This research group deals with the graduate and undergraduate education and research program for basic organic chemistry, synthetic chemistry, bioorganic chemistry and chemical biology centered on natural products.

These include the following subjects;

1. Total syntheses of biologically active compounds.
2. Development of new synthetic methodologies.
3. Elucidation and analysis of the biological functions of natural products at the molecular level.
4. Molecular design of new biologically active molecules on the basis of natural products.

Recent Publications:

1. Adachi, M.; Imazu, T.; Sakakibara, R.; Satake, Y.; Isobe, M.; Nishikawa, T. Total Synthesis of Chiriquitoxin, an Analog of Tetrodotoxin Isolated from the Skin of a Dart Frog, Chem. Eur. J. 2014, 20, 1247-1251.
2. Nakazaki, A.; Ishikawa, Y.; Sawayama, Y.; Yotsu-Yamashita, M.; Nishikawa, T. Synthesis of Crambescin B Carboxylic Acid, a Potent Inhibitor of Voltage-gated Sodium Channels, Org. Biomol. Chem. 2014, 12, 53-56.
3. Yamada, H.; Adachi, M.; Isobe, M.; Nishikawa, T. Stereocontrolled Synthesis of the Oxathiabicyclo[3.3.1]nonane Core Structure of Tagetitoxin, Chem. Commun. 2013, 49, 11221-11223.
4. Sawayama, Y.; Nishikawa, T. A Synthetic Route of the Saxitoxin Skeleton: Synthesis of Decarbamoyl-a-saxitoxinol, an Analog of Saxitoxin Produced by the Cyanobacterium Lyngbya wollei,Angew. Chem. Int. Ed. 2011, 50, 7176-7178.

The primary objective of studies in this laboratory is to investigate the bioactive natural products, which will be potentially useful for agricultural or medical application. Research in this laboratory principally concerns the isolation and structure elucidation of the natural products and their receptors, which play an important role in controlling the life cycle of plants, microorganisms and other living organisms. The biosynthesis and action mechanism of the discovered compounds are also belonging to our main research projects. The natural products or their synthetic analogues provide clues for building up new types of bio-regulators.

The following subjects are in progress:

1. Chemical biological studies on microbial hormones, antibiotics, and other pharmaceutical leads.
2. Mechanistic studies and therapeutic applications of carbohydrate-binding natural products.
3. Bioorganic studies on plant hormones and mediators of plant-microbe interactions.

Recent publications:

1. Han, C.; Furukawa, H.; Tomura, T.; Fudou, R.; Kaida, K.; Choi, B.-K.; Imokawa, G.; Ojika, M. Bioactive Maleic Anhydrides and Related Diacids from the Aquatic Hyphomycete Tricladium castaneicola, J. Nat. Prod. 2015, 78, 639-644.
2. Makoto Ojika, Shylaja D. Molli, Harumi Kanazawa, Arata Yajima, Kou Toda, Tomoo Nukada, Haimeng Mao, Ryo Murata, Tomoyo Asano, Jianhua Qi & Youji Sakagami, The second Phytophthora mating hormone defines interspecies biosynthetic crosstalk, Nat. Chem. Biol. 2011, 7, 591-593.
3. Nakagawa, Y.; Doi, T.; Masuda, Y.; Takegoshi, K.; Igarashi, Y.; Ito, Y. Mapping of the Primary Mannose-Binding Site of Pradimicin A, J. Am. Chem. Soc., 2011, 14, 17485-17493.
4. Nakagawa, Y.; Masuda, Y.; Yamada, K.; Doi, T.; Takegoshi, K.; Igarashi, Y.; Ito, Y. Solid-state NMR Spectroscopic Analysis of the Ca2^+-dependent Mannose Binding of Pradimicin A, Angew. Chem. Int. Ed., 2011, 50, 6084-6088.
5. Kondo, T.; Kajita, R.; Miyazaki, A.; Hokoyama, M.; Nakamura-Miura, M.; Mizuno, S.; Masuda, Y.; Irie, K.; Tanaka. Y.; Takada, S.; Kakimoto, T.; Sakagami, Y. Stomatal density is controlled by a mesophyll-derived signaling molecule, Plant Cell Physiol., 2010, 51, 1-8.
6. Kondo, T.; Sawa, S.; Kinoshita, A.; Mizuno, S.T; Kakimoto, T.; Fukuda, F.; Sakagami, Y. A plant peptide encoded by CLV3 identified by in situ MALDI-TOF MS analysis, Science, 2006, 313, 845-848.

The principal research objectives of this lab are to investigate diverse natural products that regulate biologically and physiologically intriguing phenomena on the basis of organic and biological organic chemistry. Our research interest is also extended to chemical biology, such as study on the target molecules and mode of actions of bioactive natural products by using their chemical probes.

The following studies are currently in progress:

1. Isolation, structure determination, synthesis, and modes of action of bioactive natural products that regulate biologically and physiologically intriguing phenomena.
2. Anesthetic substances from venomous mammals, and key substances for marine symbiotic relationships.
3. Development of new analytical methods for target molecules using fluorescent probes.

