Systems biology approach for the identification of genetic determinants of colony morphology switch in natural S. cerevisiae strain

Colony morphology is a fascinating phenotype described in unicellular organisms as a possible step towards multicellularity. The spreading of filamentous structures is used by some pathogenic fungi, as Candida albicans, to invade human tissues thus causing infection. This phenotype, rarely observed in Saccharomyces cerevisiae colonies, is present in heterozygosis in the M28 S. cerevisiae strain, isolated from damaged grapes of the Montalcino area (Italy). Meiotic segregants of M28 show mendelian inheritance of colony morphology, thus making this strain the best suitable model to study the genetic determinants of structured colonies (filigreed). We analyzed cellular and colony morphology of M28 meiotic segregants in several different carbon sources. The addition of ethanol as the only carbon source lead to an increase in filamentation: in this perspective the stable and uniform morphotype, induced by ethanol, could reflect an adaptation to stress. In order to investigate the correlation between invasiveness, filamentous morphotype and pseudohyphal growth in S. Cerevisiae, we assessed the ability of this natural strain to invade solid media. Transcriptional analysis by means of microarrays on cells grown in fermentable and not-fermentable carbon sources and Functional Enrichment Analysis identified the genes involved in the regulation of colony morphogenesis. Our results support the hypothesis of an ecological function of filamentous phenotype in creating a community adaptable to the shifts of the environmental conditions. Whole genome comparative analysis on 12 M28 sporal derivatives of three different tetrads, with Next-Generation Sequencing (NGS) approach, allowed to discover mutations in genes candidate to be the genetic determinants of the colony morphology phenotype. We demonstrate that a number of three tetrads is sufficient to map a genetic trait with mendelian inheritance. RNA-seq based transcriptomics on the all M28 sequenced genome allowed to identify a gene expression profile associated to the filamentous morphotype and to confirm the candidate morphogenesis regulatory genes