Synthetic Genomics Research Team

Accomplishments

2017

Wen-Dee Ong, Emiko Okubo-Kurihara, Yukio Kurihara, Setsuko Shimada, Yuko Makita, Mika Kawashima, Kaori Honda, Yasumitsu Kondoh, Nobumoto Watanabe, Hiroyuki Osada, Sean R. Cutler, Kumar Sudesh, Minami Matsui (2017)
Chemical-Induced Inhibition of Blue Light-Mediated Seedling Development Caused by Disruption of Upstream Signal Transduction Involving Cryptochromes in Arabidopsis thaliana.
Plant Cell Physiol.58 (1): 95-105

Hong JP, Adams E, Yanagawa Y, Matsui M, Shin R. (2017)
AtSKIP18 and AtSKIP31, F-box subunits of the SCF E3 ubiquitin ligase complex, mediate the degradation of 14-3-3 proteins in Arabidopsis.
Biochem Biophys Res Commun.S0006-291X(17)30314-5

Makita Y.,Ng KK.,Singham V.,Kawashima M., Hirakawa H., Sato S.,Othman AS., Matsui M. (2017)
Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis
Dna Research 0(0), 1–9

Kondou, Y., Manickavelu,A., Komatsu K., Arifi M., Kawashima, M., Ishii T., Hattori T., Iwata H., Tsujimoto H., Ban T., Matsui M. (2017)
Analysis of grain elements and identification of best genotypes for Fe and P in Afgan wheat landraces.
Breeding Science 66:676-682

Manickavelu A, Hattori T, Yamaoka S, Yoshimura K, Kondou Y, Onogi A, Matsui M, Iwata H, Ban T. (2017) Genetic Nature of Elemental Contents in Wheat Grains and Its Genomic Prediction: Toward the Effective Use of Wheat Landraces from Afghanistan. PLoS One. 10;12(1)

2016

Ka-Kei Sam, Nyok-Sean Lau, Amirul Al-Ashraf Abdullah, Minami Matsui (2016)
Photoautotrophic Polyhydroxyalkanoate Production in Cyanobacteria.
Cyanobacteria -Omics and Manipulation-235-251

Wang, Q., Zuo, Z., Wang, X., Gu, L., Yoshizumi, T., Yang, Z., Yang, L., Liu, Q., Liu, W., Han, Y. J., Kim, J. I., Liu, B., Wohlschlegel, J. A., Matsui, M., Oka, Y.and Lin, C. (2016)
Photoactivation and inactivation of Arabidopsis cryptochrome 2,
Science 354: 343-347.

Kim, H., Kojima, M., Choi, D., Park, S., Matsui, M., Sakakibara, H.and Hwang, I. (2016)
Overexpression of INCREASED CAMBIAL ACTIVITY, a putative methyltransferase, increases cambial activity and plant growth.
Journal of integrative plant biology 58: 874-889.

Lau, N. S., Makita, Y., Kawashima, M., Taylor, T. D., Kondo, S., Othman, A. S., Shu-Chien, A. C.and Matsui, M. (2016)
The rubber tree genome shows expansion of gene family associated with rubber biosynthesis.
Sci Rep. 6: 28594.

Okubo-Kurihara, E., Ohtani, M., Kurihara, Y., Kakegawa, K., Kobayashi, M., Nagata, N., Komatsu, T., Kikuchi, J., Cutler, S., Demura, T.and Matsui, M. (2016)
Modification of plant cell wall structure accompanied by enhancement of saccharification efficiency using a chemical, lasalocid sodium.
Sci Rep. 6: 34602.

Sugano, S., Hayashi, N., Kawagoe, Y., Mochizuki, S., Inoue, H., Mori, M., Nishizawa, Y., Jiang, C. J., Matsui, M.and Takatsuji, H. (2016)
Rice OsVAMP714, a membrane-trafficking protein localized to the chloroplast and vacuolar membrane, is involved in resistance to rice blast disease,
Plant Mol Biol. 91: 81-95.

