1
|
Sasaki Y, Saitoh K, Kagohashi K, Ose T, Kawahara S, Kitai Y, Muromoto R, Sekine Y, Ichii M, Yoshimura A, Oritani K, Kashiwakura JI, Matsuda T. STAP-2-Derived Peptide Suppresses TCR-Mediated Signals to Initiate Immune Responses. J Immunol 2023; 211:755-766. [PMID: 37417746 DOI: 10.4049/jimmunol.2200942] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 06/20/2023] [Indexed: 07/08/2023]
Abstract
Signal-transducing adaptor protein-2 (STAP-2) is an adaptor protein that contains pleckstrin and Src homology 2-like domains, as well as a proline-rich region in its C-terminal region. Our previous study demonstrated that STAP-2 positively regulates TCR signaling by associating with TCR-proximal CD3ζ ITAMs and the lymphocyte-specific protein tyrosine kinase. In this study, we identify the STAP-2 interacting regions of CD3ζ ITAMs and show that the STAP-2-derived synthetic peptide (iSP2) directly interacts with the ITAM sequence and blocks the interactions between STAP-2 and CD3ζ ITAMs. Cell-penetrating iSP2 was delivered into human and murine T cells. iSP2 suppressed cell proliferation and TCR-induced IL-2 production. Importantly, iSP2 treatment suppressed TCR-mediated activation of naive CD4+ T cells and decreased immune responses in CD4+ T cell-mediated experimental autoimmune encephalomyelitis. It is likely that iSP2 is a novel immunomodulatory tool that modulates STAP-2-mediated activation of TCR signaling and represses the progression of autoimmune diseases.
Collapse
Affiliation(s)
- Yuto Sasaki
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Kodai Saitoh
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Kota Kagohashi
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Toyoyuki Ose
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Shoya Kawahara
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Yuichi Kitai
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Ryuta Muromoto
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Yuichi Sekine
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Michiko Ichii
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Kenji Oritani
- Department of Hematology, International University of Health and Welfare, Narita, Japan
| | - Jun-Ichi Kashiwakura
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
- Department of Life Science, Faculty of Pharmaceutical Sciences, Hokkaido University of Science, Sapporo, Japan
| | - Tadashi Matsuda
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| |
Collapse
|
2
|
Wakui H, Yokoi Y, Horidome C, Ose T, Yao M, Tanaka Y, Hinou H, Nishimura SI. Structural and molecular insight into antibody recognition of dynamic neoepitopes in membrane tethered MUC1 of pancreatic cancer cells and secreted exosomes. RSC Chem Biol 2023; 4:564-572. [PMID: 37547453 PMCID: PMC10398351 DOI: 10.1039/d3cb00036b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/19/2023] [Indexed: 08/08/2023] Open
Abstract
Pancreatic cancer is highly metastatic and has poor prognosis, mainly due to delayed detection, often after metastasis has occurred. A novel method to enable early detection and disease intervention is strongly needed. Here we unveil for the first time that pancreatic cancer cells (PANC-1) and secreted exosomes express MUC1 bearing cancer-relevant dynamic epitopes recognized specifically by an anti-MUC1 antibody (SN-131), which binds specifically core 1 but not core 2 type O-glycans found in normal cells. Comprehensive assessment of the essential epitope for SN-131 indicates that PANC-1 cells produce dominantly MUC1 with aberrant O-glycoforms such as Tn, T, and sialyl T (ST) antigens. Importantly, SN-131 showed the highest affinity with MUC1 bearing ST antigen at the immunodominant DTR motif (KD = 1.58 nM) independent of the glycosylation states of other Ser/Thr residues in the MUC1 tandem repeats. The X-ray structure revealed that SN-131 interacts directly with Neu5Ac and root GalNAc of the ST antigen in addition to the proximal peptide region. Our results demonstrate that targeting O-glycosylated "dynamic neoepitopes" found in the membrane-tethered MUC1 is a promising therapeutic strategy for improving the treatment outcome of patients with pancreatic cancer.
Collapse
Affiliation(s)
- Hajime Wakui
- Field of Drug Discovery Research, Faculty of Advanced Life Science, and Graduate School of Life Science, Hokkaido University N21 W11 Kita-ku Sapporo 001-0021 Japan
| | - Yasuhiro Yokoi
- Field of Drug Discovery Research, Faculty of Advanced Life Science, and Graduate School of Life Science, Hokkaido University N21 W11 Kita-ku Sapporo 001-0021 Japan
| | - Chieko Horidome
- Field of Drug Discovery Research, Faculty of Advanced Life Science, and Graduate School of Life Science, Hokkaido University N21 W11 Kita-ku Sapporo 001-0021 Japan
| | - Toyoyuki Ose
- Field of X-ray Structural Biology, Faculty of Advanced Life Science, and Graduate School of Life Science, Hokkaido University N10 W8 Kita-ku Sapporo 060-0810 Japan
| | - Min Yao
- Field of X-ray Structural Biology, Faculty of Advanced Life Science, and Graduate School of Life Science, Hokkaido University N10 W8 Kita-ku Sapporo 060-0810 Japan
| | - Yoshikazu Tanaka
- Graduate School of Life Sciences, Tohoku University 2-1-1 Katahira Aoba-ku Sendai 980-8577 Japan
| | - Hiroshi Hinou
- Field of Drug Discovery Research, Faculty of Advanced Life Science, and Graduate School of Life Science, Hokkaido University N21 W11 Kita-ku Sapporo 001-0021 Japan
| | - Shin-Ichiro Nishimura
- Field of Drug Discovery Research, Faculty of Advanced Life Science, and Graduate School of Life Science, Hokkaido University N21 W11 Kita-ku Sapporo 001-0021 Japan
| |
Collapse
|
3
|
Wang H, Sun X, Saburi W, Hashiguchi S, Yu J, Ose T, Mori H, Yao M. Structural insights into the substrate specificity and activity of a novel mannose 2-epimerase from Runella slithyformis. Acta Crystallogr D Struct Biol 2023; 79:S205979832300390X. [PMID: 37314406 DOI: 10.1107/s205979832300390x] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/02/2023] [Indexed: 06/15/2023] Open
Abstract
Mannose 2-epimerase (ME), a member of the acylglucosamine 2-epimerase (AGE) superfamily that catalyzes epimerization of D-mannose and D-glucose, has recently been characterized to have potential for D-mannose production. However, the substrate-recognition and catalytic mechanism of ME remains unknown. In this study, structures of Runella slithyformis ME (RsME) and its D254A mutant [RsME(D254A)] were determined in their apo forms and as intermediate-analog complexes [RsME-D-glucitol and RsME(D254A)-D-glucitol]. RsME possesses the (α/α)6-barrel of the AGE superfamily members but has a unique pocket-covering long loop (loopα7-α8). The RsME-D-glucitol structure showed that loopα7-α8 moves towards D-glucitol and closes the active pocket. Trp251 and Asp254 in loopα7-α8 are only conserved in MEs and interact with D-glucitol. Kinetic analyses of the mutants confirmed the importance of these residues for RsME activity. Moreover, the structures of RsME(D254A) and RsME(D254A)-D-glucitol revealed that Asp254 is vital for binding the ligand in a correct conformation and for active-pocket closure. Docking calculations and structural comparison with other 2-epimerases show that the longer loopα7-α8 in RsME causes steric hindrance upon binding to disaccharides. A detailed substrate-recognition and catalytic mechanism for monosaccharide-specific epimerization in RsME has been proposed.
Collapse
Affiliation(s)
- Hang Wang
- Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Xiaomei Sun
- Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
| | - Saki Hashiguchi
- Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
| | - Jian Yu
- Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Toyoyuki Ose
- Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
| | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| |
Collapse
|
4
|
Maemoto T, Kitai Y, Takahashi R, Shoji H, Yamada S, Takei S, Ito D, Muromoto R, Kashiwakura JI, Handa H, Hashimoto A, Hashimoto S, Ose T, Oritani K, Matsuda T. A peptide derived from adaptor protein STAP-2 inhibits tumor progression by downregulating epidermal growth factor receptor signaling. J Biol Chem 2022; 299:102724. [PMID: 36410436 PMCID: PMC9800302 DOI: 10.1016/j.jbc.2022.102724] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 11/20/2022] Open
Abstract
Signal-transducing adaptor family member-2 (STAP-2) is an adaptor protein that regulates various intracellular signals. We previously demonstrated that STAP-2 binds to epidermal growth factor receptor (EGFR) and facilitates its stability and activation of EGFR signaling in prostate cancer cells. Inhibition of this interaction may be a promising direction for cancer treatment. Here, we found that 2D5 peptide, a STAP-2-derived peptide, blocked STAP-2-EGFR interactions and suppressed EGFR-mediated proliferation in several cancer cell lines. 2D5 peptide inhibited tumor growth of human prostate cancer cell line DU145 and human lung cancer cell line A549 in murine xenograft models. Additionally, we determined that EGFR signaling and its stability were decreased by 2D5 peptide treatment during EGF stimulation. In conclusion, our study shows that 2D5 peptide is a novel anticancer peptide that inhibits STAP-2-mediated activation of EGFR signaling and suppresses prostate and lung cancer progression.
