NIBB Departments

Plant cells can induce, degenerate and differentiate their organelles to adapt to environmental changes. Therefore, the functions, morphology and number of plant organelles dramatically change in response to the cell types, developmental stages and external stimuli. This flexibility of plant organelles is the basis of the strategy for environmental adaptation in plants. The aim of this group is to clarify the molecular mechanisms underlying the induction, differentiation, and interaction of organelles, and to understand the integrated function of individual plants through organelle dynamics. Peroxisomes are single-membrane bounded organelles, which are ubiquitously present in eukaryotic cells, and their functions, morphology and number are changeable based on cell type, developmental stage and external stimuli such as light. We have been studying the molecular mechanisms of peroxisome biogenesis, functional transition, and their functions in reproductive processes. In addition, we have been analyzing the regulatory mechanisms of organelle-organelle interactions and accumulation of seed storage proteins, and novel functions of heat shock protein 90 (HSP90).

   We built The Plant Organelles Database 3 (PODB3, http://podb.nibb.ac.jp/Organellome/) to promote a comprehensive understanding of organelle dynamics. PODB3 consists of six individual units: the electron micrograph database, the perceptive organelles database, the organelles movie database, the organellome database, the functional analysis database, and external links.
Through each database, users are able to understand the organelles dynamics easily. In addition, we maintain the website, Plant Organelles World (http://podb.nibb.ac.jp/Organellome/PODBworld/en/) as an educational tool to engage members of the non-scientific community.

The Plant Organelles Database 3  (http://podb.nibb.ac.jp/Organellome/)

• Annual Report 2014（PDF）
• Annual Report 2015（PDF）
• Annual Report 2016（PDF）

Kamigaki, A., Nito, K., Hikino, K., Goto-Yamada, S., Nishimura, M., Nakagawa, T., and Mano, S. (2016). Gateway vectors for simultaneous detection of multiple protein−protein interactions in plant cells using bimolecular fluorescence complementation. PLOS ONE 11, e0160717

Kimori, Y., Hikino, K., Nishimura, M., and Mano, S. (2016). Quantifying morphological features of actin cytoskeletal filaments in plant cells based on mathematical morphology. J. Theor. Biol. 389, 123-131.

Kanai, M., Mano, S., Kondo, M., Hayashi, M., and Nishimura, M. (2016). Extension of oil biosynthesis during the mid-phase of seed development enhances oil content in Arabidopsis seeds. Plant Biotechnol. J. 14, 1241-1250.

Oikawa, K., Matsunaga, S., Mano, S., Kondo, M., Yamada, K., Hayashi, M., Kagawa, T., Kadota, A., Sakamoto, W., Higashi, S., Watanabe, M., Mitsui, T., Shigemasa, A., Iino, T., Hosokawa, Y., and Nishimura, M. (2015). Physical interaction between peroxisomes and chloroplasts elucidated by in situ laser analysis. Nature Plants 1, 15035.

Goto-Yamada, S., Mano, S., Nakamori, C., Kondo, M., Yamawaki, R., Kato, A., and Nishimura, M. (2014). Chaperone and protease functions of LON protease 2 modulate the peroxisomal transition and degradation with autophagy. Plant Cell Physiol. 55, 482-496.

Mano, S., Nakamura, T., Kondo, M., Miwa, T., Nishikawa, S., Mimura, T., Nagatani, A., and Nishimura, M. (2014). The Plant Organelles Database 3 (PODB3) update 2014: integrating electron micrographs and new options for plant organelle research. Plant Cell Physiol. 55, e1.

Goto-Yamada, S., Mano, S., and Nishimura, M. (2014). The role of peroxisomes in plant reproductive processes. In Sexual reproduction in animals and plants. Edited by Sawada, H., Inoue, N., and Iwano, M. pp.419-429. Springer Japan.

Shibata, M., Oikawa, K., Yoshimoto, K., Kondo, M., Mano, S., Yamada, K., Hayashi, M., Sakamoto, W., Ohsumi, Y., and Nishimura, M. (2013). Highly oxidized peroxisomes are selectively degraded via autophagy in Arabidopsis thaliana. Plant Cell. 25, 4967-4983.

Mano, S., Nakamori, C., Fukao, Y., Araki, M., Matsuda, A., Kondo, M., and Nishimura, M. (2011). A defect of peroxisomal membrane protein 38 causes enlargement of peroxisomes. Plant Cell Physiol. 52, 2157-2172.

Goto, S., Mano, S., Nakamori, C., and Nishimura, M. (2011). Arabidopsis ABERRANT PEROXISOME MORPHOLOGY 9 is a peroxin that recruits the PEX1-PEX6 complex to peroxisomes. Plant Cell 23, 1573-1587.

Mano, S., Nakamori, C., Kondo, M., Hayashi, M., and Nishimura, M. (2004). An Arabidopsis dynamin-related protein, DRP3A, controls both peroxisomal and mitochondrial division. Plant J. 38, 487-498.