Recent publications:

1. Yoneda, K.; Hu, Y.; Watanabe, R.; Kita, M.; Kigoshi, H. Binding Position Analysis of Target Proteins with the Use of Amidopyrene Probes as LA-LDI Enhancing Tags. Org. Biomol. Chem. 2016, 14, 8564-8569.
2. Kita, M.; Oka, H.; Usui, A.; Ishitsuka, T.; Mogi, Y.; Watanabe, H.; Tsunoda, M.; Kigoshi, H. Total Synthesis of Mycalolides A and B Through Olefin Metathesis. Angew. Chem. Int. Ed. 2015, 54, 14174-14178.
3. Kawamura, A.; Kita, M.; Kigoshi, H. Aplysiasecosterol A: A 9,11-Secosteroid with An Unprecedented Tricyclic gamma-Diketone Structure from the Sea Hare Aplysia kurodai. Angew. Chem. Int. Ed. 2015, 54, 7073-7076.
4. Kita, M.; Kigoshi, H. Marine Natural Products That Regulate Multiple Cytoskeletal Protein Interactions. Nat. Prod. Rep. 2015, 32, 534-542.
5. Kita, M.; Hirayama, Y.; Yoneda, K.; Yamagishi, K.; Chinen, T.; Usui, T.; Sumiya, E.; Uesugi, M.; Kigoshi, H. Inhibition of Microtubule Assembly by A Complex of Actin and Antitumor Macrolide Aplyronine A. J. Am. Chem. Soc. 2013, 135, 18089-18095.

Creation of functional biomaterials is the fundamental research theme in this laboratory. The functional biomaterials include specially polymers based on biomaterials, artificial materials with sophisticated biological functions, and environmentally friendly synthetic polymers. Current research fields are: (a) Synthesis of glycoconjugates, particularly globular glycomacromolecules and their biological functions based on molecular and cellular recognition. (b) Synthesis of bio-inspired functional materials. (c) Development of functional materials via chemical modification of natural polymers, particularly, chitin. (d) Synthesis of biodegradable and biofunctional polyesters, poly(ester carbonate)s and poly(ester urethane)s utilizing natural resources. (e) Development of new methodologies for precise polymer synthesis.

Recent Publications:

1. Hasegawa, T., Kishida, H., Nomura, N. and Moriya, T. Synthesis of Crystalline Poly(lactic acid) from Glycerol By-product via Hydrothermal Reaction and Stereoselective Polymerization
   Chem. Lett., 44, 375 (2015).
2. Nomura, N., Akita, A., Ishii, R. and Mizuno, M. Random Copolymerization of ε-Caprolactone with Lactide Using a Homosalen-Al Complex. J. Am. Chem. Soc., 132, 1750 (2010).
3. Matsumi, N., Yoshioka, N. and Aoi, K. Synthesis of Boric Ester Type Ion-gels by Dehydrocoupling of Cellulose with Hydroboranes in Ionic Liquid. Solid State Ionics, 226, 37 (2012).
4. Nomura, N., Komiyama, S., Kasugai, H. and Saba, M. An Efficient Protocol of Iridium-Catalyzed Allylic Substitution Reaction and its Application to Polymer Synthesis: Complementary Regio- and Stereoselective Allylation Polycondensation via Ir- and Pd-catalyses. J. Am. Chem. Soc., 130, 812 (2008).
5. Nakamura, R., Aoi, K. and Okada, M. Controlled Synthesis of a Chitosan-Based Graft Copolymer Having Polysarcosine Side Chains Using the NCA Method with a Carboxylic Acid Additive. Macromolecular Rapid Communications, 27, 1725 (2006).
6. Nakamura, R., Aoi, K. and Okada, M. Interactions of Enzymes and a Lectin with a Chitin-Based Graft Copolymer Having Polysarcosine Side Chains. Macromolecular Bioscience, 4, 610 (2004).

The staff members of this laboratory are responsible for teaching basic courses of physical chemistry to undergraduate students. They are concerned mainly with experimental works in biochemistry and physical chemistry of macromolecules in solution with special regard to protein structure and function, as well as the interaction with various ligands. The research programs cover some of basic and applied areas related to biological and food science.

The projects now in progress are as follows;

1. Study on metabolism and new functions of D-amino acids.
2. Biochemistry of pyridoxal enzymes.
3. Biochemistry and enzymology of isoprenoid biosynthesis in archaea.
4. Metagenomic and biochemical analyses of fermentation processes.

Recent publications:

