Combined genetic and physical map of the complex genome of Agrobacterium tumefaciens

Journal of Bacteriology

Volumn 181, Issue 17, 1999, Pages 5160-5166

  Goodner, Brad W ^a   Markelz, Brian P ^a   Flanagan, M Casey ^a   Crowell Jr , Chris B ^a   Racette, Jodi L ^a   Schilling, Brittany A ^a   Halfon, Leah M ^a   Mellors, J Scott ^a   Grabowski, Gregory ^a  

^a UNIVERSITY OF RICHMOND   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ARTICLE; CHROMOSOME STRUCTURE; CONTROLLED STUDY; GENE MAPPING; GENOME; NONHUMAN; PLASMID; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; RHIZOBIUM RADIOBACTER;

AGROBACTERIUM TUMEFACIENS;

EID: 0032849712     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.181.17.5160-5166.1999     Document Type: Article

References (60)

1. Allardet-Servent, A., S. Michaux-Charachon, E. Jumas-Bilak, L. Karayan, and M. Ramuz. 1993. Presence of one linear and one circular chromosome in the Agrobacterium tumefaciens C58 genome. J. Bacteriol. 175:7869-7874.
2. Binns, A. N., and M. F. Thomashow. 1988. Cell biology of Agrobacterium infection and transformation of plants. Annu. Rev. Microbiol. 42:575-606.
3. Blattner, F. R., G. Plunkett 3rd, C. A. Bloch, N. T. Perna, V. Burland, M. Riley, J. Collado-Vides, J. D. Glasner, C. K. Rode, G. F. Mayhew, J. Gregor, N. W. Davis, H. A. Kirkpatrick, M. A. Goeden, D. J. Rose, B. Mau, and Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453-1474.
4. Bult, C. J., O. White, G. J. Olsen, L. Zhou, R. D. Fleischmann, G. G. Sutton, J. A. Blake, L. M. FitzGerald, R. A. Clayton, J. D. Gocayne, A. R. Kerlavage, B. A. Dougherty, J. F. Tomb, M. D. Adams, C. I. Reich, R. Overbeek, E. F. Kirkness, K. G. Weinstock, J. M. Merrick, A. Glodek, J. L. Scott, N. S. M. Geoghagen, and J. C. Venter. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1058-1073.
5. Charles, T. C., S. L. Doty, and E. W. Nester. 1994. Construction of Agrobacterium strains by electroporation of genomic DNA and its utility in analysis of chromosomal virulence mutations. Appl. Environ. Microbiol. 60:4192-4194.
6. Charles, T. C., and E. W. Nester. 1993. A chromosomally encoded two-component sensory transduction system is required for virulence of Agrobacterium tumefaciens. J. Bacteriol. 175:6614-6625.
7. Cheng, H.-P., and T. G. Lessie. 1994. Multiple replicons constituting the genome of Pseudomonas cepacia 17616. J. Bacteriol. 176:4034-4042.
8. T. J. Bacteriol. 176: 7694-7702.
9. T: chromosome II is a true chromosome. Microbiology 143:3085-3099.
10. 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.
11. Cooley, M. B., and C. I. Kado. 1991. Mapping of the ros virulence regulatory gene of A. tumefaciens. Mol. Gen. Genet. 230:24-27.
12. Cooley, M. B., M. R. D. Souza, and C. I. Kado. 1991. The virC and virD operons of the Agrobacterium Ti plasmid are regulated by the ros chromosome gene: analysis of the cloned ros gene. J. Bacteriol. 173:2608-2616.
13. Davis, R. W., D. Botstein, and J. R. Roth. 1980. A manual for genetic engineering: advanced bacterial genetics, p. 206-208. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
14. Deckert, G., P. V. Warren, T. Gaasterland, W. G. Young, A. L. Lenox, D. E. Graham, R. Overbeek, M. A. Snead, M. Keller, M. Aujay, R. Huber, R. A. Feldman, J. M. Short, G. J. Olsen, and R. V. Swanson. 1998. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 392: 353-358.