Collapse
Affiliation(s)
- Taiga Maemoto
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yuichi Kitai
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, Japan,For correspondence: Yuichi Kitai; Tadashi Matsuda
| | - Runa Takahashi
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Haruka Shoji
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Shunsuke Yamada
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Shiho Takei
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Daiki Ito
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Ryuta Muromoto
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Jun-ichi Kashiwakura
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Haruka Handa
- Department of Molecular Biology, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Ari Hashimoto
- Department of Molecular Biology, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Shigeru Hashimoto
- Division of Molecular Psychoimmunology, Graduate School of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Toyoyuki Ose
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Kenji Oritani
- Department of Hematology, International University of Health and Welfare, Narita, Chiba, Japan
| | - Tadashi Matsuda
- Department of Immunology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, Japan,For correspondence: Yuichi Kitai; Tadashi Matsuda
| |
Collapse
|
5
|
Yumoto K, Arisaka T, Okada K, Aoki K, Ose T, Masatani T, Sugiyama M, Ito N, Fukuhara H, Maenaka K. Characterization of Single-Chain Fv Fragments of Neutralizing Antibodies to Rabies Virus Glycoprotein. Viruses 2021; 13:v13112311. [PMID: 34835117 PMCID: PMC8624154 DOI: 10.3390/v13112311] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/10/2021] [Accepted: 11/16/2021] [Indexed: 11/28/2022] Open
Abstract
Rabies has almost a 100% case-fatality rate and kills more than 59,000 people annually around the world. There is no established treatment for rabies. The rabies virus (RABV) expresses only the glycoprotein (RABVG) at the viral surface, and it is the target for the neutralizing antibodies. We previously established mouse monoclonal antibodies, 15–13 and 12–22, which showed neutralizing activity against the RABV, targeting the sequential and conformational epitopes on the RABVG, respectively. However, the molecular basis for the neutralizing activity of these antibodies is not yet fully understood. In this study, we evaluated the binding characteristics of the Fab fragments of the 15–13 and 12–22 antibodies. The recombinant RABVG protein, in prefusion form for the binding analysis, was prepared by the silkworm–baculovirus expression system. Biolayer interferometry (BLI) analysis indicated that the 15–13 Fab interacts with the RABVG, with a KD value at the nM level, and that the 12–22 Fab has a weaker binding affinity (KD ~ μM) with the RABVG compared to the 15–13 Fab. Furthermore, we determined the amino acid sequences of both the antibodies and the designed single-chain Fv fragments (scFvs) of the 15–13 and 12–22 antibodies as another potential biopharmaceutical for targeting rabies. The 15–13 and 12–22 scFvs were successfully prepared by the refolding method and were shown to interact with the RABVG at the nM level and the μM level of the KD, respectively. These binding characteristics were similar to that of each Fab. On the other hand, differential scanning fluorometry (DSF) revealed that the thermal stability of these scFvs decreases compared to their Fabs. While the improvement of the stability of scFvs will still be required, these results provide insights into the neutralizing activity and the potential therapeutic use of antibody fragments for RABV infection.
Collapse
Affiliation(s)
- Kohei Yumoto
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan; (K.Y.); (T.A.); (K.A.); (T.O.)
| | - Tomoaki Arisaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan; (K.Y.); (T.A.); (K.A.); (T.O.)
| | - Kazuma Okada
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan; (K.O.); (T.M.); (M.S.); (N.I.)
| | - Kyosuke Aoki
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan; (K.Y.); (T.A.); (K.A.); (T.O.)
| | - Toyoyuki Ose
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan; (K.Y.); (T.A.); (K.A.); (T.O.)
| | - Tatsunori Masatani
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan; (K.O.); (T.M.); (M.S.); (N.I.)
| | - Makoto Sugiyama
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan; (K.O.); (T.M.); (M.S.); (N.I.)
| | - Naoto Ito
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan; (K.O.); (T.M.); (M.S.); (N.I.)
| | - Hideo Fukuhara
- Center for Research and Education on Drug Discovery, Hokkaido University, Sapporo 060-0812, Japan;
- Global Station for Biosurfaces and Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan; (K.Y.); (T.A.); (K.A.); (T.O.)
- Center for Research and Education on Drug Discovery, Hokkaido University, Sapporo 060-0812, Japan;
- Global Station for Biosurfaces and Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
- Correspondence:
| |
Collapse
|
6
|
Yu J, Shinoda A, Kato K, Tanaka I, Ose T, Yao M. A solution-free crystal-mounting platform for native SAD. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321088413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
7
|
Wakui H, Tanaka Y, Ose T, Matsumoto I, Kato K, Min Y, Tachibana T, Sato M, Naruchi K, Martin FG, Hinou H, Nishimura SI. Correction: A straightforward approach to antibodies recognising cancer specific glycopeptidic neoepitopes. Chem Sci 2020; 11:12588-12589. [PMID: 34125114 PMCID: PMC8162781 DOI: 10.1039/d0sc90254c] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
[This corrects the article DOI: 10.1039/D0SC00317D.].
Collapse
Affiliation(s)
- Hajime Wakui
- Field of Drug Discovery Research, Faculty of Advanced Life Science, Graduate School of Life Science, Hokkaido University N21 W11, Kita-ku Sapporo 001-0021 Japan
| | - Yoshikazu Tanaka
- Graduate School of Life Sciences, Tohoku University 2-1-1 Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Toyoyuki Ose
- Field of X-ray Structural Biology, Faculty of Advanced Life Science, Graduate School of Life Science, Hokkaido University N10 W8, Kita-ku Sapporo 060-0810 Japan
| | - Isamu Matsumoto
- Field of X-ray Structural Biology, Faculty of Advanced Life Science, Graduate School of Life Science, Hokkaido University N10 W8, Kita-ku Sapporo 060-0810 Japan
| | - Koji Kato
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University 3-1-1, Tsushima-naka, Kita-ku Okayama 700-8530 Japan
| | - Yao Min
- Field of X-ray Structural Biology, Faculty of Advanced Life Science, Graduate School of Life Science, Hokkaido University N10 W8, Kita-ku Sapporo 060-0810 Japan
| | - Taro Tachibana
- Department of Bioengineering, Graduate School of Engineering, Osaka City University Sumiyoshi-ku Osaka 558-8585 Japan
| | - Masaharu Sato
- Medicinal Chemistry Pharmaceuticals, Co., Ltd. N9 W15, Chuo-ku Sapporo 060-0009 Japan
| | - Kentaro Naruchi
- Medicinal Chemistry Pharmaceuticals, Co., Ltd. N9 W15, Chuo-ku Sapporo 060-0009 Japan
| | - Fayna Garcia Martin
- Field of Drug Discovery Research, Faculty of Advanced Life Science, Graduate School of Life Science, Hokkaido University N21 W11, Kita-ku Sapporo 001-0021 Japan
| | - Hiroshi Hinou
- Field of Drug Discovery Research, Faculty of Advanced Life Science, Graduate School of Life Science, Hokkaido University N21 W11, Kita-ku Sapporo 001-0021 Japan
| | - Shin-Ichiro Nishimura
- Field of Drug Discovery Research, Faculty of Advanced Life Science, Graduate School of Life Science, Hokkaido University N21 W11, Kita-ku Sapporo 001-0021 Japan
| |
Collapse
|
8
|
Hossain MA, Larrous F, Rawlinson SM, Zhan J, Sethi A, Ibrahim Y, Aloi M, Lieu KG, Mok YF, Griffin MDW, Ito N, Ose T, Bourhy H, Moseley GW, Gooley PR. Structural Elucidation of Viral Antagonism of Innate Immunity at the STAT1 Interface. Cell Rep 2020; 29:1934-1945.e8. [PMID: 31722208 DOI: 10.1016/j.celrep.2019.10.020] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 07/16/2019] [Accepted: 10/03/2019] [Indexed: 12/24/2022] Open
Abstract
To evade immunity, many viruses express interferon antagonists that target STAT transcription factors as a major component of pathogenesis. Because of a lack of direct structural data, these interfaces are poorly understood. We report the structural analysis of full-length STAT1 binding to an interferon antagonist of a human pathogenic virus. The interface revealed by transferred cross-saturation NMR is complex, involving multiple regions in both the viral and cellular proteins. Molecular mapping analysis, combined with biophysical characterization and in vitro/in vivo functional assays, indicates that the interface is significant in disease caused by a pathogenic field-strain lyssavirus, with critical roles for contacts between the STAT1 coiled-coil/DNA-binding domains and specific regions within the viral protein. These data elucidate the potentially complex nature of IFN antagonist/STAT interactions, and the spatial relationship of protein interfaces that mediate immune evasion and replication, providing insight into how viruses can regulate these essential functions via single multifunctional proteins.
Collapse
Affiliation(s)
- Md Alamgir Hossain
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Florence Larrous
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; Unité Lyssavirus, Epidémiologie et Neuropathologie - CNR de la RAGE, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Stephen M Rawlinson
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton Campus, VIC 3800, Australia
| | - Jingyu Zhan
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ashish Sethi
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Youssef Ibrahim
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Maria Aloi
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton Campus, VIC 3800, Australia
| | - Kim G Lieu
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton Campus, VIC 3800, Australia
| | - Yee-Foong Mok
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Naoto Ito
- Laboratory of Zoonotic Diseases, Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Toyoyuki Ose
- Faculty of Advanced Life Science, Hokkaido University, 060-0810 Sapporo, Japan
| | - Hervé Bourhy
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; Unité Lyssavirus, Epidémiologie et Neuropathologie - CNR de la RAGE, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Gregory W Moseley
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia; Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton Campus, VIC 3800, Australia.
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia.
| |
Collapse
|
9
|
Sugiyama A, Nomai T, Jiang X, Minami M, Yao M, Maenaka K, Ito N, Gooley PR, Moseley GW, Ose T. Structural comparison of the C-terminal domain of functionally divergent lyssavirus P proteins. Biochem Biophys Res Commun 2020; 529:507-512. [PMID: 32703459 DOI: 10.1016/j.bbrc.2020.05.195] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 05/26/2020] [Indexed: 12/22/2022]
Abstract
Lyssavirus P protein is a multifunctional protein that interacts with numerous host-cell proteins. The C-terminal domain (CTD) of P is important for inhibition of JAK-STAT signaling enabling the virus to evade host immunity. Several regions on the surface of rabies virus P are reported to interact with host factors. Among them, an extended, discrete hydrophobic patch of P CTD is notable. Although structures of P CTD of two strains of rabies virus, and of mokola virus have been solved, the structure of P CTD for Duvenhage virus, which is functionally divergent from these species for immune evasion function, is not known. Here, we analyze the structures of P CTD of Duvenhage and of a distinct rabies virus strain to gain further insight on the nature and potential function of the hydrophobic surface. Molecular contacts in crystals suggest that the hydrophobic patch is important to intermolecular interactions with other proteins, which differ between the lyssavirus species.
