Mika Nomura

Publications of Mika Nomura

• Copper metallochaperones are required for the assembly of bacteroid cytochrome c oxidase which is functioning for nitrogen fixation in soybean nodules.

  Authors: Hatthaya Arunothayanan, Mika Nomura, Rie Hamaguchi, Manabu Itakura, Kiwamu Minamisawa, Shigeyuki Tajima

  Plant & cell physiology. 07/2010; 51(7):1242-6.

  Bradyrhizobium japonicum, a symbiotic nitrogen-fixing bacterium for Glycine max, has complex respiratory electron transport chains. Bll4880 contained a copper-binding motif for metallochaperone,Bradyrhizobium japonicum, a symbiotic nitrogen-fixing bacterium for Glycine max, has complex respiratory electron transport chains. Bll4880 contained a copper-binding motif for metallochaperone, H(M)X(10)MX(21)HXM. A mutant strain, Bj4880, induced nodules with lower acetylene reduction activity. A double mutant, Bj4880-1131, which had inserted mutations both in blr1131, a gene of the Sco1-like protein, and in bll4880, induced nodules of significant Fix(-) phenotype and low cytochrome c oxidase (Cco) activity in the bacteroid. Our data suggest that bll4880 protein is involved in copper ion delivery to Cco through blr1131 protein, and the expression of both proteins was induced under microaerobic conditions.

• Expression and characterization of PKL01, an Ndr kinase homolog in Lotus japonicus.

  Authors: Isamu Kameshita, Sachiko Shimomura, Kazushi Nishio, Noriyuki Sueyoshi, Tetsuyuki Nishida, Mika Nomura, Shigeyuki Tajima

  Journal of biochemistry. 02/2010; 147(6):799-807.

  We isolated cDNA clones for novel protein kinases by expression cloning from Lotus japonicus. The LNZ001, one of the isolated clones, encodes a protein of 547 amino acids with a predicted molecularWe isolated cDNA clones for novel protein kinases by expression cloning from Lotus japonicus. The LNZ001, one of the isolated clones, encodes a protein of 547 amino acids with a predicted molecular weight of 63,349. Since the protein contains 12 highly conserved subdomains specific to Ser/Thr protein kinases, we designated it PKL01. When homology searches based on the PKL01 sequence were carried out, the protein was found to show sequence homology with nuclear Dbf2-related kinases (Ndr kinases). When PKL01 was produced using an Escherichia coli expression system and purified to homogeneity, it underwent intermolecular autophosphorylation. The major autophosphorylation site was identified as Ser-317 by using various point mutants, and phosphorylation at this site was found to be critical for the kinase activity. PKL01 was found to be widely distributed in the leaves, stems, roots and root nodules by northern hybridization experiments. When endogenous substrates were screened using fractionated preparations from various parts of plants, PKL01 preferentially phosphorylated basic proteins in tissue extracts. These results suggest that PKL01 is an Ndr kinase homolog in L. japonicus and may be involved in the regulation of cellular functions through phosphorylation of basic protein substrates such as histones.

• Host plant genome overcomes the lack of a bacterial gene for symbiotic nitrogen fixation.

  Authors: Tsuneo Hakoyama, Kaori Niimi, Hirokazu Watanabe, Ryohei Tabata, Junichi Matsubara, Shusei Sato, Yasukazu Nakamura, Satoshi Tabata, Li Jichun, Tsuyoshi Matsumoto, Kazuyuki Tatsumi, Mika Nomura, Shigeyuki Tajima, Masumi Ishizaka, Koji Yano, Haruko Imaizumi-Anraku, Masayoshi Kawaguchi, Hiroshi Kouchi, Norio Suganuma

  Nature. 11/2009; 462(7272):514-7.

