title: Complete genome sequence of Bradyrhizobium sp. S23321: insights into symbiosis evolution in soil oligotrophs.
abstract: Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.
authors.affiliation: Graduate School of Life Sciences, Tohoku University, Miyagi 980-8577, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Okubo
authors.forename: Takahiro
authors.initials: T
authors.lastname: Tsukui
authors.forename: Hiroko
authors.initials: H
authors.lastname: Maita
authors.forename: Shinobu
authors.initials: S
authors.lastname: Okamoto
authors.forename: Kenshiro
authors.initials: K
authors.lastname: Oshima
authors.forename: Takatomo
authors.initials: T
authors.lastname: Fujisawa
authors.forename: Akihiro
authors.initials: A
authors.lastname: Saito
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Futamata
authors.forename: Reiko
authors.initials: R
authors.lastname: Hattori
authors.forename: Yumi
authors.initials: Y
authors.lastname: Shimomura
authors.forename: Shin
authors.initials: S
authors.lastname: Haruta
authors.forename: Sho
authors.initials: S
authors.lastname: Morimoto
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
authors.forename: Yoriko
authors.initials: Y
authors.lastname: Sakai
authors.forename: Masahira
authors.initials: M
authors.lastname: Hattori
authors.forename: Shin-Ichi
authors.initials: S
authors.lastname: Aizawa
authors.forename: Kenji V P
authors.initials: KV
authors.lastname: Nagashima
authors.forename: Sachiko
authors.initials: S
authors.lastname: Masuda
authors.forename: Tsutomu
authors.initials: T
authors.lastname: Hattori
authors.forename: Akifumi
authors.initials: A
authors.lastname: Yamashita
authors.forename: Zhihua
authors.initials: Z
authors.lastname: Bao
authors.forename: Masahito
authors.initials: M
authors.lastname: Hayatsu
authors.forename: Hiromi
authors.initials: H
authors.lastname: Kajiya-Kanegae
authors.forename: Ikuo
authors.initials: I
authors.lastname: Yoshinaga
authors.forename: Kazunori
authors.initials: K
authors.lastname: Sakamoto
authors.forename: Koki
authors.initials: K
authors.lastname: Toyota
authors.forename: Mitsuteru
authors.initials: M
authors.lastname: Nakao
authors.forename: Mitsuyo
authors.initials: M
authors.lastname: Kohara
authors.forename: Mizue
authors.initials: M
authors.lastname: Anda
authors.forename: Rieko
authors.initials: R
authors.lastname: Niwa
authors.forename: Park
authors.initials: P
authors.lastname: Jung-Hwan
authors.forename: Reiko
authors.initials: R
authors.lastname: Sameshima-Saito
authors.forename: Shin-Ichi
authors.initials: S
authors.lastname: Tokuda
authors.forename: Sumiko
authors.initials: S
authors.lastname: Yamamoto
authors.forename: Syuji
authors.initials: S
authors.lastname: Yamamoto
authors.forename: Tadashi
authors.initials: T
authors.lastname: Yokoyama
authors.forename: Tomoko
authors.initials: T
authors.lastname: Akutsu
authors.forename: Yasukazu
authors.initials: Y
authors.lastname: Nakamura
authors.forename: Yuka
authors.initials: Y
authors.lastname: Nakahira-Yanaka
authors.forename: Yuko
authors.initials: Y
authors.lastname: Takada Hoshino
authors.forename: Hideki
authors.initials: H
authors.lastname: Hirakawa
authors.forename: Hisayuki
authors.initials: H
authors.lastname: Mitsui
authors.forename: Kimihiro
authors.initials: K
authors.lastname: Terasawa
authors.forename: Manabu
authors.initials: M
authors.lastname: Itakura
authors.forename: Shusei
authors.initials: S
authors.lastname: Sato
authors.forename: Wakako
authors.initials: W
authors.lastname: Ikeda-Ohtsubo
authors.forename: Natsuko
authors.initials: N
authors.lastname: Sakakura
authors.forename: Eli
authors.initials: E
authors.lastname: Kaminuma
authors.forename: Kiwamu
authors.initials: K
authors.lastname: Minamisawa
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D001482:Base Composition; D020369:Bradyrhizobium / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics*; D016680:Genome, Bacterial; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D022661:RNA, Untranslated / Q000235:genetics; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D013559:Symbiosis; D026801:Synteny
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D022661:RNA, Untranslated