[Press Release]New role of arginine metabolism in plant morphogenesis identified

Insights into the evolution of plant body architecture

Arginine metabolism boosts to make a plant body complex, according to new research by a collaborative team from Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute for Basic Biology (NIBB), RIKEN, Rikkyo University, Toyohashi University of Technology, Yamagata University, Chiba University, Hokkaido University, and University of Tokyo in Japan. The findings, now online in Cell Reports, might lead to a new understanding of amino acid metabolism with a specific role in plant morphogenesis.
In the ancestral lineage of land plants, the moss Physcomitrium patens has evolved to produce leafy shoots called gametophore. “Because metabolic reprogramming is necessary for this dramatic evolution in morphology to ensure the generation of sufficient biomass, we focused on gametophore formation as a model to uncover a mutual interaction between morphogenesis and metabolism” said Associate Professor Kensuke Kawade at ExCELLS/NIBB.

A colony of Physcomitrium patens with gametophore shoots
Filamentous protonema tissues (pale green) exhibit two dimensional growth to form a mat-like structure. On the other hand, gametophores (dark green) produce leafy shoots as a result of three dimentional growth.

In the current study, they showed that arginine metabolism is a key for gametophore formation in Physcomitrium patens and identified its underlying core pathway mediated by transcriptional co-activators ANGUSTIFOLIA3/GRF-INTERACTING FACTOR1 (AN3/GIF1) family signaling. These findings have advanced our understanding of the mechanism, by which the shoot system was established via metabolic reprogramming during the evolution of plants. More generally, this study refines the emerging concept in biology that developmental and metabolic processes influence one another for chemical force that facilitates growth, morphogenesis, and maturation. “Future work to clarify what kind of metabolite is produced from arginine in gametophores promises to unravel the physiological base of this phenomenon” explained Kawade.


Journal: Cell Reports
Title:Metabolic control of gametophore shoot formation through arginine in the moss Physcomitrium patens
Eurekalert! URL:https://www.eurekalert.org/pub_releases/2020-09/nion-nro090820.php


Kensuke Kawade
TEL: +81-564-55-7563
E-mail: kawa-ken[at]nibb.ac.jp (Please replace the “_at_” with @)

Gravity affects protein assembly related to Alzheimer’s disease
Amyloids, abnormal fibrillar aggregates of proteins, are associated with various disorders such as Alzheimer’s disease. Therefore, an in-depth understanding of the mechanisms of amyloid formation is critical for developing clinical strategies and drugs against these diseases. However, accumulating evidence suggests that amyloid formation processes and the consequent morphology of fibrils can be affected by various environmental factors. This is an obstacle for the integrative understanding of the mechanisms underlying amyloid formations. As gravity causes convectional perturbations in the microenvironments surrounding amyloid fibrils in solution, it may unavoidably affect the processes of molecular assembling. To test this possibility, the collaborative research team of Japan, involving Exploratory Research Center on Life and Living Systems (ExCELLS), Institute for Molecular Science (IMS), and National Institute for Physiological Sciences (NIPS) of National Institutes of Natural Sciences, Nagoya City University (NCU), and Japan Aerospace Exploration Agency (JAXA), characterized amyloid formation under microgravity conditions using the International Space Station (ISS). They compared the fibril formation of Alzheimer’s disease-related amyloid β (Aβ) proteins on the ISS with that on the Earth and found that the process of Aβ fibrillization significantly slowed down in the microgravity environment. Furthermore, distinct morphologies of Aβ fibrils were formed on the ISS. Therefore, the project highlights the utility of the ISS as an ideal experimental environment for investigating the mechanisms of amyloid formation without uncontrollable perturbations caused by gravity, thereby providing fundamental insights into the pathological amyloid formation.

