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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

Estimates of both positive and purifying selection at each amino acid site of SpA calculated from the ratio of non-synonymous (Ka) to synonymous substitutions (Ks) [62]. Graphical display of selecton results with FirstGlance in Jmol where the Ka/Ks scores are colored-coded. Significant positive and purifying sites (P-value < 0.05) are colored in orange (color number 1) and magenta (color number 4), respectively
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Fig6: Estimates of both positive and purifying selection at each amino acid site of SpA calculated from the ratio of non-synonymous (Ka) to synonymous substitutions (Ks) [62]. Graphical display of selecton results with FirstGlance in Jmol where the Ka/Ks scores are colored-coded. Significant positive and purifying sites (P-value < 0.05) are colored in orange (color number 1) and magenta (color number 4), respectively

Mentions: Since the previously performed LRTs indicated the presence of positive selection in spA, an empirical Bayesian analysis was performed to determine the posterior probability for each codon site to be under positive selection. For that, each partition was individually submitted to Selecton to identify the codons under positive selection. The Ka/Ks ratio was used to estimate both positive and purifying selection at each amino-acid site [74, 75]. The result for each codon was translated into a color scale graphically depicted on Fig. 6. Analyzing the obtained results one can determine that not a single residue was found to be under positive selection within the SpA Ig binding domains and signal sequence, anticipating that these SpA domains are under a strong negative constraint. However, several red and pink-colored sites were present in the partitions of SpA comprising the X region, representing positively selected codons with high statistical significance (Fig. 6).Fig. 6


The recombination dynamics of Staphylococcus aureus inferred from spA gene.

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

Estimates of both positive and purifying selection at each amino acid site of SpA calculated from the ratio of non-synonymous (Ka) to synonymous substitutions (Ks) [62]. Graphical display of selecton results with FirstGlance in Jmol where the Ka/Ks scores are colored-coded. Significant positive and purifying sites (P-value < 0.05) are colored in orange (color number 1) and magenta (color number 4), respectively
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig6: Estimates of both positive and purifying selection at each amino acid site of SpA calculated from the ratio of non-synonymous (Ka) to synonymous substitutions (Ks) [62]. Graphical display of selecton results with FirstGlance in Jmol where the Ka/Ks scores are colored-coded. Significant positive and purifying sites (P-value < 0.05) are colored in orange (color number 1) and magenta (color number 4), respectively
Mentions: Since the previously performed LRTs indicated the presence of positive selection in spA, an empirical Bayesian analysis was performed to determine the posterior probability for each codon site to be under positive selection. For that, each partition was individually submitted to Selecton to identify the codons under positive selection. The Ka/Ks ratio was used to estimate both positive and purifying selection at each amino-acid site [74, 75]. The result for each codon was translated into a color scale graphically depicted on Fig. 6. Analyzing the obtained results one can determine that not a single residue was found to be under positive selection within the SpA Ig binding domains and signal sequence, anticipating that these SpA domains are under a strong negative constraint. However, several red and pink-colored sites were present in the partitions of SpA comprising the X region, representing positively selected codons with high statistical significance (Fig. 6).Fig. 6

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