15. de Lorenzo, V., M. Herrero, U. Jakubzik, and K. N. Timmis. 1990. Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria. J. Bacteriol. 172:6568-6572.
16. DiRita, V. J., and S. B. Gelvin. 1987. Deletion analysis of the mannopine synthase gene promoter in sunflower crown gall tumors and Agrobacterium tumefaciens. Mol. Gen. Genet. 207:233-241.
17. Ditta, G., S. Stanfield, D. Corbin, and D. R. Helinski. 1980. Broad host range DNA cloning system for Gram-negative bacteria: construction of a gene bank of Rhizobium meliloti. Proc. Natl. Acad. Sci. USA 77:7347-7351.
18. Douglas, C. J., R. J. Staneloni, R. A. Rubin, and E. W. Nester. 1985. Identification and genetic analysis of an Agrobacterium tumefaciens chromosomal virulence region. J. Bacteriol. 161:850-860.
19. Figurski, D. H., and D. R. Helinski. 1979. Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. Proc. Natl. Acad. Sci. USA 76:1648-1652.
20. Fleischmann, R. D., M. D. Adams, O. White, R. A. Clayton, E. F. Kirkness, A. R. Kerlavage, C. J. Bult, J. F. Tomb, B. A. Dougherty, J. M. Merrick, K. McKenney, G. Sutton, W. FitzHugh, C. Fields, J. D. Gocayne, J. Scott, R. Shirley, L.-I. Liu, A. Glodek, J. M. Kelley, J. F. Weidman, C. A. Phillips, T. Spriggs, E. Hedblom, M. D. Cotton, T. R. Utterback, M. C. Hanna, D. T. Nguyen, D. M. Suadek, R. C. Brandon, L. D. Fine, J. L. Fritchman, J. L. Fuhrmann, N. S. M. Geoghagen, C. L. Gnehm, L. A. McDonald, K. V. Small, C. M. Fraser, H. O. Smith, and J. C. Venter. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512.
21. Friedman, A. M., S. R. Long, S. E. Brown, W. J. Buikema, and F. M. Ausubel. 1982. Construction of a broad host range cosmid cloning vector and its use in the genetic analysis of Rhizobium mutants. Gene 18:289-296.
22. Garfinkel, D. J., R. B. Simpson, L. W. Ream, F. F. White, M. P. Gordon, and E. W. Nester. 1981. Genetic analysis of crown gall: fine structure map of the T-DNA by site-directed mutagenesis. Cell 27:143-153.
23. Gelvin, S. B. 1990. Crown gall disease and hairy root disease: a sledgehammer and a tackhammer. Plant Physiol. 92:281-285.
24. Goodner, B., B. Markelz, J. Racette, C. Flanagan, C. Crowell, S. Mellors, B. Schilling, and L. Halfon. 1998. Chromosome organization in Agrobacterium, p. 1. In Proceedings of the 19th Annual Crown Gall Meeting.
25. Goodner, B. W., B. P. Markelz, M. C. Flanagan, C. B. Crowell, J. L. Racette, B. A. Schilling, J. S. Mellors, and C. M. Lappas. 1999. An Agrobacterium tumefaciens genome project at a primarily undergraduate institution - current progress and future goals. p. C24. In Microbial Genomes III: Sequencing, Functional Characterization, and Comparative Genomics. February 1999.
26. Gray, J., J. Wang, and S. B. Gelvin. 1992. Mutation of the miaA gene of Agrobacterium tumefaciens results in reduced vir gene expression. J. Bacteriol. 174:1086-1098.
27. Haas, D., and B. W. Holloway. 1978. Chromosome mobilization by the R plasmid R68.45: a tool in Pseudomonas genetics. Mol. Gen. Genet. 158:229-237.
28. Hacker, J., G. Blum-Oehler, I. Muhldorfer, and H. Tschape. 1997. Pathogenicity islands of virulent bacteria: structure, function, and impact on microbial evolution. Mol. Microbiol. 23:1089-1097.
29. Hooykaas, P. J. J., R. Peerbolte, A. J. G. Regensburg-Tuink, P. de Vries, and R. A. Schilperoort. 1982. A chromosomal linkage map of Agrobacterium tumefaciens and a comparison with the maps of Rhizobium spp. Mol. Gen. Genet. 188:12-17.
