Synthetic Genomics Research Team

Group Director

pictureGroup Director : Minami Matsui (Ph.D.)


From Exploring Science to Innovative Science- We are welcome young generations


B.A. in Biochemistry, Faculty of Science, Saitama University, Japan
Dr. of Science. in Biophysics, Faculty of Science, Kyoto University, Japan

Position Held

April 1986 - March 1989
Research Associate of the Molecular Oncology Laboratory in Nippon Veterinary and Zootechnical College
April 1989 - March 1990
Lecturer of the Molecular Oncology Laboratory in Nippon Veterinary and Zootechnical College
April 1990 - January 1992
Lecturer of the Molecular Biology Laboratory in Nippon Medical School.
January 1992 - 1994 January
Postdoctoral fellow in Xing Wang Deng's laboratory in Department of Biology in Yale University
January 1994 - March 1995
Lecturer of the Molecular Biology Laboratory in Nippon Medical School.
April 1995 - September 1999
Deputy head of Laboratory for Photoperception and Signal transduction in RIKEN Frontier Research Program (Leader: Richard E. Kendrick)
October 1999 - March 2005
Team Leader of Plant Function Exploration Team of Plant Functional Genomic Research Group in RIKEN Genomics Sciences Center
April 2005 - 2006
Team Leader of Plant Function Exploration Team of Functional Genomics Research Group in RIKEN Genomic Sciences Center
April 2006 - March 2013
Group Director of Plant Functional Genomics Research Group, RIKEN Plant Science Center
April 2010 - March 2015
Team Leader of Synthetic Genomics Research team of BMEP (Biomass Engineering Program)
April 2015 - present
Group Director of Synthetic Genomics Research team of BMEP (Biomass Engineering Program), RIKEN Center for Sustainable Resource Science