1. Okuda K, Kato S, Ito T, Shiraki S, Kawase Y, Goto M, Kawashima S, Hemmi H, Fukada H, Yoshimura T (2015) Role of the aminotransferase domain in Bacillus subtilis GabR, a pyridoxal 5'-phosphate-dependent transcriptional regulator. Mol Microbiol, 95, 245-257.
2. Ito T, Takada H, Isobe K, Suzuki M, Kitaura Y, Hemmi H, Matsuda T, Sasabe J, Yoshimura T (2015) PEGylated D-serine dehydratase as a D-serine reducing agent. J Pharm Biomed Anal, 116, 34-39.
3. Takenaka T, Ito T, Miyahara I, Hemmi H, Yoshimura T (2015) A new member of MocR/GabR-type PLP-binding regulator of D-alanyl-D-alanine ligase in Brevibacillus brevis. FEBS J, 282, 4201-4217.
4. Hattori A, Unno H, Goda S, Motoyama K, Yoshimura T, Hemmi H (2015) In vivo formation of the protein disulfide bond that enhances the thermostability of diphosphomevalonate decarboxylase, an intracellular enzyme from the hyperthermophilic archaeon Sulfolobus solfataricus. J Bacteriol, 197, 2463-3471.
5. Mori T, Isobe K, Ogawa T, Yoshimura T, Hemmi H (2015) A phytoene desaturase homolog gene from the methanogenic archaeon Methanosarcina acetivorans is responsible for hydroxyarchaeol biosynthesis. Biochem Biophys Res Commun, 466, 186-191.
6. Ito T, Matsuoka M, Koga K, Hemmi H, Yoshimura T (2014) Reaction mechanism of Zn2^+-dependent D-serine dehydratase: role of a conserved tyrosine residue interacting with pyridine ring nitrogen of pyridoxal 5'-phosphate. J Biochem, 156, 173-180.
7. Azami Y, Hattori A, Nishimura H, Kawaide H, Yoshimura T, Hemmi H (2014) (R)-mevalonate 3-phosphate is an intermediate of the mevalonate pathway in Thermoplasma acidophilum. J Biol Chem, 289, 15957-15967.
8. Ogawa T, Isobe K, Mori T, Asakawa S, Yoshimura T, Hemmi H (2014) A novel geranylgeranyl reductase from the methanogenic archaeon Methanosarcina acetivorans displays unique regiospecificity. FEBS J, 281, 3165-3176.
9. Isobe K, Ogawa T, Hirose K, Yokoi T, Yoshimura T, Hemmi H (2014) Geranylgeranyl reductase and ferredoxin from Methanosarcina acetivorans are required for the synthesis of fully reduced archaeal membrane lipid in Escherichia coli cells. J Bacteriol, 196, 417-423.
10. Ito T, Iimori J, Takayama S, Moriyama A, Yamauchi A, Hemmi H, Yoshimura T (2013) Conserved pyridoxal protein that regulates Ile and Val metabolism. J Bacteriol, 195, 5439-5449.

This laboratory is responsible for the undergraduate and graduate education in industrial biotechnology and biomolecular engineering. Our research focuses on engineering of functional proteins, such as enzymes and antibodies, enzymatic synthesis of bioactive compounds, as well as high-throughput screening of transcription factor binding sites in the genomes of microorganisms, plants and animals. In a quest for highly efficient and specific functional proteins, we utilize traditional protein engineering methods in combination with computational analysis of protein structure and dynamics, and our specialized technology for high-throughput screening of large random DNA-protein libraries.

The following research projects are currently in progress:

1. Development and application of Beads display technology (coding DNA and corresponding protein are linked and displayed on the surface of the microbeads) for various purposes such as high throughput screening of random libraries in directed evolution of enzymes (horseradish peroxidase, manganese peroxidase, cytochrome P450, transglutaminase) and comprehensive analysis of transcription factor binding sites.
2. Development of high-throughput screening system for monoclonal antibodies using single-cell RT-PCR and the cell-free protein synthesis (CFPS). Recently, we have succeeded in producing soluble and fully functional Fab fragments in E. coli CFPS system by fusing the Fab with Leucine zipper.
3. Cloning, expression and protein engineering of lipid-modifying enzymes such as phospholipase D, lipase, and phosphatase to obtain enzymes with novel functions or improved activities.
4. Efficient enzymatic synthesis of bioactive lipids with defined chemical structure, such as phosphatidylinositol and phosphatidyl-1-glucose.
5. Genome-wide identification of genes regulated by transcription factors (TFs) from various organisms, such as fungi, plants and insects, by a combinatorial analysis using genomic systematic evolution of ligands by exponential enrichment (gSELEX)-Seq, RNA-Seq and bioinformatics.

Recent publications:(2015 - , former publications are listed on https://teruyo1.wixsite.com/molbiotech/english)

1. Damnjanovic, J., Kuroiwa, C., Tanaka, H., Ishida, K., Nakano, H., and Iwasaki, Y. (2016) Directing positional specificity in enzymatic synthesis of bioactive 1-phosphatidylinositol by protein engineering of a phospholipase D. Biotechnol. Bioeng. 113, 62-71.
2. DeKosky, B. J., Kojima, T., Rodin, A., Charab, W., Ippolito, G., Ellington, A. D., and Georgiou, G. (2015) In-Depth Determination and Analysis of the Human Paired Heavy and Light Chain Antibody Repertoire. Nat. Med. 21, 86-91.
3. Mori, A., Hara, S., Sugahara, T., Kojima, T., Iwasaki, Y., Kawarasaki, Y., Sahara, T, Ohgiya, S., and Nakano, H. (2015) Signal peptide optimization tool for the secretion of recombinant protein from Saccharomyces cerevisiae. J. Biosci. Bioeng. 120, 518-525
4. Zhu, B., Mizoguchi, T., Kojima, T., and Nakano, H. (2015) Ultra-High-Throughput Screening of an In Vitro-Synthesized Horseradish Peroxidase Displayed on Microbeads Using Cell Sorter. PLoS One 10, e0127479
5. Kojima, T., Mizoguchi, T., Ota, E., Hata, J., Homma, K., Zhu, B., Hitomi, K., and Nakano, H. (2015) Immobilization of proteins onto microbeads using a DNA binding tag for enzymatic assays. J. Biosci. Bioeng. in press.
6. Ujiie, A., Nakano, H., and Iwasaki, Y. (2015) Extracellular production of Pseudozyma (Candida) antarctica lipase B with genuine primary sequence in recombinant Escherichia coli. J. Biosci. Bioeng. in press
7. Murzabaev, M., Kojima, T., Mizoguchi, T., Kobayashi, I., DeKosky, B. J., Georgiou, G., and Nakano, H. (2015) Handmade microfluidic device for biochemical applications in emulsion. J. Biosci. Bioeng. in press
8. Ojima-Kato, T., Hashimura, D., Kojima, T., Minabe, S., and Nakano, H. (2015) In vitro generation of rabbit anti- Listeria monocytogenes monoclonal antibody using single cell based RT-PCR linked cell-free expression systems. J. Immunol. Methods, 427, 58-65

