Department of Biological Mechanisms and Functions

Division of Bioresource Functions


  Fax: +81-52-789-4025
Prof. MATSUMOTO, Shogo D. Sci. shogo@
Assoc. Prof. SHIRATAKE, Katsuhiro D. Agr. shira@
Lecturer OTAGAKI, Shungo D. Agr. sotagaki@
Asst. Prof. NOTAGUCHI, Michitaka D. Sci.
Molecllar Approach to The Mechanism of Sugar Accumulation in Rasaceae Fruit

Growth and development of horticultural crops are studied for their practical application, covering pomology, vegetable crop science, floricultural science and postharvest physiology. We identify genes, which relate to important traits of horticultural crops as followings and clarify their physiological functions by biochemical and molecular biological techniques. We produce genetically modified plants of the genes.

  1. Self-incompatibility of Rosaceae family
  2. Molecular mechanisms in the reproductive/nutritional growth of Rosaceae family
  3. Coloration mechanism and effective breeding of Rosaceae family using DNA marker
  4. Long distance sugar transport and sugar metabolism in Rosaceae fruit trees, such as apple, peach and pear. (Enzyme for sorbitol metabolism, Sorbitol transporter)
  5. Functional study of transporters (aquaporin, sugar transporter, ABC transporter) in horticultural crops
  6. Molecular breeding of floricultural crops
  7. Omics study of fruits (genomics, transcriptomics, proteomics, metabolomics, ionomics)
  8. Genome editing of genes related to important traits of horticultural crops

Key Words: Omics study, Genome editing, Epigenetics, Molecular breeding, DNA marker

Recent Publications:

  1. Azuma M., Morimoto R., Hirose M., Morita Y., Hoshino A., Iida S., Oshima Y., Mitsuda N., Ohme-Takagi M. and Shiratake K. (2015) A petal-specific InMYB1 promoter from Japanese morning glory: a useful tool for molecular breeding of floricultural crops. Plant Biotechnol. J. Accepted (10.1111/pbi.12389)
  2. Otagaki S., Ogawa Y., Oyant L. H., Foucher F., Kawamura K., Horibe T. and Matsumoto S. (2015) Genotype of FLOWERING LOCUS T homologue contributes to the flowering time differences in wild and cultivated roses. Plant Biology 17: 808-815.
  3. Suzuki M., Nakabayashi R., Ogata Y., Sakurai N., Tokimatsu T., Goto S., Suzuki M., Jasinski M., Martinoia E., Otagaki S., Matsumoto S., Saito K. and Shiratake K. (2015) Multi omics in grape berry skin revealed specific induction of stilbene synthetic pathway by UV-C irradiation. Plant Physiol. 168: 47-59.
  4. Nakajima R., Otagaki S., Shiratake K. and Matsumoto S. (2015) Energy-saving seedling production system for super-forcing cultivation of June-bearing commercial strawberry. HortScience 50: 685-687.
  5. Hamada Y., Sato H., Otagaki S., Okada K., Abe K. and Matsumoto S. (2015) Breeding depression of red flesh apple progenies containing both functional MdMYB10 and MYB110a_JP genes. Plant Breeding 134: 239-246.
  6. Reuscher S., Akiyama M., Yasuda T., Aoki K., Shibata D. and Shiratake K. (2014) The sugar transporter inventory of tomato: Genome-wide identification and expression analysis. Plant Cell Physiol. 55: 1123-1141.
  7. Nakajima R., Otagaki S., Yamada K., Shiratake K. and Matsumoto S. (2014) Molecular cloning and expression analysis of FaFT, FaTFL and FaAP1 genes in cultivated strawberry: their correlation to flower bud formation. Biologia plantarum. 58: 641-648.
  8. Reuscher S., Akiyama M., Mori C., Aoki K., Shibata D. and Shiratake K. (2013) Genome-wide identification and expression analysis of aquaporins in tomato. PLoS ONE. 8: e79052.
  9. Nashima K., Shimizu T., Nishitani C., Yamamoto T., Takahashi H., Nakazono M., Itai A., Isuzugawa K., Hanada T., Takashina T., Matsumoto S., Otagaki S., Oikawa A. and Shiratake K. (2013) Microarray analysis of gene expression patterns during fruit development in European pear (Pyrus communis). Scientia Horticulturae. 164: 466–473.
  10. Umemura H., Otagaki S., Wada M., Kondo S. and Matsumoto S. (2013) Expression and functional analysis of a novel MYB gene, MdMYB110a_JP, responsible for red flesh, not skin color in apple fruit. Planta 238: 65-76.


