1
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Matsui S, Noda S, Kuwata K, Nomoto M, Tada Y, Shinohara H, Matsubayashi Y. Arabidopsis SBT5.2 and SBT1.7 subtilases mediate C-terminal cleavage of flg22 epitope from bacterial flagellin. Nat Commun 2024; 15:3762. [PMID: 38704378 PMCID: PMC11069567 DOI: 10.1038/s41467-024-48108-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 04/17/2024] [Indexed: 05/06/2024] Open
Abstract
Plants initiate specific defense responses by recognizing conserved epitope peptides within the flagellin proteins derived from bacteria. Proteolytic cleavage of epitope peptides from flagellin by plant apoplastic proteases is thought to be crucial for the perception of the epitope by the plant receptor. However, the identity of the plant proteases involved in this process remains unknown. Here, we establish an efficient identification system for the target proteases in Arabidopsis apoplastic fluid; the method employs native two-dimensional electrophoresis followed by an in-gel proteolytic assay using a fluorescence-quenching peptide substrate. We designed a substrate to specifically detect proteolytic activity at the C-terminus of the flg22 epitope in flagellin and identified two plant subtilases, SBT5.2 and SBT1.7, as specific proteases responsible for the C-terminal cleavage of flg22. In the apoplastic fluid of Arabidopsis mutant plants deficient in these two proteases, we observe a decrease in the C-terminal cleavage of the flg22 domain from flagellin, leading to a decrease in the efficiency of flg22 epitope liberation. Consequently, defensive reactive oxygen species (ROS) production is delayed in sbt5.2 sbt1.7 double-mutant leaf disks compared to wild type following flagellin exposure.
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Affiliation(s)
- Sayaka Matsui
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Saki Noda
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Mika Nomoto
- Center for Gene Research, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Yasuomi Tada
- Center for Gene Research, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Hidefumi Shinohara
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji, 910-1195, Japan
| | - Yoshikatsu Matsubayashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan.
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2
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Hayashi Y, Fukatsu K, Takahashi K, Kinoshita SN, Kato K, Sakakibara T, Kuwata K, Kinoshita T. Phosphorylation of plasma membrane H +-ATPase Thr881 participates in light-induced stomatal opening. Nat Commun 2024; 15:1194. [PMID: 38378616 PMCID: PMC10879185 DOI: 10.1038/s41467-024-45248-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024] Open
Abstract
Plasma membrane (PM) H+-ATPase is crucial for light-induced stomatal opening and phosphorylation of a penultimate residue, Thr948 (pen-Thr, numbering according to Arabidopsis AHA1) is required for enzyme activation. In this study, a comprehensive phosphoproteomic analysis using guard cell protoplasts from Vicia faba shows that both red and blue light increase the phosphorylation of Thr881, of PM H+-ATPase. Light-induced stomatal opening and the blue light-induced increase in stomatal conductance are reduced in transgenic Arabidopsis plants expressing mutant AHA1-T881A in aha1-9, whereas the blue light-induced phosphorylation of pen-Thr is unaffected. Auxin and photosynthetically active radiation induce the phosphorylation of both Thr881 and pen-Thr in etiolated seedlings and leaves, respectively. The dephosphorylation of phosphorylated Thr881 and pen-Thr are mediated by type 2 C protein phosphatase clade D isoforms. Taken together, Thr881 phosphorylation, in addition of the pen-Thr phosphorylation, are important for PM H+-ATPase function during physiological responses, such as light-induced stomatal opening in Arabidopsis thaliana.
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Affiliation(s)
- Yuki Hayashi
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Kohei Fukatsu
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Koji Takahashi
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan
| | | | - Kyohei Kato
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Taku Sakakibara
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan
| | - Toshinori Kinoshita
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan.
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan.
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3
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Kimata Y, Yamada M, Murata T, Kuwata K, Sato A, Suzuki T, Kurihara D, Hasebe M, Higashiyama T, Ueda M. Novel inhibitors of microtubule organization and phragmoplast formation in diverse plant species. Life Sci Alliance 2023; 6:e202201657. [PMID: 36849250 PMCID: PMC9971157 DOI: 10.26508/lsa.202201657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 03/01/2023] Open
Abstract
Cell division is essential for development and involves spindle assembly, chromosome separation, and cytokinesis. In plants, the genetic tools for controlling the events in cell division at the desired time are limited and ineffective owing to high redundancy and lethality. Therefore, we screened cell division-affecting compounds in Arabidopsis thaliana zygotes, whose cell division is traceable without time-lapse observations. We then determined the target events of the identified compounds using live-cell imaging of tobacco BY-2 cells. Subsequently, we isolated two compounds, PD-180970 and PP2, neither of which caused lethal damage. PD-180970 disrupted microtubule (MT) organization and, thus, nuclear separation, and PP2 blocked phragmoplast formation and impaired cytokinesis. Phosphoproteomic analysis showed that these compounds reduced the phosphorylation of diverse proteins, including MT-associated proteins (MAP70) and class II Kinesin-12. Moreover, these compounds were effective in multiple plant species, such as cucumber (Cucumis sativus) and moss (Physcomitrium patens). These properties make PD-180970 and PP2 useful tools for transiently controlling plant cell division at key manipulation nodes conserved across diverse plant species.
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Affiliation(s)
- Yusuke Kimata
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Moé Yamada
- Department of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Takashi Murata
- Department of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Daisuke Kurihara
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
- Institute for Advanced Research (IAR), Nagoya University, Nagoya, Japan
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki, Japan
- School of Life Science, The Graduate University for Advanced Studies, Okazaki, Japan
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Minako Ueda
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- Suntory Rising Stars Encouragement Program in Life Sciences (SunRiSE), Kyoto, Japan
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4
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Borgo C, Cesaro L, Hirota T, Kuwata K, D'Amore C, Ruppert T, Blatnik R, Salvi M, Pinna LA. Analysis of the phosphoproteome of CK2 α(-/-)/Δ α' C2C12 myoblasts compared to the wild-type cells. Open Biol 2023; 13:220220. [PMID: 36809799 PMCID: PMC9943641 DOI: 10.1098/rsob.220220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
CK2 is a Ser/Thr protein kinase composed of two catalytic (α/α') subunits and a non-catalytic β-subunit dimer, whose activity is often abnormally high in cancer cells. The concept that CK2 may be dispensable for cell survival has been challenged by the finding that viable CK2α/α' knock-out myoblast clones still express small amounts of an N-terminally deleted α' subunit generated during the CRISPR/Cas9 procedure. Here we show that, although the overall CK2 activity of these CK2α(-/-)/Δα' (KO) cells is less than 10% compared to wild-type (WT) cells, the number of phosphosites with the CK2 consensus is comparable to that of WT cells. A more in-depth analysis, however, reveals that the two phosphoproteomes are not superimposable according to a number of criteria, notably a functional analysis of the phosphoproteome found in the two types of cells, and variable sensitivity of the phosphosites to two structurally unrelated CK2 inhibitors. These data support the idea that a minimal CK2 activity, as in KO cells, is sufficient to perform basic housekeeping functions essential for cell survival, but not to accomplish several specialized tasks required upon cell differentiation and transformation. From this standpoint, a controlled downregulation of CK2 would represent a safe and valuable anti-cancer strategy.
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Affiliation(s)
- Christian Borgo
- Department of Biomedical Sciences, University of Padova, Padova 35122, Italy
| | - Luca Cesaro
- Department of Biomedical Sciences, University of Padova, Padova 35122, Italy
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Claudio D'Amore
- Department of Biomedical Sciences, University of Padova, Padova 35122, Italy
| | - Thomas Ruppert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Renata Blatnik
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Mauro Salvi
- Department of Biomedical Sciences, University of Padova, Padova 35122, Italy
| | - Lorenzo A. Pinna
- Department of Biomedical Sciences, University of Padova, Padova 35122, Italy,CNR Institute of Neurosciences, 35131 Padova, Italy
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5
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Kano K, Noda S, Sato S, Kuwata K, Mishiro‐Sato E. An efficient in‐gel digestion method on small amounts of protein sample from large intact gel pieces. Separation Science Plus 2023. [DOI: 10.1002/sscp.202200121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Keiko Kano
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
| | - Saki Noda
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
| | - Shinya Sato
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
| | - Keiko Kuwata
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
| | - Emi Mishiro‐Sato
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
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6
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Kato S, Misumi O, Maruyama S, Nozaki H, Tsujimoto-Inui Y, Takusagawa M, Suzuki S, Kuwata K, Noda S, Ito N, Okabe Y, Sakamoto T, Yagisawa F, Matsunaga TM, Matsubayashi Y, Yamaguchi H, Kawachi M, Kuroiwa H, Kuroiwa T, Matsunaga S. Genomic analysis of an ultrasmall freshwater green alga, Medakamo hakoo. Commun Biol 2023; 6:89. [PMID: 36690657 PMCID: PMC9871001 DOI: 10.1038/s42003-022-04367-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/12/2022] [Indexed: 01/24/2023] Open
Abstract
Ultrasmall algae have attracted the attention of biologists investigating the basic mechanisms underlying living systems. Their potential as effective organisms for producing useful substances is also of interest in bioindustry. Although genomic information is indispensable for elucidating metabolism and promoting molecular breeding, many ultrasmall algae remain genetically uncharacterized. Here, we present the nuclear genome sequence of an ultrasmall green alga of freshwater habitats, Medakamo hakoo. Evolutionary analyses suggest that this species belongs to a new genus within the class Trebouxiophyceae. Sequencing analyses revealed that its genome, comprising 15.8 Mbp and 7629 genes, is among the smallest known genomes in the Viridiplantae. Its genome has relatively few genes associated with genetic information processing, basal transcription factors, and RNA transport. Comparative analyses revealed that 1263 orthogroups were shared among 15 ultrasmall algae from distinct phylogenetic lineages. The shared gene sets will enable identification of genes essential for algal metabolism and cellular functions.
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Affiliation(s)
- Shoichi Kato
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, 278-8510, Japan
| | - Osami Misumi
- Department of Biological Science and Chemistry, Faculty of Science, Graduate School of Medicine, Yamaguchi University, Yoshida, Yamaguchi, 753-8512, Japan
| | - Shinichiro Maruyama
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobaku, Sendai, 980-8578, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, 112-8610, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Tokyo, 113-0033, Japan
- Biodiversity Division, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Yayoi Tsujimoto-Inui
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Mari Takusagawa
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Shigekatsu Suzuki
- Biodiversity Division, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Saki Noda
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Nanami Ito
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Yoji Okabe
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, 278-8510, Japan
| | - Fumi Yagisawa
- Center for Research Advancement and Collaboration, University of the Ryukyus, Okinawa, 903-0213, Japan
- Graduate School of Engineering and Science, University of the Ryukyus, Okinawa, 903-0213, Japan
| | - Tomoko M Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Yoshikatsu Matsubayashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Haruyo Yamaguchi
- Biodiversity Division, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Masanobu Kawachi
- Biodiversity Division, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Haruko Kuroiwa
- Department of Chemical and Biological Science, Faculty of Science, Japan Women's University, Tokyo, 112-8681, Japan
| | - Tsuneyoshi Kuroiwa
- Department of Chemical and Biological Science, Faculty of Science, Japan Women's University, Tokyo, 112-8681, Japan.
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, 278-8510, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.
