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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

Neighbor-net phylogenetic network showing the relationships among S. aureus strains. The split graph was estimated with SplitsTree4 from p-distances of the spA sequence alignment based on the Jukes–Cantor method. Strains highlighted according to their MLST-based CC’s (Table 1 and Fig. 1), Color code: CC8 (yellow circles), CC15 (green circles), CC1 (purple circles) and CC5 (blue circles). The relations between and within strains are illustrated by weighted splits with different colors representing simultaneously both grouping in the data and evolutionary distances between taxa, highlighting conflicting signals or alternative phylogenetic histories (recombination or gene transfer) in spA molecular evolution. MSSA strains are boxed
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Fig4: Neighbor-net phylogenetic network showing the relationships among S. aureus strains. The split graph was estimated with SplitsTree4 from p-distances of the spA sequence alignment based on the Jukes–Cantor method. Strains highlighted according to their MLST-based CC’s (Table 1 and Fig. 1), Color code: CC8 (yellow circles), CC15 (green circles), CC1 (purple circles) and CC5 (blue circles). The relations between and within strains are illustrated by weighted splits with different colors representing simultaneously both grouping in the data and evolutionary distances between taxa, highlighting conflicting signals or alternative phylogenetic histories (recombination or gene transfer) in spA molecular evolution. MSSA strains are boxed

Mentions: In order to determine the effect of recombination and horizontal gene transfer events into the phylogenetic relationships of S. aureus strains a Neighbor-Net analysis (Fig. 4) has been constructed. Evidences of a network-like evolution were clear, indicating lack of tree-like relationship between spA sequences. Nevertheless, it is still possible to reconstruct the previously defined groups from the ML phylogenetic analysis (Fig. 2b). The clusters previously identified were quite robust, presenting a complex diversifying history. Moreover, the divergence of clusters spA-I and spA-III from cluster spA-II, only group with MSSA strains, was noticeable (Fig. 4).Fig. 4


The recombination dynamics of Staphylococcus aureus inferred from spA gene.

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

Neighbor-net phylogenetic network showing the relationships among S. aureus strains. The split graph was estimated with SplitsTree4 from p-distances of the spA sequence alignment based on the Jukes–Cantor method. Strains highlighted according to their MLST-based CC’s (Table 1 and Fig. 1), Color code: CC8 (yellow circles), CC15 (green circles), CC1 (purple circles) and CC5 (blue circles). The relations between and within strains are illustrated by weighted splits with different colors representing simultaneously both grouping in the data and evolutionary distances between taxa, highlighting conflicting signals or alternative phylogenetic histories (recombination or gene transfer) in spA molecular evolution. MSSA strains are boxed
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig4: Neighbor-net phylogenetic network showing the relationships among S. aureus strains. The split graph was estimated with SplitsTree4 from p-distances of the spA sequence alignment based on the Jukes–Cantor method. Strains highlighted according to their MLST-based CC’s (Table 1 and Fig. 1), Color code: CC8 (yellow circles), CC15 (green circles), CC1 (purple circles) and CC5 (blue circles). The relations between and within strains are illustrated by weighted splits with different colors representing simultaneously both grouping in the data and evolutionary distances between taxa, highlighting conflicting signals or alternative phylogenetic histories (recombination or gene transfer) in spA molecular evolution. MSSA strains are boxed
Mentions: In order to determine the effect of recombination and horizontal gene transfer events into the phylogenetic relationships of S. aureus strains a Neighbor-Net analysis (Fig. 4) has been constructed. Evidences of a network-like evolution were clear, indicating lack of tree-like relationship between spA sequences. Nevertheless, it is still possible to reconstruct the previously defined groups from the ML phylogenetic analysis (Fig. 2b). The clusters previously identified were quite robust, presenting a complex diversifying history. Moreover, the divergence of clusters spA-I and spA-III from cluster spA-II, only group with MSSA strains, was noticeable (Fig. 4).Fig. 4

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