Comparative genomics reveals genus specific encoding of amino acids by tri-nucleotide SSRs in human pathogenic Streptococcus and Staphylococcus bacteria

Abstract

Pathogenic bacteria use phase variation of surface molecules and other characteristics as a significant adaptation mechanism. Repetitive sequences made up of numerous identical repeat units can be found in many phase variable genes. Here, we investigated the frequency and distribution of long-SSRs (Simple Sequence Repeats) in 15 human pathogenic Staphylococcus, Streptococcus, and Enterococcus bacteria. Long-SSRs were found to be distributed differently in the genic and inter-genic sequences. In the genic sequences, 61.3 SSRs were discovered on average, while 16.2 SSRs were found in the intergenic regions. Staphylococcus exhibited the highest frequency of SSRs, followed by Enterococcus, and Streptococcus had the lowest frequency of SSRs. Higher A + T content was found to be the best predictor of long-SSR in these human pathogens. Tetranucleotide repeats predominated in inte-rgenic regions, while trinucleotide repeats were in the majority in genic regions. In human pathogenic Streptococcus and Staphylococcus bacteria, genus-specific encoding of amino acids by tri-nucleotide SSRs was observed. Based on the presence of SSRs in housekeeping genes, a genetic relationship between these human pathogenic bacteria was constructed and compared to a phylogeny based on the 16 S ribosomal RNA gene.