Department of Biological Mechanisms and Functions

Division of Molecular and Cellular Biology


  Fax: +81-52-789-4087
Prof. KOBAYASHI, Tetsuo D. Agr. koba@
Assoc. Prof. KIMURA, Makoto D. Agr mkimura@
Assoc. Prof. KANAMARU, Kyoko D. Agr kanamaru@

Filamentous fungi produce high level of polysaccharide-degrading enzymes and are frequently used for production of industrial enzymes. Because of the outstanding capacity for protein secretion, filamentous fungi are desirable industrial microorganisms for production of both intrinsic and foreign proteins. Research projects are now in progress in the following areas aiming industrial application in near future:

  1. Regulation of amylolytic, cellulolytic, and xylanolytic genes in Aspergillus species. Analysis of various transcription factors, including AmyR, XlnR, AraR, Hap complex, and more, is now in progress by molecular biological approach.
  2. Signal transduction systems, especially His-Asp phosphorelays, in Aspergillus species. In response to environmental conditions, filamentous fungi change morphology, life cycle, enzyme production, etc. We are focusing on still-uncharacterized sensor proteins to solve complex signal transduction networks.

Recent publications:

  1. Genome sequencing and analysis of Aspergillus oryzae. (2005) Nature, 438: 1157-1161.
  2. Genomic sequence of the pathogenic and allergenic filamentous fungus, Aspergillus fumigatus. (2005) Nature, 438: 1151-1156.
  3. Analysis of expressed sequence tags from the fungus Aspergillus oryzae cultured under different conditions. (2007) DNA Research, 14: 47-57.
  4. In vitro analysis of His-Asp phosphorelays in Aspergillus nidulans: The first direct biochemical evidence for the existence of His-Asp phosphotransfer system in filamentous fungi. (2007) Biosci. Biotechnol. Biochem., 71: 2493-2502.
  5. Complete reconstitution of an ATP-binding cassette transporter LolCDE complex from separately isolated subunits. (2007) FEBS J., 274: 3034-3043.
  6. GFP-tagged expression analysis revealed that some histidine kinases of Aspergillus nidulans show temporally and spatially different expression during the life cycle. (2008) Biosci. Biotechnol. Biochem., 72: 428-434.
  7. Novel promoter sequence required for inductive expression of the Aspergillus nidulans endoglucanase gene eglA. (2008) Biosci. Biotechnol. Biochem., 72: 312-320.
  8. Inducer-dependent nuclear localization of a Zn(II)(2)Cys(6) transcriptional activator, AmyR, in Aspergillus nidulans. (2009) Biosci Biotechnol Biochem. 73: 391-9.
  9. Genes regulated by AoXlnR, the xylanolytic and cellulolytic transcriptional regulator, in Aspergillus oryzae. (2009) Appl Microbiol Biotechnol. 85: 141-54.
  10. Transcriptional Regulation in Aspergillus. (2010) In: M. Machida, K. Gomi, Eds., Aspergillus: Molecular Biology and Genomics. Caister Academic Press, Norfolk, pp. 85-114.


  Fax: +81-52-789-4091
Prof. FUJITA, Yuichi D. Sci. fujita@
Assoc. Prof. YAMASHINO, Takafumi D. Agr. yamasino@


  FAX: +81-52-789-4094
Prof. SAKAKIBARA, Hitoshi D. Agr. sakaki@
Assoc. Prof. ISHIGURO, Sumie D. Agr. guronyan@
Asst. Prof. MAEO, Kenichiro D. Agr. maeo@


  FAX: +81-52-789-4107
Prof. OMATA, Tatsuo D. Sci. omata@
Asst. Prof. MAEDA, Shin-ichi D. Agr. maeda@

Research at the laboratory aims at better understanding the ways plants and algae acquire energy, carbon, and nitrogen. It seeks to understand the events involved, in terms of basic mechanism, and to discover the ways they are integrated and regulated so as to determine the response of the photosynthetic organisms to different physical and chemical environments.

The research projects focus on the areas of plant biochemistry, molecular biology, and physiology and the followings are now in progress;

  1. The nature and regulatory processes of photosynthetic carbon dioxide fixation and nitrogen assimilation.
  2. Structure and expression of genes encoding enzymes or proteins involved in photosynthetic carbon and nitrogen metabolisms.
  3. Regulatory mechanisms of nitrogen-dependent gene expression for enzymes in carbon and nitrogen assimilation in plants and cyanobacteria.
  4. Enzymology and regulatory mechanisms of chlorophyll biosynthesis in photosynthetic organisms.