  Fax: +81-52-789-4029
Prof. KAWAKITA, Kazuhito D. Agr. kkawakit@
Assoc. Prof. TAKEMOTO, Daigo D. Agr. dtakemo@
Des. Assoc. Prof. CHIBA, Sotaro D. Agr. chiba@
Asst. Prof. SATO, Ikuo D. Agr. isato@

Our research group focuses on the molecular mechanisms of plant disease resistances against fungal and oomycete pathogens. We are working in particular on interaction between oomycete pathogen Phytophthora infestans and Solanaceae species. To elucidate the molecular and cellular basis of the plant-microbe interactions, we are aiming to identify and characterize genes involved in effective defense responses. Especially, we are tiring to understand the role of reactive oxygen species (ROS) and nitric oxide (NO) in disease resistance.
We also investigate the symbiotic interaction between perennial ryegrass and endophytic fungi Epichloë festucae. Recent studies have shown that the infection of this symbiotic fungi improves plant tolerance to a range of biotic and abiotic stresses, including drought, disease, and animal herbivory.
The ultimate goal of our research is to develop strategies to prevent plant diseases through the better understanding of the molecular basis of plant-microbe interactions.

The recent research projects are as follows:

  1. Characterization of genes involved in NO production in plant disease resistance.
  2. Purification and characterization of elicitors derived form P. infestans.
  3. Identification of proteins modified by NO in disease resistance.
  4. Imaging of plant-microbe interactions with GFP and modified fluorescence proteins.
  5. Identification and characterization of the genes from symbiotic fungi required initiating and maintaining mutualistic association with host plant.

Recent publications:

  1. Takemoto D., Rafiqi M., Hurley U., Lawrence G.J., Bernoux M., Hardham A.R., Ellis J.G., Dodds P.N. and Jones D.A. (2012) N-Terminal motifs in some plant disease resistance proteins function in membrane attachment and contribute to disease resistance. Mol. Plant-Microbe Interact. 25: 379-392.
  2. Takemoto D., Kamakura S., Saikia S., Becker Y., Wrenn R., Tanaka A., Sumimoto H. and Scott B. (2011) Polarity proteins Bem1 and Cdc24 are components of the filamentous fungal NADPH oxidase complex. Proc. Nat. Acad. Sci. USA 108: 2861-2866.
  3. Shibata Y., Kawakita K. and Takemoto D. (2011) SGT1 and HSP90 are essential for age-related non-host resistance of Nicotiana benthamiana against the oomycete pathogen Phytophthora infestans. Physiol. Mol. Plant Pathol. 75: 120-128.
  4. Shibata Y., Kawakita K. and Takemoto D. (2010) Age-related resistance of Nicotiana benthamiana against hemibiotrophic pathogen Phytophthora infestans requires both ethylene- and salicylic acid-mediated signaling pathways. Mol. Plant-Microbe Interact. 23: 1130-1142.
  5. Uruma S., Shibata Y., Takemoto D. and Kawakita K. (2009) N,N-dimethylsphingosine, an inhibitor of sphingosine kinase, induces phytoalexin production and hypersensitive cell death of Solanaceae plants without generation of reactive oxygen species. J. Gen. Plant Pathol. In press.
  6. Kato H., Asai S., Yamamoto-Katou A., Yoshioka H., Doke N. and Kawakita K. (2008) Involvement of NbNOA1 in NO production and defense responses in INF1-treated Nicotiana benthamiana. J. Gen. Plant Pathol. 74: 15-23.
  7. Yamamizo C., Doke N., Yoshioka H. and Kawakita K. (2007) Involvement of mitogen-activated protein kinase in the induction of StrbohC and StrbohD genes in response to pathogen signals in potato. J. Gen. Plant Pathol. 73: 304-313.
  8. Takemoto D., Tanaka A., and Scott B. (2006) A p67Phox-like regulator recruited to control hyphal branching in a fungal-plant mutualistic symbiosis. Plant Cell 18: 2807-2821.
  9. Yamamoto-Katou, A., Katou, S., Yoshioka, H., Doke, N. and Kawakita, K. (2006) Nitrate reductase is responsible for elicitin-induced nitric oxide production in Nicotiana benthamiana. Plant Cell Physiol. 47: 726-735.
  10. Saito, S., Yamamoto-Katou, A., Yoshioka, H., Doke, N. and Kawakita, K. (2006) Peroxynitrite generation and tyrosine nitration in defense responses in tobacco BY-2 cells. Plant Cell Physiol. 47: 689-697.