Collapse
Affiliation(s)
- Aoi Sugiyama
- Faculty of Advanced Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo, 060-0810, Japan
| | - Tomo Nomai
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Xinxin Jiang
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Miku Minami
- Faculty of Advanced Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo, 060-0810, Japan
| | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo, 060-0810, Japan
| | - Katsumi Maenaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Naoto Ito
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Gregory W Moseley
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton Campus, Victoria, 3800, Australia
| | - Toyoyuki Ose
- Faculty of Advanced Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo, 060-0810, Japan; Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8, Honcho Kawaguchi, Saitama, 332-0012, Japan.
| |
Collapse
|
10
|
Wakui H, Tanaka Y, Ose T, Matsumoto I, Kato K, Min Y, Tachibana T, Sato M, Naruchi K, Martin FG, Hinou H, Nishimura SI. A straightforward approach to antibodies recognising cancer specific glycopeptidic neoepitopes. Chem Sci 2020; 11:4999-5006. [PMID: 34122956 PMCID: PMC8159228 DOI: 10.1039/d0sc00317d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 11/18/2020] [Accepted: 04/23/2020] [Indexed: 12/14/2022] Open
Abstract
Aberrantly truncated immature O-glycosylation in proteins occurs in essentially all types of epithelial cancer cells, which was demonstrated to be a common feature of most adenocarcinomas and strongly associated with cancer proliferation and metastasis. Although extensive efforts have been made toward the development of anticancer antibodies targeting MUC1, one of the most studied mucins having cancer-relevant immature O-glycans, no anti-MUC1 antibody recognises carbohydrates and the proximal MUC1 peptide region, concurrently. Here we present a general strategy that allows for the creation of antibodies interacting specifically with glycopeptidic neoepitopes by using homogeneous synthetic MUC1 glycopeptides designed for the streamlined process of immunization, antibody screening, three-dimensional structure analysis, epitope mapping and biochemical analysis. The X-ray crystal structure of the anti-MUC1 monoclonal antibody SN-101 complexed with the antigenic glycopeptide provides for the first time evidence that SN-101 recognises specifically the essential epitope by forming multiple hydrogen bonds both with the proximal peptide and GalNAc linked to the threonine residue, concurrently. Remarkably, the structure of the MUC1 glycopeptide in complex with SN-101 is identical to its solution NMR structure, an extended conformation induced by site-specific glycosylation. We demonstrate that this method accelerates dramatically the development of a new class of designated antibodies targeting a variety of "dynamic neoepitopes" elaborated by disease-specific O-glycosylation in the immunodominant mucin domains and mucin-like sequences found in intrinsically disordered regions of many proteins.
Collapse
Affiliation(s)
- Hajime Wakui
- Field of Drug Discovery Research, Faculty of Advanced Life Science, Graduate School of Life Science, Hokkaido University N21 W11, Kita-ku Sapporo 001-0021 Japan
| | - Yoshikazu Tanaka
- Graduate School of Life Sciences, Tohoku University 2-1-1 Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Toyoyuki Ose
- Field of X-ray Structural Biology, Faculty of Advanced Life Science, Graduate School of Life Science, Hokkaido University N10 W8, Kita-ku Sapporo 060-0810 Japan
| | - Isamu Matsumoto
- Field of X-ray Structural Biology, Faculty of Advanced Life Science, Graduate School of Life Science, Hokkaido University N10 W8, Kita-ku Sapporo 060-0810 Japan
| | - Koji Kato
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University 3-1-1, Tsushima-naka, Kita-ku Okayama 700-8530 Japan
| | - Yao Min
- Field of X-ray Structural Biology, Faculty of Advanced Life Science, Graduate School of Life Science, Hokkaido University N10 W8, Kita-ku Sapporo 060-0810 Japan
| | - Taro Tachibana
- Department of Bioengineering, Graduate School of Engineering, Osaka City University Sumiyoshi-ku Osaka 558-8585 Japan
| | - Masaharu Sato
- Medicinal Chemistry Pharmaceuticals, Co., Ltd. N9 W15, Chuo-ku Sapporo 060-0009 Japan
| | - Kentaro Naruchi
- Medicinal Chemistry Pharmaceuticals, Co., Ltd. N9 W15, Chuo-ku Sapporo 060-0009 Japan
| | - Fayna Garcia Martin
- Field of Drug Discovery Research, Faculty of Advanced Life Science, Graduate School of Life Science, Hokkaido University N21 W11, Kita-ku Sapporo 001-0021 Japan
| | - Hiroshi Hinou
- Field of Drug Discovery Research, Faculty of Advanced Life Science, Graduate School of Life Science, Hokkaido University N21 W11, Kita-ku Sapporo 001-0021 Japan
| | - Shin-Ichiro Nishimura
- Field of Drug Discovery Research, Faculty of Advanced Life Science, Graduate School of Life Science, Hokkaido University N21 W11, Kita-ku Sapporo 001-0021 Japan
| |
Collapse
|
11
|
Kusaka H, Kita S, Tadokoro T, Yoshida K, Kasai Y, Niiyama H, Fujimoto Y, Hanashima S, Murata M, Sugiyama S, Ose T, Kuroki K, Maenaka K. Efficient preparation of human and mouse CD1d proteins using silkworm baculovirus expression system. Protein Expr Purif 2020; 172:105631. [PMID: 32213313 DOI: 10.1016/j.pep.2020.105631] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/14/2020] [Accepted: 03/20/2020] [Indexed: 10/24/2022]
Abstract
CD1d is a major histocompatibility complex (MHC) class I-like glycoprotein and binds to glycolipid antigens that are recognized by natural killer T (NKT) cells. To date, our understanding of the structural basis for glycolipid binding and receptor recognition of CD1d is still limited. Here, we established a preparation method for the ectodomain of human and mouse CD1d using a silkworm-baculovirus expression system. The co-expression of human and mouse CD1d and β2-microglobulin (β2m) in the silkworm-baculovirus system was successful, but the yield of human CD1d was low. A construct of human CD1d fused with β2m via a flexible GS linker as a single polypeptide was prepared to improve protein yield. The production of this single-chained complex was higher (50 μg/larva) than that of the co-expression complex. Furthermore, differential scanning calorimetry revealed that the linker made the CD1d complex more stable and homogenous. These results suggest that the silkworm-baculovirus expression system is useful for structural and biophysical studies of CD1d in several aspects including low cost, easy handling, biohazard-free, rapid, and high yielding.
Collapse
Affiliation(s)
- Hiroki Kusaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Shunsuke Kita
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Takashi Tadokoro
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Kouki Yoshida
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Yoshiyuki Kasai
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Harumi Niiyama
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yukari Fujimoto
- Department of Chemistry, Faculty of Science and Technology, Keio University, Yokohama, 223-8522, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Shigeru Sugiyama
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan; Faculty of Science & Technology, Kochi University, Kochi, 780-8520, Japan
| | - Toyoyuki Ose
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan; Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan; Faculty of Advanced Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kimiko Kuroki
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Katsumi Maenaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan; Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan.
| |
Collapse
|
12
|
Hirao K, Andrews S, Kuroki K, Kusaka H, Tadokoro T, Kita S, Ose T, Rowland-Jones SL, Maenaka K. Structure of HIV-2 Nef Reveals Features Distinct from HIV-1 Involved in Immune Regulation. iScience 2019; 23:100758. [PMID: 31927483 PMCID: PMC6956826 DOI: 10.1016/j.isci.2019.100758] [Citation(s) in RCA: 5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/24/2019] [Accepted: 12/03/2019] [Indexed: 01/07/2023] Open
Abstract
The human immunodeficiency virus (HIV) accessory protein Nef plays a major role in establishing and maintaining infection, particularly through immune evasion. Many HIV-2-infected people experience long-term viral control and survival, resembling HIV-1 elite control. HIV-2 Nef has overlapping but also distinct functions from HIV-1 Nef. Here we report the crystal structure of HIV-2 Nef core. The di-leucine sorting motif forms a helix bound to neighboring molecules, and moreover, isothermal titration calorimetry demonstrated that the CD3 endocytosis motif can directly bind to HIV-2 Nef, ensuring AP-2-mediated endocytosis for CD3. The highly conserved C-terminal region forms a α-helix, absent from HIV-1. We further determined the structure of simian immunodeficiency virus (SIV) Nef harboring this region, demonstrating similar C-terminal α-helix, which may contribute to AP-1 binding for MHC-I downregulation. These results provide insights into the distinct pathogenesis of HIV-2 infection. Structure of HIV-2 Nef revealed a conserved C-terminal α-helix not present in HIV-1 C-terminal structure is conserved in SIV Nef, likely involved in MHC-I downregulation Di-leucine AP-2-mediated sorting motif forms a helix bound to the α1 and α2 helices ITC demonstrated that the CD3 endocytosis motif can directly bind to HIV-2 Nef
Collapse
Affiliation(s)
- Kengo Hirao
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Sophie Andrews
- Nuffield Department of Medicine, University of Oxford, NDM Research Building, Oxford OX3 7FZ, UK
| | - Kimiko Kuroki
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Hiroki Kusaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Takashi Tadokoro
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Shunsuke Kita
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Toyoyuki Ose
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan; Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Sarah L Rowland-Jones
- Nuffield Department of Medicine, University of Oxford, NDM Research Building, Oxford OX3 7FZ, UK.
| | - Katsumi Maenaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan.
| |
Collapse
|
13
|
Kuroki K, Matsubara H, Kanda R, Miyashita N, Shiroishi M, Fukunaga Y, Kamishikiryo J, Fukunaga A, Fukuhara H, Hirose K, Hunt JS, Sugita Y, Kita S, Ose T, Maenaka K. Structural and Functional Basis for LILRB Immune Checkpoint Receptor Recognition of HLA-G Isoforms. J Immunol 2019; 203:3386-3394. [PMID: 31694909 DOI: 10.4049/jimmunol.1900562] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/05/2019] [Indexed: 01/30/2023]
Abstract
Human leukocyte Ig-like receptors (LILR) LILRB1 and LILRB2 are immune checkpoint receptors that regulate a wide range of physiological responses by binding to diverse ligands, including HLA-G. HLA-G is exclusively expressed in the placenta, some immunoregulatory cells, and tumors and has several unique isoforms. However, the recognition of HLA-G isoforms by LILRs is poorly understood. In this study, we characterized LILR binding to the β2-microglobulin (β2m)-free HLA-G1 isoform, which is synthesized by placental trophoblast cells and tends to dimerize and multimerize. The multimerized β2m-free HLA-G1 dimer lacked detectable affinity for LILRB1, but bound strongly to LILRB2. We also determined the crystal structure of the LILRB1 and HLA-G1 complex, which adopted the typical structure of a classical HLA class I complex. LILRB1 exhibits flexible binding modes with the α3 domain, but maintains tight contacts with β2m, thus accounting for β2m-dependent binding. Notably, both LILRB1 and B2 are oriented at suitable angles to permit efficient signaling upon complex formation with HLA-G1 dimers. These structural and functional features of ligand recognition by LILRs provide novel insights into their important roles in the biological regulations.
