1887

Abstract

Multi-copy single-stranded DNA (msDNA) is composed of covalently bound single-stranded DNA and RNA, and synthesized by retron-encoded reverse transcriptase. msDNA-synthesizing systems are thought to be a recent acquisition by because, to date, only seven types of msDNA, which differ markedly in their primary nucleotide sequences, have been found in a small subset of strains. The wide use of in molecular research means that it is important to understand more about these stable, covalently bound, single-stranded DNA or RNA compounds. The present review provides insights into the molecular biosynthesis, distribution and function of msDNA to raise awareness about these special molecules.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.000563
2017-12-01
2020-01-27
Loading full text...

Full text loading...

/deliver/fulltext/micro/163/12/1735.html?itemId=/content/journal/micro/10.1099/mic.0.000563&mimeType=html&fmt=ahah

References

  1. Varmus HE. Reverse transcription in bacteria. Cell 1989;56:721–724 [CrossRef][PubMed]
    [Google Scholar]
  2. Temin HM. Reverse transcriptases. Retrons in bacteria. Nature 1989;339:254–255 [CrossRef][PubMed]
    [Google Scholar]
  3. Inouye M. The first demonstration of the existence of reverse transcriptases in bacteria. Gene 2017;597:76–77 [CrossRef][PubMed]
    [Google Scholar]
  4. Inouye M, Inouye S. msDNA and bacterial reverse transcriptase. Annu Rev Microbiol 1991;45:163–186 [CrossRef][PubMed]
    [Google Scholar]
  5. Dhundale AR, Furuichi T, Inouye S, Inouye M. Distribution of multicopy single-stranded DNA among myxobacteria and related species. J Bacteriol 1985;164:914–917[PubMed]
    [Google Scholar]
  6. Elfenbein JR, Knodler LA, Nakayasu ES, Ansong C, Brewer HM et al. Multicopy single-stranded DNA directs intestinal colonization of enteric pathogens. PLoS Genet 2015;11:e1005472 [CrossRef][PubMed]
    [Google Scholar]
  7. Yoo W, Lim D, Kim S. Compiling multicopy single-stranded dna sequences from bacterial genome sequences. Genomics Inform 2016;14:29–33 [CrossRef][PubMed]
    [Google Scholar]
  8. Yee T, Furuichi T, Inouye S, Inouye M. Multicopy single-stranded DNA isolated from a gram-negative bacterium, Myxococcus xanthus. Cell 1984;38:203–209 [CrossRef][PubMed]
    [Google Scholar]
  9. Dhundale A, Lampson B, Furuichi T, Inouye M, Inouye S. Structure of msDNA from Myxococcus xanthus: evidence for a long, self-annealing RNA precursor for the covalently linked, branched RNA. Cell 1987;51:1105–1112 [CrossRef][PubMed]
    [Google Scholar]
  10. Lim D, Maas WK. Reverse transcriptase-dependent synthesis of a covalently linked, branched DNA-RNA compound in E. coli B. Cell 1989;56:891–904 [CrossRef][PubMed]
    [Google Scholar]
  11. Lampson BC, Sun J, Hsu MY, Vallejo-Ramirez J, Inouye S et al. Reverse transcriptase in a clinical strain of Escherichia coli: production of branched RNA-linked msDNA. Science 1989;243:1033–1038 [CrossRef][PubMed]
    [Google Scholar]
  12. Herzer PJ, Inouye S, Inouye M, Whittam TS. Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli. J Bacteriol 1990;172:6175–6181 [CrossRef][PubMed]
    [Google Scholar]
  13. Sun J, Herzer PJ, Weinstein MP, Lampson BC, Inouye M et al. Extensive diversity of branched-RNA-linked multicopy single-stranded DNAs in clinical strains of Escherichia coli. Proc Natl Acad Sci USA 1989;86:7208–7212 [CrossRef][PubMed]
    [Google Scholar]
  14. Inouye S, Sunshine MG, Six EW, Inouye M. Retronphage phi R73: an E. coli phage that contains a retroelement and integrates into a tRNA gene. Science 1991;252:969–971 [CrossRef][PubMed]
    [Google Scholar]
  15. Mao JR, Inouye S, Inouye M. msDNA-Ec48, the smallest multicopy single-stranded DNA from Escherichia coli. J Bacteriol 1997;179:7865–7868 [CrossRef][PubMed]
    [Google Scholar]
  16. Herzer PJ, Inouye S, Inouye M. Retron-Ec107 is inserted into the Escherichia coli genome by replacing a palindromic 34bp intergenic sequence. Mol Microbiol 1992;6:345–354 [CrossRef][PubMed]
    [Google Scholar]
  17. Zimmerly S, Wu L. An unexplored diversity of reverse transcriptases in bacteria. Microbiol Spectr 2015;3:MDNA3-0058-2014 [CrossRef][PubMed]
    [Google Scholar]
  18. Lim D, Gomes TA, Maas WK. Distribution of msDNAs among serotypes of enteropathogenic Escherichia coli strains. Mol Microbiol 1990;4:1711–1714 [CrossRef][PubMed]
    [Google Scholar]
