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
Genome Biol Evol. 2014 Sep;6(9):2557-66. doi: 10.1093/gbe/evu199.
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.
木质纤维素植物材料是生产包括乙醇和其他生物燃料在内的替代能源的可行生物质来源。然而，目前有几个因素限制了微生物生物燃料生产的效率，这些因素包括生物质预处理产生的有毒副产物以及木糖和其他戊糖的发酵不佳。为了开始了解理想性状的遗传基础，我们通过基因组和转录组测序分析，对三株在预处理的木质纤维素水解产物中生长旺盛或对与工业生物燃料生产相关的胁迫条件具有耐受性的酿酒酵母菌株进行了表征。所有抗胁迫菌株都是高度嵌合的，这表明基因混合可能有助于这些表型背后的新等位基因组合。在实验室菌株中未发现的菌株特异性基因集在功能上与特定菌株的耐受性相关。此外，具有进化选择特征的基因在对抗胁迫重要的功能类别中富集，并且包括胁迫响应信号因子。对这些菌株对热和乙醇处理（与工业生物乙醇生产相关的两种胁迫）的转录组反应进行比较，揭示了与特定抗胁迫特征相关的生理过程。许多基因型-环境表达反应发生在具有正选择特征的转录因子靶点上，这表明这些菌株在胁迫耐受性方面经历了正选择。我们的研究结果为与生物燃料生产相关的胁迫耐受性潜在机制提供了新的见解，包括对乙醇和热的耐受性，为进一步的工程改造提供了背景，并让我们得以瞥见野生酵母菌株中胁迫耐受性的自然变异情况。