30. Huang, M. W., G. A. Cangelosi, W. Halperin, and E. W. Nester. 1990. A chromosomal Agrobacterium tumefaciens gene required for effective plant signal transduction. J. Bacteriol. 172:1814-1822.
31. Jumas-Bilak, E., C. Maugard, S. Michaux-Charachon, A. Allardet-Servent, A. Perrin, D. O'Callaghan, and M. Ramuz. 1995. Study of the organization of the genomes of Escherichia coli, Brucella melitensis and Agrobacterium tumefaciens by insertion of a unique restriction site. Microbiology 141:2425-2432.
32. Jumas-Bilak, E., S. Michaux-Charachon, G. Bourg, M. Ramuz, and A. Allerdet-Servent. 1998. Unconventional genomic organization in the alpha subgroup of the Proteobacteria. J. Bacteriol. 180:2749-2755.
33. Kaneko, T., S. Sato, H. Kotani, A. Tanaka, E. Asamizu, Y. Nakamura, N. Miyajima, M. Hirosawa, M. Sugiura, S. Sasamoto, T. Kimura, T. Hosouchi, A. Matsuno, A. Muraki, N. Nakazaki, K. Naruo, S. Okumura, S. Shimpo, C. Takeuchi, T. Wada, A. Watanabe, M. Yamada, M. Yasuda, and S. Tabata. 1996. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 3:109-136.
34. Kemner, J. M., X. Liang, and E. W. Nester. 1997. The Agrobacterium tumefaciens virulence gene chvE is part of a putative ABC-type sugar transport operon. J. Bacteriol. 179:2452-2458.
35. Klenk, H. P., R. A. Clayton, J. F. Tomb, O. White, K. E. Nelson, K. A. Ketchum, R. J. Dodson, M. Gwinn, E. K. Hickey, J. D. Peterson, D. L. Richardson, A. R. Kerlavage, D. E. Graham, N. C. Kyrpides, R D. Fleischmann, J. Quackenbush, N. H. Lee, G. G. Sutton, S. Gill, E. F. Kirkness, B. A. Dougherty, K. McKenney, M. D. Adams, B. Loftus, S. Peterson, C. I. Reich, L. K. McNeil, J. H. Badger, A. Glodek, L. Zhou, R. Overbeek, J. D. Gocayne, J. F. Weidman, L. McDonald, T. Utterback, M. D. Cotton, T. Spriggs, P. Artiach, B. P. Kaine, S. M. Sykes, P. W. Sadow, K. P. D'Andrea, C. Bowman, C. Fujii, S. A. Garland, T. M. Mason, G. J. Olsen, C. M. Fraser, H. O. Smith, C. R. Woese, and J. C. Venter. 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364-370.
36. Knauf, V. C., and E. W. Nester. 1982. Wide host range cloning vectors: a cosmid clone bank of an Agrobacterium Ti plasmid. Plasmid 8:45-54.