Selected Papers

  1. The rubber tree genome shows expansion of gene family associated with rubber biosynthesis.Lau NS, Makita Y, Kawashima M, Taylor TD, Kondo S, Othman AS, Shu-Chien AC Matsui M.Sci Rep. 2016 Jun 24;6:28594. doi: 10.1038/srep28594.PMID: 27339202
  2. Modification of plant cell wall structure accompanied by enhancement of saccharification efficiency using a chemical, lasalocid sodium. Okubo-Kurihara E, Ohtani M, Kurihara Y, Kakegawa K, Kobayashi M, Nagata N, Komatsu T, Kikuchi J, Cutler S, Demura T, Matsui M. Sci Rep. 2016 Oct 3;6:34602. doi: 10.1038/srep34602.PMID: 27694977
  3. Photoactivation and inactivation mechanisms of Arabidopsis cryptochrome 2. Wang Q., Zecheng Zuo Z, Wang X, Gu L, Yoshizumi T,Yang Z, Yang L, Liu Q, Liu W, Han YJ, Kim JI, Liu B,Wohlschlegel JA, Matsui M, Oka Y, Lin C. Science 2016 Oct 21;354(6310):343-347.PMID:27846570
  4. Overexpression of INCREASED CAMBIAL ACTIVITY, a putative methyltransferase, increases cambial activity and plant growth. Kim H, Kojima M, Choi D, Park S, Matsui M, Sakakibara H, Hwang I. J Integr Plant Biol. 2016 Jun 20. doi: 10.1111/jipb.12486. PMID: 27322968
  5. Possible Involvement of MYB44-Mediated Stomatal Regulation in Systemic Resistance Induced by Penicillium simplicissimum GP17-2 in Arabidopsis. Hieno A, Naznin HA, Hyakumachi M, Higuchi-Takeuchi M, Matsui M, Yamamoto YY. Microbes Environ. 2016 Jun 25;31(2):154-9. doi: 10.1264/jsme2.ME16025. Epub 2016 Jun 10. PMID: 27301421
  6. Rice OsVAMP714, a membrane-trafficking protein localized to the chloroplast and vacuolar membrane, is involved in resistance to rice blast disease. Sugano S, Hayashi N, Kawagoe Y, Mochizuki S, Inoue H, Mori M, Nishizawa Y, Jiang CJ, Matsui M, Takatsuji H. Plant Mol Biol. 2016 May;91(1-2):81-95. doi: 10.1007/s11103-016-0444-0. Epub 2016 Feb 15.PMID: 26879413
  7. Profiling and Characterization of Small RNAs in the Liverwort, Marchantia polymorpha, Belonging to the First Diverged Land Plants.Tsuzuki M, Nishihama R, Ishizaki K, Kurihara Y, Matsui M, Bowman JL, Kohchi T, Hamada T, Watanabe Y. Plant Cell Physiol. 2016 Feb;57(2):359-72. doi: 10.1093/pcp/pcv182. Epub 2015 Nov 19.PMID: 26589267
  8. MOROKOSHI: transcriptome database in Sorghum bicolor. Makita Y, Shimada S, Kawashima M, Kondou-Kuriyama T, Toyoda T, Matsui M.Plant Cell Physiol. 2015 Jan;56(1):e6. doi: 10.1093/pcp/pcu187. Epub 2014 Dec 9.PMID: 25505007
  9. Polycistronic expression of RNA silencing suppressor protects its own mRNA from RNA silencing. Kurihara, Y. Okubo-Kurihara, E., Matsui, M. Plant Biotechnol. 32, 1-7 (2015)
  10. Profiling and Characterization of Small RNAs in the Liverwort, Marchantia polymorpha, Belonging to the First Diverged Land Plants. Tsuzuki M, Nishihama R, Ishizaki K, Kurihara Y, Matsui M, Bowman JL, Kohchi T, Hamada T, Watanabe Y.Plant Cell Physiol. 2016 Feb;57(2):359-72. doi: 10.1093/pcp/pcv182. Epub 2015 Nov 19.PMID: 26589267
  11. Functional and expression analyses of transcripts based on full-length cDNAs of Sorghum bicolor.Shimada S, Makita Y, Kuriyama-Kondou T, Kawashima M, Mochizuki Y, Hirakawa H, Sato S, Toyoda T, Matsui M. DNA Res. 2015 Dec;22(6):485-93. doi: 10.1093/dnares/dsv030. Epub 2015 Nov 5.PMID: 26546227
  12. Cyanobacteria: Photoautotrophic Microbial Factories for the Sustainable Synthesis of Industrial Products. Lau NS, Matsui M, Abdullah AA.Biomed Res Int. 2015;2015:754934. doi: 10.1155/2015/754934. Epub 2015 Jun 25. Review.PMID: 26199945
  13. Light, and Cold Stress Are Regulated by a Transcriptional Regulatory Unit Composed of Two Elements.Hayami N, Sakai Y, Kimura M, Saito T, Tokizawa M, Iuchi S, Kurihara Y, Matsui M, Nomoto M, Tada Y, Yamamoto YY. Plant Physiol. 2015 Sep;169(1):840-55. doi: 10.1104/pp.15.00398. Epub 2015 Jul 14.PMID: 26175515
  14. The ETHYLENE RESPONSE FACTORs ERF6 and ERF11 Antagonistically Regulate Mannitol- Induced Growth Inhibition in Arabidopsis. Dubois M, Van den Broeck L, Claeys H, Van Vlierberghe K, Matsui M, Inzé D.Plant Physiol. 2015 Sep;169(1):166-79. doi: 10.1104/pp.15.00335. Epub 2015 May 20.PMID: 25995327
  15. Formation and dissociation of the BSS1 protein complex regulates plant development via brassinosteroid signaling. Shimada S, Komatsu T, Yamagami A, Nakazawa M, Matsui M, Kawaide H, Natsume M, Osada H, Asami T, Nakano T.Plant Cell. 2015 Feb;27(2):375-90. doi: 10.1105/tpc.114.131508. Epub 2015 Feb 6.PMID: 25663622
  16. Whole genome amplification approach reveals novel polyhydroxyalkanoate synthases (PhaCs) from Japan Trench and Nankai Trough seawater.Foong CP, Lau NS, Deguchi S, Toyofuku T, Taylor TD, Sudesh K, Matsui M.BMC Microbiol. 2014 Dec 24;14:318. doi: 10.1186/s12866-014-0318-z.PMID: 25539583
  17. Next-generation sequencing of genomic DNA fragments bound to a transcription factor in vitro reveals its regulatory potential.Kurihara Y, Makita Y, Kawashima M, Hamasaki H, Yamamoto YY, Matsui M. Genes (Basel). 2014 Dec 19;5(4):1115-31. doi: 10.3390/genes5041115.PMID: 25534860
