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Title: Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production

Abstract

Lignocellulosic plant material is a viable source of biomass to produce alternative energy including ethanol and other biofuels. However, several factors—including toxic by products from biomass pretreatment and poor fermentation of xylose and other pentose sugars—currently limit the efficiency of microbial biofuel production. To begin to understand the genetic basis of desirable traits, we characterized three strains of Saccharomyces cerevisiae with robust growth in a pretreated lignocellulosic hydrolysate or tolerance to stress conditions relevant to industrial biofuel production, through genome and transcriptome sequencing analysis. All stress resistant strains were highly mosaic, suggesting that genetic admixture may contribute to novel allele combinations underlying these phenotypes. Strain-specific gene sets not found in the lab strain were functionally linked to the tolerances of particular strains. Furthermore, genes with signatures of evolutionary selection were enriched for functional categories important for stress resistance and included stress-responsive signaling factors. Comparison of the strains’ transcriptomic responses to heat and ethanol treatment—two stresses relevant to industrial bioethanol production—pointed to physiological processes that were related to particular stress resistance profiles. Many of the genotype-by-environment expression responses occurred at targets of transcription factors with signatures of positive selection, suggesting that these strains have undergone positive selection for stress tolerance. Ourmore » results generate new insights into potential mechanisms of tolerance to stresses relevant to biofuel production, including ethanol and heat, present a backdrop for further engineering, and provide glimpses into the natural variation of stress tolerance in wild yeast strains.« less

Authors:
 [1];  [1];  [1];  [1];  [2];  [2];  [2];  [2];  [2];  [3];  [1]
  1. Univ. of Wisconsin, Madison, WI (United States). Lab. of Genetics; Univ. of Wisconsin, Madison, WI (United States). DOE Great lakes Bioenergy Research Center
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. Univ. of Wisconsin, Madison, WI (United States). DOE Great lakes Bioenergy Research Center
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of Wisconsin, Madison, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
OSTI Identifier:
1625336
Grant/Contract Number:  
AC02-05CH11231; FC02-07ER64494
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Genome Biology and Evolution
Additional Journal Information:
Journal Volume: 6; Journal Issue: 9; Journal ID: ISSN 1759-6653
Publisher:
Society for Molecular Biology and Evolution
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Evolutionary Biology; Genetics & Heredity; bioenergy; genomics; transcriptomics; environmental stress

Citation Formats

Wohlbach, Dana J., Rovinskiy, Nikolay, Lewis, Jeffrey A., Sardi, Maria, Schackwitz, Wendy S., Martin, Joel A., Deshpande, Shweta, Daum, Christopher G., Lipzen, Anna, Sato, Trey K., and Gasch, Audrey P. Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production. United States: N. p., 2014. Web. doi:10.1093/gbe/evu199.
Wohlbach, Dana J., Rovinskiy, Nikolay, Lewis, Jeffrey A., Sardi, Maria, Schackwitz, Wendy S., Martin, Joel A., Deshpande, Shweta, Daum, Christopher G., Lipzen, Anna, Sato, Trey K., & Gasch, Audrey P. Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production. United States. https://doi.org/10.1093/gbe/evu199
Wohlbach, Dana J., Rovinskiy, Nikolay, Lewis, Jeffrey A., Sardi, Maria, Schackwitz, Wendy S., Martin, Joel A., Deshpande, Shweta, Daum, Christopher G., Lipzen, Anna, Sato, Trey K., and Gasch, Audrey P. 2014. "Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production". United States. https://doi.org/10.1093/gbe/evu199. https://www.osti.gov/servlets/purl/1625336.
@article{osti_1625336,
title = {Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production},
author = {Wohlbach, Dana J. and Rovinskiy, Nikolay and Lewis, Jeffrey A. and Sardi, Maria and Schackwitz, Wendy S. and Martin, Joel A. and Deshpande, Shweta and Daum, Christopher G. and Lipzen, Anna and Sato, Trey K. and Gasch, Audrey P.},
abstractNote = {Lignocellulosic plant material is a viable source of biomass to produce alternative energy including ethanol and other biofuels. However, several factors—including toxic by products from biomass pretreatment and poor fermentation of xylose and other pentose sugars—currently limit the efficiency of microbial biofuel production. To begin to understand the genetic basis of desirable traits, we characterized three strains of Saccharomyces cerevisiae with robust growth in a pretreated lignocellulosic hydrolysate or tolerance to stress conditions relevant to industrial biofuel production, through genome and transcriptome sequencing analysis. All stress resistant strains were highly mosaic, suggesting that genetic admixture may contribute to novel allele combinations underlying these phenotypes. Strain-specific gene sets not found in the lab strain were functionally linked to the tolerances of particular strains. Furthermore, genes with signatures of evolutionary selection were enriched for functional categories important for stress resistance and included stress-responsive signaling factors. Comparison of the strains’ transcriptomic responses to heat and ethanol treatment—two stresses relevant to industrial bioethanol production—pointed to physiological processes that were related to particular stress resistance profiles. Many of the genotype-by-environment expression responses occurred at targets of transcription factors with signatures of positive selection, suggesting that these strains have undergone positive selection for stress tolerance. Our results generate new insights into potential mechanisms of tolerance to stresses relevant to biofuel production, including ethanol and heat, present a backdrop for further engineering, and provide glimpses into the natural variation of stress tolerance in wild yeast strains.},
doi = {10.1093/gbe/evu199},
url = {https://www.osti.gov/biblio/1625336}, journal = {Genome Biology and Evolution},
issn = {1759-6653},
number = 9,
volume = 6,
place = {United States},
year = {Mon Sep 01 00:00:00 EDT 2014},
month = {Mon Sep 01 00:00:00 EDT 2014}
}

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