37. Kunst, F., N. Ogasawara, I. Moszer, A. M. Albertini, G. Alloni, V. Azevedo, M. G. Bertero, P. Bessieres, A. Bolotin, S. Borchert, R. Borriss, L. Boursier, A. Brans, M. Braun, S. C. Brignell, S. Bran, S. Brouillet, C. V. Bruschi, B. Caldwell, V. Capuano, N. M. Carter, S.-K. Choi, J.-J. Codani, I. F. Connerton, N. J. Cummings, R. A. Daniel, F. Denizot, K. M. Devine, A. Dusterhoft, S. D. Ehrlich, P. T. Emmerson, K. D. Entian, J. Errington, C. Fabret, E. Ferrari, D. Foulger, C. Fritz, M. Fujita, Y. Fujita, S. Fuma, A. Galizzi, N. Galleron, S.-Y. Ghim, P. Glaser, A. Goffeau, E. J. Golightly, G. Grandi, G. Guiseppi, B. J. Guy, K. Haga, J. Haiech, C. R. Harwood, A. Henaut, H. Hilbert, S. Holsappel, S. Hosono, M.-F. Hullo, M. Itaya, L. Jones, B. Joris, D. Karamata, Y. Kasahara, M. Klaerr-Blanchard, C. Klein, Y. Kobayashi, P. Koetter, G. Koningstein, S. Krogh, M. Kumano, K. Kurita, A. Lapidus, S. Lardinois, J. Lauber, V. Lazarevic, S.-M. Lee, A. Levine, H. Liu, S. Masuda, C. Mauel, C. Medigue, N. Medina, R. P. Mellado, M. Mizuno, D. Moestl, S. Nakai, M. Noback, D. Noone, M. O'Reilly, K. Ogawa, A. Ogiwara, B. Ouderga, S.-H. Park, V. Parro, T. M. Pohl, D. Portetelle, S. Porwollik, A. M. Prescott, E. Prescecan, P. Pujic, B. Purnelle, G. Rapaport, M. Rey, S. Reynolds, M. Rieger, C. Rivolta, E. Rocha, B. Roche, M. Rose, Y. Sadaie, T. Sato, E. Scanlan, S. Schleich, R. Schroeter, F. Scoffone, J. Sekiguchi, A. Sekowska, S. J. Seror, P. Serror, B.-S. Shin, B. Soldo, A. Sorokin, E. Tacconi, T. Takagi, H. Takahashi, K. Takemaru, M. Takeuchi, A. Tamakoshi, T. Tanaka, P. Terpstra, A. Tognoni, V. Tosato, S. Uchiyama, M. Vandenbol, F. Vannier, A. Vassarotti, A. Viari, R. Wambutt, E. Wedler, H. Wedler, T. Weitzenegger, P. Winters, A. Wipat, H. Yamamoto, K. Yamane, K. Yasumoto, K. Yata, K. Yoshida, H.-F. Yoshikawa, E. Zumstein, H. Yoshikawa, and A. Danchin. 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390:249-256.
38. Lee, C. A. 1996. Pathogenicity islands and the evolution of bacterial pathogens. Infect. Agents Dis. 5:1-7.
39. Matthysse, A. G. 1986. Initial interactions of Agrobacterium tumefaciens with plant host cells. Crit. Rev. Microbiol. 13:281-307.
40. Matthysse, A. G., S. White, and R. Lightfoot. 1995. Genes required for cellulose synthesis in Agrobacterium tumefaciens. J. Bacteriol. 177:1069-1075.
41. Matthysse, A. G., H. A. Yarnall, and N. Young. 1996. Requirement for genes with homology to ABC transport systems for attachment and virulence of Agrobacterium tumefaciens. J. Bacteriol. 178:5302-5308.
42. Metts, J., J. West, S. H. Doares, and A. G. Matthysse. 1991. Characterization of three Agrobacterium tumefaciens avirulent mutants with chromosomal mutations that affect induction of vir genes. J. Bacteriol. 173:1080-1087.
43. Michaux, S., J. Paillisoon, M.-J. Carles-Nurit, G. Bourg, A. Allardet-Servent, and M. Ramuz. 1993. Presence of two independent chromosomes in the Brucella melitensis 16M genome. J. Bacteriol. 175:701-705.
44. Miller, I. S., D. Fox, N. Saeed, P. A. Borland, C. A. Miles, and G. R. K. Sastry. 1986. Enlarged map of Agrobacterium tumefaciens C58 and the location of the chromosomal regions which affect tumorigenicity. Mol. Gen. Genet. 205:153-159.
45. Miller, J. H. 1992. A short course in bacterial genetics. A laboratory manual and handbook for Escherichia coli and related bacteria, p. 437-439. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
46. Parke, D. 1995. Supraoperonic clustering of pca genes for catabolism of the phenolic compound protocatechuate in Agrobacterium tumefaciens. J. Bacteriol. 177:3808-3817.
47. Pischl, D. L., and S. K. Farrand. 1984. Characterization of transposon Tn5-facilitated donor strains and development of a chromosomal linkage map for Agrobacterium tumefaciens. J. Bacteriol. 159:1-8.
