Kitamura Akira

Faculty of Advanced Life Science Functional Life Sciences Functional Cell ScienceAssociate Professor
Last Updated :2026/01/07

■Researcher basic information

Degree

  • Bachelor of Engineering, Kyoto University, Mar. 2003
  • M.Sci., Kyoto University, Mar. 2005
  • Ph. D., Kyoto University, Mar. 2008

Researchmap personal page

Research Keyword

  • TRAST monitoring
  • Chaperone RNA
  • proteostasis
  • FRAP
  • FRET
  • Fluorescence correlation spectroscopy
  • Amyotrophic lateral sclerosis
  • Proteostasis
  • Fluorescence imaging
  • Neurodegenerative disease
  • Molecular chaperone
  • Protein folding
  • Protein aggregation

Research Field

  • Life sciences, Functional biochemistry
  • Life sciences, Biophysics
  • Life sciences, Molecular biology
  • Life sciences, Cell biology

Educational Organization

■Career

Career

  • Apr. 2025 - Present
    Program for Forming Japan’s Peak Research Universities (J-PEAKS) "Photon Frontier", PI, Japan
  • Sep. 2024 - Present
    Hokkaido University, Faculty of Advanced Life Science, Associate Professor (PI), Japan
  • Aug. 2023 - Present
    RIKEN, Center for Biosystems Dynamics Research, Visiting Researcher, Japan
  • Oct. 2022 - Present
    PRIME, AMED
  • Oct. 2019 - Present
    Hokkaido University, Research and Education Center for Brain Science, 基幹教員, Japan
  • Aug. 2023 - Aug. 2024
    Hokkaido University, Faculty of Advanced Life Science, Senior Lecturer (Tenure and PI), Japan
  • Apr. 2019 - Jul. 2023
    Hokkaido University, Faculty of Advanced Life Science, Senior Lecturer (Tenure-track)
  • 2017 - Mar. 2020
    JSPS, Scientist for Joint International Research
  • Apr. 2010 - Mar. 2019
    Hokkaido University, Faculty of Advanced Life Science, Assistant Professor, Japan
  • Aug. 2018 - Nov. 2018
    Northwestern University, Prof. Richard Morimoto Laboratory, Visiting Scholar
  • May 2018 - Jun. 2018
    KTH Royal Institute of Technology, Department of Applied Physics, JSPS Scientist for Joint International Research
  • Oct. 2017 - Dec. 2017
    KTH Royal Institute for Technology, Dept. Applied Physics, JSPS Scientist for Joint International Research
  • Apr. 2008 - Mar. 2010
    Faculty of Advanced Life Science, Hokkaido University, JSPS Research fellow PD
  • Apr. 2006 - Mar. 2008
    Kyoto University, Institute for Frontier Medical Sciences, JSPS Research fellow DC2

Educational Background

  • 2008, Kyoto University, Graduate School of Science, Division of Biological Sciences
  • 2008, Kyoto University, Graduate School, Division of Natural Science
  • 2005, Kyoto University, Graduate School of Science, Division of Biological Sciences, Japan
  • 2003, Kyoto University, Faculty of Engineering, School of Industrial Chemistry, Japan
  • 2003, Kyoto University, Faculty of Engineering

Committee Memberships

  • Feb. 2024 - Present
    Frontiers in Biophysics, Review editor, Others
  • Jan. 2024 - Present
    Biophysics and Physicobiology (BPPB), Editorial Board Members, Society
  • 2023 - Present
    Spectroscopy Journal, Editorial Board Members
  • Jan. 2018 - Present
    日本生物物理学会, 分野別専門委員(神経変性疾患分野), Society
  • 2009 - Present
    光イメージング若手の会「光塾」, 総括塾員, Society
  • 2023 - 2023
    第32回 日本バイオイメージング学会学術集会, 実行委員, Society
  • 2022 - 2022
    日本生物物理学会, 第60回年会 実行委員, Society
  • Apr. 2012 - Mar. 2015
    日本生物物理学会, 分野別専門委員(タンパク質の品質管理), Society
  • 2014 - 2014
    日本生物物理学会第52回年会, 実行委員, Society

■Research activity information

Awards

  • Sep. 2022, The biophysical Society of Japan, 2022 Biophysics and Physicobiology (BPPB) Awards               
    Akira Kitamura

Papers

  • Advances in Conventional and Extended Fluorescence Correlation Spectroscopy for the Analysis of Biological Clusters and Aggregates
    Akira Kitamura
    Spectroscopy Journal, 3, 4, 31, 05 Nov. 2025, [Peer-reviewed], [Invited], [Lead author, Last author, Corresponding author]
    English, Scientific journal, 46048265
  • Optimizing Automated Detection for Cytoplasmic TDP25 Aggregates in Fluorescence Imaging
    Sumire Sogawa, Kotetsu Sasaki, Akira Kitamura
    Spectroscopy Journal, 3, 2, 18, 19 May 2025, [Peer-reviewed], [Last author, Corresponding author]
    English, Scientific journal, 46048265
  • Enhancement of Sensitivity in Aggregation-Based Whole-Cell Arsenite Sensor Utilizing Arsenic Metabolism Regulation
    Shiryu Abe, Rina Ayuba, Kyohei Ouchi, Yu-ki Tanaka, Ai Fujimoto, Akira Kitamura, Yasumitsu Ogra, Yuki Kimura, Daisuke Umeno, Shigeko Kawai-Noma
    ACS Omega, 15 Apr. 2025, [Peer-reviewed]
    English, Scientific journal
  • Malabaricone C isolated from edible plants as a potential inhibitor of SARS-CoV-2 infection
    Mutmainah, Yuta Murai, Ai Fujimoto, Rintaro Kawamura, Akira Kitamura, Sajeer Koolath, Seigo Usuki, Michihito Sasaki, Yasuko Orba, Yasuyuki Igarashi, Hirofumi Sawa, Akihiko Sato, Kenji Monde
    Scientific Reports, 15, 1, Springer Science and Business Media LLC, 12 Mar. 2025, [Peer-reviewed]
    English, Scientific journal
  • Short Repeat Ribonucleic Acid Reduces Cytotoxicity by Preventing the Aggregation of TDP-43 and Its 25 KDa Carboxy-Terminal Fragment
    Ai Fujimoto, Masataka Kinjo, Akira Kitamura
    JACS Au, 28 Oct. 2024, [Peer-reviewed], [Last author, Corresponding author]
    English, Scientific journal, 46048265
  • Interaction of Receptor-Binding Domain of the SARS-CoV-2 Omicron Variant with hACE2 and Actin
    Ai Fujimoto, Haruki Kawai, Rintaro Kawamura, Akira Kitamura
    Cells, 13, 16, 1318, 07 Aug. 2024, [Peer-reviewed], [Last author, Corresponding author]
    English, Scientific journal, 46048265
  • Hetero-oligomerization of TDP-43 carboxy-terminal fragments with cellular proteins contributes to proteotoxicity
    Akira Kitamura, Ai Fujimoto, Rei Kawashima, Yidan Lyu, Kotetsu Sasaki, Yuta Hamada, Kanami Moriya, Ayumi Kurata, Kazuho Takahashi, Reneé Brielmann, Laura C. Bott, Richard I. Morimoto, Masataka Kinjo
    Communications Biology, 7, 1, 743, Springer Science and Business Media LLC, 20 Jun. 2024, [Peer-reviewed], [Lead author, Corresponding author]
    English, Scientific journal, Abstract

