Conserved Target for Group II Intron Insertion in Relaxase Genes of Conjugative Elements of Gram-Positive Bacteria

Journal of Bacteriology

Volumn 186, Issue 8, 2004, Pages 2393-2401

  Staddon, Jack H ^a   Bryan, Edward M ^a,b   Manias, Dawn A ^a   Dunny, Gary M ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

^b MONOGRAM BIOSCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CHLORAMPHENICOL; DNA; ENZYME; ERYTHROMYCIN; KANAMYCIN; NUCLEOTIDE; RELAXASE; RNA; SPECTINOMYCIN; STREPTOMYCIN; TETRACYCLINE; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; GENE; GRAM POSITIVE BACTERIUM; INTRON; MINIMUM INHIBITORY CONCENTRATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY; TRANSPOSON;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CONJUGATION, GENETIC; DNA NUCLEOTIDYLTRANSFERASES; DNA TRANSPOSABLE ELEMENTS; GENE TARGETING; GENES, BACTERIAL; GRAM-POSITIVE BACTERIA; INTRONS; MOLECULAR SEQUENCE DATA; MUTAGENESIS, INSERTIONAL; OPEN READING FRAMES; PLASMIDS; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT;

BACTERIA (MICROORGANISMS); INSERTION SEQUENCES; POSIBACTERIA; PROKARYOTA; TRANSPOSONS;

EID: 1842558979     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.186.8.2393-2401.2004     Document Type: Article

References (50)

