© 2002 by Kazusa DNA Research Institute
Complete Genomic Sequence of Nitrogen-fixing Symbiotic Bacterium Bradyrhizobium japonicum USDA110
1Kazusa DNA Research Institute 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0812, Japan
2Graduate School of Life Sciences, Tohoku University Katahira, Aoba-ku, Sendai 980-8577, Japan
3Department of Chemistry and BioScience, Faculty of Science, Kagoshima University Kagoshima 890-0065, Japan
* To whom correspondence should be addressed. Tel. +81-438-52-3933, Fax. +81-438-52-3934, E-mail: tabata{at}kazusa.or.jp
The complete nucleotide sequence of the genome of a symbiotic bacterium Bradyrhizobium japonicum USDA110 was determined. The genome of B. japonicum was a single circular chromosome 9,105,828 bp in length with an average GC content of 64.1%. No plasmid was detected. The chromosome comprises 8317 potential protein-coding genes, one set of rRNA genes and 50 tRNA genes. Fifty-two percent of the potential protein genes showed sequence similarity to genes of known function and 30% to hypothetical genes. The remaining 18% had no apparent similarity to reported genes. Thirty-four percent of the B. japonicum genes showed significant sequence similarity to those of both Mesorhizobium loti and Sinorhizobium meliloti, while 23% were unique to this species. A presumptive symbiosis island 681 kb in length, which includes a 410-kb symbiotic region previously reported by Göttfert et al., was identified. Six hundred fifty-five putative protein-coding genes were assigned in this region, and the functions of 301 genes, including those related to symbiotic nitrogen fixation and DNA transmission, were deduced. A total of 167 genes for transposases/104 copies of insertion sequences were identified in the genome. It was remarkable that 100 out of 167 transposase genes are located in the presumptive symbiotic island. DNA segments of 4 to 97 kb inserted into tRNA genes were found at 14 locations in the genome, which generates partial duplication of the target tRNA genes. These observations suggest plasticity of the B. japonicum genome, which is probably due to complex genome rearrangements such as horizontal transfer and insertion of various DNA elements, and to homologous recombination.
Key words: Bradyrhizobium japonicum USDA110; genome sequencing; symbiosis; nodulation; nitrogen fixation
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D. Girlich, T. Naas, and P. Nordmann OXA-60, a Chromosomal, Inducible, and Imipenem-Hydrolyzing Class D {beta}-Lactamase from Ralstonia pickettii Antimicrob. Agents Chemother., November 1, 2004; 48(11): 4217 - 4225. [Abstract] [Full Text] [PDF]
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A. Boscari, K. Mandon, M.-C. Poggi, and D. Le Rudulier Functional Expression of Sinorhizobium meliloti BetS, a High-Affinity Betaine Transporter, in Bradyrhizobium japonicum USDA110 Appl. Envir. Microbiol., October 1, 2004; 70(10): 5916 - 5922. [Abstract] [Full Text] [PDF]
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N. Muryoi, M. Sato, S. Kaneko, H. Kawahara, H. Obata, M. W. F. Yaish, M. Griffith, and B. R. Glick Cloning and Expression of afpA, a Gene Encoding an Antifreeze Protein from the Arctic Plant Growth-Promoting Rhizobacterium Pseudomonas putida GR12-2 J. Bacteriol., September 1, 2004; 186(17): 5661 - 5671. [Abstract] [Full Text] [PDF]
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D. Perez-Mendoza, A. Dominguez-Ferreras, S. Munoz, M. J. Soto, J. Olivares, S. Brom, L. Girard, J. A. Herrera-Cervera, and J. Sanjuan Identification of Functional mob Regions in Rhizobium etli: Evidence for Self-Transmissibility of the Symbiotic Plasmid pRetCFN42d J. Bacteriol., September 1, 2004; 186(17): 5753 - 5761. [Abstract] [Full Text] [PDF]
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N. Ausmees, H. Kobayashi, W. J. Deakin, C. Marie, H. B. Krishnan, W. J. Broughton, and X. Perret Characterization of NopP, a Type III Secreted Effector of Rhizobium sp. Strain NGR234 J. Bacteriol., July 15, 2004; 186(14): 4774 - 4780. [Abstract] [Full Text] [PDF]
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D. W. Ussery and P. F. Hallin Genome Update: annotation quality in sequenced microbial genomes Microbiology, July 1, 2004; 150(7): 2015 - 2017. [Full Text] [PDF]
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L. Ferrieres, A. Francez-Charlot, J. Gouzy, S. Rouille, and D. Kahn FixJ-regulated genes evolved through promoter duplication in Sinorhizobium meliloti Microbiology, July 1, 2004; 150(7): 2335 - 2345. [Abstract] [Full Text] [PDF]