    Carboxy terminal fragments (CTFs) of TDP-43 contain an intrinsically disordered region (IDR) and form cytoplasmic condensates containing amyloid fibrils. Such condensates are toxic and associated with pathogenicity in amyotrophic lateral sclerosis. However, the molecular details of how the domain of TDP-43 CTFs leads to condensation and cytotoxicity remain elusive. Here, we show that truncated RNA/DNA-recognition motif (RRM) at the N-terminus of TDP-43 CTFs leads to the structural transition of the IDR, whereas the IDR itself of TDP-43 CTFs is difficult to assemble even if they are proximate intermolecularly. Hetero-oligomers of TDP-43 CTFs that have recruited other proteins are more toxic than homo-oligomers, implicating loss-of-function of the endogenous proteins by such oligomers is associated with cytotoxicity. Furthermore, such toxicity of TDP-43 CTFs was cell-nonautonomously affected in the nematodes. Therefore, misfolding and oligomeric characteristics of the truncated RRM at the N-terminus of TDP-43 CTFs define their condensation properties and toxicity., 46048265
  • Stress Granule Dysfunction via Chromophore-Associated Light Inactivation
    Takumi Koizumi, Ai Fujimoto, Haruka Kawaguchi, Tsumugi Kurosaki, Akira Kitamura
    ACS Omega, 14 May 2024, [Peer-reviewed], [Last author, Corresponding author]
    English, Scientific journal, 40045923
  • Axonal transport of Frizzled5 by Alcadein α-containing vesicles is associated with kinesin-1.
    Yuzuha Shiraki, Monet Mitsuma, Ritsuko Takada, Saori Hata, Akira Kitamura, Shinji Takada, Masataka Kinjo, Hidenori Taru, Ulrike C Müller, Tohru Yamamoto, Yuriko Sobu, Toshiharu Suzuki
    Molecular biology of the cell, 34, 11, ar110, 01 Oct. 2023, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Alcadein α (Alcα) and amyloid-β protein precursor (APP) are cargo receptors that associate vesicles with kinesin-1. These vesicles, which contain either Alcα or APP, transport various proteins/cargo molecules into axon nerve terminals. Here, we analyzed immune-isolated Alcα- and APP-containing vesicles of adult mouse brains with LC-MS/MS and identified proteins present in vesicles that contained either Alcα or APP. Among these proteins, Frizzled-5 (Fzd5), a Wnt receptor, was detected mainly in Alcα vesicles. Although colocalization ratios of Fzd5 with Alcα are low in the neurites of differentiating neurons by a low expression of Fzd5 in embryonic brains, the suppression of Alcα expression decreased the localization of Fzd5 in neurites of primary cultured neurons. Furthermore, Fzd5-EGFP expressed in primary cultured neurons was preferentially transported in axons with the transport velocities of Alcα vesicles. In synaptosomal fractions of adult-mice brains that express higher levels of Fzd5, the amount of Fzd5 and the phosphorylation level of calcium/calmodulin-dependent protein kinase-II were reduced in the Alcα-deficient mice. These results suggest that reduced transport of Fzd5 by Alcα-containing vesicles associated with kinesin-1 in axon terminals may impair the response to Wnt ligands in the noncanonical Ca2+-dependent signal transduction pathway at nerve terminals of mature neurons.
  • Increased intracellular crowding during hyperosmotic stress.
    Akira Kitamura, Sho Oasa, Haruka Kawaguchi, Misato Osaka, Vladana Vukojević, Masataka Kinjo
    Scientific reports, 13, 1, 11834, 11834, 22 Jul. 2023, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
    English, Scientific journal, Hyperosmotic stress activates in live cells numerous processes and also promotes intracellular protein/RNA aggregation and phase separation. However, the time course and the extent of these changes remain largely uncharacterized. To investigate dynamic changes in intracellular macromolecular crowding (MMC) induced by hyperosmotic stress in live cells, we used fluorescence lifetime imaging microscopy and fluorescence correlation spectroscopy (FCS) to quantify changes in the local environment by measuring the fluorescence lifetime and the diffusion of the monomeric enhanced green fluorescent protein (eGFP), respectively. Real-time monitoring of eGFP fluorescence lifetime showed that a faster response to environmental changes due to MMC is observed than when measuring the acceptor/donor emission ratio using the MMC-sensitive Förster resonance energy transfer sensor (GimRET). This suggests that eGFP molecular electronic states and/or collision frequency are affected by changes in the immediate surroundings due to MMC without requiring conformational changes as is the case for the GimRET sensor. Furthermore, eGFP diffusion assessed by FCS indicated higher intracellular viscosity due to increased MMC during hyperosmotic stress. Our findings reveal that changes in eGFP fluorescence lifetime and diffusion are early indicators of elevated intracellular MMC. Our approach can therefore be used to reveal in live cells short-lived transient states through which MMC builds over time, which could not be observed when measuring changes in other physical properties that occur at slower time scales., 40045923
  • Light-Induced Condensates Show Accumulation-Prone and Less Dynamic Properties in the Nucleus Compared to the Cytoplasm
    Yuta Hamada, Akira Kitamura
    Spectroscopy Journal, 10 Jul. 2023, [Peer-reviewed], [Last author, Corresponding author]
    English, Scientific journal, 40045923
  • Trans-cis isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells
    Akira Kitamura, Johan Tornmalm, Baris Demirbay, Joachim Piguet, Masataka Kinjo, Jerker Widengren
    Nucleic Acids Research, 21 Mar. 2023, [Peer-reviewed], [Lead author]
    English, Scientific journal, 40045923
  • Intracellular Conformation of Amyotrophic Lateral Sclerosis-Causative TDP-43
    Akira Kitamura, Sachiko Yuno, Rintaro Kawamura, Masataka Kinjo
    International Journal of Molecular Sciences, 24, 6, 5513, 14 Mar. 2023, [Peer-reviewed], [Lead author, Corresponding author]
    English, Scientific journal, 40045923
  • Physico- and chemical biology using nanomanipulation and micromanipulation technologies
    Akira Kitamura, Ryo Iizuka
    Biophysics and Physicobiology, Biophysical Society of Japan, 2022, [Peer-reviewed], [Invited], [Lead author, Corresponding author]
    Symposium, 40045923
  • Interaction between Spike Protein of SARS-CoV-2 and Human Virus Receptor ACE2 Using Two-Color Fluorescence Cross-Correlation Spectroscopy
    Ai Fujimoto, Yidan Lyu, Masataka Kinjo, Akira Kitamura
    Applied Sciences, 11, 22, 10697, 10697, MDPI AG, 12 Nov. 2021, [Peer-reviewed], [Invited], [Last author, Corresponding author]
    English, Scientific journal, 33376192
  • Conformational stabilization of optineurin by the dynamic interaction of linear polyubiquitin
    Akira Kitamura, Rika Numazawa, Masataka Kinjo
    Biochemical and Biophysical Research Communications, 559, 203, 209, Elsevier BV, Jun. 2021, [Peer-reviewed], [Lead author, Corresponding author]
    English, Scientific journal
  • Pinhole Closure Improves Spatial Resolution in Confocal Scanning Microscopy
    Akira Kitamura
    Methods in Molecular Biology, 385, 389, Springer US, May 2021, [Invited], [Lead author, Last author, Corresponding author]
    English, In book
  • Detection of Protein Aggregation using Fluorescence Correlation Spectroscopy
    Akira Kitamura, Ai Fujimoto, Masataka Kinjo
    Journal of Visualized Experiments, 170, e62576, MyJove Corporation, 25 Apr. 2021, [Peer-reviewed], [Invited], [Lead author, Corresponding author], [International Magazine]
    English, Scientific journal, Protein aggregation is a hallmark of neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and so on. To detect and analyze soluble or diffuse protein oligomers or aggregates, fluorescence correlation spectroscopy (FCS), which can detect the diffusion speed and brightness of a single particle with a single molecule sensitivity, has been used. However, the proper procedure and know-how for protein aggregation detection have not been widely shared. Here, we show a standard procedure of FCS measurement for diffusion properties of aggregation-prone proteins in cell lysate and live cells: ALS-associated 25 kDa carboxyl-terminal fragment of TAR DNA/RNA-binding protein 43 kDa (TDP25) and superoxide dismutase 1 (SOD1). The representative results show that a part of aggregates of green fluorescent protein (GFP)-tagged TDP25 was slightly included in the soluble fraction of murine neuroblastoma Neuro2a cell lysate. Moreover, GFP-tagged SOD1 carrying ALS-associated mutation shows a slower diffusion in live cells. Accordingly, we here introduce the procedure to detect the protein aggregation via its diffusion property using FCS.
  • Molecular basis of functional exchangeability between ezrin and other actin-membrane associated proteins during cytokinesis.
    Guang Yang, Shota Hiruma, Akira Kitamura, Masataka Kinjo, Mithilesh Mishra, Ryota Uehara
    Experimental cell research, 403, 2, 112600, 112600, 20 Apr. 2021, [Peer-reviewed], [International Magazine]
