Comparative genomics of Saccharomyces cerevisiae natural isolates for bioenergy production - PubMed (original) (raw)

Comparative Study

Comparative genomics of Saccharomyces cerevisiae natural isolates for bioenergy production

Dana J Wohlbach et al. Genome Biol Evol. 2014 Sep.

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. 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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Figures

F<sc>ig</sc>. 1.—

Fig. 1.—

Stress tolerance profiles. (A) Acquired ethanol tolerance of LEP, MUSH, CRB, and other strains from (Lewis et al. 2010). Cells were exposed to high does of ethanol with (blue) or without (gray) prior treatment of 5% v/v ethanol. (B and C) Growth rates (see Materials and Methods) of S. cerevisiae strains in YPD at 40 °C (B) or in ACSH at 42 °C (C) relative to YPD (adapted from [Sato et al. 2014]).

F<sc>ig</sc>. 2.—

Fig. 2.—

Distribution of SNPs across the genome. Homozygous (A, green) and heterozygous (B, blue) SNPs relative to the S288c reference for 16 S. cerevisiae chromosomes, with a sliding 1-kb window of 100 bp step size.

F<sc>ig</sc>. 3.—

Fig. 3.—

Population structure of 66 S. cerevisiae strains. Population structure was inferred using 11,795 evenly distributed SNPs and six ancestral populations, identified as European/wine (green), North American/oak (orange), West African (blue), Sake (purple), and Malaysian (yellow) lineages, as well as various human-associated (red) strains. For each strain indicated on the x axis, the height of each colored block represents the proportion of each population assigned to that strain. Labels indicate the source from which each strain was isolated.

F<sc>ig</sc>. 4.—

Fig. 4.—

Unique genes in CRB, LEP, and MUSH. A. Functional distribution of 25 non-S288c genes in CRB, 15 non-S288c genes in LEP, and 12 non-S288c genes in MUSH, classified according to predicted GO biological process or molecular function. CW, cell wall; other, unknown or other. (B and C). Genomic architecture of non-S288c genes in CRB and LEP (B) or in CRB and biofuel strain JAY291 (C). Black bars are spaced 2 kb apart.

F<sc>ig</sc>. 5.—

Fig. 5.—

Expression differences across environments and strains. (A) Venn diagram representing the number of differentially expressed genes responding to heat or ethanol stress, regardless of strain background. (B and C) The overlap in heat-responsive genes (independent of strain background, B) or ethanol-responsive genes (independent of strain background, C) and genes with a strain-by-stress interaction. (D) Two hundred forty-eight genes differentially expressed in at least one wild strain. Left: log2 expression differences in unstressed strains versus the average of all strains; Middle: log2-fold changes in each strain responding to heat (H) or ethanol (E) stress, compared with the strain’s starting expression before addition of stress; Right: Difference in stress-responsive expression in each strain versus the average across all strains. Red/green represents increased/decreased expression in response to each stress; yellow/blue represent higher/lower expression in the denoted strain compared with the average of all strains.

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