title: Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110.
abstract: 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.
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0812, Japan.
authors.forename: Takakazu
authors.initials: T
authors.lastname: Kaneko
authors.forename: Yasukazu
authors.initials: Y
authors.lastname: Nakamura
authors.forename: Shusei
authors.initials: S
authors.lastname: Sato
authors.forename: Kiwamu
authors.initials: K
authors.lastname: Minamisawa
authors.forename: Toshiki
authors.initials: T
authors.lastname: Uchiumi
authors.forename: Shigemi
authors.initials: S
authors.lastname: Sasamoto
authors.forename: Akiko
authors.initials: A
authors.lastname: Watanabe
authors.forename: Kumi
authors.initials: K
authors.lastname: Idesawa
authors.forename: Mayumi
authors.initials: M
authors.lastname: Iriguchi
authors.forename: Kumiko
authors.initials: K
authors.lastname: Kawashima
authors.forename: Mitsuyo
authors.initials: M
authors.lastname: Kohara
authors.forename: Midori
authors.initials: M
authors.lastname: Matsumoto
authors.forename: Sayaka
authors.initials: S
authors.lastname: Shimpo
authors.forename: Hisae
authors.initials: H
authors.lastname: Tsuruoka
authors.forename: Tsuyuko
authors.initials: T
authors.lastname: Wada
authors.forename: Manabu
authors.initials: M
authors.lastname: Yamada
authors.forename: Satoshi
authors.initials: S
authors.lastname: Tabata
mesh_terms: D020369:Bradyrhizobium / Q000235:genetics*; D016680:Genome, Bacterial; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009584:Nitrogen / Q000378:metabolism; D020560:Proteobacteria / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D016962:Sinorhizobium meliloti / Q000235:genetics; D013559:Symbiosis
chemical_list: D012335:RNA, Ribosomal; D012343:RNA, Transfer; D009584:Nitrogen