1. Ayoub, P., A. O. Kiliç, and M. N. Vijayakumar. 1991. Tn5253, the pneumococcal ω (cat tet) BM6001 element, is a composite structure of two conjugative transposons, Tn5251 and Tn5252. J. Bacteriol. 173:1617-1622.
2. Bae, T., B. Kozlowicz, and G. M. Dunny. 2002. Two targets in pCF10 DNA for PrgX binding: their role in production of Qa and prgX mRNA and in regulation of pheromone-inducible conjugation. J. Mol. Biol. 315:995-1007.
3. Bonen, L., and J. Vogel. 2001. The ins and outs of group II introns. Trends Genet. 17:322-331.
4. Bruand, C., S. D. Ehrlich, and L. Janniere. 1991. Unidirectional theta replication of the structurally stable Enterococcus faecalis plasmid pAMβ1. EMBO J. 10:217t-2177.
5. Bruand, C., E. Le Chatelier, S. D. Ehrlich, and L. Janniere. 1993. A fourth class of theta-replicating plasmids: the pAMβ1 family from gram-positive bacteria. Proc. Natl. Acad. Sci. USA 90:11668-11672.
6. Bryan, E. M., T. Bae, M. Kleerebezem, and G. M. Dunny. 2000. Improved vectors for nisin-controlled expression in gram-positive bacteria. Plasmid 44:183-190.
7. Byrd, D. R., and S. W. Matson. 1997. Nicking by transesterification: the reaction catalysed by a relaxase. Mol. Microbiol. 25:1011-1022.
8. Cousineau, B., S. Lawrence, D. Smith, and M. Belfort. 2000. Retrotransposition of a bacterial group II intron. Nature 404:1018-1021.
9. Cousineau, B., D. Smith, S. Lawrence-Cavanagh, J. E. Mueller, J. Yang, D. Mills, D. Manias, G. Dunny, A. M. Lambowitz, and M. Belfort. 1998. Retrohoming of a bacterial group II intron: mobility via complete reverse splicing, independent of homologous DNA recombination. Cell 94:451-462.
10. Dai, L., and S. Zimmerly. 2002. Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behavior. Nucleic Acids Res. 30:1091-1102.
11. Dunny, G., C. Funk, and J. Adsit. 1981. Direct stimulation of the transfer of antibiotic resistance by sex pheromones in Streptococcus faecalis. Plasmid 6:270-278.
12. Dunny, G., M. Yuhasz, and E. Ehrenfeld. 1982. Genetic and physiological analysis of conjugation in Streptococcus faecalis. J. Bacteriol. 151:855-859.
13. Dunny, G. M., B. L. Brown, and D. B. Clewell. 1978. Induced cell aggregation and mating in Streptococcus faecalis: evidence for a bacterial sex pheromone. Proc. Natl. Acad. Sci. USA 75:3479-3483.
14. Eickbush, T. H. 1999. Mobile introns: retrohoming by complete reverse splicing. Curr. Biol. 9:R11-R14.
15. Eskes, R., L. Liu, H. Ma, M. Y. Chao, L. Dickson, A. M. Lambowitz, and P. S. Perlman. 2000. Multiple homing pathways used by yeast mitochondrial group II introns. Mol. Cell. Biol. 20:8432-8446.
16. Eskes, R., J. Yang, A. M. Lambowitz, and P. S. Perlman. 1997. Mobility of yeast mitochondrial group II introns: engineering a new site specificity and retrohoming via full reverse splicing. Cell 88:865-874.
17. Francia, M. V., and D. B. Clewell. 2002. Transfer origins in the conjugative Enterococcus faecalis plasmids PAD1 and pAM373: identification of the pAD1 nic site, a specific relaxase and a possible TraG-like protein. Mol. Microbiol. 45:375-395.
18. Gold, O. G., H. V. Jordan, and J. van Houte. 1975. The prevalence of enterococei in the human mouth and their pathogenicity in animal models. Arch. Oral Biol. 20:473-477.
19. Guo, H., M. Karherg, M. Long, J. P. Jones III, B. Sullenger, and A. M. Lambowitz. 2000. Group II introns designed to insert into therapeutically relevant DNA target sites in human cells. Science 289:452-457.
20. Guo, H., S. Zimmerly, P. S. Perlman, and A. M. Lambowitz. 1997. Group II intron endonucleases use both RNA and protein subunits for recognition of specific sequences in double-stranded DNA. EMBO J. 16:6835-6848.
21. Ichiyanagi, K., A. Beauregard, S. Lawrence, D. Smith, B. Cousineau, and M. Belfort. 2002. Retrotransposition of the Ll.LtrB group II intron proceeds predominantly via reverse splicing into DNA targets. Mol. Microbiol. 46: 1259-1272.
22. Klein, J. R., and G. M. Dunny. 2002. Bacterial group II introns and their association with mobile genetic elements. Front. Biosci. 7:d1843-d1856.
23. Kulkosky, J., K. S. Jones, R. A. Katz, J. P. Mack, and A. M. Skalka. 1992. Residues critical for retrovital integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases. Mol. Cell. Biol. 12:2331-2338.
24. Lanka, E., and B. M. Wilkins. 1995. DNA processing reactions in bacterial conjugation. Annu. Rev. Biochem. 64:141-169.
25. Le Bourgeois, P., M. L. Daveran-Mingot, and P. Ritzenthaler. 2000. Genome plasticity among related Lactococcus strains: identification of genetic events associated with macrorestriction polymorphisms. J. Bacteriol. 182:2481-2491.