Recent publications:

  1. Maeda, S., Sugita, M., Sugita, C. and Omata, T. (2006) A new class of signal transducer in His-Asp phosphorelay systems. J. Biol. Chem. 281: 37868-37876.
  2. Tsujimoto, R., Yamazaki, H., Maeda, S. and Omata, T. (2007) Distinct roles of nitrate and nitrite in regulation of expression of the nitrate transport genes in the moss Physcomitrella patens. Plant Cell Physiol. 48: 484-497.
  3. Minamizaki, K., Mizoguchi, T., Goto, T., Tamiaki, H. and Fujita, Y. (2008)
    Identification of two homologous genes, chlA I and chlA II, that are differentially involved in isocyclic ring formation of chlorophyll a in the cyanobacterium Synechocystis sp. PCC 6803.
    J. Biol. Chem. 283: 2684-2692.
  4. Nishimura, T., Takahashi, Y, Yamaguchi, O., Suzuki, H., Maeda, S. and Omata, T. (2008) Mechanism of low-CO2 induced activation of the cmp bicarbonate transporter operon by a LysR family protein in the cyanobacterium Synechococcus elongatus strain PCC 7942. Mol. Microbiol. 68: 98-109.
  5. Nomata, J., Ogawa, T., Kitashima, M., Inoue, K. and Fujita, Y. (2008)
    NB-protein(BchN-BchB) of dark-operative protochlorophyllide reductase is the catalytic component containing oxygen-tolerant Fe-S clusters.
    FEBS Lett. 582: 1346-1350.
  6. Tsujimoto, R., Yamazaki, H., Maeda, S. and Omata, T. (2007) Distinct roles of nitrate and nitrite in regulation of expression of the nitrate transport genes in the moss Physcomitrella patens. Plant Cell Physiol.


  FAX: +81-52-789-4123
Prof. MORITA-TERAO, Miyo D. Sci. mimorita@
Asst. Prof. HASHIMOTO-SUGIMOTO, Mimi D. Sci. mimi@

Because most plants spend their sessile lives at the site of their germination, they rely on a number of strategies to ensure their survival in response to environmental stimuli. Plants utilize gravity as a directional cue to regulate the direction of their growth (gravitropism) so as to be in a suitable position for absorption of water or nutrients, photosynthesis, reproduction, and morphogenesis. In general, plant shoots grow upward (negative gravitropism), whereas roots grow downward (positive gravitropism). Although gravitropism has been studied for over two centuries, molecular mechanisms underlying gravity perception and signaling processes have remained elusive. The goal of our research is to understand the molecular mechanisms by analyzing structures and functions of proteins involved in plant responses to gravity. By using Arabidopsis thaliana and Marchantia polymorpha, model plants suitable for molecular genetic analyses, we are studying molecular mechanisms of gravity perception and responses.

Recent publications:

  1. Nakamura, M., Toyota, M., Tasaka, M., Morita, M. T. Live cell imaging of cytoskeletal and organelle dynamics in gravity-sensing cells in plant gravitropism. Methods Mol. Biol. 1309, 57-69 (2015).
  2. Taniguchi, M., Nakamura, M., Tasaka, M., Morita, M.T. (2014) Identification of gravitropic response indicator genes in Arabidopsis inflorescence stems. Plant Signal. Behav. 9: e29570
  3. Hashiguchi, Y., Yano, D., Nagafusa, K., Kato, T., Saito, C., Uemura, T., Ueda, T., Nakano, A., Tasaka, M., Morita, M.T. (2014) A unique HEAT repeat-containing protein SHOOT GRAVITROPISM6 is involved in vacuolar membrane dynamics in gravity sensing cells of Arabidopsis inflorescence stem. Plant Cell Physiol. 55:811-822.
  4. Negi, J.*, Hashimoto-Sugimoto, M.*, Kusumi, K. and Iba, K. (2014) New approaches to the biology of stomatal guard cells. Plant Cell Physiol. 55, 241–250.  *Co-first authors 
  5. Toyota, M., Ikeda, N., Sawai-Toyota, S., Kato, T., Gilroy, S., Tasaka, M., Morita, M.T. (2013) Amyloplast displacement is necessary for gravisensing in Arabidopsis shoots as revealed by a centrifuge microscope. Plant J. 76:648-660.
  6. Hashimoto-Sugimoto, M., Higaki, T., Yaeno, T., Nagami, A., Irie, M., Fujimi M., Miyamoto, M., Akita, K., Negi, J., Shirasu, K., Hasezawa, S. and Iba, K. (2013) A Munc13-like protein in Arabidopsis mediates H+-ATPase translocation that is essential for stomatal responses.  Nature Commun.4:2215 doi: 10.1038/ncomms3215.
  7. Morita, M.T., Nakamura, M. (2012) Dynamic behavior of plastids related to environmental response. Curr. Opin. Plant Biol. 15: 722-728.
  8. Nakamura, M., Toyota, M., Tasaka, M., Morita, M.T.  (2011) An Arabidopsis E3 Ligase SHOOT GRAVITROPISM 9 Modulates the Interaction between Statoliths and F-Actin in Gravity Sensing. Plant Cell 23: 1830-1848.
  9. Moirta, M.T. (2010) Directional gravity sensing in gravitropism. Ann. Rev. Plant Biol. 61:706-720.
  10. Hashiguchi, Y., Niihama, M., Takahashi, T., Saito, C., Nakano, A., Tasaka, M., Morita, M.T.  (2010) Loss-of-function mutations of retromer large subunits suppress the phenotype of zig mutant that lacks Qb-SNARE VTI11. Plant Cell 22:159-172.