    English, Scientific journal, The mechanism that mediates the interaction between the contractile ring and the plasma membrane during cytokinesis remains elusive. We previously found that ERM (Ezrin/Radixin/Moesin) proteins, which usually mediate cellular pole contraction, become over-accumulated at the cell equator and support furrow ingression upon the loss of other actin-membrane associated proteins, anillin and supervillin. In this study, we addressed the molecular basis of the exchangeability between ezrin and other actin-membrane associated proteins in mediating cortical contraction during cytokinesis. We found that depletion of anillin and supervillin caused over-accumulation of the membrane-associated FERM domain and actin-binding C-terminal domain (C-term) of ezrin at the cleavage furrow, respectively. This finding suggests that ezrin differentially shares its binding sites with these proteins on the actin cytoskeleton or inner membrane surface. Using chimeric mutants, we found that ezrin C-term, but not the FERM domain, can substitute for the corresponding anillin domains in cytokinesis and cell proliferation. On the other hand, either the membrane-associated or the actin/myosin-binding domains of anillin could not substitute for the corresponding ezrin domains in controlling cortical blebbing at the cell poles. Our results highlight specific designs of actin- or membrane-associated moieties of different actin-membrane associated proteins with limited exchangeability, which enables them to support diverse cortical activities on the shared actin-membrane interface during cytokinesis.
  • Analysis of the triplet-state kinetics of a photosensitizer for photoimmunotherapy by fluorescence correlation spectroscopy
    Hideo Takakura, Yuto Goto, Akira Kitamura, Toshitada Yoshihara, Seiji Tobita, Masataka Kinjo, Mikako Ogawa
    Journal of Photochemistry and Photobiology A: Chemistry, 408, 113094, 113094, Elsevier BV, Mar. 2021, [Peer-reviewed]
    English, Scientific journal
  • Membrane Surface Modulates Slow Diffusion in Small Crowded Droplets
    Kanae Harusawa, Chiho Watanabe, Yuta Kobori, Kazuho Tomita, Akira Kitamura, Masataka Kinjo, Miho Yanagisawa
    Langmuir, 37, 1, 437, 444, American Chemical Society (ACS), 12 Jan. 2021, [Peer-reviewed]
    English, Scientific journal
  • Spatial Image Correlation Spectroscopy (ICS): A Technique for Average Size Determination of Subcellular Accumulated Structures from Fluorescence Microscopic Images
    Akira Kitamura, Masakata Kinjo
    BIO-PROTOCOL, 10, 10, Bio-Protocol, LLC, 2020, [Peer-reviewed], [Invited], [Lead author, Corresponding author]
    English, Scientific journal
  • The AAA+ ATPase/ubiquitin ligase mysterin stabilizes cytoplasmic lipid droplets.
    Munechika Sugihara, Daisuke Morito, Shiori Ainuki, Yoshinobu Hirano, Kazutoyo Ogino, Akira Kitamura, Hiromi Hirata, Kazuhiro Nagata
    The Journal of cell biology, 218, 3, 949, 960, 04 Mar. 2019, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Encapsulation of biomacromolecules by soaking and co-crystallization into porous protein crystals of hemocyanin.
    Tsubasa Hashimoto, Yuxin Ye, Asuka Matsuno, Yuki Ohnishi, Akira Kitamura, Masataka Kinjo, SatoshiAbe, Takafumi Ueno, MinYao, Tomohisa Ogawa, Takashi Matsui, Yoshikazu Tanaka
    Biochemical and Biophysical Research Communications, 509, 2, 577, 584, Feb. 2019, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Encapsulation of guest molecules into the hollow spaces of crystals has been applied for a variety of purposes such as structure determination, separation, and catalysis of the guest. Although host-guest studies have been developed mainly in crystals of small molecules, those of biomacromolecules have recently been applied. In those reports, a huge hollow space in the protein crystal is commonly used for encapsulation of the guest. Our previous study revealed that cylindrical hemocyanins stack inside the crystal as a linear hollow structure. The diameter of the linear hollow is approximately 110 Å, which is large enough for most proteins to pass through. In the present study, we evaluated the potential of hemocyanin crystals as a host to encapsulate biomacromolecules. Confocal microscopy revealed that hemocyanin crystals encapsulate proteins of molecular mass up to 250 kDa, i.e., 27 kDa green fluorescence protein, 105 kDa allophycocyanin, 220 kDa C-phycocyanin, and 250 kDa phycoerythrin, and DNAs up to 200-bp long, whereas 440 kDa ferritin not. Further analysis revealed that hemocyanin crystals prefer a negatively charged guest rather than a positive charge to encapsulate. Moreover, a photobleaching experiment showed that the guest does not move once entrapped. This knowledge of the host-guest study using the hollow hemocyanin crystal should be of significance for further application of hollow proteinaceous crystals as a host.
  • Characterization of Intracellular Crowding Environments with Topology-Based DNA Quadruplex Sensors.
    Takahashi S, Yamamoto J, Kitamura A, Kinjo M, Sugimoto N
    Analytical chemistry, 91, 4, 2586, 2590, Feb. 2019, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Molecular crowding creates a unique environment in cells and imposes physical constraints such as the excluded volume effect, water activity, and dielectric constant that can affect the structure and function of biomolecules. It is therefore important to develop a method for quantifying the effects of molecular crowding in cells. In this study, we developed a Förster resonance energy transfer (FRET) probe based on a guanine-quadruplex (G4) DNA motif that shows distinct FRET signals in response to crowding conditions in the presence of salt and poly(ethylene glycol). FRET efficiencies varied in different solutions, reflecting the dependence of G4 stability and topology on salt concentration and water activity. In living cells, FRET signals in the nucleus were higher than those in the cytosol; the signals in membraneless nuclear compartments (i.e., nucleolus) were especially high, suggesting that a decrease in water activity is important for the crowding effect in the nucleus. Thus, the use of DNA sensors with variable structures can elucidate the local effects of molecular crowding in cells.
  • Determination of cytoplasmic optineurin foci sizes using image correlation spectroscopy
    Akira Kitamura, Hiroki Shimizu, Masataka Kinjo
    The Journal of Biochemistry, Oxford University Press ({OUP}), 01 Sep. 2018, [Peer-reviewed]
    English, Scientific journal
  • The cytoplasmic region of the amyloid β-protein precursor (APP) is necessary and sufficient for the enhanced fast velocity of APP transport by kinesin-1.
    Maoko Tsukamoto, Kyoko Chiba, Yuriko Sobu, Yuzuha Shiraki, Yuka Okumura, Saori Hata, Akira Kitamura, Tadashi Nakaya, Seiichi Uchida, Masataka Kinjo, Hidenori Taru, Toshiharu Suzuki
    FEBS letters, 592, 16, 2716, 2724, Aug. 2018, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Amyloid β-protein precursor (APP) is transported mainly by kinesin-1 and at a higher velocity than other kinesin-1 cargos, such as Alcadein α (Alcα); this is denoted by the enhanced fast velocity (EFV). Interaction of the APP cytoplasmic region with kinesin-1, which is essential for EFV transport, is mediated by JNK-interacting protein 1 (JIP1). To determine the roles of interactions between the APP luminal region and cargo components, we monitored transport of chimeric cargo receptors, Alcα (luminal)-APP (cytoplasmic) and APP (luminal)-Alcα (cytoplasmic). Alcα-APP is transported at the EFV, whereas APP-Alcα is transported at the same velocity as wild-type Alcα. Thus, the cytoplasmic region of APP is necessary and sufficient for the EFV of APP transport by kinesin-1.
  • Analysis of the substrate recognition state of TDP-43 to single-stranded DNA using fluorescence correlation spectroscopy.
    Akira Kitamura, Ai Shibasaki, Kayo Takeda, Ryoji Suno, Masataka Kinjo
    Biochemistry and biophysics reports, 14, 58, 63, Jul. 2018, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Normal function and abnormal aggregation of transactivation response (TAR) DNA/RNA-binding protein 43 kDa (TDP-43) are directly associated with the lethal genetic diseases: cystic fibrosis, amyotrophic lateral sclerosis (ALS), and frontotemporal lobar degeneration (FTLD). The binding of TDP-43 to single-stranded DNA (ssDNA) or RNA is involved in transcriptional repression, regulation of RNA splicing, and RNA stabilization. Equilibrium dissociation constants (Kd) of TDP-43 and ssDNA or RNA have been determined using various methods; however, methods that can measure Kd with high sensitivity in a short time using a small amount of TDP-43 in solution would be advantageous. Here, in order to determine the Kd of TDP-43 and fluorescence-labeled ssDNA as well as the binding stoichiometry, we use fluorescence correlation spectroscopy (FCS), which detects the slowed diffusion of molecular interactions in solution with single-molecule sensitivity, in addition to electrophoretic mobility shift assay (EMSA). Using tandem affinity chromatography of TDP-43 dually tagged with glutathione-S-transferase and poly-histidine tags, highly purified protein was obtained. FCS successfully detected specific interaction between purified TDP-43 and TG ssDNA repeats, with a Kd in the nanomolar range. The Kd of the TDP-43 mutant was not different from the wild type, although mutant oligomers, which did not bind ssDNA, were observed. Analysis of the fluorescence brightness per dimerized TDP-43/ssDNA complex was used to evaluate their binding stoichiometry. The results suggest that an assay combining FCS and EMSA can precisely analyze ssDNA recognition mechanisms, and that FCS may be applied for the rapid and quantitative determination of the interaction strength between TDP-43 and ssDNA or RNA. These methods will aid in the elucidation of the substrate recognition mechanism of ALS- and FTLD-associated variants of TDP-43.