Tsuzuki, M., Nishihama, R., Ishizaki, K., Kurihara, Y., Matsui, M., Bowman, J. L., Kohchi, T., Hamada, T.and Watanabe, Y. (2016)
Profiling and Characterization of Small RNAs in the Liverwort, Marchantia polymorpha, Belonging to the First Diverged Land Plants.
Plant Cell Physiol., 57: 359-372.

2015

Shimada S, Makita Y, Kuriyama-Kondou T, Kawashima M, Mochizuki Y, Hirakawa H, Sato S, Toyoda T, Matsui M. (2015)
Functional and expression analyses of transcripts based on full-length cDNAs of Sorghum bicolor.
DNA Res. 22(6):485-93.

Makita, Y., Shimada, S., Kawashima, M., Kondou-Kuriyama, T., Toyoda, T., Matsui, M.(2015)
MOROKOSHI: Transcriptome Database in Sorghum bicolor
Plant Cell Physiol.56(1):e6. doi: 10.1093/pcp/pcu187

Foong,CP., Lau,NS., Deguchi, S., Toyofuku, T., Taylor, TD., Sudesh S., Matsui, M.(2015)
Whole genome amplification approach reveals novel polyhydroxyalkanoate synthases (PhaCs) from Japan Trench and Nankai Trough seawater
Manuscript 

BMC Microbiology24;14(1):7

Kurihara, Y., Okubo-Kurihara, E., Matsui, M.(2015)
Polycistronic expression of RNA silencing suppressor protects its own mRNA from RNA silencing.(2015)
Plant Biotechnol. 32, 1-7

Shimada,S., Komatsu, T., Yamagami, A., Nakazawa, M., Matsui, M., Kawaide, H., Natsume, M., Osada, H., Asami, T., Nakano, T.(2015)
Formation and dissociation of BSS1 protein complex regulates plant development via brassinosteroid signaling
Plant Cell27(2):375-90

2014

Lau, NS., Foong, CP., Kurihara, Y., Sudesh, K., Matsui, M.(2014)
RNA-seq analysis provides insights for understanding photoautotrophic polyhydroxyalkanoate production in recombinant Synechocystis sp”  
PLOSONEdoi; 10.1371/journal.pone.0086368

Kurihara, Y., Makita, Y., Kawashima, M., Hamasaki, H., Yamamoto, YY., Matsui, M.(2014)
Next-Generation Sequencing of Genomic DNA Fragments Bound to a Transcription Factor in Vitro Reveals Its Regulatory Potential
Genes5:1115-1131

Yoshizawa E, Kaizuka M, Yamagami A, Higuchi-Takeuchi M, Matsui M, Kakei Y, Shimada Y, Sakuta M, Osada H, Asami T, Nakano T.(2014)
BPG3 is a novel chloroplast protein that involves the greening of leaves and related to brassinosteroid signaling.
Biosci Biotechnol Biochem.78(3):420-9

Kunihiro S, Kowata H, Kondou Y, Takahashi S, Matsui M, Berberich T, Youssefian S, Hidema J, Kusano T.(2014)
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.
Planta.239(5):1101-11

Higuchi-Takeuchi, M, Matsui, M.(2014)
Screening for gene function using the FOX (full-length cDNA overexpressor gene) hunting system.
Methods Mol Biol. 1056:201-210.

Adams,E., Diaz,C., Matsui,M. and Shin, R.(2014)
Overexpression of a Novel Component Induces HAK5 and Enhances Growth in Arabidopsis.
ISRN Botany490252, 9

Matsui, M.(2014)
PHA from sunlight –New route for bioplastics production in cyanobacteria via photosynthesis
Bioplastics Magazine 9 20-21

2013

Hanada K., Higuchi 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., and Matsui M. (2013)
Small open reading frames associated with morphogen- esis are hidden in plant genomes.
Proc. Natl. Acad. Sci. USA110,No.6, 2395-400

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(2013)
The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative polyadenylation.
Sci. Rep. 3:2866

