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. 2010 Feb;17(1):37-50.
doi: 10.1093/dnares/dsp026. Epub 2010 Jan 4.

Complete Genomic Structure of the Cultivated Rice Endophyte Azospirillum Sp. B510

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Free PMC article

Complete Genomic Structure of the Cultivated Rice Endophyte Azospirillum Sp. B510

Takakazu Kaneko et al. DNA Res. .
Free PMC article

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.

Figures

Figure 1
Figure 1
Schematic representation of seven circular replicons in the Azospirillum sp. B510 genome. The scale for all plasmids is the same, and the scale for the chromosome is one-half that of the plasmids. The scale indicates the location (in kb) outside the map. The bars in the two outer circles, the outermost circle and the second circle, show the positions of the putative protein-encoding genes in clockwise and counter-clockwise directions, respectively. The putative genes are represented by 25 colours, based on COG assignments (Supplementary Fig. S2). In the third circles from the outside, positions of structural RNA genes are indicated by black (tRNAs) and red (rRNAs) bars. In the fourth circles from the outside, the red bars indicate the positions of ISs, and the pale-green and blue areas show the insertion of prophages and genomic islands, respectively. The innermost and second circles from the centre show the GC-skew values (yellow and purple) and the average GC percent (blue and red), respectively, calculated using a window-size of 10 kb. The scales for GC percent are presented on the second circles. Top and bottom of each scale are shown, as follows: 73.9/58.9% in the chromosome, 74.6/57.0% in pAB510a, 72.5/60.7% in pAB510b, 72.0/60.2% in pAB510c, 74.9/48.3% in pAB510d, 71.9/59.0% in pAB510e, and 71.1/52.7% in pAB510f.
Figure 2
Figure 2
Schematic diagram of the N2-fixation gene clusters from Azospirillum sp. B510 and two Bradyrhizobium species. (A) nif gene cluster of Azospirillum sp. B510, Bradyrhizobium sp. ORS278, and Bradyrhizobium japonicum USDA110. The conservation of the gene arrangement of nif/fix is represented as boxes, with arrowheads indicating the direction of transcription. nif genes are surrounded by red boxes and are in capital letters. fix genes are in blue, lowercase font. Ferredoxin genes are shaded yellow. Black horizontal bars indicate the scale. The position on the chromosomal sequence is indicated in kb below both termini of the bars. The sequences were analysed using the tblastx function of GenomeMatcher V.1.270. The BLAST E-value of 10−10 was considered significant for the assignment of relationship. The bars connecting the maps represent close matches, with colour indicating the degree of amino acid identity determined in the BLAST alignment. The colour code is displayed at the bottom of the figure. (B) fix clusters of three bacteria. A box with a yellow border indicates that the gene cluster is located on the plasmid.

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