Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production

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.

doi:10.1093/gbe/evu199

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

Journal Article · Mon Sep 01 00:00:00 EDT 2014 · Genome Biology and Evolution

DOI:https://doi.org/10.1093/gbe/evu199· OSTI ID:1625336

Wohlbach, Dana J. ^[1]; Rovinskiy, Nikolay ^[1]; Lewis, Jeffrey A. ^[1]; Sardi, Maria ^[1]; Schackwitz, Wendy S. ^[2]; Martin, Joel A. ^[2]; Deshpande, Shweta ^[2]; Daum, Christopher G. ^[2]; Lipzen, Anna ^[2]; Sato, Trey K. ^[3]; Gasch, Audrey P. ^[1]

Univ. of Wisconsin, Madison, WI (United States). Lab. of Genetics; Univ. of Wisconsin, Madison, WI (United States). DOE Great lakes Bioenergy Research Center
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Univ. of Wisconsin, Madison, WI (United States). DOE Great lakes Bioenergy Research Center

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of Wisconsin, Madison, WI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231; FC02-07ER64494

OSTI ID:: 1625336

Journal Information:: Genome Biology and Evolution, Vol. 6, Issue 9; ISSN 1759-6653

Publisher:: Society for Molecular Biology and EvolutionCopyright Statement

Country of Publication:: United States

Language:: English

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Exploring industrial and natural Saccharomyces cerevisiae strains for the bio-based economy from biomass: the case of bioethanol Favaro, Lorenzo; Jansen, Trudy; van Zyl, Willem Heber Critical Reviews in Biotechnology, Vol. 39, Issue 6 https://doi.org/10.1080/07388551.2019.1619157	journal	May 2019
Metabolic engineering of Saccharomyces cerevisiae to produce a reduced viscosity oil from lignocellulose Tran, Tam N. T.; Breuer, Rebecca J.; Avanasi Narasimhan, Ragothaman Biotechnology for Biofuels, Vol. 10, Issue 1 https://doi.org/10.1186/s13068-017-0751-y	journal	March 2017
Shift and adapt: the costs and benefits of karyotype variations Gerstein, Aleeza C.; Berman, Judith bioRxiv https://doi.org/10.1101/025171	journal	August 2015

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