Harnessing genetic diversity in saccharomyces cerevisiae for fermentation of xylose in hydrolysates of alkaline hydrogen peroxide-pretreated biomass

Trey K. Sato, Tongjun Liu, Lucas S. Parreiras, Daniel L. Williams, Dana J. Wohlbach, Benjamin D. Bice, Irene M. Ong, Rebecca J. Breuer, Li Qin, Donald Busalacchi, Shweta Deshpande, Chris Daum, Audrey P. Gasch, David B. Hodge

    Research output: Research - peer-reviewArticle

    • 27 Citations

    Abstract

    The fermentation of lignocellulose-derived sugars, particularly xylose, into ethanol by the yeast Saccharomyces cerevisiae is known to be inhibited by compounds produced during feedstock pretreatment. We devised a strategy that combined chemical profiling of pretreated feedstocks, high-throughput phenotyping of genetically diverse S. cerevisiae strains isolated from a range of ecological niches, and directed engineering and evolution against identified inhibitors to produce strains with improved fermentation properties. We identified and quantified for the first time the major inhibitory compounds in alkaline hydrogen peroxide (AHP)-pretreated lignocellulosic hydrolysates, including Na+, acetate, and p-coumaric (pCA) and ferulic (FA) acids. By phenotyping these yeast strains for their abilities to grow in the presence of these AHP inhibitors, one heterozygous diploid strain tolerant to all four inhibitors was selected, engineered for xylose metabolism, and then allowed to evolve on xylose with increasing amounts of pCA and FA. After only 149 generations, one evolved isolate, GLBRCY87, exhibited faster xylose uptake rates in both laboratory media and AHP switchgrass hydrolysate than its ancestral GLBRCY73 strain and completely converted 115 g/liter of total sugars in undetoxified AHP hydrolysate into more than 40 g/liter ethanol. Strikingly, genome sequencing revealed that during the evolution from GLBRCY73, the GLBRCY87 strain acquired the conversion of heterozygous to homozygous alleles in chromosome VII and amplification of chromosome XIV. Our approach highlights that simultaneous selection on xylose and pCA or FA with a wild S. cerevisiae strain containing inherent tolerance to AHP pretreatment inhibitors has potential for rapid evolution of robust properties in lignocellulosic biofuel production.

    LanguageEnglish (US)
    Pages540-554
    Number of pages15
    JournalApplied and Environmental Microbiology
    Volume80
    Issue number2
    DOIs
    StatePublished - Jan 2014

    Profile

    xylose
    hydrolysates
    hydrogen peroxide
    Saccharomyces cerevisiae
    fermentation
    genetic variation
    biomass
    genetic diversity
    Xylose
    Biomass
    Hydrogen Peroxide
    Fermentation
    inhibitor
    yeast
    chromosome
    ethanol
    sugar
    Ethanol
    Chromosomes
    Yeasts

    ASJC Scopus subject areas

    • Applied Microbiology and Biotechnology
    • Food Science
    • Biotechnology
    • Ecology

    Cite this

    Harnessing genetic diversity in saccharomyces cerevisiae for fermentation of xylose in hydrolysates of alkaline hydrogen peroxide-pretreated biomass. / Sato, Trey K.; Liu, Tongjun; Parreiras, Lucas S.; Williams, Daniel L.; Wohlbach, Dana J.; Bice, Benjamin D.; Ong, Irene M.; Breuer, Rebecca J.; Qin, Li; Busalacchi, Donald; Deshpande, Shweta; Daum, Chris; Gasch, Audrey P.; Hodge, David B.

    In: Applied and Environmental Microbiology, Vol. 80, No. 2, 01.2014, p. 540-554.

    Research output: Research - peer-reviewArticle

    Sato, TK, Liu, T, Parreiras, LS, Williams, DL, Wohlbach, DJ, Bice, BD, Ong, IM, Breuer, RJ, Qin, L, Busalacchi, D, Deshpande, S, Daum, C, Gasch, AP & Hodge, DB 2014, 'Harnessing genetic diversity in saccharomyces cerevisiae for fermentation of xylose in hydrolysates of alkaline hydrogen peroxide-pretreated biomass' Applied and Environmental Microbiology, vol 80, no. 2, pp. 540-554. DOI: 10.1128/AEM.01885-13
    Sato, Trey K. ; Liu, Tongjun ; Parreiras, Lucas S. ; Williams, Daniel L. ; Wohlbach, Dana J. ; Bice, Benjamin D. ; Ong, Irene M. ; Breuer, Rebecca J. ; Qin, Li ; Busalacchi, Donald ; Deshpande, Shweta ; Daum, Chris ; Gasch, Audrey P. ; Hodge, David B./ Harnessing genetic diversity in saccharomyces cerevisiae for fermentation of xylose in hydrolysates of alkaline hydrogen peroxide-pretreated biomass. In: Applied and Environmental Microbiology. 2014 ; Vol. 80, No. 2. pp. 540-554
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    abstract = "The fermentation of lignocellulose-derived sugars, particularly xylose, into ethanol by the yeast Saccharomyces cerevisiae is known to be inhibited by compounds produced during feedstock pretreatment. We devised a strategy that combined chemical profiling of pretreated feedstocks, high-throughput phenotyping of genetically diverse S. cerevisiae strains isolated from a range of ecological niches, and directed engineering and evolution against identified inhibitors to produce strains with improved fermentation properties. We identified and quantified for the first time the major inhibitory compounds in alkaline hydrogen peroxide (AHP)-pretreated lignocellulosic hydrolysates, including Na+, acetate, and p-coumaric (pCA) and ferulic (FA) acids. By phenotyping these yeast strains for their abilities to grow in the presence of these AHP inhibitors, one heterozygous diploid strain tolerant to all four inhibitors was selected, engineered for xylose metabolism, and then allowed to evolve on xylose with increasing amounts of pCA and FA. After only 149 generations, one evolved isolate, GLBRCY87, exhibited faster xylose uptake rates in both laboratory media and AHP switchgrass hydrolysate than its ancestral GLBRCY73 strain and completely converted 115 g/liter of total sugars in undetoxified AHP hydrolysate into more than 40 g/liter ethanol. Strikingly, genome sequencing revealed that during the evolution from GLBRCY73, the GLBRCY87 strain acquired the conversion of heterozygous to homozygous alleles in chromosome VII and amplification of chromosome XIV. Our approach highlights that simultaneous selection on xylose and pCA or FA with a wild S. cerevisiae strain containing inherent tolerance to AHP pretreatment inhibitors has potential for rapid evolution of robust properties in lignocellulosic biofuel production.",
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    AU - Parreiras,Lucas S.

    AU - Williams,Daniel L.

    AU - Wohlbach,Dana J.

    AU - Bice,Benjamin D.

    AU - Ong,Irene M.

    AU - Breuer,Rebecca J.

    AU - Qin,Li

    AU - Busalacchi,Donald

    AU - Deshpande,Shweta

    AU - Daum,Chris

    AU - Gasch,Audrey P.

    AU - Hodge,David B.

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