Methods and organism with increased xylose uptake

Abstract

Provided herein are novel xylose transporters and their variants, as well as nucleic acid encoding the novel xylose transporters and their variants. Provided herein are also non-naturally occurring microbial organisms having increased xylose uptake and increased production of bioderived compounds using xylose as a substrate, as well as methods to make and use these microbial organisms.

1 . A non-naturally occurring microbial organism comprising at least one exogenous nucleic acid encoding a xylose transporter, wherein said xylose transporter has an amino acid sequence that is at least 89% identical to a  Metschnikowia  xylose transporter. 
     
     
         2 . The non-naturally occurring microbial organism of  claim 1 , comprising exogenous nucleic acids encoding at least two, at least three, at least four, at least five, at least six, or at least seven xylose transporters. 
     
     
         3 . The non-naturally occurring microbial organism of  claim 1 , wherein said xylose transporter has an amino acid sequence that is at least 90%, at least 95%, at least 98%, or at least 99%, identical to said  Metschnikowia  xylose transporter. 
     
     
         4 . The non-naturally occurring microbial organism of  claim 1 , wherein said xylose transporter is a  Metschnikowia  xylose transporter. 
     
     
         5 . The non-naturally occurring microbial organism of  claim 1 , wherein said  Metschnikowia  xylose transporter is selected from the group consisting of Xyt1p, Gxf1p, ΔGxf1p, Gxf2p/Gal2p, Gxs1p/Hgt12p, ΔGxs1p/ΔHgt12p, Hxt5p, Hxt2.6p, Qup2p, and Aps1p/Hgt19p. 
     
     
         6 . The non-naturally occurring microbial organism of  claim 1 , wherein said  Metschnikowia  xylose transporter is from a H0  Metschnikowia  sp. 
     
     
         7 . The non-naturally occurring microbial organism of  claim 1 , wherein said  Metschnikowia  xylose transporter has an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-5 and 7-12. 
     
     
         8 . The non-naturally occurring microbial organism of  claim 1 , wherein said microbial organism comprising an exogenous nucleic acid is selected from the group consisting of SEQ ID NOs: 13-17 and 19-27. 
     
     
         9 . The non-naturally occurring microbial organism of  claim 7 , wherein said microbial organism has at least one exogenous nucleic acid encoding:
 (a) SEQ ID NO:1; or   (b) SEQ ID NO: 12.   
     
     
         10 . (canceled) 
     
     
         11 . The non-naturally occurring microbial organism of  claim 1 , wherein said xylose transporter is ubiquitin-deficient. 
     
     
         12 - 13 . (canceled) 
     
     
         14 . The non-naturally occurring microbial organism of  claim 1 , wherein said exogenous nucleic acid is codon-optimized to produce said xylose transporter in said microbial organism. 
     
     
         15 . A non-naturally occurring microbial organism comprising at least one exogenous nucleic acid encoding a xylose transporter, wherein said xylose transporter has an amino acid sequence that is:
 (a) at least 74% identical to Xyt1p of a  Metschnikowia  species;   (b) at least 85% identical to Gxf1p of a  Metschnikowia  species;   (c) at least 89% identical to a ΔGxf1p of a  Metschnikowia  species;   (d) at least 71% identical to a Gxf2p/Gal2p of a  Metschnikowia  species;   (e) at least 71% identical to a Gxs1p/Hgt12p of a  Metschnikowia  species;   (f) at least 60% identical to a Hxt5p of a  Metschnikowia  species;   (g) at least 84% identical to a Hxt2.6p of a  Metschnikowia  species;   (h) at least 50% identical to a Qup2p of a  Metschnikowia  species; or   (i) at least 74% identical to a Aps1p/Hgt19p of a  Metschnikowia  species.   
     
     
         16 - 24 . (canceled) 
     
     
         25 . The non-naturally occurring microbial organism of  claim 1 , wherein said at least one exogenous nucleic acid is a heterologous nucleic acid. 
     
     
         26 . The non-naturally occurring microbial organism of  claim 1 , wherein said microbial organism is in an aerobic culture medium. 
     
     
         27 . The non-naturally occurring microbial organism of  claim 1 , wherein said microbial organism is in a substantially anaerobic culture medium. 
     
     
         28 . The non-naturally occurring microbial organism of  claim 1 , wherein the microbial organism is a species of bacteria or yeast. 
     
     
         29 - 30 . (canceled) 
     
     
         31 . The non-naturally occurring  Saccharomyces cerevisiae  of claim  30  having at least one exogenous nucleic acid encoding
 (a) SEQ ID NO:1; 
 (b) SEQ ID NO: 12; 
 (c) SEQ ID NO:21; or 
 (d) SEQ ID NO:27. 
 
     
     
         32 - 35 . (canceled) 
     
     
         36 . The non-naturally occurring microbial organism of  claim 1 , wherein said microbial organism further comprises a metabolic pathway capable of producing a bioderived compound from xylose, wherein said bioderived compound is selected from the group consisting of xylitol, ethanol, n-butanol, isobutanol, isopropanol, arabitol, ethyl acetate, phenyl-ethyl alcohol, 2-methyl-butanol, and 3-methyl-butanol. 
     
     
         37 . (canceled) 
     
     
         38 . A method of producing a bioderived compound comprising: culturing the non-naturally occurring microbial organism of  claim 36  under conditions and for a sufficient period of time to produce said bioderived compound, and wherein said microbial organism comprises a pathway capable of producing the bioderived compound from xylose. 
     
     
         39 . The method of  claim 38 , wherein the conditions comprise culturing the microbial organism in medium comprising xylose and a co-substrate selected from the group consisting of cellobiose, hemicellulose, glycerol, galactose, and glucose, or a combination thereof. 
     
     
         40 - 48 . (canceled)