Determinants of selection in yeast evolved by genome shuffling

Abstract

BackgroundGenome shuffling (GS) is a widely adopted methodology for the evolutionary engineering of desirable traits in industrially relevant microorganisms. We have previously used genome shuffling to generate a strain of Saccharomyces cerevisiae that is tolerant to the growth inhibitors found in a lignocellulosic hydrolysate. In this study, we expand on previous work by performing a population-wide genomic survey of our genome shuffling experiment and dissecting the molecular determinants of the evolved phenotype.ResultsWhole population whole-genome sequencing was used to survey mutations selected during the experiment and extract allele frequency time series. Using growth curve assays on single point mutants and backcrossed derivatives, we explored the genetic architecture of the selected phenotype and detected examples of epistasis. Our results reveal cohorts of strongly correlated mutations, suggesting prevalent genetic hitchhiking and the presence of pre-existing founder mutations. From the patterns of apparent selection and the results of direct phenotypic assays, our results identify key driver mutations and deleterious hitchhikers.ConclusionsWe use these data to propose a model of inhibitor tolerance in our GS mutants. Our results also suggest a role for compensatory evolution and epistasis in our genome shuffling experiment and illustrate the impact of historical contingency on the outcomes of evolutionary engineering.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1283-9) contains supplementary material, which is available to authorized users.

Multi-Faceted Systems Biology Approaches Present a Cellular Landscape of Phenolic Compound Inhibition in Saccharomyces cerevisiae

“…are shown in (A) . Overlapping biological processes of the deletion mutants identified in chemogenomic screens for FA, PA, CA, HBA, and Van are indicated in (B) The heatmap shown here is based on published data obtained from Endo et al (2008) , Skerker et al (2013) , Pereira et al (2014) , Piotrowski et al (2015) , Wang X. et al (2017) , Wu et al (2017) , Biot-Pelletier et al (2018) , Sardi et al (2018) , Xue et al (2018) , Fletcher et al (2019) , and Hacısalihoǧlu et al (2019) . The genes were clustered according to their associated biological process ( Robinson et al, 2002 ).…”

“…The resulting strains are sequenced to identify key mutations that can then re-constructed in the wild type to confirm the role of the selected mutations on increasing tolerance. Using genome shuffling, genes including NRG1 , GSH1 , and GDH1 were identified as key determinants required by yeast for improved tolerance to lignocellulosic hydrolysate ( Biot-Pelletier et al, 2018 ; Table 1 ). Although genome shuffling has the advantage of filtering mutations that are unrelated to phenolic tolerance, it can be laborious and time consuming.…”

“…Functional genomic screens determined that deletion of genes involved in oxidative stress response ( YAP1, STB5, GSH1, SOD1, SOD2 ) resulted in hypersensitivity to phenolics ( Skerker et al, 2013 ; Pereira et al, 2014 ; Wu et al, 2017 ; Biot-Pelletier et al, 2018 ). Also, YAP1, SOD2 and other genes with antioxidant activity ( GRX2, CTT1, CTA1 ) are upregulated during phenolic exposure as shown in the transcriptomic studies ( Park and Kim, 2014 ; Shen et al, 2014 ).…”

The renaissance of yeasts as microbial factories in the modern age of biomanufacturing

“…Despite the current limited use of diversity in industrial process, the diversity of wild yeasts is constantly being explored for new biotechnological applications in many industrial sectors. Yeasts from the wild are being screened to identify species that produce novel flavors and characteristics for beverages (Cubillos, Gibson, Grijalva-Vallejos, Krogerus, & Nikulin, 2019), enhanced robustness for biofuel (Biot-Pelletier, Pinel, Larue, & Martin, 2018;Dubey, Jakeer, & Gaur, 2016;Peris et al, 2017;Wu et al, 2017), and many other phenotypes of interest. For example, Candida antarctica, a yeast that thrives in extreme conditions, was found to produce two lipases, used as biocatalyst in several large-scale industrial processes (Siodmiak, Mangelings, Vander Heyden, Ziegler-Borowska, & Marszall, 2015).…”