Outline of the “Amyloid” project.
Decal of the project and timeline of the space experiment performed on the ISS. (©JAXA/NINS)

3D images of Aβ fibrils grown on the ISS.
Distinct morphologies of Aβ fibrils formed under microgravity conditions. (©JAXA/NINS)



Journal: NPJ Microgravity
Title:Characterization of amyloid β fibril formation under microgravity conditions
Eurekalert! URL:https://www.eurekalert.org/pub_releases/2020-06/nion-afi061620.php

In a recent study published in Molecular Cell, researchers report the role of cellular structures called PML bodies in regulating gene function
The genetic information within our cells is what makes humans unique. The cell nucleus has a complex structure that harbors this genetic information. The main component of the nucleus is chromatin, an intercalated pool of genes and proteins. Promyelocytic leukemia (PML) bodies are structures found closely associated with chromatin, suggesting that they may be involved with genetic function. However, the exact nature of the relationship between PML bodies and genes is unknown. In research conducted by a team at National Institutes of Natural Sciences (NINS) led by Yusuke Miyanari who recently joined NanoLSI at Kanazawa University, shows how PML bodies can modulate certain genes and the potential implications of these actions.

In order to visualize and track the exact location of PML bodies on the chromatin, the team developed a method known as APEX-mediated chromatin labeling and purification (ALaP). A fluorescent dye was first coupled with the PML bodies such that the light emitted by this dye could help trace the bodies. Subsequently, the PML body–chromatin complex could be isolated and the genes within it sequenced and identified.
This technique was tested in cells of mice and resulted in successful extraction of the complex without any structural damage. The chromatin region anchored to the PML bodies within this complex was then identified as YS300, a short area of the Y chromosome. What’s more, a cluster of genes in the vicinity of YS300 was also found to be impacted—some genes were suppressed and some were activated. PML bodies were thus somehow controlling the activity of these neighboring genes, which prompted the team to try and understand how.
In order for genes to be activated they must undergo a process known as DNA methylation. However, the structures of the suppressed genes suggested that they had been deprived of this process. A closer examination of the entire complex revealed that PML bodies were docked onto YS300 in a manner which prevented DNMT3A, a core regulator of DNA methylation, from accessing the genes. PML bodies were therefore physically restricting DNMT3A thereby preventing genetic activation.
“Our study sheds light on a newly discovered role of PML bodies in the regulation of the cluster genes and revealed a novel mechanism to regulate gene expression by 3D nuclear organization,” summarize the researchers. PML bodies are heavily involved in nervous system development, stress responses, and cancer suppression. Their newly found role can help understand whether and how gene regulation is involved in any of these cellular processes. Additionally, PML bodies can also be exploited as a potential switch to control the activity of certain genes.


PML bodies: PML bodies are dynamic, scaffold-like structures made up of small proteins. Each cell nucleus is known to contain 5–30 PML bodies. PML bodies are involved in a host of cellular processes such as cell growth, aging, cell division, and stress responses. While PML bodies are known to closely latch onto different regions of the chromatin, there is also evidence to show that they interact with some genes. However, the link between PML bodies and genes is still unclear.
Chromatin: Our genes are made up of long sequences of DNA molecules; these sequences can measure up to a yard when stretched out. The chromatin is an essential component of the cell that helps pack these long sequences of DNA efficiently within the cell. Chromatin is thus a complex structure within which strings of DNA are wound tightly around protein molecules. Chromatin also inevitably safeguards the genes found within it thereby acting as an entry point for molecules that interact with genes.


Misuzu Kurihara, Kagayaki Kato, Chiaki Sanbo, Shuji Shigenobu, Yasuyuki Ohkawa, Takeshi Fuchigami, Yusuke Miyanari. Genomic profiling of PML bodies by ALaP-seq reveals transcriptional regulation by PML bodies through the DNMT3A exclusion. Molecular Cell, 2020. Online 29 April 2020.
DOI: https://doi.org/10.1016/j.molcel.2020.04.004

