Distribution of restriction enzyme recognition sequences on broad host range plasmid RP4: Molecular and evolutionary implications

Journal of Molecular Biology

Volumn 258, Issue 3, 1996, Pages 447-456

  Wilkins, Brian M ^a   Chilley, Paul M ^a   Thomas, Angela T ^a   Pocklington, Michael J ^a  

^a UNIVERSITY OF LEICESTER   (United Kingdom)

Author keywords

Bacterial conjugation; IncP plasmids; Restriction avoidance; RP4; Type II restriction enzymes

Indexed keywords

OLIGONUCLEOTIDE; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE; VIRUS DNA;

ARTICLE; BINDING SITE; DNA CLEAVAGE; DNA SEQUENCE; ENZYME SPECIFICITY; ENZYME SUBSTRATE COMPLEX; EVOLUTION; MOLECULAR RECOGNITION; NONHUMAN; PLASMID; PRIORITY JOURNAL; PROTEIN DNA INTERACTION;

EID: 0029868040     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0261     Document Type: Article

References (50)

1. Arber, W. & Linn, S. (1969). DNA modification and restriction. Annu. Rev. Biochem. 38, 467-500.
2. Barcus, V. A. & Murray, N. E. (1995). Barriers to recombination: restriction. In Population Genetics of Bacteria, Society for Microbiology Symposium 52, (Baumberg, S., Young, J. P. W., Wellington, E. M. H. & Saunders, J. R., eds), pp. 31-58, Cambridge University Press, Cambridge.
3. Barth, P. T. & Grinter, N. J. (1977). Map of plasmid RP4 derived by insertion of transposon C. J. Mol. Biol. 113, 455-474.
4. Bickle, T. A. & Krüger, D. H. (1993). Biology of DNA restriction. Microbiol. Rev. 57, 434-450.
5. Boyer, H. W. (1971). DNA restriction and modification mechanisms in bacteria. Annu. Rev. Microbiol. 25, 153-176.
6. Chilley, P. M. & Wilkins, B. M. (1995). Distribution of the ardA family of antirestriction genes on conjugative plasmids. Microbiology, 141, 2157-2164.
7. Datta, N. & Hughes, V. M. (1983). Plasmids of the same Inc groups in Enterobacteria before and after the medical use of antibiotics. Nature, 306, 616-617.
8. Datta, N., Hedges, R. W., Shaw, E. J., Sykes, R. B. & Richmond, M. H. (1971). Properties of an R-factor from Pseudomonas aeruginosa. J. Bacteriol. 108, 1244-1249.
9. Delver, E. P., Kotova, V. U., Zavilgelsky, G. B. & Belogurov, A. A. (1991). Nucleotide sequence of the gene (ard) encoding the antirestriction protein of plasmid ColIb-P9. J. Bacteriol. 173, 5887-5892.
10. Frost, L. S., Ippen-Ihler, K. & Skurray, R. A. (1994). Analysis of the sequence and gene products of the transfer region of the F sex factor. Microbiol. Rev. 58, 162-210.
11. 2-fixing isolates from rice in Vietnam. Int. J. System. Bacteriol. 45, 274-289.
12. Guiney, D. G. (1982). Host range of conjugation and replication functions of Escherichia coli sex factor Flac; comparison with the broad host range plasmid RK2. J. Mol. Biol. 162, 699-703.
13. Guiney, D. G. (1993). Broad host range conjugative and mobilizable plasmids in Gram-negative bacteria. In Bacterial Conjugation (Clewell, D. B., ed.), pp. 75-103, Plenum Press, New York.
14. Haase, J., Lurz, R., Grahn, A. M., Bamford, D. H. & Lanka, E. (1995). Bacterial conjugation mediated by plasmid RP4: RSF1010 mobilization, donor-specific phage propagation, and pilus production require the same Tra2 core components of a proposed DNA transport complex. J. Bacteriol. 177, 4779-4791.
15. Heitman, J., Treisman, J., Davis, N. G. & Russel, M. (1989). Cassettes of the f1 intergenic region. Nucl. Acids Res. 17, 4413.