  Homocitrate is a component of the iron-molybdenum cofactor in nitrogenase, where nitrogen fixation occurs. NifV, which encodes homocitrate synthase (HCS), has been identified from various diazotrophsHomocitrate is a component of the iron-molybdenum cofactor in nitrogenase, where nitrogen fixation occurs. NifV, which encodes homocitrate synthase (HCS), has been identified from various diazotrophs but is not present in most rhizobial species that perform efficient nitrogen fixation only in symbiotic association with legumes. Here we show that the FEN1 gene of a model legume, Lotus japonicus, overcomes the lack of NifV in rhizobia for symbiotic nitrogen fixation. A Fix(-) (non-fixing) plant mutant, fen1, forms morphologically normal but ineffective nodules. The causal gene, FEN1, was shown to encode HCS by its ability to complement a HCS-defective mutant of Saccharomyces cerevisiae. Homocitrate was present abundantly in wild-type nodules but was absent from ineffective fen1 nodules. Inoculation with Mesorhizobium loti carrying FEN1 or Azotobacter vinelandii NifV rescued the defect in nitrogen-fixing activity of the fen1 nodules. Exogenous supply of homocitrate also recovered the nitrogen-fixing activity of the fen1 nodules through de novo nitrogenase synthesis in the rhizobial bacteroids. These results indicate that homocitrate derived from the host plant cells is essential for the efficient and continuing synthesis of the nitrogenase system in endosymbionts, and thus provide a molecular basis for the complementary and indispensable partnership between legumes and rhizobia in symbiotic nitrogen fixation.

• Barley grain with adhering hulls is controlled by an ERF family transcription factor gene regulating a lipid biosynthesis pathway.

  Authors: Shin Taketa, Satoko Amano, Yasuhiro Tsujino, Tomohiko Sato, Daisuke Saisho, Katsuyuki Kakeda, Mika Nomura, Toshisada Suzuki, Takashi Matsumoto, Kazuhiro Sato, Hiroyuki Kanamori, Shinji Kawasaki, Kazuyoshi Takeda

  Proceedings of the National Academy of Sciences of the United States of America. 04/2008; 105(10):4062-7.

  In contrast to other cereals, typical barley cultivars have caryopses with adhering hulls at maturity, known as covered (hulled) barley. However, a few barley cultivars are a free-threshing variantIn contrast to other cereals, typical barley cultivars have caryopses with adhering hulls at maturity, known as covered (hulled) barley. However, a few barley cultivars are a free-threshing variant called naked (hulless) barley. The covered/naked caryopsis is controlled by a single locus (nud) on chromosome arm 7HL. On the basis of positional cloning, we concluded that an ethylene response factor (ERF) family transcription factor gene controls the covered/naked caryopsis phenotype. This conclusion was validated by (i) fixation of the 17-kb deletion harboring the ERF gene among all 100 naked cultivars studied; (ii) two x-ray-induced nud alleles with a DNA lesion at a different site, each affecting the putative functional motif; and (iii) gene expression strictly localized to the testa. Available results indicate the monophyletic origin of naked barley. The Nud gene has homology to the Arabidopsis WIN1/SHN1 transcription factor gene, whose deduced function is control of a lipid biosynthesis pathway. Staining with a lipophilic dye (Sudan black B) detected a lipid layer on the pericarp epidermis only in covered barley. We infer that, in covered barley, the contact of the caryopsis surface, overlaid with lipids to the inner side of the hull, generates organ adhesion.

• NAD-Malic Enzyme Affects Nitrogen Fixing Activity of Bradyrhizobium japonicum USDA 110 Bacteroids in Soybean Nodules.

  Authors: Tan Van Dao, Mika Nomura, Rie Hamaguchi, Kensuke Kato, Manabu Itakura, Kiwamu Minamisawa, Suphawat Sinsuwongwat, Hoa Thi-Phuong Le, Takakazu Kaneko, Satoshi Tabata, Shigeyuki Tajima

  Microbes and environments / JSME. 01/2008; 23(3):215-20.

