Journal Article

Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast

Heil, Caiti Smukowski, Amorosi, Clara J, Hope, Elyse A, Dang, Kolena, Miller, Aaron W, Dunham, Maitreya J

2017

Overview

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.

• Publisher: Genetics Society of America
• Subject: Adaptation / Agglomeration / Baking yeast / Biofilms / Biological evolution / Cell aggregation / Cell Aggregation - genetics / Clonal deletion / Cloning / Directed Molecular Evolution / DNA Transposable Elements - genetics / Ethanol / Evolution / Experiments / Flocculation / Gene sequencing / Genes / Genetics / Genetics, Population / Genomes / Insertion / Investigations / Laboratories / Mannose-Binding Lectins - genetics / Mutation / Nuclear Proteins - genetics / Phenotype / Populations / Promoter Regions, Genetic / Repressor Proteins - genetics / Saccharomyces cerevisiae / Saccharomyces cerevisiae - genetics / Saccharomyces cerevisiae Proteins - genetics / Sequence Deletion / Transcription / Transposons / Yeast