  • State-of-the-art fluorescence fluctuation-based spectroscopic techniques for the study of protein aggregation
    Akira Kitamura, Masataka Kinjo
    International Journal of Molecular Sciences, 19, 4, 964, MDPI AG, 01 Apr. 2018, [Peer-reviewed], [Invited]
    English, Scientific journal
  • Detection of substrate binding of a collagen-specific molecular chaperone HSP47 in solution using fluorescence correlation spectroscopy
    Akira Kitamura, Yoshihito Ishida, Hiroshi Kubota, Chan-Gi Pack, Takayuki Homma, Shinya Ito, Kazutaka Araki, Masataka Kinjo, Kazuhiro Nagata
    Biochemical and Biophysical Research Communications, 497, 1, 279, 284, Elsevier B.V., 26 Feb. 2018, [Peer-reviewed]
    English, Scientific journal
  • Physicochemical properties of the mammalian molecular chaperone HSP60
    Ryuichi Ishida, Tomoya Okamoto, Fumihiro Motojima, Hiroshi Kubota, Hiroki Takahashi, Masako Tanabe, Toshihiko Oka, Akira Kitamura, Masataka Kinjo, Masasuke Yoshida, Michiro Otaka, Ewa Grave, Hideaki Itoh
    International Journal of Molecular Sciences, 19, 2, 489, MDPI AG, 06 Feb. 2018, [Peer-reviewed]
    English, Scientific journal
  • TDP-43 depletion: mechanism of neuronal cell death in ALS.
    Akira Kitamura
    Future Neurology, 13, 3, 2018, [Peer-reviewed], [Invited]
    English, Scientific journal
  • Molecular chaperone HSP70 prevents formation of inclusion bodies of the 25-kDa C-terminal fragment of TDP-43 by preventing aggregate accumulation.
    Akira Kitamura, Nodoka Iwasaki, Masataka Kinjo
    Cell Stress and Chaperones, 2018, [Peer-reviewed]
    English, Scientific journal
  • Determination of diffusion coefficients in live cells using fluorescence recovery after photobleaching with wide-field fluorescence microscopy
    Akira Kitamura, Masataka Kinjo
    Biophysics and Physicobiology, 15, 1, 7, 2018, [Peer-reviewed]
    English, Scientific journal
  • U6 snRNA expression prevents toxicity in TDP-43-knockdown cells
    Masao Yahara, Akira Kitamura, Masataka Kinjo
    PLOS ONE, 12, 11, e0187813, Nov. 2017, [Peer-reviewed]
    English, Scientific journal
  • Different aggregation states of a nuclear localization signal-tagged 25-kDa C-terminal fragment of TAR RNA/DNA-binding protein 43kDa
    Akira Kitamura, Sachiko Yuno, Hideki Muto, Masataka Kinjo
    GENES TO CELLS, 22, 6, 521, 534, Jun. 2017, [Peer-reviewed]
    English, Scientific journal
  • Development of new fusion proteins for visualizing amyloid-beta oligomers in vivo
    Tomoyo Ochiishi, Motomichi Doi, Kazuhiko Yamasaki, Keiko Hirose, Akira Kitamura, Takao Urabe, Nobutaka Hattori, Masataka Kinjo, Tatsuhiko Ebihara, Hideki Shimura
    SCIENTIFIC REPORTS, 6, 22712, Mar. 2016, [Peer-reviewed]
    English, Scientific journal
  • Dependence of fluorescent protein brightness on protein concentration in solution and enhancement of it
    Takamitsu J. Morikawa, Hideaki Fujita, Akira Kitamura, Takashi Horio, Johtaro Yamamoto, Masataka Kinjo, Akira Sasaki, Hiroaki Machiyama, Keiko Yoshizawa, Taro Ichimura, Katsumi Imada, Takeharu Nagai, Tomonobu M. Watanabe
    SCIENTIFIC REPORTS, 6, 22342, Mar. 2016, [Peer-reviewed]
    English, Scientific journal
  • In vivo fluorescence correlation spectroscopy analyses of FMBP-1, a silkworm transcription factor
    Motosuke Tsutsumi, Hideki Muto, Shohei Myoba, Mai Kimoto, Akira Kitamura, Masakatsu Kamiya, Takashi Kikukawa, Shigeharu Takiya, Makoto Demura, Keiichi Kawano, Masataka Kinjo, Tomoyasu Aizawa
    FEBS OPEN BIO, 6, 2, 106, 125, Feb. 2016, [Peer-reviewed]
    English, Scientific journal
  • Interaction of RNA with a C-terminal fragment of the amyotrophic lateral sclerosis-associated TDP43 reduces cytotoxicity
    Akira Kitamura, Yusaku Nakayama, Ai Shibasaki, Ayami Taki, Sachiko Yuno, Kayo Takeda, Masao Yahara, Naoki Tanabe, Masataka Kinjo
    SCIENTIFIC REPORTS, 6, 19230, Jan. 2016, [Peer-reviewed]
    English, Scientific journal
  • Efficient and dynamic nuclear localization of green fluorescent protein via RNA binding
    Akira Kitamura, Yusaku Nakayama, Masataka Kinjo
    BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 463, 3, 401, 406, Jul. 2015, [Peer-reviewed]
    English, Scientific journal
  • Conformational Analysis of Misfolded Protein Aggregation by FRET and Live-Cell Imaging Techniques
    Akira Kitamura, Kazuhiro Nagata, Masataka Kinjo
    INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 16, 3, 6076, 6092, Mar. 2015, [Peer-reviewed], [Invited]
    English, Scientific journal
  • 蛍光相関分光法とFRETを用いた細胞内タンパク質品質管理機構の解析
    北村 朗
    バイオイメージング, 23, 1, 12, 17, Jun. 2014, [Peer-reviewed], [Invited], [Lead author, Last author, Corresponding author]
    Japanese, Scientific journal
  • Moyamoya disease-associated protein mysterin/RNF213 is a novel AAA plus ATPase, which dynamically changes its oligomeric state
    Daisuke Morito, Kouki Nishikawa, Jun Hoseki, Akira Kitamura, Yuri Kotani, Kazumi Kiso, Masataka Kinjo, Yoshinori Fujiyoshi, Kazuhiro Nagata
    SCIENTIFIC REPORTS, 4, 4442, Mar. 2014, [Peer-reviewed]
    English, Scientific journal
  • Dysregulation of the proteasome increases the toxicity of ALS-linked mutant SOD1
    Akira Kitamura, Noriko Inada, Hiroshi Kubota, Gen Matsumoto, Masataka Kinjo, Richard I. Morimoto, Kazuhiro Nagata
    GENES TO CELLS, 19, 3, 209, 224, Mar. 2014, [Peer-reviewed]
    English, Scientific journal
  • Prefoldin prevents aggregation of alpha-synuclein
    Mariko Takano, Erika Tashiro, Akira Kitamura, Hiroshi Maita, Sanae M. M. Iguchi-Ariga, Masataka Kinjo, Hiroyoshi Ariga
    BRAIN RESEARCH, 1542, 186, 194, Jan. 2014, [Peer-reviewed]
    English, Scientific journal
  • The interaction of Hsp104 with yeast prion Sup35 as analyzed by fluorescence cross-correlation spectroscopy
    Shohei Ohta, Shigeko Kawai-Noma, Akira Kitamura, Chan-Gi Pack, Masataka Kinjo, Hideki Taguchi
    BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 442, 1-2, 28, 32, Dec. 2013, [Peer-reviewed]
    English, Scientific journal
  • Prefoldin Protects Neuronal Cells from Polyglutamine Toxicity by Preventing Aggregation Formation
    Erika Tashiro, Tamotsu Zako, Hideki Muto, Yoshinori Itoo, Karin Soergjerd, Naofumi Terada, Akira Abe, Makoto Miyazawa, Akira Kitamura, Hirotake Kitaura, Hiroshi Kubota, Mizuo Maeda, Takashi Momoi, Sanae M. M. Iguchi-Ariga, Masataka Kinjo, Hiroyoshi Ariga
    JOURNAL OF BIOLOGICAL CHEMISTRY, 288, 27, 19958, 19972, Jul. 2013, [Peer-reviewed]
    English, Scientific journal
  • Nonmuscle myosin II folds into a 10S form via two portions of tail for dynamic subcellular localization
    Takayuki Kiboku, Tsuyoshi Katoh, Akio Nakamura, Akira Kitamura, Masataka Kinjo, Yota Murakami, Masayuki Takahashi
    GENES TO CELLS, 18, 2, 90, 109, Feb. 2013, [Peer-reviewed]
    English, Scientific journal
  • Direct Association of Unfolded Proteins with Mammalian ER Stress Sensor, IRE1 beta
    Daisuke Oikawa, Akira Kitamura, Masataka Kinjo, Takao Iwawaki
    PLOS ONE, 7, 12, e51290, Dec. 2012, [Peer-reviewed]
    English, Scientific journal
  • Atg9 vesicles are an important membrane source during early steps of autophagosome formation
    Hayashi Yamamoto, Soichiro Kakuta, Tomonobu M. Watanabe, Akira Kitamura, Takayuki Sekito, Chika Kondo-Kakuta, Rie Ichikawa, Masataka Kinjo, Yoshinori Ohsumi
    JOURNAL OF CELL BIOLOGY, 198, 2, 219, 233, Jul. 2012, [Peer-reviewed]
    English, Scientific journal
  • Analyzing the aggregation of polyglutamine-expansion proteins and its modulation by molecular chaperones
    Hiroshi Kubota, Akira Kitamura, Kazuhiro Nagata
    METHODS, 53, 3, 267, 274, Mar. 2011, [Peer-reviewed]
    English
  • Amyloid oligomers: dynamics and toxicity in the cytosol and nucleus
    Akira Kitamura, Hiroshi Kubota
    FEBS JOURNAL, 277, 6, 1369, 1379, Mar. 2010, [Peer-reviewed]
    English
  • Molecular chaperone prefoldin inhibits polyglutamine aggregation and cytotoxicity
    Tashiro Erika, Muto Hideki, Zako Tamotsu, Miyazawa Makoto, Kitaura Hirotake, Kitamura Akira, Kubota Hiroshi, Maeda Mizuo, Kinjo Masataka, Ariga Hiroyoshi
    NEUROSCIENCE RESEARCH, 68, E310, 2010, [Peer-reviewed]
  • Autophagic Elimination of Misfolded Procollagen Aggregates in the Endoplasmic Reticulum as a Means of Cell Protection
    Yoshihito Ishida, Akitsugu Yamamoto, Akira Kitamura, Shireen R. Lamande, Tamotsu Yoshimori, John F. Bateman, Hiroshi Kubota, Kazuhiro Nagata
    MOLECULAR BIOLOGY OF THE CELL, 20, 11, 2744, 2754, Jun. 2009, [Peer-reviewed]
    English, Scientific journal
  • MKKS is a centrosome-shuttling protein degraded by disease-causing mutations via CHIP-mediated ubiquitination
    Shoshiro Hirayama, Yuji Yamazaki, Akira Kitamura, Yukako Oda, Daisuke Morito, Katsuya Okawa, Hiroshi Kimura, Douglas M. Cyr, Hiroshi Kubota, Kazuhiro Nagata
    MOLECULAR BIOLOGY OF THE CELL, 19, 3, 899, 911, Mar. 2008, [Peer-reviewed]
    English, Scientific journal
  • Cytosolic chaperonin prevents polyglutamine toxicity with altering the aggregation state
    Akira Kitamura, Hiroshi Kubota, Chan-Gi Pack, Gen Matsumoto, Shoshiro Hirayama, Yasuo Takahashi, Hiroshi Kimura, Masataka Kinjo, Richard I. Morimoto, Kazuhiro Nagata
    Nature Cell Biology, 8, 10, 1163, U224, Oct. 2006, [Lead author]
    English, Scientific journal
  • Type I collagen in Hsp47-null cells is aggregated in endoplasmic reticulum and deficient in N-propeptide processing and fibrillogenesis
    Y Ishida, H Kubota, A Yamamoto, A Kitamura, HP Bachinger, K Nagata
    MOLECULAR BIOLOGY OF THE CELL, 17, 5, 2346, 2355, May 2006, [Peer-reviewed]
    English, Scientific journal