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B. Boussau, E. O. Karlberg, A. C. Frank, B.-A. Legault, and S. G. E. Andersson Computational inference of scenarios for {alpha}-proteobacterial genome evolution PNAS, June 29, 2004; 101(26): 9722 - 9727. [Abstract] [Full Text] [PDF]
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D. J. Gage Infection and Invasion of Roots by Symbiotic, Nitrogen-Fixing Rhizobia during Nodulation of Temperate Legumes Microbiol. Mol. Biol. Rev., June 1, 2004; 68(2): 280 - 300. [Abstract] [Full Text] [PDF]
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R. Sameshima-Saito, K. Chiba, and K. Minamisawa New Method of Denitrification Analysis of Bradyrhizobium Field Isolates by Gas Chromatographic Determination of 15N-Labeled N2 Appl. Envir. Microbiol., May 1, 2004; 70(5): 2886 - 2891. [Abstract] [Full Text] [PDF]
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T. Uchiumi, T. Ohwada, M. Itakura, H. Mitsui, N. Nukui, P. Dawadi, T. Kaneko, S. Tabata, T. Yokoyama, K. Tejima, et al. Expression Islands Clustered on the Symbiosis Island of the Mesorhizobium loti Genome J. Bacteriol., April 15, 2004; 186(8): 2439 - 2448. [Abstract] [Full Text] [PDF]
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K. Itoh, Y. Tashiro, K. Uobe, Y. Kamagata, K. Suyama, and H. Yamamoto Root Nodule Bradyrhizobium spp. Harbor tfdA{alpha} and cadA, Homologous with Genes Encoding 2,4-Dichlorophenoxyacetic Acid-Degrading Proteins Appl. Envir. Microbiol., April 1, 2004; 70(4): 2110 - 2118. [Abstract] [Full Text] [PDF]
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M. Moris, B. Dombrecht, C. Xi, J. Vanderleyden, and J. Michiels Regulatory Role of Rhizobium etli CNPAF512 fnrN during Symbiosis Appl. Envir. Microbiol., March 1, 2004; 70(3): 1287 - 1296. [Abstract] [Full Text] [PDF]
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H. P. Benson, K. LeVier, and M. L. Guerinot A Dominant-Negative fur Mutation in Bradyrhizobium japonicum J. Bacteriol., March 1, 2004; 186(5): 1409 - 1414. [Abstract] [Full Text] [PDF]
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M. F. Dunn, G. Araiza, and J. Mora Biochemical characterization of a Rhizobium etli monovalent cation-stimulated acyl-coenzyme A carboxylase with a high substrate specificity constant for propionyl-coenzyme A Microbiology, February 1, 2004; 150(2): 399 - 406. [Abstract] [Full Text] [PDF]
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V. Seibert, M. Thiel, I.-S. Hinner, and M. Schlomann Characterization of a gene cluster encoding the maleylacetate reductase from Ralstonia eutropha 335T, an enzyme recruited for growth with 4-fluorobenzoate Microbiology, February 1, 2004; 150(2): 463 - 472. [Abstract] [Full Text] [PDF]
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W. R. Streit, R. A. Schmitz, X. Perret, C. Staehelin, W. J. Deakin, C. Raasch, H. Liesegang, and W. J. Broughton An Evolutionary Hot Spot: the pNGR234b Replicon of Rhizobium sp. Strain NGR234 J. Bacteriol., January 15, 2004; 186(2): 535 - 542. [Abstract] [Full Text] [PDF]
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L. S. Forsberg, K. D. Noel, J. Box, and R. W. Carlson Genetic Locus and Structural Characterization of the Biochemical Defect in the O-Antigenic Polysaccharide of the Symbiotically Deficient Rhizobium etli Mutant, CE166: REPLACEMENT OF N-ACETYLQUINOVOSAMINE WITH ITS HEXOSYL-4-ULOSE PRECURSOR J. Biol. Chem., December 19, 2003; 278(51): 51347 - 51359. [Abstract] [Full Text] [PDF]
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M. J. Delgado, N. Bonnard, A. Tresierra-Ayala, E. J. Bedmar, and P. Muller The Bradyrhizobium japonicum napEDABC genes encoding the periplasmic nitrate reductase are essential for nitrate respiration Microbiology, December 1, 2003; 149(12): 3395 - 3403. [Abstract] [Full Text] [PDF]
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F. Martinez-Morales, M. Schobert, I. M. Lopez-Lara, and O. Geiger Pathways for phosphatidylcholine biosynthesis in bacteria Microbiology, December 1, 2003; 149(12): 3461 - 3471. [Abstract] [Full Text] [PDF]
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S. Mesa, E. J. Bedmar, A. Chanfon, H. Hennecke, and H.-M. Fischer Bradyrhizobium japonicum NnrR, a Denitrification Regulator, Expands the FixLJ-FixK2 Regulatory Cascade J. Bacteriol., July 1, 2003; 185(13): 3978 - 3982. [Abstract] [Full Text] [PDF]
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