  19. das R, Shimamoto T, Hosen SM, Arifuzzaman M. Comparative study of different msDNA (multicopy single-stranded DNA) structures and phylogenetic comparison of reverse transcriptases (RTs): evidence for vertical inheritance. Bioinformation 2011;7:176–179 [CrossRef][PubMed]
    [Google Scholar]
  20. Hsu MY, Inouye S, Inouye M. Structural requirements of the RNA precursor for the biosynthesis of the branched RNA-linked multicopy single-stranded DNA of Myxococcus xanthus. J Biol Chem 1989;264:6214–6219[PubMed]
    [Google Scholar]
  21. Shimamoto T, Kawanishi H, Tsuchiya T, Inouye S, Inouye M. In vitro synthesis of multicopy single-stranded DNA, using separate primer and template RNAs, by Escherichia coli reverse transcriptase. J Bacteriol 1998;180:2999–3002[PubMed]
    [Google Scholar]
  22. Lim D. Structure and biosynthesis of unbranched multicopy single-stranded DNA by reverse transcriptase in a clinical Escherichia coli isolate. Mol Microbiol 1992;6:3531–3542 [CrossRef][PubMed]
    [Google Scholar]
  23. Lima TM, Lim D. A novel retron that produces RNA-less msDNA in Escherichia coli using reverse transcriptase. Plasmid 1997;38:25–33 [CrossRef][PubMed]
    [Google Scholar]
  24. Maas WK, Wang C, Lima T, Zubay G, Lim D. Multicopy single-stranded DNAs with mismatched base pairs are mutagenic in Escherichia coli. Mol Microbiol 1994;14:437–441 [CrossRef][PubMed]
    [Google Scholar]
  25. Jeong DW, Kim K, Lim D. Evidence for the complex formation between reverse transcriptase and multicopy single-stranded DNA in retron EC83. Mol Cells 1997;7:347–351[PubMed]
    [Google Scholar]
  26. Shimamoto T, Hsu MY, Inouye S, Inouye M. Reverse transcriptases from bacterial retrons require specific secondary structures at the 5'-end of the template for the cDNA priming reaction. J Biol Chem 1993;268:2684–2692[PubMed]
    [Google Scholar]
  27. Shimamoto T, Inouye M, Inouye S. The formation of the 2',5'-phosphodiester linkage in the cDNA priming reaction by bacterial reverse transcriptase in a cell-free system. J Biol Chem 1995;270:581–588 [CrossRef][PubMed]
    [Google Scholar]
  28. Shimada M, Inouye S, Inouye M. Requirements of the secondary structures in the primary transcript for multicopy single-stranded DNA synthesis by reverse transcriptase from bacterial retron-Ec107. J Biol Chem 1994;269:14553–14558[PubMed]
    [Google Scholar]
  29. Inouye S, Hsu MY, Xu A, Inouye M. Highly specific recognition of primer RNA structures for 2'-OH priming reaction by bacterial reverse transcriptases. J Biol Chem 1999;274:31236–31244 [CrossRef][PubMed]
    [Google Scholar]
  30. Lampson BC, Viswanathan M, Inouye M, Inouye S. Reverse transcriptase from Escherichia coli exists as a complex with msDNA and is able to synthesize double-stranded DNA. J Biol Chem 1990;265:8490–8496[PubMed]
    [Google Scholar]
  31. Jeong MA, Lim D. A proteomic approach to study msDNA function in Escherichia coli. J Microbiol 2004;42:200–204[PubMed]
    [Google Scholar]
  32. Jung H, Liang J, Jung Y, Lim D. Characterization of cell death in Escherichia coli mediated by XseA, a large subunit of exonuclease VII. J Microbiol 2015;53:820–828 [CrossRef][PubMed]
    [Google Scholar]
  33. Hsu MY, Inouye M, Inouye S. Retron for the 67-base multicopy single-stranded DNA from Escherichia coli: a potential transposable element encoding both reverse transcriptase and dam methylase functions. Proc Natl Acad Sci USA 1990;87:9454–9458 [CrossRef][PubMed]
    [Google Scholar]
  34. Maas WK, Wang C, Lima T, Hach A, Lim D. Multicopy single-stranded DNA of Escherichia coli enhances mutation and recombination frequencies by titrating MutS protein. Mol Microbiol 1996;19:505–509 [CrossRef][PubMed]
    [Google Scholar]
  35. Mittler JE, Lenski RE. New data on excisions of Mu from E. coli MCS2 cast doubt on directed mutation hypothesis. Nature 1990;344:173–175 [CrossRef][PubMed]
    [Google Scholar]
  36. Herzer PJ. Starvation-induced expression of retron-Ec107 and the role of ppGpp in multicopy single-stranded DNA production. J Bacteriol 1996;178:4438–4444 [CrossRef][PubMed]
    [Google Scholar]
  37. Bridges BA. Starvation-associated mutation in E. coli strains with and without reverse transcriptase. Mutat Res 1995;347:13–15 [CrossRef][PubMed]
    [Google Scholar]
  38. Mao JR, Inouye S, Inouye M. Enhancement of frame-shift mutation by the overproduction of msDNA in Escherichia coli. FEMS Microbiol Lett 1996;144:109–115 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.000563
Loading
/content/journal/micro/10.1099/mic.0.000563
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error