Other Activities and Achievements

Books and other publications

  • 新・生細胞蛍光イメージング               
    北村 朗, 第21章,実習8-2
    共立出版, Nov. 2015, [Joint work]

Lectures, oral presentations, etc.

Courses

  • Functional Cellular Sciences: Cellular and Molecular Science               
    Hokkaido University, Graduate School of Life Science
    2024 - Present
  • Cell Structural Science II               
    Hokkaido University, School of Science
    2023 - Present
  • 生命融合科学概論               
    北海道大学大学院生命科学院
    2023 - Present
  • Life science special lecture III (Advanced Light Microscope in Life Science Research) as the Hokkaido Summer Institute               
    Hokkaido University, Graduate School of Life Science
    2016 - Present
  • Functional Fluorescence Microscopy Imaging (fFMI) in Biomedical Research               
    Kalorinska Institutet
    2016 - Present
  • Laboratory Work on Bio-macromolecular Science II               
    Hokkaido University, School of Science
    2013 - Present
  • Fundamental Laboratory Work on Bio-macromolecular Science               
    Hokkaido University, School of Science
    2012 - Present
  • 脳科学研究の展開(先端脳機能イメージング)               
    北海道大学脳科学教育研究センター
    2011 - Present
  • Reaction Kinetics for Life Science               
    School of Science, Hokkaido University
    2018 - 2023
  • Experimental Biological Science               
    Hokkaido University, School of Science
    2012 - 2023
  • Cell Structural Science III               
    Hokkaido University
    2013 - 2022
  • AIST International Imaging Workshop               
    Association for Iron & Steel Technology, Japan
    2016 - 2019
  • Functional Cellular Sciences               
    Hokkaido University, Graduate School of Life Science
    2013 - 2017
  • 生物物理学               
    秋田大学工学資源学部
    2012 - 2015
  • 生命融合科学概論               
    北海道大学大学院生命科学院
    2010 - 2010

Affiliated academic society

  • JAPAN SOCIETY FOR CELL BIOLOGY               
  • THE BIOPHYSICAL SOCIETY OF JAPAN               
  • THE MOLECULAR BIOLOGY SOCIETY OF JAPAN               
  • The RNA Society of Japan               

Research Themes

  • バイオロジカルクラスター解析のための極限時空間相関分光法の確立
    科学研究費助成事業
    01 Apr. 2024 - 31 Mar. 2029
    北村 朗
    日本学術振興会, 学術変革領域研究(A), 北海道大学, 24H02286
  • Not applicable
    The 5th Research Grant (2024)
    Apr. 2025 - Mar. 2026
    Hagiwara Foundation of Japan, Principal investigator
  • Not applicable
    39th (2025 FY) Research Grant
    Apr. 2025 - Mar. 2026
    Suharakinennzaidann Co., Ltd., Principal investigator
  • 細胞内プロテオスタシスを維持するシャペロンRNAの作動機序解明
    Advanced Research & Development Programs for Medical Innovation (AMED-PRIME) "Understanding proteostasis and discovering innovative medical applications"
    Oct. 2022 - Mar. 2026
    Akira Kitamura
    AMED, Hokkaido University, Principal investigator
  • タンパク質2量体安定化機構へ与える細胞内微環境の影響解明
    科学研究費助成事業
    01 Apr. 2022 - 31 Mar. 2025
    金城 政孝, 北村 朗
    細胞情報伝達には多くのタンパク質が関与している。その中でも2量体化して細胞質から核へ移行し,情報を伝達する仕組みは,情報伝達因子や転写因子に多く存在している。しかし「2量体化」と「移行」の間には相反する要因がある。それは2量体化することで構造的には安定化すると考えられているが,2量体化することで分子量が大きくなれば,移行するためには多くのエネルギーが必要であり,また輸送時間がかかることから,情報伝達では不利になる。このようにタンパク質が2量体化をする理由については不明なことが多く,その理由は明確にされていない。


