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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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Bacteriophage diversity. A. Sites of bacteriophage integration throughout the O. oeni genome are indicated by along with the name of the specific tRNA that represents the bacteriophage attachment site. Other tRNA genes predicted to be present in the O. oeni genome are also indicated (half-height black lines). Full bacteriophage elements (pink boxes) are characterised by the presence of both integrase (int) and lytic (lys) enzymes while bacteriophage fragments (green boxes) generally only contain int ORFs. All elements are drawn to scale. B. Maximum-likelyhood phylogenetic analysis of bacteriophage int proteins from O. oeni. Colored shading is used to group proteins based on their site of integration and to define their origin as either being from a full bacteriophage element (pink) or a bacteriophage fragment (green). Previously identified phage protein sequences are indicated in bold. C. Maximum-likelyhood phylogenetic analysis of bacteriophage lys proteins from O. oeni. Shading is identical to that in part B.
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Figure 3: Bacteriophage diversity. A. Sites of bacteriophage integration throughout the O. oeni genome are indicated by along with the name of the specific tRNA that represents the bacteriophage attachment site. Other tRNA genes predicted to be present in the O. oeni genome are also indicated (half-height black lines). Full bacteriophage elements (pink boxes) are characterised by the presence of both integrase (int) and lytic (lys) enzymes while bacteriophage fragments (green boxes) generally only contain int ORFs. All elements are drawn to scale. B. Maximum-likelyhood phylogenetic analysis of bacteriophage int proteins from O. oeni. Colored shading is used to group proteins based on their site of integration and to define their origin as either being from a full bacteriophage element (pink) or a bacteriophage fragment (green). Previously identified phage protein sequences are indicated in bold. C. Maximum-likelyhood phylogenetic analysis of bacteriophage lys proteins from O. oeni. Shading is identical to that in part B.

Mentions: One of the most striking variations in intra-specific coding potential across the O. oeni strains was in the number and position of temperate bacteriophage integrations (Figure3). O. oeni has been shown previously to harbour at least four separate bacteriophages that integrate through tRNA-associated attachment sites (fOgPSU1, fOg44, fOg30 and Φ10MC) [22-25]. In this study, a total of six different tRNAs were shown to potentially be involved in the integration of bacteriophage, with four shown to be current sites of insertion of full-length and presumably functional bacteriophage (Figure3A). The remaining two tRNAs (plus a third in AWRIB129) contained bacteriophage remnants and may represent sites at which integration and then subsequent excision of a bacteriophage has occurred. It was also apparent that for two of the insertion events (at OEOE_t0506 in AWRIB548 and OEOE_t685 in AWRIB304), the entire bacteriophage sequence had been tandemly duplicated at the integration site.


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)

Bacteriophage diversity. A. Sites of bacteriophage integration throughout the O. oeni genome are indicated by along with the name of the specific tRNA that represents the bacteriophage attachment site. Other tRNA genes predicted to be present in the O. oeni genome are also indicated (half-height black lines). Full bacteriophage elements (pink boxes) are characterised by the presence of both integrase (int) and lytic (lys) enzymes while bacteriophage fragments (green boxes) generally only contain int ORFs. All elements are drawn to scale. B. Maximum-likelyhood phylogenetic analysis of bacteriophage int proteins from O. oeni. Colored shading is used to group proteins based on their site of integration and to define their origin as either being from a full bacteriophage element (pink) or a bacteriophage fragment (green). Previously identified phage protein sequences are indicated in bold. C. Maximum-likelyhood phylogenetic analysis of bacteriophage lys proteins from O. oeni. Shading is identical to that in part B.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3472311&req=5

Figure 3: Bacteriophage diversity. A. Sites of bacteriophage integration throughout the O. oeni genome are indicated by along with the name of the specific tRNA that represents the bacteriophage attachment site. Other tRNA genes predicted to be present in the O. oeni genome are also indicated (half-height black lines). Full bacteriophage elements (pink boxes) are characterised by the presence of both integrase (int) and lytic (lys) enzymes while bacteriophage fragments (green boxes) generally only contain int ORFs. All elements are drawn to scale. B. Maximum-likelyhood phylogenetic analysis of bacteriophage int proteins from O. oeni. Colored shading is used to group proteins based on their site of integration and to define their origin as either being from a full bacteriophage element (pink) or a bacteriophage fragment (green). Previously identified phage protein sequences are indicated in bold. C. Maximum-likelyhood phylogenetic analysis of bacteriophage lys proteins from O. oeni. Shading is identical to that in part B.
Mentions: One of the most striking variations in intra-specific coding potential across the O. oeni strains was in the number and position of temperate bacteriophage integrations (Figure3). O. oeni has been shown previously to harbour at least four separate bacteriophages that integrate through tRNA-associated attachment sites (fOgPSU1, fOg44, fOg30 and Φ10MC) [22-25]. In this study, a total of six different tRNAs were shown to potentially be involved in the integration of bacteriophage, with four shown to be current sites of insertion of full-length and presumably functional bacteriophage (Figure3A). The remaining two tRNAs (plus a third in AWRIB129) contained bacteriophage remnants and may represent sites at which integration and then subsequent excision of a bacteriophage has occurred. It was also apparent that for two of the insertion events (at OEOE_t0506 in AWRIB548 and OEOE_t685 in AWRIB304), the entire bacteriophage sequence had been tandemly duplicated at the integration site.

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