Unique protein acts as an inward proton pump in a distant microbial relative

Researchers investigated the group of microorganisms classified as Asgard archaea, and found a protein in their membrane which acts as a miniature light-activated pump. The schizorhodopsin protein draws protons into the organisms’ body. This research could lead to new biomolecular tools to control the pH in cells or microorganisms, and possibly more.
Asgard archaea are relatively new to science, but they are ancient and important to us in more ways than one. They are single-celled organisms and were originally found at the bottom of the ocean. Asgard archaea are what are known as a prokaryote, they do not have a cell nucleus, yet despite this, they are genetically close to single-celled organisms called eukaryotes which do contain a cell nucleus. They are like a modern analogue of an ancient common ancestor.
The race is on to investigate these small but significant organisms. Associate Professor Keiichi Inoue from the Institute for Solid State Physics at the University of Tokyo, Professor Hideki Kandori from Nagoya Institute of Technology and their team chose to study a feature of Asgard archaea that although not unique to them, is especially interesting in their case, and that is light-sensitive or photoreceptive proteins called rhodopsins. The organisms live at the bottom of oceans and lakes so it’s surprising they need any kind of sensitivity to light.
“We explored the molecular function of special rhodopsins in Asgard archaea called schizorhodopsins and found that they acted as light-activated microscopic pumps,” explained Inoue. “Schizorhodopsin uses sunlight energy to take up a proton into the cell along a pathway inside the protein. Many prokaryotes such as bacteria and other archaea use rhodopsins to pump protons out, but we find this newly characterized form in Asgard archaea particularly interesting.”
As the scale this function occurs on is nanoscopic, sophisticated measurement techniques with high sensitivity and high temporal resolution were required. Inoue, Kandori and their team used a method called laser flash photolysis which uses pulsed laser light to stimulate reactions. Color change in the protein affected by laser light was monitored by sensitive sensors. These detected the presence and nature of the short-lived activation of schizorhodopsin.
“These findings will help us better understand proton and other ion transport mechanisms. In addition, schizorhodopsin could be made into a useful molecular tool for researchers,” commented Inoue. “For example in optogenetics, which is a new methodology to control various cellular phenomena with light. Schizorhodopsins could also be used to control the pH inside cells or microorganisms with light, as pH can be altered by changing the proton concentration.



Journal: Science Advances
Title:Schizorhodopsins: A family of rhodopsins from Asgard archaea that function as light-driven inward H+ pumps
Eurekalert! URL:https://www.eurekalert.org/pub_releases/2020-04/uot-ldp041020.php
AlphaGalileo URL:https://www.alphagalileo.org/en-gb/Item-Display/ItemId/191276

Improving the secretion of biopharmaceutical glycoproteins using a molecular passport tag that is recognized by the cargo receptor

Many proteins produced by the cells are decorated with sugars and delivered out of the cells. In this secretory pathway, MCFD2 sorts and transports blood coagulation factors V and VIII as special cargos. The impairment of MCFD2 function results in a deficiency of these coagulation factors. The collaborative groups, including researchers at the Graduate School of Pharmaceutical Sciences of Nagoya City University, Exploratory Research Center on Life and Living Systems (ExCELLS), Institute for Molecular Science (IMS), and National Institute for Basic Biology (NIBB) of National Institutes of Natural Sciences, elucidated the molecular mechanisms behind MCFD2-mediated cargo transportation. The groups found that a 10-amino acid sequence is built into these coagulation factors as a “passport”, which is recognized by MCFD2, and elimination of this sequence attenuates their cellular secretion. Moreover, they discovered that the intracellular transportation and consequent secretion of recombinant erythropoietin, a glycoprotein that is used to treat anemia, are significantly enhanced simply by tagging it with the factor VIII-derived passport sequence. Presently, most biopharmaceuticals are produced using mammalian cell cultures. The collaborative group findings provide the molecular basis for the intracellular trafficking of blood coagulation factors and an explanation for genetic deficiency as well as offer this “passport sequence” as a potentially useful tool for improving production yields of recombinant glycoproteins of biopharmaceutical interest.

Passport tagging for express cargo transportation in cells
(A) The passport sequence built in coagulation factor VIII.
(B) Secretion enhancement of biopharmaceuticals by tagging them with the passport sequence


Journal: Nature Communications
Title: Improved secretion of glycoproteins using an N-glycan-restricted passport sequence tag recognized by cargo receptor
DOI: 10.1038/s41467-020-15192-1
Eurekalert! URL:https://www.eurekalert.org/pub_releases/2020-03/ncu-ptf031720.php


Koichi Kato
Exploratory Research Center on Life and Living Systems (ExCELLS)/
Institute for Molecular Science, Natural Institutes of Natural Sciences
TEL: +81-564-59-5225
E-mail: kkato[at]excells.orion.ac.jp (Please replace the “_at_” with @)

A unique archaeal protein complex having a spacious center surrounded by five columns

