Study on Shigella virulence genes and development of molecular diagnostic tools

Abstract

Simple sequence repeats (SSRs) are a class of DNA sequences consisting of simple motif that are tandemly repeated at a locus. They are omnipresent in prokaryotes and eukaryotes, even in the smallest bacterial genomes, and are found anywhere in the genome in both protein-encoding and noncoding regions. In present study the whole genome sequences of 10 chromosomes and 7 plasmids, Genes Distributed by COGs, Pathogenicity islands, Pseudogenes, Plasmid virulence genes and chromosome virulence genes were downloaded in FASTA format from ftp://ncbi.nlm.nih.gov/genbank/genomes/ and SHIBASE for identifying abundance, distribution, composition of SSRs and determine difference between the observed and the expected tandem repeats in genome of the organisms. in this study. VNTR Loci and 1 MLVA locus have been selected for Molecular typing of Shigella flexneri 2a. The result obtained in the present study show that: (i) tandem repeats are widely distributed throughout the genomes (ii) SSRs are differentially distributed among coding and noncoding regions in investigated genomes. (iii) total frequency of SSRs innoncoding regions are higher than coding regions. (iv) in all investigated chromosomes ratio of Trinucleotide SSRs are much higher than randomized genome and Di nucleotide SSRs are lower.(v) Ratio of mononucleotide SSRs in real genome is higher than randomized genome in E.coli K12 , Sh.f 301 , S.saprophyticus , while it is lower in Sh.f 2457T, Sh.sonnei and M.tuberculosis and it is approximately same in M.leprae. (vi) Frequency of codon repetitions vary considerably depending on the type of encoded amino acid. (vii) SSR in Shigella pathogenesity islands are overrepresented rather than other gene clusters of Shigella. (viii) Amino acid repeats pattern and codon repeats frequency in Shigella islands is different with other gene clusters (ix) SSR is overrepresented in ipaH genes, mxi, spa, osp genes particularly plasmid ipaH genes.