Cox, RS, Nishikata, K, Shimoyama, S, Yoshida, Y, Matsui, M, Makita, Y, Toyoda, T.(2013)
PromoterCAD: Data-driven design of plant regulatory DNA.
Nucleic Acids Res., 41 W569-74

Hong, JP, Takeshi, Y, Kondou, Y, Schachtman, DP, Matsui, M, Shin, R.(2013)
Identification and Characterization of Transcription Factors Regulating Arabidopsis HAK5.
Plant Cell Physiol. 54:1478-1490

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(2013)
The Arabidopsis COP9 SIGNALOSOME INTERACTING F-BOX KELCH 1 protein forms an SCF ubiquitin ligase and regulates hypocotyl elongation.
Mol. Plant. 6(5):1616-1629

Bekh-Ochir, D, Shimada, S, Yamagami, A, Kanda, S, Ogawa, K, Nakazawa, M, Matsui, M, Sakuta, M, Osada, H, Asami, T, Nakano, T.(2013)
A novel mitochondrial DnaJ/Hsp40 family protein BIL2 promotes plant growth and resistance against environmental stress in brassinosteroid signaling.
Planta237:1509-25

Higuchi-Takeuchi, M, Mori, M, Matsui, M.(2013)
High-throughput analysis of rice genes by means of the heterologous full-length cDNA overexpressor (FOX)-hunting system.
Int J Dev Biol.575:17-523

2012

Kim J., Mizoi J., Kidokoro S., Maruyama K., Nakajima J., Nakashima K., Mitsuda N., Takiguchi Y., Takagi-Ohme M., Kondou Y., Matsui M., Shinozaki K., and Shinozaki-Yamaguchi K. (2012)
Arabidopsis GROWTH- REGULATING FACTOR7 functions as a transcrip- tional repressor of abscisic acid- and osmotic stress- responsive genes, including DREB2A
Plant Cell24(8):3393–33405

Utsumi Y., Tanaka M., Morosawa T., Kurotani A., Yoshida T., Mochida K., Matsui A., Umemura Y., Ishitani M., Shinozaki K., Sakurai T., and Seki M (2012)
Transcriptome analysis using a high-density oligomi- croarray under drought stress in various genotypes of cassava: an important tropical crop
DNA Res.19(4):335–345

Kurihara Y., Schmitz R. J., Nery J. R., Schultz M. D., Kurihara E., Morosawa T., Tanaka M., Toyoda T., Seki M., and Ecker J. R. (2012)
Surveillance of 3’ Noncoding Tran- scripts Requires FIERY1 and XRN3 in Arabidopsis
Genes, Genomes, Genetics2(4):487–498

Utsumi Y., Sakurai T., Umemura Y., Ayling S., Ishitani M., Narangajavana J., Sojikul P., Triwitayakorn K., Matsui M., Manabe R., Shinozaki K., and Seki M.
RIKEN Cassava Initiative: Establishment of a Cassava unctional Genomics Platform
Tropical Plant Biol.5:110–116

2011

Higuchi M., Ichikawa T., Kondou Y., Matsui K., Hasegawa Y., Kawashima M., Sonoike K., Mori M., Hirochika H., and Matsui M. (2011)
Functional analysis of two iso- forms of leaf-type ferredoxin-NADP+-oxidoreductase in rice using heterologous expression system of Arabidopsis thaliana
Plant Physiol.157:96–108

Kurihara Y. and Seki M. (2011)
Genome-wide analysis of RNA degradation in Arabidopsis
RNA Technologies79–89

Kondou Y, Higuchi M, Ichikawa T, Matsui M. (2011)
Application of full-length cDNA resources to gain-of-function technology for characterization of plant.
Methods Mol Biol.729:183-97

2010

Kondou Y, Higuchi M, Matsui M. (2010)
High-throughput characterization of plant gene functions by using gain-of-function technology.
Annual review of Plant Biology 61:373-393

Higuchi M, Kondou Y, Ichikawa T, Matsui M. (2010)
Full-length cDNA overexpressor gene hunting system (FOX hunting system).
Plant Reverse Genetics Methods in Molecular Biology 678:77-89