16. Holloway, B. W. & Richmond, M. H. (1973). R-factors used for genetic studies in strains of Pseudomonas aeruginosa and their origin. Genet. Res. 12, 103-105.
17. Hooykaas, P. J. J. & Beijersbergen, A. G. M. (1994). The virulence system of Agrobacterium tumefaciens. Annu. Rev. Phytopathol. 32, 157-179.
18. Kulakauskas, S., Lubys, A. & Ehrlich, S. D. (1995). DNA restriction-modification systems mediate plasmid maintenance. J. Bacteriol. 177, 3451-3454.
19. Ingram, L. C., Richmond, M. H. & Sykes, R. B. (1973). Molecular characterization of the R factors implicated in the carbenicillin resistance of a sequence of Pseudomonas aeruginosa strains isolated from burns. Antimicrob. Agents Chemother. 3, 279-288.
20. Jacoby, G. A. (1977). Classification of plasmids in Pseudomonas aeruginosa. In Microbiology-1977 (Schlessinger, D., ed.), pp. 119-126, American Society for Microbiology, Washington DC.
21. Karlin, S., Burge, C. & Campbell, A. M. (1992). Statistical analyses of counts and distributions of restriction sites in DNA sequences. Nucl. Acids Res. 20, 1363-1370.
22. Korona, R., Korona, B. & Levin, B. R. (1993). Sensitivity of naturally occurring coliphages to type I and type II restriction and modification. J. Gen. Microbiol. 139, 1283-1290.
23. Lanka, E. & Wilkins, B. M. (1995). DNA processing reactions in bacterial conjugation. Annu. Rev. Biochem. 64, 141-169.
24. Lanka, E., Lurz, R. & Fürste, J. P. (1983). Molecular cloning and mapping of SphI restriction fragments of plasmid RP4. Plasmid, 10, 303-307.
25. Larsen, M. H. & Figurski, D. H. (1994). Structure, expression, and regulation of the kilC operon of promiscuous IncPα plasmids. J. Bacteriol. 176, 5022-5032.
26. Lessl, M., Balzer, D., Pansegrau, W. & Lanka, E. (1992). Sequence similarities between the RP4 Tra2 and Ti VirB region strongly support the conjugation model for T-DNA transfer. J. Biol. Chem. 267, 20471-20480.
27. Lessl, M., Balzer, D., Weyrauch, K. & Lanka, E. (1993). The mating pair formation system of plasmid RP4 defined by RSF1010 mobilization and donor-specific phage propagation. J. Bacteriol. 175, 6415-6425.
28. Lowbury, E. J. L., Kidson, A., Lilly, H. A., Ayliffe, G. A. J. & Jones, R. J. (1969). Sensitivity of Pseudomonas aeruginosa to antibiotics: emergence of strains highly resistant to carbenicillin. Lancet, ii, 448-452.
29. McClelland, M. (1985). Selection against dam methylation sites in the genomes of DNA of enterobacteriophages. J. Mol. Evol. 21, 317-322.
30. McKane, M. & Milkman, R. (1995). Transduction, restriction and recombination patterns in Escherichia coli. Genetics, 139, 35-43.
31. Meyer, R., Figurski, D. & Helinski, D. R. (1977). Physical and genetic studies with restriction endonucleases on the broad host range plasmid RK2. Mol. Gen. Genet. 152, 129-135.
32. Naito, T., Kusano, K. & Kobayashi, I. (1995). Selfish behaviour of restriction-modification systems. Science, 267, 897-899.
33. Palleroni, N. J. (1992). Introduction to the Family Pseudomonadaceae. In The Prokaryotes (Balows, A., Trüper, H. G., Dworkin, M., Harder, H. & Schleifer, K.-H., eds), 2nd edit., vol. 3, pp. 3071-3085, Springer-Verlag, New York.
34. Pansegrau, W. & Lanka, E. (1987). Conservation of a common 'backbone' in the genetic organization of the IncP plasmids RP4 and R751. Nucl. Acids Res. 15, 2385.