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.

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.

The principal research objectives of this lab are to understand the relevance of a variety of small molecules as ligands and triggers of chemical reactions related to our health and diseases, particularly regarding chemicals generated within our bodies and/or encountered in the environment. We are studying these foundational areas using a variety of approaches including organic chemistry, biochemistry, and chemical biology.

The following studies are currently in progress:

1. Covalent modification of proteins by endogenous molecules including lipid peroxidation-derived compounds.
2. Biological significance of protein modification as triggers of innate immunity and inflammatory responses.
3. Molecular basis of health benefits of functional food components including phytochemicals.

Cellular responses mediated by oxidized fatty acids and functional food components.

Recent publications:

1. Miyashita, H., Chikazawa, M., Otaki, N., Hioki, Y., Shimozu, Y., Nakashima, F., Shibata, T., Hagihara, Y., Maruyama, S., Matsumi, N., and Uchida, K. (2014) Lysine pyrrolation is a naturally-occurring covalent modification involved in the production of DNA mimic proteins. Sci. Rep. 4, 5343.
2. Shibata, T., Nakashima, F., Honda, K., Lu, Y.J., Kondo, T., Ushida, Y., Aizawa, K., Suganuma, H., Oe, S., Tanaka, H., Takahashi, T., and Uchida, K. (2014) Toll-like receptors as a target of food-derived anti-inflammatory compounds. J. Biol. Chem. 289, 32757-32772.
3. Chikazawa, M., Otaki, N., Shibata, T., Miyashita, H., Kawai, Y., Maruyama, S., Toyokuni, S., Kitaura, Y., Matsuda, T., and Uchida, K. (2013) Multispecificity of immunoglobulin M antibodies raised against advanced glycation end products: involvement of electronegative potential of antigens. J. Biol. Chem. 288, 13204-13214.
4. Shibata, T., Shimozu, Y., Wakita, C., Shibata, N., Kobayashi, M., Machida, S., Kato, R., Itabe, H., Zhu, X., Sayre, L. M., and Uchida, K. (2011) Lipid peroxidation modification of protein generates Nepsilon-(4-oxononanoyl)lysine as a pro-inflammatory ligand. J. Biol. Chem. 286, 19943-19957.
5. Shimozu, Y., Hirano, K., Shibata, T., Shibata, N., and Uchida, K. (2011) 4-Hydroperoxy-2-nonenal is not just an intermediate, but a reactive molecule that covalently modifies proteins to generate unique intramolecular oxidation products. J. Biol. Chem. 286, 29313-29324.
6. Shibata, T., Kimura, Y., Mukai, A., Mori, H., Ito, S., Asaka, Y., Oe, S., Tanaka, H., Takahashi, T., and Uchida, K. (2011) Transthiocarbamoylation of proteins by thiolated isothiocyanates. J. Biol. Chem. 286, 42150-42161.
7. Ishino, K., Wakita, C., Shibata, T., Toyokuni, S., Machida, S., Matsuda, S., Matsuda, T., and Uchida, K. (2010) Lipid peroxidation generates a body odor component trans-2-nonenal covalently bound to protein in vivo. J. Biol. Chem. 285, 15302-15313.
8. Yamaguchi, S., Aldini, G., Ito, S., Morishita, N., Shibata, T., Vistoli, G., Carini, M., and Uchida, K. (2010) Δ12-Prostaglandin J2 as a product and ligand of human serum albumin: Formation of an unusual covalent adduct at His146. J. Am. Chem. Soc. 132, 824-832.
9. Wakita, C., Maeshima, T., Yamazaki, A., Shibata, T., Ito, S., Akagawa, M., Ojika, M., Yodoi, J., and Uchida, K. (2009) Stereochemical configuration of 4-hydroxy-2-nonenal-cysteine adducts and their stereoselective formation in a redox-regulated protein. J. Biol. Chem. 284, 28810-28822.
10. Kanayama, M., Yamaguchi, S., Shibata, T., Shibata, N., Kobayashi, M., Nagai, R., Arai, H., Takahashi, K., and Uchida, K. (2007) Identification of a serum component that regulates cyclooxygenase-2 gene expression in cooperation with 4-hydroxy-2-nonenal. J. Biol. Chem. 282, 24166-24174.