Collapse
Affiliation(s)
- Kimiko Kuroki
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Haruki Matsubara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Ryo Kanda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Naoyuki Miyashita
- RIKEN, Kobe 650-0047, Japan.,Department of Computational Systems Biology, Kindai University, Kinokawa 649-6493, Japan
| | - Mitsunori Shiroishi
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuko Fukunaga
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Jun Kamishikiryo
- Faculty of Pharmaceutical Sciences, Fukuyama University, Fukuyama 729-0292, Japan; and
| | - Atsushi Fukunaga
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Hideo Fukuhara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Kaoru Hirose
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Joan S Hunt
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | | | - Shunsuke Kita
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Toyoyuki Ose
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Katsumi Maenaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan;
| |
Collapse
|
14
|
Sasaki M, Anindita PD, Ito N, Sugiyama M, Carr M, Fukuhara H, Ose T, Maenaka K, Takada A, Hall WW, Orba Y, Sawa H. The Role of Heparan Sulfate Proteoglycans as an Attachment Factor for Rabies Virus Entry and Infection. J Infect Dis 2019. [PMID: 29529215 DOI: 10.1093/infdis/jiy081] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rabies virus (RABV) is the causative agent of fatal neurological disease. Cellular attachment is the initial and essential step for viral infections. Although extensive studies have demonstrated that RABV uses various target cell molecules to mediate infection, no specific molecule has been identified as an attachment factor for RABV infection. Here we demonstrate that cellular heparan sulfate (HS) supports RABV adhesion and subsequent entry into target cells. Enzymatic removal of HS reduced cellular susceptibility to RABV infection, and heparin, a highly sulfated form of HS, blocked viral adhesion and infection. The direct binding between RABV glycoprotein and heparin was demonstrated, and this interaction was shown to require HS N- and 6-O-sulfation. We also revealed that basic amino acids in the ectodomain of RABV glycoprotein serve as major determinants for the RABV-HS interaction. Collectively, our study highlights a previously undescribed role of HS as an attachment factor for RABV infection.
Collapse
Affiliation(s)
- Michihito Sasaki
- Division of Molecular Pathobiology, Hokkaido University, Sapporo
| | | | - Naoto Ito
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, Japan
| | - Makoto Sugiyama
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, Japan
| | - Michael Carr
- Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo.,National Virus Reference Laboratory, School of Medicine, University College Dublin, Ireland
| | - Hideo Fukuhara
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Science, Hokkaido University, Sapporo
| | - Toyoyuki Ose
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Science, Hokkaido University, Sapporo
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Science, Hokkaido University, Sapporo
| | - Ayato Takada
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo.,Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo
| | - William W Hall
- Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo.,Center for Research in Infectious Diseases, University College Dublin, Ireland.,Global Virus Network, Baltimore, Maryland
| | - Yasuko Orba
- Division of Molecular Pathobiology, Hokkaido University, Sapporo
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, Hokkaido University, Sapporo.,Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo.,Global Virus Network, Baltimore, Maryland
| |
Collapse
|
15
|
Fukuhara H, Ito Y, Sako M, Kajikawa M, Yoshida K, Seki F, Mwaba MH, Hashiguchi T, Higashibata MA, Ose T, Kuroki K, Takeda M, Maenaka K. Specificity of Morbillivirus Hemagglutinins to Recognize SLAM of Different Species. Viruses 2019; 11:v11080761. [PMID: 31430904 PMCID: PMC6722581 DOI: 10.3390/v11080761] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 12/15/2022] Open
Abstract
Measles virus (MV) and canine distemper virus (CDV) are highly contagious and deadly, forming part of the morbillivirus genus. The receptor recognition by morbillivirus hemagglutinin (H) is important for determining tissue tropism and host range. Recent reports largely urge caution as regards to the potential expansion of host specificities of morbilliviruses. Nonetheless, the receptor-binding potential in different species of morbillivirus H proteins is largely unknown. Herein, we show that the CDV-H protein binds to the dog signaling lymphocyte activation molecule (SLAM), but not to the human, tamarin, or mouse SLAM. In contrast, MV-H can bind to human, tamarin and dog SLAM, but not to that of mice. Notably, MV binding to dog SLAM showed a lower affinity and faster kinetics than that of human SLAM, and MV exhibits a similar entry activity in dog SLAM- and human SLAM-expressing Vero cells. The mutagenesis study using a fusion assay, based on the MV-H–SLAM complex structure, revealed differences in tolerance for the receptor specificity between MV-H and CDV-H. These results provide insights into H-SLAM specificity related to potential host expansion.
Collapse
Affiliation(s)
- Hideo Fukuhara
- Center for Research and Education on Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Yuri Ito
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Miyuki Sako
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Mizuho Kajikawa
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Koki Yoshida
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Fumio Seki
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Mwila Hilton Mwaba
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Takao Hashiguchi
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Masa-Aki Higashibata
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Toyoyuki Ose
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kimiko Kuroki
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Makoto Takeda
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Katsumi Maenaka
- Center for Research and Education on Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
| |
Collapse
|
16
|
Tanzawa T, Kato K, Girodat D, Ose T, Kumakura Y, Wieden HJ, Uchiumi T, Tanaka I, Yao M. The C-terminal helix of ribosomal P stalk recognizes a hydrophobic groove of elongation factor 2 in a novel fashion. Nucleic Acids Res 2019; 46:3232-3244. [PMID: 29471537 PMCID: PMC5887453 DOI: 10.1093/nar/gky115] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/09/2018] [Indexed: 01/17/2023] Open
Abstract
Archaea and eukaryotes have ribosomal P stalks composed of anchor protein P0 and aP1 homodimers (archaea) or P1•P2 heterodimers (eukaryotes). These P stalks recruit translational GTPases to the GTPase-associated center in ribosomes to provide energy during translation. The C-terminus of the P stalk is known to selectively recognize GTPases. Here we investigated the interaction between the P stalk and elongation factor 2 by determining the structures of Pyrococcus horikoshii EF-2 (PhoEF-2) in the Apo-form, GDP-form, GMPPCP-form (GTP-form), and GMPPCP-form bound with 11 C-terminal residues of P1 (P1C11). Helical structured P1C11 binds to a hydrophobic groove between domain G and subdomain G′ of PhoEF-2, where is completely different from that of aEF-1α in terms of both position and sequence, implying that such interaction characteristic may be requested by how GTPases perform their functions on the ribosome. Combining PhoEF-2 P1-binding assays with a structural comparison of current PhoEF-2 structures and molecular dynamics model of a P1C11-bound GDP form, the conformational changes of the P1C11-binding groove in each form suggest that in response to the translation process, the groove has three states: closed, open, and release for recruiting and releasing GTPases.
Collapse
Affiliation(s)
- Takehito Tanzawa
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Koji Kato
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.,Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Dylan Girodat
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge AB T1K 3M4, Canada
| | - Toyoyuki Ose
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.,Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yuki Kumakura
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Hans-Joachim Wieden
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge AB T1K 3M4, Canada
| | - Toshio Uchiumi
- Department of Biology, Faculty of Science, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan
| | - Isao Tanaka
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Min Yao
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.,Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| |
Collapse
|
17
|
Tadokoro T, Jahan ML, Ito Y, Tahara M, Chen S, Imai A, Sugimura N, Yoshida K, Saito M, Ose T, Hashiguchi T, Takeda M, Fukuhara H, Maenaka K. Biophysical characterization and single-chain Fv construction of a neutralizing antibody to measles virus. FEBS J 2019; 287:145-159. [PMID: 31287622 DOI: 10.1111/febs.14991] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 12/02/2018] [Revised: 05/01/2019] [Accepted: 07/06/2019] [Indexed: 12/22/2022]
Abstract
The measles virus (MV) is a major cause of childhood morbidity and mortality worldwide. We previously established a mouse monoclonal antibody, 2F4, which shows high neutralizing titers against eight different genotypes of MV. However, the molecular basis for the neutralizing activity of the 2F4 antibody remains incompletely understood. Here, we have evaluated the binding characteristics of a Fab fragment of the 2F4 antibody. Using the MV infectious assay, we demonstrated that 2F4 Fab inhibits viral entry via either of two cellular receptors, SLAM and Nectin4. Surface plasmon resonance (SPR) analysis of recombinant proteins indicated that 2F4 Fab interacts with MV hemagglutinin (MV-H) with a KD value at the nm level. Furthermore, we designed a single-chain Fv fragment of 2F4 antibody as another potential biopharmaceutical to target measles. The stable 2F4 scFv was successfully prepared by the refolding method and shown to interact with MV-H at the μm level. Like 2F4 Fab, scFv inhibited receptor binding and viral entry. This indicates that 2F4 mAb uses the receptor-binding site and/or a neighboring region as an epitope with high affinity. These results provide insight into the neutralizing activity and potential therapeutic use of antibody fragments for MV infection.
