Genomic structural variations contribute to trait improvement during whole-genome shuffling of yeast

Abstract

Whole-genome shuffling (WGS) is a powerful technology of improving the complex traits of many microorganisms. However, the molecular mechanisms underlying the altered phenotypes in isolates were less clarified. Isolates with significantly enhanced stress tolerance and ethanol titer under very-high-gravity conditions were obtained after WGS of the bioethanol Saccharomyces cerevisiae strain ZTW1. Karyotype analysis and RT-qPCR showed that chromosomal rearrangement occurred frequently in genome shuffling. Thus, the phenotypic effects of genomic structural variations were determined in this study. RNA-Seq and physiological analyses revealed the diverse transcription pattern and physiological status of the isolate S3-110 and ZTW1. Our observations suggest that the improved stress tolerance of S3-110 can be largely attributed to the copy number variations in large DNA regions, which would adjust the ploidy of yeast cells and expression levels of certain genes involved in stress response. Overall, this work not only constructed shuffled S. cerevisiae strains that have potential industrial applications but also provided novel insights into the molecular mechanisms of WGS and enhanced our knowledge on this useful breeding strategy.

Improving industrial yeast strains: exploiting natural and artificial diversity

“…Firstly, it is possible to carry out a prescreening by subjecting the hybrid population to a severe stress by plating the cells on medium that contains for instance high ethanol or acetic acid levels, conditions encountered during fermentation. Next, only fast-growing colonies are tested individually in small-scale fermentations, and only superior hybrids are used for a next round of shuffling (Shi et al ., 2009; Zheng et al ., 2011a, b, 2013a, b; Tao et al ., 2012). Other investigators have instead tried to first improve stress tolerance and found that hybrids generated after multiple rounds of genome shuffling and selection also showed increased general fermentation performance (Wei et al ., 2008; Cao et al ., 2009, 2010, 2012; Hou, 2009; Wang & Hou, 2010; Jingping et al ., 2012; Lu et al ., 2012; Wang et al ., 2012a).…”

Industrial Relevance of Chromosomal Copy Number Variation in Saccharomyces Yeasts

“…cerevisiae strains used in dough leavening, bioethanol production, ale-type beer fermentation, and distilled-beverage production. In these strains, aneuploidy typically involves small deviations in copy number of one or a few chromosomes (117–119). Since accurate information is available for only a few of the many hundreds of such strains stored in culture collections, the incidence of CCNV may well be underestimated.…”

“…Use of the mitotic inhibitor methyl benzimidazole-2-yl-carbamate (MBC) to mutagenize the aneuploid bioethanol strain ZTW1 demonstrates the potential of this approach (153). Treatment of strain ZTW1 with MBC yielded strains with an improved fermentative capacity under industrial high-gravity conditions (119), enhanced viability after drying (154), and higher final ethanol titer (124). These observations and the frequent appearance of CCNV in ALE suggest that such interference with chromosome segregation may deserve reconsideration in industrial yeast strain improvement.…”

Large-scale robot-assisted genome shuffling yields industrial Saccharomyces cerevisiae yeasts with increased ethanol tolerance

“…Some researchers used laboratory strains [10,11], which likely do not perform well under industrial conditions. In other studies, the novel hybrids were not tested on a pilot scale [12-15]. Moreover, genome shuffling is often combined with genetic engineering [16,17], making some industrial applications problematic.…”