Genetic and sequence analysis of the pTiC58 trb locus, encoding a mating-pair formation system related to members of the type IV secretion family

Journal of Bacteriology

Volumn 180, Issue 23, 1998, Pages 6164-6172

  Li, Pei Li ^a   Everhart, Dawn M ^a,b   Farrand, Stephen K ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b Family Practice Residency Program   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PLASMID DNA;

ARTICLE; DNA SEQUENCE; DNA TRANSFER; ESCHERICHIA COLI; GENE LOCUS; NONHUMAN; OPEN READING FRAME; PLASMID; PRIORITY JOURNAL; RHIZOBIUM RADIOBACTER;

AGROBACTERIUM; AGROBACTERIUM TUMEFACIENS; ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA; UNIDENTIFIED BACTERIOPHAGE;

EID: 0031786870     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/.180.23.6164-6172.1998     Document Type: Article

References (68)

1. Alt-Mörbe, J., J. L. Stryker, C. Fuqua, P.-L. Li, S. K. Farrand, and S. C. Winans. 1996. The conjugal transfer system of Agrobacterium tumefaciens octopine-type Ti plasmids is closely related to the transfer system of an IncP plasmid and distantly related to Ti plasmid vir genes. J. Bacteriol. 178:4248-4257.
2. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
3. Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
4. Beck von Bodman, S., G. T. Hayman, and S. K. Farrand. 1992. Opine catabolism and conjugal transfer of the nopaline Ti plasmid pTiC58 are coordinately regulated by a single repressor. Proc. Natl. Acad. Sci. USA 89: 643-647.
5. Beck von Bodman, S., J. E. McCutchan, and S. K. Farrand. 1989. Characterization of conjugal transfer functions of Agrobacterium tumefaciens Ti plasmid pTiC58. J. Bacteriol. 171:5281-5289.
6. Beijersbergen, A., A. D. Dulk-Ras, R. A. Schilperoort, and P. J. J. Hooykaas. 1992, Conjugative transfer by the virulence system of Agrobacterium tumefaciens. Science 256:1324-1327.
7. Berger, B. R., and P. J. Christie. 1993. The Agrobacterium tumefaciens virB4 gene product is an essential virulence protein requiring an intact nucleoside triphosphate-binding domain. J. Bacteriol. 175:1723-1734.
8. Binns, A. N., C. E. Beaupré, and E. M. Dale. 1995. Inhibition of VirB-mediated transfer of diverse substrates from Agrobacterium tumefaciens by the IncQ plasmid RSF1010. J. Bacteriol. 177:4890-4899.
9. Binns, A. N., and M. F. Thomashow. 1988. Cell biology of Agrobacterium infection and transformation of plants. Annu. Rev. Microbiol. 42:575-606.
10. Censini, S., C. Lange, Z. Xiang, J. E. Crabtree, P. Ghiara, M. Borodovsky, R. Rappuoli, and A. Covacci. 1996. cag, a pathogenicity island of Helicobacter pylori, encodes type I-specific and disease-associated virulence factors. Proc. Natl. Acad. Sci. USA 93:14648-14653.
11. Chilton, M. D., T. C. Currier, S. K. Farrand, A. J. Bendich, M. P. Gordon, and E. W. Nester. 1974. Agrobacterium tumefaciens DNA and PS8 bacteriophage DNA not detected in crown gall tumors. Proc. Natl. Acad. Sci. USA 71:3672-3676.
12. Christie, P. J. 1997. Agrobacterium tumefaciens T-complex transport apparatus: a paradigm for a new family of multifunctional transporters in eubacteria. J. Bacteriol. 179:3085-3094.
13. Christie, P. J., J. E. Ward, Jr., M. P. Gordon, and E. W. Nester. 1989. A gene required for transfer of T-DNA to plants encodes an ATPase with autophosphorylating activity. Proc. Natl. Acad. Sci. USA 86:9677-9681.