  18. BPG3 is a novel chloroplast protein that involves the greening of leaves and related to brassinosteroid signaling. Yoshizawa E, Kaizuka M, Yamagami A, Higuchi-Takeuchi M, Matsui M, Kakei Y, Shimada Y, Sakuta M, Osada H, Asami T, Nakano T.Biosci Biotechnol Biochem. 2014;78(3):420-9. doi: 10.1080/09168451.2014.885831. Epub 2014 Apr 16.PMID: 25036828
  19. Overexpression of rice OsREX1-S, encoding a putative component of the core general transcription and DNA repair factor IIH, renders plant cells tolerant to cadmium- and UV-induced damage by enhancing DNA excision repair.Kunihiro S, Kowata H, Kondou Y, Takahashi S, Matsui M, Berberich T, Youssefian S, Hidema J, Kusano T.Planta. 2014 May;239(5):1101-11. doi: 10.1007/s00425-014-2042-1. Epub 2014 PMID: 24563249
  20. RNA-Seq analysis provides insights for understanding photoautotrophic polyhydroxyalkanoate production in recombinant Synechocystis Sp.Lau NS, Foong CP, Kurihara Y, Sudesh K, Matsui M.PLoS One. 2014 Jan 22;9(1):e86368. doi: 10.1371/journal.pone.0086368. eCollection 2014.PMID: 24466058
  21. Database construction for PromoterCAD: synthetic promoter design for mammals and plants.Nishikata K, Cox RS 3rd, Shimoyama S, Yoshida Y, Matsui M, Makita Y, Toyoda T.ACS Synth Biol. 2014 Mar 21;3(3):192-6. doi: 10.1021/sb400178c. Epub 2014 Jan 6.PMID: 24364365
  22. Screening for gene function using the FOX (full-length cDNA overexpressor gene) hunting system.Higuchi-Takeuchi M, Matsui M. Methods Mol Biol. 2014;1056:201-10. doi: 10.1007/978-1-62703-592-7_19.PMID: 24306875
  23. High-throughput analysis of rice genes by means of the heterologous full-length cDNA overexpressor (FOX)-hunting system.Higuchi-Takeuchi M, Mori M, Matsui M.Int J Dev Biol. 2013;57(6-8):517-23. doi: 10.1387/ijdb.130176mm. Review.PMID: 24166434
  24. The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative polyadenylation.Lyons R, Iwase A, Gänsewig T, Sherstnev A, Duc C, Barton GJ, Hanada K, Higuchi-Takeuchi M, Matsui M, Sugimoto K, Kazan K, Simpson GG, Shirasu K. Sci Rep. 2013 Oct 9;3:2866. doi: 10.1038/srep02866.PMID: 24104185
  25. Identification and characterization of transcription factors regulating Arabidopsis HAK5.Hong JP, Takeshi Y, Kondou Y, Schachtman DP, Matsui M, Shin R. Plant Cell Physiol. 2013 Sep;54(9):1478-90. doi: 10.1093/pcp/pct094. Epub 2013 Jul 2.PMID: 23825216
  26. PromoterCAD: Data-driven design of plant regulatory DNA.Cox RS 3rd, Nishikata K, Shimoyama S, Yoshida Y, Matsui M, Makita Y, Toyoda T.Nucleic Acids Res. 2013 Jul;41(Web Server issue):W569-74. doi: 10.1093/nar/gkt518. Epub 2013 Jun 12.PMID: 23766287
  27. Ethylene Response Factor6 acts as a central regulator of leaf growth under waterlimiting conditions in Arabidopsis.Dubois M, Skirycz A, Claeys H, Maleux K, Dhondt S, De Bodt S, Vanden Bossche R, De Milde L, Yoshizumi T, Matsui M, Inzé D.Plant Physiol. 2013 May;162(1):319-32. doi: 10.1104/pp.113.216341. Epub 2013 Apr 3.PMID: 23553636
  28. A novel mitochondrial DnaJ/Hsp40 family protein BIL2 promotes plant growth and resistance against environmental stress in brassinosteroid signaling.Bekh-Ochir D, Shimada S, Yamagami A, Kanda S, Ogawa K, Nakazawa M, Matsui M, Sakuta M, Osada H, Asami T, Nakano T.Planta. 2013 Jun;237(6):1509-25. doi: 10.1007/s00425-013-1859-3. Epub 2013 Mar 15.PMID: 23494613
  29. The Arabidopsis COP9 SIGNALOSOME INTERACTING F-BOX KELCH 1 protein forms an SCF ubiquitin ligase and regulates hypocotyl elongation.Franciosini A, Lombardi B, Iafrate S, Pecce V, Mele G, Lupacchini L, Rinaldi G, Kondou Y, Gusmaroli G, Aki S, Tsuge T, Deng XW, Matsui M, Vittorioso P, Costantino P, Serino G.Mol Plant. 2013 Sep;6(5):1616-29. doi: 10.1093/mp/sst045. Epub 2013 Mar 9.PMID: 23475998
  30. Small open reading frames associated with morphogenesis are hidden in plant genomes. Hanada K, Higuchi-Takeuchi M, Okamoto M, Yoshizumi T, Shimizu M, Nakaminami K, Nishi R, Ohashi C, Iida K, Tanaka M, Horii Y, Kawashima M, Matsui K, Toyoda T, Shinozaki K, Seki M, Matsui M. Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2395-400. doi: 10.1073/pnas.1213958110. Epub 2013 Jan 22. PMID: 23341627
  31. A comprehensive analysis of interaction and localization of Arabidopsis SKP1-like (ASK) and F-box (FBX) proteins. Kuroda H, Yanagawa Y, Takahashi N, Horii Y, Matsui M. PLoS One. 2012;7(11):e50009. doi: 10.1371/journal.pone.0050009. Epub 2012 Nov 15.PMID: 23166809
  32. Arabidopsis PIZZA has the capacity to acylate brassinosteroids. Schneider K, Breuer C, Kawamura A, Jikumaru Y, Hanada A, Fujioka S, Ichikawa T, Kondou Y, Matsui M, Kamiya Y, Yamaguchi S, Sugimoto K. PLoS One. 2012;7(10):e46805. doi: 10.1371/journal.pone.0046805. Epub 2012 Oct 5.PMID: 23071642
  33. BAT1, a putative acyltransferase, modulates brassinosteroid levels in Arabidopsis. Choi S, Cho YH, Kim K, Matsui M, Son SH, Kim SK, Fujioka S, Hwang I. Plant J. 2013 Feb;73(3):380-91. doi: 10.1111/tpj.12036. Epub 2012 Dec 31.PMID: 23020607