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. 2012;7(1):e29626.
doi: 10.1371/journal.pone.0029626. Epub 2012 Jan 3.

Functional divergence in the genus Oenococcus as predicted by genome sequencing of the newly-described species, Oenococcus kitaharae

Anthony R Borneman  1 , Jane M McCarthy, Paul J Chambers, Eveline J Bartowsky
Affiliations

Functional divergence in the genus Oenococcus as predicted by genome sequencing of the newly-described species, Oenococcus kitaharae

Anthony R Borneman et al. PLoS One. 2012.

Abstract

Oenococcus kitaharae is only the second member of the genus Oenococcus to be identified and is the closest relative of the industrially important wine bacterium Oenococcus oeni. To provide insight into this new species, the genome of the type strain of O. kitaharae, DSM 17330, was sequenced. Comparison of the sequenced genomes of both species show that the genome of O. kitaharae DSM 17330 contains many genes with predicted functions in cellular defence (bacteriocins, antimicrobials, restriction-modification systems and a CRISPR locus) which are lacking in O. oeni. The two genomes also appear to differentially encode several metabolic pathways associated with amino acid biosynthesis and carbohydrate utilization and which have direct phenotypic consequences. This would indicate that the two species have evolved different survival techniques to suit their particular environmental niches. O. oeni has adapted to survive in the harsh, but predictable, environment of wine that provides very few competitive species. However O. kitaharae appears to have adapted to a growth environment in which biological competition provides a significant selective pressure by accumulating biological defence molecules, such as bacteriocins and restriction-modification systems, throughout its genome.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Circular representation of the chromosomal and plasmid replicons of Oenococcus kitaharae.
Tracks represent (from largest to smallest) plus strand ORFs (red), minus strand ORFs (blue), RNA (tRNA light green, rRNA dark green), %GC and GC skew. The location of the five, two-copy repeats that are present in the O. kitaharae genome are also shown (light blue bars). Each of the five repeat groups are connected by arcs with the associated level of homology between each repeat listed.
Figure 2
Figure 2. Evolutionary relationship of Oenococcus kitaharae and members of the LAB family.
(A) The distribution of BLAST best-hits by genus for each ORF predicted in the O. kitaharae genome. (B) Whole genome phylogenetic relationship between O. kitaharae and other LAB based upon a conserved group of 95 proteins.
Figure 3
Figure 3. Conservation of the Oenococcus kitaharae genome.
Homologs of each of the predicted O. kitaharae ORFs were sought from thirteen strains of LAB using BLAST and individual results are displayed for each strain color-coded by individual protein identity scores. In addition, an overall median identity was calculated by applying a sliding window of syntenic ORFs (n = 9, step = 1) to obtain a median percent identity for each strain with regions of low conservation highlighted (grey shading). Both the average GC percentage (5000 bp window, 200 bp step) and alien hunter foreign DNA likelihood scores across the genome are also shown to compare areas of low sequence conservation with possible instances of HGT. The position of sequences associated with either toxin-antitoxin modules, phage integrase proteins, conjugative transposons or the CRISPR array are also shown.
Figure 4
Figure 4. Schematic representation of two putative conjugative transposons present in the Oenococcus kitaharae genome.
The ORFs present in each genomic element are colour coded by predicted function. The conserved conjugation-associated region present in the centre of each element is also highlighted (red shading).
Figure 5
Figure 5. The malate operon of Oenococcus kitaharae.
(A) Schematic representation of the genomic region surrounding the non-functional malate operon in O. kitaharae. O. kitaharae ORFs (blue) are shown above their orthologs from O. oeni with regions of microsynteny indicated by the differential shading of the O. oeni ORFs (green, red, yellow, pink and orange). (B) Partial alignment of the ORF which encodes malate enzyme O. oeni (red) with the homologous region from O. kitaharae (blue). Both the DNA and predicted protein sequences are listed.
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