Genome Survey Sequencing of the Wine Spoilage YeastDekkera (Brettanomyces) bruxellensis

Abstract

The hemiascomycete yeast Dekkera bruxellensis, also known as Brettanomyces bruxellensis, is a major cause of wine spoilage worldwide. Wines infected with D. bruxellensis develop distinctive, unpleasant aromas due to volatile phenols produced by this species, which is highly ethanol tolerant and facultatively anaerobic. Despite its importance, however, D. bruxellensis has been poorly genetically characterized until now. We performed genome survey sequencing of a wine strain of D. bruxellensis to obtain 0.4؋ coverage of the genome. We identified approximately 3,000 genes, whose products averaged 49% amino acid identity to their Saccharomyces cerevisiae orthologs, with similar intron contents. Maximum likelihood phylogenetic analyses suggest that the relationship between D. bruxellensis, S. cerevisiae, and Candida albicans is close to a trichotomy. The estimated rate of chromosomal rearrangement in D. bruxellensis is slower than that calculated for C. albicans, while its rate of amino acid evolution is somewhat higher. The proteome of D. bruxellensis is enriched for transporters and genes involved in nitrogen and lipid metabolism, among other functions, which may reflect adaptations to its low-nutrient, high-ethanol niche. We also identified an adenyl deaminase gene that has high similarity to a gene in bacteria of the Burkholderia cepacia species complex and appears to be the result of horizontal gene transfer. These data provide a resource for further analyses of the population genetics and evolution of D. bruxellensis and of the genetic bases of its physiological capabilities.

Assessing Genetic Diversity among Brettanomyces Yeasts by DNA Fingerprinting and Whole-Genome Sequencing

“…Further, sugars such as arabinose, lactose, and raffinose did not support the growth of most isolates (2). Woolfit et al (22) reported the presence of five genes involved in nitrate assimilation in B. bruxellensis CBS 2499, including genes encoding a nitrate reductase, a nitrite reductase, and a nitrate transporter, as well as two regulatory genes encoding a Zn(II) 2 Cys 6 transcriptional factor for nitrate induction. Strains of Hansenula polymorpha in which any of these genes were disrupted lost their ability to grow on nitrate (64,69,70), showing their necessity in the assimilation of nitrate.…”

“…Woolfit et al reported a partial genome sequence of a B. bruxellensis wine contaminant (CBS 2499) and identified approximately 3,000 genes (22). Recently, the full genome sequence of this strain was determined and used to deduce the genetic background of some food-relevant properties and the evolutionary history of this yeast (23).…”

“…Apart from isolations from beer and wine, Brettanomyces species have been detected and isolated in other foods, such as cider, soft drinks, dairy products, and olives (9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20). Despite its economic importance either as a spoilage contaminant in wine and nonalcoholic beverages or as a vital component of the fermentation biota in the production of certain beers, the physiology and ecology of Brettanomyces yeasts have only recently been the subject of intensive research (1,(21)(22)(23)(24)(25). However, little is still known about the level of genomic interstrain variation within B. bruxellensis or within the genus Brettanomyces.…”

Complex Nature of the Genome in a Wine Spoilage Yeast, Dekkera bruxellensis

“…To analyze species-specific sequence variation, five regions from the D. bruxellensis sequence were randomly chosen (40) a The Centraalbureau Vor Schimmelcultures (CBS) collection of Dekkera bruxellensis strains was used in this study. Shown are GenBank accession numbers for nuclear 26S rDNA (D1/D2 fragment) and mitochondrial 15S rDNA.…”

“…The lineages of D. bruxellensis and S. cerevisiae separated at approximately the same time as the lineages of S. cerevisiae and C. albicans separated, approximately 200 million years ago (40). However, D. bruxellensis and S. cerevisiae share several characteristics, such as the production of ethanol, the ability to propagate in the absence of oxygen (anaerobic growth), and petite positivity (the ability to produce offspring without mitochondrial DNA [mtDNA]), that are rarely found among other yeasts (16,20).…”