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7
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Nomura K, Kawano K, Kawaguchi Y, Kawamura Y, Michibata J, Kuwata K, Sugiyama K, Kusumoto K, Futaki S. Hemopexin as a Potential Binding Partner of Arginine-Rich Cell-Penetrating Peptides in Serum. ACS Pharmacol Transl Sci 2022; 5:603-615. [DOI: 10.1021/acsptsci.2c00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Kayo Nomura
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kenichi Kawano
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yoshimasa Kawaguchi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yuki Kawamura
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Junya Michibata
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Koji Sugiyama
- Formulation Research Laboratory, Taiho Pharmaceutical Co., Ltd., 224-2, Ebisuno, Hiraishi, Kawauchi-cho, Tokushima 771-0194, Japan
| | - Kenji Kusumoto
- Formulation Research Laboratory, Taiho Pharmaceutical Co., Ltd., 224-2, Ebisuno, Hiraishi, Kawauchi-cho, Tokushima 771-0194, Japan
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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8
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Kajiwara K, Osaki H, Greßies S, Kuwata K, Kim JH, Gensch T, Sato Y, Glorius F, Yamaguchi S, Taki M. A negative-solvatochromic fluorescent probe for visualizing intracellular distributions of fatty acid metabolites. Nat Commun 2022; 13:2533. [PMID: 35534485 PMCID: PMC9085894 DOI: 10.1038/s41467-022-30153-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 04/19/2022] [Indexed: 01/25/2023] Open
Abstract
Metabolic distribution of fatty acid to organelles is an essential biological process for energy homeostasis as well as for the maintenance of membrane integrity, and the metabolic pathways are strictly regulated in response to environmental stimuli. Herein, we report a fluorescent fatty acid probe, which bears an azapyrene dye that changes its absorption and emission features depending on the microenvironment polarity of the organelle into which it is transported. Owing to the environmental sensitivity of this dye, the distribution of the metabolically incorporated probe in non-polar lipid droplets, medium-polarity membranes, and the polar aqueous regions, can be visualized in different colors. Based on density scatter plots of the fluorophore, we demonstrate that the degradation of triacylglycerols in lipid droplets occurs predominantly via lipolysis rather than lipophagy in nutrition-starved hepatocytes. This tool can thus be expected to significantly advance our understanding of the lipid metabolism in living organisms. Metabolic distribution of fatty acids to organelles is an essential biological process for energy homeostasis. Here the authors report a fluorescent probe that allows multicolour visualisation of the intracellular distribution of exogenous fatty acids, metabolically incorporated as lipid components.
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9
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Iida T, Mizutani Y, Esaki N, Ponik SM, Burkel BM, Weng L, Kuwata K, Masamune A, Ishihara S, Haga H, Kataoka K, Mii S, Shiraki Y, Ishikawa T, Ohno E, Kawashima H, Hirooka Y, Fujishiro M, Takahashi M, Enomoto A. Pharmacologic conversion of cancer-associated fibroblasts from a protumor phenotype to an antitumor phenotype improves the sensitivity of pancreatic cancer to chemotherapeutics. Oncogene 2022; 41:2764-2777. [PMID: 35414659 DOI: 10.1038/s41388-022-02288-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 03/05/2022] [Accepted: 03/18/2022] [Indexed: 12/17/2022]
Abstract
Previous therapeutic attempts to deplete cancer-associated fibroblasts (CAFs) or inhibit their proliferation in pancreatic ductal adenocarcinoma (PDAC) were not successful in mice or patients. Thus, CAFs may be tumor suppressive or heterogeneous, with distinct cancer-restraining and -promoting CAFs (rCAFs and pCAFs, respectively). Here, we showed that induced expression of the glycosylphosphatidylinositol-anchored protein Meflin, a rCAF-specific marker, in CAFs by genetic and pharmacological approaches improved the chemosensitivity of mouse PDAC. A chemical library screen identified Am80, a synthetic, nonnatural retinoid, as a reagent that effectively induced Meflin expression in CAFs. Am80 administration improved the sensitivity of PDAC to chemotherapeutics, accompanied by increases in tumor vessel area and intratumoral drug delivery. Mechanistically, Meflin was involved in the suppression of tissue stiffening by interacting with lysyl oxidase to inhibit its collagen crosslinking activity. These data suggested that modulation of CAF heterogeneity may represent a strategy for PDAC treatment.
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Affiliation(s)
- Tadashi Iida
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuyuki Mizutani
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobutoshi Esaki
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Suzanne M Ponik
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Brian M Burkel
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Liang Weng
- Department of Oncology, Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, China
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Hisashi Haga
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Kunio Kataoka
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shinji Mii
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yukihiro Shiraki
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takuya Ishikawa
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Eizaburo Ohno
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroki Kawashima
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Endoscopy, Nagoya University Hospital, Nagoya, Japan
| | - Yoshiki Hirooka
- Department of Gastroenterology and Hepatology, Fujita Health University, Toyoake, Aichi, Japan
| | - Mitsuhiro Fujishiro
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masahide Takahashi
- International Center for Cell and Gene Therapy, Fujita Health University, Toyoake, Japan
| | - Atsushi Enomoto
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
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10
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Uehara TN, Nonoyama T, Taki K, Kuwata K, Sato A, Fujimoto KJ, Hirota T, Matsuo H, Maeda AE, Ono A, Takahara TT, Tsutsui H, Suzuki T, Yanai T, Kay SA, Itami K, Kinoshita T, Yamaguchi J, Nakamichi N. Phosphorylation of RNA Polymerase II by CDKC;2 Maintains the Arabidopsis Circadian Clock Period. Plant Cell Physiol 2022; 63:450-462. [PMID: 35086143 PMCID: PMC9016870 DOI: 10.1093/pcp/pcac011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
The circadian clock is an internal timekeeping system that governs about 24 h biological rhythms of a broad range of developmental and metabolic activities. The clocks in eukaryotes are thought to rely on lineage-specific transcriptional-translational feedback loops. However, the mechanisms underlying the basic transcriptional regulation events for clock function have not yet been fully explored. Here, through a combination of chemical biology and genetic approaches, we demonstrate that phosphorylation of RNA polymerase II by CYCLIN DEPENDENT KINASE C; 2 (CDKC;2) is required for maintaining the circadian period in Arabidopsis. Chemical screening identified BML-259, the inhibitor of mammalian CDK2/CDK5, as a compound lengthening the circadian period of Arabidopsis. Short-term BML-259 treatment resulted in decreased expression of most clock-associated genes. Development of a chemical probe followed by affinity proteomics revealed that BML-259 binds to CDKC;2. Loss-of-function mutations of cdkc;2 caused a long period phenotype. In vitro experiments demonstrated that the CDKC;2 immunocomplex phosphorylates the C-terminal domain of RNA polymerase II, and BML-259 inhibits this phosphorylation. Collectively, this study suggests that transcriptional activity maintained by CDKC;2 is required for proper period length, which is an essential feature of the circadian clock in Arabidopsis.
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Affiliation(s)
| | | | | | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Kazuhiro J Fujimoto
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Hiromi Matsuo
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Akari E Maeda
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Azusa Ono
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Tomoaki T Takahara
- Department of Applied Chemistry, Waseda University, 513 Wasedatsurumakicho, Shinjuku, Tokyo, 162-0041 Japan
| | - Hiroki Tsutsui
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, 487-8501 Japan
| | - Takeshi Yanai
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Steve A Kay
- Keck School of Medicine, University of Southern California, 1975 Zonal Avenue, Los Angeles, CA 90033, USA
| | - Kenichiro Itami
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
- JST ERATO, Itami Molecular Nanocarbon Project, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Toshinori Kinoshita
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Junichiro Yamaguchi
- *Corresponding authors: Norihito Nakamichi, E-mail, ; Junichiro Yamaguchi, E-mail,
| | - Norihito Nakamichi
- *Corresponding authors: Norihito Nakamichi, E-mail, ; Junichiro Yamaguchi, E-mail,
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11
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Obara K, Yoshikawa T, Yamaguchi R, Kuwata K, Nakatsukasa K, Nishimura K, Kamura T. Proteolysis of adaptor protein Mmr1 during budding is necessary for mitochondrial homeostasis in Saccharomyces cerevisiae. Nat Commun 2022; 13:2005. [PMID: 35422486 PMCID: PMC9010424 DOI: 10.1038/s41467-022-29704-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 03/29/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractIn yeast, mitochondria are passed on to daughter cells via the actin cable, motor protein Myo2, and adaptor protein Mmr1. They are released from the actin-myosin machinery after reaching the daughter cells. We report that Mmr1 is rapidly degraded by the ubiquitin-proteasome system in Saccharomyces cerevisiae. Redundant ubiquitin ligases Dma1 and Dma2 are responsible for Mmr1 ubiquitination. Dma1/2-mediated Mmr1 ubiquitination requires phosphorylation, most likely at S414 residue by Ste20 and Cla4. These kinases are mostly localized to the growing bud and nearly absent from mother cells, ensuring phosphorylation and ubiquitination of Mmr1 after the mitochondria enter the growing bud. In dma1Δ dma2Δ cells, transported mitochondria are first stacked at the bud-tip and then pulled back to the bud-neck. Stacked mitochondria in dma1Δ dma2Δ cells exhibit abnormal morphology, elevated respiratory activity, and increased level of reactive oxygen species, along with hypersensitivity to oxidative stresses. Collectively, spatiotemporally-regulated Mmr1 turnover guarantees mitochondrial homeostasis.
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12
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Nagano Y, Arafiles JVV, Kuwata K, Kawaguchi Y, Imanishi M, Hirose H, Futaki S. Grafting Hydrophobic Amino Acids Critical for Inhibition of Protein-Protein Interactions on a Cell-Penetrating Peptide Scaffold. Mol Pharm 2021; 19:558-567. [PMID: 34958576 DOI: 10.1021/acs.molpharmaceut.1c00671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Stapled peptides are a promising class of conformationally restricted peptides for modulating protein-protein interactions (PPIs). However, the low membrane permeability of these peptides is an obstacle to their therapeutic applications. It is common that only a few hydrophobic amino acid residues are mandatory for stapled peptides to bind to their target proteins. Hoping to create a novel class of membrane-permeable PPI inhibitors, the phenylalanine, tryptophan, and leucine residues that play a critical role in inhibiting the p53-HDM2 interaction were grafted into the framework of CADY2─a cell-penetrating peptide (CPP) having a helical propensity. Two analogues (CADY-3FWL and CADY-10FWL) induced apoptotic cell death but lacked the intended HDM2 interaction. Pull-down experiments followed by proteomic analysis led to the elucidation of nesprin-2 as a candidate binding target. Nesprin-2 is considered to play a role in the nuclear translocation of β-catenin upon activation of the Wnt signaling pathway, which leads to the expression of antiapoptosis proteins and cell survival. Cells treated with the two analogues showed decreased nuclear localization of β-catenin and reduced mRNA expression of related antiapoptotic proteins. These data suggest inhibition of β-catenin nuclear translocation as a possible mode of action of the described cell-penetrating stapled peptides.
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Affiliation(s)
- Yuki Nagano
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | | | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yoshimasa Kawaguchi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Miki Imanishi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hisaaki Hirose
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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13
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Hayashi Y, Takahashi Y, Fukatsu K, Tada Y, Takahashi K, Kuwata K, Suzuki T, Kinoshita T. Identification of Abscisic Acid-Dependent Phosphorylated Basic Helix-Loop-Helix Transcription Factors in Guard Cells of Vicia faba by Mass Spectrometry. Front Plant Sci 2021; 12:735271. [PMID: 34987530 PMCID: PMC8721282 DOI: 10.3389/fpls.2021.735271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/24/2021] [Indexed: 05/28/2023]
Abstract
An unknown 61 kDa protein is phosphorylated by abscisic acid (ABA)-activated protein kinase in response to ABA and binds to 14-3-3 protein in a phosphorylation-dependent manner in guard-cell protoplasts (GCPs) from Vicia faba. Subsequently, ABA-dependent phosphorylated proteins were identified as basic helix-loop-helix transcription factors, named ABA-responsive kinase substrates (AKSs) in GCPs from Arabidopsis thaliana. However, whether the 61 kDa protein in Vicia GCPs is an AKS is unclear. We performed immunoprecipitation of ABA-treated Vicia GCPs using anti-14-3-3 protein antibodies and identified several AKS isoforms in V. faba (VfAKSs) by mass spectrometry. The 61 kDa protein was identified as VfAKS1. Phosphoproteomic analysis revealed that VfAKSs are phosphorylated at Ser residues, which are important for 14-3-3 protein binding and monomerisation, in response to ABA in GCPs. Orthologs of AtABCG40, an ABA importer in guard cells, and CHC1, a clathrin heavy chain and a regulator of stomatal movement, also co-immunoprecipitated with 14-3-3 protein from guard cells.
