Route 66: investigations into the organisation and distribution of the IS66 family of prokaryotic insertion sequences

Research in Microbiology

Volumn 161, Issue 2, 2010, Pages 136-143

  Gourbeyre, Edith ^a   Siguier, Patricia ^a   Chandler, Michael ^a  

^a UMR   (France)

Author keywords

Archaea; IS distribution; IS families; Transposase

Indexed keywords

TRANSPOSASE; TRANSPOSASE A; TRANSPOSASE B; TRANSPOSASE C; UNCLASSIFIED DRUG;

ACTINOBACTERIA; ARCHAEBACTERIUM; ARTICLE; BACTERIOPLANKTON; CYANOBACTERIUM; DEINOCOCCUS; DNA BINDING; FIRMICUTES; GENE INSERTION SEQUENCE; INVERTED REPEAT; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLUM; PRIORITY JOURNAL; PROKARYOTE; PROTEOBACTERIA; RHIZOBIUM; THERMUS; TRANSPOSON;

ARCHAEA; BACTERIA; CONSERVED SEQUENCE; DNA TRANSPOSABLE ELEMENTS; DNA, ARCHAEAL; DNA, BACTERIAL; OPEN READING FRAMES; PHYLOGENY; SEQUENCE HOMOLOGY; TERMINAL REPEAT SEQUENCES;

ACTINOBACTERIA; ARCHAEA; BACTERIA (MICROORGANISMS); CRENARCHAEOTA; CYANOBACTERIA; EURYARCHAEOTA; FIRMICUTES; PLANCTOMYCETES; PROKARYOTA; PROTEOBACTERIA;

EID: 77949917114     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2009.11.005     Document Type: Article

References (24)

1. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
2. Brugger K., Redder P., She Q., Confalonieri F., Zivanovic Y., Garrett R.A. Mobile elements in archaeal genomes. FEMS Microbiol Lett 2002, 206:131-141.
3. Clamp M., Cuff J., Searle S.M., Barton G.J. The Jalview Java alignment editor. Bioinformatics 2004, 20:426-427.
4. Combet C., Blanchet C., Geourjon C., Deleage G. NPS@ network protein sequence analysis. Trends Biochem Sci 2000, 25:147-150.
5. Crooks G.E., Hon G., Chandonia J.-M., Brenner S.E. WebLogo: a sequence logo generator. Genome Res. 2004, 14:1188-1190.
6. Egelseer E.M., Idris R., Jarosch M., Danhorn T., Sleytr U.B., Sara M. ISBst12, a novel type of insertion-sequence element causing loss of S-layer-gene expression in bacillus stearothermophilus ATCC 12980. Microbiology 2000, 146:2175-2183.
7. Enright A.J., Van Dongen S., Ouzounis C.A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002, 30:1575-1584.
8. Filee J., Siguier P., Chandler M. Insertion sequence diversity in archaea. Microbiol Mol Biol Rev 2007, 71:121-157.
9. Galtier N., Gouy M., Gautier C. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 1996, 12:543-548.
10. Han C.G., Shiga Y., Tobe T., Sasakawa C., Ohtsubo E. Structural and functional characterization of IS679 and IS66-family elements. J Bacteriol 2001, 183:4296-4304.
11. Haren L., Polard P., Ton-Hoang B., Chandler M. Multiple oligomerisation domains in the IS911 transposase: a leucine zipper motif is essential for activity. J Mol Biol 1998, 283:29-41.
12. Haren L., Ton-Hoang B., Chandler M. Integrating DNA: transposases and retroviral integrases. Ann Rev Microbiol 1999, 53:245-281.
13. Jones D.T., Taylor W.R., Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992, 8:275-282.
14. Machida Y., Sakurai M., Kiyokawa S., Ubasawa A., Suzuki Y., Ikeda J.E. Nucleotide sequence of the insertion sequence found in the T-DNA region of mutant Ti plasmid pTiA66 and distribution of its homologues in octopine Ti plasmid. Proc Natl Acad Sci USA 1984, 81:7495-7499.
15. Mahillon J., Chandler M. Insertion sequences. Microbiol Mol Biol Rev 1998, 62:725-774.
16. Nunes-Duby S.E., Kwon H.J., Tirumalai R.S., Ellenberger T., Landy A. Similarities and differences among 105 members of the Int family of site-specific recombinases. Nucleic Acids Res 1998, 26:391-406.
17. Ohta S., Tsuchida K., Choi S., Sekine Y., Shiga Y., Ohtsubo E. Presence of a characteristic D-D-E motif in IS1 transposase. J Bacteriol 2002, 184:6146-6154.
18. Page R.D. TreeView, an application to display phylogenetic trees on personal computers. Comput Appl Biosci 1996, 12:357-358.
19. Serre M.C., Turlan C., Bortolin M., Chandler M. Mutagenesis of the IS1 transposase: importance of a His-Arg-Tyr triad for activity. J Bacteriol 1995, 177:5070-5077.
20. Siguier P., Gagnevin L., Chandler M. The new IS1595 family, its relation to IS1 and the frontier between insertion sequences and transposons. Res Microbiol 2009, 160:232-241.
21. Siguier P., Perochon J., Lestrade L., Mahillon J., Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006, 34:D32-D36.
22. Thompson J.D., Higgins D.G., 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 1994, 22:4673-4680.
23. Ton-Hoang B., Turlan C., Chandler M. Functional domains of the IS1 transposase: analysis in vivo and in vitro. Mol Microbiol 2004, 53:1529-1543.
24. Van Dongen S. A cluster algorithm for graphs 2000, Technical Report INS-R0010, National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam.