Naomi Nakazaki

Publications of Naomi Nakazaki

• Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L.

  Authors: Shusei Sato, Hideki Hirakawa, Sachiko Isobe, Eigo Fukai, Akiko Watanabe, Midori Kato, Kumiko Kawashima, Chiharu Minami, Akiko Muraki, Naomi Nakazaki [......] Eri Makigano, Nobuko Ohmido, Nakako Shibagaki, Joyce A Cartagena, Naoki Wada, Tsutomu Kohinata, Alipour Atefeh, Shota Yuasa, Sachihiro Matsunaga, Kiichi Fukui

  DNA research : an international journal for rapid publication of reports on genes and genomes. 01/2011; 18(1):65-76.

  The whole genome of Jatropha curcas was sequenced, using a combination of the conventional Sanger method and new-generation multiplex sequencing methods. Total length of the non-redundant sequencesThe whole genome of Jatropha curcas was sequenced, using a combination of the conventional Sanger method and new-generation multiplex sequencing methods. Total length of the non-redundant sequences thus obtained was 285 858 490 bp consisting of 120 586 contigs and 29 831 singlets. They accounted for ~95% of the gene-containing regions with the average G + C content was 34.3%. A total of 40 929 complete and partial structures of protein encoding genes have been deduced. Comparison with genes of other plant species indicated that 1529 (4%) of the putative protein-encoding genes are specific to the Euphorbiaceae family. A high degree of microsynteny was observed with the genome of castor bean and, to a lesser extent, with those of soybean and Arabidopsis thaliana. In parallel with genome sequencing, cDNAs derived from leaf and callus tissues were subjected to pyrosequencing, and a total of 21 225 unigene data have been generated. Polymorphism analysis using microsatellite markers developed from the genomic sequence data obtained was performed with 12 J. curcas lines collected from various parts of the world to estimate their genetic diversity. The genomic sequence and accompanying information presented here are expected to serve as valuable resources for the acceleration of fundamental and applied research with J. curcas, especially in the fields of environment-related research such as biofuel production. Further information on the genomic sequences and DNA markers is available at http://www.kazusa.or.jp/jatropha/.

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

  Authors: Takakazu Kaneko, Kiwamu Minamisawa, Tsuyoshi Isawa, Hiroki Nakatsukasa, Hisayuki Mitsui, Yasuyuki Kawaharada, Yasukazu Nakamura, Akiko Watanabe, Kumiko Kawashima, Akiko Ono [......] Chika Takahashi, Chiharu Minami, Tsunakazu Fujishiro, Mitsuyo Kohara, Midori Katoh, Naomi Nakazaki, Shinobu Nakayama, Manabu Yamada, Satoshi Tabata, Shusei Sato

  DNA research : an international journal for rapid publication of reports on genes and genomes. 02/2010; 17(1):37-50.

  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 sativaWe 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.

• Genome Structure of the Legume, Lotus japonicus.

  Authors: Shusei Sato, Yasukazu Nakamura, Takakazu Kaneko, Erika Asamizu, Tomohiko Kato, Mitsuteru Nakao, Shigemi Sasamoto, Akiko Watanabe, Akiko Ono, Kumiko Kawashima [......] Chika Takahashi, Tsuyuko Wada, Manabu Yamada, Nobuko Ohmido, Makoto Hayashi, Kiichi Fukui, Tomoya Baba, Tomoko Nakamichi, Hirotada Mori, Satoshi Tabata

  DNA research : an international journal for rapid publication of reports on genes and genomes. 06/2008;

  The legume Lotus japonicus has been widely used as a model system to investigate the genetic background of legume-specific phenomena such as symbiotic nitrogen fixation. Here, we report structuralThe legume Lotus japonicus has been widely used as a model system to investigate the genetic background of legume-specific phenomena such as symbiotic nitrogen fixation. Here, we report structural features of the L. japonicus genome. The 315.1-Mb sequences determined in this and previous studies correspond to 67% of the genome (472 Mb), and are likely to cover 91.3% of the gene space. Linkage mapping anchored 130-Mb sequences onto the six linkage groups. A total of 10 951 complete and 19 848 partial structures of protein-encoding genes were assigned to the genome. Comparative analysis of these genes revealed the expansion of several functional domains and gene families that are characteristic of L. japonicus. Synteny analysis detected traces of whole-genome duplication and the presence of synteny blocks with other plant genomes to various degrees. This study provides the first opportunity to look into the complex and unique genetic system of legumes.

• Complete genomic structure of the bloom-forming toxic cyanobacterium Microcystis aeruginosa NIES-843.

