Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110
Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110
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DOI：
10.1093/dnares/9.6.189
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发表时间：
2002-12-31
期刊：
影响因子：
4.1
通讯作者：
Tabata, S
中科院分区：
文献类型：
--
作者：
Kaneko, T;Nakamura, Y;Tabata, S
测定了一株共生菌慢生菌USDA110的基因组全序列。日本血吸虫基因组为一条9,105,828个碱基的单环形染色体，平均GC含量为64.1%。未检测到任何质粒。该染色体由8317个潜在的蛋白质编码基因、一组rRNA基因和50个tRNA基因组成。52%的潜在蛋白质基因与已知功能基因序列相似，30%与假设基因序列相似。剩下的18%与已报道的基因没有明显的相似性。34%的日本芽孢杆菌基因与洛提中根瘤菌和苜蓿中华根瘤菌的序列有显著的相似性，23%是该物种所特有的。确定了一个681kb的推定共生岛，其中包括Gottfert等人以前报道的410kb的共生区。在该区域共定位了655个编码蛋白质的基因，推测了与共生固氮和DNA传递相关的基因的功能。基因组中共鉴定出167个转座酶基因/104个插入序列拷贝。值得注意的是，167个转座酶基因中有100个位于假定的共生岛上。在基因组的14个位置发现插入tRNA基因的4kb到97kb的DNA片段，这产生了目标tRNA基因的部分复制。这些观察结果表明，日本血吸虫基因组具有可塑性，这可能是由于复杂的基因组重排，如各种DNA元件的水平转移和插入，以及同源重组。
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 Gottfert 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.