The impact of genomic variability on gene expression in environmental Saccharomyces cerevisiae strains

Abstract

Environmental Saccharomyces cerevisiae strains are crucially important, as they represent the large pool from which domesticated industrial yeasts have been selected, and vineyard strains can be considered the genetic reservoir from which industrial wine strains with strong fermentative behaviour are selected. Four vineyard strains with different fermentation performances were chosen from a large collection of strains isolated from Italian vineyards. Their genomes were sequenced to identify how genetic variations influence gene expression during fermentation and to clarify the evolutionary relationship between vineyard isolates and industrial wine strains. RNA sequencing was performed on the four vineyard strains, as well as on the industrial wine yeast strain EC1118 and on the laboratory strain S288c, at two stages of fermentation. We showed that there was a large gene cluster with variable promoter regions modifying gene expression in the strains. Our results indicate that it is the evolvability of the yeast promoter regions, rather than structural variations or strain-specific genes, that is the main cause of the differences in gene expression. This promoter variability, determined by variable tandem repeats and a high number of single-nucleotide polymorphisms together with 49 differentially expressed transcription factors, explained the strong phenotypic differences in the strains.

Saccharomyces cerevisiae FLO1Gene Demonstrates Genetic Linkage to Increased Fermentation Rate at Low Temperatures

“…The transcriptional response to low temperature fermentation is initiated in two steps, first via the induction of cold-specific stress genes, followed by the more generalized environmental stress response and fermentation stress response (Gasch and Werner-Washburne 2002; Beltran et al 2006; Marks et al 2008; Deed et al 2015). It has been well documented that different S. cerevisiae strains vary greatly in their ability to grow and ferment at lower temperatures (Charoenchai et al 1998; Torija et al 2003), and it has been suggested that these phenotypic differences are due to strain differences in gene expression, particularly via variation in gene promoter regions and the expression of transcription factors (Beltran et al 2006; Chiva et al 2012; Treu et al 2014; Deed et al 2015). …”

Saccharomyces cerevisiaevineyard strains have different nitrogen requirements that affect their fermentation performances

“…In previous work, a pool of S. cerevisiae strains was isolated from the vineyards and significant differences in terms of fermentation and nitrogen utilization were evidenced among the strains (Treu et al . ). Seven vineyard yeasts were chosen, from the pool, on the basis of the isolation origins, the technological characteristics and the mt‐DNA profiles that allowed yeast identification at strain level.…”

“…); Characterization at strain level was performed by means of mt‐DNA analysis (Treu et al . ). Strain physiological characterization was performed for all the yeasts to evaluate the presence of technological trait interesting for winemaking (Treu et al .…”

“…; Treu et al . ). In particular, vineyard strain genome analysis demonstrated that in those strains gene sequences involved in nitrogen metabolism are more variable than those present in industrial strains, suggesting a different aptitude in nitrogen uptake and management (Treu et al .…”

Single TRAM domain RNA‐binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii

“…meme was used to illustrate the compositions of identified motifs. Statistical over‐representation of tRNA and 5S rRNA sequences in the Ctr3‐bound data was assessed using procedures described previously (Treu et al ., ). Briefly, 100 000 random samplings were performed using 64 and 53 genes (representing transcripts defined from 4°C and 23°C cultures respectively; see Ctr3 RNA binding specificity ) across the entire M. burtonii genome sequence (2497 genes) using custom Perl script implementing Perl ‘rand()’ function.…”