Proteins often form assemblies and thereby perform sophisticated functions in cells as best exemplified by proteasomes, which are huge enzyme complexes functioning as proteolytic machines. In eukaryotes, this proteasome formation is not a spontaneous process but is assisted by several other proteins, termed proteasome-assembling chaperones. Paradoxically, archaeal genomes encode proteasome-assembling chaperone homologs, denoting a shared ancestry between genes, although archaeal proteasome formation is a spontaneous process not requiring these chaperones. Therefore, the functional roles of the archaeal chaperone-like proteins remain unknown. The collaborative groups, including researchers at Exploratory Research Center on Life and Living Systems (ExCELLS), Institute for Molecular Science (IMS), and National Institute for Physiological Sciences (NIPS) of National Institutes of Natural Sciences found that a chaperone-like protein originating from a hyperthermophilic archaeon together with another protein from the same species, whose function is also unknown, are assembled together into unique structures. The integrated biophysical data they obtained using native mass spectrometry, solution scattering, high-speed atomic force microscopy, and electron microscopy, along with atomic structure modeling, revealed that this complex forms a five-column tholos-like architecture, harboring a large central cavity, which can potentially accommodate biomolecules, such as proteins. This characteristic architecture of archaeal protein complex provides insight into the molecular evolution between archaeal and eukaryotic proteins. Furthermore, their findings offer a novel framework for designing functional protein cages as molecular warehouses or shelters that are stable in high temperatures.

The two functionally unannotated archaeal proteins, PbaA and PF0014, are co-assembled into a unique ancient Greek tholos-like architecture, having a spacious space in the middle surrounded by two pentameric PbaA, a chaperone-like protein, and five columns of dimeric PF0014.


Journal: Scientific Reports
Title: Supramolecular tholos-like architecture constituted by archaeal proteins without functional annotation
Author: Maho Yagi-Utsumi, Arunima Sikdar, Chihong Song, Jimin Park, Rintaro Inoue, Hiroki Watanabe, Raymond N. Burton-Smith, Toshiya Kozai, Tatsuya Suzuki, Atsuji Kodama, Kentaro Ishii, Hirokazu Yagi, Tadashi Satoh, Susumu Uchiyama, Takayuki Uchihashi, Keehyoung Joo, Jooyoung Lee, Masaaki Sugiyama, Kazuyoshi Murata, and Koichi Kato.
DOI: 10.1038/s41598-020-58371-2
Eurekalert! URL:https://eurekalert.org/pub_releases/2020-02/nion-agt020320.php


Koichi Kato
Exploratory Research Center on Life and Living Systems (ExCELLS)/
Institute for Molecular Science, Natural Institutes of Natural Sciences
TEL: +81-564-59-5225
E-mail: kkato[at]excells.orion.ac.jp (Please replace the “_at_” with @)

The dynamic assembly of antibodies for recruiting complements on an antigenic membrane.

Antibodies are key players in our immune system. These antibodies recognize antigens displayed on foreign cell membranes and thereby recruit attacking forces, called complements. This mechanism is detrimental to our own immune system at times when our own cells exhibit some molecules that resemble infectious bacterial ones. Guillain–Barré syndrome is a postinfectious autoimmune disorder which is characterized by antibodies misdirected against GM1, self-molecule found in our neuronal cells. Although molecular mimicry between GM1 and the infectious bacterial lipo-oligosaccharide has been proven, the detailed mechanisms linking autoantigen recognition and complement activation remain unexplored.

The collaborative groups, including researchers at Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS) of National Institutes of Natural Sciences and Graduate School of Pharmaceutical Sciences of Nagoya City University investigated this mechanism utilizing high-speed atomic force microscopy. They successfully visualized the dynamic process by which the autoantibodies that are bound to GM1 contained in membranes spontaneously assemble to form a hexameric ring structure on the membrane. They also revealed that the assembled antibodies serve as a landing place for the first charge commander C1q on the membrane, which is the initial step of complement-mediated cell lysis. The groups’ findings will provide deep insights into the molecular mechanisms behind Guillain–Barré syndrome and offer clues for controlling antibody assembly and consequent complement activation.

The antibodies assembled into a hexameric ring (white circle) transiently interact with the complement component C1q (white arrow) on the membrane containing GM1 as antigen.