    特に核内受容体の一つであるグルココルチコイドレセプター (GR)は,細胞情報伝達分子として糖代謝のみならず,免疫制御・抗炎症作用から精神的な情緒まで広く関与している。GRのシグナル伝達の最終段階は2量体化しDNAに結合する転写活性にあるが,申請者らはその前段階のホモならびにヘテロ2量体形成量が核内受容体の多様な機能を支えると考えた。
    本研究ではGRの2量体化量とそれに与える細胞内微環境の影響を同時に解明するために分子量サイズの変化に敏感で回転拡散測定可能な偏光蛍光相互相関分光装置(Pol-FCCS)の新規構築を続ける。特にPol-FCCSから得られるパラメーターのうち,分子数を決定することのため,Alexa系蛍光色素と,Fluorescein系蛍光色素を用いて,共焦点領域の大きさの決定を行った。
    また,細胞測定に向けて,細胞内タンパク質の発現パターンを調べる必要性から科研費予算を利用して外注してNeuro2a並びに293細胞のtoral RNA解析を行った。
    日本学術振興会, 基盤研究(B), 北海道大学, 23K23842
  • タンパク質2量体安定化機構へ与える細胞内微環境の影響解明
    科学研究費助成事業
    Apr. 2022 - Mar. 2025
    金城 政孝, 北村 朗
    日本学術振興会, 基盤研究(B), 北海道大学, Coinvestigator, 22H02578
  • 神経変性疾患の核酸医薬創薬に向けたシャペロン RNA の実証
    研究助成
    Apr. 2021 - Mar. 2025
    Hoansha, 北海道大学, Principal investigator
  • 細胞由来微粒子迅速測定のための蛍光と散乱光測定の融合
    科学研究費助成事業
    30 Jun. 2022 - 31 Mar. 2024
    金城 政孝, 北村 朗
    細胞内の液-液相分離による分子集合体やタンパク質凝縮体、また細胞外に放出される細胞外小胞など、様々な形態や大きさを有する新規の構造体が細胞情報伝達や疾患など生体の重要な機能に関連することが認識されている。本研究では、そのような多彩な構造と幅広いサイズ分布を持つ分子集合体を一括して『細胞由来微粒子』として捉え、それらを対象とした散乱光による網羅的検出と蛍光による特異的検出を統合した新規定量的検出法の確立を目指している。
    生体分子を対象とした蛍光と散乱光測定を融合した同時計測方法はこれまでになく、シグナル強度だけを見ると、散乱強度は極端に強く、蛍光は微弱であり、単純に比較することは困難である。申請者等は溶液中の分子や微粒子の特徴の一つである「揺れ動く」性質に着目した。蛍光・散乱測定に共通する時系列シグナル変化を基礎とする「自己相関解析」と、さらに蛍光と散乱光シグナル間の「相互相関解析」の同時利用で蛍光と散乱測定の二つの情報の統合と高度利用法を目指している。
    具体的測定手段は申請者等が構築した不等分割光ファイバー型蛍光相関分光装置の散乱同時測定への展開と高度化である。本研究では特に細胞外微粒子の中でもガン診断の指標等として注目されている抗原提示エクソソームの定量的検出・同定法の確立を通してその性能を実証し、新規細胞由来微粒子検出法としての可能性を実証する
    不当分割光ファイバーを利用した2色蛍光相互相関分光装置(FCrossCS)は、通常の励起光ダイクロイックミラー(第1次DM)を必要としないことから、これまで測定毎に必要とされた光軸・ピンホール調整等のキャリブレーションは一切不要となり、小型で長期安定な蛍光測定装置として利用でき、光軸調整不要なことから広い拡張性を有する。その拡張性の一つに、検出側の蛍光分光ダイクロイックミラー(2次)をハーフミラーに交換することで蛍光と散乱の同時測定を行なった。
    日本学術振興会, 挑戦的研究(萌芽), 北海道大学, 22K19886
  • 非公開
    Translational Research Network Program (Seeds A)
    Apr. 2023 - Mar. 2024
    AMED, Hokkaido University, Principal investigator
  • 非公開
    Translational Research Network Program (Seeds H)
    Sep. 2022 - Mar. 2024
    Akira Kitamura
    AMED, Hokkaido University, Principal investigator, JP22ym0126814
  • 蛍光動的消光測定による生細胞内RNA立体構造の情報物理解析
    Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
    Apr. 2022 - Mar. 2024
    北村 朗
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Hokkaido University, Principal investigator, 22H04826
  • 次世代画像相関分光法の確立による液滴内分子運動解析
    2021 2nd Grant Program
    Apr. 2022 - Mar. 2023
    Akira Kitamura
    HAGIWARA Foundation, Hokkaido University, Principal investigator
  • 二量体特異的発色団補助光不活化法の確立とそれを用いた光破壊による細胞内機能解析
    Grant Program
    Apr. 2022 - Mar. 2023
    Akira Kitamura
    NAKATANI Foundation, Hokkaido University, Principal investigator
  • 単一分子感度蛍光測定法を用いた新型コロナウイルス感染阻害剤スクリーニング法の確立
    新型コロナウイルス感染症対策 助成プログラム
    Jul. 2020 - Jun. 2021
    NAKATANI Foundation, 北海道大学, Principal investigator
  • 神経変性疾患に関連したタンパク質凝集形成を防ぐシャペロンRNAの実証
    Grant-in-Aid for Scientific Research (C)
    Apr. 2018 - Mar. 2021
    Akira Kitamura
    JSPS, Principal investigator, Competitive research funding
  • 光ファイバー型蛍光相関分光システムの研究開発と生物応用               
    Research fund
    Apr. 2018 - Mar. 2020
    Akira Kitamura
    Canon fundation, Principal investigator, Competitive research funding
  • Development of polarization-dependent fluorescence correlation spectroscopy for initial process analysis of protein aggregation
    Grants-in-Aid for Scientific Research
    Apr. 2016 - Mar. 2019
    Yamamoto Johtaro, Kitamura Akira
    In this work, we developed a polarization-dependent fluorescence correlation spectroscopy (Pol-FCS), which analyzes translational and rotational diffusion of molecules such as proteins. Size measurement of molecular aggregation using Pol-FCS inside living cells was successfully demonstrated. In addition, we found the Pol-FCS can also estimate orientation of molecules (ordered/disordered) and degree of macromolecular crowding. Thus, the Pol-FCS was a more powerful tool than we expected. In future, we expect the Pol-FCS will be widely used in biology such as the researches about aggregation prone proteins.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Coinvestigator, 16K07312
  • Elucidation for the regulation of motility and lifespan by proteostasis(Fostering Joint International Research)
    Grants-in-Aid for Scientific Research
    2017 - 2019
    Kitamura Akira
    The accumulation of misfolded proteins formed upon disruption of intracellular proteinstasis often results in the formation of aggregates in the cell. Such protein aggregates are thought to be toxic and cause death of neurons. However, the mechanism of reducing the toxicity of the aggregates formed in the cells at the individual level has not been elucidated, and its application to the treatment of specific neurodegenerative diseases has not been possible. In this study, we established a nematode strain expressing TDP25, a causative protein of amyotrophic lateral sclerosis (ALS), and analyzed its motility and lifespan. We further established a novel fluorescence spectroscopy method and a system to read out the structure of RNAs that bind to aggregate proteins in living cells. We also established a method to read out the status of intracellular macromolecular crowding, which is thought to be involved in aggregation formation, using the fluorescence lifetime of GFP.
    Japan Society for the Promotion of Science, Fund for the Promotion of Joint International Research (Fostering Joint International Research), Hokkaido University, 16KK0156
  • TDP43に潜在する非古典的核内輸送シグナル配列の同定と, 細胞質における神経細胞毒性低減機構の解明               
    ALS基金
    Jun. 2016 - Mar. 2017
    北村 朗
    一般社団法人 日本ALS協会, Principal investigator, Competitive research funding
  • ALSのRNA治療に向けたTDP43のプリオン様構造転移および凝集形成を抑制するRNA分子の同定               
    「生命の彩」ALS研究助成基金
    May 2016 - Mar. 2017
    北村 朗
    三井住友信託銀行公益信託, Principal investigator, Competitive research funding
  • Establishment of unified theory of cellular inclusion bodies including misfolded protein
    KAKENHI
    Apr. 2014 - Mar. 2017
    Akira Kitamura
    Accumulation of misfolded proteins due to inappropriate stabilization results in neurodegenerative diseases including amyotrophic lateral sclerosis (ALS). In this study, we clarify structural differences of carboxyl terminal fragments of ALS-causative TDP43 (TDP35 or TDP25) by using fluorescence resonance energy transfer (FRET) or related procedure. We elucidate that nuclear localization signal sequence (NLS)-tagged TDP25 can reduce cytotoxicity through the structural change.