  Authors: Takakazu Kaneko, Nobuyoshi Nakajima, Shinobu Okamoto, Iwane Suzuki, Yuuhiko Tanabe, Masanori Tamaoki, Yasukazu Nakamura, Fumie Kasai, Akiko Watanabe, Kumiko Kawashima [......] Chika Takahashi, Chiharu Minami, Tsunakazu Fujishiro, Mitsuyo Kohara, Midori Katoh, Naomi Nakazaki, Shinobu Nakayama, Manabu Yamada, Satoshi Tabata, Makoto M Watanabe

  DNA research : an international journal for rapid publication of reports on genes and genomes. 01/2008; 14(6):247-56.

  The nucleotide sequence of the complete genome of a cyanobacterium, Microcystis aeruginosa NIES-843, was determined. The genome of M. aeruginosa is a single, circular chromosome of 5,842,795 baseThe nucleotide sequence of the complete genome of a cyanobacterium, Microcystis aeruginosa NIES-843, was determined. The genome of M. aeruginosa is a single, circular chromosome of 5,842,795 base pairs (bp) in length, with an average GC content of 42.3%. The chromosome comprises 6312 putative protein-encoding genes, two sets of rRNA genes, 42 tRNA genes representing 41 tRNA species, and genes for tmRNA, the B subunit of RNase P, SRP RNA, and 6Sa RNA. Forty-five percent of the putative protein-encoding sequences showed sequence similarity to genes of known function, 32% were similar to hypothetical genes, and the remaining 23% had no apparent similarity to reported genes. A total of 688 kb of the genome, equivalent to 11.8% of the entire genome, were composed of both insertion sequences and miniature inverted-repeat transposable elements. This is indicative of a plasticity of the M. aeruginosa genome, through a mechanism that involves homologous recombination mediated by repetitive DNA elements. In addition to known gene clusters related to the synthesis of microcystin and cyanopeptolin, novel gene clusters that may be involved in the synthesis and modification of toxic small polypeptides were identified. Compared with other cyanobacteria, a relatively small number of genes for two component systems and a large number of genes for restriction-modification systems were notable characteristics of the M. aeruginosa genome.

• Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids.

  Authors: Yasukazu Nakamura, Takakazu Kaneko, Shusei Sato, Mamoru Mimuro, Hideaki Miyashita, Tohru Tsuchiya, Shigemi Sasamoto, Akiko Watanabe, Kumiko Kawashima, Yoshie Kishida, Chiaki Kiyokawa, Mitsuyo Kohara, Midori Matsumoto, Ai Matsuno, Naomi Nakazaki, Sayaka Shimpo, Chie Takeuchi, Manabu Yamada, Satoshi Tabata

  DNA research : an international journal for rapid publication of reports on genes and genomes. 09/2003; 10(4):137-45.

  The nucleotide sequence of the entire genome of a cyanobacterium Gloeobacter violaceus PCC 7421 was determined. The genome of G. violaceus was a single circular chromosome 4,659,019 bp long with anThe nucleotide sequence of the entire genome of a cyanobacterium Gloeobacter violaceus PCC 7421 was determined. The genome of G. violaceus was a single circular chromosome 4,659,019 bp long with an average GC content of 62%. No plasmid was detected. The chromosome comprises 4430 potential protein-encoding genes, one set of rRNA genes, 45 tRNA genes representing 44 tRNA species and genes for tmRNA, B subunit of RNase P, SRP RNA and 6Sa RNA. Forty-one percent of the potential protein-encoding genes showed sequence similarity to genes of known function, 37% to hypothetical genes, and the remaining 22% had no apparent similarity to reported genes. Comparison of the assigned gene components with those of other cyanobacteria has unveiled distinctive features of the G. violaceus genome. Genes for PsaI, PsaJ, PsaK, and PsaX for Photosystem I and PsbY, PsbZ and Psb27 for Photosystem II were missing, and those for PsaF, PsbO, PsbU, and PsbV were poorly conserved. cpcG for a rod core linker peptide for phycobilisomes and nblA related to the degradation of phycobilisomes were also missing. Potential signal peptides of the presumptive products of petJ and petE for soluble electron transfer catalysts were less conserved than the remaining portions. These observations may be related to the fact that photosynthesis in G. violaceus takes place not in thylakoid membranes but in the cytoplasmic membrane. A large number of genes for sigma factors and transcription factors in the LuxR, LysR, PadR, TetR, and MarR families could be identified, while those for major elements for circadian clock, kaiABC were not found. These differences may reflect the phylogenetic distance between G. violaceus and other cyanobacteria.

• Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1.