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Affiliation(s)
- Yuki Hayashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yohei Takahashi
- Cell and Developmental Biology Section, Division of Biological Sciences, University of California San Diego, San Diego, CA, United States
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Kohei Fukatsu
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yasuomi Tada
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Koji Takahashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Toshinori Kinoshita
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
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14
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Nomoto M, Skelly MJ, Itaya T, Mori T, Suzuki T, Matsushita T, Tokizawa M, Kuwata K, Mori H, Yamamoto YY, Higashiyama T, Tsukagoshi H, Spoel SH, Tada Y. Suppression of MYC transcription activators by the immune cofactor NPR1 fine-tunes plant immune responses. Cell Rep 2021; 37:110125. [PMID: 34910911 DOI: 10.1016/j.celrep.2021.110125] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 10/05/2021] [Accepted: 11/23/2021] [Indexed: 12/13/2022] Open
Abstract
Plants tailor immune responses to defend against pathogens with different lifestyles. In this process, antagonism between the immune hormones salicylic acid (SA) and jasmonic acid (JA) optimizes transcriptional signatures specifically to the attacker encountered. Antagonism is controlled by the transcription cofactor NPR1. The indispensable role of NPR1 in activating SA-responsive genes is well understood, but how it functions as a repressor of JA-responsive genes remains unclear. Here, we demonstrate that SA-induced NPR1 is recruited to JA-responsive promoter regions that are co-occupied by a JA-induced transcription complex consisting of the MYC2 activator and MED25 Mediator subunit. In the presence of SA, NPR1 physically associates with JA-induced MYC2 and inhibits transcriptional activation by disrupting its interaction with MED25. Importantly, NPR1-mediated inhibition of MYC2 is a major immune mechanism for suppressing pathogen virulence. Thus, NPR1 orchestrates the immune transcriptome not only by activating SA-responsive genes but also by acting as a corepressor of JA-responsive MYC2.
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Affiliation(s)
- Mika Nomoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Aichi 464-8602, Japan; Center for Gene Research, Nagoya University, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Michael J Skelly
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Tomotaka Itaya
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Tsuyoshi Mori
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Takamasa Suzuki
- JST ERATO Higashiyama Live-Holonics Project, Nagoya University, Chikusa, Nagoya, Aichi 464-8602, Japan; College of Bioscience and Biotechnology, Chubu University, Aichi 487-8501, Japan
| | - Tomonao Matsushita
- Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Mutsutomo Tokizawa
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Hitoshi Mori
- Graduate School of Agriculture, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan
| | | | - Tetsuya Higashiyama
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Aichi 464-8602, Japan; JST ERATO Higashiyama Live-Holonics Project, Nagoya University, Chikusa, Nagoya, Aichi 464-8602, Japan; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Hironaka Tsukagoshi
- Faculty of Agriculture, Meijo University, Tenpaku, Nagoya, Aichi 468-8502, Japan
| | - Steven H Spoel
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
| | - Yasuomi Tada
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Aichi 464-8602, Japan; Center for Gene Research, Nagoya University, Chikusa, Nagoya, Aichi 464-8602, Japan.
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15
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Takeuchi T, Tatsukawa H, Shinoda Y, Kuwata K, Nishiga M, Takahashi H, Hase N, Hitomi K. Spatially Resolved Identification of Transglutaminase Substrates by Proteomics in Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2021; 65:319-330. [PMID: 34264172 DOI: 10.1165/rcmb.2021-0012oc/suppl_file/disclosures.pdf] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is characterized by the invariably progressive deposition of fibrotic tissue in the lungs and overall poor prognosis. TG2 (transglutaminase 2) is an enzyme that crosslinks glutamine and lysine residues and is involved in IPF pathogenesis. Despite the accumulating evidence implicating TG2 as a critical enzyme, the causative function and direct target of TG2 relating to this pathogenesis remain unelucidated. Here, we clarified the distributions of TG2 protein/activity and conducted quantitative proteomics analyses of possible substrates crosslinked by TG2 on unfixed lung sections in a mouse pulmonary fibrosis model. We identified 126 possible substrates as markedly TG2-dependently increased in fibrotic lung. Gene ontology analysis revealed that these identified proteins were mostly enriched in the lipid metabolic process, immune system process, and protein transport. In addition, these proteins were enriched in 21 pathways, including phagosome, lipid metabolism, several immune responses, and protein processing in endoplasmic reticulum. Furthermore, the network analyses screened out the six clusters and top 20 hub proteins with higher scores, which are related to endoplasmic reticulum stress and peroxisome proliferator-activated receptor signals. Several enriched pathways and categories were identified, some of which were the same terms based on transcription analysis in IPF. Our results provide novel pathological molecular networks driven by protein crosslinking via TG2, which can lead to the development of new therapeutic targets for IPF.
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Affiliation(s)
- Taishu Takeuchi
- Cellular Biochemistry Laboratory, Graduate School of Pharmaceutical Sciences, and
| | - Hideki Tatsukawa
- Cellular Biochemistry Laboratory, Graduate School of Pharmaceutical Sciences, and
| | - Yoshiki Shinoda
- Cellular Biochemistry Laboratory, Graduate School of Pharmaceutical Sciences, and
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules, Nagoya University, Tokai National Higher Education and Research System, Furo-cho, Chikusa, Nagoya, Japan; and
| | - Miyuki Nishiga
- Teijin Institute for Bio-Medical Research, Teijin Pharma Limited, Hino, Tokyo, Japan
| | - Hiroshi Takahashi
- Teijin Institute for Bio-Medical Research, Teijin Pharma Limited, Hino, Tokyo, Japan
| | - Naoki Hase
- Teijin Institute for Bio-Medical Research, Teijin Pharma Limited, Hino, Tokyo, Japan
| | - Kiyotaka Hitomi
- Cellular Biochemistry Laboratory, Graduate School of Pharmaceutical Sciences, and
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16
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Yoshii T, Oki C, Watahiki R, Nakamura A, Tahara K, Kuwata K, Furuta T, Tsukiji S. Chemo-optogenetic Protein Translocation System Using a Photoactivatable Self-Localizing Ligand. ACS Chem Biol 2021; 16:1557-1565. [PMID: 34339163 DOI: 10.1021/acschembio.1c00416] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Manipulating subcellular protein localization using light is a powerful approach for controlling signaling processes with high spatiotemporal precision. The most widely used strategy for this is based on light-induced protein heterodimerization. The use of small synthetic molecules that can control the localization of target proteins in response to light without the need for a second protein has several advantages. However, such methods have not been well established. Herein, we present a chemo-optogenetic approach for controlling protein localization using a photoactivatable self-localizing ligand (paSL). We developed a paSL that can recruit tag-fused proteins of interest from the cytoplasm to the plasma membrane within seconds upon light illumination. This paSL-induced protein translocation (paSLIPT) is reversible and enables the spatiotemporal control of signaling processes in living cells, even in a local region. paSLIPT can also be used to implement simultaneous optical stimulation and multiplexed imaging of molecular processes in a single cell, offering an attractive and novel chemo-optogenetic platform for interrogating and engineering dynamic cellular functions.
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Affiliation(s)
- Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Choji Oki
- Department of Nanopharmaceutical Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Rei Watahiki
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan
| | - Akinobu Nakamura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
| | - Kai Tahara
- Department of Nanopharmaceutical Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Toshiaki Furuta
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
- Department of Nanopharmaceutical Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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17
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18
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Takeuchi T, Tatsukawa H, Shinoda Y, Kuwata K, Nishiga M, Takahashi H, Hase N, Hitomi K. Spatially Resolved Identification of Transglutaminase Substrates by Proteomics in Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2021; 65:319-330. [PMID: 34264172 DOI: 10.1165/rcmb.2021-0012oc] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is characterized by the invariably progressive deposition of fibrotic tissue in the lungs and overall poor prognosis. Transglutaminase 2 (TG2) is an enzyme that crosslinks glutamine and lysine residues and is involved in IPF pathogenesis. Despite the accumulating evidence implicating TG2 as a critical enzyme, the causative function and direct target of TG2 relating to this pathogenesis remain unelucidated. Here, we clarified the distributions of TG2 protein/activity and conducted quantitative proteomics analyses of possible substrates crosslinked by TG2 on unfixed lung sections in a mouse pulmonary fibrosis model. We identified 126 possible substrates as markedly increased TG2-dependently in fibrotic lung. Gene ontology analysis revealed that these identified proteins were mostly enriched in the lipid metabolic process, immune system process, and protein transport. In addition, these proteins enriched in the 21 pathways including phagosome, lipid metabolism, several immune responses, and protein processing in endoplasmic reticulum. Furthermore, the network analyses screened out the 6 clusters and top 20 hub proteins with higher scores, which are related to ER stress and peroxisome proliferator-activated receptor signals. Several enriched pathways and categories were identified, and some of which were the same terms based on transcription analysis in IPF. Our results provide novel pathological molecular networks driven by protein crosslinking via TG2, which can lead to the development of new therapeutic targets for IPF.
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Affiliation(s)
- Taishu Takeuchi
- Tokai National Higher Education and Research System, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Hideki Tatsukawa
- Tokai National Higher Education and Research System, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan;
| | - Yoshiki Shinoda
- Tokai National Higher Education and Research System, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Keiko Kuwata
- Tokai National Higher Education and Research System, Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Nagoya, Japan
| | | | | | | | - Kiyotaka Hitomi
- Tokai National Higher Education and Research System, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
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19
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Eguchi A, Ueki A, Hoshiyama J, Kuwata K, Chikaoka Y, Kawamura T, Nagatoishi S, Tsumoto K, Ueki R, Sando S. A DNA Aptamer That Inhibits the Aberrant Signaling of Fibroblast Growth Factor Receptor in Cancer Cells. JACS Au 2021; 1:578-585. [PMID: 34467321 PMCID: PMC8395645 DOI: 10.1021/jacsau.0c00121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Indexed: 06/13/2023]
Abstract
Growth factor receptors are activated through dimerization by the binding of their ligands and play pivotal roles in normal cell function. However, the aberrant activity of the receptors has been associated with cancer malignancy. One of the main causes of the aberrant receptor activation is the overexpression of receptors and the resultant formation of unliganded receptor dimers, which can be activated in the absence of external ligand molecules. Thus, the unliganded receptor dimer is a promising target to inhibit aberrant signaling in cancer. Here, we report an aptamer that specifically binds to fibroblast growth factor receptor 2b and inhibits the aberrant receptor activation and signaling. Our investigation suggests that this aptamer inhibits the formation of the receptor dimer occurring in the absence of external ligand molecules. This work presents a new inhibitory function of aptamers and the possibility of oligonucleotide-based therapeutics for cancer.