  FAX: +81-52-789-4136
Prof. ASAKAWA, Susumu D. Agr. asakawa@
Assoc. Prof. MURASE, Jun D. Agr. murase@
Lecturer WATANABE, Takeshi D. Agr. watanabe@
Microorganisms in a paddy field ecosystem
Upper right, bacteriophage isolated from flood water
Lower left, methane producing archaea (Methanosarcina mazei)

Rice is a staple food for more than half of world population, and landscape of paddy fields is an unspoiled scenery in Japan. In our lab., we have studied the biochemical phenomena in paddy field to clarify the whole picture of paddy field ecosystem from the standpoint of soil microbiology, paddy soil chemistry and global environmental problems. Of these, dynamics of soil microorganisms and their interactions in a paddy field ecosystem are the current central themes of this research group. The aim is to elucidate the facts and mechanisms of microbial diversity and functions in cycling of bioelements in a paddy field ecosystem.

Current researches

  1. Microorganisms involving methane cycling in paddy field
  2. Microbial ecology during decomposition of organic matter in paddy soil
  3. Ecology of protists in paddy field
  4. Virus ecology in paddy field

Research keywords

  1. Isolation and characterization of novel soil microorganisms
  2. Molecular analysis of microbial community
  3. Biogeochemical cycles
  4. Gene expression and physiology of soil microorganisms

Recent publications:

  1. Ashraf Khalifa, Chol Gyu Lee, Takuya Ogiso, Chihoko Ueno, Dayeri Dianou, Toyoko Demachi, Arata Katayama, Susumu Asakawa 2015: Methylomagnum ishizawai gen. nov., sp. nov., a mesophilic type I methanotroph isolated from rice rhizosphere. Int. J. Syst. Evol. Microbiol., 65, 3527-3534.
  2. Rasit Asiloglu, Hiroki Honjo, Norikuni Saka, Susumu Asakawa, Jun Murase 2015: Community structure of microeukariotes in a rice rhizosphere revealed by DNA-based PCR-DGGE. Soil Sci. Plant Nutr., 61, 761-768.
  3. Kazunori Yokoe, Masahiro Maesaka, Jun Murase, Susumu Asakawa 2015: Solarization makes a great impact on the abundance and composition of microbial communities in soil. Soil Sci. Plant Nutr., 61, 641-652.
  4. Dongyan Liu, Hiroki Ishikawa, Mizuhiko Nishida, Kazunari Tsuchiya, Tomoki Takahashi, Makoto Kimura, Susumu Asakawa 2015: Effect of paddy-upland rotation on methanogenic archaeal community structure in paddy field soil. Microb. Ecol., 69, 160-168.
  5. Jun Murase, Azusa Hida, Kaori Ogawa, Toshihiro Nonoyama, Nanako Yoshikawa, Katsuhiko Imai 2015: Impact of long-term fertilizer treatment on the microeukaryotic community structure of a rice field soil. Soil Biol. Biochem., 80, 237-243.
  6. Kohei Yamashita, Hiroki Honjo, Mizuhiko Nishida, Makoto Kimura, Susumu Asakawa 2014: Estimation of microbial biomass potassium in paddy field soil. Soil Sci. Plant Nutr., 60, 512-519.
  7. Yong Li, Takeshi Watanabe, Jun Murase, Susumu Asakawa, Makoto Kimura 2014: Abundance and composition of ammonia oxidizers in response to degradation of root cap cells of rice in soil microcosms. J. Soils Sediments, 14, 1587-1598.
  8. Jun Murase, Yuriko Takenouchi, Kazufumi Iwasaki, Makoto Kimura 2014: Microeukaryotic community and oxygen response in rice field soil revealed using a combined rRNA-gene and rRNA-based approach. Microbes Environ., 29, 74-81.
  9. Ryuko Baba, Makoto Kimura, Susumu Asakawa, Takeshi Watanabe 2014: Analysis of [FeFe]-hydrogenase genes for the elucidation of a hydrogen-producing bacterial community in paddy field soil. FEMS Microbiol. Lett., 350, 249-256.
  10. Yong Li, Takeshi Watanabe, Jun Murase, Susumu Asakawa, Makoto Kimura 2013: Growth of hydrogenotrophic and acetoclastic methanogens on substrate from rice plant callus cells in anaerobic soil: an estimation to the role of slough-off root cap cells to their growth. Soil Sci. Plant Nutr. 59, 548-558.