  The NAD(+)-dependent malic enzyme (DME) has been reported to play a key role supporting nitrogenase activity in bacteroids of Sinorhizobium meliloti. Genetic evidence for a similar role inThe NAD(+)-dependent malic enzyme (DME) has been reported to play a key role supporting nitrogenase activity in bacteroids of Sinorhizobium meliloti. Genetic evidence for a similar role in Bradyrhizobium japonicum USDA110 was obtained by constructing a dme mutant. Soybean plants inoculated with a dme mutant did not show delayed nodulation, but formed small root nodules and exhibited significant nitrogen-deficiency symptoms. Nodule numbers and the acetylene reducting activity per nodule as a dry weight value 14 and 28 days after inoculation with the dme mutant were comparable to those of plants inoculated with wild-type B. japonicum. However, shoot dry weight and acetylene reducting activity per nodule decreased to ca. 30% of the values in plants with wild-type B. japonicum. The sucrose and organic acid (malate, succinate, acetate, α-ketoglutarate and lactate) contents of the nodules were investigated. Amounts of sucrose, malate and a-ketoglutarate increased on inoculation with the dme mutant, suggesting that the decreased DME and nitrogenase activities in the bacteroids resulted in a reduction in the consumption of these respiratory metabolites by the nodules. The data suggest that the DME activity of B. japonicum bacteroids plays a role in nodule metabolism and supports nitrogen fixation.

• LjnsRING, a novel RING finger protein, is required for symbiotic interactions between Mesorhizobium loti and Lotus japonicus.

  Authors: Kenshiro Shimomura, Mika Nomura, Shigeyuki Tajima, Hiroshi Kouchi

  Plant & cell physiology. 12/2006; 47(11):1572-81.

  Nodule-specific (nodulin) genes are thought to play crucial roles during establishment of the nitrogen-fixing symbiosis between legume plants and Rhizobium bacteria. On the basis of a gene expressionNodule-specific (nodulin) genes are thought to play crucial roles during establishment of the nitrogen-fixing symbiosis between legume plants and Rhizobium bacteria. On the basis of a gene expression database for early stages of the nodulation process of Lotus japonicus, previously constructed by a cDNA macroarray analysis, we identified a novel nodulin gene, LjnsRING, which encodes a protein with a typical RING-H2 finger domain that is well conserved in a number of plant E3 ubiquitin ligases. LjnsRING transcripts were almost exclusively expressed in nodules, and very low expression was detected in roots and shoots. RNA interference (RNAi) knockdown of LjnsRING by hairy root transformation caused impaired root growth together with abortion of nodule formation. Examination with lacZ-labeled Mesorhizobium loti indicated that infection thread formation in the RNAi transgenic hairy roots was significantly inhibited. Analysis using a chimeric gene of LjnsRING promoter and beta-glucuronidase (GUS) coding region demonstrated that LjnsRING transcription in nodules was restricted to the infected cells. These results suggest the requirement for LjnsRING in rhizobial infection and the subsequent nodule formation process.

• Identification of a Sed5-like SNARE gene LjSYP32-1 that contributes to nodule tissue formation of Lotus japonicus.

  Authors: Ha Thu Mai, Mika Nomura, Kaoru Takegawa, Erika Asamizu, Syusei Sato, Tomohiko Kato, Satoshi Tabata, Shigeyuki Tajima

  Plant & cell physiology. 08/2006; 47(7):829-38.

  We identified a Sed5-like clone LjSYP32-1 which contributes to nodule tissue formation and plant growth in Lotus japonicus. In the L. japonicus expressed sequence tag (EST) clone databases of KazusaWe identified a Sed5-like clone LjSYP32-1 which contributes to nodule tissue formation and plant growth in Lotus japonicus. In the L. japonicus expressed sequence tag (EST) clone databases of Kazusa DNA Research Institute, another syntaxin-related clone (LjSYP32-2) was also detected, and the nucleotide and amino acid sequences of these two clone are very similar to each other. Real-time PCR and promoter analysis indicated that expression of LjSYP32-1 was dominant compared with LjSYP32-2 in the various plant organs. Promoter analysis and in situ hybridization revealed that LjSYP32-1 was expressed significantly in the inner cortex cell layer surrounding the infected zone of young nodules and in the meristem area of developing lateral root. To explore the function and physiological role of LjSYP32-1 in nodules and other plant organs, stable transformation lines of L. japonicus expressing either sense or antisense LjSYP32-1 were prepared. The antisense plants showed a significantly retarded plant growth phenotype, suggesting a role for LjSYP32-1 in supporting plant growth. In the same transgenic lines, the plants were capable of forming nodules, but the acetylene reduction activity was reduced by around 50% per plant. The nodules were much smaller and some nodules were fused to each other by sharing the inner cortex. The rate of occurrence of such irregular nodules was twice that observed in wild-type plants. The data suggest that LjSYP32-1 contributes to the support of plant growth and normal nodule tissue differentiation.

