Limits...
The recombination dynamics of Staphylococcus aureus inferred from spA gene.

Santos-Júnior CD, Veríssimo A, Costa J - BMC Microbiol. (2016)

Bottom Line: The alignment of SpA sequences enabled the clustering of several isoforms as a result of non-randomly distributed amino acid variations, located in two clusters of polymorphic sites in domains D to B and Xr (a).The detection of positive selection operating on spA combined with frequent non-synonymous mutations, domain duplication and frequent intragenic recombination events represent important mechanisms acting in the evolutionary adaptive mechanism promoting spA genetic plasticity.These findings argue that crucial allelic forms correlated with pathogenicity can be identified by sequences analysis enabling the design of more robust schemes.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Evolutionary Genetics, Federal University of São Carlos (UFSCar), São Paulo, Brazil.

ABSTRACT

Background: Given the role of spA as a pivotal virulence factor decisive for Staphylococcus aureus ability to escape from innate and adaptive immune responses, one can consider it as an object subject to adaptive evolution and that variations in spA may uncover pathogenicity variations.

Results: The population genetic structure was deduced from the extracellular domains of SpA gene sequence (domains A-E and the X-region) and compared to the MLST-analysis of 41 genetically diverse methicillin-resistant (MRSA) and methicillin-susceptible (MSSA) S. aureus strains. Incongruence between tree topologies was noticeable and in the inferred spA tree most MSSA isolates were clustered in a distinct group. Conversely, the distribution of strains according to their spA-type was not always congruent with the tree inferred from the complete spA gene foreseeing that spA is a mosaic gene composed of different segments exhibiting different evolutionary histories. Evidences of a network-like organization were identified through several conflicting phylogenetic signals and indeed several intragenic recombination events (within subdomains of the gene) were detected within and between CC's of MRSA strains. The alignment of SpA sequences enabled the clustering of several isoforms as a result of non-randomly distributed amino acid variations, located in two clusters of polymorphic sites in domains D to B and Xr (a). Nevertheless, evidences of cluster specific structural arrangements were detected reflecting alterations on specific residues with potential impact on S. aureus pathogenicity.

Conclusions: The detection of positive selection operating on spA combined with frequent non-synonymous mutations, domain duplication and frequent intragenic recombination events represent important mechanisms acting in the evolutionary adaptive mechanism promoting spA genetic plasticity. These findings argue that crucial allelic forms correlated with pathogenicity can be identified by sequences analysis enabling the design of more robust schemes.

No MeSH data available.


Related in: MedlinePlus

Unique recombination events detected on spA alignment. Each sequence is represented by a color and the recombination is evidenced by donor and is mapped onto the corresponding breaking point positions in the alignment. All analyses were evaluated with RDP and the most significant P value to support the findings are shown at Additional file 4: Table S1
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4940709&req=5

Fig5: Unique recombination events detected on spA alignment. Each sequence is represented by a color and the recombination is evidenced by donor and is mapped onto the corresponding breaking point positions in the alignment. All analyses were evaluated with RDP and the most significant P value to support the findings are shown at Additional file 4: Table S1

Mentions: The abovementioned results corroborate the occurrence of recombination events between and within distinct spA clusters. Indeed, evidences of individual recombination events were detected by two distinct approaches. Namely, GARD found evidences with statistical significance (p < 0.001, KH test) for at least 5 breaking-points, corroborated by Recco analysis from 1000 bootstraps. RDP analysis showed the same breaking-points with at least three different algorithms that were mapped into the corresponding ML phylogenetic tree (Fig. 5 and Additional file 4: Table S1).Fig. 5


The recombination dynamics of Staphylococcus aureus inferred from spA gene.

Santos-Júnior CD, Veríssimo A, Costa J - BMC Microbiol. (2016)

Unique recombination events detected on spA alignment. Each sequence is represented by a color and the recombination is evidenced by donor and is mapped onto the corresponding breaking point positions in the alignment. All analyses were evaluated with RDP and the most significant P value to support the findings are shown at Additional file 4: Table S1
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4940709&req=5

Fig5: Unique recombination events detected on spA alignment. Each sequence is represented by a color and the recombination is evidenced by donor and is mapped onto the corresponding breaking point positions in the alignment. All analyses were evaluated with RDP and the most significant P value to support the findings are shown at Additional file 4: Table S1
Mentions: The abovementioned results corroborate the occurrence of recombination events between and within distinct spA clusters. Indeed, evidences of individual recombination events were detected by two distinct approaches. Namely, GARD found evidences with statistical significance (p < 0.001, KH test) for at least 5 breaking-points, corroborated by Recco analysis from 1000 bootstraps. RDP analysis showed the same breaking-points with at least three different algorithms that were mapped into the corresponding ML phylogenetic tree (Fig. 5 and Additional file 4: Table S1).Fig. 5

Bottom Line: The alignment of SpA sequences enabled the clustering of several isoforms as a result of non-randomly distributed amino acid variations, located in two clusters of polymorphic sites in domains D to B and Xr (a).The detection of positive selection operating on spA combined with frequent non-synonymous mutations, domain duplication and frequent intragenic recombination events represent important mechanisms acting in the evolutionary adaptive mechanism promoting spA genetic plasticity.These findings argue that crucial allelic forms correlated with pathogenicity can be identified by sequences analysis enabling the design of more robust schemes.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Evolutionary Genetics, Federal University of São Carlos (UFSCar), São Paulo, Brazil.

ABSTRACT

Background: Given the role of spA as a pivotal virulence factor decisive for Staphylococcus aureus ability to escape from innate and adaptive immune responses, one can consider it as an object subject to adaptive evolution and that variations in spA may uncover pathogenicity variations.

Results: The population genetic structure was deduced from the extracellular domains of SpA gene sequence (domains A-E and the X-region) and compared to the MLST-analysis of 41 genetically diverse methicillin-resistant (MRSA) and methicillin-susceptible (MSSA) S. aureus strains. Incongruence between tree topologies was noticeable and in the inferred spA tree most MSSA isolates were clustered in a distinct group. Conversely, the distribution of strains according to their spA-type was not always congruent with the tree inferred from the complete spA gene foreseeing that spA is a mosaic gene composed of different segments exhibiting different evolutionary histories. Evidences of a network-like organization were identified through several conflicting phylogenetic signals and indeed several intragenic recombination events (within subdomains of the gene) were detected within and between CC's of MRSA strains. The alignment of SpA sequences enabled the clustering of several isoforms as a result of non-randomly distributed amino acid variations, located in two clusters of polymorphic sites in domains D to B and Xr (a). Nevertheless, evidences of cluster specific structural arrangements were detected reflecting alterations on specific residues with potential impact on S. aureus pathogenicity.

Conclusions: The detection of positive selection operating on spA combined with frequent non-synonymous mutations, domain duplication and frequent intragenic recombination events represent important mechanisms acting in the evolutionary adaptive mechanism promoting spA genetic plasticity. These findings argue that crucial allelic forms correlated with pathogenicity can be identified by sequences analysis enabling the design of more robust schemes.

No MeSH data available.


Related in: MedlinePlus