Using genomic data to determine the diversity and distribution of target site motifs recognized by class C-attC group II introns

Journal of Molecular Evolution

Volumn 68, Issue 5, 2009, Pages 539-549

  Quiroga, Cecilia ^a   Centrón, Daniela ^a  

^a UNIVERSIDAD DE BUENOS AIRES   (Argentina)

Author keywords

AttC sites; Group II introns; Integron integrase; Retrotransposon; Secondary structure

Indexed keywords

ATTC; GENOMIC DNA; PALINDROMIC DNA; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENOME; CLASS C ATTC GROUP II INTRON; COMPUTER PROGRAM; GENETIC ANALYSIS; HORIZONTAL GENE TRANSFER; INTEGRON; INTRON; NUCLEOTIDE SEQUENCE;

ATTACHMENT SITES, MICROBIOLOGICAL; BASE COMPOSITION; BASE SEQUENCE; GENETIC VARIATION; GENOME, BACTERIAL; HOST-PATHOGEN INTERACTIONS; INTEGRASES; INTEGRONS; INTRONS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; REGULATORY SEQUENCES, NUCLEIC ACID; SEQUENCE ALIGNMENT;

BACTERIA (MICROORGANISMS); SHEWANELLA;

EID: 67349109465     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-009-9228-3     Document Type: Article

References (39)

