Tobes R, Ramos JL: REP code: defining bacterial identity in extragenic space. Environ Microbiol. 2005, 7: 225-228. 10.1111/j.1462-2920.2004.00704.x.
Article
PubMed
CAS
Google Scholar
Espeli O, Moulin L, Boccard F: Transcription attenuation associated with bacterial repetitive extragenic BIME elements. J Mol Biol. 2001, 314: 375-386. 10.1006/jmbi.2001.5150.
Article
PubMed
CAS
Google Scholar
Aranda-Olmedo I, Tobes R, Manzanera M, Ramos JL, Marques S: Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida. Nucleic Acids Res. 2002, 30: 1826-1833. 10.1093/nar/30.8.1826.
Article
PubMed
CAS
PubMed Central
Google Scholar
Khemici V, Carpousis AJ: The RNA degradosome and poly(A) polymerase of Escherichia coli are required in vivo for the degradation of small mRNA decay intermediates containing REP-stabilizers. Mol Microbiol. 2004, 51: 777-790. 10.1046/j.1365-2958.2003.03862.x.
Article
PubMed
CAS
Google Scholar
Tobes R, Pareja E: Repetitive extragenic palindromic sequences in the Pseudomonas syringae pv. tomato DC3000 genome: extragenic signals for genome reannotation. Res Microbiol. 2005, 156: 424-433. 10.1016/j.resmic.2004.10.014.
Article
PubMed
CAS
Google Scholar
Gilson E, Perrin D, Hofnung M: DNA polymerase I and a protein complex bind specifically to E. coli palindromic unit highly repetitive DNA: implications for bacterial chromosome organization. Nucleic Acids Res. 1990, 18: 3941-3952.
Article
PubMed
CAS
PubMed Central
Google Scholar
Espeli O, Boccard F: In vivo cleavage of Escherichia coli BIME-2 repeats by DNA gyrase: genetic characterization of the target and identification of the cut site. Mol Microbiol. 1997, 26: 767-777. 10.1046/j.1365-2958.1997.6121983.x.
Article
PubMed
CAS
Google Scholar
Engelhorn M, Boccard F, Murtin C, Prentki P, Geiselmann J: In vivo interaction of the Escherichia coli integration host factor with its specific binding sites. Nucleic Acids Res. 1995, 23: 2959-2965.
Article
PubMed Central
Google Scholar
Clement JM, Wilde C, Bachellier S, Lambert P, Hofnung M: IS1397 is active for transposition into the chromosome of Escherichia coli K-12 and inserts specifically into palindromic units of bacterial interspersed mosaic elements. J Bacteriol. 1999, 181: 6929-6936.
PubMed
CAS
PubMed Central
Google Scholar
Choi S, Ohta S, Ohtsubo E: A novel IS element, IS621, of the ISPa110/IS492 family transposes to a specific site in repetitive extragenic palindromic sequences in Escherichia coli . J Bacteriol. 2003, 185: 4891-4900. 10.1128/JB.185.16.4891-4900.2003.
Article
PubMed
CAS
PubMed Central
Google Scholar
Wilde C, Bachellier S, Hofnung M, Clement JM: Transposition of IS1397 in the family Enterobacteriaceae and first characterization of ISKpn1, a new insertion sequence associated with Klebsiella pneumoniae palindromic units. J Bacteriol. 2001, 183: 4395-4404. 10.1128/JB.183.15.4395-4404.2001.
Article
PubMed
CAS
PubMed Central
Google Scholar
Wilde C, Escartin F, Kokeguchi S, Latour-Lambert P, Lectard A, Clement JM: Transposases are responsible for the target specificity of IS1397 and ISKpn1 for two different types of palindromic units (PUs). Nucleic Acids Res. 2003, 31: 4345-4353. 10.1093/nar/gkg494.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kumagai M, Ikeda H: Molecular analysis of the recombination junctions of lambda bio transducing phages. Mol Gen Genet. 1991, 230: 60-64. 10.1007/BF00290651.
Article
PubMed
CAS
Google Scholar
Kofoid E, Bergthorsson U, Slechta ES, Roth JR: Formation of an F' plasmid by recombination between imperfectly repeated chromosomal Rep sequences: a closer look at an old friend (F'(128) pro lac). J Bacteriol. 2003, 185: 660-663. 10.1128/JB.185.2.660-663.2003.
