Potential role of group IIC-attC introns in integron cassette formation

Journal of Bacteriology

Volumn 191, Issue 19, 2009, Pages 6040-6051

  Léon, Grégory ^a,b   Roy, Paul H ^a,b  

^a LAVAL UNIVERSITY   (Canada)

^b UNIVERSITÉ LAVAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED DNA POLYMERASE; RNA DIRECTED DNA POLYMERASE;

ARTICLE; BACTERIAL GENOME; BACTERIUM ISOLATE; CONTROLLED STUDY; ENZYME ACTIVITY; ESCHERICHIA COLI; GENE CASSETTE; GENE EXPRESSION; GENE SEQUENCE; GENE TARGETING; GENETIC TRANSCRIPTION; HOMOLOGOUS RECOMBINATION; IN VITRO STUDY; INTEGRON; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN MOTIF; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION; RNA SPLICING; SERRATIA MARCESCENS; TRANSCRIPTION TERMINATION;

ESCHERICHIA COLI; SERRATIA MARCESCENS;

EID: 70349133579     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.00674-09     Document Type: Article

References (49)

1. Beauregard, A., M. J. Curcio, and M. Belfort. 2008. The take and give between retrotransposable elements and their hosts. Annu. Rev. Genet. 42:587-617.
2. Boucher, Y., M. Labbate, J. E. Koenig, and H. W. Stokes. 2007. Integrons: mobilizable platforms that promote genetic diversity in bacteria. Trends Microbiol. 15:301-309. (Pubitemid 47017712)
3. Boucher, Y., C. L. Nesbo, M. J. Joss, A. Robinson, B. C. Mabbutt, M. R. Gillings, W. F. Doolittle, and H. W. Stokes. 2006. Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio. BMC Evol. Biol. 6:3. (Pubitemid 43301287)
4. Centron, D., and P. H. 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.
5. Chen, C. Y., K. M. Wu, Y. C. Chang, C. H. Chang, H. C. Tsai, T. L. Liao, Y. M. Liu, H. J. Chen, A. B. Shen, J. C. Li, T. L. Su, C. P. Shao, C. T. Lee, L. I. Hor, and S. F. Tsai. 2003. Comparative genome analysis of Vibrio vulnificus, a marine pathogen. Genome Res. 13:2577-2587.
6. Coleman, N., S. Tetu, N. Wilson, and A. Holmes. 2004. An unusual integron in Treponema denticola. Microbiology 150:3524-3526.
7. da Silva, A. C., J. A. Ferro, F. C. Reinach, C. S. Farah, L. R. Furlan, R. B. Quaggio, C. B. Monteiro-Vitorello, M. A. Van Sluys, N. F. Almeida, L. M. Alves, A. M. do Amaral, M. C. Bertolini, L. E. Camargo, G. Camarotte, F. Cannavan, J. Cardozo, F. Chambergo, L. P. Ciapina, R. M. Cicarelli, L. L. Coutinho, J. R. Cursino-Santos, H. El-Dorry, J. B. Faria, A. J. Ferreira, R. C. Ferreira, M. I. Ferro, E. F. Formighieri, M. C. Franco, C. C. Greggio, A. Gruber, A. M. Katsuyama, L. T. Kishi, R. P. Leite, E. G. Lemos, M. V. Lemos, E. C. Locali, M. A. Machado, A. M. Madeira, N. M. Martinez-Rossi, E. C. Martins, J. Meidanis, C. F. Menck, C. Y. Miyaki, D. H. Moon, L. M. Moreira, M. T. Novo, V. K. Okura, M. C. Oliveira, V. R. Oliveira, H. A. Pereira, A. Rossi, J. A. Sena, C. Silva, R. F. de Souza, L. A. Spinola, M. A. Takita, R. E. Tamura, E. C. Teixeira, R. I. Tezza, M. Trindade dos Santos, D. Truffi, S. M. Tsai, F. F. White, J. C. Setubal, and J. P. Kitajima. 2002. Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417:459-463.
8. Fluit, A. C., and F. J. Schmitz. 1999. Class 1 integrons, gene cassettes, mobility, and epidemiology. Eur. J. Clin. Microbiol. Infect. Dis. 18:761-770.
9. Fluit, A. C., and F. J. Schmitz. 2004. Resistance integrons and super-integrons. Clin. Microbiol. Infect. 10:272-288.
10. Gillings, M. R., M. P. Holley, H. W. Stokes, and A. J. Holmes. 2005. Integrons in Xanthomonas: a source of species genome diversity. Proc. Natl. Acad. Sci. USA 102:4419-4424.
11. Hall, R. M., D. E. Brookes, and H. W. 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.
12. Hall, R. M., and C. M. Collis. 1995. Mobile gene cassettes and integrons: capture and spread of genes by site-specific recombination. Mol. Microbiol. 15:593-600.
