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Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways.

Borneman AR, McCarthy JM, Chambers PJ, Bartowsky EJ - BMC Genomics (2012)

Bottom Line: These benefits are realised primarily through catalysing malolactic fermentation, but also through imparting other positive sensory properties.While any single strain of O. oeni was shown to contain around 1800 protein-coding genes, in-depth comparative annotation based on genomic synteny and protein orthology identified over 2800 orthologous open reading frames that comprise the pan genome of this species, and less than 1200 genes that make up the conserved genomic core present in all of the strains.This data is vital to understanding and harnessing the phenotypic variation present in this economically-important species.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Australian Wine Research Institute, Glen Osmond, South Australia 5064, Australia. anthony.borneman@awri.com.au

ABSTRACT

Background: Oenococcus oeni, a member of the lactic acid bacteria, is one of a limited number of microorganisms that not only survive, but actively proliferate in wine. It is also unusual as, unlike the majority of bacteria present in wine, it is beneficial to wine quality rather than causing spoilage. These benefits are realised primarily through catalysing malolactic fermentation, but also through imparting other positive sensory properties. However, many of these industrially-important secondary attributes have been shown to be strain-dependent and their genetic basis it yet to be determined.

Results: In order to investigate the scale and scope of genetic variation in O. oeni, we have performed whole-genome sequencing on eleven strains of this bacterium, bringing the total number of strains for which genome sequences are available to fourteen. While any single strain of O. oeni was shown to contain around 1800 protein-coding genes, in-depth comparative annotation based on genomic synteny and protein orthology identified over 2800 orthologous open reading frames that comprise the pan genome of this species, and less than 1200 genes that make up the conserved genomic core present in all of the strains. The expansion of the pan genome relative to the coding potential of individual strains was shown to be due to the varied presence and location of multiple distinct bacteriophage sequences and also in various metabolic functions with potential impacts on the industrial performance of this species, including cell wall exopolysaccharide biosynthesis, sugar transport and utilisation and amino acid biosynthesis.

Conclusions: By providing a large cohort of sequenced strains, this study provides a broad insight into the genetic variation present within O. oeni. This data is vital to understanding and harnessing the phenotypic variation present in this economically-important species.

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Horizontal gene transfer in O. oeni. A. The probability of genomic regions being present due to horizontal gene transfer (HGT). A region of high probability of strain-specific HGT is indicated (black arrow). B. Maximum-likelyhood phylogeny of a horizontally-acquired transmembrane protein within the region highlighted in (A). Bacterial genera are indicated by colored shading (Oenococcus spp., blue; Lactobacillus spp., pink; Weissella spp., green; Pediococcus spp., yellow). C. Homology between O. oeni and Lactococcus spp. A representative protein for each pan_genome locus was used in homology searches against the combined predicted protein sequences from each Lactococcus spp. genome available in Genbank. Average identity values were calculated using a 10 ORF sliding window (blue line). Regions predicted to be result of HGT in which >5 adjacent ORFs displayed >90% amino acid identity between an O. oeni protein and a protein from Lactococcus spp. are also indicated (red boxes).
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Figure 2: Horizontal gene transfer in O. oeni. A. The probability of genomic regions being present due to horizontal gene transfer (HGT). A region of high probability of strain-specific HGT is indicated (black arrow). B. Maximum-likelyhood phylogeny of a horizontally-acquired transmembrane protein within the region highlighted in (A). Bacterial genera are indicated by colored shading (Oenococcus spp., blue; Lactobacillus spp., pink; Weissella spp., green; Pediococcus spp., yellow). C. Homology between O. oeni and Lactococcus spp. A representative protein for each pan_genome locus was used in homology searches against the combined predicted protein sequences from each Lactococcus spp. genome available in Genbank. Average identity values were calculated using a 10 ORF sliding window (blue line). Regions predicted to be result of HGT in which >5 adjacent ORFs displayed >90% amino acid identity between an O. oeni protein and a protein from Lactococcus spp. are also indicated (red boxes).

Mentions: In order to determine if any of the strain-specific genes in the O. oeni genome were the result of horizontal gene transfer (HGT), the genome of each strain was interrogated for regions with an increased probability of being horizontally-acquired [18]. While there were numerous regions that exceeded the threshold for being potentially horizontally acquired (Additional file 4), one region, present in at least seven of the strains, had a very high probability of resulting from HGT , (Figure2A). This region was subsequently shown to contain evidence of two independent HGT events (separated by ~65 kb) involving IS element insertions that appear to have been horizontally transferred from Lactobacillus spp. The first of these (pan_genome loci 1725–1734) appears to be associated with an IS30 element insertion that was first discovered in AWRIB429 [11,19]. The second region (pan_genome loci 1802–1816) is associated with an insertion event within an ORF that encodes an arginine deaminase (OEOE_1118 of PSU-1). The last 3.5 kb of this 7.5 kb fragment has ~99% identity to a large portion of a genetic element that has been characterised in beer-spoilage strains of Lactobacillus spp. and Pedicoccus spp. [20]. This element has been postulated to be horizontally-transferred and, due to the presence of the HorC efflux pump, to provide resistance to antibacterial compounds present in hops [21]. However, the portion of the element present in strains of O. oeni lacks the horC gene, while still encoding the glycosyltransferase, an integral membrane protein, and a cell wall teichoic acid glycosylation protein that are present in the 3’ half of the element. As expected for a HGT event, these proteins share a higher than expected degree of relatedness compared to the evolutionary distance that separates Oenococcus spp. and Lactobacillus spp. (Figure2B, Additional file 2).


Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways.