Collapse
Affiliation(s)
- Takashi Tadokoro
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Mst Lubna Jahan
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Yuri Ito
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Maino Tahara
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Surui Chen
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Atsutoshi Imai
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Natsumi Sugimura
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Koki Yoshida
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Mizuki Saito
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Toyoyuki Ose
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Takao Hashiguchi
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Makoto Takeda
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideo Fukuhara
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Katsumi Maenaka
- Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| |
Collapse
|
18
|
Zhan J, Hossain MA, Sethi A, Ose T, Moseley GW, Gooley PR. 1H, 15N and 13C resonance assignments of the C-terminal domain of the P protein of the Nishigahara strain of rabies virus. Biomol NMR Assign 2019; 13:5-8. [PMID: 30238347 DOI: 10.1007/s12104-018-9841-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 06/04/2018] [Accepted: 09/14/2018] [Indexed: 06/08/2023]
Abstract
The C-terminal domain of the P protein of rabies virus is a multifunctional domain that interacts with both viral and host cell proteins. Here we report the 1H, 13C and 15N chemical shift assignments of this domain from P protein of the Nishigahara strain of rabies virus, a pathogenic laboratory strain well established for studies of virulence functions of rabies virus proteins, including P protein. The data and secondary structure analysis are in good agreement with the reported predominantly helical structure of the same domain from the CVS strain of rabies solved by crystallography. These assignments will enable future solution studies of the interactions of the P protein with viral and host proteins, and the effects of post-translational modifications.
Collapse
Affiliation(s)
- Jingyu Zhan
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Md Alamgir Hossain
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ashish Sethi
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Toyoyuki Ose
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Gregory W Moseley
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton Campus, Clayton, VIC, 3800, Australia
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.
| |
Collapse
|
19
|
Li L, Adachi M, Yu J, Kato K, Shinoda A, Ostermann A, Schrader TE, Ose T, Yao M. Neutron crystallographic study of heterotrimeric glutamine amidotransferase CAB. Acta Crystallogr F Struct Biol Commun 2019; 75:193-196. [PMID: 30839294 DOI: 10.1107/s2053230x19000220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 01/05/2019] [Indexed: 11/10/2022]
Abstract
Heterotrimeric glutamine amidotransferase CAB (GatCAB) possesses an ammonia-self-sufficient mechanism in which ammonia is produced and used in the inner complex by GatA and GatB, respectively. The X-ray structure of GatCAB revealed that the two identified active sites of GatA and GatB are markedly distant, but are connected in the complex by a channel of 30 Å in length. In order to clarify whether ammonia is transferred through this channel in GatCAB by visualizing ammonia, neutron diffraction studies are indispensable. Here, GatCAB crystals were grown to approximate dimensions of 2.8 × 0.8 × 0.8 mm (a volume of 1.8 mm3) with the aid of a polymer using microseeding and macroseeding processes. Monochromatic neutron diffraction data were collected using the neutron single-crystal diffractometer BIODIFF at the Heinz Maier-Leibnitz Zentrum, Germany. The GatCAB crystals belonged to space group P212121, with unit-cell parameters a = 74.6, b = 94.5, c = 182.5 Å and with one GatCAB complex (molecular mass 119 kDa) in the asymmetric unit. This study represented a challenge in current neutron diffraction technology.
Collapse
Affiliation(s)
- Long Li
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Motoyasu Adachi
- National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Jian Yu
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Koji Kato
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Akira Shinoda
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Tobias E Schrader
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Toyoyuki Ose
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Min Yao
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| |
Collapse
|
20
|
Shioi N, Tadokoro T, Shioi S, Okabe Y, Matsubara H, Kita S, Ose T, Kuroki K, Terada S, Maenaka K. Crystal structure of the complex between venom toxin and serum inhibitor from Viperidae snake. J Biol Chem 2019; 294:1250-1256. [PMID: 30504218 PMCID: PMC6349104 DOI: 10.1074/jbc.ra118.006840] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 11/27/2018] [Indexed: 01/07/2023] Open
Abstract
Venomous snakes have endogenous proteins that neutralize the toxicity of their venom components. We previously identified five small serum proteins (SSP-1-SSP-5) from a highly venomous snake belonging to the family Viperidae as inhibitors of various toxins from snake venom. The endogenous inhibitors belong to the prostate secretory protein of 94 amino acids (PSP94) family. SSP-2 interacts with triflin, which is a member of the cysteine-rich secretory protein (CRISP) family that blocks smooth muscle contraction. However, the structural basis for the interaction and the biological roles of these inhibitors are largely unknown. Here, we determined the crystal structure of the SSP-2-triflin complex at 2.3 Å resolution. A concave region centrally located in the N-terminal domain of triflin is fully occupied by the terminal β-strands of SSP-2. SSP-2 does not bind tightly to the C-terminal cysteine-rich domain of triflin; this domain is thought to be responsible for its channel-blocker function. Instead, the cysteine-rich domain is tilted 7.7° upon binding to SSP-2, and the inhibitor appears to sterically hinder triflin binding to calcium channels. These results help explain how an endogenous inhibitor prevents the venomous protein from maintaining homeostasis in the host. Furthermore, this interaction also sheds light on the binding interface between the human homologues PSP94 and CRISP-3, which are up-regulated in prostate and ovarian cancers.
Collapse
Affiliation(s)
- Narumi Shioi
- From the Department of Chemistry, Faculty of Science, Fukuoka University, 19-1, 8-chome Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan, , To whom correspondence may be addressed. Tel.:
81-92-870-6631 ext. 6215; Fax:
81-92-865-6030; E-mail:
| | - Takashi Tadokoro
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan, and , To whom correspondence may be addressed. Tel.:
81-11-706-3764; Fax:
81-11-706-4986; E-mail:
| | - Seijiro Shioi
- Radioisotope Center, Fukuoka University, Fukuoka 814-0180, Japan
| | - Yuki Okabe
- From the Department of Chemistry, Faculty of Science, Fukuoka University, 19-1, 8-chome Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Haruki Matsubara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan, and
| | - Shunsuke Kita
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan, and
| | - Toyoyuki Ose
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan, and
| | - Kimiko Kuroki
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan, and
| | - Shigeyuki Terada
- From the Department of Chemistry, Faculty of Science, Fukuoka University, 19-1, 8-chome Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Katsumi Maenaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan, and , To whom correspondence may be addressed. Tel.:
81-11-706-3970; Fax:
81-11-706-4986; E-mail:
| |
Collapse
|
21
|
Kajikawa M, Ose T, Fukunaga Y, Okabe Y, Matsumoto N, Yonezawa K, Shimizu N, Kollnberger S, Kasahara M, Maenaka K. Structure of MHC class I-like MILL2 reveals heparan-sulfate binding and interdomain flexibility. Nat Commun 2018; 9:4330. [PMID: 30337538 PMCID: PMC6193965 DOI: 10.1038/s41467-018-06797-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 10/12/2017] [Accepted: 09/27/2018] [Indexed: 12/23/2022] Open
Abstract
The MILL family, composed of MILL1 and MILL2, is a group of nonclassical MHC class I molecules that occur in some orders of mammals. It has been reported that mouse MILL2 is involved in wound healing; however, the molecular mechanisms remain unknown. Here, we determine the crystal structure of MILL2 at 2.15 Å resolution, revealing an organization similar to classical MHC class I. However, the α1-α2 domains are not tightly fixed on the α3-β2m domains, indicating unusual interdomain flexibility. The groove between the two helices in the α1-α2 domains is too narrow to permit ligand binding. Notably, an unusual basic patch on the α3 domain is involved in the binding to heparan sulfate which is essential for MILL2 interactions with fibroblasts. These findings suggest that MILL2 has a unique structural architecture and physiological role, with binding to heparan sulfate proteoglycans on fibroblasts possibly regulating cellular recruitment in biological events. The MILL (MHC-I-like located near the leukocyte receptor complex) family is a group of related nonclassical MHC-I molecules. Here the authors present the crystal structure of MILL2, which reveals an unusual interdomain flexibility, and show that MILL2 binds heparan sulfate on the surface of fibroblasts through a basic patch.
Collapse
Affiliation(s)
- Mizuho Kajikawa
- Laboratory of Microbiology, Showa Pharmaceutical University, Machida, Tokyo, 190-8543, Japan.,Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Toyoyuki Ose
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Yuko Fukunaga
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yuki Okabe
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.,Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Naoki Matsumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Kento Yonezawa
- Photon Factory, High Energy Accelerator Research Organization, Tsukuba, Ibaraki, 305-0801, Japan
| | - Nobutaka Shimizu
- Photon Factory, High Energy Accelerator Research Organization, Tsukuba, Ibaraki, 305-0801, Japan
| | - Simon Kollnberger
- Cardiff Institute of Infection & Immunity, University of Cardiff, Henry Wellcome Building, Heath Park, Cardiff, CF14 4XN, UK
| | - Masanori Kasahara
- Department of Pathology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Katsumi Maenaka
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan. .,Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan.
| |
Collapse
|
22
|
Furukawa A, Kakita K, Yamada T, Ishizuka M, Sakamoto J, Hatori N, Maeda N, Ohsaka F, Saitoh T, Nomura T, Kuroki K, Nambu H, Arase H, Matsunaga S, Anada M, Ose T, Hashimoto S, Maenaka K. Structural and thermodynamic analyses reveal critical features of glycopeptide recognition by the human PILRα immune cell receptor. J Biol Chem 2017; 292:21128-21136. [PMID: 29046357 DOI: 10.1074/jbc.m117.799239] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 05/31/2017] [Revised: 10/11/2017] [Indexed: 11/06/2022] Open
Abstract
Before entering host cells, herpes simplex virus-1 uses its envelope glycoprotein B to bind paired immunoglobulin-like type 2 receptor α (PILRα) on immune cells. PILRα belongs to the Siglec (sialic acid (SA)-binding immunoglobulin-like lectin)-like family, members of which bind SA. PILRα is the only Siglec member to recognize not only the sialylated O-linked sugar T antigen (sTn) but also its attached peptide region. We previously determined the crystal structure of PILRα complexed with the sTn-linked glycopeptide of glycoprotein B, revealing the simultaneous recognition of sTn and peptide by the receptor. However, the contribution of each glycopeptide component to PILRα binding was largely unclear. Here, we chemically synthesized glycopeptide derivatives and determined the thermodynamic parameters of their interaction with PILRα. We show that glycopeptides with different sugar units linking SA and peptides (i.e. "GlcNAc-type" and "deoxy-GlcNAc-type" glycopeptides) have lower affinity and more enthalpy-driven binding than the wild type (i.e. GalNAc-type glycopeptide). The crystal structures of PILRα complexed with these glycopeptides highlighted the importance of stereochemical positioning of the O4 atom of the sugar moiety. These results provide insights both for understanding the unique O-glycosylated peptide recognition by the PILRα and for the rational design of herpes simplex virus-1 entry inhibitors.