• Phosphoenolpyruvate carboxylase plays a crucial role in limiting nitrogen fixation in Lotus japonicus nodules.

  Authors: Mika Nomura, Ha Thu Mai, Miho Fujii, Shingo Hata, Katsura Izui, Shigeyuki Tajima

  Plant & cell physiology. 06/2006; 47(5):613-21.

  Phosphoenolpyruvate carboxylase (PEPC, EC 4.1.1.31) is believed to play a significant role in supporting nitrogen fixation via anaplerotic CO2 fixation for recycling carbon in nodules. Using thePhosphoenolpyruvate carboxylase (PEPC, EC 4.1.1.31) is believed to play a significant role in supporting nitrogen fixation via anaplerotic CO2 fixation for recycling carbon in nodules. Using the antisense technique, we decreased the expression levels of the nodule-enhanced PEPC gene (Ljpepc1) in a determinate legume plant (Lotus japonicus) in order to look at the influence of the symbiotic phenotype and biochemical parameters. Three independent transgenic L. japonicus plants (designated as Asppc1, Asppc2 and Asppc3) were prepared using a Ljpepc1 DNA fragment which is under the control of the cauliflower mosaic virus 35S promoter. Extensive suppression of the Ljpepc1 transcript in nodules of Asppc plants (T3 homologous plants) was confirmed by RNA gel blot, Western blot and enzyme activity assays. In nodules of Asppc plants, PEPC activity was reduced to about 10% of that of non-transformants and the plants showed typical nitrogen-deficient symptoms without a supply of nitrogen nutrient, and returned to normal growth when nitrate was supplied at 2.5 mM. The acetylene reduction activity per fresh weight of nodules of these Asppc plants decreased by 29% at 35 dai (days after infection). Various enzyme activities and metabolite levels were surveyed using Asppc plants at 35 dai. Significant reduction of sucrose synthase and asparagine aminotransferase activities was observed in Asppc nodules. In addition, sucrose, succinate, asparagine, aspartate and glutamate contents also decreased in Asppc nodules. The data are discussed in terms of a role for PEPC in the carbon/nitrogen metabolic flux in nodules.

• Differential expression pattern of C4 bundle sheath expression genes in rice, a C3 plant.

  Authors: Mika Nomura, Tomonori Higuchi, Yuji Ishida, Shozo Ohta, Toshihiko Komari, Nobuyuki Imaizumi, Mitsue Miyao-Tokutomi, Makoto Matsuoka, Shigeyuki Tajima

  Plant & cell physiology. 06/2005; 46(5):754-61.

  NADP-malic enzyme (NADP-ME) and phosphoenolpyruvate carboxykinase (PCK) are specifically expressed in bundle sheath cells (BSCs) in NADP-ME-type and PCK-type C4 plants, respectively. Unlike the highNADP-malic enzyme (NADP-ME) and phosphoenolpyruvate carboxykinase (PCK) are specifically expressed in bundle sheath cells (BSCs) in NADP-ME-type and PCK-type C4 plants, respectively. Unlike the high activities of these enzymes in the green leaves of C4 plants, their low activities have been detected in the leaves of C3 plants. In order to elucidate the differences in the gene expression system between C3 and C4 plants, we have produced chimeric constructs with the beta-glucuronidase (GUS) reporter gene under the control of the maize NADP-Me (ZmMe) or Zoysia japonica Pck (ZjPck) promoter and introduced these constructs into rice. In leaves of transgenic rice, the ZmMe promoter directed GUS expression not only in mesophyll cells (MCs) but also in BSCs and vascular cells, whereas the ZjPck promoter directed GUS expression only in BSCs and vascular cells. Neither the ZjPck nor ZmMe promoters induced GUS expression due to light. In rice leaves, the endogenous NADP-Me (OsMe1) was expressed in MCs, BSCs and vascular cells, whereas the rice Pck (OsPck1) was expressed only in BSCs and vascular cells. Taken together, the results obtained from transgenic rice demonstrate that the expression pattern of ZmMe or ZjPck in transgenic rice was reflected by that of its counterpart gene in rice.

• The promoter for C4-type mitochondrial aspartate aminotransferase does not direct bundle sheath-specific expression in transgenic rice plants.

  Authors: Mika Nomura, Tomonori Higuchi, Kenichi Katayama, Mitsutaka Taniguchi, Mitsue Miyao-Tokutomi, Makoto Matsuoka, Shigeyuki Tajima

  Plant & cell physiology. 06/2005; 46(5):743-53.

  For NAD-malic enzyme (NAD-ME)-type C4 photosynthesis, two types of aspartate aminotransferase (AAT) are involved. We examined the expression pattern of the Panicum miliaceum mitochondrial Aat geneFor NAD-malic enzyme (NAD-ME)-type C4 photosynthesis, two types of aspartate aminotransferase (AAT) are involved. We examined the expression pattern of the Panicum miliaceum mitochondrial Aat gene (PmAat) and P. miliaceum cytosolic Aat gene (PcAat) in transgenic rice plants, which were specifically expressed in bundle sheath cells (BSCs) and mesophyll cells (MCs), respectively. Expression of a beta-glucuronidase (GUS) reporter gene under the control of the PcAat promoter was regulated in an organ-preferential and light-dependent manner in the transgenic rice plants. However, the PmAat promoter drove the GUS expression in all organs we tested without light dependency, and this non-preferential expression pattern was also observed in transgenic rice with introduction of the intact PmAat gene. The expression patterns of the rice counterpart Aat genes to PmAat or PcAat showed that the rice mitochondrial Aat (RmAat1) gene was expressed in all organs tested in a light-independent manner, while expression of the rice cytosolic Aat (RcAat1) gene showed an organ-preferential and light-dependent pattern. Taking these results together, we can generalize that the regulatory system of BSC-specific or light-dependent expression of mitochondrial Aat is not shared between P. miliaceum (C4) and rice (C3) and that the expression of the C4 genes introduced into rice mimics that of their counterpart genes in rice.

• Expression cloning of a variety of novel protein kinases in Lotus japonicus.

  Authors: Isamu Kameshita, Tetsuyuki Nishida, Satoko Nakamura, Yasunori Sugiyama, Noriyuki Sueyoshi, Yosuke Umehara, Mika Nomura, Shigeyuki Tajima

  Journal of biochemistry. 02/2005; 137(1):33-9.

  To investigate protein kinases expressed in Lotus japonicus, a cDNA expression library of the root-nodule of L. japonicus was immunologically screened with monoclonal antibodies directed to a highlyTo investigate protein kinases expressed in Lotus japonicus, a cDNA expression library of the root-nodule of L. japonicus was immunologically screened with monoclonal antibodies directed to a highly conserved region in protein serine/threonine kinases (Ser/Thr kinases). Among 178 positive clones obtained from the lambdaZAPII cDNA library, 164 clones were found to encode novel proteins possessing the subdomain VIB sequences characteristic of Ser/Thr kinases. By phylogenetic analysis on the basis of deduced amino acid sequences, the isolated clones could be classified into five different families of Ser/Thr kinases : the SnRK family, GSK-3 family, Ndr kinase family, Ark family, and receptor kinase family. These results suggest that this expression cloning using the kinase-specific antibodies will provide new clues for investigations of a wide variety of known and novel protein kinases in higher plants.

• Ureide biosynthesis in legume nodules.

  Authors: Shigeyuki Tajima, Mika Nomura, Hiroshi Kouchi

  Frontiers in bioscience : a journal and virtual library. 06/2004; 9:1374-81.

  In tropical legumes like Glycine, Phaseolus and Vigna sp., ammonia as direct product of symbiotic nitrogen fixation is converted to ureides (allantoin and allantoic acid) and they were translocatedIn tropical legumes like Glycine, Phaseolus and Vigna sp., ammonia as direct product of symbiotic nitrogen fixation is converted to ureides (allantoin and allantoic acid) and they were translocated to the shoots as nitrogen source. In the xylem sap of soybean in reproductive phase the ureides reached to 60-75% of soluble nitrogen. In nodules infected cells (plastid and mitochondria) and uninfected cells (peroxisome) shares de novo purine biosynthesis and urate oxidation to produce ureides respectively. Current research revealed unique feathers on this symbiotic metabolism, especially on regulation of purine biosynthesis, uricase gene expression and feedback inhibition of ureides to nitrogen fixing activity.

