOs:35 and 36); Lactobacillus casei ATCC 334 (SEQ ID NOs:37 and 38); Bifidobacterium adolescentis (SEQ ID NOs:39 and 40); Bifidobacterium longum NCC2705 (SEQ ID NOs:41 and 42); Bifidobacterium longum DJO10A (SEQ ID NOs:43 and 44); Bifidobacterium animalis DSM 10140 (SEQ ID NOs:45 and 46); Clostridium cellulolyticum (SEQ ID NOs:47 and 48); Escherichia coli (SEQ ID NOs:49 and 50);

[0167] pflB sequences from bacteria include: Bacillus licheniformis DSM13 (SEQ ID

NOs:51 and 52); Bacillus licheniformis ATCC14580 (SEQ ID NOs:53 and 54);

[0168] Streptococcus thermophilus CNRZ1066 (SEQ ID NOs:55 and 56); Streptococcus thermophilus LMG18311 (SEQ ID NOs:57 and 58); Streptococcus thermophilus LMD-9 (SEQ ID NOs:59 and 60); Lactobacillus plantarum WCFS1 (Gene Accession No. lp_2598) (SEQ ID NOs:61 and 62); Lactobacillus plantarum WCFS1 (Gene Accession No: lp_3313) (SEQ ID NOs:63 and 64); Lactobacillus plantarum JDMl (Gene Accession No: JDM1 2695) (SEQ ID NOs:65 and 66); Lactobacillus plantarum JDMl (Gene Accession No: JDM1_2087) (SEQ ID NOs:67 and 68); Lactobacillus casei bl23 (SEQ ID NOs:69 and 70); Lactobacillus casei ATCC 334 (SEQ ID NOs:71 and 72); Bifidobacterium adolescentis (SEQ ID NOs:73 and 74); Bifidobacterium longum NCC2705 (SEQ ID NOs:75 and 76); Bifidobacterium longum DJO10A (SEQ ID NOs:77 and 78); Bifidobacterium animalis DSM 10140 (SEQ ID NOs:79 and 80); Clostridium cellulolyticum (SEQ ID NOs:81 and 82); Escherichia coli (SEQ ID NOs:83 and 84);

[0169] Examples of eukaryotic PFL include, but are not limited to, Chlamydomonas reinhardtii PflAl, Piromyces sp. E2, or Neocallimastix frontalis, Acetabularia acetabulum, Haematococcus pluvialis, Volvox carteri, Ostreococcus tauri, Ostreococcus lucimarinus, Micromonas pusilla, Micromonas sp., Porphyra haitanensis, and Cyanophora paradoxa), an opisthokont (Amoebidium parasiticum), an amoebozoan (Mastigamoeba balamuthi), a stramenopile (Thalassiosira pseudonana (2)) and a haptophyte (Prymnesium parvum), M. pusilla, Micromonas sp. O. tauri and O. lucimarinus) an amoebozoan (M. balamuthi), and a stramenopile (T. pseudonana). See Stairs, C.W., et al, "Eukaryotic pyruvate formate lyase and its activating enzyme were acquired laterally from a firmicute," Mol. Biol, and Evol., published on-line on Feb. 3, 2011, at http://mbe.oxfordjournals.org/. [0170] pflA sequences from eukaryotes include: Chlamydomonas reinhardtii PflAl (SEQ

ID NOs:85 and 86); Neocallimastix frontalis (SEQ ID NOs:87 and 88);

[0171] pfll sequences from eukaryotes include: Chlamydomonas reinhardtii PflA (SEQ

ID NOs:89 and 90); Piromyces sp. E2 (SEQ ID NOs:91 and 92); Neocallimastix frontalis (nucleotide - partial CDS, missing start; SEQ ID NO:93); and Neocallimastix frontalis (amino acid - partial CDS, missing start; SEQ ID NO:94).

[0172] In certain embodiments, the recombinant microorganism comprises a deletion or disruption of one or more formate dehydrogenase genes. FDH sequences from eukaryotes include: S. cerevisiae fdhl (SEQ ID NOs: 199 and 200) and S. cerevisiae fdh2 (SEQ ID NOs: 201 and 202). In some embodiments, the one or more pyruvate dehydrogenase genes are selected from FDH1, FDH2, or both.

Acetaldehyde/ Alcohol Dehydrogenases

[0173] Engineering of acetaldehyde dehydrogenases, alcohol dehydrogenases, and/or bifunctional acetylaldehyde/alcohol dehydrogenases into a cell can increase the production of ethanol. However, because the production of ethanol is redox neutral, an acetaldehyde/alcohol dehydrogenase activity cannot serve as an alternative for the redox balancing that the production of glycerol provides to a cell in anaerobic metabolism. When Medina attempted to express an acetylaldehyde dehydrogenase, mhpF, from E. coli in an S. cerevisiae gpdl/2 deletion strain, the strain did not grow under anaerobic conditions in the presence of glucose as the sole source of carbon. Medina, V.G., et al., Appl. Env. Microbiol. 7(5: 190-195 (2010); see also EP 2277989. Rather, the anaerobic growth of the glycerol-deletion strain required the presence of acetic acid. However, an acetylaldehyde dehydrogenase has not been expressed in combination with PFL or with the recombinant host cells of the invention. Additionally, replacing the endogenous acetylaldehyde dehydrogenase activity with either an improved acetaldehyde dehydrogenase or using a bifunctional acetaldehyde/alcohol dehydrogenase (AADH) can positively affect the in vivo kinetics of the reaction providing for improved growth of the host strain.

[0174] AADH enzymes for use in the recombinant host cells of the invention can come from a bacterial or eukaryotic source. Examples of bacterial AADH include, but are not limited to, Clostridium phytofermentans, Escherichia coli, Bacillus coagulans, Bacillus lentus, Bacillus licheniformis, Bacillus pumilus, Bacillus subtilis, Bacteroides amylophilus, Bacteroides capillosus, Bacteroides ruminocola, Bacteroides suis, Bifidobacterium adolescentis, Bifidobacterium animalis, Bifidobacterium bifidum, Bifidobacterium infantis, Bifidobacterium longum, Bifidobacterium thermophilum, Lactobacillus acidophilus, Lactobacillus brevis, Lactobacillus buchneri (cattle only), Lactobacillus bulgaricus, Lactobacillus casei, Lactobacillus cellobiosus, Lactobacillus curvatus, Lactobacillus delbruekii, Lactobacillus farciminis (swine only), Lactobacillus fermentum, Lactobacillus helveticus, Lactobacillus lactis, Lactobacillus plantarum, Lactobacillus reuterii, Leuconostoc mesenteroides, Pediococcus acidilacticii, Pediococcus pentosaceus, Propionibacterium acidpropionici (cattle only), Propionibacterium freudenreichii, Propionibacterium shermanii, Enterococcus cremoris, Enterococcus diacety lactis, Enterococcus faecium, Enterococcus intermedius, Enterococcus lactis, or Enterococcus thermophilus

[0175] AdhE bacterial sequences include: Clostridium phytofermentans (SEQ ID NOs:95 and 96); Escherichia coli (SEQ ID NOs:97 and 98); Bifidobacterium adolescentis (amino acid; SEQ ID NO: 103); Bacillus coagulans (amino acid; SEQ ID NO: 104); Bacillus licheniformis (amino acid; SEQ ID NO: 105); Enterococcus faecium TX1330 (amino acid; SEQ ID NO: 106);

[0176] Examples of eukaryotic AdhE include, but are not limited to, Chlamydomonas reinhardtii AdhE, Piromyces sp. E2, or Neocallimastix frontalis. AdhE sequences from eukaryotes include: Chlamydomonas reinhardtii AdhE (SEQ ID NOs: 99 and 100) and Piromyces sp. E2 (SEQ ID NOs: 101 and 102).

[0177] The recombinant microorganism of the present invention can be capable of overexpressing one or more alcohol dehydrogenases. In some embodiments, the recombinant host cell overexpresses AdhE. In one particular embodiment, the AdhE is from B. adolescentis.

Consolidated Bioprocessing

[0178] Consolidated bioprocessing (CBP) is a processing strategy for cellulosic biomass that involves consolidating into a single process step four biologically-mediated events: enzyme production, hydrolysis, hexose fermentation, and pentose fermentation. Implementing this strategy requires development of microorganisms that both utilize cellulose, hemicellulosics, and other biomass components while also producing a product of interest at sufficiently high yield and concentrations. The feasibility of CBP is supported by kinetic and bioenergetic analysis. See van Walsum and Lynd (1998) Biotech. Bioeng. 55:316.

[0179] CBP offers the potential for lower cost and higher efficiency than processes featuring dedicated saccharolytic enzyme production. The benefits result in part from avoided capital costs, substrate and other raw materials, and utilities associated with saccharolytic enzyme production. In addition, several factors support the realization of higher rates of hydrolysis, and hence reduced reactor volume and capital investment using CBP, including enzyme -microbe synergy and the use of thermophilic organisms and/or complexed saccharolytic systems. Moreover, cellulose-adherent cellulolytic microorganisms are likely to compete successfully for products of cellulose hydrolysis with non-adhered microbes, e.g., contaminants, which could increase the stability of industrial processes based on microbial cellulose utilization. Progress in developing CBP-enabling microorganisms is being made through two strategies: engineering naturally occurring saccharolytic microorganisms to improve product-related properties, such as yield and titer; and engineering non-saccharolytic organisms that exhibit high product yields and titers to express a heterologous saccharolytic enzyme system enabling starch, cellulose, and, hemicellulose utilization.

Starch and Cellulose Degradation

[0180] The degradation of starch into component sugar units proceeds via amylo lytic enzymes. Amylase is an example of an amylolytic enzyme that is present in human saliva, where it begins the chemical process of digestion. The pancreas also makes amylase (alpha amylase) to hydrolyze dietary starch into disaccharides and trisaccharides which are converted by other enzymes to glucose to supply the body with energy. Plants and some bacteria also produce amylases. Amylases are glycoside hydrolases and act on a-l,4-glycosidic bonds.

[0181] Several amylolytic enzymes are implicated in starch hydrolysis. Alpha-amylases

(EC 3.2.1.1) (alternate names: 1 ,4-a-D-glucan glucanohydrolase; glycogenase) are calcium metalloenzymes, i.e., completely unable to function in the absence of calcium. By acting at random locations along the starch chain, alpha-amylase breaks down long- chain carbohydrates, ultimately yielding maltotriose and maltose from amylose, or maltose, glucose and "limit dextrin" from amylopectin. Because it can act anywhere on the substrate, alpha-amylase tends to be faster-acting than beta-amylase. Another form of amylase, beta-amylase (EC 3.2.1.2) (alternate names: 1 ,4-a-D-glucan maltohydrolase; glycogenase; saccharogen amylase) catalyzes the hydrolysis of the second a- 1,4 glycosidic bond, cleaving off two glucose units (maltose) at a time. The third amylase is gamma-amylase (EC 3.2.1.3) (alternate names: Glucan 1,4-a-glucosidase; amyloglucosidase; Exo- 1,4-a-glucosidase; glucoamylase; lysosomal a-glucosidase; 1,4-a- D-glucan glucohydrolase). In addition to cleaving the last a(l-4)glycosidic linkages at the nonreducing end of amylose and amylopectin, yielding glucose, gamma-amylase will cleave a(l-6) glycosidic linkages.

[0182] A fourth enzyme, alpha-glucosidase, acts on maltose and other short malto- oligosaccharides produced by alpha-, beta-, and gamma-amylases, converting them to glucose.

[0183] Three major types of enzymatic activities degrade native cellulose. The first type is endoglucanases (l ,4-P-D-glucan 4-glucanohydrolases; EC 3.2.1.4). Endoglucanases cut at random in the cellulose polysaccharide chain of amorphous cellulose, generating oligosaccharides of varying lengths and consequently new chain ends. The second type are exoglucanases, including cellodextrinases (l,4- -D-glucan glucanohydrolases; EC 3.2.1.74) and cellobiohydrolases (1,4-P-D-glucan cellobiohydrolases; EC 3.2.1.91). Exoglucanases act in a processive manner on the reducing or non-reducing ends of cellulose polysaccharide chains, liberating either glucose (glucanohydrolases) or cellobiose (cellobiohydrolase) as major products. Exoglucanases can also act on microcrystallme cellulose, presumably peeling cellulose chains from the microcrystallme structure. The third type are β-glucosidases (β-glucoside glucohydrolases; EC 3.2.1.21). β-Glucosidases hydrolyze soluble cellodextrins and cellobiose to glucose units.