The major interest in this laboratory is to understand how cellular functions such as signal transduction, membrane traffic, transport, growth and secretion are regulated in a Ca²⁺-dependent manner by biomolecular interactions of enzymes, receptors, adaptor proteins and other protein factors. Basic knowledge in biochemistry, cell biology and molecular biology is required.

Current projects are as follows:

1. Cellular response to Ca²⁺ -stimulation by drugs, amino acids, cytokines etc.
2. Structures, functions and ligand-recognition mechanisms of the penta-EF-hand Ca²⁺-binding protein ALG-2.
3. Regulation of cell death by cellular factors in relation to Ca²⁺.
4. Regulation of intracellular transport of macromolecules by Ca²⁺.

Recent publications:

1. Analysis of limited proteolytic activity of calpain-7 using non-physiological substrates in mammalian cells. Maemoto Y, Kiso S, Shibata H, Maki M. FEBS J. 280(11):2594-607 (2013).
2. Nuclear ALG-2 protein interacts with Ca²⁺ homeostasis endoplasmic reticulum protein (CHERP) Ca²⁺-dependently and participates in regulation of alternative splicing of inositol trisphosphate receptor type 1 (IP3R1) pre-mRNA. Sasaki-Osugi K, Imoto C, Takahara T, Shibata H, Maki M. J Biol Chem. 288(46):33361-3375 (2013).
3. Involvement of calpain-7 in epidermal growth factor receptor degradation via the endosomal sorting pathway. Maemoto Y, Ono Y, Kiso S, Shibata H, Takahara T, Sorimachi H, Maki M.FEBS J. 281(16):3642-3655 (2014).
4. A new role for annexin A11 in the early secretory pathway via stabilizing Sec31A protein at the endoplasmic reticulum exit sites (ERES). Shibata H, Kanadome T, Sugiura H, Yokoyama T, Yamamuro M, Moss SE, Maki M. J Biol Chem. 290(8):4981-93 (2015).
5. Structural analysis of the complex between penta-EF-hand ALG-2 protein and Sec31A peptide reveals a novel target recognition mechanism of ALG-2. Takahashi T, Kojima K, Zhang W, Sasaki K, Ito M, Suzuki H, Kawasaki M, Wakatsuki S, Takahara T, Shibata H, Maki M. Int J Mol Sci. 16(2):3677-99 (2015).

The aims of this laboratory are the elucidation of molecular mechanisms in regulation of biological systems in higher animals and plants useful in agriculture and biological industries. In our laboratory a variety of biochemical, molecular- and cell-biological researches is ongoing on the biosynthesis, functions and dynamics of proteins, nucleic acids, and glycoconjugates in development, differentiation, reproduction, and immunity. Goals of these researches are agricultural, industrial, and medical applications of biological products and systems.

The recent research projects are as follows:

1. Functional interaction of intestinal epithelium and mucosal immune system with exogenous macromolecules and microbes.
2. Biosynthesis and functional regulation of mammalian ribosomes.
3. Molecular and cellular biology of reproductive organs and cells (mammary gland, ovary, and testis).
4. Intercellular signaling networks mediated by exovesicles.

Recent publications:

1. Yasueda T, Oshima K, Nakatani H, Tabuchi K, Nadano D, Matsuda T. A protective effect of milk fat globule EGF factor VIII (MFG-E8) on the spontaneous fusion of milk fat globules in breast milk. J Biochem., 158(1): 25-35, 2015.
2. Nishio S, Kohno Y, Iwata Y, Arai M, Okumura H, Oshima K, Nadano D, Matsuda T. Glycosylated chicken ZP2 accumulates in the egg coat of immature oocytes and remains localized to the germinal disc region of mature eggs. Biol Reprod., 91(5): 107, 1-10, 2014.
3. Oshima K, Yasueda T, Nishio S and Matsuda T, MFG-E8: Origin, Structure, Expression, Functions and Regulation, in "MFG-E8 and Inflammation", P. Wang (ed.), Springer, 2014, pp 1-31.
4. Yonezawa, K., Sugihara, Y., Oshima, K., Matsuda, T., and Nadano, D. Lyar, a cell growth-regulating zinc finger protein, was identified to be associated with cytoplasmic ribosomes in male germ and cancer cells. Mol. Cell. Biochem., 395 (1-2): 221-229, 2014.
5. Sugihara, Y., Sadohara, E., Yonezawa, K., Kugo, M., Oshima, K., Matsuda, T., and Nadano, D. Identification and expression of an autosomal paralogue of ribosomal protein S4, X-linked, in mice: Potential involvement of testis-specific ribosomal proteins in translation and spermatogenesis. Gene, 521 (1): 91-99, 2013.

Glycan chains are covalently attached to proteins and lipids to form glycoproteins and glycolipids, i.e., “glycoconjugates”, and cover the entire surface of cells in any bioorganisms on our planet. They play important roles in a myriad of biological processes, such as cell adhesion, tissue and organ formation, and host recognition to pathogens or symbionts. In most cases, they play roles in various cell societies. However, there are still many glycan chains that remain to be elucidated for their biological functions. Thus, our research goal is to understand how glycan chains function on the cell surface as well as soluble glycoconjugates.