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Affiliation(s)
- Akihiro Eguchi
- Department of Chemistry and Biotechnology andDepartment of Bioengineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ayaka Ueki
- Department of Chemistry and Biotechnology andDepartment of Bioengineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Junya Hoshiyama
- Department of Chemistry and Biotechnology andDepartment of Bioengineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Keiko Kuwata
- Institute
of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Yoko Chikaoka
- Proteomics
Laboratory, Isotope Science Center, The
University of Tokyo, 2-11-16, Yayoi, Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Takeshi Kawamura
- Proteomics
Laboratory, Isotope Science Center, The
University of Tokyo, 2-11-16, Yayoi, Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Satoru Nagatoishi
- The
Institute of Medical Science, The University
of Tokyo, 4-6-1 Shirokanedai,
Minato-ku, Tokyo 108-8639, Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology andDepartment of Bioengineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- The
Institute of Medical Science, The University
of Tokyo, 4-6-1 Shirokanedai,
Minato-ku, Tokyo 108-8639, Japan
| | - Ryosuke Ueki
- Department of Chemistry and Biotechnology andDepartment of Bioengineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology andDepartment of Bioengineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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20
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Moriya SS, Shibasaki H, Kohara M, Kuwata K, Imamura Y, Demizu Y, Kurihara M, Kittaka A, Sugiyama T. Synthesis and characterization of PNA oligomers containing preQ 1 as a positively charged guanine analogue. Bioorg Med Chem Lett 2021; 39:127850. [PMID: 33662538 DOI: 10.1016/j.bmcl.2021.127850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/28/2021] [Accepted: 02/05/2021] [Indexed: 10/22/2022]
Abstract
We report the synthesis of a peptide nucleic acid (PNA) monomer containing preQ1, a positively charged guanine analogue. The new monomer was incorporated into PNA oligomers using standard Fmoc-chemistry-based solid-phase synthesis. The preQ1 unit-containing PNA oligomers exhibited improved affinity for their complementary DNA through electrostatic attraction, and their sequence specificity was not compromised. It could be beneficial to incorporate preQ1 into PNA oligomers instead of guanine when creating antisense/antigene agents or research tools.
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Affiliation(s)
- Shun-Suke Moriya
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Hatsune Shibasaki
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Misaki Kohara
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yasutada Imamura
- Faculty of Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, Ministry of Health and Welfare, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Masaaki Kurihara
- School of Pharmacy, International University of Health and Welfare, 2600-1, Kitakanemaru, Ohtawara, Tochigi 324-8501, Japan
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan.
| | - Toru Sugiyama
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan.
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21
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Islam M, Inoue T, Hiraide M, Khatun N, Jahan A, Kuwata K, Katagiri S, Umezawa T, Yotsui I, Sakata Y, Takezawa D. Activation of SnRK2 by Raf-like kinase ARK represents a primary mechanism of ABA and abiotic stress responses. Plant Physiol 2021; 185:533-546. [PMID: 33655297 PMCID: PMC8133623 DOI: 10.1093/plphys/kiaa046] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 11/10/2020] [Indexed: 05/25/2023]
Abstract
The Raf-like protein kinase abscisic acid (ABA) and abiotic stress-responsive Raf-like kinase (ARK) previously identified in the moss Physcomitrium (Physcomitrella) patens acts as an upstream regulator of subgroup III SNF1-related protein kinase2 (SnRK2), the key regulator of ABA and abiotic stress responses. However, the mechanisms underlying activation of ARK by ABA and abiotic stress for the regulation of SnRK2, including the role of ABA receptor-associated group A PP2C (PP2C-A), are not understood. We identified Ser1029 as the phosphorylation site in the activation loop of ARK, which provided a possible mechanism for regulation of its activity. Analysis of transgenic P. patens ark lines expressing ARK-GFP with Ser1029-to-Ala mutation indicated that this replacement causes reductions in ABA-induced gene expression, stress tolerance, and SnRK2 activity. Immunoblot analysis using an anti-phosphopeptide antibody indicated that ABA treatments rapidly stimulate Ser1029 phosphorylation in the wild type (WT). The phosphorylation profile of Ser1029 in ABA-hypersensitive ppabi1 lacking protein phosphatase 2C-A (PP2C-A) was similar to that in the WT, whereas little Ser1029 phosphorylation was observed in ABA-insensitive ark missense mutant lines. Furthermore, newly isolated ppabi1 ark lines showed ABA-insensitive phenotypes similar to those of ark lines. Therefore, ARK is a primary activator of SnRK2, preceding negative regulation by PP2C-A in bryophytes, which provides a prototype mechanism for ABA and abiotic stress responses in plants.
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Affiliation(s)
- Mousona Islam
- Graduate School of Science and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
- Plant Tissue Culture Section, Biological Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka 1205, Bangladesh
| | - Takumi Inoue
- Graduate School of Science and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Mayuka Hiraide
- Graduate School of Science and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Nobiza Khatun
- Graduate School of Science and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Akida Jahan
- Graduate School of Science and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Sotaro Katagiri
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei City, Tokyo 184-8588, Japan
| | - Taishi Umezawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei City, Tokyo 184-8588, Japan
| | - Izumi Yotsui
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yoichi Sakata
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Daisuke Takezawa
- Graduate School of Science and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan
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22
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Ohkubo Y, Kuwata K, Matsubayashi Y. A type 2C protein phosphatase activates high-affinity nitrate uptake by dephosphorylating NRT2.1. Nat Plants 2021; 7:310-316. [PMID: 33686225 DOI: 10.1038/s41477-021-00870-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
The nitrate transporter NRT2.1, which plays a central role in high-affinity nitrate uptake in roots, is activated at the post-translational level in response to nitrogen (N) starvation1,2. However, the critical enzymes required for the post-translational activation of NRT2.1 remain to be identified. Here, we show that a type 2C protein phosphatase, designated CEPD-induced phosphatase (CEPH), activates high-affinity nitrate uptake by directly dephosphorylating Ser501 of NRT2.1, a residue that functions as a negative phospho-switch in Arabidopsis2. CEPH is predominantly expressed in epidermal and cortex cells in roots and is upregulated by N starvation via a CEPDL2/CEPD1/2-mediated long-distance signalling from shoots3,4. The loss of CEPH leads to marked decreases in high-affinity nitrate uptake, tissue nitrate content and plant biomass. Collectively, our results identify CEPH as a crucial enzyme in the N-starvation-dependent activation of NRT2.1 and provide molecular and mechanistic insights into how plants regulate high-affinity nitrate uptake at the post-translational level in response to the N environment.
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Affiliation(s)
- Yuri Ohkubo
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Yoshikatsu Matsubayashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan.
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23
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Inukai R, Mori K, Kuwata K, Suzuki C, Maki M, Takahara T, Shibata H. The Novel ALG-2 Target Protein CDIP1 Promotes Cell Death by Interacting with ESCRT-I and VAPA/B. Int J Mol Sci 2021; 22:ijms22031175. [PMID: 33503978 PMCID: PMC7865452 DOI: 10.3390/ijms22031175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 12/15/2022] Open
Abstract
Apoptosis-linked gene 2 (ALG-2, also known as PDCD6) is a member of the penta-EF-hand (PEF) family of Ca2+-binding proteins. The murine gene encoding ALG-2 was originally reported to be an essential gene for apoptosis. However, the role of ALG-2 in cell death pathways has remained elusive. In the present study, we found that cell death-inducing p53 target protein 1 (CDIP1), a pro-apoptotic protein, interacts with ALG-2 in a Ca2+-dependent manner. Co-immunoprecipitation analysis of GFP-fused CDIP1 (GFP-CDIP1) revealed that GFP-CDIP1 associates with tumor susceptibility gene 101 (TSG101), a known target of ALG-2 and a subunit of endosomal sorting complex required for transport-I (ESCRT-I). ESCRT-I is a heterotetrameric complex composed of TSG101, VPS28, VPS37 and MVB12/UBAP1. Of diverse ESCRT-I species originating from four VPS37 isoforms (A, B, C, and D), CDIP1 preferentially associates with ESCRT-I containing VPS37B or VPS37C in part through the adaptor function of ALG-2. Overexpression of GFP-CDIP1 in HEK293 cells caused caspase-3/7-mediated cell death. In addition, the cell death was enhanced by co-expression of ALG-2 and ESCRT-I, indicating that ALG-2 likely promotes CDIP1-induced cell death by promoting the association between CDIP1 and ESCRT-I. We also found that CDIP1 binds to vesicle-associated membrane protein-associated protein (VAP)A and VAPB through the two phenylalanines in an acidic tract (FFAT)-like motif in the C-terminal region of CDIP1, mutations of which resulted in reduction of CDIP1-induced cell death. Therefore, our findings suggest that different expression levels of ALG-2, ESCRT-I subunits, VAPA and VAPB may have an impact on sensitivity of anticancer drugs associated with CDIP1 expression.
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Affiliation(s)
- Ryuta Inukai
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; (R.I.); (K.M.); (C.S.); (M.M.); (T.T.)
| | - Kanako Mori
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; (R.I.); (K.M.); (C.S.); (M.M.); (T.T.)
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan;
| | - Chihiro Suzuki
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; (R.I.); (K.M.); (C.S.); (M.M.); (T.T.)
| | - Masatoshi Maki
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; (R.I.); (K.M.); (C.S.); (M.M.); (T.T.)
| | - Terunao Takahara
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; (R.I.); (K.M.); (C.S.); (M.M.); (T.T.)
| | - Hideki Shibata
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; (R.I.); (K.M.); (C.S.); (M.M.); (T.T.)
- Correspondence:
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24
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Lu Y, Maruyama J, Kuwata K, Fukuda H, kiIwasa H, Arimoto-Matsuzaki K, Sugimura H, Hata Y. Retraction notice to "Doublecortin-like kinase 1 compromises DNA repair and induces chromosomal instability" [BBREP 16C (2018) 130-137]. Biochem Biophys Rep 2020; 24:100799. [PMID: 33381661 PMCID: PMC7767794 DOI: 10.1016/j.bbrep.2020.100799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
[This retracts the article DOI: 10.1016/j.bbrep.2018.10.014.].
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Affiliation(s)
- Yuxiong Lu
- Department of Medical Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Junichi Maruyama
- Department of Medical Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601, Japan
| | - Hiroyuki Fukuda
- Agilent Technologies Research Alliance Laboratory, Graduate School of Science, Osaka University, Osaka, 565-0871 Japan
- Agilent Technologies Japan, Ltd., Hachioji-shi, Tokyo, 192-8510, Japan
| | - Hiroa kiIwasa
- Department of Medical Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Kyoko Arimoto-Matsuzaki
- Department of Medical Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Haruhiko Sugimura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Hamamatsu, 431-3152, Japan
| | - Yutaka Hata
- Department of Medical Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
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25
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Miura C, Shindo N, Okamoto K, Kuwata K, Ojida A. Fragment-Based Discovery of Irreversible Covalent Inhibitors of Cysteine Proteases Using Chlorofluoroacetamide Library. Chem Pharm Bull (Tokyo) 2020; 68:1074-1081. [PMID: 33132374 DOI: 10.1248/cpb.c20-00547] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fragment-based approach combined with electrophilic reactive compounds is a powerful strategy to discover novel covalent ligands for protein target. However, the promiscuous reactivity often interferes with identification of the fragments possessing specific binding affinity to the targeted protein. In our study, we report the fragment-based covalent drug discovery using the chemically tuned weak reactivity of chlorofluoroacetamide (CFA). We constructed a small fragment library composed of 30 CFA-appended compounds and applied it to the covalent ligand screening for cysteine protease papain as a model protein target. Using the fluorescence enzymatic assay, we identified CFA-benzothiazole 30 as a papain inhibitor, which was found to irreversibly inactivate papain upon enzyme kinetic analysis. The formation of the covalent papain-30 adduct was confirmed using electrospray ionization mass spectrometry analysis. The activity-based protein profiling (ABPP) experiment using an alkynylated analog of 30 (i.e., 30-yne) revealed that 30-yne covalently labeled papain with high selectivity. These data demonstrate potential utility of the CFA-fragment library for de novo discovery of target selective covalent inhibitors.
