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Complete genomic structure of the cultivated rice endophyte Azospirillum sp. B510.

Kaneko T, Minamisawa K, Isawa T, Nakatsukasa H, Mitsui H, Kawaharada Y, Nakamura Y, Watanabe A, Kawashima K, Ono A, Shimizu Y, Takahashi C, Minami C, Fujishiro T, Kohara M, Katoh M, Nakazaki N, Nakayama S, Yamada M, Tabata S, Sato S - DNA Res. (2010)

Bottom Line: B510.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.

View Article: PubMed Central - PubMed

Affiliation: Kazusa DNA Research Institute, Kisarazu, Chiba, Japan.

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.

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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.
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DSP026F1: 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.

Mentions: A GC-skew analysis was performed to locate the probable origin of DNA replication. We established that the shift of GC-skew values occurred in two regions of the chromosome, at coordinates 35 and 1710 kb, as shown in Fig. 1 (the innermost circle). The hemE locus, which is known to associate with the origins of replication in alpha-proteobacteria,36 was found to be adjacent to the shift point of the GC skew. A cluster of nine genes, rho–hypothetical–hemH–hemE–hypothetical–maf–aroE–coaE–dnaQ (AZL028900–AZL028930–AZL000010– AZL000050: these codes are hereinafter defined in the Protein-encoding genes section), occurring at ∼0 kb on the B510 chromosome (Supplementary Fig. S2) was commonly found in the Magnetospirillum sp. AMB-1 genome.37 parA (AZL000140) and parB (AZL000150) were found downstream of dnaQ (AZL000050; Supplementary Fig. S2). These findings strongly suggest that the ori region of the chromosome is located between AZL028930 and AZL000010. This location of the ori is also supported by the KOPS motif distribution analysis (Supplementary Fig. S3).


Complete genomic structure of the cultivated rice endophyte Azospirillum sp. B510.

Kaneko T, Minamisawa K, Isawa T, Nakatsukasa H, Mitsui H, Kawaharada Y, Nakamura Y, Watanabe A, Kawashima K, Ono A, Shimizu Y, Takahashi C, Minami C, Fujishiro T, Kohara M, Katoh M, Nakazaki N, Nakayama S, Yamada M, Tabata S, Sato S - DNA Res. (2010)

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.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2818188&req=5

DSP026F1: 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.
Mentions: A GC-skew analysis was performed to locate the probable origin of DNA replication. We established that the shift of GC-skew values occurred in two regions of the chromosome, at coordinates 35 and 1710 kb, as shown in Fig. 1 (the innermost circle). The hemE locus, which is known to associate with the origins of replication in alpha-proteobacteria,36 was found to be adjacent to the shift point of the GC skew. A cluster of nine genes, rho–hypothetical–hemH–hemE–hypothetical–maf–aroE–coaE–dnaQ (AZL028900–AZL028930–AZL000010– AZL000050: these codes are hereinafter defined in the Protein-encoding genes section), occurring at ∼0 kb on the B510 chromosome (Supplementary Fig. S2) was commonly found in the Magnetospirillum sp. AMB-1 genome.37 parA (AZL000140) and parB (AZL000150) were found downstream of dnaQ (AZL000050; Supplementary Fig. S2). These findings strongly suggest that the ori region of the chromosome is located between AZL028930 and AZL000010. This location of the ori is also supported by the KOPS motif distribution analysis (Supplementary Fig. S3).

Bottom Line: B510.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.

View Article: PubMed Central - PubMed

Affiliation: Kazusa DNA Research Institute, Kisarazu, Chiba, Japan.

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.

Show MeSH
Related in: MedlinePlus