Construction of physical map and mapping of chromosomal virulence genes of the biovar 3 Agrobacterium (Rhizobium vitis) strain K-Ag-1

Genes and Genetic Systems

Volumn 81, Issue 6, 2006, Pages 373-380

  Tanaka, Katsuyuki ^a   Urbanczyk, Henryk ^a   Matsui, Hiroki ^a   Sawada, Hiroyuki ^b   Suzuki, Katsunori ^a  

^a HIROSHIMA UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

Author keywords

Genomic organization; Pathogenesis genes; Plant disease; Plasmid; Rhizobia

Indexed keywords

BACTERIAL DNA; RIBOSOME DNA; RNA 16S;

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BIOTYPE; CHROMOSOME MAP; GENE LOCUS; GENE MAPPING; GRAPE; JAPAN; KIWIFRUIT; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PULSED FIELD GEL ELECTROPHORESIS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RHIZOBIUM; RHIZOBIUM VITIS;

DNA, BACTERIAL; DNA, RIBOSOMAL; ELECTROPHORESIS, GEL, PULSED-FIELD; GENOME, BACTERIAL; PHYSICAL CHROMOSOME MAPPING; PLASMIDS; RESTRICTION MAPPING; RHIZOBIUM; RNA, RIBOSOMAL, 16S; VIRULENCE FACTORS;

ACTINIDIA DELICIOSA; AGROBACTERIUM; AGROBACTERIUM RHIZOGENES; AGROBACTERIUM TUMEFACIENS; AGROBACTERIUM VITIS; VITIS;

EID: 33846924341     PISSN: 13417568     EISSN: None     Source Type: Journal    
DOI: 10.1266/ggs.81.373     Document Type: Article

References (31)

