Novel Centromeric Loci of the Wine and Beer Yeast Dekkera bruxellensis CEN1 and CEN2

Abstract

The wine and beer yeast Dekkera bruxellensis thrives in environments that are harsh and limiting, especially in concentrations with low oxygen and high ethanol. Its different strains’ chromosomes greatly vary in number (karyotype). This study isolates two novel centromeric loci (CEN1 and CEN2), which support both the yeast’s autonomous replication and the stable maintenance of plasmids. In the sequenced genome of the D. bruxellensis strain CBS 2499, CEN1 and CEN2 are each present in one copy. They differ from the known “point” CEN elements, and their biological activity is retained within ~900–1300 bp DNA segments. CEN1 and CEN2 have features of both “point” and “regional” centromeres: They contain conserved DNA elements, ARSs, short repeats, one tRNA gene, and transposon-like elements within less than 1 kb. Our discovery of a miniature inverted-repeat transposable element (MITE) next to CEN2 is the first report of such transposons in yeast. The transformants carrying circular plasmids with cloned CEN1 and CEN2 undergo a phenotypic switch: They form fluffy colonies and produce three times more biofilm. The introduction of extra copies of CEN1 and CEN2 promotes both genome rearrangements and ploidy shifts, with these effects mediated by homologous recombination (between circular plasmid and genome centromere copy) or by chromosome breakage when integrated. Also, the proximity of the MITE-like transposon to CEN2 could translocate CEN2 within the genome or cause chromosomal breaks, so promoting genome dynamics. With extra copies of CEN1 and CEN2, the yeast’s enhanced capacities to rearrange its genome and to change its gene expression could increase its abilities for exploiting new and demanding niches.

Brettanomyces bruxellensis population survey reveals a diploid-triploid complex structured according to substrate of isolation and geographical distribution

“…Hybrids are also a widespread state among wine yeast, where natural or laboratory obtained combinations between two species could have interesting technological properties 62 , 66 – 69 . Other form of genome dynamics was also highlighted for the diploid CBS 2499 strain possessing specific centromeric loci configuration that enables genome rearrangements and ploidy shifts 43 . Based on the body of knowledge concerning other polyploid micro- and macro-organisms and the prevalence of polyploid strains highlighted in this study, we assume that B. bruxellensis has adapted to environmental stress factors by the means of genome plasticity, namely polyploidy.…”

“…Several studies highlight an important intraspecific diversity of B. bruxellensis 14 , 20 , 38 , 40 which makes the prediction of its occurrence and behaviour in industrial fermentations difficult. Further, recent genetic studies on a limited number of strains 24 , 41 , 42 have suggested that polyploidy and hybridisation may play a significant role in microevolution of the species, along with plasticity in chromosomal structure due to “untraditional” centromeres 43 . The role of polyploidy in adaptive changes to suit environment and/or lifestyle has been observed in other organisms 44 – 47 , notably for S. cerevisiae which shares similar fermentation niches to those occupied by B. bruxellensis .…”

Assessing Population Diversity of Brettanomyces Yeast Species and Identification of Strains for Brewing Applications

“…Despite the genome of Brettanomyces being highly dynamic and karyotypes strongly variable (Hellborg and Piškur, 2009;Curtin and Pretorius, 2014), we could display an overview of the polymorphic subtelomeric regions where more variation is expected (Brown et al, 2010). The centromeric loci CEN1, CEN2, responsible for chromosome rearrangements and change of ploidy (Ishchuk et al, 2016) is located in scaffold I. Scaffold I also contains a maltose assimilation cluster (MAL31, MAL11, IMA1), similar to the one already described in brewer's yeast in which is essential for maltose degradation (Needleman et al, 1984;Horák, 2013;Needleman and Michels, 2015). In this case, no transcriptional activator such as ScMAL13 is present, but just an α-glucosidase surrounded by maltose permeases and transporters.…”

New genome assemblies reveal patterns of domestication and adaptation acrossBrettanomyces(Dekkera) species

“…Brettanomyces [17,[35][36][37][38][39]. This genome plasticity is thought to be a mechanism in yeast for adaptation…”

“…Brettanomyces (Landry et al, 2006, Hellborg and Piskur, 2009, Vigentini et al, 2012, Borneman et al, 2014, Ishchuk et al, 2016, Avramova et al, 2018. This genome plasticity is thought to be a mechanism in yeast for adaptation to new environments and niches, and in response to new stressors (see Marsit et al (2017)…”