[0184] Even though yeast strains expressing enzymes for the production of fuel ethanol from whole grain or starch have been previously disclosed, the application has not been commercialized in the grain-based fuel ethanol industry, due to the relatively poor ability of the resulting strains to produce/tolerate high levels of ethanol. For example, U.S. Pat. No. 7,226,776 discloses that a polysaccharase enzyme expressing ethanologen can make ethanol directly from carbohydrate polymers, but the maximal ethanol titer demonstrated is 3.9 g/L. U.S. Pat. No. 5,422,267 discloses the use of a glucoamylase in yeast for production of alcoholic beverages; however, no commercially relevant titers of ethanol are disclosed. Heterologous Saccharolytic Enzymes

[0185] According to one aspect of the present invention, the expression of heterologous saccharolytic enzymes the recombinant microorganisms of the invention can be used advantageously to produce products such as ethanol from biomass sources. For example, cellulases from a variety of sources can be heterologously expressed to successfully increase efficiency of ethanol production. The saccharolytic enzymes can be from fungi, yeast, bacteria, plant, protozoan or termite sources. In some embodiments, the saccharolytic enzyme is from H. grisea, T. aurantiacus, T. emersonii, T. reesei, C. lacteus, C. formosanus, N. takasagoensis, C. acinaciformis, M. darwinensis, N. walkeri, S. fibuligera, C. lucknowense R. speratus, Thermobfida fusca, Clostridum thermocellum, Clostridium cellulolyticum, Clostridum josui, Bacillus pumilis, Cellulomonas fimi, Saccharophagus degradans, Piromyces equii, Neocallimastix patricarum or Arabidopsis thaliana.

[0186] In some embodiments, the cellulase for expression in the recombinant microorganisms of the invention is any cellulase disclosed in Table 4 or Table 7 in International Publication No. WO2011/153516, incorporated by reference herein in its entirety, or any cellulase suitable for expression in an appropriate host cell. In other embodiments, the amylase for expression in the recombinant microorganisms of the invention is any amylase such as alpha-amylases, beta-amylases, glucoamylases, alpha- glucosidases, pullulanase, or isopullulanase paralogues or orthologues, any amylase disclosed in Tables 15-19, preferably in Table 19, in International Publication No. WO2011/153516, incorporated by reference herein in its entirety, or any amylase suitable for expression in an appropriate host cell. In some embodiments of the invention, multiple saccharolytic enzymes from a single organism are co-expressed in the same recombinant microorganism. In some embodiments of the invention, multiple saccharolytic enzymes from different organisms are co-expressed in the same recombinant microorganism. In particular, saccharolytic enzymes from two, three, four, five, six, seven, eight, nine or more organisms can be co-expressed in the same recombinant microorganism. Similarly, the invention can encompass co-cultures of yeast strains, wherein the yeast strains express different saccharolytic enzymes. Co-cultures can include yeast strains expressing heterologous saccharolytic enzymes from the same organisms or from different organisms. Co-cultures can include yeast strains expressing saccharolytic enzymes from two, three, four, five, six, seven, eight, nine or more organisms.

[0187] Lignocellulases for expression in the recombinant microorganisms of the present invention include both endoglucanases and exoglucanases. Other lignocellulases for expression in the recombinant microorganisms of the invention include accessory enzymes which can act on the lignocellulosic material. The lignocellulases can be, for example, endoglucanases, glucosidases, cellobiohydrolases, xylanases, glucanases, xylosidases, xylan esterases, arabinofuranosidases, galactosidases, cellobiose phosphorylases, cellodextrin phosphorylases, mannanases, mannosidases, xyloglucanases, endoxylanases, glucuronidases, acetylxylanesterases, arabinofuranohydrolases, swollenins, glucuronyl esterases, expansins, pectinases, and feruoyl esterases. In some embodiments, the lignocellulases of the invention can be any suitable enzyme for digesting the desired lignocellulosic material.

[0188] In certain embodiments of the invention, the lignocellulase can be an endoglucanase, glucosidase, cellobiohydrolase, xylanase, glucanase, xylosidase, xylan esterase, arabinofuranosidase, galactosidase, cellobiose phosphorylase, cellodextrin phosphorylase, mannanase, mannosidase, xyloglucanase, endoxylanase, glucuronidase, acetylxylanesterase, arabinofuranohydrolase, swollenin, glucuronyl esterase, expansin, pectinase, and feruoyl esterase paralogue or orthologue. In particular embodiments, the lignocellulase is derived from any species named in Tables 4 and 7, in copending International Publication No. WO2011/153516, incorporated by reference herein.

Xylose metabolism

[0189] Xylose is a five-carbon monosaccharide that can be metabolized into useful products by a variety of organisms. There are two main pathways of xylose metabolism, each unique in the characteristic enzymes they utilize. One pathway is called the "Xylose Reductase-Xylitol Dehydrogenase" or XR-XDH pathway. Xylose reductase (XR) and xylitol dehydrogenase (XDH) are the two main enzymes used in this method of xylose degradation. XR, encoded by the XYL1 gene, is responsible for the reduction of xylose to xylitol and is aided by cofactors NADH or NADPH. Xylitol is then oxidized to xylulose by XDH, which is expressed through the XYL2 gene, and accomplished exclusively with the cofactor NAD ⁺ . Because of the varying cofactors needed in this pathway and the degree to which they are available for usage, an imbalance can result in an overproduction of xylitol byproduct and an inefficient production of desirable ethanol. Varying expression of the XR and XDH enzyme levels have been tested in the laboratory in the attempt to optimize the efficiency of the xylose metabolism pathway.

[0190] The other pathway for xylose metabolism is called the "Xylose Isomerase" (XI) pathway. Enzyme XI is responsible for direct conversion of xylose into xylulose, and does not proceed via a xylitol intermediate. Both pathways create xylulose, although the enzymes utilized are different. After production of xylulose both the XR-XDH and XI pathways proceed through the enzyme xylulokinase (XK), encoded on gene XKS1, to further modify xylulose into xylulose-5 -phosphate where it then enters the pentose phosphate pathway for further catabolism. XI includes those enzymes that correspond to Enzyme Commission Number 5.3.1.5. Suitable xylose isomerases of the present invention include xylose isomerases derived from, for example, Piromyces sp., and B. thetaiotaomicron, although any xylose isomerase that functions when expressed in host cells of the invention can be used, including chimeric enzymes.

[0191] Piromyces sp. xylose isomerase nucleotide and amino acid sequences correspond to SEQ ID NO:107 and SEQ ID NO: 108, respectively. B. thetaiotaomicron xylose isomerase nucleotide and amino acid sequences correspond to SEQ ID NO: 109 and SEQ ID NO:l 10, respectively.

[0192] Studies on flux through the pentose phosphate pathway during xylose metabolism have revealed that limiting the speed of this step may be beneficial to the efficiency of fermentation to ethanol. Modifications to this flux that may improve ethanol production include a) lowering phosphoglucose isomerase activity, b) deleting the GNDl gene, and c) deleting the ZWF1 gene (Jeppsson et ah, Appl. Environ. Microbiol. 68: 1604-09 (2002)). Since the pentose phosphate pathway produces additional NADPH during metabolism, limiting this step will help to correct the already evident imbalance between NAD(P)H and NAD ⁺ cofactors and reduce xylitol byproduct. In an additional embodiment, a native and/or heterologous phosphoketolase, an enzyme that participates in the PPP pathway, may be expressed in a recombinant microorganism of the invention. Phosphoketolases include enzymes that catalyze the conversion of D-xylulose 5- phosphate to D-glyceraldehyde 3-phosphate and dual specificity phosphoketolases that catalyze the conversion of D-fructose 6-phosphate to D-erythrose 4-phosphate. Phosphoketolases that can be employed in the invention include those disclosed in commonly owned U.S. Provisional Patent Application Nos. 61/728,450 and 61/792,731, which are incorporated by reference herein in their entireties.

[0193] An alternative approach is to improve the kinetics of the oxidative branch of the

PPP over those of competing pathways. This could be achieved by various approaches, e.g., by directly increasing the expression of the rate-limiting enzyme(s) of the oxidative branch of the PPP pathway, such as glucose-6-P dehydrogenase (encoded endogenously by ZWF1), changing the expression of regulating transcription factors like Stb5p (Cadiere, A., et al, "The Saccharomyces cerevisiae zinc factor protein Stb5p is required as a basal regulator of the pentose phosphate pathway," FEMS Yeast Research 10:819- 827 (2010)), or directly down-regulating the expression of genes involved in competing pathways like glucose-6-P isomerase (encoded by PGI1). Producing more C0 ₂ in the oxidative branch of the PPP would increase the availability of NADPH and increase the NADPH/NADP ratio. This would stimulate the flux of acetate-consuming pathways that (at least partially) consume NADPH, as would for example be the case for ethanol-to- isopropanol conversion that relies on a NADPH-consuming secondary alcohol dehydrogenase to convert acetone to isopropanol, or an acetate-to-ethanol pathway that uses a NADPH-consuming acetaldehyde dehydrogenase and/or alcohol dehydrogenase.

[0194] Another experiment comparing the two xylose metabolizing pathways revealed that the XI pathway was best able to metabolize xylose to produce the greatest ethanol yield, while the XR-XDH pathway reached a much faster rate of ethanol production (Karhumaa et al., Microb Cell Fact. 2007 Feb 5, 6:5). See also International Publication No. WO2006/009434, incorporated herein by reference in its entirety.

[0195] In some embodiments, the recombinant microorganisms of the invention have the ability to metabolize xylose using one or more of the above enzymes.

[0196] Various genes involved in xylose metabolism may be overexpressed by the recombinant microorganisms of the present invention. In some embodiments, the recombinant microorganism overexpresses one or more of xylose isomerase (XylA), xylulokinase (XKS1), transketolase (TKL2), transaldolase (TALI), ribose-5 -phosphate ketol-isomerase (R I1) and any combination thereof. Table 3 provides exemplary genes involved in xylose metabolism that can be engineered, as indicated, in the recombinant microorganisms of the invention:

Table 3 Gene name Modification Organism SEQ ID NO

Saccharomyces 226

TALI Overexpression cerevisiae

Saccharomyces 227

XKS1 Overexpression cerevisiae

Saccharomyces 228

TKL1 Overexpression cerevisiae

Saccharomyces 229

RKI1 Overexpression cerevisiae

Bacteroides 109

BtXI Overexpression thetaiotaomicron

Arabinose Metabolism

[0197] Arabinose is a five-carbon monosaccharide that can be metabolized into useful products by a variety of organisms. L-Arabinose residues are found widely distributed among many heteropolysaccharides of different plant tissues, such as arabinans, arabinogalactans, xylans and arabinoxylans. Bacillus species in the soil participate in the early stages of plant material decomposition, and B. subtilis secretes three enzymes, an endo-arabanase and two arabinosidases, capable of releasing arabinosyl oligomers and L- arabinose from plant cell.

[0198] Three pathways for L-arabinose metabolism in microorganisms have been described. Many bacteria, including Escherichia coli, use arabinose isomerase (AraA; E.C. 5.3.1.4), ribulokinase (AraB; E.C. 2.7.1.16), and ribulose phosphate epimerase (AraD; E.C. 5.1.3.4) to sequentially convert L-arabinose to D-xylulose-5 -phosphate through L-ribulose and L-ribulose 5-phosphate. See, e.g., Sa-Nogueira I, et ah, Microbiology 143:957-69 (1997). The D-xylulose-5 -phosphate then enters the pentose phosphate pathway for further catabolism. In the second pathway, L-arabinose is converted to L-2-keto-3-deoxyarabonate (L-KDA) by the consecutive action of enzymes arabinose dehydrogenase (ADH), arabinolactone (AL), and arabinonate dehydratase (AraC). See, e.g., Watanabe, S, et al, J. Biol. Chem. 281: 2612-2623 (2006). L-KDA can be further metabolized in two alternative pathways: 1) L-KDA conversion to 2- ketoglutarate via 2-ketoglutaric semialdehyde (KGSA) by L-KDA dehydratase and KGSA dehydrogenase or 2) L-KDA conversion to pyruvate and glycolaldehyde by L- KDA aldolase. In the third, fungal pathway, L-arabinose is converted to D-xylulose-5- phosphate through L-arabinitol, L-xylulose, and xylitol, by enzymes such as NAD(P)H- dependent aldose reductase (AR), L-arabinitol 4-dehydrogenase (ALDH), L-xylulose reductase (LXR), xylitol dehydrogenase (XylD), and xylulokinase (XylB). These, and additional proteins involved in arabinose metabolism and regulation may be found at http://www.nmpdr.org/FIG/subsys. cgi?user=&ssa_name=L-Arabinose_utilization& request =show_ssa, visited June 20, 2013, which is incorporated by reference herein in its entirety.