1. Bazzi, C., and Rosciglione, B. (1982) Agrobacterium tumefaciens biovar 3, causal agent of crown gall on Chysanthemum in Italy. Phytopathology 103, 280-284.
2. Burr, T. J., and Otten, L. (1999) Crown gall of grape: Biology and Disease Management. Annu. Rev. Phytopathol. 37, 53-80.
3. Casjens, S. (1998) The diverse and dynamic structure of bacterial genomes. Annu. Rev. Genet. 32, 339-377.
4. Capela, D., Barloy-Hubler, F., Gouzy, J., Bothe, G., Ampe, F., Batut. J., Boistard, P., Becker, A., Boutry, M., Cadieu, E., Dreano, S., Gloux, S., Godrie, T., Goffeau, A., Kahn, D., Kiss, E., Lelaure, V., Masuy, D., Pohl, T., Portetelle, D., Puhler, A., Purnelle, B., Ramsperger, U., Renard, C., Thebault, P., Vandenbol, M., Weidner, S., and Galibert, F. (2001) Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021. Proc. Natl. Acad. Sci. U.S.A. 98, 9877-9882.
5. Chilton, M. D., Currier, T. C., Farrand, S. K., Bendich, A. J., Gordon, M. P., and Nester, E. W. (1974) Agrobacterium tumefaciens DNA and PS8 bacteriophage DNA not detected in crown gall tumors. Proc. Natl. Acad. Sci. U.S.A. 71, 3672-3676.
6. Church, G. M., and Gilbert, W. (1984) Genomic sequencing. Proc. Natl. Acad. Sci. U.S.A. 81, 1991-1995.
7. Galibert, F., Finan, T. M., Long, S. R., Puhler, A., Abola, P., Ampe, F., Barloy-Hubler, F., Barnett, M. J., Becker, A., Boistard, P., Bothe, G., Boutry, M., Bowser, L., Buhrmester, J., Cadieu, E., Capela, D., Chain, P., Cowie, A., Davis, R. W., Dreano, S., Federspiel, N. A., Fisher, R. F., Gloux, S., Godrie, T., Goffeau, A., Golding, B., Gouzy, J., Gurjal, M., Hernandez-Lucas, I., Hong, A., Huizar, L., Hyman, R. W., Jones, T., Kahn, D., Kahn, M. L., Kalman, S., Keating, D. H., Kiss, E., Komp, C., Lelaure, V., Masuy, D., Palm, C., Peck, M. C., Pohl, T. M., Portetelle, D., Purnelle, B., Ramsperger, U., Surzycki, R., Thebault, P., Vandenbol, M., Vorholter, F. J., Weidner, S., Wells, D. H., Wong, K., Yeh, K. C., and Batut, J. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668-672.
8. Gonzalez, V., Santamaria, R. I., Bustos, P., Hernandez-Gonzalez, I., Medrano-Soto, A., Moreno-Hagelsieb, G., Janga, S.C., Ramirez, M.A., Jimenez-Jacinto, V., Collado-Vides, J., and Davila, G. (2006) The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons. Proc. Natl. Acad. Sci. U.S.A. 103, 3834-3839.
9. Goodner, B., Hinkle, G., Gattung, S., Miller, N., Blanchard, M., Qurollo, B., Goldman, B. S., Cao, Y., Askenazi, M., Halling, C., Mullin, L., Houmiel, K., Gordon, J., Vaudin, M., Iartchouk, O., Epp, A., Liu, F., Wollam, C., Allinger, M., Doughty, D., Scott, C., Lappas, C., Markelz, B., Flanagan, C., Crowell, C., Gurson, J., Lomo, C., Sear, C., Strub, G., Cielo, C., and Slater, S. (2001) Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 294, 2323-2328.
10. Goodner, B. W., Markaelz, B. P., Flanagan, M. C., Crowell, C. B. Jr., Racette, J. L., Schilling, B. A., Halfon, L. M., Mellors, J. S., and Grabowski, G. (1999) Combined genetic and physical map of the complex genome of Agrobacterium tumefaciens. J. Bacteriol. 181, 5160-5166.
11. Holmes, B., and Robert, P. (1981) The classification, identification and nomenclature of agrobacteria. J. Appl. Bacteriol. 50, 443-467.
12. Jumas-Bilak, E., Michaux-Charachon, S., Bourg, G., Ramuz, M., and Allardet-Servenet, A. (1998) Unconventional genome organization in the alpha subgroup of proteobacteria. J. Bacteriol. 180, 2749-2755.
13. Kaneko, T., Nakamura, Y., Sato, S., Asamizu, E., Kato, T., Sasamoto, S., Watanabe, A., Idesawa, K., Ishikawa, A., Kawashima, K., Kimura, T., Kishida, Y., Kiyokawa, C., Kohara, M., Matsumoto, M., Matsuno, A., Mochizuki, Y., Nakayama, S., Nakazaki, N., Shimpo, S., Sugimoto, M., Takeuchi, C., Yamada, M., and Tabata, S. (2000) Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res. 7, 331-338.
14. Kaneko, T., Nakamura, Y., Sato, S., Minamisawa, K., Uchiumi, T., Sasamoto, S., Watanabe, A., Idesawa, K., Iriguchi, M., Kawashima, K., Kohara, M., Matsumoto, M., Shimpo, S., Tsuruoka, H., Wada, T., Yamada, M., and Tabata, S. (2002) Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res. 9, 189-197.