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Affiliation(s)
- Chizuru Miura
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | - Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | - Kei Okamoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University
| | - Keiko Kuwata
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University
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26
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Inoue S, Morita R, Kuwata K, Ishii K, Minami Y. Detection of candidate proteins in the indican biosynthetic pathway of Persicaria tinctoria (Polygonum tinctorium) using protein-protein interactions and transcriptome analyses. Phytochemistry 2020; 179:112507. [PMID: 32931962 DOI: 10.1016/j.phytochem.2020.112507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
Persicaria tinctoria (Polygonum tinctorium) synthesizes indican (indoxyl-β-D-glucoside) as a specialized metabolite. Indican is synthesized in the cytosol of leaf cells from indoxyl and UDP-glucose by the catalysis of indoxyl-β-D-glucoside synthase (PtIGS), then transported into vacuoles. As a portion of PtIGS is found on the microsomal membrane, we assume that it is present on the ER membrane as a large complex involving other indican metabolism-related proteins. Based on this hypothesis, the existence of such a complex was investigated using two separate approaches: a protein-protein interaction assay and transcriptome analysis. We first performed a co-immunoprecipitation using the anti-PtIGS antibody and a pull-down assay using recombinant PtIGS, then identified the candidate proteins through MS/MS analysis. Secondly, we performed a transcriptome analysis to examine the differential gene expression between the first and the second leaves. The expressions of candidate genes detected by protein-protein interaction analyses were collated with transcriptome data and validated by quantitative reverse transcription polymerase chain reaction, showing that the expression of sucrose synthase and cytochrome P450 genes decreased in the second leaves compared with the first leaves. Furthermore, we detected several additional proteins, such as heat shock and cytoskeletal proteins, suggesting that PtIGS may form a large complex, a metabolon.
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Affiliation(s)
- Shintaro Inoue
- Okayama University of Science, Department of Biochemistry, Faculty of Science, 1-1 Ridai-cho, Kita-ku, Okayama, 700-0005, Japan
| | - Rihito Morita
- Okayama University of Science, Department of Biochemistry, Faculty of Science, 1-1 Ridai-cho, Kita-ku, Okayama, 700-0005, Japan
| | - Keiko Kuwata
- Nagoya University, Institute of Transformative Bio-Molecules (WPI-ITbM), Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Kazuo Ishii
- Kurume University, Biostatistics Center, 67 Asahi-machi, Kurume, 830-0011, Japan
| | - Yoshiko Minami
- Okayama University of Science, Department of Biochemistry, Faculty of Science, 1-1 Ridai-cho, Kita-ku, Okayama, 700-0005, Japan.
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27
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Tokunaga K, Sato M, Kuwata K, Miura C, Fuchida H, Matsunaga N, Koyanagi S, Ohdo S, Shindo N, Ojida A. Bicyclobutane Carboxylic Amide as a Cysteine-Directed Strained Electrophile for Selective Targeting of Proteins. J Am Chem Soc 2020; 142:18522-18531. [PMID: 33047956 DOI: 10.1021/jacs.0c07490] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Expanding the repertoire of electrophiles with unique reactivity features would facilitate the development of covalent inhibitors with desirable reactivity profiles. We herein introduce bicyclo[1.1.0]butane (BCB) carboxylic amide as a new class of thiol-reactive electrophiles for selective and irreversible inhibition of targeted proteins. We first streamlined the synthetic routes to generate a variety of BCB amides. The strain-driven nucleophilic addition to BCB amides proceeded chemoselectively with cysteine thiols under neutral aqueous conditions, the rate of which was significantly slower than that of acrylamide. This reactivity profile of BCB amide was successfully exploited to develop covalent ligands targeting Bruton's tyrosine kinase (BTK). By tuning BCB amide reactivity and optimizing its disposition on the ligand, we obtained a selective covalent inhibitor of BTK. The in-gel activity-based protein profiling and mass spectrometry-based chemical proteomics revealed that the selected BCB amide had a higher target selectivity for BTK in human cells than did a Michael acceptor probe. Further chemical proteomic study revealed that BTK probes bearing different classes of electrophiles exhibited distinct off-target profiles. This result suggests that incorporation of BCB amide as a cysteine-directed electrophile could expand the capability to develop covalent inhibitors with the desired proteome reactivity profile.
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Affiliation(s)
- Keisuke Tokunaga
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mami Sato
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furocho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Chizuru Miura
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hirokazu Fuchida
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Matsunaga
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Satoru Koyanagi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shigehiro Ohdo
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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28
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Hasegawa K, Kuwata K, Yoshitake J, Shimomura S, Uchida K, Shibata T. Extracellular vesicles derived from inflamed murine colorectal tissue induce fibroblast proliferation via epidermal growth factor receptor. FEBS J 2020; 288:1906-1917. [PMID: 32894891 DOI: 10.1111/febs.15557] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/22/2020] [Accepted: 09/01/2020] [Indexed: 12/26/2022]
Abstract
Inflammatory bowel diseases (IBDs), such as Crohn's disease and ulcerative colitis, are chronic inflammatory disorders of the gastrointestinal tract. Although IBDs increase the risk of colitis-associated colon cancer, the underlying mechanisms are not fully understood. Extracellular vesicles (EVs) are lipid-bound sacs that transport proteins, RNA, and lipids between cells and are key mediators of cellular communication in both physiological and pathological settings. EVs have been implicated in many cancer hallmarks, including uncontrolled tumor growth and metastasis. In this study, we investigated the effects of colon-derived EVs on the proliferation of fibroblasts. We used comparative proteomics to characterize protein profiles of colorectal EVs isolated from healthy mice (Con-EVs) and those with dextran sulfate sodium-induced colitis (IBD-EVs). The results showed that 109 proteins were upregulated in IBD-EVs. Notably, expression of epidermal growth factor receptor (EGFR), which plays important roles in cell proliferation and development, was increased in IBD-EVs. We then examined the effect of EVs on murine NIH3T3 fibroblasts and found that IBD-EVs significantly promoted cell proliferation in EGFR- and ERK-dependent manner. Our findings suggest that inflamed colon-derived EVs promote tumor development thorough activation of fibroblasts.
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Affiliation(s)
- Kana Hasegawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Japan
| | - Jun Yoshitake
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Japan
| | - Sayako Shimomura
- Graduate School of Bioagricultural Sciences, Nagoya University, Japan
| | - Koji Uchida
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.,Japan Agency for Medical Research and Development, CREST, Tokyo, Japan
| | - Takahiro Shibata
- Graduate School of Bioagricultural Sciences, Nagoya University, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Japan
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29
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Yoshii T, Tahara K, Suzuki S, Hatano Y, Kuwata K, Tsukiji S. An Improved Intracellular Synthetic Lipidation-Induced Plasma Membrane Anchoring System for SNAP-Tag Fusion Proteins. Biochemistry 2020; 59:3044-3050. [DOI: 10.1021/acs.biochem.0c00410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kai Tahara
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
| | - Sachio Suzuki
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
| | - Yuka Hatano
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
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30
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Sato M, Fuchida H, Shindo N, Kuwata K, Tokunaga K, Xiao-Lin G, Inamori R, Hosokawa K, Watari K, Shibata T, Matsunaga N, Koyanagi S, Ohdo S, Ono M, Ojida A. Selective Covalent Targeting of Mutated EGFR(T790M) with Chlorofluoroacetamide-Pyrimidines. ACS Med Chem Lett 2020; 11:1137-1144. [PMID: 32550993 DOI: 10.1021/acsmedchemlett.9b00574] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/08/2020] [Indexed: 12/14/2022] Open
Abstract
Covalent modification of disease-associated proteins with small molecules is a powerful approach for achieving an increased and sustained pharmacological effect. To reduce the potential risk of nonselective covalent modification, molecular design of covalent inhibitors is critically important. We report herein the development of a targeted covalent inhibitor for mutated epidermal growth factor receptor (EGFR) (L858R/T790M) using α-chlorofluoroacetamide (CFA) as the reactive group. The chemically tuned weak reactivity of CFA was suitable for the design of third-generation EGFR inhibitors that possess the pyrimidine scaffold. The structure-activity relationship study revealed that CFA inhibitor 18 (NSP-037) possessed higher inhibition selectivity to the mutated EGFR over wild-type EGFR when compared to clinically approved osimertinib. Mass-based chemical proteomics analyses further revealed that 18 displayed high covalent modification selectivity for the mutated EGFR in living cells. These findings highlight the utility of CFA as a warhead of targeted covalent inhibitors and the potential application of the CFA-pyrimidines for treatment of non-small-cell lung cancer.
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Affiliation(s)
- Mami Sato
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hirokazu Fuchida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan
| | - Keisuke Tokunaga
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Guo Xiao-Lin
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Ryo Inamori
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Keitaro Hosokawa
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kosuke Watari
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Tomohiro Shibata
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Matsunaga
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Satoru Koyanagi
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shigehiro Ohdo
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mayumi Ono
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Kuwata K, Itou K, Kotani M, Ohmura T, Naito Y. DIUTHAME enables matrix-free mass spectrometry imaging of frozen tissue sections. Rapid Commun Mass Spectrom 2020; 34:e8729. [PMID: 31951673 DOI: 10.1002/rcm.8729] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/10/2020] [Accepted: 01/15/2020] [Indexed: 06/10/2023]
Abstract
RATIONALE A recently developed matrix-free laser desorption/ionization method, DIUTHAME (desorption ionization using through-hole alumina membrane), was examined for the feasibility of mass spectrometry imaging (MSI) applied to frozen tissue sections. The permeation behavior of DIUTHAME is potentially useful for MSI as positional information may not be distorted during the extraction of analytes from a sample. METHODS The through-hole porous alumina membranes used in the DIUTHAME chips were fabricated by wet anodization, were 5 μm thick, and had the desired values of 200 nm through-hole diameter and 50% open aperture ratio. Mouse brain frozen tissue sections on indium tin oxide (ITO)-coated slides were covered using the DIUTHAME chips and were subjected to MSI experiments in commercial time-of-flight mass spectrometers equipped with solid-state UV lasers after thawing and drying without matrix application. RESULT Mass spectra and mass images were successfully obtained from the frozen tissue sections using DIUTHAME as the ionization method. The mass spectra contained rich peaks in the phospholipid mass range free from the chemical background owing to there being no matrix-derived peaks in that range. DIUTHAME-MSI delivered high-quality mass images that reflected the anatomy of the brain tissue. CONCLUSIONS Analytes can be extracted from frozen tissue by capillary action of the through-holes in DIUTHAME and moisture contained in the tissue without distorting positional information of the analytes. The sample preparation for frozen tissue sections in DIUTHAME-MSI is simple, requiring no specialized skills or dedicated apparatus for matrix application. DIUTHAME can facilitate MSI at a low mass, as there is no interference from matrix-derived peaks, and should provide high-quality, reproducible mass images more easily than MALDI-MSI.
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Affiliation(s)
- Keiko Kuwata
- Nagoya University Institute of Transformative Bio-Molecules (WPI-ITbM), Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Kayoko Itou
- Nagoya University Institute of Transformative Bio-Molecules (WPI-ITbM), Furo-cho, Chikusa-ku, Nagoya, Japan
| | | | | | - Yasuhide Naito
- The Graduate School for the Creation of New Photonics Industries, 1955-1 Kurematsu-cho, Nishi-ku, Hamamatsu, Japan
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Nakamura A, Oki C, Sawada S, Yoshii T, Kuwata K, Rudd AK, Devaraj NK, Noma K, Tsukiji S. Designer Palmitoylation Motif-Based Self-Localizing Ligand for Sustained Control of Protein Localization in Living Cells and Caenorhabditis elegans. ACS Chem Biol 2020; 15:837-843. [PMID: 32182034 DOI: 10.1021/acschembio.0c00014] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Inducing protein translocation to the plasma membrane (PM) is an important approach for manipulating diverse signaling molecules/pathways in living cells. We previously devised a new chemogenetic system, in which a protein fused to Escherichia coli dihydrofolate reductase (eDHFR) can be rapidly translocated from the cytoplasm to the PM using a trimethoprim (TMP)-based self-localizing ligand (SL), mgcTMP. However, mgcTMP-induced protein translocation turned out to be transient and spontaneously reversed within 1 h, limiting its application. Here, we first demonstrated that the spontaneous reverse translocation was caused by cellular degradation of mgcTMP, presumably by proteases. To address this problem, we newly developed a proteolysis-resistant SL, mDcTMP. This mDcTMP now allows sustained PM localization of eDHFR-fusion proteins (over several hours to a day), and it was applicable to inducing prolonged signal activation and cell differentiation. mDcTMP also worked in live nematodes, making it an attractive new tool for probing and controlling living systems.