Collapse
Affiliation(s)
| | - Kosuke Kakita
- Synthetic and Industrial Chemistry, Faculty of Pharmaceutical Sciences and
| | - Tomoki Yamada
- Center for Research and Education on Drug Discovery, Hokkaido University, Sapporo 060-0812, Japan and
| | | | | | - Nanao Hatori
- Synthetic and Industrial Chemistry, Faculty of Pharmaceutical Sciences and
| | - Naoyoshi Maeda
- Center for Research and Education on Drug Discovery, Hokkaido University, Sapporo 060-0812, Japan and
| | - Fumina Ohsaka
- Center for Research and Education on Drug Discovery, Hokkaido University, Sapporo 060-0812, Japan and
| | - Takashi Saitoh
- Center for Research and Education on Drug Discovery, Hokkaido University, Sapporo 060-0812, Japan and
| | - Takao Nomura
- Center for Research and Education on Drug Discovery, Hokkaido University, Sapporo 060-0812, Japan and
| | | | - Hisanori Nambu
- Synthetic and Industrial Chemistry, Faculty of Pharmaceutical Sciences and
| | - Hisashi Arase
- World Premier International Immunology Frontier Research Center and.,Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shigeki Matsunaga
- Synthetic and Industrial Chemistry, Faculty of Pharmaceutical Sciences and
| | - Masahiro Anada
- Synthetic and Industrial Chemistry, Faculty of Pharmaceutical Sciences and
| | - Toyoyuki Ose
- From the Laboratories of Biomolecular Science and
| | - Shunichi Hashimoto
- Synthetic and Industrial Chemistry, Faculty of Pharmaceutical Sciences and
| | - Katsumi Maenaka
- From the Laboratories of Biomolecular Science and .,Center for Research and Education on Drug Discovery, Hokkaido University, Sapporo 060-0812, Japan and
| |
Collapse
|
23
|
Maeda N, Furukawa A, Kakita K, Anada M, Hashimoto S, Matsunaga S, Kuroki K, Ose T, Kato A, Arii J, Kawaguchi Y, Arase H, Maenaka K. Rapid Screening by Cell-Based Fusion Assay for Identifying Novel Antivirals of Glycoprotein B-Mediated Herpes Simplex Virus Type 1 Infection. Biol Pharm Bull 2017; 39:1897-1902. [PMID: 27803463 DOI: 10.1248/bpb.b16-00533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Herpes simplex virus type 1 (HSV-1) is a causative agent for a variety of diseases. Although antiherpetic drugs such as acyclovir have been developed to inhibit virus replication through interaction with DNA kinases, their continuous administration leads to an increase in the frequency of drug-resistant HSV-1, which is an important clinical issue that requires urgent solution. Recently, we reported that the sialylated O-linked sugar T antigen (sTn) and its attached peptide region (O-glycosylated sTn peptide) derived from the HSV-1 glycoprotein B (gB) protein inhibited HSV-1 infection by specifically targeting paired immunoglobulin-like type 2 receptor alpha (PILRα) in vitro. In this study, to further identify novel inhibitors of gB-mediated HSV-1 infection in vitro, we established a cell-based fusion assay for rapid drug screening. Chinese hamster ovary (CHO) cells were transfected with expression plasmids for HSV-1 gB, gD, gH, and gL, and T7 RNA polymerase, and were designated as the effector cells. The CHO-K1 cells stably expressing PILRα were transfected with the expression plasmid for firefly luciferase under the T7 promoter, and were designated as the target cells. The effector and target cells were co-cultured, and luminescence was measured when both cells were successfully fused. Importantly, we found that cell-to-cell fusion was specifically inhibited by O-glycosylated sTn peptide in a dose dependent manner. Our results suggested that this virus-free cell-based fusion assay system could be a useful and promising approach to identify novel inhibitors of gB-mediated HSV-1 infection, and will aid in the development of antiviral therapeutic strategies for HSV-1-associated diseases.
Collapse
Affiliation(s)
- Naoyoshi Maeda
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Takahashi A, Kuroki K, Okabe Y, Kasai Y, Matsumoto N, Yamada C, Takai T, Ose T, Kon S, Matsuda T, Maenaka K. The immunosuppressive effect of domain-deleted dimer of HLA-G2 isoform in collagen-induced arthritis mice. Hum Immunol 2016; 77:754-9. [DOI: 10.1016/j.humimm.2016.01.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/11/2016] [Indexed: 11/26/2022]
|
25
|
Hirata Y, Brems H, Suzuki M, Kanamori M, Okada M, Morita R, Llano-Rivas I, Ose T, Messiaen L, Legius E, Yoshimura A. Interaction between a Domain of the Negative Regulator of the Ras-ERK Pathway, SPRED1 Protein, and the GTPase-activating Protein-related Domain of Neurofibromin Is Implicated in Legius Syndrome and Neurofibromatosis Type 1. J Biol Chem 2015; 291:3124-34. [PMID: 26635368 DOI: 10.1074/jbc.m115.703710] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [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: 11/11/2015] [Indexed: 11/06/2022] Open
Abstract
Constitutional heterozygous loss-of-function mutations in the SPRED1 gene cause a phenotype known as Legius syndrome, which consists of symptoms of multiple café-au-lait macules, axillary freckling, learning disabilities, and macrocephaly. Legius syndrome resembles a mild neurofibromatosis type 1 (NF1) phenotype. It has been demonstrated that SPRED1 functions as a negative regulator of the Ras-ERK pathway and interacts with neurofibromin, the NF1 gene product. However, the molecular details of this interaction and the effects of the mutations identified in Legius syndrome and NF1 on this interaction have not yet been investigated. In this study, using a yeast two-hybrid system and an immunoprecipitation assay in HEK293 cells, we found that the SPRED1 EVH1 domain interacts with the N-terminal 16 amino acids and the C-terminal 20 amino acids of the GTPase-activating protein (GAP)-related domain (GRD) of neurofibromin, which form two crossing α-helix coils outside the GAP domain. These regions have been shown to be dispensable for GAP activity and are not present in p120(GAP). Several mutations in these N- and C-terminal regions of the GRD in NF1 patients and pathogenic missense mutations in the EVH1 domain of SPRED1 in Legius syndrome reduced the binding affinity between the EVH1 domain and the GRD. EVH1 domain mutations with reduced binding to the GRD also disrupted the ERK suppression activity of SPRED1. These data clearly demonstrate that SPRED1 inhibits the Ras-ERK pathway by recruiting neurofibromin to Ras through the EVH1-GRD interaction, and this study also provides molecular basis for the pathogenic mutations of NF1 and Legius syndrome.
Collapse
Affiliation(s)
- Yasuko Hirata
- From the Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Hilde Brems
- the Department of Human Genetics, Catholic University of Leuven, 3000 Leuven, Belgium
| | - Mayu Suzuki
- From the Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Mitsuhiro Kanamori
- From the Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masahiro Okada
- From the Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Rimpei Morita
- From the Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Isabel Llano-Rivas
- the Department of Genetics, Hospital Universitario Cruces, BioCruces Health Research Institute, Biscay, Spain
| | - Toyoyuki Ose
- Department of Pharmaceutical Sciences, Hokkaido University, N12W6, Sapporo 060-0812, Japan, and
| | - Ludwine Messiaen
- the Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Eric Legius
- the Department of Human Genetics, Catholic University of Leuven, 3000 Leuven, Belgium
| | - Akihiko Yoshimura
- From the Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan,
| |
Collapse
|
26
|
Ose T, Oikawa A, Nakamura Y, Maenaka K, Higuchi Y, Satoh Y, Fujiwara S, Demura M, Sone T, Kamiya M. Solution structure of an avirulence protein, AVR-Pia, from Magnaporthe oryzae. J Biomol NMR 2015; 63:229-235. [PMID: 26362280 DOI: 10.1007/s10858-015-9979-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/18/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Toyoyuki Ose
- Faculty of Pharmaceutical Sciences, Hokkaido University, N12, W6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Azusa Oikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, N12, W6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Yukiko Nakamura
- Faculty of Pharmaceutical Sciences, Hokkaido University, N12, W6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Katsumi Maenaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, N12, W6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Yuya Higuchi
- Graduate School of Agriculture, Hokkaido University, N9, W9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Yuki Satoh
- Graduate School of Agriculture, Hokkaido University, N9, W9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Shiho Fujiwara
- Graduate School of Agriculture, Hokkaido University, N9, W9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University, N10, W8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan
| | - Teruo Sone
- Graduate School of Agriculture, Hokkaido University, N9, W9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan.
| | - Masakatsu Kamiya
- Faculty of Advanced Life Science, Hokkaido University, N10, W8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan.
