Laboratory evolution of aSaccharomyces cerevisiaexS. eubayanushybrid under simulated lager-brewing conditions: genetic diversity and phenotypic convergence

Abstract

Saccharomyces pastorianus lager-brewing yeasts are domesticated hybrids of S. cerevisiae x S. eubayanus that display extensive inter-strain chromosome copy number variation and chromosomal recombinations. It is unclear to what extent such genome rearrangements are intrinsic to the domestication of hybrid brewing yeasts and whether they contribute to their industrial performance.Here, an allodiploid laboratory hybrid of S. cerevisiae and S. eubayanus was evolved for up to 418 generations on wort under simulated lager-brewing conditions in six independent sequential batch bioreactors. Characterization of 55 single-cell isolates from the evolved cultures showed large phenotypic diversity and whole-genome sequencing revealed a large array of mutations. Frequent loss of heterozygosity involved diverse, strain-specific chromosomal translocations, which differed from those observed in domesticated, aneuploid S. pastorianus brewing strains. In contrast to the extensive aneuploidy of domesticated S. pastorianus strains, the evolved isolates only showed limited (segmental) aneuploidy. Specific mutations could be linked to calcium-dependent flocculation, loss of maltotriose utilisation and loss of mitochondrial activity, three industrially relevant traits that also occur in domesticated S. pastorianus strains. This study indicates that fast acquisition of extensive aneuploidy is not required for genetic adaptation of S. cerevisiae x S. eubayanus hybrids to brewing environments. In addition, this work demonstrates that, consistent with the diversity of brewing strains for maltotriose utilization, domestication under brewing conditions can result in loss of this industrially relevant trait. These observations have important implications for the design of strategies to improve industrial performance of novel laboratory-made hybrids.

Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast

“…Numerous laboratory evolution studies selecting for improved growth identified mutations in PKA signaling, including in strains evolved under sugar and nitrogen limitation, continuous growth in rich medium, growth on non-preferred carbon sources, and on industrial wort [32–34,36,38,39]. These studies often identify mutations in RAS and RAS regulators, adenylate cyclase that generates cAMP, and especially IRA2 .…”

“…The mutations identified in Y128 promote xylose utilization in multiple strain backgrounds [29], and similar mutations were identified in an independent study [27], revealing that they have a generalizable impact on strains with the metabolic potential for xylose consumption. Furthermore, mutations in PKA regulators, including IRA2 , frequently emerge in laboratory evolution studies that select for improved growth under various conditions [32–39]. Yet the physiological impacts of these mutations that enable improved phenotypes, in particular anaerobic xylose fermentation, remain unclear.…”

No evidence for whole-chromosome dosage compensation or global transcriptomic expression differences in spontaneously-aneuploid mutation accumulation lines ofSaccharomyces cerevisiae

“…While autosomal aneuploidies are generally deleterious in most organisms, presumably because of dosage problems (CHUNDURI AND STORCHOVA 2019), in some species, aneuploidies are surprisingly common, such as in some wild yeast (Saccharomyces cerevisiae) isolates (STROPE et al 2015). It has been shown experimentally that the accumulation or loss of chromosomes can be adaptive in certain environments (SELMECKI et al 2006;PAVELKA et al 2010;CHEN et al 2012;YONA et al 2012;SELMECKI et al 2015;DE VRIES et al 2018).…”

“…While dosage compensation has been observed for autosomes in Drosophila (DEVLIN et al 1982;BIRCHLER et al 1990; MCANALLY AND YAMPOLSKY 2009; CHEN AND OLIVER 2015; HANGNOH LEE 2016;LEE et al 2016), it is unknown whether such an intrinsic mechanism exists in yeast. The fact that yeast are often found to be aneuploid in natural isolates (STROPE et al 2015) and develop aneuploidies in response to certain environmental conditions (SELMECKI et al 2006;PAVELKA et al 2010;CHEN et al 2012;YONA et al 2012;SELMECKI et al 2015;DE VRIES et al 2018) could suggest that aneuploidy causes changes in gene expression that are adaptive, and no DC exists (KAYA et al 2015;LINDER et al 2017). Alternatively, yeast may be naturally robust to aneuploidy, so that aneuploid strains do not differ in fitness and thus occur in nature as neutral variants.…”