48. Robertson, J. L., T. Holliday, and A. G. Matthysse. 1988. Mapping of Agrobacterium tumefaciens chromosomal genes affecting cellulose synthesis and bacterial attachment to host cells. J. Bacteriol. 170:1408-1411.
49. Rong, L., N. C. Carpita, A. Mort, and S. B. Gelvin. 1994. Soluble cell wall compounds from carrot roots induce the picA and pgl loci of Agrobacterium tumefaciens. Mol. Plant-Microbe Interact. 7:5-14.
50. Rong, L., S. J. Karcher, and S. B. Gelvin. 1991. Genetic and molecular analyses of picA, a plant-inducible locus on the Agrobacterium tumefaciens chromosome. J. Bacteriol. 173:5110-5120.
51. Smith, D. R., L. A. Doucette-Stamm, C. Deloughery, H. Lee, J. Dubois, T. Aldredge, R. Bashirzadeh, D. Blakely, R. Cook, K. Gilbert, D. Harrison, L. Hoang, P. Keagle, W. Lumm, B. Pothier, D. Qiu, R. Spadafora, R. Vicaire, Y. Wang, J. Wierzbowski, R. Gibson, N. Jiwani, A. Caruso, D. Bush, H. Safer, D. Patwell, S. Prabhakar, S. McDougall, G. Shimer, A. Goyal, S. Pietrokovski, G. Church, C. Daniels, J. Mao, P. Rice, J. Nolling, and J. N. Reeve. 1997. Complete genome sequence of Methanobacterium thermoautotrophicum △H: functional analysis and comparative genomics. J. Bacteriol. 179: 7135-7155.
52. Smith, E. F., and C. O. Townsend. 1907. A plant tumor of bacterial origin. Science 25:671-673.
53. Sobral, B. W. S., and A. G. Atherly. 1989. A rapid and cost-effective method for preparing genomic DNA from gram-negative bacteria in agarose plugs for pulsed-field gel electrophoresis. BioTechniques 7:938.
54. Suwanto, A., and S. Kaplan. 1989. Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: presence of two unique circular chromosomes. J. Bacteriol. 171:5850-5859.
55. Thomashow, M. F., J. Karlinsey, J. R. Marks, and R. E. Hurlbert. 1987. Identification of a new virulence locus in Agrobacterium tumefaciens that affects polysaccharide composition and plant cell attachment. J. Bacteriol. 169:3209-3216.
56. Tomb, J. F., O. White, A. R. Kerlavage, R. A. Clayton, G. G. Sutton, R. D. Fleischmann, K. A. Ketchum, H. P. Klenk, S. Gill, B. A. Dougherty, K. Nelson, J. Quackenbush, L. Zhou, E. F. Kirkness, S. Peterson, B. Loftus, D. Richardson, R. Dodson, H. G. Khalak, A. Glodek, K. McKenney, L. M. Fitzgerald, N. Lee, M. D. Adams, E. K. Hickey, D. E. Berg, J. D. Gocayne, T. R. Utterback, J. D. Peterson, J. M. Kelley, M. D. Cotton, J. M. Weidman, C. Fujii, C. Bowman, L. Watthey, E. Wallin, W. S. Hayes, M. Borodovsky, P. D. Karp, H. O. Smith, C. M. Fraser, and J. C. Venter. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388: 539-547.
57. Trucksis, M., J. Mickalski, Y. K. Deng, and J. B. Kaper. 1998. The Vibrio cholerai genome contains two unique circular chromosomes. Proc. Natl. Acad. Sci. USA 95:14464-14469.
58. Winans, S. C. 1992. Two-way chemical signalling in Agrobacterium-plant interactions. Microbiol. Rev. 56:12-31.
59. Winans, S. C., R. A. Kerstetter, and E. W. Nester. 1988. Transcriptional regulation of the virA and virG genes of Agrobacterium tumefaciens. J. Bacteriol. 170:4047-4054.
60. Wong, K. K., and M. McClelland. 1992. Dissection of the Salmonella typhimurium genome by use of a Tn5 derivative carrying rare restriction sites. J. Bacteriol. 174:3807-3811.