26. Lebmann, K., and U. Schmidt. 2003. Group II introns: structure and catalytic versatility of large natural ribozymes. Crit. Rev. Biochem. Mol. Biol. 38:249-303.
27. Martinez-Abarca, F., and N. Toro. 2000. Group II introns in the bacterial world. Mol. Microbiol. 38:917-926.
28. Matsuura, M., R. Saldanha, H. Ma, H. Wank, J. Yang, G. Mohr, S. Cavanagh, G. M. Dunny, M. Belfort, and A. M. Lambowitz. 1997. A bacterial group II intron encoding reverse transcriptase, maturase, and DNA endonuclease activities: biochemical demonstration of maturase activity and insertion of new genetic information within the intron. Genes Dev. 11:2910-2924.
29. Michel, F., K. Umesono, and H. Ozeki. 1989. Comparative and functional anatomy of group II catalytic introns-a review. Gene 82:5-30.
30. Mills, D. A., D. A. Manias, L. L. McKay, and G. M. Dunny. 1997. Homing of a group II intron from Lactococcus lactis subsp. lactis ML3. J. Bacteriol. 179:6t07-6t11.
31. Mills, D. A., L. L. McKay, and G. M. Dunny. 1996. Splicing of a group II intron involved in the conjugative transfer of pRS01 in lactococci. J. Bacteriol. 178:3531-3538.
32. Mills, D. A., T. G. Phister, G. M. Dunny, and L. L. McKay. 1998. An origin of transfer (oriT) on the conjugative element pRS01 from Lactococcus lactis subsp. lactis ML3. Appl. Environ. Microbiol. 64:1541-1544.
33. Mohr, G., P. S. Perlman, and A. M. Lambowitz. 1993. Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function. Nucleic Acids Res. 21:4991-4997.
34. 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.
35. O'Sullivan, D., R. P. Ross, D. P. Twomey, G. F. Fitzgerald, C. Hill, and A. Coffey. 2001. Naturally occurring lactococcal plasmid pAH90 links bacteriophage resistance and mobility functions to a food-grade selectable marker. Appl. Environ. Microbiol. 67:929-937.
36. Pansegrau, W., W. Schröder, and E. Lanka. 1994. Concerted action of three distinct domains in the DNA cleaving-joining reaction catalyzed by relaxase (TraI) of conjugative plasmid RP4. J. Biol. Chem. 269:2782-2789.
37. Paulsen, I. T., L. Banerjei, G. S. Myers, K. E. Nelson, R. Seshadri, T. D. Read, D. E. Fouts, J. A. Eisen, S. R. Gill, J. F. Heidelberg, H. Tettelin, R. J. Dodson, L. Umayam, L. Brinkac, M. Beanan, S. Daugherty, R. T. DeBoy, S. Durkin, J. Kolonay, R. Madupu, W. Nelson, J. Vamathevan, B. Tran, J. Upton, T. Hansen, J. Shetty, H. Khouri, T. Utterback, D. Radune, K. A. Ketchum, B. A. Dougherty, and C. M. Fraser. 2003. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 299:2071-2074.
38. Sharp, P. A. 1991. "Five easy pieces." Science 254:663.
39. Shearman, C., J. J. Godon, and M. Gasson. 1996. Splicing of a group II intron in a functional transfer gene of Lactococcus lactis. Mol. Microbiol. 21:45-53.
40. 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.
41. Srinivas, P., A. O. Kiliç, and M. N. Vijayakumar. 1997. Site-specific nicking in vitro at oriT by the DNA relaxase of Ta5252. Plasmid 37:42-50.
42. Streisinger, G., Y. Okada, J. Emrich, J. Newton, A. Tsugita, E. Terzaghi, and M. Inouye. 1966. Frameshift mutations and the genetic code. Cold Spring Harbor Symp. Quant. Biol. 31:77-84.
43. 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.
44. Trieu-Cuot, P., and P. Courvalin. 1983. Nucleotide sequence of the Streptococcus faecalis plasmid gene encoding the 3′5′ -aminoglycoside phosphotransferase type III. Gene 23:331-341.
45. Varsaki, A., M. Lucas, A. S. Afendra, C. Drainas, and F. De La Cruz. 2003. Genetic nd biochemical characterization of MbeA, the relaxase involved in plasmid ColE1 conjugative mobilization. Mol. Microbiol. 48:481-493.
46. Vijayakumar, M. N., and S. Ayalew. 1993. Nucleotide sequence analysis of the termini and chromosomal locus involved in site-specific integration of the streptococcal conjugative transposon Tn5252. J. Bacteriol. 175:2713-2719.
47. Yagi, Y., and D. B. Clewell. 1980. Recombination-deficient mutant of Streptococcus faecalis. J. Bacteriol. 143:966-970.
48. Zhong, J., M. Karherg, and A. M. Lambowitz. 2003. Targeted and random bacterial gene disruption using a group II intron (targetron) vector containing a retrotransposition-activated selectable marker. Nucleic Acids Res. 31: 1656-1664.
49. Zhou, L., D. A. Manias, and G. M. Dunny. 2000. Regulation of intron function: efficient splicing in vivo of a bacterial group II intron requires a functional promoter within the intron. Mol. Microbiol. 37:639-651.
50. Zimmerly, S., G. Hausner, and X. Wu. 2001. Phylogenetic relationships among group II intron ORFs. Nucleic Acids Res. 29:1238-1250.