[0199] AraC protein regulates expression of its own synthesis and the other genes of the

Ara system. See Schleif, R., Trends Genet. i<5(12):559-65 (2000). In the E. coli, the AraC protein positively and negatively regulates expression of the proteins required for the uptake and catabolism of the sugar L-arabinose. Homologs of AraC, such as regulatory proteins RhaR and RhaS of the rhamnose operon, have been identified that contain regions homologous to the DNA-binding domain of AraC (Leal, T.F. and de Sa- Nogueira, I., FEMS Microbiol Lett. 24i(l):41-48 (2004)). Such arabinose regulatory proteins are referred to as the AraC/XylS family. See also, Mota, L.J., et ah, Mol. Microbiol. JJ(3):476-89 (1999); Mota, L.J., et al., J Bacteriol. 7SJ(14):4190-201 (2001).

[0200] In E. coli, the transport of L-arabinose across the E. coli cytoplasmic membrane requires the expression of either the high-affinity transport operon, araFGH, a binding protein-dependent system on the low-affinity transport operon, araE, a proton symporter. Additional arabinose transporters include those identified from K. marxianus and P. guilliermondii, disclosed in U.S. Patent No. 7,846,712, which is incorporated by reference herein.

[0201] In some embodiments, the recombinant microorganisms of the invention have the ability to metabolize arabinose using one or more of the above enzymes. Additional enzymes and/or strategies that can be employed for the metabolism of arabinose in the invention include those disclosed in commonly owned International Publication No. WO 2013/071112, which is incorporated by reference herein in its entirety.

Trehalose Metabolism

[0202] Trehalose is an alpha-linked disaccharide formed through an α,α-Ι,Ι-glucoside bond between two a-glucose molecules. Trehalose is known to play a role as a storage carbohydrate in yeast and can be broken down into glucose by enzymes such as trehalase. Intracellular levels of trehalose in the yeast S. cerevisiae are well-regulated through balancing enzymatic synthesis and degradation. See Jules, M., et al., "New Insights into Trehalose Metabolism by Saccharomyces cerevisiae: NHT2 Encodes a Functional Cytosolic Trehalase, and Deletion of TPS1 Reveals ATHlp-Dependent Trehalose Mobilization," Appl. Environ. Microbiol. 74 (3) :605-614 (2008). Trehalose also functions as a potential carbon source for microorganisms, including yeast. Yeast genes involved in the metabolism of trehalose include, but are not limited to, Athlp, which is thought to extracellularly hydrolyze trehalose into two glucose units; the trehalose transporter Agtlp; and Nthlp, which is believed to hydrolyse the imported disaccharide. See Jules, M., et al. (2008).

[0203] In some embodiments, the recombinant microorganisms of the invention have the ability to metabolize trehalose using one or more of the above enzymes. Additionally, over expression of TPS 1 and/or TPS2, and/or TSLl may increase the intracellular pool of trehalose allowing for improved robustness. It was recently shown that overexpression of TPS1 and TPS2 improved the performance of a GPD1 mutant engineered to express GAPN from Bacillus cereus. See Guo, Z-P., et al., "Minimization of glycerol synthesis in industrial ethanol yeast without influencing its fermentation performance," Metabolic Engineering 7J(l):49-59 (2011). It has not been shown that overexpression of trehalose synthesis improves the performance of strains engineered to make formate nor has it been shown in combination with glycerol uptake genes such as STL1. In some embodiments TPS1 is from S. cerevisiae. S. cerevisiae TPS1 nucleotide and amino acid sequences correspond to SEQ ID NO:l 11 and SEQ ID NO: 112, respectively. In some embodiments TPS2 is from S. cerevisiae. S. cerevisiae TPS2 nucleotide and amino acid sequences correspond to SEQ ID NO: 113 and SEQ ID NO: 114, respectively. In some embodiments TSLl is from S. cerevisiae. S. cerevisiae TSLl nucleotide and amino acid sequences correspond to SEQ ID NO: 115 and SEQ ID NO: 116, respectively. In some embodiments NTH1 is from S. cerevisiae. S. cerevisiae NTH1 nucleotide and amino acid sequences correspond to SEQ ID NO: 1 17 and SEQ ID NO: 118, respectively.

Isopropanol Production

[0204] Production of isopropanol from carbohydrates has been shown to occur natively in certain organisms including those related to C. acetobutylicum. In addition, pathways for the recombinant production of isopropanol from carbohydrates in microorganisms have been engineered in E. coli and yeast. See, e.g., U.S. Patent Appl. Pub. No. 2008/0293125, which is incorporated by reference herein in its entirety. Additional methods and enzymes for recombinantly producing isopropanol are disclosed in commonly owned International Publication No. WO 2011/140386, which is incorporated by reference herein in its entirety. In certain embodiments, any of the above pathways may be engineered into the recombinant microorganism of the invention for the production of isopropanol.

Microorganisms

[0205] The present invention includes multiple strategies for the development of microorganisms with the combination of substrate-utilization and product-formation properties required for CBP. The "native cellulolytic strategy" involves engineering naturally occurring cellulolytic microorganisms to improve product-related properties, such as yield and titer. The "recombinant cellulolytic strategy" involves engineering natively non-cellulolytic organisms that exhibit high product yields and titers to express a heterologous cellulase system that enables cellulose utilization or hemicellulose utilization or both.

[0206] Many bacteria have the ability to ferment simple hexose sugars into a mixture of acidic and pH-neutral products via the process of glycolysis. The glycolytic pathway is abundant and comprises a series of enzymatic steps whereby a six carbon glucose molecule is broken down, via multiple intermediates, into two molecules of the three carbon compound pyruvate. This process results in the net generation of ATP (biological energy supply) and the reduced cofactor NADH.

[0207] Pyruvate is an important intermediary compound of metabolism. For example, under aerobic conditions pyruvate may be oxidized to acetyl coenzyme A (acetyl-CoA), which then enters the tricarboxylic acid cycle (TCA), which in turn generates synthetic precursors, C0 ₂ , and reduced cofactors. The cofactors are then oxidized by donating hydrogen equivalents, via a series of enzymatic steps, to oxygen resulting in the formation of water and ATP. This process of energy formation is known as oxidative phosphorylation.

[0208] Under anaerobic conditions (no available oxygen), fermentation occurs in which the degradation products of organic compounds serve as hydrogen donors and acceptors. Excess NADH from glycolysis is oxidized in reactions involving the reduction of organic substrates to products, such as lactate and ethanol. In addition, ATP is regenerated from the production of organic acids, such as acetate, in a process known as substrate level phosphorylation. Therefore, the fermentation products of glycolysis and pyruvate metabolism include a variety of organic acids, alcohols and C0 ₂ .

[0209] Most facultative anaerobes metabolize pyruvate aerobically via pyruvate dehydrogenase (PDH) and the tricarboxylic acid cycle (TCA). Under anaerobic conditions, the main energy pathway for the metabolism of pyruvate is via pyruvate- formate-lyase (PFL) pathway to give formate and acetyl-CoA. Acetyl-CoA is then converted to acetate, via phosphotransacetylase (PTA) and acetate kinase (ACK) with the co-production of ATP, or reduced to ethanol via acetalaldehyde dehydrogenase (ACDH) and alcohol dehydrogenase (ADH). In order to maintain a balance of reducing equivalents, excess NADH produced from glycolysis is re-oxidized to NAD ⁺ by lactate dehydrogenase (LDH) during the reduction of pyruvate to lactate. NADH can also be re- oxidized by ACDH and ADH during the reduction of acetyl-CoA to ethanol, but this is a minor reaction in cells with a functional LDH.

[0210] Alternate pathways from acetate to acetyl-CoA can be achieved by the expression of the bacterial system of PTA and ACK. These two enzymes can act sequentially to produce acetyl-CoA from acetate. Due to the difference in co-factors between PTA/ACK and ACS, this pathway could have higher activity in vivo when heterologously expressed. Sources for PTA and ACK can come from a large variety of bacterial sources including but not limited to Escherichia, Thermoanaerobacter, Clostridia, and Bacillus species. Examples of expression of PTA and ACK for the production of alcohols and other desired products are disclosed in commonly owned International Publication No. WO 2011/140386, which is incorporated by reference herein in its entirety.

[0211] In some embodiments, the PTA is from Bifidobacterium adolescentis.

Bifidobacterium adolescentis PTA nucleotide and amino acid sequences correspond to SEQ ID NO: 1 19 and SEQ ID NO: 120, respectively. In some embodiments, the PTA is from Leuconostoc mesenteroides. Leuconostoc mesenteroides PTA nucleotide and amino acid sequences correspond to SEQ ID NO: 121 and SEQ ID NO: 122, respectively. In some embodiments, the PTA is from Oenococcus oenii. Oenococcus oenii PTA nucleotide and amino acid sequences correspond to SEQ ID NO: 123 and SEQ ID NO: 124, respectively. In some embodiments, the ACK is from Bifidobacterium adolescentis. Bifidobacterium adolescentis ACK nucleotide and amino acid sequences correspond to SEQ ID NO: 125 and SEQ ID NO: 126, respectively. In some embodiments, ACK is from Leuconostoc mesenteroides. Leuconostoc mesenteroides ACK nucleotide and amino acid sequences correspond to SEQ ID NO: 127 and SEQ ID NO:128, respectively. In some embodiments, the ACK is from Oenococcus oenii. Oenococcus oenii ACK nucleotide and amino acid sequences correspond to SEQ ID NO: 129 and SEQ ID NO: 130, respectively.

Host Cells

[0212] Host cells useful in the present invention include any prokaryotic or eukaryotic cells; for example, microorganisms selected from bacterial, algal, and yeast cells. Among host cells thus suitable for the present invention are microorganisms, for example, of the genera Aeromonas, Aspergillus, Bacillus, Escherichia, Kluyveromyces, Pichia, Rhodococcus, Saccharomyces and Streptomyces.

[0213] In some embodiments, the host cells are microorganisms. In one embodiment the microorganism is a yeast. According to the present invention the yeast host cell can be, for example, from the genera Saccharomyces, Kluyveromyces, Candida, Pichia, Schizosaccharomyces, Hansenula, Kloeckera, Schwanniomyces, and Yarrowia. Yeast species as host cells may include, for example, S. cerevisiae, S. bulderi, S. barnetti, S. exiguus, S. uvarum, S. diastaticus, K. lactis, K. marxianus, or K. fragilis. In some embodiments, the yeast is selected from the group consisting of Saccharomyces cerevisiae, Schizzosaccharomyces pombe, Candida albicans, Pichia pastoris, Pichia stipitis, Yarrowia lipolytica, Hansenula polymorpha, Phajfia rhodozyma, Candida utilis, Arxula adeninivorans, Debaryomyces hansenii, Debaryomyces polymorphus, Schizosaccharomyces pombe and Schwanniomyces occidentalis. In one particular embodiment, the yeast is Saccharomyces cerevisiae. In another embodiment, the yeast is the S. cerevisiae strain PE-2. In yet another embodiment, the yeast is a thermotolerant Saccharomyces cerevisiae. The selection of an appropriate host is deemed to be within the scope of those skilled in the art from the teachings herein.

