<i>In silico</i> characterisation of the two-component system regulators of <i>Streptococcus pyogenes</i>

<div><p>Bacteria respond to environmental changes through the co-ordinated regulation of gene expression, often mediated by two-component regulatory systems (TCS). Group A <i>Streptococcus</i> (GAS), a bacterium which infects multiple human body sites and causes multiple diseases, possesses up to 14 TCS. In this study we examined genetic variation in the coding sequences and non-coding DNA upstream of these TCS as a method for evaluating relationships between different GAS <i>emm</i>-types, and potential associations with GAS disease. Twelve of the 14 TCS were present in 90% of the genomes examined. The length of the intergenic regions (IGRs) upstream of TCS coding regions varied from 39 to 345 nucleotides, with an average nucleotide diversity of 0.0064. Overall, IGR allelic variation was generally conserved with an <i>emm</i>-type. Subsequent phylogenetic analysis of concatenated sequences based on all TCS IGR sequences grouped genomes of the same <i>emm</i>-type together. However grouping with <i>emm</i>-pattern and <i>emm</i>-cluster-types was much weaker, suggesting epidemiological and functional properties associated with the latter are not due to evolutionary relatedness of <i>emm</i>-types. All <i>emm</i>5, <i>emm</i>6 and most of the <i>emm</i>18 genomes, all historically considered rheumatogenic <i>emm</i>-types clustered together, suggesting a shared evolutionary history. However <i>emm</i>1, <i>emm</i>3 and several <i>emm</i>18 genomes did not cluster within this group. These latter <i>emm</i>18 isolates were epidemiologically distinct from other <i>emm</i>18 genomes in study, providing evidence for local variation. <i>emm</i>-types associated with invasive disease or nephritogenicity also did not cluster together. Considering the TCS coding sequences (cds), correlation with <i>emm</i>-type was weaker than for the IGRs, and no strong correlation with disease was observed. Deletion of the malate transporter, <i>maeP</i>, was identified that serves as a putative marker for the <i>emm</i>89.0 subtype, which has been implicated in invasive outbreaks. A recombination-related, subclade-forming DNA motif was identified in the putative receiver domain of the Spy1556 response regulator that correlated with throat-associated <i>emm</i>-pattern-type A-C strains.</p>