Two projects are going on in our laboratory:

(1) Glyco-atmosphere, a field of glycans on the surface of cells and glycoconjugates: Demonstration of its existence and biological significance;
(2) Diversity and heterogeneity of sialic acids and polysialic acids: Their structure, biosynthesis, function, and applications.
Glycobiology, our research field, is relatively young and challenging, but has become more and more important as a leading area of biological sciences, especially in the current post-genomic era.
See the details

Glycan chains are covalently attached to proteins and lipids to form glycoproteins and glycolipids, i.e., “glycoconjugates”, and cover the entire surface of cells in any bioorganisms on our planet. They play important roles in a myriad of biological processes, such as cell adhesion, tissue and organ formation, and host recognition to pathogens or symbionts. In most cases, they play roles in various cell societies. However, there are still many glycan chains that remain to be elucidated for their biological functions. Thus, our research goal is to understand how glycan chains function on the cell surface as well as soluble glycoconjugates.

Two projects are going on in our laboratory:

(1) Glyco-atmosphere, a field of glycans on the surface of cells and glycoconjugates: Demonstration of its existence and biological significance;
(2) Diversity and heterogeneity of sialic acids and polysialic acids: Their structure, biosynthesis, function, and applications.
Glycobiology, our research field, is relatively young and challenging, but has become more and more important as a leading area of biological sciences, especially in the current post-genomic era.
See the details

Our team aims to develop biotechnology-based materials and devices for dedicating to human health, which are based on the molecular cell biological analyses of cell signaling mechanisms of humans and animals.

1. Analysis of the functions of scaffold proteins-recruited signaling complexes in cardiac myocytes.
2. Identification of the regulatory proteins or factors controlling the expression and activity of ion channels.
3. Analysis of signal transduction mechanism for novel bone morphogenetic protein, NELL1.

Recent publications:

1. Takahashi, K., Imai, A., Iijima, M., Yoshimoto, N., Maturana, A. D., Kuroda, S., and Niimi, T. (2015) Mapping the heparin-binding site of the osteoinductive protein NELL1 by site-directed mutagenesis. FEBS Lett. 589, 4026-4032.
2. Ito, J., Iijima, M., Yoshimoto, N., Niimi, T., Kuroda, S., and Maturana, A. D. (2015) Scaffold protein Enigma Homolog activates CREB whereas a short splice variant prevents CREB activation in cardiomyocytes. Cell. Signal. 27, 2425-2433.
3. Nakamura, Y., Hasebe, A., Takahashi, K., Iijima, M., Yoshimoto, N., Maturana, A.D., Ting, K., Kuroda, S. and Niimi, T. (2014) Oligomerization-induced conformational change in the C-terminal region of Nel-like molecule 1 (NELL1) protein is necessary for the efficient mediation of murine MC3T3-E1 cell adhesion and spreading. J. Biol. Chem., 289, 9781-9794.
4. Kumazaki, K., Chiba, S., Takemoto, M., Furukawa, A., Nishiyama, K., Sugano, Y., Mori, T., Dohmae, N., Hirata, K., Nakada-Nakura, Y., Maturana, A.D., Tanaka, Y., Mori, H., Sugita, Y., Arisaka, F., Ito, K., Ishitani, R., Tsukazaki, T., and Nureki, O. (2014) Structural basis of Sec-independent membrane protein insertion by YidC. Nature, 509, 516-520.
5. Takeda, H., Hattori, M., Nishizawa, T., Yamashita, K., Shah, S.T., Caffrey, M., Maturana, A.D., Ishitani, R., and Nureki, O. (2014) Structural basis for ion selectivity revealed by high-resolution crystal structure of Mg2⁺ channel MgtE. Nat. Commun., 5, 5374.
6. Nishizawa, T., Kita, S, Maturana, A.D., Furuya, N., Hirata, K., Kasuya, G., Ogasawara, S., Dohmae, N., Iwamoto, T., Ishitani, R., and Nureki, O. (2013) Structural basis for counter-transport mechanism of H⁺/Ca2⁺ exchanger. Science, 341, 168-172.
7. Ito, J., Takita, M., Takimoto, K., and Maturana, A.D. (2013) Enigma homolog 1 promotes myogenic gene expression and differentiation of C2C12 cells. Biochem. Biophys. Res. Commun., 435, 483-487.
8. Tanaka, Y., Hipolito, C.J., Maturana, A.D., Ito, K., Kuroda, T., Higuchi, T., Katoh, T., Kato, H.E., Hattori, M., Kumazaki, K., Tsukazaki, T., Ishitani, R., Suga, H. and Nureki, O. (2013) Structural basis for the drug extrusion mechanism by a MATE multidrug transporter. Nature, 496, 247-251.
9. Hasebe, A., Nakamura, Y., Tashima, H., Takahashi, K., Iijima, M., Yoshimoto, N., Ting, K., Kuroda, S., and Niimi, T. (2012) The C-terminal region of NELL1 mediates osteoblastic cell adhesion through integrin alpha3beta1. FEBS Lett., 586, 2500-2506.
10. Ito, J., Hashimoto, T., Nakamura, S., Aita, Y., Yamazaki, T., Schlegel, W., Takimoto, K. and Maturana, A.D. (2012) Splicing transitions of the anchoring protein ENH during striated muscle development. Biochem. Biophys. Res. Commun., 421, 232-238.