[0214] In some embodiments, the host cell is an oleaginous cell. The oleaginous host cell can be an oleaginous yeast cell. For example, the oleaginous yeast host cell can be from the genera Blakeslea, Candida, Cryptococcus, Cunninghamella, Lipomyces, Mortierella, Mucor, Phy corny ces, Pythium, Rhodosporidum, Rhodotorula, Trichosporon or Yarrowia. According to the present invention, the oleaginous host cell can be an oleaginous microalgae host cell. For example, the oleaginous microalgea host cell can be from the genera Thraustochytrium or Schizochytrium. Biodiesel could then be produced from the triglyceride produced by the oleaginous organisms using conventional lipid transesterification processes. In some particular embodiments, the oleaginous host cells can be induced to secrete synthesized lipids. Embodiments using oleaginous host cells are advantageous because they can produce biodiesel from lignocellulosic feedstocks which, relative to oilseed substrates, are cheaper, can be grown more densely, show lower life cycle carbon dioxide emissions, and can be cultivated on marginal lands.

[0215] In some embodiments, the host cell is a thermotolerant host cell. Thermotolerant host cells can be particularly useful in simultaneous saccharification and fermentation processes by allowing externally produced cellulases and ethanol-producing host cells to perform optimally in similar temperature ranges.

[0216] Thermotolerant host cells can include, for example, Issatchenkia orientalis, Pichia mississippiensis, Pichia mexicana, Pichia farinosa, Clavispora opuntiae, Clavispora lusitaniae, Candida mexicana, Hansenula polymorpha and Kluyveromyces host cells. In some embodiments, the thermotolerant cell is an S. cerevisiae strain, or other yeast strain, that has been adapted to grow in high temperatures, for example, by selection for growth at high temperatures in a cytostat.

[0217] In some particular embodiments, the host cell is a Kluyveromyces host cell. For example, the Kluyveromyces host cell can be a K lactis, K marxianus, K. blattae, K phqffii, K. yarrowii, K. aestuarii, K. dobzhanskii, K. wickerhamii K. thermotolerans, or K waltii host cell. In one embodiment, the host cell is a K lactis, or K marxianus host cell. In another embodiment, the host cell is a K marxianus host cell.

[0218] In some embodiments, the thermotolerant host cell can grow at temperatures above about 30° C, about 31° C, about 32° C, about 33° C, about 34° C, about 35° C, about 36° C, about 37° C, about 38° C, about 39° C, about 40° C, about 41° C or about 42° C. In some embodiments of the present invention the thermotolerant host cell can produce ethanol from cellulose at temperatures above about 30° C, about 31° C, about 32° C, about 33° C, about 34° C, about 35° C, about 36° C, about 37° C, about 38° C, about 39° C, about 40° C, about 41° C, about 42° C, or about 43 °C, or about 44 °C, or about 45 °C, or about 50° C.

[0219] In some embodiments of the present invention, the thermotolerant host cell can grow at temperatures from about 30° C to 60° C, about 30° C to 55° C, about 30° C to 50° C, about 40° C to 60° C, about 40° C to 55° C or about 40° C to 50° C. In some embodiments of the present invention, the thermotolterant host cell can produce ethanol from cellulose at temperatures from about 30° C to 60° C, about 30° C to 55° C, about 30° C to 50° C, about 40° C to 60° C, about 40° C to 55° C or about 40° C to 50° C.

[0220] In some embodiments, the host cell has the ability to metabolize xylose. Detailed information regarding the development of the xylose-utilizing technology can be found in the following publications: Kuyper M et al. FEMS Yeast Res. 4: 655-64 (2004), Kuyper M et al. FEMS Yeast Res. 5:399-409 (2005), and Kuyper M et al. FEMS Yeast Res. 5:925-34 (2005), which are herein incorporated by reference in their entirety. For example, xylose-utilization can be accomplished in S. cerevisiae by heterologously expressing the xylose isomerase gene, XylA, e.g., from the anaerobic fungus Piromyces sp. E2, overexpressing five S. cerevisiae enzymes involved in the conversion of xylulose to glycolytic intermediates (xylulokinase, ribulose 5-phosphate isomerase, ribulose 5- phosphate epimerase, transketolase and transaldolase) and deleting the GRE3 gene encoding aldose reductase to minimize xylitol production.

[0221] In some embodiments, the host cell has the ability to metabolize arabinose. For example, arabinose-utilization can be accomplished by heterologously expressing, e.g., one or more of arabinose isomerase, ribulokinase, or ribulose phosphate epimerase. The host cells can contain antibiotic markers or can contain no antibiotic markers.

[0222] In certain embodiments, the host cell is a microorganism that is a species of the genera Thermoanaerobacterium, Thermoanaerobacter, Clostridium, Geobacillus, Saccharococcus, Paenibacillus, Bacillus, Caldicellulosiruptor, Anaerocellum, or Anoxybacillus. In certain embodiments, the host cell is a bacterium selected from the group consisting of: Thermoanaerobacterium thermosulfurigenes, Thermoanaerobacterium aotearoense, Thermoanaerobacterium polysaccharolyticum, Thermoanaerobacterium zeae, Thermoanaerobacterium xylanolyticum,

Thermoanaerobacterium saccharolyticum, Thermoanaerobium brockii,

Thermoanaerobacterium thermosaccharolyticum, Thermoanaerobacter thermohydrosulfuricus, Thermoanaerobacter ethanolicus, Thermoanaerobacter brocki, Clostridium thermocellum, Clostridium cellulolyticum, Clostridium phytofermentans, Clostridium straminosolvens, Geobacillus thermoglucosidasius, Geobacillus stearothermophilus, Saccharococcus caldoxylosilyticus, Saccharoccus thermophilus, Paenibacillus campinasensis, Bacillus flavothermus, Anoxybacillus kamchatkensis, Anoxybacillus gonensis, Caldicellulosiruptor acetigenus, Caldicellulosiruptor saccharolyticus, Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor owensensis, Caldicellulosiruptor lactoaceticus, and Anaerocellum thermophilum. In certain embodiments, the host cell is Clostridium thermocellum, Clostridium cellulolyticum, or Thermoanaerobacterium saccharolyticum.

Codon Optimized Polynucleotides

[0223] The polynucleotides encoding heterologous cellulases can be codon-optimized.

As used herein the term "codon-optimized coding region" means a nucleic acid coding region that has been adapted for expression in the cells of a given organism by replacing at least one, or more than one, or a significant number, of codons with one or more codons that are more frequently used in the genes of that organism.

[0224] In general, highly expressed genes in an organism are biased towards codons that are recognized by the most abundant tR A species in that organism. One measure of this bias is the "codon adaptation index" or "CAI," which measures the extent to which the codons used to encode each amino acid in a particular gene are those which occur most frequently in a reference set of highly expressed genes from an organism.

[0225] The CAI of codon optimized sequences of the present invention corresponds to between about 0.8 and 1.0, between about 0.8 and 0.9, or about 1.0. A codon optimized sequence may be further modified for expression in a particular organism, depending on that organism's biological constraints. For example, large runs of "As" or "Ts" (e.g., runs greater than 3, 4, 5, 6, 7, 8, 9, or 10 consecutive bases) can be removed from the sequences if these are known to effect transcription negatively. Furthermore, specific restriction enzyme sites may be removed for molecular cloning purposes. Examples of such restriction enzyme sites include Pad, Ascl, BamHI, Bglll, EcoRI and Xhol. Additionally, the DNA sequence can be checked for direct repeats, inverted repeats and mirror repeats with lengths of ten bases or longer, which can be modified manually by replacing codons with "second best" codons, i.e., codons that occur at the second highest frequency within the particular organism for which the sequence is being optimized.

Deviations in the nucleotide sequence that comprise the codons encoding the amino acids of any polypeptide chain allow for variations in the sequence coding for the gene. Since each codon consists of three nucleotides, and the nucleotides comprising DNA are restricted to four specific bases, there are 64 possible combinations of nucleotides, 61 of which encode amino acids (the remaining three codons encode signals ending translation). The "genetic code" which shows which codons encode which amino acids is reproduced herein as Table 4. As a result, many amino acids are designated by more than one codon. For example, the amino acids alanine and proline are coded for by four triplets, serine and arginine by six, whereas tryptophan and methionine are coded by just one triplet. This degeneracy allows for DNA base composition to vary over a wide range without altering the amino acid sequence of the proteins encoded by the DNA.

TABLE 4: The Standard Genetic Code

[0227] Many organisms display a bias for use of particular codons to code for insertion of a particular amino acid in a growing peptide chain. Codon preference or codon bias, differences in codon usage between organisms, is afforded by degeneracy of the genetic code, and is well documented among many organisms. Codon bias often correlates with the efficiency of translation of messenger RNA (mRNA), which is in turn believed to be dependent on, inter alia, the properties of the codons being translated and the availability of particular transfer RNA (tRNA) molecules. The predominance of selected tRNAs in a cell is generally a reflection of the codons used most frequently in peptide synthesis. Accordingly, genes can be tailored for optimal gene expression in a given organism based on codon optimization.

[0228] Given the large number of gene sequences available for a wide variety of animal, plant and microbial species, it is possible to calculate the relative frequencies of codon usage. Codon usage tables are readily available, for example, at www.kazusa.or.jp/codon/ (visited June 20, 2013), and these tables can be adapted in a number of ways. See Nakamura, Y., et al. "Codon usage tabulated from the international DNA sequence databases: status for the year 2000," Nucl. Acids Res. 28:292 (2000). Codon usage tables for yeast, calculated from GenBank Release 128.0 [15 February 2002], are reproduced below as Table 52. This table uses mRNA nomenclature, and so instead of thymine (T) which is found in DNA, the tables use uracil (U) which is found in RNA. The table has been adapted so that frequencies are calculated for each amino acid, rather than for all 64 codons.

TABLE 5 : Codon Usage Table for Saccharomyces cerevisiae Genes

Amino Acid Codon Number Frequency per

hundred

Phe UUU 170666 26.1

Phe UUC 120510 18.4

Leu UUA 170884 26.2

Leu UUG 177573 27.2

Leu CUU 80076 12.3

Leu CUC 35545 5.4

Leu CUA 87619 13.4

Leu CUG 68494 10.5

He AUU 196893 30.1

He AUC 112176 17.2

[0229] By utilizing this or similar tables, one of ordinary skill in the art can apply the frequencies to any given polypeptide sequence, and produce a nucleic acid fragment of a codon-optimized coding region which encodes the polypeptide, but which uses codons optimal for a given species. Codon-optimized coding regions can be designed by various different methods.

[0230] In one method, a codon usage table is used to find the single most frequent codon used for any given amino acid, and that codon is used each time that particular amino acid appears in the polypeptide sequence. For example, referring to Table 4 above, for leucine, the most frequent codon is UUG, which is used 27.2% of the time. Thus all the leucine residues in a given amino acid sequence would be assigned the codon UUG.

[0231] In another method, the actual frequencies of the codons are distributed randomly throughout the coding sequence. Thus, using this method for optimization, if a hypothetical polypeptide sequence had 100 leucine residues, referring to Table 4 for frequency of usage in the S. cerevisiae, about 5, or 5% of the leucine codons would be CUC, about 11, or 11% of the leucine codons would be CUG, about 12, or 12% of the leucine codons would be CUU, about 13, or 13% of the leucine codons would be CUA, about 26, or 26% of the leucine codons would be UUA, and about 27, or 27% of the leucine codons would be UUG.

[0232] These frequencies would be distributed randomly throughout the leucine codons in the coding region encoding the hypothetical polypeptide. As will be understood by those of ordinary skill in the art, the distribution of codons in the sequence can vary significantly using this method; however, the sequence always encodes the same polypeptide.

[0233] When using the methods above, the term "about" is used precisely to account for fractional percentages of codon frequencies for a given amino acid. As used herein, "about" is defined as one amino acid more or one amino acid less than the value given. The whole number value of amino acids is rounded up if the fractional frequency of usage is 0.50 or greater, and is rounded down if the fractional frequency of use is 0.49 or less. Using again the example of the frequency of usage of leucine in human genes for a hypothetical polypeptide having 62 leucine residues, the fractional frequency of codon usage would be calculated by multiplying 62 by the frequencies for the various codons. Thus, 7.28 percent of 62 equals 4.51 UUA codons, or "about 5," i.e., 4, 5, or 6 UUA codons, 12.66 percent of 62 equals 7.85 UUG codons or "about 8," i.e., 7, 8, or 9 UUG codons, 12.87 percent of 62 equals 7.98 CUU codons, or "about 8," i.e., 7, 8, or 9 CUU codons, 19.56 percent of 62 equals 12.13 CUC codons or "about 12," i.e., 11, 12, or 13 CUC codons, 7.00 percent of 62 equals 4.34 CUA codons or "about 4," i.e., 3, 4, or 5 CUA codons, and 40.62 percent of 62 equals 25.19 CUG codons, or "about 25," i.e., 24, 25, or 26 CUG codons.

[0234] Randomly assigning codons at an optimized frequency to encode a given polypeptide sequence, can be done manually by calculating codon frequencies for each amino acid, and then assigning the codons to the polypeptide sequence randomly. Additionally, various algorithms and computer software programs are readily available to those of ordinary skill in the art. For example, the "EditSeq" function in the Lasergene Package, available from DNAstar, Inc., Madison, WI, the backtranslation function in the VectorNTI Suite, available from InforMax, Inc., Bethesda, MD, and the "backtranslate" function in the GCG~Wisconsin Package, available from Accelrys, Inc., San Diego, CA. In addition, various resources are publicly available to codon-optimize coding region sequences, e.g., the "backtranslation" function at www.entelechon.com/2008/10/backtranslation-tool/ (visited June 20, 2013) and the "backtranseq" function June 20, 2013). Constructing a rudimentary algorithm to assign codons based on a given frequency can also easily be accomplished with basic mathematical functions by one of ordinary skill in the art.

A number of options are available for synthesizing codon optimized coding regions designed by any of the methods described above, using standard and routine molecular biological manipulations well known to those of ordinary skill in the art. In one approach, a series of complementary oligonucleotide pairs of 80-90 nucleotides each in length and spanning the length of the desired sequence is synthesized by standard methods. These oligonucleotide pairs are synthesized such that upon annealing, they form double stranded fragments of 80-90 base pairs, containing cohesive ends, e.g., each oligonucleotide in the pair is synthesized to extend 3, 4, 5, 6, 7, 8, 9, 10, or more bases beyond the region that is complementary to the other oligonucleotide in the pair. The single-stranded ends of each pair of oligonucleotides is designed to anneal with the single-stranded end of another pair of oligonucleotides. The oligonucleotide pairs are allowed to anneal, and approximately five to six of these double-stranded fragments are then allowed to anneal together via the cohesive single stranded ends, and then they ligated together and cloned into a standard bacterial cloning vector, for example, a TOPO ^® vector available from Invitrogen Corporation, Carlsbad, CA. The construct is then sequenced by standard methods. Several of these constructs consisting of 5 to 6 fragments of 80 to 90 base pair fragments ligated together, i.e., fragments of about 500 base pairs, are prepared, such that the entire desired sequence is represented in a series of plasmid constructs. The inserts of these plasmids are then cut with appropriate restriction enzymes and ligated together to form the final construct. The final construct is then cloned into a standard bacterial cloning vector, and sequenced. Additional methods would be immediately apparent to the skilled artisan. In addition, gene synthesis is readily available commercially.

[0236] In additional embodiments, a full-length polypeptide sequence is codon-optimized for a given species resulting in a codon-optimized coding region encoding the entire polypeptide, and then nucleic acid fragments of the codon-optimized coding region, which encode fragments, variants, and derivatives of the polypeptide are made from the original codon-optimized coding region. As would be well understood by those of ordinary skill in the art, if codons have been randomly assigned to the full-length coding region based on their frequency of use in a given species, nucleic acid fragments encoding fragments, variants, and derivatives would not necessarily be fully codon optimized for the given species. However, such sequences are still much closer to the codon usage of the desired species than the native codon usage. The advantage of this approach is that synthesizing codon-optimized nucleic acid fragments encoding each fragment, variant, and derivative of a given polypeptide, although routine, would be time consuming and would result in significant expense.

Transposons

[0237] To select for foreign DNA that has entered a host it is preferable that the DNA be stably maintained in the organism of interest. With regard to plasmids, there are two processes by which this can occur. One is through the use of replicative plasmids. These plasmids have origins of replication that are recognized by the host and allow the plasmids to replicate as stable, autonomous, extrachromosomal elements that are partitioned during cell division into daughter cells. The second process occurs through the integration of a plasmid onto the chromosome. This predominately happens by homologous recombination and results in the insertion of the entire plasmid, or parts of the plasmid, into the host chromosome. Thus, the plasmid and selectable marker(s) are replicated as an integral piece of the chromosome and segregated into daughter cells. Therefore, to ascertain if plasmid DNA is entering a cell during a transformation event through the use of selectable markers requires the use of a replicative plasmid or the ability to recombine the plasmid onto the chromosome. These qualifiers cannot always be met, especially when handling organisms that do not have a suite of genetic tools. [0238] One way to avoid issues regarding plasmid-associated markers is through the use of transposons. A transposon is a mobile DNA element, defined by mosaic DNA sequences that are recognized by enzymatic machinery referred to as a transposase. The function of the transposase is to randomly insert the transposon DNA into host or target DNA. A selectable marker can be cloned onto a transposon by standard genetic engineering. The resulting DNA fragment can be coupled to the transposase machinery in an in vitro reaction and the complex can be introduced into target cells by electroporation. Stable insertion of the marker onto the chromosome requires only the function of the transposase machinery and alleviates the need for homologous recombination or replicative plasmids.

[0239] The random nature associated with the integration of transposons has the added advantage of acting as a form of mutagenesis. Libraries can be created that comprise amalgamations of transposon mutants. These libraries can be used in screens or selections to produce mutants with desired phenotypes. For instance, a transposon library of a CBP organism could be screened for the ability to produce more ethanol, or less lactic acid and/or more acetate.

Native cellulolytic strategy

[0240] Naturally occurring cellulolytic microorganisms are starting points for CBP organism development via the native strategy. Anaerobes and facultative anaerobes are of particular interest. The primary objective is to engineer the metabolization of biomass to solvents, including but not limited to, acetone, isopropanol, ethyl acetate, or ethanol. Metabolic engineering of mixed-acid fermentations in relation to, for example, ethanol production, has been successful in the case of mesophilic, non-cellulolytic, enteric bacteria. Recent developments in suitable gene -transfer techniques allow for this type of work to be undertaken with cellulolytic bacteria.

Recombinant cellulolytic strategy

[0241] Non-cellulolytic microorganisms with desired product- formation properties are starting points for CBP organism development by the recombinant cellulolytic strategy. The primary objective of such developments is to engineer a heterologous cellulase system that enables growth and fermentation on pretreated lignocellulose. The heterologous production of cellulases has been pursued primarily with bacterial hosts producing ethanol at high yield (engineered strains of E. coli, Klebsiella oxytoca, and Zymomonas mobilis) and the yeast Saccharomyces cerevisiae. Cellulase expression in strains of K oxytoca resulted in increased hydrolysis yields - but not growth without added cellulase - for microcrystalline cellulose, and anaerobic growth on amorphous cellulose. Although dozens of saccharolytic enzymes have been functionally expressed in S. cerevisiae, anaerobic growth on cellulose as the result of such expression has not been definitively demonstrated.

Aspects of the present invention relate to the use of thermophilic or mesophilic microorganisms as hosts for modification via the native cellulolytic strategy. Their potential in process applications in biotechnology stems from their ability to grow at relatively high temperatures with attendant high metabolic rates, production of physically and chemically stable enzymes, and elevated yields of end products. Major groups of thermophilic bacteria include eubacteria and archaebacteria. Thermophilic eubacteria include: phototropic bacteria, such as cyanobacteria, purple bacteria, and green bacteria; Gram-positive bacteria, such as Bacillus, Clostridium, Lactic acid bacteria, and Actinomyces; and other eubacteria, such as Thiobacillus, Spirochete, Desulfotomaculum, Gram-negative aerobes, Gram-negative anaerobes, and Thermotoga. Within archaebacteria are considered Methanogens, extreme thermophiles (an art-recognized term), and Thermoplasma. In certain embodiments, the present invention relates to Gram-negative organotrophic thermophiles of the genera Thermus, Gram-positive eubacteria, such as genera Clostridium, and also which comprise both rods and cocci, genera in group of eubacteria, such as Thermosipho and Thermotoga, genera of Archaebacteria, such as Thermococcus, Thermoproteus (rod-shaped), Thermofilum (rod- shaped), Pyrodictium, Acidianus, Sulfolobus, Pyrobaculum, Pyrococcus, Thermodiscus, Staphylothermus, Desulfurococcus, Archaeoglobus, and Methanopyrus. Some examples of thermophilic or mesophilic (including bacteria, prokaryotic microorganism, and fungi), which may be suitable for the present invention include, but are not limited to: Clostridium thermosulfurogenes, Clostridium cellulolyticum, Clostridium thermocellum, Clostridium thermohydrosulfuricum, Clostridium thermoaceticum, Clostridium thermosaccharolyticum, Clostridium tartarivorum, Clostridium thermocellulaseum, Clostridium phytofermentans, Clostridium straminosolvens, Thermoanaerobacterium thermosaccarolyticum, Thermoanaerobacterium saccharolyticum, Thermobacteroides acetoethylicus, Thermoanaerobium brockii, Methanobacterium thermoautotrophicum, Anaerocellum thermophilium, Pyrodictium occultum, Thermoproteus neutrophilus, Thermofilum librum, Thermothrix thioparus, Desulfovibrio thermophilus, Thermoplasma acidophilum, Hydrogenomonas thermophilus, Thermomicrobium roseum, Thermus flavas, Thermus ruber, Pyrococcus furiosus, Thermus aquaticus, Thermus thermophilus, Chloroflexus aurantiacus, Thermococcus litoralis, Pyrodictium abyssi, Bacillus stearothermophilus, Cyanidium caldarium, Mastigocladus laminosus, Chlamydothrix calidissima, Chlamydothrix penicillata, Thiothrix carnea, Phormidium tenuissimum, Phormidium geysericola, Phormidium subterraneum, Phormidium bijahensi, Oscillatoria flliformis, Synechococcus lividus, Chloroflexus aurantiacus, Pyrodictium brockii, Thiobacillus thiooxidans, Sulfolobus acidocaldarius, Thiobacillus thermophilica, Bacillus stearothermophilus, Cercosulcifer hamathensis, Vahlkampfia reichi, Cyclidium citrullus, Dactylaria gallopava, Synechococcus lividus, Synechococcus elongatus, Synechococcus minervae, Synechocystis aquatilus, Aphanocapsa thermalis, Oscillatoria terebriformis, Oscillatoria amphibia, Oscillatoria germinata, Oscillatoria okenii, Phormidium laminosum, Phormidium parparasiens, Symploca thermalis, Bacillus acidocaldarias, Bacillus coagulans, Bacillus thermocatenalatus, Bacillus licheniformis, Bacillus pamilas, Bacillus macerans, Bacillus circulans, Bacillus laterosporus, Bacillus brevis, Bacillus subtilis, Bacillus sphaericus, Desulfotomaculum nigrificans, Streptococcus thermophilus, Lactobacillus thermophilus, Lactobacillus bulgaricus, Bifidobacterium thermophilum, Streptomyces fragmentosporus, Streptomyces thermonitrificans, Streptomyces thermovulgaris, Pseudonocardia thermophila, Thermoactinomyces vulgaris, Thermoactinomyces sacchari, Thermoactinomyces Candidas, Thermomonospora curvata, Thermomonospora viridis, Thermomonospora citrina, Microbispora thermodiastatica, Microbispora aerata, Microbispora bispora, Actinobifida dichotomica, Actinobifida chromogena, Micropolyspora caesia, Micropolyspora faeni, Micropolyspora cectivugida, Micropolyspora cabrobrunea, Micropolyspora thermovirida, Micropolyspora viridinigra, Methanobacterium thermoautothropicum, Caldicellulosiruptor acetigenus, Caldicellulosiruptor saccharolyticus, Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor owensensis, Caldicellulosiruptor lactoaceticus, variants thereof, and/or progeny thereof. [0243] In particular embodiments, the present invention relates to thermophilic bacteria selected from the group consisting of Clostridium cellulolyticum, Clostridium thermocellum, and Thermoanaerobacterium saccharolyticum.

[0244] In certain embodiments, the present invention relates to thermophilic bacteria selected from the group consisting of Fervidobacterium gondwanense, Clostridium thermolacticum, Moorella sp., and Rhodothermus marinus.

[0245] In certain embodiments, the present invention relates to thermophilic bacteria of the genera Thermoanaerobacterium or Thermoanaerobacter, including, but not limited to, species selected from the group consisting of: Thermoanaerobacterium thermosulfurigenes, Thermoanaerobacterium aotearoense, Thermoanaerobacterium poly saccharolyticum, Thermoanaerobacterium zeae, Thermoanaerobacterium xylanolyticum, Thermoanaerobacterium saccharolyticum, Thermoanaerobium brockii, Thermoanaerobacterium thermosaccharolyticum, Thermoanaerobacter thermohydrosulfuricus, Thermoanaerobacter ethanolicus, Thermoanaerobacter brockii, variants thereof, and progeny thereof.

[0246] In certain embodiments, the present invention relates to microorganisms of the genera Geobacillus, Saccharococcus, Paenibacillus, Bacillus, and Anoxybacillus, including, but not limited to, species selected from the group consisting of: Geobacillus thermoglucosidasius, Geobacillus stearothermophilus, Saccharococcus caldoxylosilyticus, Saccharoccus thermophilus, Paenibacillus campinasensis, Bacillus flavothermus, Anoxybacillus kamchatkensis, Anoxybacillus gonensis, variants thereof, and progeny thereof.

[0247] In certain embodiments, the present invention relates to mesophilic bacteria selected from the group consisting of Saccharophagus degradans; Flavobacterium johnsoniae; Fibrobacter succinogenes; Clostridium hungatei; Clostridium phytofermentans; Clostridium cellulolyticum; Clostridium aldrichii; Clostridium termitididis; Acetivibrio cellulolyticus; Acetivibrio ethanolgignens; Acetivibrio multivorans; Bacteroides cellulosolvens; and Alkalibacter saccharofomentans, variants thereof and progeny thereof.

Organism development via the native cellulolytic strategy

[0248] One approach to organism development for CBP begins with organisms that naturally utilize cellulose, hemicellulose and/or other biomass components, which are then genetically engineered to enhance product yield and tolerance. For example, Clostridium thermocellum is a thermophilic bacterium that has among the highest rates of cellulose utilization reported. Other organisms of interest are xylose-utilizing thermophiles such as Thermoanaerobacterium saccharolyticum and Thermoanaerobacterium thermosaccharolyticum. Organic acid production may be responsible for the low concentrations of produced ethanol generally associated with these organisms. Thus, one objective is to eliminate production of acetic and lactic acid in these organisms via metabolic engineering. Substantial efforts have been devoted to developing gene transfer systems for the above-described target organisms and multiple C. thermocellum isolates from nature have been characterized. See McLaughlin et al. (2002) Environ. Sci. Technol. 36:2122. Metabolic engineering of thermophilic, saccharolytic bacteria is an active area of interest, and knockout of lactate dehydrogenase in T. saccharolyticum has recently been reported. See Desai et al. (2004) Appl. Microbiol. Biotechnol. 65:600. Knockout of acetate kinase and phosphotransacetylase in this organism is also possible.

Organism development via the recombinant cellulolytic strategy

[0249] An alternative approach to organism development for CBP involves conferring the ability to grow on lignocellulosic materials to microorganisms that naturally have high product yield and tolerance via expression of a heterologous cellulasic system and perhaps other features. For example, Saccharomyces cerevisiae has been engineered to express over two dozen different saccharolytic enzymes. See Lynd et al. (2002) Microbiol. Mol. Biol. Rev. 66:506.

[0250] Whereas cellulosic hydrolysis has been approached in the literature primarily in the context of an enzymatically-oriented intellectual paradigm, the CBP processing strategy requires that cellulosic hydrolysis be viewed in terms of a microbial paradigm. This microbial paradigm naturally leads to an emphasis on different fundamental issues, organisms, cellulasic systems, and applied milestones compared to those of the enzymatic paradigm. In this context, C. thermocellum has been a model organism because of its high growth rate on cellulose together with its potential utility for CBP.

[0251] In certain embodiments, organisms useful in the present invention may be applicable to the process known as simultaneous saccharification and fermentation (SSF), which is intended to include the use of said microorganisms and/or one or more recombinant hosts (or extracts thereof, including purified or unpurified extracts) for the contemporaneous degradation or depolymerization of a complex sugar (i.e., cellulosic biomass) and bioconversion of that sugar residue into ethanol by fermentation.

Ethanol Production

[0252] According to the present invention, a recombinant microorganism can be used to produce ethanol from biomass, which is referred to herein as lignocellulosic material, lignocellulosic substrate, or cellulosic biomass. Methods of producing ethanol can be accomplished, for example, by contacting the biomass with a recombinant microorganism as described herein, and as described in commonly owned U.S. Patent Application Publication No. 2011/0189744 Al, U.S. Patent Application Publication No. 2011/0312054 Al, U.S. Patent Application Publication No. 2012/0003701, International Publication No. WO 2010/060056, International Publication No. WO 2010/075529, International Publication No. WO 2010/056805, International Publication No. WO 2009/138877, and International Publication No. WO 2010/060056, the contents of each are incorporated by reference herein in their entireties.

[0253] Numerous cellulosic substrates can be used in accordance with the present invention. Substrates for cellulose activity assays can be divided into two categories, soluble and insoluble, based on their solubility in water. Soluble substrates include cellodextrins or derivatives, carboxymethyl cellulose (CMC), or hydroxyethyl cellulose (HEC). Insoluble substrates include crystalline cellulose, microcrystalline cellulose (Avicel), amorphous cellulose, such as phosphoric acid swollen cellulose (PASC), dyed or fluorescent cellulose, and pretreated lignocellulosic biomass. These substrates are generally highly ordered cellulosic material and thus only sparingly soluble.

[0254] It will be appreciated that suitable lignocellulosic material may be any feedstock that contains soluble and/or insoluble cellulose, where the insoluble cellulose may be in a crystalline or non-crystalline form. In various embodiments, the lignocellulosic biomass comprises, for example, wood, corn, corn stover, sawdust, bark, leaves, agricultural and forestry residues, grasses such as switchgrass, ruminant digestion products, municipal wastes, paper mill effluent, newspaper, cardboard or combinations thereof.

[0255] In some embodiments, the invention is directed to a method for hydrolyzing a cellulosic substrate, for example a cellulosic substrate as described above, by contacting the cellulosic substrate with a recombinant microorganism of the invention. In some embodiments, the invention is directed to a method for hydrolyzing a cellulosic substrate, for example a cellulosic substrate as described above, by contacting the cellulosic substrate with a co-culture comprising yeast cells expressing heterologous cellulases.

[0256] In some embodiments, the invention is directed to a method for fermenting cellulose. Such methods can be accomplished, for example, by culturing a host cell or co- culture in a medium that contains insoluble cellulose to allow saccharification and fermentation of the cellulose.

[0257] The production of ethanol can, according to the present invention, be performed at temperatures of at least about 30° C, about 31° C, about 32° C, about 33° C, about 34° C, about 35° C, about 36° C, about 37° C, about 38° C, about 39° C, about 40° C, about 41° C, about 42° C, about 43 °C, about 44 °C, about 45 °C, about 46 °C, about 47 °C, about 48 °C, about 49 °C, or about 50° C. In some embodiments of the present invention the thermotolerant host cell can produce ethanol from cellulose at temperatures above about 30° C, about 31° C, about 32° C, about 33° C, about 34° C, about 35° C, about 36° C, about 37° C, about 38° C, about 39° C, about 40° C, about 41° C, about 42° C, or about 43 °C, or about 44 °C, or about 45 °C, or about 50° C. In some embodiments of the present invention, the thermotolterant host cell can produce ethanol from cellulose at temperatures from about 30° C to 60° C, about 30° C to 55° C, about 30° C to 50° C, about 40° C to 60° C, about 40° C to 55° C or about 40° C to 50° C.

[0258] The production of ethanol (or other products and co-products) can, according to the present invention, further be performed according to the "Brazil process." Under the "Brazil process," non-sterilized cane juice and/or molasses is fermented at a high inoculum to achieve fast fermentations. During the fermentation process, the yeast is repeatedly recycled over the 200+ day crop season by centrifuging the cells and washing them in sulphuric acid to decrease contamination and break up flocculation of cells. Industrial strains isolated from cane ethanol fermentations in Brazil have been shown to have characteristics that allow them to survive the acid washing and fermentation conditions better than typical lab yeast or other industrial yeast isolates. One commonly used S. cerevisiae strain in Brazil, PE-2, is a wild isolate from cane ethanol fermentation. The PE-2 strain has been described by Argueso et ah, 2009, which is incorporated by reference herein in its entirety. Argueso et al., "Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production," Genome Res. 19(12) :225%-70 (2009); see also JAY291 genome, Saccharomyces Genome Database (SGD), yeastgenome.org/. In the Brazil cane ethanol fermentations, PE-2 and other industrial strains produce an average of 4.5g/L glycerol. In some embodiments, the PE-2 strain, or a modified version thereof, is used as the host organism. In certain embodiments, ethanol is produced through the fermentation of a host cell according to the Brazil process. In some embodiments, the recombinant microorganism is used to ferment a carbohydrate source wherein the microorganisms are reused after one or more fermentations, and wherein the microorganisms are washed with an acid following each fermentation. In some embodiments, the acid has a pH of between 2.0 and 2.2. In certain embodiments, the acid is sulphuric acid.

[0259] In some embodiments, methods of producing ethanol can comprise contacting a cellulosic substrate with a recombinant microorganism or co-culture of the invention and additionally contacting the cellulosic substrate with externally produced cellulase enzymes. Exemplary externally produced cellulase enzymes are commercially available and are known to those of skill in the art.

[0260] In some embodiments, the methods comprise producing ethanol at a particular rate. For example, in some embodiments, ethanol is produced at a rate of at least about 0.1 mg per hour per liter, at least about 0.25 mg per hour per liter, at least about 0.5 mg per hour per liter, at least about 0.75 mg per hour per liter, at least about 1.0 mg per hour per liter, at least about 2.0 mg per hour per liter, at least about 5.0 mg per hour per liter, at least about 10 mg per hour per liter, at least about 15 mg per hour per liter, at least about 20.0 mg per hour per liter, at least about 25 mg per hour per liter, at least about 30 mg per hour per liter, at least about 50 mg per hour per liter, at least about 100 mg per hour per liter, at least about 200 mg per hour per liter, at least about 300 mg per hour per liter, at least about 400 mg per hour per liter, at least about 500 mg per hour per liter, at least about 600 mg per hour per liter, at least about 700 mg per hour per liter, at least about 800 mg per hour per liter, at least about 900 mg per hour per liter, at least about 1 g per hour per liter, at least about 1.5 g per hour per liter, at least about 2 g per hour per liter, at least about 2.5 g per hour per liter, at least about 3 g per hour per liter, at least about 3.5 g per hour per liter, at least about 4 g per hour per liter, at least about 4.5 g per hour per liter, or at least about 5 g per hour per liter. [0261] In some embodiments, the host cells of the present invention can produce ethanol at a rate of at least about 0.1 mg per hour per liter, at least about 0.25 mg per hour per liter, at least about 0.5 mg per hour per liter, at least about 0.75 mg per hour per liter, at least about 1.0 mg per hour per liter, at least about 2.0 mg per hour per liter, at least about 5.0 mg per hour per liter, at least about 10 mg per hour per liter, at least about 15 mg per hour per liter, at least about 20.0 mg per hour per liter, at least about 25 mg per hour per liter, at least about 30 mg per hour per liter, at least about 50 mg per hour per liter, at least about 100 mg per hour per liter, at least about 200 mg per hour per liter, at least about 300 mg per hour per liter, at least about 400 mg per hour per liter, at least about 500 mg per hour per liter, at least about 600 mg per hour per liter, at least about 700 mg per hour per liter, at least about 800 mg per hour per liter, at least about 900 mg per hour per liter, at least about 1 g per hour per liter, at least about 1.5 g per hour per liter, at least about 2 g per hour per liter, at least about 2.5 g per hour per liter, at least about 3 g per hour per liter, at least about 3.5 g per hour per liter, at least about 4 g per hour per liter, at least about 4.5 g per hour per liter, or at least about 5 g per hour per liter more than a control strain (e.g., a wild-type strain) and grown under the same conditions. In some embodiments, the ethanol can be produced in the absence of any externally added cellulases.

