Molecular Characterization of a Chromosomal Rearrangement Involved in the Adaptive Evolution of Yeast Strains

Abstract

Wine yeast strains show a high level of chromosome length polymorphism. This polymorphism is mainly generated by illegitimate recombination mediated by Ty transposons or subtelomeric repeated sequences. We have found, however, that the SSU1-R allele, which confers sulfite resistance to yeast cells, is the product of a reciprocal translocation between chromosomes VIII and XVI due to unequal crossing-over mediated by microhomology between very short sequences on the 5Ј upstream regions of the SSU1 and ECM34 genes. We also show that this translocation is only present in wine yeast strains, suggesting that the use for millennia of sulfite as a preservative in wine production could have favored its selection. This is the first time that a gross chromosomal rearrangement is shown to be involved in the adaptive evolution of Saccharomyces cerevisiae.[The sequence data from this study have been submitted to EMBL under accession nos. AF239757, AF239758, and AJ458340-AJ458367. The following individual kindly provided reagents, samples, or unpublished information as indicated in the paper: N. Goto-Yamamoto.] The unaware use of yeast for winemaking by the first agricultural civilizations has been reported as far back as 7400 years ago. Until the middle of the last millennium, wines were mainly produced around the Mediterranean Sea and the Caucasus. Since then, winemaking has spread with the European colonizers throughout the temperate regions of the world (Pretorius 2000).Although different genera and species of yeasts are found in musts, the species Saccharomyces cerevisiae is mainly responsible for the transformation of musts into wines. The origin of S. cerevisiae is controversial. Some authors propose that this species is a "natural" organism present in plant fruits (Mortimer and Polsinelli 1999). Others argue that S. cerevisiae is a domesticated species originated from its closest relative S. paradoxus, a wild species found all around the world (Vaughan-Martini and Martini 1995). This debate is important in postulating the original genome of S. cerevisiae and how the strong selective pressure applied since its first unconscious use in controlled fermentation processes has reshaped it. Useful phenotypic traits such as fast growth in sugar-rich media, high alcohol production and tolerance, and good flavor production selected for billions of generations have had strong influences on the S. cerevisiae genome.In contrast to most S. cerevisiae strains used in the laboratory, which are either haploid or diploid and have a constant chromosome electrophoretic profile, wine yeast strains are mainly diploid, aneuploid, or polyploid, homothallic, and . Their exacerbated capacity to reorganize its genome by chromosome rearrangements such as Ty-promoted chromosomal translocations (Longo and Vézinhet 1993;Rachidi et al. 1999), mitotic crossing-over (Aguilera et al. 2000), and gene conversion (Puig et al. 2000) promotes a faster adaptation to environmental changes than spontaneous mutations, which occur at comparatively very low rat...

A sulphite-inducible form of the sulphite efflux gene SSU1 in a Saccharomyces cerevisiae wine yeast

“…It has been shown that the expression of SSU1 varied considerably among vineyard isolates (Townsend et al, 2003) and that high levels of SSU1 mRNA were correlated with increased sulphite resistance (Goto-Yamamoto et al, 1998;Hauser et al, 2001;Perez-Ortin et al, 2002). Several studies have demonstrated or suggested different mechanisms of activation for SSU1 (Park & Bakalinsky, 2000;Perez-Ortin et al, 2002;Yuasa et al, 2004Yuasa et al, , 2005, involving either its conventional activator FZF1 or an alternative system based on the new promoter resulting from chromosome translocation.…”

“…SSU1-R is expressed at much higher levels than SSU1 (Goto-Yamamoto et al, 1998). It has also been shown that at least two repeats of the 76 bp enhancer sequence are required for SSU1-R expression (Perez-Ortin et al, 2002;Yuasa et al, 2005) and that SSU1-R is not directly regulated by Fzf1p (Yuasa et al, 2005).…”

“…Several studies have demonstrated or suggested different mechanisms of activation for SSU1 (Park & Bakalinsky, 2000;Perez-Ortin et al, 2002;Yuasa et al, 2004Yuasa et al, , 2005, involving either its conventional activator FZF1 or an alternative system based on the new promoter resulting from chromosome translocation. The mechanisms described in these studies were constitutive, with no suggestion of inducible transcriptional activation of SSU1.…”

“…Some highly sulphiteresistant wine strains have an SSU1 allele (SSU1-R) on chromosome VIII (Goto-Yamamoto et al, 1998). The upstream sequence is no longer present on this allele due to a reciprocal translocation between chromosomes VIII and XVI (Perez-Ortin et al, 2002). The SSU1-R promoter contains up to six repeats of a 76 bp enhancer sequence from the promoter of ECM34, a highly expressed protein of unknown function.…”

“…The SSU1-R allele is only present in wine yeasts; thus the genomic organization of the SSU1 locus in oenological strains has been studied extensively as a marker of the adaptive evolution of S. cerevisiae (Perez-Ortin et al, 2002). Moreover, a high level of polymorphism has been observed in the SSU1 gene among vineyard-isolated strains (Aa et al, 2006), suggesting that this transport system is important in the evolution of SO 2 resistance mechanisms.…”