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Affiliation(s)
- Akinobu Nakamura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Choji Oki
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Shunsuke Sawada
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Andrew K. Rudd
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Neal K. Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Kentaro Noma
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Group of Nutritional Neuroscience, Neuroscience Institute, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- Frontier Research Institute for Materials Science (FRIMS), Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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Nakamura A, Oki C, Kato K, Fujinuma S, Maryu G, Kuwata K, Yoshii T, Matsuda M, Aoki K, Tsukiji S. Engineering Orthogonal, Plasma Membrane-Specific SLIPT Systems for Multiplexed Chemical Control of Signaling Pathways in Living Single Cells. ACS Chem Biol 2020; 15:1004-1015. [PMID: 32162909 DOI: 10.1021/acschembio.0c00024] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Most cell behaviors are the outcome of processing information from multiple signals generated upon cell stimulation. Thus, a systematic understanding of cellular systems requires methods that allow the activation of more than one specific signaling molecule or pathway within a cell. However, the construction of tools suitable for such multiplexed signal control remains challenging. In this work, we aimed to develop a platform for chemically manipulating multiple signaling molecules/pathways in living mammalian cells based on self-localizing ligand-induced protein translocation (SLIPT). SLIPT is an emerging chemogenetic tool that controls protein localization and cell signaling using synthetic self-localizing ligands (SLs). Focusing on the inner leaflet of the plasma membrane (PM), where there is a hub of intracellular signaling networks, here we present the design and engineering of two new PM-specific SLIPT systems based on an orthogonal eDHFR and SNAP-tag pair. These systems rapidly induce translocation of eDHFR- and SNAP-tag-fusion proteins from the cytoplasm to the PM specifically in a time scale of minutes upon addition of the corresponding SL. We then show that the combined use of the two systems enables chemically inducible, individual translocation of two distinct proteins in the same cell. Finally, by integrating the orthogonal SLIPT systems with fluorescent reporters, we demonstrate simultaneous multiplexed activation and fluorescence imaging of endogenous ERK and Akt activities in a single cell. Collectively, orthogonal PM-specific SLIPT systems provide a powerful new platform for multiplexed chemical signal control in living single cells, offering new opportunities for dissecting cell signaling networks and synthetic cell manipulation.
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Affiliation(s)
- Akinobu Nakamura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Choji Oki
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Kenya Kato
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Satoko Fujinuma
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Gembu Maryu
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Michiyuki Matsuda
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhiro Aoki
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, Faculty of Life Science, SOKENDAI, The Graduate University for Advanced Studies, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- Frontier Research Institute for Materials Science (FRIMS), Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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34
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Yamada K, Goto-Yamada S, Nakazaki A, Kunieda T, Kuwata K, Nagano AJ, Nishimura M, Hara-Nishimura I. Endoplasmic reticulum-derived bodies enable a single-cell chemical defense in Brassicaceae plants. Commun Biol 2020; 3:21. [PMID: 31937912 PMCID: PMC6959254 DOI: 10.1038/s42003-019-0739-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/10/2019] [Indexed: 01/23/2023] Open
Abstract
Brassicaceae plants have a dual-cell type of chemical defense against herbivory. Here, we show a novel single-cell defense involving endoplasmic reticulum (ER)-derived organelles (ER bodies) and the vacuoles. We identify various glucosinolates as endogenous substrates of the ER-body β-glucosidases BGLU23 and BGLU21. Woodlice strongly prefer to eat seedlings of bglu23 bglu21 or a glucosinolate-deficient mutant over wild-type seedlings, confirming that the β-glucosidases have a role in chemical defense: production of toxic compounds upon organellar damage. Deficiency of the Brassicaceae-specific protein NAI2 prevents ER-body formation, which results in a loss of BGLU23 and a loss of resistance to woodlice. Hence, NAI2 that interacts with BGLU23 is essential for sequestering BGLU23 in ER bodies and preventing its degradation. Artificial expression of NAI2 and BGLU23 in non-Brassicaceae plants results in the formation of ER bodies, indicating that acquisition of NAI2 by Brassicaceae plants is a key step in developing their single-cell defense system. Kenji Yamada et al. describe a single-cell chemical defense strategy in Brassicaceae plants that requires formation of endoplasmic reticulum-derived organelles for the accumulation of β-glucosidases. They find that seedlings lacking a specific β-glucosidase lose their resistance to predation by woodlice.
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Affiliation(s)
- Kenji Yamada
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387, Krakow, Poland. .,Department of Cell Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan. .,Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan.
| | - Shino Goto-Yamada
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387, Krakow, Poland.,Department of Cell Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan.,Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Akiko Nakazaki
- Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Tadashi Kunieda
- Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan.,Faculty of Science and Engineering, Konan University, Kobe, 658-8501, Japan.,Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Mikio Nishimura
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan. .,Faculty of Science and Engineering, Konan University, Kobe, 658-8501, Japan.
| | - Ikuko Hara-Nishimura
- Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan. .,Faculty of Science and Engineering, Konan University, Kobe, 658-8501, Japan.
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35
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Sawada S, Nakamura A, Yoshii T, Kuwata K, Nakatsu F, Tsukiji S. Protein-recruiting synthetic molecules targeting the Golgi surface. Chem Commun (Camb) 2020; 56:15422-15425. [DOI: 10.1039/d0cc06908f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthetic molecules consisting of a small-molecule ligand and a tri-N-methylated myristoyl-Gly-Cys lipopeptide serve as chemical tools to rapidly recruit their target proteins from the cytoplasm to the Golgi surface in living cells.
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Affiliation(s)
- Shunsuke Sawada
- Department of Nanopharmaceutical Sciences
- Graduate School of Engineering
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Akinobu Nakamura
- Department of Life Science and Applied Chemistry
- Graduate School of Engineering
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry
- Graduate School of Engineering
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM)
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Fubito Nakatsu
- Department of Neurochemistry and Molecular Cell Biology
- Graduate School of Medical and Dental Sciences
- Niigata University
- Niigata 951-8510
- Japan
| | - Shinya Tsukiji
- Department of Nanopharmaceutical Sciences
- Graduate School of Engineering
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
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36
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Suzuki S, Ikuta M, Yoshii T, Nakamura A, Kuwata K, Tsukiji S. Golgi recruitment assay for visualizing small-molecule ligand–target engagement in cells. Chem Commun (Camb) 2020; 56:7961-7964. [DOI: 10.1039/d0cc02020f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A Golgi recruitment (G-REC) assay is developed as a new method for visualizing small-molecule ligand–target engagement in living cells.
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Affiliation(s)
- Sachio Suzuki
- Department of Nanopharmaceutical Sciences
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Masahiro Ikuta
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- PRESTO, Japan Science and Technology Agency (JST)
| | - Akinobu Nakamura
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM)
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Shinya Tsukiji
- Department of Nanopharmaceutical Sciences
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- Department of Life Science and Applied Chemistry
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37
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Bessho-Uehara M, Yamamoto N, Shigenobu S, Mori H, Kuwata K, Oba Y. Kleptoprotein bioluminescence: Parapriacanthus fish obtain luciferase from ostracod prey. Sci Adv 2020; 6:eaax4942. [PMID: 31934625 PMCID: PMC6949039 DOI: 10.1126/sciadv.aax4942] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
Through their diet, animals can obtain substances essential for imparting special characteristics, such as toxins in monarch butterflies and luminescent substances in jellyfishes. These substances are typically small molecules because they are less likely to be digested and may be hard for the consumer to biosynthesize. Here, we report that Parapriacanthus ransonneti, a bioluminescent fish, obtains not only its luciferin but also its luciferase enzyme from bioluminescent ostracod prey. The enzyme purified from the fish's light organs was identical to the luciferase of Cypridina noctiluca, a bioluminescent ostracod that they feed upon. Experiments where fish were fed with a related ostracod, Vargula hilgendorfii, demonstrated the specific uptake of the luciferase to the fish's light organs. This "kleptoprotein" system allows an organism to use novel functional proteins that are not encoded in its genome and provides an evolutionary alternative to DNA-based molecular evolution.
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Affiliation(s)
- Manabu Bessho-Uehara
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
- Department of Environmental Biology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Naoyuki Yamamoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Hitoshi Mori
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Keiko Kuwata
- Graduate School of Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yuichi Oba
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
- Department of Environmental Biology, Chubu University, Kasugai, Aichi 487-8501, Japan
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38
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Shimada TL, Shimada T, Okazaki Y, Higashi Y, Saito K, Kuwata K, Oyama K, Kato M, Ueda H, Nakano A, Ueda T, Takano Y, Hara-Nishimura I. HIGH STEROL ESTER 1 is a key factor in plant sterol homeostasis. Nat Plants 2019; 5:1154-1166. [PMID: 31712757 DOI: 10.1038/s41477-019-0537-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 09/18/2019] [Indexed: 05/21/2023]
Abstract
Plants strictly regulate the levels of sterol in their cells, as high sterol levels are toxic. However, how plants achieve sterol homeostasis is not fully understood. We isolated an Arabidopsis thaliana mutant that abundantly accumulated sterol esters in structures of about 1 µm in diameter in leaf cells. We designated the mutant high sterol ester 1 (hise1) and called the structures sterol ester bodies. Here, we show that HISE1, the gene product that is altered in this mutant, functions as a key factor in plant sterol homeostasis on the endoplasmic reticulum (ER) and participates in a fail-safe regulatory system comprising two processes. First, HISE1 downregulates the protein levels of the β-hydroxy β-methylglutaryl-CoA reductases HMGR1 and HMGR2, which are rate-limiting enzymes in the sterol synthesis pathway, resulting in suppression of sterol overproduction. Second, if the first process is not successful, excess sterols are converted to sterol esters by phospholipid sterol acyltransferase1 (PSAT1) on ER microdomains and then segregated in SE bodies.
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Affiliation(s)
- Takashi L Shimada
- Graduate School of Science, Kyoto University, Kyoto, Japan
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
- Graduate School of Horticulture, Chiba University, Matsudo, Japan
| | - Tomoo Shimada
- Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioresources, Mie University, Tsu, Japan
| | | | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Kaori Oyama
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Misako Kato
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Haruko Ueda
- Faculty of Science and Engineering, Konan University, Kobe, Japan
| | - Akihiko Nakano
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
- RIKEN Center for Advanced Photonics, Wako, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
- JST, PRESTO, Kawaguchi, Japan
- SOKENDAI (Graduate University for Advanced Studies), Okazaki, Japan
| | | | - Ikuko Hara-Nishimura
- Graduate School of Science, Kyoto University, Kyoto, Japan.
- Faculty of Science and Engineering, Konan University, Kobe, Japan.
