Systemic aneuploidization events drive phenotype switching in Saccharomyces cerevisiae

Abstract

How cells leverage their phenotypic potential to adapt and survive in a changing environment is a complex biological problem, with important implications for pathogenesis and species evolution. One particularly fascinating adaptive approach is the bet hedging strategy known as phenotype switching, which introduces phenotypic variation into a population through stochastic processes. Phenotype switching has long been observed in species across the tree of life, yet the mechanistic causes of switching in these organisms have remained difficult to define. Here we describe the causative basis of colony morphology phenotype switching which occurs among cells of the pathogenic isolate of Saccharomyces cerevisiae, YJM311. From clonal populations of YJM311 cells grown in identical conditions, we identified colonies which displayed altered colony architectures, yet could revert to the wild-type morphology after passaging. Whole genome sequence analysis revealed that these variant clones had all acquired whole chromosome copy number alterations (i.e., aneuploidies). Cumulatively, the variant clones we characterized harbored an exceptional spectrum of karyotypic alterations, with individual variants carrying between 1 and 16 aneuploidies. Most variants harbored unique collections of aneuploidies, indicating that numerous distinct karyotypes could manifest in the same morphological variation. Intriguingly, the genomic stability of these newly aneuploid variant clones modulated how often cells reverted back to the wild-type phenotypic state. We found that such revertant switches were also driven by chromosome missegregation events, and in some cases occurred through a return to euploidy. Together, our results demonstrate that colony morphology switching in this yeast strain is driven by stochastic and systemic aneuploidization events. These findings add an important new perspective to our current understanding of phenotype switching and bet hedging strategies, as well as how environmental pressures perpetuate organismal adaption and genome evolution.

Genomic characterization of a pathogenic isolate of Saccharomyces cerevisiae reveals an extensive and dynamic landscape of structural variation

“…Before initiating our studies of YJM311 18 , we first assessed the homogeneity of our stock by purifying individual clones for comparative karyotype analysis using pulsed-field gel electrophoresis (PFGE)(i.e., YJM311-1 through YJM311-7)(Fig. 1).…”

“…1). We also used this subclone to characterize the sources of stochastic phenotype switching displayed by YJM311 18 .…”

“…We next verified that the Longshot haplotype calling was accurate. Our investigation of phenotype switching in YJM311 revealed that this behavior is primarily driven by stochastic and systemic genomic instability events resulting in the gain and loss of unique combinations of chromosomes 18 . As such, we had assembled a collection of YJM311-3 derived phenotypic variants, each of which harbored at least one aneuploidy.…”

“…One such phenotype, called the colony morphology response, enables YJM311 cells to transition from a unicellular growth state to a cooperative 'multicellular' growth state in response to environmental changes in carbon source (i.e., glucose) availability 16,17 . On media rich in glucose, YJM311 cells form a typical smooth and simple colony architecture, but when plated on glucose-poor media, cells form complex colonies with a highly patterned organization [16][17][18] . Previously, studies using YJM311 as a model with which to investigate the genetic regulation of the colony morphology response demonstrated that allelic variations at numerous sites in the diploid genome modulate this complex phenotypic trait 17 .…”

“…Recently, we observed that some YJM311 cells stochastically switched between these simple and complex phenotypic states, even when grown in identical conditions. While investigating the sources of this phenotypic variation 18 , we also took the opportunity to explore the structural composition the YJM311 genome. By combining the of strengths short-and long read WGS analyses, we assembled the fully phased heterozygous diploid genome of YJM311 and explored the myriad structural complexities comprising the genomic architecture of this strain.…”