The human health is closely related with the metabolic conditions, which is greatly affected by nutrition. In this lab, we are investigating the nutritional regulation of energy and protein-amino acid metabolism. It has been recently elucidated that branched-chain amino acids (BCAA) have great effects on the protein and glucose metabolism.
How can liver, a metabolic center organ, keep hepatocyte-phenotype? We have found that cultured hepatocytes with spherical cell shape can keep high levels of liver specific phenotype and that some liver-enriched transcription factors such as HNF-4. We are now focusing our effort on 1) identification of a regulatory transcription factors controlling HNF-4 by cell shape and 2) molecular mechanism of signal transduction pathway from cell shape to nucleus. Recently we are also trying to establish artificial liver support system by using spherical human hepatoma cells.

Current projects are follows:

1. Nutritional regulation of gene expression in animals.
2. Molecular mechanism of hepatocytes differentiation of 3-dimentional culture.
3. Physiological significance of liver clock.
4. Regulatory mechanism for the BCAA catabolism.
5. Regulation of glucose metabolism by BCAA.

Current projects are follows:

1. Zhen H, Nakamura K, Kitaura Y, Kadota Y, Ishikawa T, Kondo Y, Xu M, Shimomura Y. (2015) Regulation of the plasma amino acid profile by leucine via the system L amino acid transporter. Biosci Biotechnol Biochem. 79(12): 2057-2062.
2. Kadota Y, Toyoda T, Hayashi-Kato M, Kitaura Y, Shimomura Y. (2015) Octanoic acid promotes branched-chain amino acid catabolism via the inhibition of hepatic branched-chain alpha-keto acid dehydrogenase kinase in rats. Metabolism 64: 1157-1164.
3. Kitaura Y, Inoue K, Kato N, Matsushita N, Shimomura Y. (2015) Enhanced oleate uptake and lipotoxicity associated with laurate. FEBS Open Bio 5: 485-491.
4. Yamada K, Aiba K, Kitaura K, Kondo Y, Nomura N, Nakamura Y, Fukushi D, Murayama K, Shimomura Y, Pitt J, Yamaguchi S, Yokochi K, Wakamatsu N. (2015) Clinical, biochemical, and metabolic characterization of mild forms of human short-chain enoyl-CoA hydratase deficiency: significance of increased N-acetyl-S-(2-carboxypropyl)cysteine excretion. J Med Genet. 52(10): 691-698.
5. Oda, H., Okuda, Y., Yoshida, Y., Kimura, N. and Kakinuma, A. (2015) Phenobarbital reduces blood glucose and gluconeogenesis through down-regulation of phosphoenolpyruvate carboxykinase (GTP) gene expression in rats. Biochem. Biophys. Res. Commun. 466, 306-311
6. Chijimatsu, T., Umeki, M., Kataoka, Y., Kobayashi, S, Yamada, K., Oda, H. and Mochizuki, S. (2013) Lipid components prepared from a freshwater clam (Corbicula fluminea) extract ameliorate hypercholesterolemia in rats fed high-cholesterol diet. Food Chem. 136, 328-334.
7. Yamajuku, D., Inagaki, T., Haruma, T., Okubo, S., Kataoka, Y., Kobayashi, S., Ikegami, K., Laurent, T., Kojima, T., Noutomi, K., Hashimoto, S. and Oda, H. (2012) Real-time monitoring in three-dimensional hepatocytes reveals that insulin acts as a synchronizer for liver clock. Scientific Rep. 2, 439; DOI:10.1038/srep00439
8. Laurent, T., Murase, D., Tsukioka1, S., Matsuura, T., Nagamori, S. and Oda, H. (2012) A novel human hepatoma cell line, FLC-4, exhibits highly enhanced liver differentiation functions through the three-dimensional cell shape. J. Cell. Physiol. 227, 2898-2906.
9. Yamajuku, D., Okubo, S., Haruma, T., Inagaki, T., Okuda, Y., Kojima T, Noutomi, K., Hashimoto, S. and Oda, H. (2009) Regular feeding plays an important role in cholesterol homeostasis through the liver circadian clock. Circulation Res.,105, 545-548.

Food is composed of diverse factors including tastants and nutrients. Although the neural mechanisms of calorie intake are well studied recently, the mechanisms for food preference are still unclear. Our research interests are [1] the neural system for taste perception [2] the formation mechanism of experience-dependent plasticity in food preference [3] the brain mechanism that senses various food factors such as micronutrients.

