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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

Molecular phylogenetic analysis by maximum likelihood method of S. aureus strains from a MLST concatenated genes and bspA gene. Bootstrap support values (1,000 replicates) for nodes higher than 50 % are indicated next to the corresponding node. Scale bar, 1 inferred amino acid substitutions per 100 nucleotides. CC’s and spA clusters are indicated next to corresponding strain. MSSA strains are boxed
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Fig2: Molecular phylogenetic analysis by maximum likelihood method of S. aureus strains from a MLST concatenated genes and bspA gene. Bootstrap support values (1,000 replicates) for nodes higher than 50 % are indicated next to the corresponding node. Scale bar, 1 inferred amino acid substitutions per 100 nucleotides. CC’s and spA clusters are indicated next to corresponding strain. MSSA strains are boxed

Mentions: In order to identify the mechanisms underlying spA molecular gene evolution, ML phylogenetic trees were obtained from the alignment of extracellular domains of spA locus and, for comparison purposes, from the MLST-concatenated alignment (Fig. 2). The MLST-concatenated inferred ML tree was in accordance with previously obtained eBURST analysis since each CC tends to cluster together (Fig. 2a). Conversely, the distribution of strains according to their spA-type was not always congruent with the topology of ML tree inferred from the spA sequences (Fig. 2b). Namely, strains Mu50, N315 and Mu, and strains ECTR2, JH1 and JH9, identified as spA-t002, were split into distinct clusters, respectively. While the Ridom SpaServer database [23] assigns spA sequences to distinct spA types according to variation in the tandem repeat region X from spA, the ML tree was inferred from complete extracellular domains of spA sequence. All other S. aureus strains that shared the same spA-type tend to cluster together and were distinct from all other groups (Fig. 2b).Fig. 2


The recombination dynamics of Staphylococcus aureus inferred from spA gene.

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

Molecular phylogenetic analysis by maximum likelihood method of S. aureus strains from a MLST concatenated genes and bspA gene. Bootstrap support values (1,000 replicates) for nodes higher than 50 % are indicated next to the corresponding node. Scale bar, 1 inferred amino acid substitutions per 100 nucleotides. CC’s and spA clusters are indicated next to corresponding strain. MSSA strains are boxed
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Molecular phylogenetic analysis by maximum likelihood method of S. aureus strains from a MLST concatenated genes and bspA gene. Bootstrap support values (1,000 replicates) for nodes higher than 50 % are indicated next to the corresponding node. Scale bar, 1 inferred amino acid substitutions per 100 nucleotides. CC’s and spA clusters are indicated next to corresponding strain. MSSA strains are boxed
Mentions: In order to identify the mechanisms underlying spA molecular gene evolution, ML phylogenetic trees were obtained from the alignment of extracellular domains of spA locus and, for comparison purposes, from the MLST-concatenated alignment (Fig. 2). The MLST-concatenated inferred ML tree was in accordance with previously obtained eBURST analysis since each CC tends to cluster together (Fig. 2a). Conversely, the distribution of strains according to their spA-type was not always congruent with the topology of ML tree inferred from the spA sequences (Fig. 2b). Namely, strains Mu50, N315 and Mu, and strains ECTR2, JH1 and JH9, identified as spA-t002, were split into distinct clusters, respectively. While the Ridom SpaServer database [23] assigns spA sequences to distinct spA types according to variation in the tandem repeat region X from spA, the ML tree was inferred from complete extracellular domains of spA sequence. All other S. aureus strains that shared the same spA-type tend to cluster together and were distinct from all other groups (Fig. 2b).Fig. 2

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