Plant Molecular Breeding Research Group

Welcome to Plant Molecular Breeding Research Group at Osaka Metropolitan University!

Overview

Plant Molecular Breeding Research Group is a collaborative research group co-directed by Dr. Nozomu Koizumi and Dr. Yuji Iwata. We are interested in understanding molecular mechanisms of regulation of gene expression that governs various aspects of plant development and stress adaptation. We are also interested in developing plants with useful traits using plant genetic engineering. In addition to research activities, we are also involved in science communication regarding plant science and biotechnology.

For international students and postdocs

We welcome international students and postdocs to join our research team. If interested, please do not hesitate to contact us. You can also take a look at the following websites for your information.
For students, JASSO website, OMU website
For postdocs, JSPS website

Lab members

Faculty

Nozomu Koizumi,  Professor   orcid.logo.icon
    nkoizumi[at]omu.ac.jp

Yuji Iwata,  Assocate Professor   orcid.logo.icon
    yuji.iwata[at]omu.ac.jp

Staff

Yoko Sogabe
Ayumi Sakei

Graduate Students

Ryo Nakamoto
Ayaka Hieda
Hiroyuki Mizoguchi
Rei Yamada
Tomo Ikuta
Natsumi Kajiwara
Ryuga Matsuyoshi
Kota Wada

Undergraduate Students

Yuka Kawaura
Yu Kimura
Mizuki Nakagawa

Research

Unfolded protein response in plants

The endoplasmic reticulum (ER) has a central role in protein folding and maturation of secretory and membrane proteins, which constitute approximately one-third of all proteins synthesized in eukaryotes. They are cotranslationally inserted into the ER lumen and undergo folding and posttranslational modification to mature into functional proteins. The disturbance of this process culminates in accumulation of unfolded proteins in the ER, a condition termed ER stress. The ER responds to ER stress by activating a signal transduction pathway known as the unfolded protein response (UPR) (also known as the ER stress response) to assure protein-folding capacity. We have characterized the components of the UPR signaling pathway and their roles in plant development and environmental stress responses using Arabidopsis thaliana. For more details, please see our review article (Yuji Iwata and Nozomu Koizumi (2012) Trends Plant Sci 17:720-7 [PubMed]).

Selected publication:

  • Takeda S, Taisuke T, Mishiba KI, Yamato KT, Iwata Y, Koizumi N (2022) IRE1-mediated cytoplasmic splicing and regulated IRE1-dependent decay of mRNA in the liverwort Marchantia polymorpha. Plant Biotechnol 39:303-310 [PubMed]

  • Mishiba K, Iwata Y, Mochizuki T, Matsumura A, Nishioka N, Hirata R, Koizumi N (2019) Unfolded protein-independent IRE1 activation contributes to multifaceted developmental processes in Arabidopsis. Life Sci Alliance 2:e201900459 [PubMed]