13. Heidelberg, J. F., J. A. Eisen, W. C. Nelson, R. A. Clayton, M. L. Gwinn, R. J. Dodson, D. H. Haft, E. K. Hickey, J. D. Peterson, L. Umayam, S. R. Gill, K. E. Nelson, T. D. Read, H. Tettelin, D. Richardson, M. D. Ermolaeva, J. Vamathevan, S. Bass, H. Qin, I. Dragoi, P. Sellers, L. McDonald, T. Utterback, R. D. Fleishmann, W. C. Nierman, O. White, S. L. Salzberg, H. O. Smith, R. R. Colwell, J. J. Mekalanos, J. C. Venter, and C. M. Fraser. 2000. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406:477-483.
14. Holmes, A. J., M. R. Gillings, B. S. Nield, B. C. Mabbutt, K. M. Nevalainen, and H. W. Stokes. 2003. The gene cassette metagenome is a basic resource for bacterial genome evolution. Environ. Microbiol. 5:383-394.
15. Holmes, A. J., M. P. Holley, A. Mahon, B. Nield, M. Gillings, and H. W. Stokes. 2003. Recombination activity of a distinctive integron-gene cassette system associated with Pseudomonas stutzeri populations in soil. J. Bacteriol. 185:918-928.
16. Jeong, S. H., K. Lee, Y. Chong, J. H. Yum, S. H. Lee, H. J. Choi, J. M. Kim, K. H. Park, B. H. Han, S. W. Lee, and T. S. Jeong. 2003. Characterization of a new integron containing VIM-2, a metallo-beta-lactamase gene cassette, in a clinical isolate of Enterobacter cloacae. J. Antimicrob. Chemother. 51:397-400.
17. Lambowitz, A. M., and S. Zimmerly. 2004. Mobile group II introns. Annu. Rev. Genet. 38:1-35.
18. Léon, G., and P. H. Roy. 2003. Excision and integration of cassettes by an integron integrase of Nitrosomonas europaea. J. Bacteriol. 185:2036-2041.
19. Léon, G., and P. H. Roy. 2009. Group IIC intron mobility into attC sites involves a bulged DNA stem-loop motif. RNA 15:1543-1553.
20. Martinez-Abarca, F., A. Barrientos-Duran, M. Fernandez-Lopez, and N. Toro. 2004. The RmInt1 group II intron has two different retrohoming pathways for mobility using predominantly the nascent lagging strand at DNA replication forks for priming. Nucleic Acids Res. 32:2880-2888. (Pubitemid 38898626)
21. Mazel, D. 2006. Integrons: agents of bacterial evolution. Nat. Rev. Microbiol. 4:608-620.
22. Mazel, D., B. Dychinco, V. A. Webb, and J. Davies. 1998. A distinctive class of integron in the Vibrio cholerae genome. Science 280:605-608.
23. Michael, G. B., M. Cardoso, and S. Schwarz. 2008. Molecular analysis of multiresistant porcine Salmonella enterica subsp. enterica serovar Bredeney isolates from southern Brazil: identification of resistance genes, integrons and a group II intron. Int. J. Antimicrob. Agents 32:120-129.
24. Mohr, G., D. Smith, M. Belfort, and A. M. Lambowitz. 2000. Rules for DNA target-site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences. Genes Dev. 14:559-573. (Pubitemid 30159775)
25. Moran, J. V., S. Zimmerly, R. Eskes, J. C. Kennell, A. M. Lambowitz, R. A. Butow, and P. S. Perlman. 1995. Mobile group II introns of yeast mitochondrial DNA are novel site-specific retroelements. Mol. Cell. Biol. 15:2828-2838.
26. Munoz-Adelantado, E., J. San Filippo, F. Martinez-Abarca, F. M. Garcia- Rodriguez, A. M. Lambowitz, and N. Toro. 2003. Mobility of the Sinorhizobium meliloti group II intron RmInt1 occurs by reverse splicing into DNA, but requires an unknown reverse transcriptase priming mechanism. J. Mol. Biol. 327:931-943.
27. Pan, J. C., R. Ye, H. Q. Wang, H. Q. Xiang, W. Zhang, X. F. Yu, D. M. Meng, and Z. S. He. 2008. Vibrio cholerae O139 multiple-drug resistance mediated by Yersinia pestis pIP1202-like conjugative plasmids. Antimicrob. Agents Chemother. 52:3829-3836.
28. Quiroga, C., and D. Centron. 2009. Using genomic data to determine the diversity and distribution of target site motifs recognized by class C-attC group II introns. J. Mol. Evol. 68:539-549.
