Engineered microorganisms with enhanced fermentation activity

Abstract

Provided herein are genetically modified microorganisms that have enhanced fermentation activity, and methods for making and using such microorganisms.

1 - 52 . (canceled) 
     
     
         53 . A eukaryotic cell comprising a polypeptide having xylose isomerase activity, which polypeptide comprises an amino acid sequence greater than that 65.8% identical to SEQ ID NO: 31. 
     
     
         54 . The eukaryotic cell of  claim 53 , wherein the polypeptide comprises an amino acid sequence that is 75% or more identical to SEQ ID NO: 31. 
     
     
         55 . The eukaryotic cell of  claim 54 , wherein the polypeptide comprises an amino acid sequence that is 80% or more identical to SEQ ID NO: 31. 
     
     
         56 . The eukaryotic cell of  claim 55 , wherein the polypeptide comprises an amino acid sequence that is 85% or more identical to SEQ ID NO: 31. 
     
     
         57 . The eukaryotic cell of  claim 56 , wherein the polypeptide comprises an amino acid sequence that is 90% or more identical to SEQ ID NO: 31. 
     
     
         58 . The eukaryotic cell of  claim 57 , wherein the polypeptide comprises an amino acid sequence that is 95% or more identical to SEQ ID NO: 31. 
     
     
         59 . The eukaryotic cell of  claim 58 , wherein the polypeptide comprises an amino acid sequence of SEQ ID NO: 31. 
     
     
         60 . The eukaryotic cell of  claim 59 , wherein the polypeptide consists of an amino acid sequence of SEQ ID NO: 31. 
     
     
         61 . The eukaryotic cell of  claim 53 , which is a yeast cell. 
     
     
         62 . The eukaryotic cell of  claim 61 , which is a  Saccharomyces  spp. cell. 
     
     
         63 . The eukaryotic cell of  claim 62 , which is a  Saccharomyces cerevisiae  cell. 
     
     
         64 . An engineered yeast comprising a chimeric enzyme having xylose isomerase activity, wherein:
 the C-terminal region of the chimeric enzyme comprises at least 5 contiguous amino acids from a bacterial xylose isomerase enzyme; and   the N-terminal region of the chimeric enzyme comprises at least 5 contiguous amino acids from a fungal xylose isomerase enzyme.   
     
     
         65 . The engineered yeast of  claim 64 , wherein the bacterial xylose isomerase enzyme is a  Ruminococcus  spp. xylose isomerase enzyme. 
     
     
         66 . The engineered yeast of  claim 65 , wherein the  Ruminococcus  spp. xylose isomerase enzyme is from a  Ruminococcus flavefaciens  strain. 
     
     
         67 . The engineered yeast of  claim 66 , wherein the  Ruminococcus flavefaciens  strain is selected from the group consisting of  Ruminococcus flavefaciens  strain 17 , Ruminococcus flavefaciens  strain Siijpesteijn 1948, and  Ruminococcus flavefaciens  strain FD1. 
     
     
         68 . The engineered yeast of  claim 66 , wherein the at least 5 contiguous amino acids from the bacterial xylose isomerase enzyme are from SEQ ID NO: 31. 
     
     
         69 . The engineered yeast of  claim 64 , wherein the fungal xylose isomerase enzyme is from a fungus selected from the group consisting of an  Aspergillus  spp. fungus,  Thraustochytrium  spp. fungus,  Schizochytrium  spp. fungus,  Rhizopus  spp. fungus,  Orpinomyces  spp. fungus and  Piromyces  spp. fungus. 
     
     
         70 . The engineered yeast of  claim 69 , wherein the fungal xylose isomerase enzyme is from a  Piromyces  spp. fungus. 
     
     
         71 . The engineered yeast of  claim 70 , wherein the  Piromyces  spp. fungus is a  Piromyces  strain E2 fungus. 
     
     
         72 . The engineered yeast of  claim 71 , wherein the at least 5 contiguous amino acids from the fungal xylose isomerase enzyme are from SEQ ID NO: 35. 
     
     
         73 . The engineered yeast of  claim 64 , which is an engineered  Saccharomyces  spp. yeast. 
     
     
         74 . The engineered yeast of  claim 73 , which is an engineered  Saccharomyces cerevisiae  yeast.