    JSPS, Grant-in-Aid for Scientific Research (C), Hokkaido University, Principal investigator, Competitive research funding, 26440090
  • 細胞内化学反応解析のための超高速光計測システムの開発               
    Development of systems and technology for advanced measurement and analysis
    Oct. 2013 - Mar. 2017
    Yasushi Hiraoka
    JST, Competitive research funding
  • Analysis of neuronal cell death by ALS-associated misfolded protein aggregation with modulation of cellular RNA homeostasis
    KAKENHI
    Apr. 2011 - Mar. 2015
    Akira Kitamura
    TAR-RNA/DNA binding protein 43 kDa is a disease gene product associated with amyotrophic lateral sclerosis (ALS), a motor neuron disease. In this research, fluorescence correlation spectroscopy (FCS) measurement in cell lysate revealed that a 25 kDa carboxyl-terminal fragment of TDP43 (TDP25) formed aggregation after dissociation of RNA. Next, TDP43 was sequestrated into cytoplasmic inclusion bodies of TDP25 in living cells. Neuronal cells expressing TDP25 showed higher cell death efficiency than that of TDP43. These results suggest that TDP25 may be an aggregation-causative and toxic seed, and RNA may play an important role for inhibition of aggregation-formation of TDP25.
    JSPS, Grant-in-Aid for Young Scientists (B), Hokkaido University, Principal investigator, Competitive research funding, 23770215
  • 多点時空間相関解析法による細胞内分子複合体研究
    KAKENHI
    May 2009 - Mar. 2014
    Masataka Kinjo
    蛍光相関分光法(Fluorescence Correlation Spectroscopy,FCS)はダイナミックな分子間相互作用を単一分子レベルで解析する手法でるが、その一方で、励起光源にレーザー光が必要であり、その焦点領域である、特定の1点でしか測定出来ない。このことは生細胞が様々な区画に分かれていて、さらにその区画の中も不均一であるため、細胞生物学的応用の際の問題となっている。その解決のために本年も引き続き多点同時測定FCSの構築と生細胞測定への応用を目指ざしている。
    そこでこれまで多点測定のためのまず、多点の焦点領域を作る必要がある。そのために空間光変調素子を利用したホログラフィ技術により複数照射の励起光パターンを作りだすことを可能とした。次に検出側としてマルチ光ファイバーと各端面に光電子増倍管を接続した多点検出装置を用いて,実際に生細胞内の多点におけるタンパク質の拡散運動を検出する装置を作成した。
    次に本年は細胞応用測定に重点を置き、細胞質ならび細胞核を区別して7点同時測定を行った。
    生細胞内GFPを対象としてガラス面からZ軸方向(上方向)に0.5ミクロンステップの空間分解能があることを証明し、次に細胞核膜を境にして同時7点測定FCS測定が可能であることを実証した。次に機能性タンパク質としてリガンド刺激により、細胞質から核へ移行するグルココルチコイドレセプター(GR)のGFP融合タンパク質を対象とした測定を行い、15秒おきのFCS多点同時測定に成功した。さらに本年は精度を上げるために細胞運動の抑制方法を種々検討し、ノコダゾール処理と、緩衝液を調整することで、長期の観測を可能とした。
    安定測定が可能となったので、さらに時間分解を上げることが可能となったので、単一タンパク質分子の動態について、検出と解析を試みている。
    MEXT, 基盤研究(S), 北海道大学, Competitive research funding, 21221006
  • Regulation of cellular functions by highly evolved two chaperonins
    Grants-in-Aid for Scientific Research
    2011 - 2013
    KUBOTA HIROSHI, NAGATA Kazuhiro, KINJO Masataka, KITAMURA Akira
    Chaperonins are a group of molecular chaperone that assists in protein folding in the cell. In this project, we analyzed two eukaryotic chaperonins: cytosolic chaperonin CCT and mitochondrial chaperonin HSP60. In the study of CCT, we found that CCT possesses GTPase activity in addition to the ATPase activity. In the study of HSP60, we found that football-like complex plays an important role in the function of HSP60 after formation of the football-like complex from single-ring complex via double-ring complex. These results contain important findings to understand chaperonin functions.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Akita University, 23570220
  • Study of membrane binding protein complex using total internal reflection fluorescence correlation spectroscopy
    KAKENHI
    2007 - 2011
    Masataka Kinjo
    The functional molecules move around in the cell and interact with other molecules, and then support higher function of the cell. Moreover, even aggregate prone protein acts as aggregate and disaggregate under specific condition, so that each element of these aggregate protein is exchanged with free its molecules in solution. FCS (fluorescence correlation spectroscopy) detects the fluorescence fluctuations, the diffusion coefficient, molecular concentration and molecular interactions of molecules. We developed a multipoint FCS system which was based on an objective-type total internal reflection-FCS (TIR-FCS) in order to analysis molecular interaction in living cell and system of protein community.
    MEXT, Grant-in-Aid for Scientific Research on Priority Areas, Hokkaido University, Competitive research funding, 19058001
  • 神経変性疾患を引き起こすタンパク質凝集体形成と神経細胞死機構の時空間的解析
    科学研究費助成事業
    2008 - 2010
    北村 朗
    神経変性疾患に共通してみられる現象として,神経細胞の機能低下とそれに続く細胞死がある.このような神経細胞死を引き起こす原因として,細胞内外に蓄積したタンパク質凝集体があげられる.筋萎縮性側索硬化症(Amyotrophic Lateral Screlosis ; ALS)では,原因遺伝子の約20%をSuperoxide dismutase 1(SOD1)が占めており,このSOD1タンパク質に変異が入ると凝集体を形成することが知られている.これらの変異タンパク質の凝集体が,細胞内のどのような場所でどのような構造にあるとき,細胞毒性を持つのか.そして細胞死に至るのかといった問題点を解明するため,細胞内の分解機構の一つであるプロテアソーム経路の阻害剤を用いたところ,変異型SOD1は細胞内で凝集体を形成した.さらに,プロテアソームの活性を回復させたところ,凝集体は脱凝集を介して消失した.これらの脱凝集過程は,プロテアソームの活性に大きく依存しており,細胞内における別の分解経路として知られているオートファジー・リソソーム経路は必須ではないことを見出した.また,蛍光相関分光法技術を用いることで,変異型SOD1タンパク質は生細胞のサイトゾルで複合体を形成していることが判明した.蛍光相関分光法の解析により,この複合体は変異型SOD1タンパク質のみを含むものではなく,他の細胞内因子が含まれていることが示唆された.さらに,免疫共沈降法・マススペクトル解析により,分子シャペロンHsc70などが含まれていることが明らかとなった.このことから,細胞内において凝集体の毒性を抑制する際に,分子シャペロンが関与していることが示唆された.
    日本学術振興会, 特別研究員奨励費, 北海道大学, 08J04474
  • 細胞質シャペロニンの機能解析
    科学研究費助成事業
    2006 - 2007
    北村 朗
    本年度は,従来より研究を進めていたポリグルタミンタンパク質のように変異によって凝集体を形成し,神経細胞死を招くと考えられている変異型SOD1タンパク質の凝集体形成について主に解析を行った.SOD1タンパク質は,難病指定された神経変性疾患の一つである家族性筋萎縮性側索硬化症(fALS)の原因遺伝子である.最初に,プロテアソーム阻害剤であるMG-132処理により,変異型SOD1では,核近傍に,ユビキチン化されたタンパク質や分子シャペロンなどが集積したアグレソーム様の凝集体構造を形成していることを明らかにした.さらに,MG-132処理によって形成された凝集体構造は,プロテアソームの活性回復に伴い,消失することを見出した.この消失過程を詳細に解析した結果,一度形成された凝集体を解きほぐす脱凝集機構が関与していることが示唆された.また,凝集過程よりも脱凝集過程における細胞死の頻度が高いことから,脱凝集過程において発生する分子の構造もしくは多量体化状態が毒性を発揮する可能性があると考え,蛍光相関分光法による分子サイズの解析より,脱凝集過程において,可溶性のオリゴマーはすみやかに消失することから,毒性を発揮するのは,大きな多量体ではなく,低分子で構造の転移したものではないかという仮説提唱に至った.これらの結果は,昨年度公開した研究成果のようなポリグルタミンタンパク質で得られた知見とは異なり,SOD1の場合は,多量体化したオリゴマーが毒性を発揮するのではなく,低分子であっても毒性を発揮しうる状態があるのではないかと考えられる.
    続いて,細胞質シャペロニンCCTと弱い相同性を持つタンパク質であるMKKSPについても解析を行った.MKKSPは中心体に豊富に局在していることが,これまでの解析から明らかにされていたが,今年度の研究では,MKKSPが中心体と細胞質の間をすみやかに移動しているが,少ない割合の成分は中心体に滞留し,何かしらの機能を発現していることが示唆された.
    日本学術振興会, 特別研究員奨励費, 京都大学, 06J03037

