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
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 5′ end of the DNA molecule is joined to an internal guanine base (G) residue of the RNA molecule by a unique 2′, 5′-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cholerae [10], Salmonella enterica serovar Typhimurium [5], V. parahaemolyticus and V. mimicus (Shimamoto T, 2003, unpublished data).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
References
[1]
K. Yamanaka, T. Shimamoto, S. Inouye, and M. Inouye, “Retrons,” in Mobile DNA II, N. L. Craig, R. Craigie, M. Gellert, and A. M. Lambowitz, Eds., pp. 784–795, ASM press, Washington, DC, USA, 2002.
[2]
H. M. Temin and S. Mizutani, “Viral RNA-dependent DNA polymerase: RNA-dependent DNA polymerase in virions of Rous sarcoma virus,” Nature, vol. 226, no. 5252, pp. 1211–1213, 1970.
[3]
B. C. Lampson, M. Inouye, and S. Inouye, “Reverse transcriptase with concomitant ribonuclease H activity in the cell-free synthesis of branched RNA-linked msDNA of Myxococcus xanthus,” Cell, vol. 56, no. 4, pp. 701–707, 1989.
[4]
B. C. Lampson, J. Sun, M. Y. Hsu, J. Vallejo-Ramirez, S. Inouye, and M. Inouye, “Reverse transcriptase in a clinical strain of Escherichia coli: production of branched RNA-linked msDNA,” Science, vol. 243, no. 4894, pp. 1033–1038, 1989.
[5]
A. M. Ahmed and T. Shimamoto, “msDNA-St85, a multicopy single-stranded DNA isolated from Salmonella enterica serovar Typhimurium LT2 with the genomic analysis of its retron,” FEMS Microbiology Letters, vol. 224, no. 2, pp. 291–297, 2003.
[6]
B. C. Lampson, M. Inouye, and S. Inouye, “Retrons, msDNA, and the bacterial genome,” Cytogenetic and Genome Research, vol. 110, no. 1–4, pp. 491–499, 2005.
[7]
T. Yee, T. Furuichi, S. Inouye, and M. Inouye, “Multicopy single-stranded DNA isolated from a Gram-negative bacterium, Myxococcus xanthus,” Cell, vol. 38, no. 1, pp. 203–209, 1984.
[8]
D. Lim, “Structure and biosynthesis of unbranched multi-copy single-stranded DNA by reverse transcriptase in a clinical Esscherichia coli isolate,” Molecular Microbiology, vol. 6, pp. 3531–3542, 1992.
[9]
T. M. O. Lima and D. Lim, “A novel retron that produces RNA-less msDNA in Escherichia coli using reverse transcriptase,” Plasmid, vol. 38, no. 1, pp. 25–33, 1997.
[10]
T. Shimamoto, M. Kobayashi, T. Tsuchiya et al., “A retroelement in Vibrio cholerae,” Molecular Microbiology, vol. 34, no. 3, pp. 631–632, 1999.
[11]
P. E. Chen, C. Cook, A. C. Stewart et al., “Genomic characterization of the Yersinia genus,” Genome Biology, vol. 11, no. 1, article R1, 2010.
[12]
J. D. Thompson, D. G. Higgins, and T. J. Gibson, “CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research, vol. 22, no. 22, pp. 4673–4680, 1994.
[13]
M. Hamada, H. Kiryu, K. Sato, T. Mituyama, and K. Asai, “Prediction of RNA secondary structure using generalized centroid estimators,” Bioinformatics, vol. 25, no. 4, pp. 465–473, 2009.
[14]
M. E. Mulligan, D. K. Hawley, R. Entriken, and W. R. Mcclure, “Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity,” Nucleic Acids Research, vol. 12, no. 1, pp. 789–800, 1984.
[15]
T. Maruyama, T. Gojobori, S. Aota, and T. Ikemura, “Codon usage tabulated from the GenBank genetic sequence data,” Nucleic acids research, vol. 14, supplement, pp. r151–197, 1986.
[16]
W. K. Maas, C. Wang, T. Lima, G. Zubay, and D. Lim, “Multicopy single-stranded DNAs with mismatched base pairs are mutagenic in Escherichia coli,” Molecular Microbiology, vol. 14, no. 3, pp. 437–441, 1994.
[17]
J. R. Mao, S. Inouye, and M. Inouye, “Enhancement of frame-shift mutation by the overproduction of msDNA in Escherichia coli,” FEMS Microbiology Letters, vol. 144, no. 1, pp. 109–115, 1996.
