Adaptation ofSaccharomyces cerevisiaeto saline stress through laboratory evolution

Abstract

Most laboratory evolution studies that characterize evolutionary adaptation genomically focus on genetically simple traits that can be altered by one or few mutations. Such traits are important, but they are few compared with complex, polygenic traits influenced by many genes. We know much less about complex traits, and about the changes that occur in the genome and in gene expression during their evolutionary adaptation. Salt stress tolerance is such a trait. It is especially attractive for evolutionary studies, because the physiological response to salt stress is well‐characterized on the molecular and transcriptome level. This provides a unique opportunity to compare evolutionary adaptation and physiological adaptation to salt stress. The yeast Saccharomyces cerevisiae is a good model system to study salt stress tolerance, because it contains several highly conserved pathways that mediate the salt stress response. We evolved three replicate lines of yeast under continuous salt (NaCl) stress for 300 generations. All three lines evolved faster growth rate in high salt conditions than their ancestor. In these lines, we studied gene expression changes through microarray analysis and genetic changes through next generation population sequencing. We found two principal kinds of gene expression changes, changes in basal expression (82 genes) and changes in regulation (62 genes). The genes that change their expression involve several well‐known physiological stress‐response genes, including CTT1, MSN4 and HLR1. Next generation sequencing revealed only one high‐frequency single‐nucleotide change, in the gene MOT2, that caused increased fitness when introduced into the ancestral strain. Analysis of DNA content per cell revealed ploidy increases in all the three lines. Our observations suggest that evolutionary adaptation of yeast to salt stress is associated with genome size increase and modest expression changes in several genes.

Large and variable genome size unrelated to serpentine adaptation but supportive of cryptic sexuality in Cenococcum geophilum

“…Differential selection across ploidy levels has been observed in different abiotic environments (e.g., Dhar et al 2011) and increased ploidy has been suggested to provide a selective advantage in adaptation to new environmental conditions (Pawlowska and Taylor 2004;Ma et al 2009). However, despite the strong selection pressure that is expected in serpentine soils and a report of possible influences of serpentine on the evolution of polyploids in K. arvensis (Kolář et al 2012), we did not find significant differentiation in genome size between the C. geophilum populations included in this study, suggesting that genetic and demographic processes are more important in shaping the genome size variation of this species than environmental selection in the form of home soil chemistry.…”

“…Candida glabrata on the other hand is a haploid fungal species that displays frequent changes in its chromosome complement in relation with pathogenicity and a changing environment (Poláková et al 2009). Specific environmental factors that have been shown to affect fungal genome size include salt stress (Dhar et al 2011), fungicide treatments (Welker and Williams 1980), heat shock treatments (Hilton et al 1985), and host-pathogen interactions (Raffaele and Kamoun 2012).…”

Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris

“…For instance, in E. coli, mutations have been identified in the proline ABC transporter gene proV (Dragosits et al, 2013;Winkler et al, 2014), and in the osmoprotectant biosynthesis genes otsBA (Stoebel et al, 2009). In yeast, mutations were found in the proton efflux pump gene pma1, the global transcriptional repressor gene cyc8 (Anderson et al, 2010) and the mot2 gene that has an unknown role in salt tolerance (Dhar et al, 2011). Here, we employ experimental evolution coupled with whole-genome whole-population sequencing and site-directed mutagenesis to discover and verify the functional genes conferring salt tolerance in an anaerobic environmental bacterium Desulfovibrio vulgaris.…”

Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution

“…Salt-stress tolerance is a polygenic trait especially attractive for evolutionary studies (Dhar et al, 2011).…”