The new IS1595 family, its relation to IS1 and the frontier between insertion sequences and transposons

Research in Microbiology

Volumn 160, Issue 3, 2009, Pages 232-241

  Siguier, Patricia ^a   Gagnevin, Lionel ^b   Chandler, Michael ^a  

^a UPS   (France)

^b UNIVERSITÉ DE LA RÉUNION   (France)

Author keywords

Insertion sequence (IS) diversity; IS1 family; IS1595 family; ISfinder; Prokaryotic genomes; Transposable elements; Transposases

Indexed keywords

TRANSPOSASE;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; GENE INSERTION SEQUENCE; GENETIC ORGANIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; SEQUENCE ANALYSIS; TRANSPOSON;

DNA TRANSPOSABLE ELEMENTS; DNA, BACTERIAL; GENETIC VARIATION; GENOME, BACTERIAL; SEQUENCE HOMOLOGY;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 67349260702     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2009.02.003     Document Type: Article

References (28)

1. Achard A., and Leclercq R. Characterization of a small mobilizable transposon, MTnSag1, in Streptococcus agalactiae. J. Bacteriol. 189 (2007) 4328-4331
2. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
3. Baranov P.V., Fayet O., Hendrix R.W., and Atkins J.F. Recoding in bacteriophages and bacterial IS elements. Trends Genet. 22 (2006) 174-181
4. Chandler M., and Mahillon J. Insertion sequences revisited. In: Craig N.L., Craigie R., Gellert M., and Lambowitz A. (Eds). Mobile DNA vol. II (2002), ASM Press, Washington DC 305-366
5. Clamp M., Cuff J., Searle S.M., and Barton G.J. The Jalview Java alignment editor. Bioinformatics 20 (2004) 426-427
6. Crooks G.E., Hon G., Chandonia J.M., and Brenner S.E. WebLogo: a sequence logo generator. Genome Res. 14 (2004) 1188-1190 10.1101/gr.849004
7. De Palmenaer D., Siguier P., and Mahillon J. IS4 family goes genomic. BMC Evol. Biol. 8 (2008) 18
8. De Palmenaer D., Vermeiren C., and Mahillon J. IS231-MIC231 elements from Bacillus cereus sensu lato are modular. Mol. Microbiol. 53 (2004) 457-467
9. Dodd I.B., and Egan J.B. Improved detection of helix-turn-helix DNA-binding motifs in protein sequences. Nucleic Acids Res. 18 (1990) 5019-5026
10. Enright A.J., Van Dongen S., and Ouzounis C.A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30 (2002) 1575-1584
11. Fayet O., Ramond P., Polard P., Prere M.F., and Chandler M. Functional similarities between retroviruses and the IS3 family of bacterial insertion sequences?. Mol. Microbiol. 4 (1990) 771-777
12. Filée J., Siguier P., and Chandler M. I am what I eat and I eat what I am: acquisition of bacterial genes by giant viruses. Trends Genet. 23 (2007) 10-15
13. Filée J., Siguier P., and Chandler M. Insertion sequence diversity in archaea. Microbiol. Mol. Biol. Rev. 71 (2007) 121-157
14. Jones D.T., Taylor W.R., and Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8 (1992) 275-282
15. Kulkosky J., Jones K.S., Katz R.A., Mack J.P., and Skalka A.M. Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases. Mol. Cell Biol. 12 (1992) 2331-2338
16. Mahillon J., and Chandler M. Insertion sequences. Microbiol. Mol. Biol. Rev. 62 (1998) 725-774
17. Mazel D. Integrons: agents of bacterial evolution. Nat. Rev. Microbiol. 4 (2006) 608-620
18. Nakatsu C., Ng J., Singh R., Straus N., and Wyndham C. Chlorobenzoate catabolic transposon Tn5271 is a composite class I element with flanking class II insertion sequences. Proc. Natl. Acad. Sci. U.S.A. 88 (1991) 8312-8316
19. Nirdnoy W., Mason C.J., and Guerry P. Mosaic structure of a multiple-drug-resistant, conjugative plasmid from Campylobacter jejuni. Antimicrob. Agents Chemother. 49 (2005) 2454-2459
20. Ohta S., Tsuchida K., Choi S., Sekine Y., Shiga Y., and Ohtsubo E. Presence of a characteristic D-D-E motif in IS1 transposase. J. Bacteriol. 184 (2002) 6146-6154
21. Ohta S., Yoshimura E., and Ohtsubo E. Involvement of two domains with helix-turn-helix and zinc finger motifs in the binding of IS1 transposase to terminal inverted repeats. Mol. Microbiol. 53 (2004) 193-202
22. Parkhill J., Achtman M., James K.D., Bentley S.D., Churcher C., Klee S.R., Morelli G., Basham D., et al. Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. Nature 404 (2000) 502-506
23. Rice P., Craigie R., and Davies D.R. Retroviral integrases and their cousins. Curr. Opin. Struct. Biol. 6 (1996) 76-83
24. Siguier P., Perochon J., Lestrade L., Mahillon J., and Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 34 (2006) D32-D36
25. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
26. Ton-Hoang B., Turlan C., and Chandler M. Functional domains of the IS1 transposase: analysis in vivo and in vitro. Mol. Microbiol. 53 (2004) 1529-1543
27. Touchon M., and Rocha E.P. Causes of insertion sequences abundance in prokaryotic genomes. Mol. Biol. Evol. 24 (2007) 969-981
28. Van Dongen S. A Cluster Algorithm for Graphs. Technical Report INS-R0010 (2000), National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam