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Open Access Research article

Global changes in gene expression associated with phenotypic switching of wild yeast

Vratislav Šťovíček13, Libuše Váchová12, Markéta Begany2, Derek Wilkinson1 and Zdena Palková1*

Author Affiliations

1 Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 44 Prague 2, Czech Republic

2 Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic

3 Current Address: The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, 2970 Hørsholm, Denmark

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BMC Genomics 2014, 15:136  doi:10.1186/1471-2164-15-136

Published: 17 February 2014

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.

Keywords:
Biofilm colony; Histone deacetylase; Phenotypic switching; Wild yeast strains