15. Kersters, K., and De Lay, J. (1984) Genus III Agrobacterium conn 1942, In: Bergey's manual of systematic bacteriology Vol. 1 (eds.: Kreig, N. R., and Holt, J. G.) , pp. 244-254. Williams & Wilkins, Baltimore.
16. Moriguchi, K., Maeda, Y., Satou, M., Handayani, N.S., Kataoka, M., Tanaka, N., and Yoshida, K. (2001) The complete nucleotide sequence of a plant root-inducing (Ri) plasmid indicates its chimeric structure and evolutionary relationship between tumor-inducing (Ti) and symbiotic (Sym) plasmids in Rhizobiaceae. J. Mol. Biol. 307, 771-784.
17. Otten, L., Crouzet, P., Salomone, J.Y., de Ruffray, P., and Szegedi, E. (1995) Agrobacterium vitis strain AB3 harbors two independent tartrate utilization systems, one of which is encoded by the Ti plasmid. Mol. Plant-Microbe Interact. 8, 138-146.
18. Otten, L., de Ruffray, P., de Lajudie, P., and Michot, B. (1996) Sequence and characterisation of a ribosomal RNA operon from Agrobacterium vitis. Mol. Gen. Genet. 251, 99-107.
19. Sawada, H., and Ieki, H. (1992a) Phenotypic characteristics of the genus Agrobacterium. Ann. Phytopathol. Soc. Jpn. 58, 37-45.
20. Sawada, H., and Ieki, H. (1992b) Crown gall of kiwi caused by Agrobacterium tumefaciens in Japan, Plant Disease. 76, 212.
21. Sawada, H., Ieki, H., and Takikawa, Y. (1990) Identification of grapevine crown gall bacteria isolated in Japan. Ann. Phytopathol. Soc. Jpn. 56, 199-206.
22. Sule, S. (1978) Biotypes of Agrobacterium tumefaciens in Hungary. J. Appl. Bacteriol., 44, 207-213.
23. Suzuki, K., Iwata, K., and Yoshida, K. (2001) Genome analysis of Agrobacterium tumefaciens: construction of physical maps for linear and circular chromosomal DNAs, determination of copy number ratio and mapping of chromosomal virulence genes. DNA Res. 8, 141-152.
24. Suzuki, K., Hattori, Y., Uraji, M., Ohta, N., Iwata, M., Murata, K., Kato, A., and Yoshida, K. (2000) Complete nucleotide sequence of a plant tumor-inducing Ti plasmid. Gene 242, 331-336.
25. Szegedi, E. (1985) Host range and specific L(+)-tartrate utilization of biotype 3 Agrobacterium tumefaciens. Acta Phytopath. Acad. Sci. Hungary 20, 17-22.
26. Takami, H., Nakasone, K., Hirama, C., Takaki, Y., Masui, N., Fuji, F., Nakamura, Y., and Inoue, A. (1999) An improved physical and genetic map of the genome of alkaliphilic Bacillus sp. C-125. Extremophiles 3, 21-28.
27. Urbanczyk, H., Suzuki, K., Yoshida, K., and Kondo, K. (2003) Physical and gene maps of Agrobacterium biovar 2 strains and their relationship to biovar 1 chromosomes. Microbiology 149, 3035-3042.
28. Young, J. P., Crossman, L. C., Johnston, A. W., Thomson, N. R., Ghazoui, Z. F., Hull, K. H., Wexler, M., Curson, A. R., Todd, J. D., Poole, P. S., Mauchline, T. H., East, A. K., Quail, M. A., Churcher, C., Arrowsmith, C., Cherevach, I., Chillingworth, T., Clarke, K., Cronin, A., Davis, P., Fraser, A., Hance, Z., Hauser, H., Jagels, K., Moule, S., Mungall, K., Norbertczak, H., Rabbinowitsch, E., Sanders, M., Simmonds, M., Whitehead, S., and Parkhill, J. (2006) The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol. 7, R34.
29. nd ed. (eds.: Brenner, R. K., Krieg, S., and G. M. Garrity), Volume 2 Part C, pp. 340-345. Springer-Verlag, New York.
30. Young, J. M., Kuykendall, L. D., Martinez-Romero, E., Kerr, A., and Sawada, H. (2001) A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis. Int. J. Syst. Bacteriol. 51, 89-103.
31. Wood, D. W., Setubal, J. C., Kaul, R., Monks, D. E., Kitajima, J. P., Okura, V. K., Zhou, Y., Chen, L., Wood, G. E., Almeida, N. F. Jr., Woo, L., Chen, Y., Paulsen, I. T., Eisen, J. A., Karp, P. D., Bovee, D. Sr., Chapman, P., Clendenning, J., Deatherage, G., Gillet, W., Grant, C., Kutyavin, T., Levy, R., Li, M. J., McClelland, E., Palmieri, A., Raymond, C., Rouse, G., Saenphimmachak, C., Wu, Z., Romero, P., Gordon, D., Zhang, S., Yoo, H., Tao, Y., Biddle, P., Jung, M., Krespan, W., Perry, M., Gordon-Kamm, B., Liao, L., Kim, S., Hendrick, C., Zhao, Z. Y., Dolan, M., Chumley, F., Tingey, S. V., Tomb, J. F., Gordon, M. P., Olson, M. V., and Nester, E. W. (2001) The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294, 2317-2323.