| |
Collapse
|
27
|
Sone T, Haraguchi Y, Kuwahara A, Ose T, Takano M, Abe A, Tanaka M, Tanaka I, Asano K. Structural characterization reveals the keratinolytic activity of an arthrobacter nicotinovorans protease. Protein Pept Lett 2015; 22:63-72. [PMID: 25256266 DOI: 10.2174/0929866521666140919100851] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/23/2014] [Accepted: 09/04/2014] [Indexed: 11/22/2022]
Abstract
Elevated cadmium (Cd) concentrations in fishery byproducts are an environmental concern, that might be reduced by enzymatic removal and adsorption of the contaminants during recycling the byproducts as animal food. We cloned the gene for Arthrobacter nicotinovorans serine protease (ANISEP), which was isolated from the hepatopancreas of the Japanese scallop (Patiopecten yessoensis) and has been found to be an effective enzyme for Cd(II) removal. The gene is 993 bp in length and encodes 330 amino acids, including the pre (1-30) and pro (31-111) sequences. The catalytic triad consists of His, Asp, and Ser. Sequence similarities indicate that ANISEP is a extracellular serine protease. X-ray crystallography revealed structural similarities between ANISEP and the trypsin-like serine protease NAALP from Nesterenkonia sp. Site-directed mutagenesis identified Ser171 as catalytic residue. The keratinolytic activity of ANISEP was 10-fold greater than that of trypsin. ANISEP digested Cd(II)-bound recombinant metallothionein MT-10a from Laternula elliptica, but did not release Cd. These results further suggest ANISEP is a trypsin-like serine protease that can release Cd from the Japanese scallop hepatopancreas because of its strong keratinolytic activity.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Kozo Asano
- Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan.
| |
Collapse
|
28
|
Kita S, Matsubara H, Kasai Y, Tamaoki T, Okabe Y, Fukuhara H, Kamishikiryo J, Krayukhina E, Uchiyama S, Ose T, Kuroki K, Maenaka K. Crystal structure of extracellular domain of human lectin-like transcript 1 (LLT1), the ligand for natural killer receptor-P1A. Eur J Immunol 2015; 45:1605-13. [DOI: 10.1002/eji.201545509] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 03/01/2015] [Accepted: 03/26/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Shunsuke Kita
- Laboratory of Biomolecular Science; Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Japan
| | - Haruki Matsubara
- Laboratory of Biomolecular Science; Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Japan
- Department of Materials Structure Science; Structural Biology Research Center; Photon Factory; Institute of Materials Structure Science; High Energy Accelerator Research Organization (KEK); The Graduate University for Advanced Studies; Tsukuba Ibaraki Japan
| | - Yoshiyuki Kasai
- Laboratory of Biomolecular Science; Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Japan
| | - Takaharu Tamaoki
- Laboratory of Biomolecular Science; Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Japan
| | - Yuki Okabe
- Laboratory of Biomolecular Science; Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Japan
- Research Center for Hepatitis and Immunology; National Center for Global Health and Medicine; 1-7-1 Kohnodai Ichikawa Chiba Japan
| | - Hideo Fukuhara
- Laboratory of Biomolecular Science; Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Japan
| | - Jun Kamishikiryo
- Faculty of Pharmacy and Pharmaceutical Sciences; Fukuyama University; Fukuyama Japan
| | - Elena Krayukhina
- Department of Biotechnology; Graduate School of Engineering; Osaka University; Osaka Japan
- U-Medico Corporation; Osaka Japan
| | - Susumu Uchiyama
- Department of Biotechnology; Graduate School of Engineering; Osaka University; Osaka Japan
| | - Toyoyuki Ose
- Laboratory of Biomolecular Science; Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Japan
| | - Kimiko Kuroki
- Laboratory of Biomolecular Science; Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Japan
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science; Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Japan
| |
Collapse
|
29
|
Srivastava M, Duan G, Kershaw NJ, Athanasopoulos V, Yeo JHC, Ose T, Hu D, Brown SHJ, Jergic S, Patel HR, Pratama A, Richards S, Verma A, Jones EY, Heissmeyer V, Preiss T, Dixon NE, Chong MMW, Babon JJ, Vinuesa CG. Roquin binds microRNA-146a and Argonaute2 to regulate microRNA homeostasis. Nat Commun 2015; 6:6253. [PMID: 25697406 PMCID: PMC4346627 DOI: 10.1038/ncomms7253] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [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: 06/03/2014] [Accepted: 01/09/2015] [Indexed: 12/26/2022] Open
Abstract
Roquin is an RNA-binding protein that prevents autoimmunity and inflammation via repression of bound target mRNAs such as inducible costimulator (Icos). When Roquin is absent or mutated (Roquinsan), Icos is overexpressed in T cells. Here we show that Roquin enhances Dicer-mediated processing of pre-miR-146a. Roquin also directly binds Argonaute2, a central component of the RNA-induced silencing complex, and miR-146a, a microRNA that targets Icos mRNA. In the absence of functional Roquin, miR-146a accumulates in T cells. Its accumulation is not due to increased transcription or processing, rather due to enhanced stability of mature miR-146a. This is associated with decreased 3′ end uridylation of the miRNA. Crystallographic studies reveal that Roquin contains a unique HEPN domain and identify the structural basis of the ‘san’ mutation and Roquin’s ability to bind multiple RNAs. Roquin emerges as a protein that can bind Ago2, miRNAs and target mRNAs, to control homeostasis of both RNA species. Roquin is an RNA-binding protein that promotes the degradation of specific mRNAs and is crucial for the maintenance of peripheral immune tolerance. Here the authors show that, in addition to its target mRNAs, Roquin can bind miR-146a and the RISC component Ago2 to control homeostasis of both RNA species.
Collapse
Affiliation(s)
- Monika Srivastava
- Department of Pathogens and Immunity, John Curtin School of Medical Research, Canberra, Australian Capital Territory 2601, Australia
| | - Guowen Duan
- Department of Pathogens and Immunity, John Curtin School of Medical Research, Canberra, Australian Capital Territory 2601, Australia
| | - Nadia J Kershaw
- Division of Structural Biology, Walter and Eliza Hall Institute and The University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Vicki Athanasopoulos
- Department of Pathogens and Immunity, John Curtin School of Medical Research, Canberra, Australian Capital Territory 2601, Australia
| | - Janet H C Yeo
- Genomics and Immunology laboratory, St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Toyoyuki Ose
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Desheng Hu
- Helmholtz Zentrum München, Institute of Molecular Immunology, D-81377 München, Germany
| | - Simon H J Brown
- Centre for Medical and Molecular Bioscience, University of Wollongong and Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Slobodan Jergic
- Centre for Medical and Molecular Bioscience, University of Wollongong and Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Hardip R Patel
- 1] Department of Genome Biology, John Curtin School of Medical Research, Canberra, Australian Capital Territory 2601, Australia [2] Genome Discovery Unit, John Curtin School of Medical Research, Canberra, Australian Capital Territory 2601, Australia
| | - Alvin Pratama
- Department of Pathogens and Immunity, John Curtin School of Medical Research, Canberra, Australian Capital Territory 2601, Australia
| | - Sashika Richards
- Department of Pathogens and Immunity, John Curtin School of Medical Research, Canberra, Australian Capital Territory 2601, Australia
| | - Anil Verma
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - E Yvonne Jones
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Vigo Heissmeyer
- 1] Helmholtz Zentrum München, Institute of Molecular Immunology, D-81377 München, Germany [2] Ludwig-Maximilians-Universität München, Institute for Immunology, D-80336 München, Germany
| | - Thomas Preiss
- 1] Department of Genome Biology, John Curtin School of Medical Research, Canberra, Australian Capital Territory 2601, Australia [2] Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - Nicholas E Dixon
- Centre for Medical and Molecular Bioscience, University of Wollongong and Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Mark M W Chong
- Genomics and Immunology laboratory, St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Jeffrey J Babon
- Division of Structural Biology, Walter and Eliza Hall Institute and The University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Carola G Vinuesa
- Department of Pathogens and Immunity, John Curtin School of Medical Research, Canberra, Australian Capital Territory 2601, Australia
| |
Collapse
|
30
|
Zheng A, Yu J, Yamamoto R, Ose T, Tanaka I, Yao M. X-ray structures of eIF5B and the eIF5B-eIF1A complex: the conformational flexibility of eIF5B is restricted on the ribosome by interaction with eIF1A. ACTA ACUST UNITED AC 2014; 70:3090-8. [PMID: 25478828 DOI: 10.1107/s1399004714021476] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [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: 03/13/2014] [Accepted: 09/29/2014] [Indexed: 11/11/2022]
Abstract
eIF5B and eIF1A are two translation-initiation factors that are universally conserved among all kingdoms. They show a unique interaction in eukaryotes which is important for ribosomal subunit joining. Here, the structures of two isolated forms of yeast eIF5B and of the eIF5B-eIF1A complex (eIF1A and eIF5B do not contain the respective N-terminal domains) are reported. The eIF5B-eIF1A structure shows that the C-terminal tail of eIF1A binds to eIF5B domain IV, while the core domain of eIF1A is invisible in the electron-density map. Although the individual domains in all structures of eIF5B or archaeal IF5B (aIF5B) are similar, their domain arrangements are significantly different, indicating high structural flexibility, which is advantageous for conformational change during ribosomal subunit joining. Based on these structures, models of eIF5B, eIF1A and tRNAi(Met) on the 80S ribosome were built. The models suggest that the interaction between the eIF1A C-terminal tail and eIF5B helps tRNAi(Met) to bind to eIF5B domain IV, thus preventing tRNAi(Met) dissociation, stabilizing the interface for subunit joining and providing a checkpoint for correct ribosome assembly.