Industrial Property Rights

  • BDNF分泌促進剤及び緑内障を治療又は予防するための薬剤
    Patent right, 北村朗, 藤本愛, 河村綸太郎
    特願2025-104771, 20 Jun. 2025
    40045923
  • TDP43、TDP35、またはTDP25の凝集を特徴とする神経変性疾患の治療剤、進行抑制剤、および予防剤               
    Patent right, 北村朗, 藤本愛, 国立大学法人 北海道大学
    特願PCT/JP2022/041001, 02 Nov. 2022
  • ヘモシアニン会合体を用いた包摂体の製造方法               
    Patent right, 田中 良和, 松野 明日香, 北村 朗, 金城 政孝, 姚 閔, 上野 隆史, 安部 聡
    特願2016-110309, 01 Jun. 2016
    特開2017-214339, 07 Dec. 2017

syllabus

  • ソフトマター科学概論, 2024年, 修士課程, 生命科学院
  • 生命融合科学概論, 2024年, 修士課程, 生命科学院
  • 生命科学特別講義Ⅲ, 2024年, 修士課程, 生命科学院
  • 生命科学特別講義Ⅲ, 2024年, 修士課程, 生命科学院
  • 生命科学特別講義Ⅲ, 2024年, 修士課程, 生命科学院
  • 細胞機能科学特論, 2024年, 修士課程, 生命科学院
  • 統合物質生命科学特論, 2024年, 修士課程, 生命科学院
  • 統合物質生命科学特論, 2024年, 修士課程, 生命科学院
  • 大学院共通授業科目(一般科目):自然科学・応用科学, 2024年, 修士課程, 大学院共通科目
  • 大学院共通授業科目(一般科目):自然科学・応用科学, 2024年, 修士課程, 大学院共通科目
  • 大学院共通授業科目(一般科目):自然科学・応用科学, 2024年, 修士課程, 大学院共通科目
  • 細胞構造科学Ⅱ, 2024年, 学士課程, 理学部
  • 生体高分子学実験Ⅱ, 2024年, 学士課程, 理学部
  • 高分子機能学基礎実験, 2024年, 学士課程, 理学部