Article
PubMed
CAS
PubMed Central
Google Scholar
Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins dos Santos VA, Fouts DE, Gill SR, Pop M, Holmes M, Brinkac L, Beanan M, DeBoy RT, Daugherty S, Kolonay J, Madupu R, Nelson W, White O, Peterson J, Khouri H, Hance I, Chris Lee P, Holtzapple E, Scanlan D, Tran K, Moazzez A, Utterback T, Rizzo M, Lee K, Kosack D, Moestl D, Wedler H, Lauber J, Stjepandic D, Hoheisel J, Straetz M, Heim S, Kiewitz C, Eisen JA, Timmis KN, Dusterhoft A, Tummler B, Fraser CM: Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol. 2002, 4: 799-808. 10.1046/j.1462-2920.2002.00366.x.
Article
PubMed
CAS
Google Scholar
Mahillon J, Chandler M: Insertion sequences. Microbiol Mol Biol Rev. 1998, 62: 725-774.
PubMed
CAS
PubMed Central
Google Scholar
Bachellier S, Clément JM, Hofnung M, Gilson E: Bacterial Interspersed Mosaic Elements (BIMEs) are a major source of sequence polymorphism in Escherichia coli intergenic regions including specific associations with a new insertion sequence. Genetics. 1997, 145: 551-562.
PubMed
CAS
PubMed Central
Google Scholar
Craig NL: Target site selection in transposition. Annu Rev Biochem. 1997, 66: 437-474. 10.1146/annurev.biochem.66.1.437.
Article
PubMed
CAS
Google Scholar
Fayet O, Ramond P, Polard P, Prere MF, Chandler M: Functional similarities between retroviruses and the IS3 family of bacterial insertion sequences?. Mol Microbiol. 1990, 4 (10): 1771-7.
Article
PubMed
CAS
Google Scholar
Haren L, Ton-Hoang B, Chandler M: Transposases and Retroviral Integrases. Annu Rev Microbiol. 1990, 53: 245-281. 10.1146/annurev.micro.53.1.245.
Article
Google Scholar
Schwartz E, Kröger M, Rak B: IS150: distribution, nucleotide sequence and phylogenetic relationships of a new E. coli insertion element. Nucleic Acids Res. 1988, 16: 6789-6802.
Article
PubMed
CAS
PubMed Central
Google Scholar
Rousseau P, Gueguen E, Duval-Valentin G, Chandler M: The helix-turn-helix motif of bacterial insertion sequence IS911 transposase is required for DNA binding. Nucleic Acids Res. 2004, 32: 1335-1344. 10.1093/nar/gkh276.
Article
PubMed
CAS
PubMed Central
Google Scholar
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. 10.1006/jmbi.1998.2053.
Article
PubMed
CAS
Google Scholar
Nagy Z, Szabo M, Chandler M, Olasz F: Analysis of the N-terminal DNA binding domain of the IS30 transposase. Mol Microbiol. 2004, 54: 478-488. 10.1111/j.1365-2958.2004.04279.x.
Article
PubMed
CAS
Google Scholar
Mahillon J, Leonard C, Chandler M: IS elements as constituents of bacterial genomes. Res Microbiol. 1999, 150: 675-687. 10.1016/S0923-2508(99)00124-2.
Article
PubMed
CAS
Google Scholar
Chandler M, Mahillon J: Insertion Sequences Revisited. Mobile DNA II. Edited by: Craig NL, Gragie R, Gellert M, Lambowitz AM. 2002, ASM Press, 305-366.
Chapter
Google Scholar
Tobiason DM, Buchner JM, Thiel WH, Gernert KM, Karls AC: Conserved amino acid motifs from the novel Piv/MooV family of transposases and site-specific recombinases are required for catalysis of DNA inversion by Piv. Mol Microbiol. 2001, 39: 641-651. 10.1046/j.1365-2958.2001.02276.x.
Article
PubMed
CAS
Google Scholar
Dyda F, Hickman AB, Jenkins TM, Engelman A, Craigie R, Davies DR: Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. Science. 1994, 266: 1981-1986.
