Histone chaperones and the Rrm3p helicase regulate flocculation in S. cerevisiae

Hollie Rowlands,Barret Foster,Kholoud Shaban,Yannic Proteau,Krassimir Yankulov

doi:10.1186/s13072-019-0303-8

Abstract

BackgroundBiofilm formation or flocculation is a major phenotype in wild type budding yeasts but rarely seen in laboratory yeast strains. Here, we analysed flocculation phenotypes and the expression of FLO genes in laboratory strains with various genetic backgrounds.ResultsWe show that mutations in histone chaperones, the helicase RRM3 and the Histone Deacetylase HDA1 de-repress the FLO genes and partially reconstitute flocculation. We demonstrate that the loss of repression correlates to elevated expression of several FLO genes, to increased acetylation of histones at the promoter of FLO1 and to variegated expression of FLO11. We show that these effects are related to the activity of CAF-1 at the replication forks. We also demonstrate that nitrogen starvation or inhibition of histone deacetylases do not produce flocculation in W303 and BY4742 strains but do so in strains compromised for chromatin maintenance. Finally, we correlate the de-repression of FLO genes to the loss of silencing at the subtelomeric and mating type gene loci.ConclusionsWe conclude that the deregulation of chromatin maintenance and transmission is sufficient to reconstitute flocculation in laboratory yeast strains. Consequently, we propose that a gain in epigenetic silencing is a major contributing factor for the loss of flocculation phenotypes in these strains. We suggest that flocculation in yeasts provides an excellent model for addressing the challenging issue of how epigenetic mechanisms contribute to evolution.

Highlights

Biofilm formation or flocculation is a major phenotype in wild type budding yeasts but rarely seen in laboratory yeast strains
Flocculation‐like phenotypes in laboratory strains While analysing epistatic interactions of histone chaperones with the RRM3 helicase, we noticed that some mutant strains produced clusters in liquid cultures
This was surprising as all mutations were in haploid BY4742 or W303 backgrounds, which do not flocculate under normal laboratory conditions

Summary

Introduction

Biofilm formation or flocculation is a major phenotype in wild type budding yeasts but rarely seen in laboratory yeast strains. We analysed flocculation phenotypes and the expression of FLO genes in laboratory strains with various genetic backgrounds. The non-sexual aggregation of single cell organisms into clusters is referred to as flocculation or biofilm [1, 2]. In industrial yeast strains flocculation is a highly desired phenotype and in many cases can be readily activated by starvation, exposure to ethanol and/or other stressors [1, 2]. The key regulators of flocculation in S. cerevisiae are the FLO genes. They are positioned 20–40 kb away from the telomeres and encode lectin-like cell surface proteins [3, 4]. FLO1 acts as a regulator of biofilm formation [6] while FLO11 is known to control the switch

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