%0 Journal Article
%T A Novel msDNA (Multicopy Single-Stranded DNA) Strain Present in Yersinia frederiksenii ATCC 33641 Contig01029 Enteropathogenic Bacteria with the Genomic Analysis of It's Retron
%A Rasel Das
%A Tadashi Shimamoto
%A Md. Arifuzzaman
%J Journal of Pathogens
%D 2011
%I Hindawi Publishing Corporation
%R 10.4061/2011/693769
%X Retron is a retroelement that encodes msDNA (multicopy single-stranded DNA) which was significantly found mainly in Gram-negative pathogenic bacteria. We screened Yersinia frederiksenii ATCC 33641 contig01029 for the presence of retroelement by using bioinformatics tools and characterized a novel retron-Yf79 on the chromosome that encodes msDNA-Yf79. In this study, we perceived that, the codon usage of retron-Yf79 were noteworthy different from those of the Y. frederiksenii genome. It demonstrates that, the retron-Yf79 was a foreign DNA element and integrated into this organism genome during their evolution. In addition to this, we have observed a transposase gene which is located just downstream of retron-Yf79. So, the enzyme might be responsible for the transposition of this novel retron element. 1. Introduction For the past 21 years, it has been shown that some pathogenic Gram-negative bacteria strains contain genetic elements called retrons. Retron is a retroelement consisting of msr, which encodes the RNA part of msDNA, msd, which encodes the DNA part of msDNA, and the ret gene for reverse transcriptase (RT) [1]. The reverse transcriptase (RT) was originally discovered in virus [2] as an essential enzyme for the replication of retroviruses. Since the discovery of RT in myxobacteria [3] and Escherichia coli [4] an intriguing question have been raised concerning its origin and function in the prokaryotes [5]. The msDNA (multicopy single-stranded DNA) is composed of a small, single-stranded DNA, linked to a small, single-stranded RNA molecule. The 5กไ end of the DNA molecule is joined to an internal guanine base (G) residue of the RNA molecule by a unique 2กไ, 5กไ-phosphodiester bond [6]. Since msDNA was originally discovered in the Gram-negative soil bacterium, Myxococcus xanthus [7] it was also isolated from aggregative adherence E. coli (AAEC) [8], a classical enteropathogenic E. coli (EPEC) [9] and more recently from Vibrio cholerae [10], Salmonella enterica serovar Typhimurium [5], V. parahaemolyticus and V. mimicus (Shimamoto T, 2003, unpublished data). Hence, RT might have a role in diversification of pathogenic bacteria genomes. Although msDNAs have been isolated over the pathogenic Gram-negative bacteria, in this study we characterized a novel retron region by screening the complete genome sequence of Yersinia frederiksenii [11] which encodes msr, msd with a ret gene by best hits RT sequence similarity along with V. cholerae, V. parahaemolyticus and S. Typhimurium. These provide insight into the important roles of this mysterious element in
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