Article
PubMed
CAS
Google Scholar
Bujacz G, Jaskolski M, Alexandratos J, Wlodawer A, Merkel G, Katz RA, Skalka AM: High-resolution structure of the catalytic domain of avian sarcoma virus integrase. J Mol Biol. 1995, 253: 333-346. 10.1006/jmbi.1995.0556.
Article
PubMed
CAS
Google Scholar
Davies DR, Braam LM, Reznikoff WS, Rayment I: The three-dimensional structure of a Tn5 transposase-related protein determined to 2.9-A resolution. J Biol Chem. 1999, 274: 11904-11913. 10.1074/jbc.274.17.11904.
Article
PubMed
CAS
Google Scholar
Chiapello H, Bourgait I, Sourivong F, Heuclin G, Gendrault-Jacquemard A, Petit MA, ElKaroui M: Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops. BMC Bioinformatics. 2005, 6: 171-10.1186/1471-2105-6-171.
Article
PubMed
CAS
PubMed Central
Google Scholar
Schneider D, Duperchy E, Depeyrot J, Coursange E, Lenski R, Blot M: Genomic comparisons among Escherichia coli strains B, K-12, and O157:H7 using IS elements as molecular markers. BMC Microbiol. 2002, 2:
Google Scholar
Goryshin IY, Miller JA, Kil YV, Lanzov VA, Reznikoff WS: Tn5/IS50 target recognition. Proc Natl Acad Sci USA. 1998, 95: 10716-10721. 10.1073/pnas.95.18.10716.
Article
PubMed
CAS
PubMed Central
Google Scholar
Lodge JK, Weston-Hafer K, Berg DE: Transposon Tn5 target specificity: preference for insertion at G/C pairs. Genetics. 1988, 120: 645-650.
PubMed
CAS
PubMed Central
Google Scholar
Sasakawa C, Uno Y, Yoshikawa M: The requirement for both DNA polymerase and 5' to 3' exonuclease activities of DNA polymerase I during Tn5 transposition. Mol Gen Genet. 1981, 182: 19-24. 10.1007/BF00422761.
Article
PubMed
CAS
Google Scholar
Syvanen M, Hopkins JD, Clements M: A new class of mutants in DNA polymerase I that affects gene transposition. J Mol Biol. 1982, 158: 203-212. 10.1016/0022-2836(82)90429-6.
Article
PubMed
CAS
Google Scholar
Isberg RR, Lazaar AL, Syvanen M: Regulation of Tn5 by the right-repeat proteins: control at the level of the transposition reaction?. Cell. 1982, 30: 883-892. 10.1016/0092-8674(82)90293-8.
Article
PubMed
CAS
Google Scholar
Pato ML, Banerjee M: The Mu strong gyrase-binding site promotes efficient synapsis of the prophage termini. Mol Microbiol. 1996, 22: 283-292. 10.1046/j.1365-2958.1996.00115.x.
Article
PubMed
CAS
Google Scholar
Sternglanz R, DiNardo S, Voelkel KA, Nishimura Y, Hirota Y, Becherer K, Zumstein L, Wang JC: Mutations in the gene coding for Escherichia coli DNA topoisomerase I affect transcription and transposition. Proc Natl Acad Sci USA. 1981, 78: 2747-2751. 10.1073/pnas.78.5.2747.
Article
PubMed
CAS
PubMed Central
Google Scholar
Wang X, Higgins NP: 'Muprints' of the lac operon demonstrate physiological control over the randomness of in vivo transposition. Mol Microbiol. 1994, 12: 665-677.
Article
PubMed
CAS
Google Scholar
Franco AA: The Bacteroides fragilis pathogenicity island is contained in a putative novel conjugative transposon. J Bacteriol. 2004, 186: 6077-6092. 10.1128/JB.186.18.6077-6092.2004.
Article
PubMed
CAS
PubMed Central
Google Scholar
Okitsu N, Kaieda S, Yano H, Nakano R, Hosaka Y, Okamoto R, Kobayashi T, Inoue M: Characterization of ermB gene transposition by Tn1545 and Tn917 in macrolide-resistant Streptococcus pneumoniae isolates. J Clin Microbiol. 2005, 43: 168-173. 10.1128/JCM.43.1.168-173.2005.