[0262] Ethanol production can be measured using any method known in the art. For example, the quantity of ethanol in fermentation samples can be assessed using HPLC analysis. Many ethanol assay kits are commercially available that use, for example, alcohol oxidase enzyme based assays. Methods of determining ethanol production are within the scope of those skilled in the art from the teachings herein. The U.S. Department of Energy (DOE) provides a method for calculating theoretical ethanol yield. Accordingly, if the weight percentages are known of C6 sugars (i.e., glucan, galactan, mannan), the theoretical yield of ethanol in gallons per dry ton of total C6 polymers can be determined by applying a conversion factor as follows:

(1.11 pounds of C6 sugar/pound of polymeric sugar) x (0.51 pounds of ethanol/pound of sugar) x (2000 pounds of ethanol/ton of C6 polymeric sugar) x (1 gallon of ethanol/6.55 pounds of ethanol) x (1/100%), wherein the factor (1 gallon of ethanol/6.55 pounds of ethanol) is taken as the specific gravity of ethanol at 20°C.

[0263] And if the weight percentages are known of C5 sugars (i.e., xylan, arabinan), the theoretical yield of ethanol in gallons per dry ton of total C5 polymers can be determined by applying a conversion factor as follows: (1.136 pounds of C5 sugar/pound of C5 polymeric sugar) x (0.51 pounds of ethanol/pound of sugar) x (2000 pounds of ethanol/ton of C5 polymeric sugar) x (1 gallon of ethanol/6.55 pounds of ethanol) x (1/100%), wherein the factor (1 gallon of ethanol/6.55 pounds of ethanol) is taken as the specific gravity of ethanol at 20°C.

[0264] It follows that by adding the theoretical yield of ethanol in gallons per dry ton of the total C6 polymers to the theoretical yield of ethanol in gallons per dry ton of the total C5 polymers gives the total theoretical yield of ethanol in gallons per dry ton of feedstock.

[0265] Applying this analysis, the DOE provides the following examples of theoretical yield of ethanol in gallons per dry ton of feedstock: corn grain, 124.4; corn stover, 113.0; rice straw, 109.9; cotton gin trash, 56.8; forest thinnings, 81.5; hardwood sawdust, 100.8; bagasse, 111.5; and mixed paper, 116.2. It is important to note that these are theoretical yields. The DOE warns that depending on the nature of the feedstock and the process employed, actual yield could be anywhere from 60% to 90% of theoretical, and further states that "achieving high yield may be costly, however, so lower yield processes may often be more cost effective."

EXEMPLIFICATION

[0266] The invention now being generally described, it will be more readily understood by reference to the following examples, which are included merely for purposes of illustration of certain aspects and embodiments of the present invention, and are not intended to limit the invention.

EXAMPLE 1

STL1 Overexpression in Wild Type Strain

[0267] An STL1 expression cassette comprising S. cerevisiae STL1 (Figure 9 and SEQ

ID NOs: 139 and 140) was genetically engineered into M2390 (Ethanol Red (new) from LaSaffre (pahc.com/Phibro/Performance-Products/Catalog/23/Ethanol-Red .html)) using the primers listed in Table 6 below. The transformed strain was compared to the non- transformed host strain M2390 during fermentation of laboratory medium YMD-280 (280 g/L maltodextrin, 20 g/L yeast extract,2 g/L urea, 1 g/L citrate, +/1 5 g/L glycerol ) with or without externally supplied glycerol (5 g/L glycerol). YMD-280 medium with or without glycerol was inoculated with M2390 and M2390 + STLl to starting concentration of 0.1 g/L dry cell weight (DCW) and allowed to ferment for 72 hrs. Samples were withdrawn and metabolite concentrations where determined by HPLC. Ethanol concentrations were higher in the strains overexpressing the STLl gene (Figure 2 A) when compared to the control strain. The increase in ethanol titer was independent of externally supplied glycerol (Figure 2A). In addition, total glycerol was reduced by approximately 2 g/L in the STLl expressing strain compared to the control strain, regardless of whether external glycerol was supplied (Figure 2B).

TABLE 6: Primers to create assembly MA0415.6 (STLl cassette integrated into the FCY1 locus)

MA0415.6

Expected

Fragment Primers Template Size

M2390

FCY 5 ^* Flank X21754/X24389 gDNA 2018bp

TEF2 pro-STL 1-ADH3

ter X24388/X19513 pMU3636 2709bp

ADH1 pro-STL 1-PDCl

ter X19514/X18955 pMU3635 2950bp

M2390

FCY 3 ^* Flank X19950/X18869 gDNA 2159bp

EXAMPLE 2

STLl Overexpression in Wild Type Strain An additional fermentation was performed to determine the effect of STLl expression in the wild type M2390 background using YMD-2300 medium (300 g/L maltodextrin, 20 g/L yeast extract, 2 g/L urea, 1 g/L citrate, 5 g/L glycerol). M2390 and M5975 (M2390 + STLl) were inoculated into 50 mL of YMD-300 to a starting concentration of 0.1 g/L DCW and allowed to ferment for 48 hrs, at which point samples were withdrawn and metabolite concentrations where determined by HPLC. M5975 consumed significantly more sugar and reached a significantly higher titer of ethanol than the M2390 control strain (Figures 3 A and 3B). Relative to M2390, expression of STLl in M5975 resulted in extracellular glycerol concentrations that were reduced by 3.3 g/L (Figure 3C).

EXAMPLE 3

Overexpression of STLl in Wild Type Yeast Results in Higher Intracellular

Glycerol Concentrations

[0269] An intracellular assay was used to determine whether expression of STLl resulted in higher intracellular glycerol concentrations. Strain M5975 overexpresses STLl due to engineering of STLl into the FCY1 site on the S. cerevisiae chromosome (the same cassette as described above in Example 1). Both M2390 and M5975 were grown overnight in YPD medium (20 g/L peptone, 10 g/L yeast extract, 20 g/g dextrose), after which cells were harvested and quenched. See Gonzalez, et al., "A Rapid and Reliable Method for Metabolite Extraction in Yeast using Boiling Buffered Ethanol," Yeast 75: 1347-56 (1997). Briefly, cells were grown overnight in YPD and the culture was diluted to an OD ₆ 6o of 1.9. Ten milliliters of ice cold methanol were added to 10 mL of the OD ₆ 6o 1.9 culture. The suspension was centrifuged at 5,000 RPMs for 5 min, after which the supernatant was discarded. To each pellet, 5 mL of boiling 75% ethanol/250mM HEPES pH 7.5 was added and allowed to cool on ice for ten minutes. These samples were dehydrated in a speed vac overnight and reconstituted in 500 of DI H ₂ 0. This suspension was centrifuged and the supernatant was used to assay for glycerol concentration using the Free Glycerol Reagent (Sigma catalog # F6428).

[0270] The data of Figure 4 demonstrates that M5975 has increased intracellular glycerol concentration compared to the parental control, M2390.

EXAMPLE 4

STLl Overexpression in Wild Type Strain Reaches a Higher Titer on Corn Mash

[0271] Several strains were constructed that contained modifications of STLl overexpression levels in M2390 and fermentation performance was evaluated on 33% solids corn mash. Strains M2390 and M5975 are described above. Strain M6173 was created using the primers listed in Table 47 below and contains the same promoters and terminators used in MA0415.6 Example 1 above; however, the assembly was integrated in the STL1 locus. See Figure 10.

[0272] Both strains containing upregulation of STL1 (M5975 and M6173) made ~2.5 g/L more ethanol than the parental control (M2390) with a concomitant reduction in glycerol production (Figures 5A and 5B). These results indicate that glycerol uptake through STL1 overexpression can reduce overall glycerol production without sacrificing performance in industrially relevant conditions, e.g., fermentation on corn mash.

TABLE 7: Primers to create assembly MA0998 (STL1 cassette integrated into the STL1 locus)

STLl ::4copies STL1

Expected

Fragment Primers Template Size

5 ^* Flank X24000/X24109 M2390 gDNA ~2kb

tef2pro X24108 X19513 pMU3636 2709bp

adhlpro X19514/X24111 pMU3635 2950bp

3 ^* Flank X24110/X24003 M2390 gDNA ~2kb

EXAMPLE 5

STL1 Overexpression in S. cerevisiae Strains Engineered to Secrete a

Glucoamylase

[0273] An S. fibuligera glucoamylase expression cassette was engineered into S. cerevisiae strain M2390 (described in U.S. Patent Appl. No. 13/696,207 and U.S. Patent Appl. No. 13/701,652, both of which are incorporated by reference herein in their entireties) to create strain M4080. The S. fibuligera glucoamylase nucleotide and amino acid sequences correspond to SEQ ID NO:131 and SEQ ID NO:132, respectively. M4080 was subsequently engineered with the STL1 expression cassette of Example 1 above to create strain M6308. Strains M2390, M4080, and M6308 were each inoculated into 50 mL of 33% solids industrial corn mash and allowed to ferment for 68 hrs prior to sampling and HPLC-based determination of metabolite concentrations. Glucoamylase (Sprizyme ultra, Novozymes) was added to the control (strain M2390) at 0.6 AGU/gTS and at 0.3 AGU/gTS for both M4080 and M6308. The results shown in Figure 6A demonstrate that expression of STL1 in M6308 enabled the strain to reach a higher titer of ethanol than the wild type yeast (strain M2390) using 50%> less externally added glucoamylase. A 0.9 g/L reduction in glycerol was also observed in strain M6308 compared to the control strain (Figure 6B).

EXAMPLE 6

STLl Overexpression in S. cerevisiae Strains Engineered to Produce Formate as an

Alternate Electron Sink

[0274] Strain M3465 was previously engineered to produce formate as an alternative electron sink and the creation of strain M3465 is described in International Publication No. WO 2012/138942, which is incorporated by reference herein in its entirety. M3465 was subsequently engineered with the STLl expression cassette of Example 1 above to create strain M6211. Strains M2390 (control strain), M3465, and M6211 were each inoculated into 50 mL of 33% solids industrial corn mash and allowed to ferment for 72 hrs prior to sampling and HPLC-based determination of metabolite concentrations. The results shown in Figure 7A demonstrate that the expression of STLl in M6211 enabled the strain to reach a higher titer of ethanol production than the wild type yeast strain M2390 and strain M3465. A 2.3 g/L reduction in glycerol production was also observed when compared to the parent strain, M3465. (Figure 7B).

EXAMPLE 7

STLl Overexpression in S. cerevisiae Strains Engineered to Produce Formate as an

Alternate Electron Sink and Secrete a Heterologous Glucoamylase

[0275] Strain M3465 (described above) was further engineered with the glucoamylase expression cassette of Example 5 above to create strain M4361. Strain M4361 was subsequently engineered with the STLl expression cassette of Example 4 above to create strain M6307. Strains M2390, M4361, and M6307 were each inoculated into 50 mL of 33% solids industrial corn mash and allowed to ferment for 68 hrs prior to sampling and HPLC-based determination of metabolite concentrations. The results shown in Figure 8A demonstrate that the expression of STLl in M6307 enabled the strain to reach a higher titer of ethanol production than the wild type yeast (M2390) and strain M4361, which produces formate as an alternative electron sink and expresses an S. fibuligera glucoamylase. A 3.7 g/L reduction in glycerol production relative to M2390 was also observed for strain M6307 (Figure 8B).

EXAMPLE 8

Creation of S. cerevisiae PE-2 Strains that Overexpress STL1

[0276] As described above, industrial strains isolated from cane ethanol fermentations in

Brazil have been shown to have characteristics that allow them to survive acid washing and fermentation conditions better than typical lab yeast or other industrial yeast isolates. The most commonly used S. cerevisiae strain currently in Brazil, PE-2, is a wild isolate from cane ethanol fermentation. PE-2 and other industrial used strains, produce an average of 4.5g/L glycerol in the Brazil process. This glycerol passes through the system unused. The Brazil industrial isolate PE-2 was engineered to overexpress the glycerol transporter STL1. One of the isolated Brazilian fuel ethanol strains, BG-1, was found to have additional copies of the STL1 gene located on a translocated region from Saccharomyces paradoxus. See Della-Bianca, et al., "What do we know about the yeast strains from the Brazilian fuel ethanol industry?," Appl. Microbiol. Biotechnol. 97(3):9Ί9- 91 (2013), which is incorporated by reference herein in its entirety.