• Expression islands clustered on the symbiosis island of the Mesorhizobium loti genome.

  Authors: Toshiki Uchiumi, Takuji Ohwada, Manabu Itakura, Hisayuki Mitsui, Noriyuki Nukui, Pramod Dawadi, Takakazu Kaneko, Satoshi Tabata, Tadashi Yokoyama, Kouhei Tejima [......] Rutchadaporn Sriprang, Yoshikatsu Murooka, Shigeyuki Tajima, Kenshiro Simomura, Mika Nomura, Akihiro Suzuki, Yoshikazu Shimoda, Kouki Sioya, Mikiko Abe, Kiwamu Minamisawa

  Journal of bacteriology. 05/2004; 186(8):2439-48.

  Rhizobia are symbiotic nitrogen-fixing soil bacteria that are associated with host legumes. The establishment of rhizobial symbiosis requires signal exchanges between partners in microaerobicRhizobia are symbiotic nitrogen-fixing soil bacteria that are associated with host legumes. The establishment of rhizobial symbiosis requires signal exchanges between partners in microaerobic environments that result in mutualism for the two partners. We developed a macroarray for Mesorhizobium loti MAFF303099, a microsymbiont of the model legume Lotus japonicus, and monitored the transcriptional dynamics of the bacterium during symbiosis, microaerobiosis, and starvation. Global transcriptional profiling demonstrated that the clusters of genes within the symbiosis island (611 kb), a transmissible region distinct from other chromosomal regions, are collectively expressed during symbiosis, whereas genes outside the island are downregulated. This finding implies that the huge symbiosis island functions as clustered expression islands to support symbiotic nitrogen fixation. Interestingly, most transposase genes on the symbiosis island were highly upregulated in bacteroids, as were nif, fix, fdx, and rpoN. The genome region containing the fixNOPQ genes outside the symbiosis island was markedly upregulated as another expression island under both microaerobic and symbiotic conditions. The symbiosis profiling data suggested that there was activation of amino acid metabolism, as well as nif-fix gene expression. In contrast, genes for cell wall synthesis, cell division, DNA replication, and flagella were strongly repressed in differentiated bacteroids. A highly upregulated gene in bacteroids, mlr5932 (encoding 1-aminocyclopropane-1-carboxylate deaminase), was disrupted and was confirmed to be involved in nodulation enhancement, indicating that disruption of highly expressed genes is a useful strategy for exploring novel gene functions in symbiosis.

• Proteomic analysis on symbiotic differentiation of mitochondria in soybean nodules.

  Authors: Le Thi-Phuong Hoa, Mika Nomura, Hideyuki Kajiwara, David Alexander Day, Shigeyuki Tajima

  Plant & cell physiology. 04/2004; 45(3):300-8.

  Symbiotic interactions between legume plants and rhizobia induce specific metabolisms and intracellular organelles in nodules. For surveying symbiotic differentiation of a key organelle,Symbiotic interactions between legume plants and rhizobia induce specific metabolisms and intracellular organelles in nodules. For surveying symbiotic differentiation of a key organelle, mitochondria, protein constituents of soybean nodule and root mitochondria were compared after two-dimensional (2-D) electrophoresis, and the proteins were characterized in combination with matrix-assisted desorption/ionization time-of-flight mass spectrometry, electrospray ionization mass spectrometry and N-terminal amino acid sequencing. Of the proteins that were detected only in nodule mitochondria, phosphoserine aminotransferase, flavanone 3-hydroxylase, coproporphyrinogen III oxidase, one ribonucleoprotein and three unknown proteins were identified. Seven up-regulated, eight down-regulated and two strongly suppressed protein spots in nodule mitochondria were also assigned protein identities. The physiological roles of these differential expressions were discussed in relation to nodule-specific metabolisms in soybean nodules.