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

By T. Kaneko, Yasukazu Nakamura, Shusei Sato, K. Minamisawa, T. Uchiumi, S. Sasamoto, A. Watanabe, K. Idesawa, Mayumi Iriguchi, K. Kawashima and 7 more. DNA Research, 2002

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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.

Subfields: Plant Science

View Paper: https://www.semanticscholar.org/paper/8cbfcb00ac0f84b4b46c14d61e912a64f30eab6d

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In Plant Science

1. B. R. Glick
2. A. Sessitsch
3. S. Compant
4. Zhenyu Cheng
5. J. Czarny
6. J. Duan
7. Brendan J. McConkey
8. B. Todorovic

Citations in the corpus

• Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization (2010, background): “Sequenced genomes of nodule-forming bacteria such as A. caulinodans ORS 571, Bradyrhizobium japonicum USDA110 (Kaneko et al., 2002), Burkholderia phymatum strain STM815, Cupriavidus taiwanensis strain R1 (Amadou et al., 2008) and Frankia spp. strain CcI3 (Normand et al., 2007) have moreover…”
• Root-based N2-fixing Symbioses: Legumes, Actinorhizal Plants, Parasponia sp. and Cycads (2005, background): “…the ‘model’ legumes, Lotus japonicus and Medicago truncatulata (Colebatch et al., 2002b), and the complete sequencing of the genomes of a several of the rhizobial microsymbionts (Galibert et al., 2001; Kaneko et al., 2000, 2002) will further help to accelerate the investigation of these symbioses.”
• Promotion of Plant Growth by Bacterial ACC Deaminase (2007, background): “…(Klee and Kishore, 1992; Jacobson et al., 1994; Glick et al., 1995, 1998; Burd et al., 1998; Kaneko et al., 2000; Belimov et al., 2001, 2005; Kaneko et al., 2002; Babalola et al., 2003; Ma et al., 2003; Ghosh et al., 2003; Dey et al., 2004; Mayak et al., 2004a; Hontzeas et al., 2005;…”
• Modulation of plant ethylene levels by the bacterial enzyme ACC deaminase. (2005, background): “viciae 128C53K,Variovarax paradoxus 5C2, and Achromobacter xylosoxidans A551 [39,41,49,50], and is consistent with the notion that the entire region of DNA containing the ACC deaminase structural and regulatory genes was acquired by lateral gene transfer.”
• Bacterial Associations with Legumes (2015, background): “…by genes harboured in autoconjugative plasmids in fast-growing rhizobia (Zurkowski and Lorkiewic, 1979) and in 2000s decade it was discovered that these genes are harboured in symbiotic islands in the case of most intermediate and slow-growing rhizobia (Kaneko et al., 2002; Sullivan et al., 2002).”