The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties
Highlights
► Genome sequence of an important wine spoiling yeast ► Genomics of food related microorganisms ► Genetic background for aromatic compounds in wine ► Comparative genomics reveals evolutionary strategies.
Introduction
There is an enormous diversity among yeast species, including those that play important roles in traditional food processes, often in mixed cultures in spontaneous fermentations. One such yeast is Dekkera/Brettanomyces bruxellensis, associated with lambic beer fermentation and wine production, especially as a contributor, in a positive or negative manner, to flavor development (Du Toit and Pretorius, 2000). This yeast can produce phenolic compounds, such as 4-ethylguaiacol and 4-ethylphenol, which could lead to wine spoilage if present in high enough concentration (Heresztyn, 1986, Vigentini et al., 2008). In fact, D. bruxellensis represents a serious problem in wine industry, causing enormous economic losses as a consequence of wine spoilage (Wedral et al., 2010). However, in spite of the economic impact of D. bruxellensis, this yeast remains poorly studied.
D. bruxellensis is apparently not a close relative of baker's yeast Saccharomyces cerevisiae, but the phylogenetic position of the D. bruxellensis group has so far been rather impossible to determine (Woolfit et al., 2007). Both yeasts share several “peculiar” and rather “unusual” traits important for food-related properties, such as production of high ethanol levels, high tolerance towards ethanol, and the ability to grow without oxygen and in acidic environments (Rozpędowska et al., 2011). Apparently, given the lack of relatedness, these traits evolved in parallel in both groups, but it is unclear if the molecular mechanisms behind these properties are similar or different (Rozpędowska et al., 2011). In other words, these two yeasts represent an ideal model to study molecular processes involved in convergent and parallel evolutionary routes.
Ethanol production and capability to survive without oxygen are highly relevant in food fermentations. In S. cerevisiae, but not in D. bruxellensis, the corresponding genetic factors that underlie these traits have been relatively well studied. For example, the whole genome duplication (WGD), duplicated gene profiles, the horizontal transfer of the URA1 gene (coding for the DHODase, dihydroorotate dehydrogenase, catalyzing the fourth pyrimidine de novo pathway step), and lineage-specific duplication of the ADH genes (encoding alcohol dehydrogenases), have been shown to be at least partially responsible for the development of the S. cerevisiae high fermentation capacity and/or anaerobic properties (reviewed in Piskur and Langkjaer, 2004, Piskur et al., 2006). It is not known whether similar molecular strategies are responsible for the domination of the same environment by D. bruxellensis.
Recently, a partial genome sequence of one strain of D. bruxellensis has been reported, and the analysis estimated that this yeast has around 7.500 genes, of which many lack a homolog in the S. cerevisiae genome (Woolfit et al., 2007). Further analysis of the partial sequence has revealed that D. bruxellensis is not a simple haploid. Its genome contains approximately 1% polymorphic sites but the exact physical background for this heterozygocity is not known (Hellborg and Piskur, 2009).
Here we determined the whole genome sequence of the D. bruxellensis strain Y879 (CBS2499) and used it to deduce several “food-relevant” properties and evolution pathways of this yeast.
Section snippets
Genome sequencing and assembly
The genome of D. bruxellensis strain Y879 (CBS2499) was sequenced using a combination of 454 and Illumina sequencing platforms (GYBS 454 standard rapid, GYHO 454 standard rapid, GYHG 454 titanium 4 kb, GYFW 454 titanium 4 kb, GXXW Illumina 2 × 76 300 bp, ICHI Illumna 2 × 150 270 bp, and ICCY Illumina 2 × 100 4 kb CLIP). All general aspects of library construction and sequencing can be found at the JGI website (http://www.jgi.doe.gov/). An initial assembly of GXXW was conducted for QC purposes using the
General genome parameters
The 13.4 Megabase genome of D. bruxellensis CBS2499 was sequenced using a combination of 454 and Illumina platforms, assembled with AllPaths assembler and annotated using JGI annotation pipeline to predict 5600 genes (Table 1A, B, C, D, E). The obtained genome size is significantly smaller from the one deduced from the previously determined partial sequence (Woolfit et al., 2007). The previous wrong prediction was likely due to the problems with ploidy because D. bruxellensis is not a simple
Acknowledgments
JP acknowledges a Slovenian ARRS grant and a Swedish Sörensen Foundation grant to support his work on wine yeasts. TG and MMH acknowledge a grant from the Spanish Ministry of Science (BFU09-09268). The sequencing and annotations were conducted by the U.S. Department of Energy Joint Genome Institute and was supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231.
References (51)
- et al.
Basic local alignment search tool
Journal of Molecular Biology
(1990) - et al.
Reliability measures for membrane protein topology prediction algorithms
Journal of Molecular Biology
(2003) - et al.
How did Saccharomyces evolve to become a good brewer?
Trends in Genetics
(2006) - et al.
Identification of common molecular subsequences
Journal of Molecular Biology
(1981) - et al.
The challenge of Brettanomyces in wine
LWT—Food Science and Technology
(2010) Information theory and extension of the maximum likelihood principle
- et al.
Using GeneWise in the Drosophila annotation experiment
Genome Research
(2000) - et al.
Fermentation characteristics of Dekkera bruxellensis strains
Applied Microbiology and Biotechnology
(2010) - et al.
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Bioinformatics
(2009) - et al.
Genome sequence of the recombinant protein production host Pichia pastoris
Nature Biotechnology
(2009)