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39
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Nakamura A, Katahira R, Sawada S, Shinoda E, Kuwata K, Yoshii T, Tsukiji S. Chemogenetic Control of Protein Anchoring to Endomembranes in Living Cells with Lipid-Tethered Small Molecules. Biochemistry 2019; 59:205-211. [DOI: 10.1021/acs.biochem.9b00807] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Akinobu Nakamura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
| | - Rika Katahira
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Shunsuke Sawada
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
| | - Eri Shinoda
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
- PRESTO, Japan Science and Technology (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
- Frontier Research Institute for Materials Science (FRIMS), Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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40
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Hirakawa T, Kuwata K, Gallego ME, White CI, Nomoto M, Tada Y, Matsunaga S. LSD1-LIKE1-Mediated H3K4me2 Demethylation Is Required for Homologous Recombination Repair. Plant Physiol 2019; 181:499-509. [PMID: 31366719 PMCID: PMC6776857 DOI: 10.1104/pp.19.00530] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/22/2019] [Indexed: 05/18/2023]
Abstract
Homologous recombination is a key process for maintaining genome integrity and diversity. In eukaryotes, the nucleosome structure of chromatin inhibits the progression of homologous recombination. The DNA repair and recombination protein RAD54 alters the chromatin structure via nucleosome sliding to enable homology searches. For homologous recombination to progress, appropriate recruitment and dissociation of RAD54 is required at the site of homologous recombination; however, little is known about the mechanism regulating RAD54 dynamics in chromatin. Here, we reveal that the histone demethylase LYSINE-SPECIFIC DEMETHYLASE1-LIKE 1 (LDL1) regulates the dissociation of RAD54 at damaged sites during homologous recombination repair in the somatic cells of Arabidopsis (Arabidopsis thaliana). Depletion of LDL1 leads to an overaccumulation of RAD54 at damaged sites with DNA double-strand breaks. Moreover, RAD54 accumulates at damaged sites by recognizing histone H3 Lys 4 di-methylation (H3K4me2); the frequency of the interaction between RAD54 and H3K4me2 increased in the ldl1 mutant with DNA double-strand breaks. We propose that LDL1 removes RAD54 at damaged sites by demethylating H3K4me2 during homologous recombination repair and thereby maintains genome stability in Arabidopsis.
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Affiliation(s)
- Takeshi Hirakawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Maria E Gallego
- Génétique, Reproduction et Développement, Unité de Mixte de Recherche, Centre National de la Recherche Scientifique 6293, Clermont Université, Institut National de la Santé et de la Recherche Médicale U1103, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Charles I White
- Génétique, Reproduction et Développement, Unité de Mixte de Recherche, Centre National de la Recherche Scientifique 6293, Clermont Université, Institut National de la Santé et de la Recherche Médicale U1103, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Mika Nomoto
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Yasuomi Tada
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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41
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Zhang Y, Hirota T, Kuwata K, Oishi S, Gramani SG, Bode JW. Chemical Synthesis of Atomically Tailored SUMO E2 Conjugating Enzymes for the Formation of Covalently Linked SUMO-E2-E3 Ligase Ternary Complexes. J Am Chem Soc 2019; 141:14742-14751. [PMID: 31436980 DOI: 10.1021/jacs.9b06820] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
E2 conjugating enzymes are the key catalytic actors in the transfer of ubiquitin, SUMO, and other ubiquitin-like modifiers to their substrate proteins. Their high rates of transfer and promiscuous binding complicate studies of their interactions and binding partners. To access specific, covalently linked conjugates of the SUMO E2 conjugating enzyme Ubc9, we prepared synthetic variants bearing site-specific non-native modifications including the following: (1) replacement of Cys93 to 2,3-diaminopropionic acid to form the amide-linked stable E2-SUMO conjugate, which is known to have high affinity for E3 ligases; (2) a photoreactive group (diazirine) to trap E3 ligases upon UV irradiation; and (3) an N-terminal biotin for purification and detection. To construct these Ubc9 variants in a flexible, convergent manner, we combined the three leading methods: native chemical ligation (NCL), α-ketoacid-hydroxylamine (KAHA) ligation, and serine/threonine ligation (STL). Using the synthetic proteins, we demonstrated the selective formation of Ubc9-SUMO conjugates and the trapping of an E3 ligase (RanBP2) to form the stable, covalently linked SUMO1-Ubc9-RanBP2 ternary complex. The powerful combination of ligation methods-which minimizes challenges of functional group manipulations-will enable chemical probes based on E2 conjugating enzymes to trap E3 ligases and facilitate the synthesis of other protein classes.
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Affiliation(s)
- Yinfeng Zhang
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Shunsuke Oishi
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Subramanian G Gramani
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Jeffrey W Bode
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan.,Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences , ETH Zürich , Zürich 8093 , Switzerland
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42
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Saito AN, Matsuo H, Kuwata K, Ono A, Kinoshita T, Yamaguchi J, Nakamichi N. Structure-function study of a novel inhibitor of the casein kinase 1 family in Arabidopsis thaliana. Plant Direct 2019; 3:e00172. [PMID: 31549020 PMCID: PMC6747015 DOI: 10.1002/pld3.172] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 08/31/2019] [Accepted: 09/03/2019] [Indexed: 05/16/2023]
Abstract
Casein kinase 1 (CK1) is an evolutionarily conserved protein kinase family among eukaryotes. Studies in non-plants have shown CK1-dependent divergent biological processes, but the collective knowledge regarding the biological roles of plant CK1 lags far behind other members of the Eukarya. One reason for this is that plants have many more genes encoding CK1 than do animals. To accelerate our understanding of the plant CK1 family, a strong CK1 inhibitor that efficiently inhibits multiple members of the CK1 protein family in vivo (i.e., in planta) is required. Here, we report a novel, specific, and effective CK1 inhibitor in Arabidopsis. Using circadian period-lengthening activity as an estimation of the CK1 inhibitor effect in vivo, we performed a structure-activity relationship study of analogues of the CK1 inhibitor PHA767491 (1,5,6,7-tetrahydro-2-(4-pyridinyl)-4H-pyrrolo[3,2-c]pyridin-4-one hydrochloride). A propargyl group at the pyrrole nitrogen atom (AMI-212) or a bromine atom at the pyrrole C3 position (AMI-23) had stronger CK1 inhibitory activity than PHA767491. A hybrid molecule of AMI-212 and AMI-23 (AMI-331) was about 100-fold more inhibitory than the parent molecule PHA767491. Affinity proteomics using an AMI-331 probe showed that the targets of AMI-331 inhibition are mostly CK1 kinases. As such, AMI-331 is a potent and selective CK1 inhibitor that shows promise in the research of CK1 in plants.
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Affiliation(s)
- Ami N. Saito
- Department of Applied ChemistryWaseda UniversityShinjuku, TokyoJapan
| | - Hiromi Matsuo
- Institute of Transformative Bio‐molecules (WPI‐ITbM)Nagoya UniversityChikusa, NagoyaJapan
| | - Keiko Kuwata
- Institute of Transformative Bio‐molecules (WPI‐ITbM)Nagoya UniversityChikusa, NagoyaJapan
| | - Azusa Ono
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityChikusa, NagoyaJapan
| | - Toshinori Kinoshita
- Institute of Transformative Bio‐molecules (WPI‐ITbM)Nagoya UniversityChikusa, NagoyaJapan
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityChikusa, NagoyaJapan
| | | | - Norihito Nakamichi
- Institute of Transformative Bio‐molecules (WPI‐ITbM)Nagoya UniversityChikusa, NagoyaJapan
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityChikusa, NagoyaJapan
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43
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Nishikawa Y, Miki T, Awa M, Kuwata K, Tamura T, Hamachi I. Development of a Nitric Oxide-Responsive Labeling Reagent for Proteome Analysis of Live Cells. ACS Chem Biol 2019; 14:397-404. [PMID: 30715847 DOI: 10.1021/acschembio.8b01021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nitric oxide (NO) is a pleiotropic signaling molecule involved in the regulation of diverse physiological and pathophysiological mechanisms in cardiovascular, nervous, and immunological systems. To understand the biological functions of NO in detail, comprehensive characterization of proteins found in high-NO concentration environments is crucial. Herein, we describe the design of NO-responsive protein labeling reagents based on N-alkoxyacyl- o-phenylenediamine as an optimal reactive scaffold. The designed molecules can label proteins in murine macrophage cells in response to endogenously produced NO. The combination of NO-responsive protein labeling and liquid chromatography-tandem mass spectrometry technology allowed the characterization of the proteome under NO-generated conditions. Moreover, we demonstrated that our reagent was able to selectively mark and be used to fluorescently visualize NO-producing cells in a mixed cell culture system.
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Affiliation(s)
- Yuki Nishikawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takayuki Miki
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Masashi Awa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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44
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Shishido Y, Tomoike F, Kuwata K, Fujikawa H, Sekido Y, Murakami-Tonami Y, Kameda T, Abe N, Kimura Y, Shuto S, Abe H. A Covalent Inhibitor for Glutathione S-Transferase Pi (GSTP 1-1 ) in Human Cells. Chembiochem 2019; 20:900-905. [PMID: 30548113 DOI: 10.1002/cbic.201800671] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Indexed: 11/08/2022]
Abstract
Glutathione S-transferase π (GSTP1-1 ) is overexpressed in many types of cancer and is involved in drug resistance. Therefore, GSTP1-1 is an important target in cancer therapy, and many GST inhibitors have been reported. We had previously developed an irreversible inhibitor, GS-ESF, as an effective GST inhibitor; however, its cellular permeability was too low for it to be used in inhibiting intracellular GST. We have now developed new irreversible inhibitors by introducing sulfonyl fluoride (SF) into chloronitrobenzene (CNB). The mechanism of action was revealed to be that CNBSF first reacts with glutathione (GSH) through an aromatic substitution in the cell, then the sulfonyl group on the GSH conjugate with CNBSF reacts with Tyr108 of GST to form a sulfonyl ester bond. Our new inhibitor irreversible inhibited GSTP1-1 both in vitro and in cellulo with a long duration of action.
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Affiliation(s)
- Yuko Shishido
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan.,Faculty of Pharmaceutical Science, Hokkaido University, Kita-12, Nishi-6, Kita-Ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Fumiaki Tomoike
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
| | - Haruka Fujikawa
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
| | - Yoshitaka Sekido
- Division of Cancer Biology, Aichi Cancer Center Research Institute, 1-1, Kanokoden, Chikusa-Ku, Nagoya, Aichi, 464-8681, Japan
| | - Yuko Murakami-Tonami
- Division of Cancer Biology, Aichi Cancer Center Research Institute, 1-1, Kanokoden, Chikusa-Ku, Nagoya, Aichi, 464-8681, Japan.,Juntendo University, Graduate School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7, Aomi, Ko-to-ku, Tokyo, 135-0064, Japan
| | - Naoko Abe
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
| | - Yasuaki Kimura
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
| | - Satoshi Shuto
- Faculty of Pharmaceutical Science, Hokkaido University, Kita-12, Nishi-6, Kita-Ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Hiroshi Abe
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
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45
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Shindo N, Fuchida H, Sato M, Watari K, Shibata T, Kuwata K, Miura C, Okamoto K, Hatsuyama Y, Tokunaga K, Sakamoto S, Morimoto S, Abe Y, Shiroishi M, Caaveiro JMM, Ueda T, Tamura T, Matsunaga N, Nakao T, Koyanagi S, Ohdo S, Yamaguchi Y, Hamachi I, Ono M, Ojida A. Selective and reversible modification of kinase cysteines with chlorofluoroacetamides. Nat Chem Biol 2019; 15:250-258. [PMID: 30643284 DOI: 10.1038/s41589-018-0204-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/16/2018] [Indexed: 01/27/2023]
Abstract
Irreversible inhibition of disease-associated proteins with small molecules is a powerful approach for achieving increased and sustained pharmacological potency. Here, we introduce α-chlorofluoroacetamide (CFA) as a novel warhead of targeted covalent inhibitor (TCI). Despite weak intrinsic reactivity, CFA-appended quinazoline showed high reactivity toward Cys797 of epidermal growth factor receptor (EGFR). In cells, CFA-quinazoline showed higher target specificity for EGFR than the corresponding Michael acceptors in a wide concentration range (0.1-10 μM). The cysteine adduct of the CFA derivative was susceptible to hydrolysis and reversibly yielded intact thiol but was stable in solvent-sequestered ATP-binding pocket of EGFR. This environment-dependent hydrolysis can potentially reduce off-target protein modification by CFA-based drugs. Oral administration of CFA quinazoline NS-062 significantly suppressed tumor growth in a mouse xenograft model. Further, CFA-appended pyrazolopyrimidine irreversibly inhibited Bruton's tyrosine kinase with higher target specificity. These results demonstrate the utility of CFA as a new class warheads for TCI.
