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Title: Directed evolution reveals unexpected epistatic interactions that alter metabolic regulation and enable anaerobic xylose use by Saccharomyces cerevisiae

The inability of native Saccharomyces cerevisiae to convert xylose from plant biomass into biofuels remains a major challenge for the production of renewable bioenergy. Despite extensive knowledge of the regulatory networks controlling carbon metabolism in yeast, little is known about how to reprogram S. cerevisiae to ferment xylose at rates comparable to glucose. Here we combined genome sequencing, proteomic profiling, and metabolomic analyses to identify and characterize the responsible mutations in a series of evolved strains capable of metabolizing xylose aerobically or anaerobically. We report that rapid xylose conversion by engineered and evolved S. cerevisiae strains depends upon epistatic interactions among genes encoding a xylose reductase ( GRE3), a component of MAP Kinase (MAPK) signaling ( HOG1), a regulator of Protein Kinase A (PKA) signaling ( IRA2), and a scaffolding protein for mitochondrial iron-sulfur (Fe-S) cluster biogenesis ( ISU1). Interestingly, the mutation in IRA2 only impacted anaerobic xylose consumption and required the loss of ISU1 function, indicating a previously unknown connection between PKA signaling, Fe-S cluster biogenesis, and anaerobiosis. Proteomic and metabolomic comparisons revealed that the xylose-metabolizing mutant strains exhibit altered metabolic pathways relative to the parental strain when grown in xylose. Further analyses revealed that interacting mutations in HOG1more » and ISU1 unexpectedly elevated mitochondrial respiratory proteins and enabled rapid aerobic respiration of xylose and other non-fermentable carbon substrates. Lastly, our findings suggest a surprising connection between Fe-S cluster biogenesis and signaling that facilitates aerobic respiration and anaerobic fermentation of xylose, underscoring how much remains unknown about the eukaryotic signaling systems that regulate carbon metabolism.« less
Authors:
ORCiD logo [1] ;  [1] ; ORCiD logo [1] ;  [2] ;  [3] ; ORCiD logo [4] ;  [5] ; ORCiD logo [1] ; ORCiD logo [1] ; ORCiD logo [1] ; ORCiD logo [1] ; ORCiD logo [1] ;  [1] ; ORCiD logo [1] ; ORCiD logo [1] ; ORCiD logo [6] ;  [6] ;  [1] ;  [7] ;  [8] more »;  [5] ;  [9] ;  [10] « less
  1. Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center
  2. Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center and Genome Center of Wisconsin
  3. Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center, Genome Center of Wisconsin and Lab. of Genetics
  4. Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center, Genome Center of Wisconsin and Dept. of Chemistry
  5. Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center, Genome Center of Wisconsin, Lab. of Genetics and Microbiology Doctoral Training Program
  6. Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center and Dept. of Chemical and Biological Engineering
  7. Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center, Genome Center of Wisconsin, Dept. of Chemistry and Dept. of Biomolecular Chemistry
  8. Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center, Genome Center of Wisconsin, Lab. of Genetics, Microbiology Doctoral Training Program and Wisconsin Energy Institute
  9. Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center, Microbiology Doctoral Training Program and Dept. of Biochemistry
  10. Univ. of Toronto, Toronto, ON (Canada)
Publication Date:
Grant/Contract Number:
FC02-07ER64494
Type:
Published Article
Journal Name:
PLoS Genetics
Additional Journal Information:
Journal Volume: 12; Journal Issue: 10; Journal ID: ISSN 1553-7404
Publisher:
Public Library of Science
Research Org:
Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1338424
Alternate Identifier(s):
OSTI ID: 1363955

Sato, Trey K., Tremaine, Mary, Parreiras, Lucas S., Hebert, Alexander S., Myers, Kevin S., Higbee, Alan J., Sardi, Maria, McIlwain, Sean J., Ong, Irene M., Breuer, Rebecca J., Narasimhan, Ragothaman Avanasi, McGee, Mick A., Dickinson, Quinn, La Reau, Alex, Xie, Dan, Tian, Mingyuan, Reed, Jennifer L., Zhang, Yaoping, Coon, Joshua J., Hittinger, Chris Todd, Gasch, Audrey P., Landick, Robert, and Caudy, Amy. Directed evolution reveals unexpected epistatic interactions that alter metabolic regulation and enable anaerobic xylose use by Saccharomyces cerevisiae. United States: N. p., Web. doi:10.1371/journal.pgen.1006372.
