Plant Molecular Biology Laboratory

Dr. Kenji Yamada

·         Phone: +48 12 664 6323

·         e-mail: kenji.yamada[a.t]

·         MCB, Gronostajowa 7a str

ER body formation and function

Plant cells develop various types of endoplasmic reticulum (ER)-derived structures with specific functions. ER bodies are ER-derived compartments observed in plants of the order Brassicales, including Arabidopsis thaliana. In the endoplasmic reticulum (ER) of transgenic Arabidopsis expressing green fluorescent protein (GFP), spindle shaped ER bodies were observed in the epidermis of seedlings and roots, in addition to the regular ER network (Figure 1). Normally, ER bodies are not observed in the rosette leaves, however wounding the leaf or application of methyl jasmonate (a wounding hormone in plants) induces ER bodies, suggesting that they are involved in a defense system against pests or pathogens in Arabidopsis. ER bodies accumulate high levels of ß-glucosidase named PYK10. Since ß-glucosidases are responsible for the production of toxic and defensive compounds in various plant species, the finding suggests that PYK10 might be involved in the production of defense molecules from glucosides in Arabidopsis.

      The basic helix-loop-helix- (bHLH) type transcription factor NAI1 (also known as AtbHLH20) regulates ER body formation, as shown by the fact that disruption of this gene in Arabidopsis completely disrupts ER body formation in seedlings and roots. NAI1 regulates the expression of genes encoding ER body proteins, such as those encoded by PYK10, NAI2, MEMBRANE OF ER BODY (MEB) 1 and MEB2 in the seedlings and roots. A unique ER body protein NAI2 is necessary for the ER body formation in seedlings and roots, and the nai2 mutant lacks ER bodies. Based on sequence similarity, NAI2 homologues are only observed in the plants of order Brassicales that produce ER bodies, further suggesting that NAI2 has a specific function in the formation of these organelles. MEB1 and MEB2 have been identified to accumulate specifically at ER body membranes, and are homologous to each other with multiple membrane-spanning regions.

      We recently found that PYK10 is able to hydrolyze glucosinolates, which are thioglucosides in the plants of order Brassicales. These findings strongly suggest that PYK10 is a thioglucosidase able to produce repellent isothiocyanates from glucosinolates. ER bodies accumulate in seedlings and roots, suggesting that they are naturally involved in the main defense system of these organs. Understanding the ER body defense system at the molecular level will explain the defense systems active in seedlings and roots.

Figure 1. ER bodies in the epidermal cells of Arabidopsis cotyledons. Fluorescent image of transgenic plants expressing ER-targeted GFP. Arrowheads indicate ER bodies. Scale bar = 10 µm.


Nakano, R.T., Yamada, K., Bednarek, P., Nishimura, M., Hara-Nishimura, I. (2014) ER bodies in plants of the Brassicales order: Biogenesis and association with innate immunity. Front. Plant Sci. 5, 73.

Yamada, K., Hara-Nishimura, I., Nishimura, M. (2011) Unique defense strategy by the endoplasmic reticulum body in plants. Plant Cell Physiol. 52 (12), 2039-2049.

Original publications

Yamada, K., Nagano, A.J., Nishina, M., Hara-Nishimura, I., Nishimura, M. (2013) Identification of two novel endoplasmic reticulum body-specific integral membrane proteins. Plant Physiol. 161 (1), 108-120.

Yamada, K., Nagano, A.J., Nishina, M., Hara-Nishimura, I., & Nishimura, M. (2008) NAI2 is an endoplasmic reticulum body component that enables ER body formation in Arabidopsis thaliana. Plant Cell 20 (9), 2529-2540.

Hayashi, Y., Yamada, K., Shimada, T., Matsushima, R., Nishizawa, N. K., Nishimura, M., Hara-Nishimura, I. (2001) A protease-storing body that prepares for cell death or stress in the epidermal cells of Arabidopsis. Plant Cell Physiol 42 (9), 894-899.

Quality control of peroxisomes

Mechanisms to remove useless and/or toxic cellular components are found in various organelles and cellular processes during maintenance of homeostasis of organisms. Peroxisomes, one of the ubiquitous organelles found in eukaryotic cells, contain appropriate enzymes and change metabolic systems depending on cellular state, plant developmental stage and environmental stimuli. During this functional transition, useless enzymes are degraded rapidly. In addition, peroxisomes produce hydrogen peroxide (H2O2) in the course of their metabolism. Since H2O2 can be the source of the most highly reactive and toxic form of reactive oxygen species (ROS), peroxisomal proteins must inevitably be damaged. Therefore, a quality control system to remove abnormal and toxic proteins is crucial for the maintenance of optimal performance of peroxisomes.

      In a previous study, we demonstrated that there are two important actors in the quality control of plant peroxisomes, LON proteinase 2 (LON2) and autophagy. LON2 is one of the protease inside peroxisomes. The C-terminal peptidase domain of LON2 contributes to degradation of unnecessary peroxisomal proteins during the functional transition of peroxisomes. On the other hand, autophagy degrades peroxisomes whole. We showed that autophagy is responsible for degradation of peroxisomes that are highly oxidized and damaged by H2O2. Interestingly, the N-terminus chaperone domain of LON2 is responsible for suppression of peroxisome degradation by autophagy. The present study aims to understand the role of LON2 in peroxisome maintenance and the molecular mechanism whereby autophagy recognizes damaged peroxisomes.


Goto-Yamada, S., Mano, S., Yamada, K., Oikawa, K., Hosokawa, Y., Hara-Nishimura, I., Nishimura, M. (2015) Dynamics of the light-dependent transition of plant peroxisomes. Plant Cell Physiol. 56(7), 1264-1271.

Original publications

Goto-Yamada, S., Mano, S., Nakamori, C., Kondo, M., Yamawaki, R., Kato, A., Nishimura, M. (2014) Chaperone and protease functions of LON protease 2 modulate the peroxisomal transition and degradation with autophagy. Plant Cell Physiol. 55(3), 482-496.

Shibata, M., Oikawa, K., Yoshimoto, K., Kondo, M., Mano, S., Yamada, K., Hayashi, M., Sakamoto, W., Ohsumi, Y., Nishimura, M. (2013) Highly oxidized peroxisomes are selectively degraded via autophagy in Arabidopsis. Plant Cell 25(12), 4967-4983.

Goto, S., Mano, S., Nakamori, C., Nishimura, M. (2011) Arabidopsis ABERRANT PEOXISOME MORPHOLOGY 9 is a peroxin that recruits the PEX1-PEX6 complex to peroxisomes. Plant Cell 23(4), 1537-1587.

Lab Members

Kenji Yamada (group leader)
Katarzyna Tarnawska-Glatt (postdoc)
Shino Goto-Yamada (JSPS postdoc)
Katarzyna Sieńko (postdoc)
Olga Długosz-Grochowska (postdoc)
Kaichiro Endo (postdoc)
Jakub Bizan
Natalia Stefanik (PhD student)
Alwine Wilkens (PhD student)
Arpan Kumar Basak (PhD student)
Karolina Małek

Job Opportunities

We are always seeking for interested and highly motivated Master, PhD or Postdoc candidates. Please contact us for further details ( kenji.yamada[a.t] )