Journal: International Journal of Molecular Sciences
Title: On-Membrane Dynamic Interplay between Anti-GM1 IgG Antibodies and Complement Component C1q
Author: Saeko Yanaka,Rina Yogo,Hiroki Watanabe,Yuki Taniguchi,Tadashi Satoh,Naoko Komura,Hiromune Ando,Hirokazu Yagi,Nobuhiro Yuki,Takayuki Uchihashi,and Koichi Kato
DOI: 10.3390/ijms21010147
Eurekalert! URL:https://www.eurekalert.org/pub_releases/2020-01/nion-aga010620.php
Article URL:: https://www.mdpi.com/1422-0067/21/1/147


Koichi Kato
Exploratory Research Center on Life and Living Systems (ExCELLS)/
Institute for Molecular Science, Natural Institutes of Natural Sciences
TEL: +81-564-59-5225
E-mail: kkato[at]excells.orion.ac.jp (Please replace the “_at_” with @)

Researchers at the Korea Advanced Institute of Science and Technology (KAIST), Ulsan National Institute of Science and Technology (UNIST), and The National Institutes of Natural Sciences (NINS), revealed the first molecular structure of the ATAD2 family of histone chaperones, a factor that is strongly correlated with the development of malignant tumors. This research was published online at Nature Communications on December 17, 2019.

Research Background

ATAD2 is a gene that is highly overexpressed in many human cancers such as prostate, lung, pancreatic, and colorectal cancer. Due to its clinical importance, many studies are investigating ATAD2 as a potential cancer drug target. Despite such attention to its therapeutic potential, the molecular structure of ATAD has been unknown.


Now, taking advantage of recent advances in cryo-electron microscopy (cryo-EM), researchers have solved the full structure of the yeast counterpart of ATAD2 to atomic resolution. The structures show that ATAD2 undergoes ATP energy-dependent changes shifting between a ring and spiral shape. These changes were also observed by utilizing high-speed atomic force microscopy (HS-AFM).
The authors also find that ATAD2 binds histones and helps deposit them onto DNA, a process that is likely important in the chromatin assembly and the regulation of gene expression. This is the first example where it has been shown that a histone chaperone protein uses ATP energy to deliver histones.

Figure 1. Cryo-EM and HS-AFM structures of the histone chaperone Abo1, and demonstration of histone loading activity onto DNA by single molecule fluorescence studies.

Social significance of this research

“This study highlights how the advance and combination of biophysical tools can be used to further our understanding of disease, the lead author Carol Cho says. “This structure should provide new leads to developing anti-cancer drugs targeted towards ATAD2” says professor Song, the corresponding author.


Cho et al. (2019) “Structural basis of nucleosome assembly by the Abo1 AAA+ ATPase histone chaperone” Nature Communications

Main Authors

Ji-Joon Song (KAIST)
Carol Cho (KAIST)
Ja Yil Lee (UNIST)
Juwon Jang (KAIST)
Takayuki Uchihashi (NINS)
Hiroki Watanabe (NINS)
Koichi Kato (NINS)

Contact Person

Koichi Kato
Exploratory Research Center on Life and Living Systems (ExCELLS)/
Institute for Molecular Science, Natural Institutes of Natural Sciences
TEL: +81-564-59-5225
E-mail: kkato[at]excells.orion.ac.jp (Please replace the “_at_” with @)

The research group including researchers of Exploratory Research Center on Life and Living Systems (ExCELLS), Institute for Molecular Science (IMS) in National Institutes of Natural Sciences and Hokkaido University determined the structures of “heme uptake system” that is used to uptake essential iron ions, and revealed the detail mechanism of the heme uptake in Corynebacteria such as Corynebacterium diphtheriae. The results of this study are expected to provide the basic knowledge for the development of new antibiotics against diphtheria. Their findings have been published in the online version of Chemical Communications (Royal Society of Chemistry).

Research Background

Iron ion is an essential trace element for all organisms. The organisms utilize the various molecular systems for uptake iron ions into their cells. Pathogenic bacteria have a molecular system for extracting heme from heme proteins in infected hosts, by which extracted heme molecules are transported into the bacterial cells so that they utilize heme proteins in infected hosts as the major iron source. Before this study, the heme uptake systems from several bacteria have been studied, but the detail studies of the heme uptake system from Corynebacteria including Corynebacterium diphtheriae has not progressed.