  Authors: Yasukazu Nakamura, Takakazu Kaneko, Shusei Sato, Masahiko Ikeuchi, Hiroshi Katoh, Shigemi Sasamoto, Akiko Watanabe, Mayumi Iriguchi, Kumiko Kawashima, Takaharu Kimura [......] Chiaki Kiyokawa, Mitsuyo Kohara, Midori Matsumoto, Ai Matsuno, Naomi Nakazaki, Sayaka Shimpo, Masako Sugimoto, Chie Takeuchi, Manabu Yamada, Satoshi Tabata

  DNA research : an international journal for rapid publication of reports on genes and genomes. 09/2002; 9(4):123-30.

  The entire genome of a thermophilic unicellular cyanobacterium, Thermosynechococcus elongatus BP-1, was sequenced. The genome consisted of a circular chromosome 2,593,857 bp long, and no plasmid wasThe entire genome of a thermophilic unicellular cyanobacterium, Thermosynechococcus elongatus BP-1, was sequenced. The genome consisted of a circular chromosome 2,593,857 bp long, and no plasmid was detected. A total of 2475 potential protein-encoding genes, one set of rRNA genes, 42 tRNA genes representing 42 tRNA species and 4 genes for small structural RNAs were assigned to the chromosome by similarity search and computer prediction. The translated products of 56% of the potential protein-encoding genes showed sequence similarity to experimentally identified and predicted proteins of known function, and the products of 34% of these genes showed sequence similarity to the translated products of hypothetical genes. The remaining 10% lacked significant similarity to genes for predicted proteins in the public DNA databases. Sixty-three percent of the T. elongatus genes showed significant sequence similarity to those of both Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120, while 22% of the genes were unique to this species, indicating a high degree of divergence of the gene information among cyanobacterial strains. The lack of genes for typical fatty acid desaturases and the presence of more genes for heat-shock proteins in comparison with other mesophilic cyanobacteria may be genomic features of thermophilic strains. A remarkable feature of the genome is the presence of 28 copies of group II introns, 8 of which contained a presumptive gene for maturase/reverse transcriptase. A trace of genome rearrangement mediated by the group II introns was also observed.

• Complete Genome Structure of the Nitrogen-fixing Symbiotic Bacterium Mesorhizobium loti (Supplement)

  Authors: Takakazu Kaneko, Yasukazu Nakamura, Shusei Sato, Erika Asamizu, Tomohiko Kato, Shigemi Sasamoto, Akiko Watanabe, Kumi Idesawa, Atsuko Ishikawa, Kumiko Kawashima [......] Midori Matsumoto, Ai Matsuno, Yoko Mochizuki, Shinobu Nakayama, Naomi Nakazaki, Sayaka Shimpo, Masako Sugimoto, Chie Takeuchi, Manabu Yamada, Satoshi Tabata

• Complete Genome Structure of the Nitrogen-fixing Symbiotic Bacterium Mesorhizobium loti

  Authors: Takakazu Kaneko, Yasukazu Nakamura, Shusei Sato, Erika Asamizu, Tomohiko Kato, Shigemi Sasamoto, Akiko Watanabe, Kumi Idesawa, Atsuko Ishikawa, Kumiko Kawashima [......] Midori Matsumoto, Ai Matsuno, Yoko Mochizuki, Shinobu Nakayama, Naomi Nakazaki, Sayaka Shimpo, Masako Sugimoto, Chie Takeuchi, Manabu Yamada, Satoshi Tabata

  The complete nucleotide sequence of the genome of a symbiotic bacterium Mesorhizobium loti strain MAFF303099 was determined. The genome of M. loti consisted of a single chromosome (7, 036, 071 bp)The complete nucleotide sequence of the genome of a symbiotic bacterium Mesorhizobium loti strain MAFF303099 was determined. The genome of M. loti consisted of a single chromosome (7, 036, 071 bp) and two plasmids, designated as pMLa (351, 911 bp) and pMLb (208, 315 bp). The chromosome comprises 6752 potential protein-coding genes, two sets of rRNA genes and 50 tRNA genes representing 47 tRNA species. Fifty-four percent of the potential protein genes showed sequence similarity to genes of known function, 21% to hypothetical genes, and the remaining 25% hadno apparent similarity to reported genes. A 611-kb DNA segment, a highly probable candidate of a symbiotic island, was identified, and 30 genes for nitrogen fixation and 24 genes for nodulation were assigned in this region. Codon usage analysis suggested that the symbiotic islandas well as the plasmids originated andw ere transmittedfrom other genetic systems. The genomes of two plasmids, pMLa and pMLb, contained 320 and 209 potential protein-coding genes, respectively, for a variety of biological functions. These include genes for the ABC-transporter system, phosphate assimilation, two-component system, DNA replication and conjugation, but only one gene for nodulation was identified.