Methods and compositions for improving the production of products in microorganisms

Abstract

Methods and compositions are provided for improving the production of products, such as fuel products like ethanol, in microorganisms. In particular, methods and compositions are described for improving ethanol production utilizing genes identified in Clostridium phytofermentans.

1 - 21 . (canceled) 
     
     
         22 . A method of producing one or more fermentation end products comprising:
 a. contacting a biomass with a recombinant microorganism wherein said recombinant microorganism comprises an isolated nucleic acid sequence encoding:
 i. at least one hydrolase from  C. phytofermentans , wherein said isolated nucleic acid is selected from Table 6; or 
 ii. at least one ABC-transporter from  C. phytofermentans , wherein said isolated nucleic acid is selected from ABC-transporter genes in Table 7, 
 wherein at least one of said isolated nucleic acid sequence encoding at least one hydrolase or at least one ABC-transporter from  C. phytofermentans  is heterologous to the microorganism or is an additional copy of an endogenous nucleic acid sequence; and, 
   b. fermenting said biomass with said recombinant microorganism to produce said one or more fermentation end products.   
     
     
         23 . The method of  claim 22 , wherein said recombinant microorganism further comprises an isolated nucleic acid sequence encoding at least one transcriptional regulator from  C. phytofermentans.    
     
     
         24 . The method of  claim 22 , wherein said at least one hydrolase is Cphy1163, Cphy2058, Cphy3202, Cphy3367, Cphy3368, Cphy0430, Cphy3854, Cphy0857, Cphy0694 or Cphy1929. 
     
     
         25 . The method of  claim 22 , wherein said at least one ABC-transporter is Cphy3854, Cphy3855, Cphy3857, Cphy3858, Cphy3859, Cphy3860, Cphy3861 or Cphy3862. 
     
     
         26 . The method of  claim 22 , wherein said recombinant microorganism is  Clostridium cellulovorans, Clostridium cellulolyticum, Clostridium thermocellum, Clostridium josui, Clostridium papyrosolvens, Clostridium cellobioparum, Clostridium hungatei, Clostridium cellulosi, Clostridium stercorarium, Clostridium termitidis, Clostridium thermocopriae, Clostridium celerecrescens, Clostridium polysaccharolyticum, Clostridium populeti, Clostridium lentocellum, Clostridium chartatabidum, Clostridium aldrichii, Clostridium herbivorans, Acetivibrio cellulolyticus, Bacteroides celluosolvens, Caldicellulosiruptor saccharolyticum, Ruminococcus albus, Ruminococcus flavefaciens, Fibrobacter succinogenes, Eubacterium cellulosolvens, Butyrivibrio fibrisolvens, Anaerocellum thermophilum, Halocella celluloytica, Thermoanaerobacterium thermosaccharolyticum  or  Thermoanaerobacterium saccharolyticum.    
     
     
         27 . The method of  claim 22 , wherein said biomass comprises cellulosic, hemicellulosic or lignocellulosic material. 
     
     
         28 . The method of  claim 22 , wherein said biomass comprises saw dust, wood flour, wood pulp, paper pulp, paper pulp waste streams, grasses, switchgrass, plants, crops, crambe, algae, hulls, bagasse, jute, leaves, grass clippings, corn stover, corn cobs, corn grain, corn grind, distillers grains, pectin or mixtures thereof. 
     
     
         29 . The method of  claim 22 , wherein said fermentation end product comprises one or more of butanol, propanol, methanol, hydrogen, lactic acid, acetic acid, formic acid, acetone, formaldehyde, 1,2-propanediol, 1,3-propanediol, acetic acid, succinic acid or pyruvic acid. 
     
     
         30 . The method of  claim 22 , wherein said fermentation end product comprises ethanol. 
     
     
         31 . The method of  claim 22 , wherein said recombinant microorganism is capable of hydrolyzing and fermenting hemicellulose or lignocellulose. 
     
     
         32 . A system for the production of one or more fermentation end products comprising a
 a. fermentor;   b. a biomass; and,   c. a recombinant microorganism, said recombinant microorganism comprising an isolated nucleic acid sequence encoding:
 i. at least one hydrolase from  C. phytofermentans , wherein said isolated nucleic acid is selected from Table 6; or 
 ii. at least one ABC-transporter from  C. phytofermentans , wherein said isolated nucleic acid is selected from ABC-transporter genes in Table 7, 
 wherein at least one of said isolated nucleic acid sequence encoding at least one hydrolase or at least one ABC-transporter from  C. phytofermentans  is heterologous to the microorganism or is an additional copy of an endogenous nucleic acid sequence, 
   wherein said fermentor maintains conditions conducive for said recombinant microorganism to ferment said biomass.   
     
     
         33 . The system of  claim 32 , wherein said recombinant microorganism further comprises an isolated nucleic acid sequence encoding at least one transcriptional regulator from  C. phytofermentans.    
     
     
         34 . The system of  claim 32 , wherein said at least one hydrolase is Cphy1163, Cphy2058, Cphy3202, Cphy3367, Cphy3368, Cphy0430, Cphy3854, Cphy0857, Cphy0694 or Cphy1929. 
     
     
         35 . The system of  claim 32 , wherein said at least one ABC-transporter is Cphy3854, Cphy3855, Cphy3857, Cphy3858, Cphy3859, Cphy3860, Cphy3861 or Cphy3862. 
     
     
         36 . The system of  claim 32 , wherein said recombinant microorganism is  Clostridium cellulovorans, Clostridium cellulolyticum, Clostridium thermocellum, Clostridium josui, Clostridium papyrosolvens, Clostridium cellobioparum, Clostridium hungatei, i cellulosi, Clostridium stercorarium, Clostridium termitidis, Clostridium thermocopriae, Clostridium celerecrescens, Clostridium polysaccharolyticum, Clostridium populeti, Clostridium lentocellum, Clostridium chartatabidum, Clostridium aldrichii, Clostridium herbivorans, Acetivibrio cellulolyticus, Bacteroides cellulosolvens, Caldicellulosiruptor saccharolyticum, Ruminococcus albus, Ruminococcus flavefaciens, Fibrobacter succinogenes, Eubacterium cellulosolvens, Butyrivibrio fibrisolvens, Anaerocellum thermophilum, Halocella Thermoanaerobacterium thermosaccharolyticum or Thermoanaerobacterium saccharolyicum.    
     
     
         37 . The system of  claim 32 , wherein said biomass comprises cellulosic, hemicellulosic or lignocellulosic material. 
     
     
         38 . The system of  claim 32 , wherein said biomass comprises saw dust, wood flour, wood pulp, paper pulp, paper pulp waste streams, grasses, switchgrass, plants, crops, crambe, algae, hulls, bagasse, jute, leaves, grass clippings, corn stover, corn cobs, corn grain, corn grind, distillers grains, pectin or mixtures thereof. 
     
     
         39 . The system of  claim 32 , wherein said fermentation end product comprises one or more of ethanol, butanol, propanol, methanol, hydrogen, lactic acid, acetic acid, formic acid, acetone, formaldehyde, 1,2-propanediol, 1,3-propanediol, acetic acid, succinic acid or pyruvic acid. 
     
     
         40 . The system of  claim 32 , wherein said fermentation end product comprises ethanol. 
     
     
         41 . The system of  claim 32 , wherein said recombinant microorganism is capable of hydrolyzing and fermenting hemicellulose or lignocellulose.