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Affiliation(s)
- Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Hirokazu Fuchida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Mami Sato
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kosuke Watari
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomohiro Shibata
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Chizuru Miura
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kei Okamoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuji Hatsuyama
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Keisuke Tokunaga
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Seiichi Sakamoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Satoshi Morimoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshito Abe
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Mitsunori Shiroishi
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Jose M M Caaveiro
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Tadashi Ueda
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomonori Tamura
- Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Naoya Matsunaga
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Takaharu Nakao
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Satoru Koyanagi
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Shigehiro Ohdo
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuchika Yamaguchi
- Faculty of Pharmaceutical Sciences, Nagasaki International University, Sasebo, Japan
| | - Itaru Hamachi
- Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Mayumi Ono
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
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46
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Oshima T, Niwa Y, Kuwata K, Srivastava A, Hyoda T, Tsuchiya Y, Kumagai M, Tsuyuguchi M, Tamaru T, Sugiyama A, Ono N, Zolboot N, Aikawa Y, Oishi S, Nonami A, Arai F, Hagihara S, Yamaguchi J, Tama F, Kunisaki Y, Yagita K, Ikeda M, Kinoshita T, Kay SA, Itami K, Hirota T. Cell-based screen identifies a new potent and highly selective CK2 inhibitor for modulation of circadian rhythms and cancer cell growth. Sci Adv 2019; 5:eaau9060. [PMID: 30746467 PMCID: PMC6357737 DOI: 10.1126/sciadv.aau9060] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 12/11/2018] [Indexed: 05/08/2023]
Abstract
Compounds targeting the circadian clock have been identified as potential treatments for clock-related diseases, including cancer. Our cell-based phenotypic screen revealed uncharacterized clock-modulating compounds. Through affinity-based target deconvolution, we identified GO289, which strongly lengthened circadian period, as a potent and selective inhibitor of CK2. Phosphoproteomics identified multiple phosphorylation sites inhibited by GO289 on clock proteins, including PER2 S693. Furthermore, GO289 exhibited cell type-dependent inhibition of cancer cell growth that correlated with cellular clock function. The x-ray crystal structure of the CK2α-GO289 complex revealed critical interactions between GO289 and CK2-specific residues and no direct interaction of GO289 with the hinge region that is highly conserved among kinases. The discovery of GO289 provides a direct link between the circadian clock and cancer regulation and reveals unique design principles underlying kinase selectivity.
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Affiliation(s)
- Tsuyoshi Oshima
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan
| | - Yoshimi Niwa
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Ashutosh Srivastava
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Tomoko Hyoda
- Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yoshiki Tsuchiya
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Megumi Kumagai
- Department of Physiology, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan
| | - Masato Tsuyuguchi
- Graduate School of Science, Osaka Prefecture University, Osaka 599-8531, Japan
| | - Teruya Tamaru
- Department of Physiology and Advanced Research Center for Medical Science, Toho University School of Medicine, Tokyo 143-8540, Japan
| | - Akiko Sugiyama
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Natsuko Ono
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Norjin Zolboot
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Yoshiki Aikawa
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Shunsuke Oishi
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Atsushi Nonami
- Center for Advanced Medical Innovation, Kyushu University, Fukuoka 812-8582, Japan
| | - Fumio Arai
- Department of Stem Cell Biology and Medicine/Cancer Stem Cell Research, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Shinya Hagihara
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan
- PRESTO, JST, Nagoya 464-8601, Japan
| | | | - Florence Tama
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan, and RIKEN Center for Computational Science, Kobe 650-0047, Japan
| | - Yuya Kunisaki
- Department of Stem Cell Biology and Medicine/Cancer Stem Cell Research, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Kazuhiro Yagita
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Masaaki Ikeda
- Department of Physiology, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan
| | - Takayoshi Kinoshita
- Graduate School of Science, Osaka Prefecture University, Osaka 599-8531, Japan
| | - Steve A. Kay
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Kenichiro Itami
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan
- ERATO Itami Molecular Nanocarbon Project, JST, Nagoya 464-8601, Japan
- Corresponding author. (T.H.); (K.I.)
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
- PRESTO, JST, Nagoya 464-8601, Japan
- Corresponding author. (T.H.); (K.I.)
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Uraguchi D, Kuwata K, Hijikata Y, Yamaguchi R, Imaizumi H, AM S, Rakers C, Mori N, Akiyama K, Irle S, McCourt P, Kinoshita T, Ooi T, Tsuchiya Y. A femtomolar-range suicide germination stimulant for the parasitic plantStriga hermonthica. Science 2018; 362:1301-1305. [DOI: 10.1126/science.aau5445] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/25/2018] [Indexed: 01/05/2023]
Abstract
The parasitic plantStriga hermonthicahas been causing devastating damage to the crop production in Africa. BecauseStrigarequires host-generated strigolactones to germinate, the identification of selective and potent strigolactone agonists could help control these noxious weeds. We developed a selective agonist, sphynolactone-7, a hybrid molecule originated from chemical screening, that contains two functional modules derived from a synthetic scaffold and a core component of strigolactones. Cooperative action of these modules in the activation of a high-affinity strigolactone receptor ShHTL7 allows sphynolactone-7 to provokeStrigagermination with potency in the femtomolar range. We demonstrate that sphynolactone-7 is effective for reducingStrigaparasitism without impinging on host strigolactone-related processes.
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48
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Fujisawa A, Tamura T, Yasueda Y, Kuwata K, Hamachi I. Chemical Profiling of the Endoplasmic Reticulum Proteome Using Designer Labeling Reagents. J Am Chem Soc 2018; 140:17060-17070. [DOI: 10.1021/jacs.8b08606] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Alma Fujisawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yuki Yasueda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency,
Sanbancho, Chiyodaku, Tokyo 102-0075, Japan
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49
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Inoue S, Morita R, Kuwata K, Kunieda T, Ueda H, Hara-Nishimura I, Minami Y. Tissue-specific and intracellular localization of indican synthase from Polygonum tinctorium. Plant Physiol Biochem 2018; 132:138-144. [PMID: 30189417 DOI: 10.1016/j.plaphy.2018.08.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 08/25/2018] [Indexed: 05/09/2023]
Abstract
The plant Polygonum tinctorium produces the secondary metabolite indican (indoxyl-β-D-glucoside), a precursor of the blue dye indigo. P. tinctorium synthesizes indican through the actions of the UDP-glucosyltransferase (UGT), indican synthase. Herein, we partially purified an indican synthase from the leaves and subsequently performed peptide mass fingerprinting analysis. Consequently, we identified a fragment that was homologous to a UDP-glucosyltransferase 72B (UGT72B) family member. We named it PtIgs (P. tinctoriumindoxyl-β-D-glucoside synthase) and obtained the full-length cDNA using rapid amplification of the cDNA ends. The primary structure of PtIGS, which PtIgs encoded, showed high identity with indican synthases (ItUGT1 and ItUGT2) from Indigofera tinctoria (Inoue et al., 2017). Moreover, in expression analyses of P. tinctorium, PtIGS mRNA was virtually found only in the leaves, was most highly expressed in the 1st leaves, and decreased with leaf age. Because PtIGS expression tended to reflect indican contents and synthesis activities, we concluded that PtIGS functions as an indican synthase in plant cells. To examine intracellular localization of PtIGS, crude leaf extracts were separated into cytosol and microsome fractions, and found PtIGS in the cytosol and in microsome fractions. Furthermore, microsomal PtIGS was soluble in the presence of detergents and urea and was strongly associated with membranes. Finally, we confirmed endoplasmic reticulum (ER) membrane localization of PtIGS using ultracentrifugation with a sucrose density gradient. These data suggest that PtIGS interacts with some kind of proteins on ER membranes to certainly carry out a delivery of substrate.
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Affiliation(s)
- Shintaro Inoue
- Okayama University of Science, Department of Biochemistry, Faculty of Science, 1-1 Ridai-cho, Kita-ku, Okayama, 700-0005, Japan
| | - Rihito Morita
- Okayama University of Science, Department of Biochemistry, Faculty of Science, 1-1 Ridai-cho, Kita-ku, Okayama, 700-0005, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Tadashi Kunieda
- Konan University, Department of Biology, Faculty of Science and Engineering, 8-9-1 Okamoto, Higashinada-ku, Kobe, Hyogo, 658-8501, Japan
| | - Haruko Ueda
- Konan University, Department of Biology, Faculty of Science and Engineering, 8-9-1 Okamoto, Higashinada-ku, Kobe, Hyogo, 658-8501, Japan
| | - Ikuko Hara-Nishimura
- Konan University, Department of Biology, Faculty of Science and Engineering, 8-9-1 Okamoto, Higashinada-ku, Kobe, Hyogo, 658-8501, Japan
| | - Yoshiko Minami
- Okayama University of Science, Department of Biochemistry, Faculty of Science, 1-1 Ridai-cho, Kita-ku, Okayama, 700-0005, Japan.
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Lu Y, Maruyama J, Kuwata K, Fukuda H, Iwasa H, Arimoto-Matsuzaki K, Sugimura H, Hata Y. Doublecortin-like kinase 1 compromises DNA repair and induces chromosomal instability. Biochem Biophys Rep 2018; 16:130-137. [PMID: 30417131 PMCID: PMC6216093 DOI: 10.1016/j.bbrep.2018.10.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/17/2018] [Accepted: 10/21/2018] [Indexed: 12/14/2022] Open
Abstract
Doublecortin-like kinase 1 (DCLK1) is a serine/threonine-kinase with two doublecortin (DCX) domains. DCLK1 is associated with microtubules via DCX domains and regulates microtubule polymerization. DCLK1 is known to be expressed in cancer stem cells and provides cancer cells with tumor-initiating capacity. Accumulating clinical evidence supports that DCLK1 is associated with tumor aggressiveness and is an important prognostic marker in various human cancers. However, the mechanism, by which DCLK1 causes oncogenesis, is not yet elucidated. In this study, we showed that DCLK1 empowers human mammary epithelial MCF10A cells to form spheres under floating condition in serum-free medium, which are reminiscent of mammospheres formed by mammary epithelial stem cells. We demonstrated that DCLK1 causes chromatin instability in MCF10A cells. DCLK1 impairs DNA repairs in human colon cancer HCT116 and lung cancer H1299 cells. The kinase-negative DCLK1 mutant and the mutant that is not associated with microtubules compromise DNA repair. In conclusion, DCLK1 interferes with DNA repair and induces tumorigenesis through genomic instability and this function is independent of the kinase activity and the regulation of microtubules. Doublecortin-like kinase 1 (DCLK1) confers stemness to cancer cells. Mammary epithelial cells expressing DCLK1 form spheres under floating condition. DCLK1 causes robust chromosomal abnormalities in mammary epithelial cells. DCLK1 impairs DNA repair in cancer cells. The kinase-negative DCLK1 shows similar effects.
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Affiliation(s)
- Yuxiong Lu
- Department of Medical Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Junichi Maruyama
- Department of Medical Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya 464-8601, Japan
| | - Hiroyuki Fukuda
- Agilent Technologies Research Alliance Laboratory, Graduate School of Science, Osaka University, Osaka 565-0871, Japan.,Agilent Technologies Japan, Ltd., Hachioji-shi, Tokyo 192-8510, Japan
| | - Hiroaki Iwasa
- Department of Medical Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Kyoko Arimoto-Matsuzaki
- Department of Medical Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Haruhiko Sugimura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Hamamatsu 431-3152, Japan
| | - Yutaka Hata
- Department of Medical Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8519, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
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