Journal of Proteomics & Bioinformatics
Open Access
ISSN: 0974-276X
ISSN: 0974-276X
Rasel Das, Tadashi Shimamoto and Md. Arifuzzaman
Posters: J Proteomics Bioinform
Yersinia frederiksenii is a Gram negative enteropathogenic bacterium and is reclassified from Yersinia enterocolitica. It causes enterocolitis with other diseases in human. On the other hand, retron DNAs are commonly associated with prophage DNA and are found in the genomes of a wide variety of different pathogenic bacteria like in (Vibrio cholerae, Vibrio parahaemolyticus, Salmonella typhimurium, Escherichia coli species and also in other pathogenic bacteria). The retron reverse transcriptase (RT) is used to synthesize a strange msDNA (multicopy single-stranded DNA). This msDNA is a satellite DNA and is composed of a small, single-stranded DNA, linked to a small, single-stranded RNA molecule by a unique 2?, 5?- Phosphodiester bond which is synthesized by the bacterial reverse transcriptase (RT). The present study was undertaken to investigate whether the enteropathogenic Yersinia frederiksenii may contain such type of novel retron element in their genome sequences. This study has assigned the retron-Yf79 in Yersinia frederiksenii ATCC 33641 Contig01029, together with its codon bias and G+C content which have analyzed by using Bioinformatics tools. The region (retron-Yf79) required for the biosynthesis of a branched RNA-linked msDNA-Yf79 and the element consist of a unique 2.8 kilo base sequence, contain genes for msDNA-RNA (msd,msr), a gene (Yfred0001_42830) for reverse transcriptase (RT) and a gene (Yfred0001_42840) for an open reading frame (ORF-541), consisting of 541 amino acids. The conserved guanine (G) residue at position 12 in RNA part of msDNA-Yf79 has also been found in msDNA-RNA complexes and is essential for branch formation. The RT-Yf79 (reverse transcriptase in Yersinia frederiksenii) and open reading frame-541 (ORF-541) genes used AAA codon for lysine with a frequency of 55% and 74%, respectively whereas Yersinia frederiksenii genome itself only used AAA codon for lysine with a frequency of 20% of the time. Subsequently we perceived that, the (G+C) content of RT-Yf79 and (G+C) content of open reading frame-541 (ORF-541) genes was same (41%) indicating that, the open reading frame-541 (ORF-541) was a member of this retron (retron-Yf79) element. Whereas, the general (G+C) content of the Yersinia frederiksenii ATCC 33641 contig01029 genome was 45 %. The codon bias, G+C content, phylogenetic analysis of reverse transcriptase (RTs) and also the 16S rRNA from pathogenic bacteria revealed that, this retron (retron-Yf79) was a foreign DNA element. It might have integrated at once upon a time during their evolution through the vertical descent rather than the horizontal transformations by a mechanism related to phage recognition and transposition. Because, it contains a transposase gene located just downstream of retron-Yf79 element which might participate in transposition of this novel retronelement. All of these results document evidence, in support of the importance of retron element towards the expression of pathogenic potential of Yersinia frederiksenii.