35. Pansegrau, W., Lanka, E., Barth, P. T., Figurski, D. H., Guiney, D. G., Haas, D., Helinski, D. R., Schwab, H., Stanisich, V. A. & Thomas, C. M. (1994). Complete nucleotide sequence of Birmingham IncPα plasmids: compilation and comparative analysis of sequence data. J. Mol. Biol. 239, 623-663.
36. Rådström, P., Sköld, O., Swedberg, G., Flensburg, J., Roy, P. H. & Sundström, L. (1994). Transposon Tn5090 of plasmid R751, which carries an integron, is related to Tn7, Mu and the retroelements. J. Bacteriol. 176, 3257-3268.
37. Read, T. D., Thomas, A. T. & Wilkins, B. M. (1992). Evasion of type I and type II DNA restriction systems by IncI1 plasmid ColIb-P9 during transfer by bacterial conjugation. Mol. Microbiol. 6, 1933-1941.
38. 1 plasmid ColIb-P9. Plasmid, 18, 223-236.
39. Roberts, R. J. & Macelis, D. (1994). REBASE - restriction enzymes and methylases. Nucl. Acids Res. 22, 3628-3639.
40. Rogowsky, P. M., Powell, B. S., Shirasu, K., Lin, T.-S., Morel, P., Zyprian, E. M., Steck, T. R. & Kado, C. I. (1990). Molecular characterization of the vir regulon of Agrobacterium tumefaciens: complete nucleotide sequence and gene organization of the 28.63-kbp regulon cloned as a single unit. Plasmid, 23, 85-106.
41. Rosenberg, A. H., Simon, M. N., Studier, F. W. & Roberts, R. J. (1979). Survey and mapping of restriction endonuclease cleavage sites in bacteriophage T7 DNA. J. Mol. Biol. 135, 907-915.
42. Schroeder, C., Jurkschat, H., Meisel, A., Reich, J-G. & Krüger, D. (1986). Unusual occurrence of EcoPl and EcoP15 recognition sites and counterselection of type II methylation and restriction sequences in bacteriophage T7 DNA. Gene, 45, 77-86.
43. Sharp, P. M. (1986). Molecular evolution of bacteriophages: evidence of selection against the recognition sites of host restriction enzymes. Mol. Biol. Evol. 3, 75-83.
44. Smith, C. A. & Thomas, C. M. (1989). Relationships and evolution of IncP plasmids. In Promiscuous Plasmids of Gram-negative Bacteria (Thomas, C. M., ed.), pp. 57-77, Academic Press, London.
45. Smith, H. R., Humphreys, G. O., Willshaw, G. A. & Anderson, E. S. (1976). Characterisation of plasmids coding for restriction endonuclease EcoRI. Mol. Gen. Genet. 143, 319-325.
46. Thorstenson, Y. R., Kuldau, G. A. & Zambryski, P. C. (1993). Subcellular localization of seven VirB proteins of Agrobacterium tumefaciens: implications for the formation of a T-DNA transport structure. J. Bacteriol. 175, 5233-5241.
47. van Veen, R. J. M., den Dulk-Ras, H., Bisseling, T., Schilperoort, R. A. & Hooykaas, P. J. J. (1988). Crown gall tumor and root nodule formation by the bacterium Phyllobacterium myrsinacearum after the introduction of an Agrobacterium Ti plasmid or a Rhizobium Sym plasmid. Mol. Plant Microbe Interact. 1, 231-234.
48. Wilkins, B. M. (1995). Gene transfer by bacterial conjugation: diversity of systems and functional specializations. In Population Genetics of Bacteria, Society for Microbiology Symposium 52 (Baumberg, S., Young, J. P. W., Wellington, E. M. H. & Saunders, J. R., eds), pp. 59-88, Cambridge University Press, Cambridge.
49. Wilson, G. G. & Murray, N. E. (1991). Restriction and modification systems. Annu. Rev. Genet. 25, 585-627.
50. Womble, D. D. & Rownd, R. H. (1988). Genetic and physical map of plasmid NR1: comparison with other IncFII antibiotic resistance plasmids. Microbiol. Rev. 52, 433-451.