Article
PubMed
CAS
PubMed Central
Google Scholar
Lupski JR: Molecular mechanisms for transposition of drug-resistance genes and other movable genetic elements. Rev Infect Dis. 1987, 9: 357-368.
Article
PubMed
CAS
Google Scholar
Ziebuhr W, Krimmer V, Rachid S, Lossner I, Gotz F, Hacker J: A novel mechanism of phase variation of virulence in Staphylococcus epidermidis : evidence for control of the polysaccharide intercellular adhesin synthesis by alternating insertion and excision of the insertion sequence element IS256. Mol Microbiol. 1999, 32: 345-356. 10.1046/j.1365-2958.1999.01353.x.
Article
PubMed
CAS
Google Scholar
Brunder W, Karch H: Genome plasticity in Enterobacteriaceae. Int J Med Microbiol. 2000, 153-165.
Google Scholar
Arber W: Genetic variation: molecular mechanisms and impact on microbial evolution. FEMS Microbiol Rev. 2000, 24: 1-7. 10.1111/j.1574-6976.2000.tb00529.x.
Article
PubMed
CAS
Google Scholar
NCBI Complete Microbial Genomes. [http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?view=1]
Corpet F: Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 1988, 16: 10881-10890.
Article
PubMed
CAS
PubMed Central
Google Scholar
MultAlin: Multiple sequence alignment. [http://prodes.toulouse.inra.fr/multalin/multalin.html]
Thompson JD, Higgins DG, Gibson TJ: 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.
Article
PubMed
CAS
PubMed Central
Google Scholar
EMBL-EBI. ClustalW. [http://www.ebi.ac.uk/clustalw/#]
ISfinder database. [http://www-is.biotoul.fr/is.html]
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR: The Pfam protein families database. Nucleic Acids Res. 2004, 32: 138-141. 10.1093/nar/gkh121.
Article
Google Scholar
Sanger Institute: Pfam database. [http://www.sanger.ac.uk/Software/Pfam/search.shtml]
Gilson E, Bachellier S, Perrin S, Perrin D, Grimont PA, Grimont F, Hofnung M: Palindromic unit highly repetitive DNA sequences exhibit species specificity within Enterobacteriaceae. Res Microbiol. 1990, 141: 1103-1116. 10.1016/0923-2508(90)90084-4.
Article
PubMed
CAS
Google Scholar
Parkhill J, Achtman M, James KD, Bentley SD, Churcher C, Klee SR, Morelli G, Basham D, Brown D, Chillingworth T, Davies RM, Davis P, Devlin K, Feltwell T, Hamlin N, Holroyd S, Jagels K, Leather S, Moule S, Mungall K, Quail MA, Rajandream MA, Rutherford KM, Simmonds M, Skelton J, Whitehead S, Spratt BG, Barrell BG: Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. Nature. 2000, 404: 502-506. 10.1038/35006655.
Article
PubMed
CAS
Google Scholar
Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dreano S, Federspiel NA, Fisher RF, Gloux S, Godrie T, Goffeau A, Golding B, Gouzy J, Gurjal M, Hernandez-Lucas I, Hong A, Huizar L, Hyman RW, Jones T, Kahn D, Kahn ML, Kalman S, Keating DH, Kiss E, Komp C, Lelaure V, Masuy D, Palm C, Peck MC, Pohl TM, Portetelle D, Purnelle B, Ramsperger U, Surzycki R, Thebault P, Vandenbol M, Vorholter FJ, Weidner S, Wells DH, Wong K, Yeh KC, Batut J: The composite genome of the legume symbiont Sinorhizobium meliloti . Science. 2001, 293: 668-672. 10.1126/science.1060966.
Article
PubMed
CAS
Google Scholar
Makarova KS, Wolf YI, White O, Minton K, Daly MJ: Short repeats and IS elements in the extremely radiation-resistant bacterium Deinococcus radiodurans and comparison to other bacterial species. Res Microbiol. 2001, 150: 711-724. 10.1016/S0923-2508(99)00121-7.
Article
Google Scholar
Ogata H, Audic S, Abergel C, Fournier PE, Claverie JM: Protein coding palindromes are a unique but recurrent feature in Rickettsia. Genome Res. 2002, 12: 808-816. 10.1101/gr.227602.
Article
PubMed
CAS
PubMed Central
Google Scholar