The heme uptake system from Corynebacteria consists of HtaA and HtaB, which are located on the cell surface and are responsible for heme binding and transport, and HmuT-HmuU-HmuV, which is responsible for heme transport into the cell. HtaA extracts heme from the host heme protein and transfers extracted heme to HtaB. HtaB transfers heme to HmuT. At last, heme was transported into the cell by HmuUV heme transporter. Our research group has previously reported the crystal structure of HmuT from Corynebacterium glutamicum (Muraki et al., Chem. Lett., 2016, Muraki et al., Int. J. Mol. Sci., 2016). In this study, we have succeeded to determine the crystal structures of HtaA and HtaB to find that HtaA and HtaB have a novel fold for heme-binding/transport proteins.
HtaA consists of an N-terminal domain and a C-terminal domain, in which the CR (conserved region) domain is adopted for heme-binding/transport. HtaB consists of a single domain. We determined the crystal structures of the N- and the C-terminal domains of HtaA and HtaB at 2.0 Å, 1.3 Å and 1.7 Å resolution, respectively. These structures are homologous to each other, and consist of eleven βa-strands, which formed antiparallel β-sheets and two short α-helices. A part of antiparallel β-sheets formed a barrel-like structure (Fig. 1).

Fig. 1. Crystal structures of (a) N-terminal domain of HtaA, (b) C-terminal domain of HtaA, and (c) HtaB.

We have determined the crystal structures of HtaA/HtaB in the holo-form. One heme molecule is bound in the heme pocket formed by the loop region at the end of β-sheet and α-helix (α1). The propionate group of heme forms hydrogen bonds with serine (Ser54 in HtaA) and tyrosine (Tyr201 in HtaA). The ring of heme was stabilized by a π-π interaction with phenylalanine (Phe200 in HtaA). Heme Iron had a five-coordinate structure with tyrosine (Tyr58 in HtaA) (Fig. 2). This tyrosine forms a hydrogen bond with histidine (His111 in HtaA). These amino acids involved in heme recognition are highly conserved between HtaA / HtaB CR domains.

Fig. 2. Interactions between heme and proteins in (a) N-terminal domain of HtaA, (b) C-terminal domain of HtaA, and (c) HtaB.

We have found that the hydrogen bond between the axial ligand Tyr and His plays an important role for the regulation of heme-binding affinity fo HtaA/HtaB. By replacing this His with Ala, we prepared an apo-protein, and determined the apo-form structure of the C-terminal domain of HtaA. The apo form of HtaA forms a domain swapped dimer (Fig. 3). In this structure, α-helix (α1) in one protomer is located close to the heme pocket of the other protomer. This domain-swapped dimer seems to mimic the reaction intermediate of the heme transfer reaction in HtaA/HtaB.

Fig. 3. Crystal structure of the apo-form of HtaA. Different protomers are shown in different colors.

Social significance of this research

In this study, we have determined the crystal structures of the heme uptake system from Corynebacterium glutamicum, which is a non-pathogenic bacterium, but the same heme uptake system is also used by Corynebacterium diphtheriae. The results of this research may contribute to the development of new antibiotics that inhibit the growth of Corynebacterium diphtheriae by blocking the uptake of iron ions (heme) essential for growth.

Information of the paper

Authors: Norifumi Muraki, Chihiro Kitatsuji, Yasunori Okamoto, Takeshi Uchida, Koichiro Ishimori and Shigetoshi Aono
Journal Name: Chemical Communications
Journal Title:“Structural basis for heme transfer reaction in heme uptake machinery from Corynebacteria”
DOI: 10.1039 / C9CC07369H

Financial Supports

Grant-in-Aid for Scientific Research
Scientific Research on Innovative Areas “Integrated Bio-metal Science”

17H03093, 19H05762


Contact Person

Shigetoshi Aono
Exploratory Research Center on Life and Living Systems (ExCELLS)/
Institute for Molecular Science, Natural Institutes of Natural Sciences
TEL: +81-564-59-5575 / FAX: +81-564-59-5576
E-mail: aono_at_ims.ac.jp (Please replace the “_at_” with @)

The ExCELLS Retreat for Young Scientists (FY2019) will be held next February.
Please check here for the details.