29. Quiroga, C., P. H. Roy, and D. Centron. 2008. The S.ma.I2 class C group II intron inserts at integron attC sites. Microbiology 154:1341-1353.
30. Recchia, G. D., and R. M. Hall. 1997. Origins of the mobile gene cassettes found in integrons. Trends Microbiol. 5:389-394.
31. Robart, A. R., W. Seo, and S. Zimmerly. 2007. Insertion of group II intron retroelements after intrinsic transcriptional terminators. Proc. Natl. Acad. Sci. USA 104:6620-6625.
32. Rowe-Magnus, D. A., A. M. Guerout, L. Biskri, P. Bouige, and D. Mazel. 2003. Comparative analysis of superintegrons: engineering extensive genetic diversity in the Vibrionaceae. Genome Res. 13:428-442.
33. Rowe-Magnus, D. A., A. M. Guerout, P. Ploncard, B. Dychinco, J. Davies, and D. Mazel. 2001. The evolutionary history of chromosomal super-integrons provides an ancestry for multiresistant integrons. Proc. Natl. Acad. Sci. USA 98:652-657.
34. Sambrook, J., and D. W. Russell. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
35. Schmelzer, C., and R. J. Schweyen. 1986. Self-splicing of group II introns in vitro: mapping of the branch point and mutational inhibition of lariat formation. Cell 46:557-565.
36. Simon, D. M., N. A. Clarke, B. A. McNeil, I. Johnson, D. Pantuso, L. Dai, D. Chai, and S. Zimmerly. 2008. Group II introns in Eubacteria and Archaea: ORF-less introns and new varieties. RNA 14:1704-1713.
37. Singh, N. N., and A. M. Lambowitz. 2001. Interaction of a group II intron ribonucleoprotein endonuclease with its DNA target site investigated by DNA footprinting and modification interference. J. Mol. Biol. 309:361-386.
38. Smith, D., J. Zhong, M. Matsuura, A. M. Lambowitz, and M. Belfort. 2005. Recruitment of host functions suggests a repair pathway for late steps in group II intron retrohoming. Genes Dev. 19:2477-2487. (Pubitemid 41483695)
39. Stokes, H. W., and R. M. Hall. 1989. A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons. Mol. Microbiol. 3:1669-1683.
40. Stokes, H. W., D. B. O'Gorman, G. D. Recchia, M. Parsekhian, and R. M. Hall. 1997. Structure and function of 59-base element recombination sites associated with mobile gene cassettes. Mol. Microbiol. 26:731-745.
41. Sunde, M. 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.
42. Toor, N., G. Hausner, and S. Zimmerly. 2001. Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases. RNA 7:1142-1152. (Pubitemid 32726912)
43. Vaisvila, R., R. D. Morgan, J. Posfai, and E. A. Raleigh. 2001. Discovery and distribution of super-integrons among pseudomonads. Mol. Microbiol. 42:587-601.
44. Vellore, J., S. E. Moretz, and B. C. Lampson. 2004. A group II intron-type open reading frame from the thermophile Bacillus (Geobacillus) stearothermophilus encodes a heat-stable reverse transcriptase. Appl. Environ. Microbiol. 70:7140-7147.
45. Venter, J. C., K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch, J. A. Eisen, D. Wu, I. Paulsen, K. E. Nelson, W. Nelson, D. E. Fouts, S. Levy, A. H. Knap, M. W. Lomas, K. Nealson, O. White, J. Peterson, J. Hoffman, R. Parsons, H. Baden-Tillson, C. Pfannkoch, Y. H. Rogers, and H. O. Smith. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74. (Pubitemid 38451457)
46. VIM-2 gene cassettes. J. Antimicrob. Chemother. 49:837-840.
47. Zhong, J., and A. M. Lambowitz. 2003. Group II intron mobility using nascent strands at DNA replication forks to prime reverse transcription. EMBO J. 22:4555-4565. (Pubitemid 37087208)
48. Zimmerly, S., G. Hausner, and X. Wu. 2001. Phylogenetic relationships among group II intron ORFs. Nucleic Acids Res. 29:1238-1250.
49. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31:3406-3415. (Pubitemid 37442169)