14. Cook, D. M., and S. K. Farrand. 1992. The oriT region of the Agrobacterium tumefaciens Ti plasmid pTiC58 shares DNA sequence identity with the transfer origins of RSF1010 and RK2/RP4 and with T-region borders. J. Bacteriol. 174:6238-6246.
15. Cook, D. M., P.-L. Li, F. Ruchaud, S. Padden, and S. K. Farrand. 1997. Ti plasmid conjugation is independent of vir: reconstitution of the tra functions from pTiC58 as a binary system. J. Bacteriol. 179:1291-1297.
16. Depicker, A., M. de Wilde, G. de Vos, R. de Vos, M. Van Montagu, and J. Schell. 1980. Molecular cloning of overlapping segments of the nopaline Ti-plasmid pTiC58 as a means to restriction endonuclease mapping. Plasmid 3:193-211.
17. Engler, G., R. Depicker, R. Maenhaut, R. Villarroel, M. Van Montagu, and J. Schell. 1981. Physical mapping of DNA base sequence homologies between an octopine and a nopaline Ti plasmid of Agrobacterium tumefaciens. J. Mol. Biol. 152:183-208.
18. Farrand, S. K. 1993. Conjugation of Agrobacterium plasmids, p. 255-291. In D. B. Clewell (ed.), Bacterial conjugation. Plenum Press, Inc., New York, N.Y.
19. Farrand, S. K., I. Hwang, and D. M. Cook. 1996. The tra region of the nopaline-type Ti plasmid is a chimera with elements related to the transfer systems of RSF1010, RP4, and F. J. Bacteriol. 178:4233-4247.
20. Farrand, S. K., S. P. O'Morchoe, and J. McCutchan. 1989. Construction of an Agrobacterium tumefaciens C58 recA mutant. J. Bacteriol. 171:5314-5321.
21. Freiberg, C., R. Fellay, A. Bairoch, W. J. Broughton, A. Rosenthal, and X. Perret. 1997. Molecular basis of symbiosis between Rhizobium and legumes. Nature (London) 387:394-401.
22. Frost, L. S. 1993. Conjugative pili and pilus-specitic phages, p. 189-221. In D. B. Clewell (ed.), Bacterial conjugation. Plenum Press, Inc., New York, NY.
23. Frost, L. S., K. Ippen-Ihler, and R. A. Skurray. 1994. An analysis of the sequence and gene products of the transfer region of the F sex factor. Microbiol. Rev. 58:162-210.
24. Fullner, K. J., K. M. Stephens, and E. W. Nester. 1994. An essential virulence protein of Agrobacterium tumefaciens, VirB4, requires an intact mononucleotide binding domain to function in transfer of T-DNA. Mol. Gen. Genet. 245:704-715.
25. Fuqua, C., and S. C. Winans. 1996. Conserved cis-acting promoter elements are required for density-dependent transcription of Agrobacterium tumefaciens conjugal transfer genes. J. Bacteriol. 178:435-440.
26. Fuqua, W. C., S. C. Winans, and E. P. Greenberg. 1994. Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators. J. Bacteriol. 176:269-275.
27. Gallie, D. R., M. Hagiya, and C. I. Kudo. 1985. Analysis of Agrobacterium tumefaciens plasmid pTiC58 replication region with a novel high-copy-number derivative. J. Bacteriol. 161:1034-1041.
28. Grahn, A. M., J. Haase, E. Lanka, and D. H. Bamford. 1997. Assembly of a functional phage PRD1 receptor depends on 11 genes of the IncP plasmid mating pair formation complex. J. Bacteriol. 179:4733-4740.
29. Haase, J., M. Kalkum, and E. Lanka. 1996. TrbK, a small cytoplasmic membrane lipoprotein, functions in entry exclusion of the IncPα plasmid RP4. J. Bacteriol. 178:6720-6729.
30. Haase, J., and E. Lanka. 1997. A specific protease encoded by the conjugative DNA transfer systems of IncP and Ti plasmids is essential for pilus synthesis. J. Bacteriol. 179:5728-5735.
31. Haase, J., R. Lurz, A. M. Grahn, D. H. Bamford, and E. Lanka. 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.
