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.

Characterization of Bacteroid Proteins in Soybean Nodules Formed with Bradyrhizobium japonicum USDA110

“…Table 1 shows the list of proteins identified as up-regulated or specific in bacteroids compared to cultured cells. Among them, enzymes for the nitrogenase system (nitrogenase iron protein, nifH; nitrogenase Mo-Fe protein beta chain, nifK; NifAregulated gene product, NrgC) were detected as abundant proteins as previously reported using Sinorhizobium meliloti 10) , and in addition, many other genes localized in the symbiosis island region A of the B. japonicum genome were detected (nodule formation efficiency; nfeC, probable dioxygenase, 1-aminocyclopropane-1-carboxylate deaminase, 60 kDa chaperonin 3, alkyl hydroperoxide reductase; ahpC and hypothetical proteins) 5) . Their physiological roles were not clear, but an enzyme, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, degrades a precursor (ACC) of the plant hormone ethylene and acts to lower the ethylene concentration around bacteroids 12) .…”

“…The proteomic analysis of cultured cells and bacteroids in Sinorhizobium meliloti has provided insight into how microsymbionts alter metabolism to establish an endo-symbiotic relationship with the host plant cells 10) . In soybean, the genomic DNA of Bradyrhizobium japonicum USDA110 has been completely sequenced by the Kazusa DNA Research Institute 5) , and a large scale macroarray analysis is being conducted by comparing gene expression profiles among rhizosphere cells, cultured cells and bacteroids (Minamisawa et al, personal communication). In cooperation with these transcriptome analyses, we compared protein profiles between bacteroids and cultured cells of B. japonicum USDA110 and examined the physiological role of bacteroid specific proteins.…”

New Method of Denitrification Analysis of Bradyrhizobium Field Isolates by Gas Chromatographic Determination of 15 N-Labeled N 2

“…Strain USDA110 was used as a standard strain of B. japonicum (11). A total of 65 field isolates of Bradyrhizobium were isolated from the soils of the Nakazawa fields at the Niigata Agricultural Experiment Station (Nagaoka, Niigata, Japan) and the Tokachi field at the Tokachi Agricultural Station (Memuro, Tokachi, Hokkaido, Japan) as described previously (9,15,18 (26).…”

Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California

“…Rhizobial genomes are subdivided into genome regions specific for their life stages, with chromosomal loci expressed during free-living phases in the soil and symbiosis loci expressed inside of host cells [13,14]. Symbiosis loci required for host nodulation and nitrogen fixation are clustered onto large plasmids or genomic islands [15][16][17][18][19], that can be transferred among lineages, presumably via conjugation [20][21][22]. Non-nodulating rhizobia are also common [23,24], and these strains often lack some or all of the characterized symbiosis loci [23][24][25][26][27][28].…”