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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 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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DSP026F2: 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.

Mentions: B510 is a bacterium capable of performing N2 fixation in a modified Rennie semi-solid medium.13 Furthermore, we demonstrated its ability to fix N2 in planta in this study (see the Colonization and N2 fixation in rice plants section). The genes encoding the nitrogenase core and assembly proteins were separately clustered in three loci on the B510 chromosome. These three gene clusters were arranged in nifA [1 gene]–nifB [3 genes]–nifZ [1 gene]–nifST (AZL022440–AZL022530), nifWV [1 gene]–nifSU (AZL006520–AZL006560), and nifHDK [2 genes]–nifENX (AZL007710–AZL007640; Fig. 2A). nifQ (AZL010780) was located at a distance from above other nif gene clusters. The fixABCX (AZL006470–AZL006500) cluster, which encoded components participating in the transport of electrons to nitrogenase,44,45 was adjacent to the nifWVSU cluster and in an opposite orientation (Fig. 2A). Not all of the major components of N2 fixation were encoded by genes on the chromosome; AZLc04520, which is a homologue of nifJ encoding pyruvate–flavodoxin oxidoreductase, was solely found on the pAB510c plasmid. However, considering that a homologue of nifF, which encodes flavodoxin, an electron donor of NifJ, was not found in the B510 genome, AZLc04520 may not be involved in the major pathway for electron transfer to nitrogenase in B510.


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

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getmorefigures.php?uid=PMC2818188&req=5

DSP026F2: 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.
Mentions: B510 is a bacterium capable of performing N2 fixation in a modified Rennie semi-solid medium.13 Furthermore, we demonstrated its ability to fix N2 in planta in this study (see the Colonization and N2 fixation in rice plants section). The genes encoding the nitrogenase core and assembly proteins were separately clustered in three loci on the B510 chromosome. These three gene clusters were arranged in nifA [1 gene]–nifB [3 genes]–nifZ [1 gene]–nifST (AZL022440–AZL022530), nifWV [1 gene]–nifSU (AZL006520–AZL006560), and nifHDK [2 genes]–nifENX (AZL007710–AZL007640; Fig. 2A). nifQ (AZL010780) was located at a distance from above other nif gene clusters. The fixABCX (AZL006470–AZL006500) cluster, which encoded components participating in the transport of electrons to nitrogenase,44,45 was adjacent to the nifWVSU cluster and in an opposite orientation (Fig. 2A). Not all of the major components of N2 fixation were encoded by genes on the chromosome; AZLc04520, which is a homologue of nifJ encoding pyruvate–flavodoxin oxidoreductase, was solely found on the pAB510c plasmid. However, considering that a homologue of nifF, which encodes flavodoxin, an electron donor of NifJ, was not found in the B510 genome, AZLc04520 may not be involved in the major pathway for electron transfer to nitrogenase in B510.

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