32. Hayman, G. T., and S. K. Farrand. 1988. Characterization and mapping of the agrocinopine-agrocin 84 locus on the nopaline Ti plasmid pTiC58. J. Bacteriol. 170:1759-1767.
33. Hofmann, K., and W. Stoffel. 1993. TMBASE-A database of membrane spanning protein segments. Biol. Chem. Hoppe-Seyler 374:166.
34. Hooykaas, P. J. J., and A. G. M. Beijersbergen. 1994. The virulence system of Agrobacterium tumefaciens. Annu. Rev. Phytopathol. 32:157-179.
35. Hwang, I., D. M. Cook, and S. K. Farrand. 1995. A new regulatory element modulates homoserine lactone-mediated autoinduction of Ti plasmid conjugal transfer. J. Bacteriol. 177:449-458.
36. Hwang, I., P.-L. Li, L. Zhang, K. R. Piper, D. M. Cook, M. E. Tate, and S. K. Farrand. 1994. TraI, a LuxI homologue, is responsible for production of conjugation factor, the Ti plasmid N-acylhomoserine lactone autoinducer. Proc. Natl. Acad. Sci. USA 91:4639-4643.
37. Johnson, F. D., and D. L. Burns. 1994. Detection and subcellular localization of three Ptl proteins involved in the secretion of pertussis toxin from Bodetella pertussis. J. Bacteriol. 176:5350-5356.
38. Keen, N. T., S. Tamaki, D. Kobayashi, and D. Trollinger. 1988. Improved broad-host-range plasmids for DNA cloning in Gram-negative bacteria. Gene 70:191-197.
39. Lessl, M., D. Balzer, W. Pansegrau, and E. Lanka. 1992. Sequence similarities between the RP4 Tra2 and the Ti VirB region strongly support the conjugation model for T-DNA transfer. J. Biol. Chem. 267:20471-20480.
40. Lessl, M., D. Balzer, K. Weyrauch, and E. Lanka. 1993. The mating pair formation system of plasmid RP4 defined by RSF1010 mobilization and donor-specific phage propagation. J. Bacteriol. 175:6415-6425.
41. Lessl, M., and E. Lanka. 1994. Common mechanisms in bacterial conjugation and Ti-mediated T-DNA transfer to plant cells. Cell 77:321-324.
42. Li, P.-L., and S. K. Farrand. Unpublished data.
43. Mark, C. 1988. "DNA Strider": a "C" program for the fast analysis of DNA and protein sequences on the Apple Macintosh family of computers. Nucleic Acids Res. 16:1829-1836.
44. Moré, M. I., L. D. Finger, J. L. Stryker, C. Fuqua, A. Eberhard, and S. C. Winans. 1996. Enzymatic synthesis of a quorum-sensing autoinducer through use of defined substrates. Science 272:1655-1658.
45. Nelson, C. D., C. E. Bratis, and S. K. Farrand. Unpublished data.
46. Nielsen, H., J. Engelbrecht, S. Brunak, and G. von Heijne. 1997. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10:1-6.
47. Pansegrau, W., E. Lanka, P. T. Barth, D. H. Figurski, D. G. Guiney, D. Haas, D. R. Helinski, H. Schwab, V. A. Stanisich, and C. M. Thomas. 1994. Complete nucleotide sequence of Birmingham IncPα plasmids. Compilation and comparative analysis. J. Mol. Biol. 239:623-663.
48. Piper, K. R., S. Beck von Bodman, and S. K. Farrand. 1993. Conjugation factor of Agrobacterium tumefaciens regulates Ti plasmid transfer by autoinduction. Nature (London) 362:448-450.
49. Piper, K. R., S. Beck von Bodman, I. Hwang, and S. K. Farrand. Submitted for publication.
50. Pohlman, R. F., H. D. Genetti, and S. C. Winans. 1994. Common ancestry between IncN conjugal transfer genes and macromolecular export systems of plant and animal pathogens. Mol. Microbiol. 14:655-668.
51. Rashkova, S., G. M. Spudich, and P. J. Christie. 1997. Characterization of membrane and protein interaction determinants of the Agrobacterium tumefaciens VirB11 ATPase. J. Bacteriol. 179:583-591.
