title: Global changes in gene expression associated with phenotypic switching of wild yeast.
abstract: BACKGROUND
  Saccharomyces cerevisiae strains isolated from natural settings form structured biofilm colonies that are equipped with intricate protective mechanisms. These wild strains are able to reprogram themselves with a certain frequency during cultivation in plentiful laboratory conditions. The resulting domesticated strains switch off certain protective mechanisms and form smooth colonies that resemble those of common laboratory strains.
  
  
  RESULTS
  Here, we show that domestication can be reversed when a domesticated strain is challenged by various adverse conditions; the resulting feral strain restores its ability to form structured biofilm colonies. Phenotypic, microscopic and transcriptomic analyses show that phenotypic transition is a complex process that affects various aspects of feral strain physiology; it leads to a phenotype that resembles the original wild strain in some aspects and the domesticated derivative in others. We specify the genetic determinants that are likely involved in the formation of a structured biofilm colonies. In addition to FLO11, these determinants include genes that affect the cell wall and membrane composition. We also identify changes occurring during phenotypic transitions that affect other properties of phenotypic strain-variants, such as resistance to the impact of environmental stress. Here we document the regulatory role of the histone deacetylase Hda1p in developing such a resistance.
  
  
  CONCLUSIONS
  We provide detailed analysis of transcriptomic and phenotypic modulations of three related S. cerevisiae strains that arose by phenotypic switching under diverse environmental conditions. We identify changes specifically related to a strain's ability to create complex structured colonies; we also show that other changes, such as genome rearrangement(s), are unrelated to this ability. Finally, we identify the importance of histone deacetylase Hda1p in strain resistance to stresses.
authors.forename: Vratislav
authors.initials: V
authors.lastname: Šťovíček
authors.forename: Libuše
authors.initials: L
authors.lastname: Váchová
authors.forename: Markéta
authors.initials: M
authors.lastname: Begany
authors.forename: Derek
authors.initials: D
authors.lastname: Wilkinson
authors.affiliation: Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 44 Prague 2, Czech Republic. zdenap@natur.cuni.cz.
authors.forename: Zdena
authors.initials: Z
authors.lastname: Palková
mesh_terms: D018441:Biofilms; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D006023:Glycoproteins / Q000235:genetics / Q000378:metabolism; D006655:Histone Deacetylases / Q000235:genetics / Q000378:metabolism; D008562:Membrane Glycoproteins / Q000235:genetics / Q000378:metabolism; D010641:Phenotype; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000502:physiology / Q000648:ultrastructure; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: C110690:FLO11 protein, S cerevisiae; D006023:Glycoproteins; D008562:Membrane Glycoproteins; D029701:Saccharomyces cerevisiae Proteins; D006655:Histone Deacetylases