Natural Variation in Diauxic Shift between Patagonian Saccharomyces eubayanus Strains

Abstract

The study of natural variation can untap novel alleles with immense value for biotechnological applications. Saccharomyces eubayanus Patagonian isolates exhibit differences in the diauxic shift between glucose and maltose, representing a suitable model to study their natural genetic variation for novel strains for brewing. However, little is known about the genetic variants and chromatin regulators responsible for these differences. Here, we show how genome-wide chromatin accessibility and gene expression differences underlie distinct diauxic shift profiles in S. eubayanus. We identified two strains with a rapid diauxic shift between glucose and maltose (CL467.1 and CBS12357) and one strain with a remarkably low fermentation efficiency and longer lag phase during diauxic shift (QC18). This is associated in the QC18 strain to lower transcriptional activity and chromatin accessibility of specific genes of maltose metabolism, and higher expression levels of glucose transporters. These differences are governed by the HAP complex, which differentially regulates gene expression depending on the genetic background. We found in the QC18 strain a contrasting phenotype to those described in S. cerevisiae, where hap4, hap5 and cin5 knockouts significantly improved the QC18 growth rate in the glucose-maltose shift. The most profound effects were found between CIN5 allelic variants, suggesting that Cin5p could strongly activate a repressor of the diauxic shift in the QC18 strain, but not necessarily in the other strains. The differences between strains could originate from the tree host from which the strains were obtained, which might determine the sugar source preference and the brewing potential of the strain.

Wild Patagonian yeast improve the evolutionary potential of novel interspecific hybrid strains for Lager brewing

“…Previous studies using hybridization and experimental evolution demonstrated that Lager yeast hybrids could be improved through selection under fermentation conditions (Krogerus, Preiss, et al, 2018) without polyploidization (Krogerus et al, 2015). While these studies have expanded the diversity of Lager yeast phenotypes, they are primarily based on a single S. eubayanus genetic background, CBS 12357T (belonging to PB-1), which is not representative of the overall species' genetic and phenotypic diversity (Burini et al, 2021;Molinet, Eizaguirre, et al, 2022;Nespolo et al, 2020;Urbina et al, 2020). S. eubayanus lineages vary widely in fermentation capacity and aroma profiles during beer fermentation, suggesting that the natural diversity of S. eubayanus is also well-suited for making innovative Lager hybrid strains (Burini et al, 2021;Mardones et al, 2021;Urbina et al, 2020).…”

“…Hybrids and parental strains were phenotypically characterized under microculture conditions as previously described (Molinet, Urbina, et al, 2022). Briefly, we estimated mitotic growth in 96-well plates containing Yeast Nitrogen Base (YNB) supplemented with 2% glucose, 2% maltose, 2% maltotriose, 2% glucose and 9% ethanol, 2% glucose and 10% sorbitol, and under carbon source switching from glucose to maltose as previously described (Molinet, Eizaguirre, et al, 2022). All conditions were evaluated at 25 °C.…”

“…Gene expression analysis was performed on ancestral and evolved hybrid strains H3-A and H3-E. RNA was obtained and processed after 24 h under beer wort fermentation in triplicates, using the E.Z.N.A Total RNA kit I (OMEGA) as previously described (Molinet, Eizaguirre, et al, 2022;Venegas et al, 2023). Total RNA was recovered using the RNA Clean and Concentrator Kit (Zymo Research).…”