Recent publications:

1. Nakajima K. Neural insights into sweet taste transduction and hunger-induced taste modification in mice. Biosci. Biotechnol. Biochem. 86,11,1485-1489 (2022).
2. Fu O, Minokoshi Y, Nakajima K. Recent Advances in Neural Circuits for Taste Perception in Hunger. Front. Neural. Circuits. 15, 609824 (2021)
3. Fu O, Iwai Y, Narukawa M, Ishikawa WA, Ishii KK, Murata K, Yoshimura Y, Touhara K, Misaka T, Minokoshi Y, Nakajima K. Hypothalamic neuronal circuits regulating hunger-induced taste modification. Nat. Commun.8, 4560 (2019).
4. Fu O, Iwai Y, Kondoh K, Misaka T, Minokoshi Y, Nakajima K. SatB2-Expressing Neurons in the Parabrachial Nucleus Encode Sweet Taste. Cell Reports, 27, 1650-1656 (2019)
5. Nakajima K*, Cui Z*, Li C, Meister J, Cui Y, Fu Ou, Smith SA, Jain S, Lowell BB, Krashes MJ, Wess J. Gs-coupled GPCR signalling in AgRP neurons triggers sustained increase in food intake. Nat. Commun.7, 10268 (2016) (*K.N. and Z.C. contributed equally)

Our group is studying basic and applied plant sciences, focusing on molecular aspects of plant growth and development. The goal of our study is to establish basic knowledge on how plants develop into defined shape and size, and to apply such knowledge for creation of plants with high productivity for food and biofuel. Following projects are currently under way.

1. Regulatory mechanisms of ethylene production, a gaseous plant hormone, focusing on ACC synthase that acts as a key enzyme of its biosynthetic pathway.
2. Studies on molecular mechanisms of parthenocarpic fruit development in tomato, by comparing parthenocarpic and non-parthenocarpic tomato varieties.
3. Studies on hormonal control of apical dominance in pea.
4. Studies on transcription factors that regulate cell division during development of Arabidopsis.
5. Cell size control that is mediated by increase of cellular ploidy.

Recent publications:

1. Goto, H., Okuda, S., Mizukami, A., Mori, H., Sasaki, N., Kurihara, D. and Higashiyama, T. (2011) Chemical Visualization of an Attractant Peptide, LURE. Plant Cell Physiol., 52, 49-58.
2. Iwata, E., Ikeda, S., Matsunaga, S., Kurata, M., Yoshioka, Y., Criqui, M-C, Genschik, P. and Ito, M. (2011) GIGAS CELL1, a novel negative regulator of the anaphase-promoting complex/cyclosome, is required for proper mitotic progression and cell fate determination in Arabidopsis. Plant Cell, 23, 4382-4393.
3. Haga, N., Kobayashi, K., Suzuki, T., Maeo, K., Kubo, M., Ohtani, M., Mitsuda, N., Demura, T., Nakamura, K., Jurgens, G., and Ito, M. (2011) Mutations in MYB3R1 and MYB3R4 cause pleiotropic developmental defects and preferential down-regulation of multiple G2/M-specific genes in Arabidopsis thaliana. Plant Physiol., 157, 706-17. 2011.
4. Kamiyoshihara, Y., Iwata, M., Fukaya, T., Tatsuki, M. and Mori, H. (2010) Turnover of LeACS2, a wound-inducible 1-aminocyclopropane-1-carboxylic acid synthase in tomato, is regulated by phosphorylation/dephosphorylation. Plant J., 64, 140-150.
5. Mori, H. (2010) Ethylene in “Plant Hormones, Comprehensive Natural Products Chemistry II”, 4. 02. 8, 87-90.
6. Hirano, K., Asano, K., Tsuji, H., Kawamura, M., Mori, H., Kitano, H., Ueguchi-Tanaka, M. and Matsuoka, M. (2010) Characterization of the molecular mechanism underlying gibberellin perception complex formation in rice. Plant Cell, 22, 2680-2696.
7. Hattori, Y., Nagai, K., Furukawa, S., Song, X-J., Kawano, R., Sakakibara, H., Wu, J., Matsumoto, T., Yoshimura, A., Kitano, H., Matsuoka, M., Mori, H. and Ashikari, M. (2009) The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. Nature, 460, 1026-1030.
8. Shimizu-Sato, S., Tanaka, M. and Mori, H. (2009) Auxin-cytokinin interactions in the control of shoot branching. Plant Mol. Biol., 69, 429-435.
9. Kato, K., Galis, I., Suzuki, S., Araki, S., Demura, T., Criqui, M.C., Potuschak., T, Genschik, P., Fukuda, H., Matsuoka, K., and Ito, M. (2009) Preferential up-regulation of G2/M phase-specific genes by overexpression of the hyperactive form of NtmybA2 lacking its negative regulation domain in tobacco BY-2 cells. Plant Physiol., 149, 1945-1957.
10. Ito-Inaba, Y., Hida, Y., Mori, H. and Inaba, T. (2008) Molecular identity of uncoupling proteins in thermogenic skunk cabbage. Plant Cell Physiol., 49, 1911-1916.
11. Shimizu-Sato, S., Ike, Y. and Mori, H. (2008) PsRBR1 encodes a pea retinoblastoma-related protein that is phosphorylated in axillary buds during dormancy-to-growth transition. Plant Mol. Biol., 66, 125-135.
12. Haga, N., Kato, K., Murase, M., Araki, S., Kubo, M., Demura, T., Suzuki, K., Muller, I., Vos, U., Jurgens, G. and Ito, M. (2007) R1R2R3-Myb proteins positively regulate cytokinesis through activation of KNOLLE transcription in Arabidopsis thaliana. Development, 134, 1101-1110.