  Tel: +81-52-789-4017
Prof. NAKAZONO, Mikio D. Agr. nakazono@
Asst. Prof. TAKAHASHI, Hirokazu D. Agr. hiro_t@

The primary research objective of this laboratory is to study the principles of genetics and breeding of crop plants. For this purpose, we are trying to understand molecular and genetic mechanisms of shoot and root development in rice using mutants or natural variations as genetic resources. We also try to understand molecular mechanism of adaptation of crops to environmental stresses such as flooding and drought, with the aim of producing crops tolerant to these stresses.

Our recent research projects seek to understand

  1. The mechanisms of formation of aerenchyma and radial oxygen loss barrier, which contribute to flooding tolerance, in plant roots.
  2. The molecular and genetic mechanisms of shoot development and embryogenesis in rice.
  3. The molecular evolution of small RNAs in the rice genome.
  4. The molecular and genetic mechanisms of root development and root system development in rice and soybean
  5. QTL analysis of iron toxicity tolerance in rice.

Recent publications:

  1. Suzuki, M., Sato, Y., Wu, S., Kang, B. and McCartly, D.R. (2015) Conserved functions of the MATE transporter BIG EMBRYO 1 in regulation of lateral organ size and initiation rate. Plant Cell, 27: 2288-2300.
  2. Yamauchi, T., Shiono, K., Nagano, M., Fukazawa, A., Ando, M., Takamure, I., Mori, H., Nishizawa, N.K., Kawai-Yamada, M., Tsutsumi, N., Kato, K. and Nakazono, M. (2015) Ethylene biosynthesis is promoted by very-long-chain fatty acids during lysigenous aerenchyma formation in rice roots. Plant Physiology, 169: 180-193.
  3. Takahashi, H., Yamauchi, T., Rajhi, I., Nishizawa, N.K. and Nakazono, M. (2015) Transcript profiles in cortical cells of maize primary root during ethylene-induced lysigenous aerenchyma formation under aerobic conditions. Annals of Botany, 115: 879-894.
  4. Shiono, K., Ando, M., Nishiuchi, S., Takahashi, H., Watanabe, K., Nakamura, M., Matsuo, Y., Yasuno, N., Yamanouchi, U., Fujimoto, M., Takanashi, H., Ranathunge, K., Franke, R., Shitan, N., Nishizawa, N.K., Takamure, I., Yano, M., Tsutsumi, N., Schreiber, L., Yazaki, K., Nakazono, M. and Kato, K. (2014) RCN1/OsABCG5, an ATP-binding cassette (ABC) transporter, is required for hypodermal suberization of roots in rice (Oryza sativa). Plant Journal, 80: 40-51.
  5. Kulichikhin, K., Yamauchi, T., Watanabe, K. and Nakazono, M.: Biochemical and molecular characterization of rice (Oryza sativa L.) roots forming a barrier to radial oxygen loss. (2014) Plant, Cell & Environment, 37: 2406-2420.
  6. Yamauchi, T., Watanabe, K., Fukazawa, A., Mori, H., Abe, F., Kawaguchi, K., Oyanagi, A. and Nakazono, M. (2014) Ethylene and reactive oxygen species are involved in root aerenchyma formation and adaptation of wheat seedlings to oxygen-deficient conditions. Journal of Experimental Botany, 65: 261-273.
  7. Ishiwata, A., Ozawa, M., Nagasaki, H., Kato, M., Noda, Y., Yamaguchi, T., Nosaka, M., Shimizu-Sato, S., Nagasaki, A., Maekawa, M., Hirano, H. and Sato, Y. (2013) Two WUSCHEL- related homeobox genes, narrow leaf2 and narrow leaf3, control leaf width in rice. Plant and Cell Physiology 54: 779-792.
  8. Nosaka, M., Ono, A., Ishiwata, A., Shimizu-Sato, S., Ishimoto, K., Noda, Y. and Sato, Y. (2013) Expression of the rice microRNA miR820 is associated with epigenetic modifications at its own locus. Genes & Genetic Systems, 88: 105-112.
  9. Nosaka, M., Itoh, J., Nagato, Y., Ono, A., Ishiwata, A. and Sato, Y. (2012) Role of transposon-derived small RNAs in the interplay between genomes and parasitic DNA in rice. PLoS Genetics, 8: e1002953.
  10. Tabuchi, H., Zhang, Y., Hattori, S., Omae, M., Shimizu-Sato, S., Oikawa, T., Qian, Q., Nishimura, M., Kitano, H., Xie, H., Fang, X., Yoshida, H., Kyozuka, J., Chen, F. and Sato, Y. (2011) LAX PANICLE2 of rice encodes a novel nuclear protein and regulates the formation of axillary meristems. Plant Cell, 23: 3276-3287.