title: Complete genomic structure of the cultivated rice endophyte Azospirillum sp. B510.
abstract: We determined the nucleotide sequence of the entire genome of a diazotrophic endophyte, Azospirillum sp. B510. Strain B510 is an endophytic bacterium isolated from stems of rice plants (Oryza sativa cv. Nipponbare). The genome of B510 consisted of a single chromosome (3,311,395 bp) and six plasmids, designated as pAB510a (1,455,109 bp), pAB510b (723,779 bp), pAB510c (681,723 bp), pAB510d (628,837 bp), pAB510e (537,299 bp), and pAB510f (261,596 bp). The chromosome bears 2893 potential protein-encoding genes, two sets of rRNA gene clusters (rrns), and 45 tRNA genes representing 37 tRNA species. The genomes of the six plasmids contained a total of 3416 protein-encoding genes, seven sets of rrns, and 34 tRNAs representing 19 tRNA species. Eight genes for plasmid-specific tRNA species are located on either pAB510a or pAB510d. Two out of eight genomic islands are inserted in the plasmids, pAB510b and pAB510e, and one of the islands is inserted into trnfM-CAU in the rrn located on pAB510e. Genes other than the nif gene cluster that are involved in N(2) fixation and are homologues of Bradyrhizobium japonicum USDA110 include fixABCX, fixNOQP, fixHIS, fixG, and fixLJK. Three putative plant hormone-related genes encoding tryptophan 2-monooxytenase (iaaM) and indole-3-acetaldehyde hydrolase (iaaH), which are involved in IAA biosynthesis, and ACC deaminase (acdS), which reduces ethylene levels, were identified. Multiple gene-clusters for tripartite ATP-independent periplasmic-transport systems and a diverse set of malic enzymes were identified, suggesting that B510 utilizes C(4)-dicarboxylate during its symbiotic relationship with the host plant.
authors.affiliation: Kazusa DNA Research Institute, Kisarazu, Chiba, Japan.
authors.forename: Takakazu
authors.initials: T
authors.lastname: Kaneko
authors.forename: Kiwamu
authors.initials: K
authors.lastname: Minamisawa
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Isawa
authors.forename: Hiroki
authors.initials: H
authors.lastname: Nakatsukasa
authors.forename: Hisayuki
authors.initials: H
authors.lastname: Mitsui
authors.forename: Yasuyuki
authors.initials: Y
authors.lastname: Kawaharada
authors.forename: Yasukazu
authors.initials: Y
authors.lastname: Nakamura
authors.forename: Akiko
authors.initials: A
authors.lastname: Watanabe
authors.forename: Kumiko
authors.initials: K
authors.lastname: Kawashima
authors.forename: Akiko
authors.initials: A
authors.lastname: Ono
authors.forename: Yoshimi
authors.initials: Y
authors.lastname: Shimizu
authors.forename: Chika
authors.initials: C
authors.lastname: Takahashi
authors.forename: Chiharu
authors.initials: C
authors.lastname: Minami
authors.forename: Tsunakazu
authors.initials: T
authors.lastname: Fujishiro
authors.forename: Mitsuyo
authors.initials: M
authors.lastname: Kohara
authors.forename: Midori
authors.initials: M
authors.lastname: Katoh
authors.forename: Naomi
authors.initials: N
authors.lastname: Nakazaki
authors.forename: Shinobu
authors.initials: S
authors.lastname: Nakayama
authors.forename: Manabu
authors.initials: M
authors.lastname: Yamada
authors.forename: Satoshi
authors.initials: S
authors.lastname: Tabata
authors.forename: Shusei
authors.initials: S
authors.lastname: Sato
mesh_terms: D000383:Agriculture; D016949:Azospirillum / Q000235:genetics* / Q000254:growth & development; D001426:Bacterial Proteins / Q000235:genetics; D001692:Biological Transport / Q000235:genetics; D015169:Colony Count, Microbial; D004251:DNA Transposable Elements / Q000235:genetics; D005798:Genes, Bacterial; D016680:Genome, Bacterial / Q000235:genetics*; D044404:Genomic Islands / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family; D009586:Nitrogen Fixation / Q000235:genetics; D012275:Oryza / Q000254:growth & development* / Q000382:microbiology*; D010937:Plant Growth Regulators / Q000378:metabolism; D012329:RNA, Bacterial / Q000235:genetics; D018741:Replication Origin / Q000235:genetics; D012093:Replicon / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D004251:DNA Transposable Elements; D010937:Plant Growth Regulators; D012329:RNA, Bacterial