Genome-wide array-CGH analysis revealsYRF1gene copy number variation that modulates genetic stability in distillery yeasts

Abstract

Industrial yeasts, economically important microorganisms, are widely used in diverse biotechnological processes including brewing, winemaking and distilling. In contrast to a well-established genome of brewer's and wine yeast strains, the comprehensive evaluation of genomic features of distillery strains is lacking. In the present study, twenty two distillery yeast strains were subjected to electrophoretic karyotyping and array-based comparative genomic hybridization (array-CGH). The strains analyzed were assigned to the Saccharomyces sensu stricto complex and grouped into four species categories: S. bayanus, S. paradoxus, S. cerevisiae and S. kudriavzevii. The genomic diversity was mainly revealed within subtelomeric regions and the losses and/or gains of fragments of chromosomes I, III, VI and IX were the most frequently observed. Statistically significant differences in the gene copy number were documented in six functional gene categories: 1) telomere maintenance via recombination, DNA helicase activity or DNA binding, 2) maltose metabolism process, glucose transmembrane transporter activity; 3) asparagine catabolism, cellular response to nitrogen starvation, localized in cell wall-bounded periplasmic space, 4) siderophore transport, 5) response to copper ion, cadmium ion binding and 6) L-iditol 2- dehydrogenase activity. The losses of YRF1 genes (Y' element ATP-dependent helicase) were accompanied by decreased level of Y' sequences and an increase in DNA double and single strand breaks, and oxidative DNA damage in the S. paradoxus group compared to the S. bayanus group. We postulate that naturally occurring diversity in the YRF1 gene copy number may promote genetic stability in the S. bayanus group of distillery yeast strains.

Detecting differential growth of microbial populations with Gaussian process regression

“…S13; Liti et al 2009). S. paradoxus harbors higher levels of ROS (Deregowska et al 2015), and our results suggest that this may lead to a higher susceptibility to oxidative stress. Many other large-scale population growth studies have been performed to differentiate biological function through population growth phenotypes in the yeast community, and we anticipate that future applications of B-GREAT will highlight additional results from these studies (Warringer et al 2003;Fernandez-Ricaud et al 2005).…”

Aneuploidy in yeast: Segregation error or adaptation mechanism?

“…Aneuploidy has also been found in the yeasts used for the distilling of spirits such and vodka and whisky (Adamczyk et al, 2016;Deregowska et al, 2015;Naumova, Sadykova, Martynenko, & Naumov, 2013). Aneuploidies in distilling strains have been linked with increased copy number of MAL and SUC genes, which are known to play important roles in the distilling process (Naumova et al, 2013).…”

Copy number variations of genes involved in stress responses reflect the redox state and DNA damage in brewing yeasts

“…The dendrogram of chromosomal DNA-based similarity was created using Free-Tree software using unweighted pair group method with arithmetic mean (UPGMA) algorithm, Jaccard similarity coefficient, and Java TreeView 1.1.6.r2 (http://jtreeview.sourceforge.net/) (Deregowska et al 2015b). …”

“…Oxidative DNA damage as a level of 8-hydroxy-2′-deoxyguanosine (8-OHdG, 8-oxo-dG) was measured using Epigentek EpiQuik 8-OHdG DNA Damage Quantification Direct Kit (Gentaur, Poland) as previously described (Deregowska et al 2015b). …”