[0277] The genetic modification techniques utilized to develop STL1 overexpressing strains rely on direct integration of the STL1 cassette onto both chromosomes in the diploid yeast M7101 {see Figure 15), a colony isolate of PE-2. The directed integration approach creates transgenic strains with integration events that are stable and easy to characterize.

[0278] The modified S. cerevisiae strains described herein contain four additional copies of the native S. cerevisiae gene STL1 (M7772; ScSTLl), or heterologous STL1 genes from Saccharomyces paradoxus (M9725; SpSTLl) or Pichia sorbitophila (M9208; PsSTLl) engineered into the PE-2 strain background. See Table 8. Information regarding the genes, donors, and sources are summarized in Table 8. Detailed information regarding the genetic description such as gene copy number is provided in Table 9. The genetic constructs are described in Table 10, and Table 11 describes plasmids used as DNA templates and for transformation purposes. A strain tree depicting the final strains, M7772, M9208 and M9725, is provided in Figure 13. TABLE 8: STLl genes used in S. cerevisiae PE-2 STLl overexpression strains.

TABLE 9: STLl assemblies in S. cerevisiae PE-2 strain M7101.

The STLl genes of MA415.6, MA1356 and MAP33 (Table 9), were amplified from the templates in Table 10 and gel purified prior to transformation into M7101. The recombinant STLl gene copies in MA415.6, MA1356 and MAP33 are under the control of native S. cerevisiae promoters TEF2 and ADH1 , as shown in Table 10, which are oriented on opposing DNA strands of the chromosome to minimize the possibility of recombination between the recombinant STLl genes at a given locus. These PCR- amplified products were engineered with overlapping ends having homology to DNA flanking the 5 ' and 3 ' region of the FCY1 locus to promote homologous recombination in vivo at the FCY1 locus of S. cerevisiae. A 2-micron plasmid, pMU228, (Figure 14) with a hygromycin resistance marker (hph) was co-transformed with the PCR products to enable selection against untransformed cells. The pMU228 plasmid contains the hph gene which confers resistance to hygromycin. This vector can be used for co-transformation with PCR products during the construction of strains. This vector is capable of replicating in both yeast (2μιη ori) and E.coli (PMB1 ori). This vector also contains the bla gene for ampicillin resistance in E.coli and the S. cerevisiae URA3 gene for selection in ura auxotrophs. Without antibiotic selection in yeast, the plasmid is typically lost in two plate passages. Loss of this co-transformation plasmid is confirmed by screening for hygromycin sensitivity.

The transformed cells were first cultivated overnight in YPDS (20 g/L yeast extract, lOg g/L peptone, 20 g/L dextrose, and 90 g/L sorbitol) + hygromycin (300μg/ml) broth and then plated on a medium containing 5-FC to select against [functional?] FCYl and simultaneously assemble and integrate the STLl cassettes into the chromosome, knocking out the FCYl gene. Figure 15 demonstrates how the STLl expression cassettes were integrated into the FCYl loci of strain M7101. The 4 DNA fragments: (pi) FCYl 5' flank, (p2) the STLl cassette with the TEF2 promoter and ADH3 terminator, (p3) the STLl cassette with the ADH1 promoter and PDC1 terminator, and (p4) the FCYl 3' flank, were engineered with overlapping ends to promote homologous recombination in vivo. Counter-selection against FCYl using 5-fluorocytosine (5-FC) selects for integration of the STLl expression cassette. See Hartzog, P. E., et ah, "Cytosine deaminase MX cassettes as positive/negative selectable markers in S. cerevisiae," Yeast 22:789-798 (2005). Because removal of both copies of FCYl is necessary for resistance to 5-FC, the expression cassette was found to be integrated at both chromosomes.

TABLE 10: Gene cassettes for STLl overexpression at the FCYl locus.

MA415.6 (Afcyl::ScSTLl)

Fragment Primers Template Expected Size

FCY 5' Flank X21754/X19552 M2390 gDNA 2018 bp

TEF2 pro-STLl-ADH3 ter X19551/X19513 pMU3636 2709

PDC1 ter-STLl-ADHl pro X19514/X18955 pMU3635 2950

FCY 3' Flank X19950/X18869 M2390 gDNA 2159

MA1356 (Afcylr.PsSTLl)

Fragment Primers Template Expected size

FCYl 5' flank (JAY291) X26376/X26801 M7101 1558 bp

TEF2p-STLl

(P. sorbitophila)-AOH3t X26802/X26792 pMU3432 2812

PDClt-STLl

(P. sorbitophila)-AOHl ) X26793/X23413 YCL482-3 3036

FCYl 3' flank (JAY291) X26822/X26379 M7101 1268

MAP33(Afcyl::SpSTLl)

Fragment Primers Template Expected size FCY1 5' flank (JAY291) X26376/X26377 M7101 1517 bp

(building) Tef2p-STL1

(S. paradoxus)-AOH3t X26802/X26792 M9441 2788

(building) ADHlp-STLl

(S. p r doxus)-VOClt X26793/X23413 M9442 3030

FCY1 3' flank (JAY291) X26378/X26379 M7101 1226

TABLE 1 1 : Summary of plasmids used in the construction of strain M7772.

[0281] Genetic confirmation of the cassette integration was achieved through PCR genotyping of the FCY1 locus using chromosomal DNA isolated from individual transformants. To confirm that the MA451.6, MA1356, and MAP33 cassettes were inserted at the FCY1 site of strain M7101 , PCR products were amplified from genomic DNA that crossed all junctions of the inserted DNA pieces. These products were run on an agarose gel, which showed that the cassettes had integrated correctly and that the insertions removed the native FCY1 gene. The deletion of FCY1 allows for the easy and unique detection of the engineered strains in the lab or industrial environment due to the resistance of the AFCYl strains to 5-FC as well as their inability to grow on minimal media with cytosine as the sole nitrogen source. FCY1 functions in the pyrimidine salvage pathway for DNA synthesis and is required for utilization of cytosine as a nitrogen source. S. cerevisiae strains that have FCY1 knocked out (fcylA) therefore cannot grow on media where cytosine is the sole nitrogen source.

[0282] The strains with the correct genotype were passaged several times in the absence of antibiotic selection to ensure that plasmid pMU228 (Figure 14; Table 1 1) was cured from the strain. Loss of pMU228 was confirmed by lack of growth when cells were plated on agar plates containing 300μg/ml hygromycin. Strains M7772, M9208 and M9725 were confirmed to be hygromycin sensitive. EXAMPLE 9

Fermentation of S. cerevisiae PE-2 Strains Overexpressing STL1

Minimal media fermentations with PE-2 STL1 strains

[0283] STL1 overexpression strains were initially screened in anaerobic fermentations on minimal media. Strains were propagated aerobically on YPD20 broth (yeast extract 20 g/L, peptone 10 g/L, and 20g/L dextrose) at 35°C with shaking at 225 rpm. Cultures of 100 g/L glucose Verduyn media, as described in Verduyn, et αί, "Effect of benzoic acid on metabolic fluxes in yeasts: A continuous-culture study on the regulation of respiration and alcoholic fermentation," Yeast 8: 501-17 (1992), which is incorporated by reference herein in its entirety, at pH 4.8 were inoculated with 0.5 g/L cells and incubated with shaking at 225 rpm at 35°C for 48hrs, and the concentration of glycerol and ethanol were determined by HPLC. M7772, which comprises S. cerevisiae STL1 (ScSTLl), showed a 15% decrease in glycerol in the media as well as about a 2% increase in ethanol production compared to the wild-type parental strain, M7101 (Figure 16A). Fhe expression of the heterologous SFL1 genes from P. sorbitophila and S. paradoxus showed similar results to the S. cerevisiae SFL1 overexpression. Fhe P. sorbitophila SFL1 expressing strain, M9208, had a 23% reduction in glycerol and a 4% increase in ethanol titer compared to the wild-type PE-2 strain, M7101 (Figure 16A). Fhe S. paradoxus SFL1 expressing strain, M9725, had a 12% reduction in glycerol and a 4% increase in ethanol titer compared to the wild-type PE-2 strain, M7101 (Figure 16A).

Acid treatment-Brazilian cane ethanol fermentations

[0284] Fhe wild-type parental strain, M7101 (PE-2 isolate), and the S. cerevisiae SFL1 overexpression strain, M7772, were compared for their fermentation performance in a lab-scale batch must fermentation and acid wash test. Strains were propagated overnight aerobically in YPD50 medium (yeast extract 20 g/L, peptone 10 g/,L, and 50g/L dextrose) at 35°C with shaking at 225 rpm. Strains were then inoculated at 10% w/w into an initial fermentation on a must and incubated for 6 hours at 35°C. Must is a mixture of cane syrup and cane molasses at approximately 160 g/L total reducing sugars (FRS) (70:30 mixture based on FRS). Fhe cells were then isolated by centrifugation, stored overnight at 4°C and then washed with sulphuric acid at pH2.0-2.2 for 30 minutes at room temperature. A second fermentation on must was carried out on the acid washed cells at 35°C. Fermentations were sampled at 6 hours and ethanol and glycerol levels were determined using HPLC as described above. The engineered yeast overexpressing S. cerevisiae STL1, strain M7772, showed a 4.7% increase in ethanol and a 20% reduction in glycerol compared to the parental strain M7101 (Figure 16B).

[0285] We then further tested the S. cerevisiae STL1 strain (M7772) in a scaled down version of the Brazil process that included feeding of the must and acid recycle to assess how glycerol uptake would affect the cells under more process relevant conditions. The wild-type parental strain, M7101 (PE-2 isolate), and the S. cerevisiae STL1 overexpression strain, M7772, were compared for their fermentation performance in a lab-scale fed-batch must fermentation. The strains were taken from glycerol stocks and plated to YPD30 (yeast extract 20 g/L, peptone 10 g/L, and 30g/L dextrose) plates for 24 hours at 30° C. The strains were then transferred to 40mL of liquid YPS40 (yeast extract 20 g/L, peptone 10 g/L, and 40 g/L sucrose) medium with an additional 75g/L molasses added. This step occurred at 30°C in a 250 mL shake flasks under 175 RPM of agitation. After 24 hours, an additional 40 mL of YPS40 media was added and the process was continued for an additional 12 hours. The cells were then pelleted in 50 mL conical tubes and stored overnight at 4°C. The cell pellets were then reduced to 5 g and 9 mL of water was then added. The pH was then reduced to between 2.0 and 2.2 using 72% sulfuric acid. The reactors were allowed to sit at room temperature for 40 minutes after which they were placed in an incubator at 32°C and shaken at 250 RPM. 28 g of must was then added to a final concentration of 160g/L total reducing sugars ("TRS") over 4.5 hours. The fermentation was allowed to continue incubating with shaking for an additional 3-4 hours for a total fermentation time of 7.5-8.5 hours. The reactors were then centrifuged, the supernatant was decanted off, and the supernatant and cell pellets were stored overnight at 4°C. A sample of supernatant was run on HPLC (H and N column) for compositional analysis. The process was then repeated the next day with the only difference being instead of adding 9 mL of water, 2 mL of the supernatant from the previous run was added as well as 7 mL of water. This process was repeated for a total of 14 fermentations and acid treatments.

[0286] Results for runs 4 through 14 (F4-F14) are shown in Figure 17. The S. cerevisiae

STL1 engineered strain, M7772, shows an average of a 1% increase in ethanol titer over the wild-type M7101 over these 10 fermentations and an average 14% decrease in glycerol from the fermentation media compared to M7101 (Figure 17A and 17B). In addition, the cell mass accumulation was measured in the fermentations as well as the viability of these cells after the acid washing. Cell mass accumulation from each run was measured as the difference between the started wet weight (5g) and the final wet pellet weight in each of the reactors. Viability of the cell population was measured post-acid treatment using a Cellometer that stains for live and dead cells. M7772 showed similar biomass accumulation as wild-type M7101 (Figure 17D) and similar viability (within 4%) after acid treatment as M7101 (Figure 17C). This data suggests that glycerol uptake by STL1 leads to an increase in ethanol yield in the Brazil cane ethanol fermentations, and these cells are able to withstand acid treatment and multiple rounds of cell recycle while maintaining this yield improvement.

Incorporation by Reference

[0287] All of the references cited herein are hereby incorporated by reference in their entirety.

Equivalents

[0288] Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.