Oncotarget

Research Papers: Chromosome:

Genome-wide array-CGH analysis reveals YRF1 gene copy number variation that modulates genetic stability in distillery yeasts

Anna Deregowska _, Marek Skoneczny, Jagoda Adamczyk, Aleksandra Kwiatkowska, Ewa Rawska, Adrianna Skoneczna, Anna Lewinska and Maciej Wnuk

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Oncotarget. 2015; 6:30650-30663. https://doi.org/10.18632/oncotarget.5594

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Abstract

Anna Deregowska1,*, Marek Skoneczny2,*, Jagoda Adamczyk1, Aleksandra Kwiatkowska1, Ewa Rawska1, Adrianna Skoneczna3, Anna Lewinska4,** and Maciej Wnuk1,**

1 Department of Genetics, University of Rzeszow, Rzeszow, Poland

2 Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland

3 Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland

4 Department of Biochemistry and Cell Biology, University of Rzeszow, Poland

* These authors have contributed equally as first authors

** These authors have contributed equally as last authors

Correspondence to:

Anna Lewinska, email:

Maciej Wnuk, email:

Keywords: distillery yeasts, genome, array-CGH, chromosomes, genetic instability

Received: July 19, 2015 Accepted: August 24, 2015 Published: September 10, 2015

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.


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