Borneman AR, McCarthy JM, Chambers PJ, Bartowsky EJ - BMC Genomics (2012)

Horizontal gene transfer in O. oeni. A. The probability of genomic regions being present due to horizontal gene transfer (HGT). A region of high probability of strain-specific HGT is indicated (black arrow). B. Maximum-likelyhood phylogeny of a horizontally-acquired transmembrane protein within the region highlighted in (A). Bacterial genera are indicated by colored shading (Oenococcus spp., blue; Lactobacillus spp., pink; Weissella spp., green; Pediococcus spp., yellow). C. Homology between O. oeni and Lactococcus spp. A representative protein for each pan_genome locus was used in homology searches against the combined predicted protein sequences from each Lactococcus spp. genome available in Genbank. Average identity values were calculated using a 10 ORF sliding window (blue line). Regions predicted to be result of HGT in which >5 adjacent ORFs displayed >90% amino acid identity between an O. oeni protein and a protein from Lactococcus spp. are also indicated (red boxes).
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Figure 2: Horizontal gene transfer in O. oeni. A. The probability of genomic regions being present due to horizontal gene transfer (HGT). A region of high probability of strain-specific HGT is indicated (black arrow). B. Maximum-likelyhood phylogeny of a horizontally-acquired transmembrane protein within the region highlighted in (A). Bacterial genera are indicated by colored shading (Oenococcus spp., blue; Lactobacillus spp., pink; Weissella spp., green; Pediococcus spp., yellow). C. Homology between O. oeni and Lactococcus spp. A representative protein for each pan_genome locus was used in homology searches against the combined predicted protein sequences from each Lactococcus spp. genome available in Genbank. Average identity values were calculated using a 10 ORF sliding window (blue line). Regions predicted to be result of HGT in which >5 adjacent ORFs displayed >90% amino acid identity between an O. oeni protein and a protein from Lactococcus spp. are also indicated (red boxes).
Mentions: In order to determine if any of the strain-specific genes in the O. oeni genome were the result of horizontal gene transfer (HGT), the genome of each strain was interrogated for regions with an increased probability of being horizontally-acquired [18]. While there were numerous regions that exceeded the threshold for being potentially horizontally acquired (Additional file 4), one region, present in at least seven of the strains, had a very high probability of resulting from HGT , (Figure2A). This region was subsequently shown to contain evidence of two independent HGT events (separated by ~65 kb) involving IS element insertions that appear to have been horizontally transferred from Lactobacillus spp. The first of these (pan_genome loci 1725–1734) appears to be associated with an IS30 element insertion that was first discovered in AWRIB429 [11,19]. The second region (pan_genome loci 1802–1816) is associated with an insertion event within an ORF that encodes an arginine deaminase (OEOE_1118 of PSU-1). The last 3.5 kb of this 7.5 kb fragment has ~99% identity to a large portion of a genetic element that has been characterised in beer-spoilage strains of Lactobacillus spp. and Pedicoccus spp. [20]. This element has been postulated to be horizontally-transferred and, due to the presence of the HorC efflux pump, to provide resistance to antibacterial compounds present in hops [21]. However, the portion of the element present in strains of O. oeni lacks the horC gene, while still encoding the glycosyltransferase, an integral membrane protein, and a cell wall teichoic acid glycosylation protein that are present in the 3’ half of the element. As expected for a HGT event, these proteins share a higher than expected degree of relatedness compared to the evolutionary distance that separates Oenococcus spp. and Lactobacillus spp. (Figure2B, Additional file 2).

Bottom Line: These benefits are realised primarily through catalysing malolactic fermentation, but also through imparting other positive sensory properties.While any single strain of O. oeni was shown to contain around 1800 protein-coding genes, in-depth comparative annotation based on genomic synteny and protein orthology identified over 2800 orthologous open reading frames that comprise the pan genome of this species, and less than 1200 genes that make up the conserved genomic core present in all of the strains.This data is vital to understanding and harnessing the phenotypic variation present in this economically-important species.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Australian Wine Research Institute, Glen Osmond, South Australia 5064, Australia. anthony.borneman@awri.com.au

ABSTRACT

Background: Oenococcus oeni, a member of the lactic acid bacteria, is one of a limited number of microorganisms that not only survive, but actively proliferate in wine. It is also unusual as, unlike the majority of bacteria present in wine, it is beneficial to wine quality rather than causing spoilage. These benefits are realised primarily through catalysing malolactic fermentation, but also through imparting other positive sensory properties. However, many of these industrially-important secondary attributes have been shown to be strain-dependent and their genetic basis it yet to be determined.

Results: In order to investigate the scale and scope of genetic variation in O. oeni, we have performed whole-genome sequencing on eleven strains of this bacterium, bringing the total number of strains for which genome sequences are available to fourteen. While any single strain of O. oeni was shown to contain around 1800 protein-coding genes, in-depth comparative annotation based on genomic synteny and protein orthology identified over 2800 orthologous open reading frames that comprise the pan genome of this species, and less than 1200 genes that make up the conserved genomic core present in all of the strains. The expansion of the pan genome relative to the coding potential of individual strains was shown to be due to the varied presence and location of multiple distinct bacteriophage sequences and also in various metabolic functions with potential impacts on the industrial performance of this species, including cell wall exopolysaccharide biosynthesis, sugar transport and utilisation and amino acid biosynthesis.

Conclusions: By providing a large cohort of sequenced strains, this study provides a broad insight into the genetic variation present within O. oeni. This data is vital to understanding and harnessing the phenotypic variation present in this economically-important species.

Show MeSH
Related in: MedlinePlus