1. Y Boucher CL Nesbo MJ Joss A Robinson BC Mabbutt MR Gillings WF Doolittle HW Stokes 2006 Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio BMC Evol Biol 6 3
2. Y Boucher M Labbate JE Koenig HW Stokes 2007 Integrons: mobilizable platforms that promote genetic diversity in bacteria Trends Microbiol 15 301 309 (Pubitemid 47017712)
3. M Bouvier G Demarre D Mazel 2005 Integron cassette insertion: a recombination process involving a folded single strand substrate EMBO J 24 4356 4367 (Pubitemid 41828910)
4. D Centrón PH Roy 2002 Presence of a group II intron in a multiresistant Serratia marcescens strain that harbors three integrons and a novel gene fusion Antimicrob Agents Chemother 46 1402 1409 (Pubitemid 34415321)
5. S Chen S Zhao DG White CM Schroeder R Lu H Yang PF McDermott S Ayers J Meng 2004 Characterization of multiple-antimicrobial-resistant Salmonella serovars isolated from retail meats Appl Environ Microbiol 70 1 7 (Pubitemid 38090181)
6. B Cousineau D Smith S Lawrence-Cavanagh JE Mueller J Yang D Mills D Manias G Dunny AM Lambowitz M Belfort 1998 Retrohoming of a bacterial group II intron: mobility via complete reverse splicing, independent of homologous DNA recombination Cell 94 451 462 (Pubitemid 28391861)
7. B Cousineau S Lawrence D Smith M Belfort 2000 Retrotransposition of a bacterial group II intron Nature 404 1018 1021 (Pubitemid 30243599)
8. GE Crooks G Hon JM Chandonia SE Brenner 2004 WebLogo: a sequence logo generator Genome Res 14 1188 1190 (Pubitemid 38811555)
9. L Dai S Zimmerly 2002 Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behavior Nucleic Acids Res 30 1091 1102 (Pubitemid 34679680)
10. MV Francia JC Zabala F de la Cruz JM Garcia Lobo 1999 The IntI1 integron integrase preferentially binds single-stranded DNA of the attC site J Bacteriol 181 6844 6849 (Pubitemid 29518004)
11. RM Hall HW Stokes 1993 Integrons: novel DNA elements which capture genes by site-specific recombination Genetica 90 115 132 (Pubitemid 2032213)
12. RM Hall DE Brookes HW Stokes 1991 Site-specific insertion of genes into integrons: role of the 59-base element and determination of the recombination cross-over point Mol Microbiol 5 1941 1959 (Pubitemid 21896225)
13. HH Hau JA Gralnick 2007 Ecology and biotechnology of the genus Shewanella Annu Rev Microbiol 61 237 258 (Pubitemid 350058208)
14. AJ Holmes MR Gillings BS Nield BC Mabbutt KM Nevalainen HW Stokes 2003 The gene cassette metagenome is a basic resource for bacterial genome evolution Environ Microbiol 5 383 394 (Pubitemid 36572800)
15. HM Holt B Gahrn-Hansen B Bruun 2005 Shewanella algae and Shewanella putrefaciens: clinical and microbiological characteristics Clin Microbiol Infect 11 347 352 (Pubitemid 40575816)
16. C Johansson M Kamali-Moghaddam L Sundstrom 2004 Integron integrase binds to bulged hairpin DNA Nucleic Acids Res 32 4033 4043 (Pubitemid 39199095)
17. M Labbate Y Boucher MJ Joss CA Michael MR Gillings HW Stokes 2007 Use of chromosomal integron arrays as a phylogenetic typing system for Vibrio cholerae pandemic strains Microbiol 153 1488 1498 (Pubitemid 46780005)
18. AM Lambowitz M Belfort 1993 Introns as mobile genetic elements Annu Rev Biochem 62 587 622
19. AM Lambowitz S Zimmerly 2004 Mobile group II introns Annu Rev Genet 38 1 35 (Pubitemid 40013722)
20. G Leon PH Roy 2003 Excision and integration of cassettes by an integron integrase of Nitrosomonas europaea J Bacteriol 185 2036 2041 (Pubitemid 36297907)
21. D MacDonald G Demarre M Bouvier D Mazel DN Gopaul 2006 Structural basis for broad DNA-specificity in integron recombination Nature 440 1157 1162
22. N Messier PH Roy 2001 Integron integrases possess a unique additional domain necessary for activity J Bacteriol 183 6699 6706 (Pubitemid 33026764)
23. WW Navarre M McClelland SJ Libby FC Fang 2007 Silencing of xenogeneic DNA by H-NS-facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA Genes Dev 21 1456 1471 (Pubitemid 46955718)
24. DR Nemergut MS Robeson RF Kysela AP Martin SK Schmidt R Knight 2008 Insights and inferences about integron evolution from genomic data BMC Genomics 9 261
25. BE Orman SA Pineiro S Arduino M Galas R Melano MI Caffer DO Sordelli D Centron 2002 Evolution of multiresistance in nontyphoid Salmonella serovars from 1984 to 1998 in Argentina Antimicrob Agents Chemother 46 3963 3970 (Pubitemid 35403275)
26. M Petrillo G Silvestro PP Di Nocera A Boccia G Paolella 2006 Stem-loop structures in prokaryotic genomes BMC Genomics 7 170
27. C Quiroga PH Roy D Centron 2008 The S.ma.I2 class C group II intron inserts at integron attC sites Microbiology 154 1341 1353
28. AR Robart W Seo S Zimmerly 2007 Insertion of group II intron retroelements after intrinsic transcriptional terminators Proc Natl Acad Sci U S A 104 6620 6625 (Pubitemid 47175550)
29. DA Rowe-Magnus AM Guerout L Biskri P Bouige D Mazel 2003 Comparative analysis of superintegrons: engineering extensive genetic diversity in the Vibrionaceae Genome Res 13 428 442 (Pubitemid 36395401)
30. K Rutherford J Parkhill J Crook T Horsnell P Rice MA Rajandream B Barrell 2000 Artemis: sequence visualization and annotation Bioinformatics 16 944 945
31. HW Stokes DB O'Gorman GD Recchia M Parsekhian RM Hall 1997 Structure and function of 59-base element recombination sites associated with mobile gene cassettes Mol Microbiol 26 731 745 (Pubitemid 27489335)
32. M Sunde 2005 Class I integron with a group II intron detected in an Escherichia coli strain from a free-range reindeer Antimicrob Agents Chemother 49 2512 2514 (Pubitemid 40734492)
33. K Tamura J Dudley M Nei S Kumar 2007 MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 Mol Biol Evol 24 1596 1599 (Pubitemid 47236692)
34. SG Tetu AJ Holmes 2008 A family of insertion sequences that impacts integrons by specific targeting of gene cassette recombination sites, the IS1111-attC Group J Bacteriol 190 4959 4970
35. R Tobes E Pareja 2006 Bacterial repetitive extragenic palindromic sequences are DNA targets for insertion sequence elements BMC Genomics 7 62
36. N Toor G Hausner S Zimmerly 2001 Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases RNA 7 1142 1152 (Pubitemid 32726912)
37. ME Val M Bouvier J Campos D Sherratt F Cornet D Mazel FX Barre 2005 The single-stranded genome of phage CTX is the form used for integration into the genome of Vibrio cholerae Mol Cell 19 559 566 (Pubitemid 41140012)
38. (VIM-2) gene cassettes J Antimicrob Chemother 49 837 840 (Pubitemid 34537647)
39. M Zuker 2003 Mfold web server for nucleic acid folding and hybridization prediction Nucleic Acids Res 31 3406 3415 (Pubitemid 37442169)