Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110

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 pote...

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Bibliographic Details
Published in:DNA research 2002, Vol.9 (6), p.189-197
Main Authors: KANEKO, Takakazu, NAKAMURA, Yasukazu, KOHARA, Mitsuyo, MATSUMOTO, Midori, SHIMPO, Sayaka, TSURUOKA, Hisae, WADA, Tsuyuko, YAMADA, Manabu, TABATA, Satoshi, SATO, Shusei, MINAMISAWA, Kiwamu, UCHIUMI, Toshiki, SASAMOTO, Shigemi, WATANABE, Akiko, IDESAWA, Kumi, IRIGUCHI, Mayumi, KAWASHIMA, Kumiko
Format: Article
Language:English
Subjects:
Bacteria
Biological and medical sciences
Bradyrhizobium - genetics
Bradyrhizobium japonicum
Fundamental and applied biological sciences. Psychology
Genome, Bacterial
homologous recombination
homologous recomnbination
Models, Genetic
Molecular Sequence Data
Nitrogen - metabolism
Parasitism and symbiosis
Plant physiology and development
Proteobacteria - genetics
Recombination, Genetic
RNA, Ribosomal - genetics
RNA, Transfer - genetics
Sequence Analysis, DNA
Sinorhizobium meliloti - genetics
Symbiosis
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Summary: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.
ISSN:1340-2838
1756-1663
DOI:10.1093/dnares/9.6.189