  • Iwata Y, Iida T, Matsunami T, Yamada Y, Mishiba K, Ogawa T, Kurata T, Koizumi N (2018) Constitutive BiP protein accumulation in Arabidopsis mutants defective in a gene encoding chloroplastt-resident stearoyl-acyl carrier protein desaturase. Genes Cells 23:456-465 [PubMed]
  • Iwata Y, Ashida M, Hasegawa C, Tabara K, Mishiba KI, Nozomu Koizumi N (2017) Activation of the Arabidopsis membrane-bound transcription factor bZIP28 is mediated by site-2 protease, but not site-1 protease. Plant J, 91, 408-15.[PubMed]
  • Nagashima Y, Iwata Y, Mishiba KI, Koizumi N (2016) Arabidopsis tRNA ligase completes the cytoplasmic splicing of bZIP60 mRNA in the unfolded protein response. Biochem Biophys Res Commun 470, 941-6.[PubMed]
  • Nagashima Y, Iwata Y, Ashida M, Mishiba KI, Koizumi N (2014) Exogenous salicylic acid activates two signaling arms of the unfolded protein response in Arabidopsis. Plant Cell Physiol 55: 1772-8. [PubMed]
  • Mishiba KI, Nagashima Y, Suzuki E, Hayashi N, Ogata Y, Shimada Y, Koizumi N (2013) Defects in IRE1 enhance cell death and fail to degrade mRNAs encoding secretory pathway proteins in the Arabidopsis unfolded protein response. Proc Natl Acad Sci USA 110:5713-5718. [PubMed]
  • Iwata Y, Koizumi N (2012) Plant transducers of the endoplasmic reticulum unfolded protein response. Trends Plant Sci 17:720-727. [PubMed]
  • Iwata Y, Nishino T, Iwano M, Takayama S, Koizumi N (2012) Role of the plant-specific endoplasmic reticulum stress-inducible gene TIN1 in the formation of pollen surface structure in Arabidopsis thaliana. Plant Biotechnol 29:51-56. [J-STAGE]
  • Nagashima Y, Mishiba KI, Suzuki E, Shimada Y, Iwata Y, Koizumi N (2011) Arabidopsis IRE1 catalyses unconventional splicing of bZIP60 mRNA to produce the active transcription factor. Sci Rep 1:29. [PubMed]
  • Iwata Y, Sakiyama M, Lee MH, Koizumi N (2010) Transcriptomic response of Arabidopsis thaliana to tunicamycin-induced endoplasmic reticulum stress. Plant Biotechnol 27:161-171. [J-STAGE]
  • Iwata Y, Fedoroff NV, Koizumi N (2008) Arabidopsis bZIP60 is a proteolysis-activated transcription factor involved in the endoplasmic reticulum stress response. Plant Cell 20:3107-3121. [PubMed]
  • Tajima H, Iwata Y, Iwano M, Takayama S, Koizumi N (2008) Identification of an Arabidopsis transmembrane bZIP transcription factor involved in the endoplasmic reticulum stress response. Biochem Biophys Res Commun 374:242-247. [PubMed]
  • Iwata Y, Koizumi N (2005) An Arabidopsis transcription factor, AtbZIP60, regulates the endoplasmic reticulum stress response in a manner unique to plants. Proc Natl Acad Sci USA 102:5280-5285. [PubMed]
  • Koizumi N, Martinez IM, Kimata Y, Kohno K, Sano H, Chrispeels MJ (2001) Molecular characterization of two Arabidopsis Ire1 homologs, endoplasmic reticulum-located transmembrane protein kinases. Plant Physiol 127:949-962. [PubMed]

Plant microRNA biogenesis

MicroRNA (miRNA) is a class of small non-coding RNA found in plants, animals and other diverse eukaryotes. Plant miRNA is 20 – 22 nucleotides in length, regulates gene expression by guiding mRNA cleavage and translational repression, and is critical for various aspects of plant biology such as plant growth, development and stress adaptation. Our main focus has been on understanding the molecular mechanism of miRNA biogenesis using Arabidopsis thaliana.

Selected publications:
  • Hirata R, Makabe T, Mishiba K, Koizumi N, Hamdan SM, Iwata Y (2022) Unpaired nucleotides on the stem of microRNA precursor are important for precise cleavage by Dicer-Like1 in Arabidopsis. Genes Cells 27: 280-292[PubMed]
  • Hirata R, Mishiba K, Koizumi N, Iwata Y (2019) Deficiency in the double-stranded RNA binding protein HYPONASTIC LEAVES1 increases sensitivity to the endoplasmic reticulum stress inducer tunicamycin in Arabidopsis. BMC Res Notes 12:580 [PubMed]
  • Iwata Y, Takahashi M, Fedoroff NV, Hamdan SM (2013) Dissecting the interactions of SERRATE with RNA and DICER-LIKE 1 in Arabidopsis microRNA precursor processing. Nucleic Acids Res 41:9129-9140. [PubMed]

Generation of eggplants with higher carotenoid contents

(more details coming soon.)

Selected publications:
  • Mishiba KI, Nishida K, Inoue N, Fujiwara T, Teranishi S, Iwata Y, Takeda S, Koizumi N (2020) Genetic engineering of eggplant accumulating β-carotene in fruit. Plant Cell Rep 39:1029-1039. [PubMed]

Mailing Address

Graduate School of Agriculture
Osaka Metropolitan University

Building C17, Room 303 (Koizumi) or Room 306 (Iwata)
1-1 Gakuen-cho, Naka-ku
Sakai, Osaka 599-8531
Japan