52. Rost, B., R. Casadio, and P. Fariselli. 1996. Refining neural network predictions for helical transmembrane protein by dynamic programming, p. 192-200. In D. States, et al. (ed.), Fourth International Conference on Intelligent Systems for Molecular Biology, St. Louis, Mo. AAAI Press, Menlo Park, Calif.
53. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Press, Cold Spring Harbor, N.Y.
54. Schröder, J., J. von Lintig, and H. Zanker. 1990. Functional organization of the regions responsible for nopaline and octopine catabolism in Ti plasmids of Agrobacterium tumefaciens, p. 28-31. In H. Hennecke and D. P. S. Verma (ed.), Advances in molecular genetics of plant-microbe interactions, vol. 1. Kluwer Academic Publishers, Amsterdam, The Netherlands.
55. Shirasu, K., Z. Koukolikova-Nicola, B. Hohn, and C. I. Kado. 1994. An inner-membrane-associated virulence protein essential for T-DNA transfer from Agrobacterium tumefaciens to plants exhibits ATPase activity and similarities to conjugative transfer genes. Mol. Microbiol. 11:581-588.
56. Shirasu, K., P. Morel, and C. I. Kado. 1990. Characterization of the virB operon of an Agrobacterium tumefaciens Ti plasmid: nucleotide sequence and protein analysis. Mol. Microbiol. 4:1153-1163.
57. Stephens, K. M., C. Roush, and E. Nester. 1995. Agrobacterium tumefaciens VirB11 protein requires a consensus nucleotide-binding site for function in virulence. J. Bacteriol. 177:27-36.
58. Suzuki, K., N. Ohta, Y. Hattori, M. Uraji, A. Kato, and K. Yoshida. 1998. Novel structural difference between nopaline- and octopine-rype trbJ genes: construction of genetic and physical map and sequencing of trb/traI and rep gene clusters of a new Ti plasmid pTi-SAKURA. Biochim. Biophys. Acta 1396:1-7.
59. Tabata, S., P. J. J. Hooykaas, and A. Oka. 1989. Sequence determination and characterization of the replicator region in the tumor-inducing plasmid pTiB6S3. J. Bacteriol. 171:1665-1672.
60. Tummuru, M. K. R., S. A. Sharma, and M. J. Blaser. 1995. Helicobacter pylori picB, a homologue of the Bordetella pertussis toxin secretion protein, is required for induction of IL-8 in gastric epithelial cells. Mol. Microbiol. 18: 867-876.
61. Vogel, J. P., H. L. Andrews, S. K. Wong, and R. R. Isberg. 1998. Conjugative transfer by the virulence system of Legionella pneumophila. Science 279:873-876.
62. von Heijne, G. 1986. A new method for predicting signal sequence cleavage sites. Nucleic Acids Res. 14:4683-4690.
63. von Lintig, J., H. Zanker, and J. Schröder. 1991. Positive regulators of opine-inducible promoters in the nopaline and octopine catabolism regions of Ti plasmids. Mol. Plant-Microbe Interact. 4:370-378.
64. Walker, J. E., M. Saraste, M. J. Runswick, and N. J. Gay. 1982. Distantly related sequences in the α- and β-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1:945-951.
65. Ward, J. E., D. E. Akiyoshi, D. Regier, A. Datta, M. P. Gordon, and E. W. Nester. 1988. Characterization of the virB operon from an Agrobacterium tumefaciens Ti plasmid. J. Biol. Chem. 263:5804-5814.
66. Weiss, A. A., F. D. Johnson, and D. L. Burns. 1993. Molecular characterization of an operon required for pertussis toxin secretion. Proc. Natl. Acad. Sci. USA 90:2970-2974.
67. Zambryski, P. C. 1992. Chronicles from the Agrobacterium-plant cell DNA transfer story. Annu. Rev. Plant Physiol. Plant Mol. Biol. 43:465-490.
68. Zhang, L., P. J. Murphy, A. Kerr, and M. E, Tate. 1993. Agrobacterium conjugation and gene regulation by N-acyl-L-homoserine lactones. Nature (London) 362:446-448.