Experimental evolution reveals favored adaptive routes to cell aggregation in yeast

Abstract

Yeast flocculation is a community-building cell aggregation trait that is an important mechanism of stress resistance and a useful phenotype for brewers; however, it is also a nuisance in many industrial processes, in clinical settings, and in the laboratory. Chemostat-based evolution experiments are impaired by inadvertent selection for aggregation, which we observe in 35% of populations. These populations provide a testing ground for understanding the breadth of genetic mechanisms Saccharomyces cerevisiae uses to flocculate, and which of those mechanisms provide the biggest adaptive advantages. In this study, we employed experimental evolution as a tool to ask whether one or many routes to flocculation are favored, and to engineer a strain with reduced flocculation potential. Using a combination of whole genome sequencing and bulk segregant analysis, we identified causal mutations in 23 independent clones that had evolved cell aggregation during hundreds of generations of chemostat growth. In 12 of those clones, we identified a transposable element insertion in the promoter region of known flocculation gene FLO1, and, in an additional five clones, we recovered loss-of-function mutations in transcriptional repressor TUP1, which regulates FLO1 and other related genes. Other causal mutations were found in genes that have not been previously connected to flocculation. Evolving a flo1 deletion strain revealed that this single deletion reduces flocculation occurrences to 3%, and demonstrated the efficacy of using experimental evolution as a tool to identify and eliminate the primary adaptive routes for undesirable traits.

Flocculation of Saccharomyces cerevisiae is dependent on activation of Slt2 and Rlm1 regulated by the cell wall integrity pathway

“…Flocculation is a natural phenomenon of yeast cells which allows them to survive under stress conditions by the formation of multicellular clumps (Stratford, ; Bony et al , ; Hope et al , ) and/or biofilms; develop resistance to drugs (Chandra et al , ). The genetic, epigenetic and environmental factors; mutations in certain genes, nutritional stress, temperature, pH, oxygen supply and alteration in cell wall composition have been shown to induce flocculation phenotypes (Soares, ; Kim and Rose, ; Liu et al , ).…”

Multiplexing Mutation Rate Assessment: Determining Pathogenicity of Msh2 Variants inS. cerevisiae

“…DNA was once again extracted with the Mira-Prep protocol, and then used to transform YMD4328: FY4 msh2Δ and his3Δ flo1Δ FY4. The flo1Δ is present to reduce the prevalence of flocs (Hope et al, 2017). Transformants were collected such that there was 20X coverage of each barcode.…”