Sato, Trey K., Tremaine, Mary, Parreiras, Lucas S., Hebert, Alexander S., Myers, Kevin S., Higbee, Alan J., Sardi, Maria, McIlwain, Sean J., Ong, Irene M., Breuer, Rebecca J., Narasimhan, Ragothaman Avanasi, McGee, Mick A., Dickinson, Quinn, La Reau, Alex, Xie, Dan, Tian, Mingyuan, Reed, Jennifer L., Zhang, Yaoping, Coon, Joshua J., Hittinger, Chris Todd, Gasch, Audrey P., Landick, Robert, & Caudy, Amy. Directed evolution reveals unexpected epistatic interactions that alter metabolic regulation and enable anaerobic xylose use by Saccharomyces cerevisiae. United States. doi:10.1371/journal.pgen.1006372.
Sato, Trey K., Tremaine, Mary, Parreiras, Lucas S., Hebert, Alexander S., Myers, Kevin S., Higbee, Alan J., Sardi, Maria, McIlwain, Sean J., Ong, Irene M., Breuer, Rebecca J., Narasimhan, Ragothaman Avanasi, McGee, Mick A., Dickinson, Quinn, La Reau, Alex, Xie, Dan, Tian, Mingyuan, Reed, Jennifer L., Zhang, Yaoping, Coon, Joshua J., Hittinger, Chris Todd, Gasch, Audrey P., Landick, Robert, and Caudy, Amy. 2016. "Directed evolution reveals unexpected epistatic interactions that alter metabolic regulation and enable anaerobic xylose use by Saccharomyces cerevisiae". United States. doi:10.1371/journal.pgen.1006372.
@article{osti_1338424,
title = {Directed evolution reveals unexpected epistatic interactions that alter metabolic regulation and enable anaerobic xylose use by Saccharomyces cerevisiae},
author = {Sato, Trey K. and Tremaine, Mary and Parreiras, Lucas S. and Hebert, Alexander S. and Myers, Kevin S. and Higbee, Alan J. and Sardi, Maria and McIlwain, Sean J. and Ong, Irene M. and Breuer, Rebecca J. and Narasimhan, Ragothaman Avanasi and McGee, Mick A. and Dickinson, Quinn and La Reau, Alex and Xie, Dan and Tian, Mingyuan and Reed, Jennifer L. and Zhang, Yaoping and Coon, Joshua J. and Hittinger, Chris Todd and Gasch, Audrey P. and Landick, Robert and Caudy, Amy},
abstractNote = {The inability of native Saccharomyces cerevisiae to convert xylose from plant biomass into biofuels remains a major challenge for the production of renewable bioenergy. Despite extensive knowledge of the regulatory networks controlling carbon metabolism in yeast, little is known about how to reprogram S. cerevisiae to ferment xylose at rates comparable to glucose. Here we combined genome sequencing, proteomic profiling, and metabolomic analyses to identify and characterize the responsible mutations in a series of evolved strains capable of metabolizing xylose aerobically or anaerobically. We report that rapid xylose conversion by engineered and evolved S. cerevisiae strains depends upon epistatic interactions among genes encoding a xylose reductase (GRE3), a component of MAP Kinase (MAPK) signaling (HOG1), a regulator of Protein Kinase A (PKA) signaling (IRA2), and a scaffolding protein for mitochondrial iron-sulfur (Fe-S) cluster biogenesis (ISU1). Interestingly, the mutation in IRA2 only impacted anaerobic xylose consumption and required the loss of ISU1 function, indicating a previously unknown connection between PKA signaling, Fe-S cluster biogenesis, and anaerobiosis. Proteomic and metabolomic comparisons revealed that the xylose-metabolizing mutant strains exhibit altered metabolic pathways relative to the parental strain when grown in xylose. Further analyses revealed that interacting mutations in HOG1 and ISU1 unexpectedly elevated mitochondrial respiratory proteins and enabled rapid aerobic respiration of xylose and other non-fermentable carbon substrates. Lastly, our findings suggest a surprising connection between Fe-S cluster biogenesis and signaling that facilitates aerobic respiration and anaerobic fermentation of xylose, underscoring how much remains unknown about the eukaryotic signaling systems that regulate carbon metabolism.},
doi = {10.1371/journal.pgen.1006372},
journal = {PLoS Genetics},
number = 10,
volume = 12,
place = {United States},
year = {2016},
month = {10}
}