Collapse
Affiliation(s)
- Aiping Zheng
- Graduate School of Life Sciences, Hokkaido University, Kita 10 Nishi 8 Kita-Ku, Sapporo, Hokkaido 060-0810, Japan
| | - Jian Yu
- Graduate School of Life Sciences, Hokkaido University, Kita 10 Nishi 8 Kita-Ku, Sapporo, Hokkaido 060-0810, Japan
| | - Reo Yamamoto
- Graduate School of Life Sciences, Hokkaido University, Kita 10 Nishi 8 Kita-Ku, Sapporo, Hokkaido 060-0810, Japan
| | - Toyoyuki Ose
- Graduate School of Life Sciences, Hokkaido University, Kita 10 Nishi 8 Kita-Ku, Sapporo, Hokkaido 060-0810, Japan
| | - Isao Tanaka
- Graduate School of Life Sciences, Hokkaido University, Kita 10 Nishi 8 Kita-Ku, Sapporo, Hokkaido 060-0810, Japan
| | - Min Yao
- Graduate School of Life Sciences, Hokkaido University, Kita 10 Nishi 8 Kita-Ku, Sapporo, Hokkaido 060-0810, Japan
| |
Collapse
|
31
|
Wiltzer L, Brice A, Lieu K, Harrison A, Oksayan S, Bell T, Whelan D, Hossain A, Shillling P, Okada K, Yamaoka S, Larrous F, Bourhy H, Ose T, Gooley P, Jans DA, Blondel D, Ito N, Moseley G. 133. Cytokine 2014. [DOI: 10.1016/j.cyto.2014.07.140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
32
|
Satoh Y, Miki S, Ose T, Oikawa A, Maenaka K, Terauchi R, Asano K, Sone T. Heterologous production, purification, and immunodetection of Magnaporthe oryzae avirulence protein AVR-Pia. Biosci Biotechnol Biochem 2014; 78:680-6. [PMID: 25036967 DOI: 10.1080/09168451.2014.893186] [Citation(s) in RCA: 3] [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: 10/25/2022]
Abstract
The avirulence gene AVR-Pia of Magnaporthe oryzae, which induces a hypersensitive reaction in rice cultivars containing the resistance gene Pia, was expressed in Escherichia coli. AVR-Pia protein was collected as inclusion bodies, denatured, and refolded. Finally, recombinant AVR-Pia (rAVR-Pia) protein was purified by column chromatography. Infiltration of rAVR-Pia triggered cell browning in the leaves of rice cultivar Aichiasahi (Pia), with accumulation of H2O2 and induction of PR1a expression in rice. On the other hand, these reactions were not observed in Shin-2 (pia) leaves after the same treatment. This observation indicated that rAVR-Pia had the function of an avirulence protein. rAVR-Pia was used for immunization of a rabbit, and anti-AVR-Pia antiserum was prepared. The specificity of this antibody was appraised by detecting native AVR-Pia in the inoculated leaf sheath extract using Western blotting in combination with immunoprecipitation. Native AVR-Pia was successfully detected, and its molecular weight was estimated to be 7.4 kDa, indicating signal peptide cleavage. Additionally, secreted native AVR-Pia was quantified as 3.7 ng/g rice sheath.
Collapse
Affiliation(s)
- Yuki Satoh
- a Graduate School of Agriculture, Hokkaido University , Sapporo , Japan
| | | | | | | | | | | | | | | |
Collapse
|
33
|
Minami A, Ose T, Sato K, Oikawa A, Kuroki K, Maenaka K, Oguri H, Oikawa H. Allosteric regulation of epoxide opening cascades by a pair of epoxide hydrolases in monensin biosynthesis. ACS Chem Biol 2014; 9:562-9. [PMID: 24320215 DOI: 10.1021/cb4006485] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Multistep catalysis of epoxide hydrolase/cyclase in the epoxide opening cascade is an intriguing issue in polyether biosynthesis. A pair of structurally homologous epoxide hydrolases was found in gene clusters of ionophore polyethers. In the epoxide opening reactions with MonBI and MonBII involved in monensin biosynthesis, we found that MonBII and catalytically inactive MonBI mutant catalyzed two-step reactions of bisepoxide substrate analogue to afford bicyclic product although MonBII alone catalyzed only the first cyclization. The X-ray crystal structure of MonBI dimers suggested the importance of the KSD motif in MonBI/MonBI interaction, which was further supported by gel filtration chromatography of wild-type MonBI and mutant MonBI. The involvement of the KSD motif in heterodimer formation was confirmed by in vitro assay. Direct evidence of MonBI/MonBII interaction was obtained by native mass spectrometry. Its dissociation constant was determined as 2.21 × 10(-5) M by surface plasmon resonance. Our results suggested the involvement of an allosteric regulation mechanism by MonBI/MonBII interaction in monensin skeletal construction.
Collapse
Affiliation(s)
- Atsushi Minami
- Division of Chemistry, Graduate School of Science and ‡Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Toyoyuki Ose
- Division of Chemistry, Graduate School of Science and ‡Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Kyohei Sato
- Division of Chemistry, Graduate School of Science and ‡Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Azusa Oikawa
- Division of Chemistry, Graduate School of Science and ‡Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Kimiko Kuroki
- Division of Chemistry, Graduate School of Science and ‡Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Katsumi Maenaka
- Division of Chemistry, Graduate School of Science and ‡Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Hiroki Oguri
- Division of Chemistry, Graduate School of Science and ‡Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Hideaki Oikawa
- Division of Chemistry, Graduate School of Science and ‡Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| |
Collapse
|
34
|
Kanda R, Sutoh Y, Kasamatsu J, Maenaka K, Kasahara M, Ose T. Crystal structure of the lamprey variable lymphocyte receptor C reveals an unusual feature in its N-terminal capping module. PLoS One 2014; 9:e85875. [PMID: 24465760 PMCID: PMC3900441 DOI: 10.1371/journal.pone.0085875] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Accepted: 12/02/2013] [Indexed: 01/02/2023] Open
Abstract
Jawless vertebrates represented by lampreys and hagfish use variable lymphocyte receptors (VLRs) as antigen receptors to mount adaptive immune responses. VLRs generate diversity that is comparable to immunoglobulins and T-cell receptors by a gene conversion-like mechanism, which is mediated by cytosine deaminases. Currently, three types of VLRs, VLRA, VLRB, and VLRC, have been identified in lampreys. Crystal structures of VLRA and VLRB in complex with antigens have been reported recently, but no structural information is available for VLRC. Here, we present the first crystal structure of VLRC from the Japanese lamprey (Lethenteron japonicum). Similar to VLRA and VLRB, VLRC forms a typical horseshoe-like solenoid structure with a variable concave surface. Strikingly, its N-terminal cap has a long loop with limited sequence variability that protrudes toward the concave surface, which is the putative antigen-binding surface. Furthermore, as predicted previously, its C-terminal cap lacks a highly variable protruding loop that plays an important role in antigen recognition by lamprey VLRA and VLRB. Recent work suggests that VLRC+ lymphocytes in jawless vertebrates might be akin to γδ T cells in jawed vertebrates. Structural features of lamprey VLRC described here suggest that it may recognize antigens in a unique manner.
Collapse
Affiliation(s)
- Ryo Kanda
- Graduate School of Life Sciences, Hokkaido University, Sapporo, Japan
| | - Yoichi Sutoh
- Department of Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Jun Kasamatsu
- Department of Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Katsumi Maenaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Masanori Kasahara
- Department of Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Toyoyuki Ose
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| |
Collapse
|
35
|
Ariyawutthiphan O, Ose T, Minami A, Shinde S, Tsuda M, Gao YG, Yao M, Oikawa H, Tanaka I. Structure analysis of geranyl pyrophosphate methyltransferase and the proposed reaction mechanism of SAM-dependent C-methylation. Corrigendum. Acta Crystallogr D Biol Cryst 2013. [DOI: 10.1107/s0907444913029247] [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] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The name of one of the authors in the article by Ariyawutthiphanet al.[(2012),Acta Cryst.D68, 1558–1569] is corrected.
Collapse
|
36
|
Ariyawutthiphan O, Ose T, Minami A, Sinde S, Tsuda M, Gao YG, Yao M, Oikawa H, Tanaka I. Structure analysis of geranyl pyrophosphate methyltransferase and the proposed reaction mechanism of SAM-dependentC-methylation. Acta Crystallogr D Biol Crystallogr 2012; 68:1558-69. [DOI: 10.1107/s0907444912038486] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 09/07/2012] [Indexed: 11/10/2022]
Abstract
In the typical isoprenoid-biosynthesis pathway, condensation of the universal C5-unit precursors isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) occursviathe common intermediates prenyl pyrophosphates (C10–C20). The diversity of isoprenoids reflects differences in chain length, cyclization and further additional modification after cyclization. In contrast, the biosynthesis of 2-methylisonorneol (2-MIB), which is responsible for taste and odour problems in drinking water, is unique in that it primes the enzymatic methylation of geranyl pyrophosphate (GPP) before cyclization, which is catalyzed by anS-adenosyl-L-methionine-dependent methyltransferase (GPPMT). The substrate of GPPMT contains a nonconjugated olefin and the reaction mechanism is expected to be similar to that of the steroid methyltransferase (SMT) family. Here, structural analysis of GPPMT in complex with its cofactor and substrate revealed the mechanisms of substrate recognition and possible enzymatic reaction. Using the structures of these complexes, methyl-group transfer and the subsequent proton-abstraction mechanism are discussed. GPPMT and SMTs contain a conserved glutamate residue that is likely to play a role as a general base. Comparison with the reaction mechanism of the mycolic acid cyclopropane synthase (MACS) family also supports this result. This enzyme represented here is the first model of the enzymaticC-methylation of a nonconjugated olefin in the isoprenoid-biosynthesis pathway. In addition, an elaborate system to avoid methylation of incorrect substrates is proposed.
Collapse
|
37
|
Arai R, Tsuda M, Watanabe T, Ose T, Obuse C, Maenaka K, Minami A, Ohba Y. Simultaneous inhibition of Src and Aurora kinases by SU6656 induces therapeutic synergy in human synovial sarcoma growth, invasion and angiogenesis in vivo. Eur J Cancer 2012; 48:2417-30. [PMID: 22244830 DOI: 10.1016/j.ejca.2011.12.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 12/21/2011] [Accepted: 12/21/2011] [Indexed: 11/26/2022]
Abstract
Synovial sarcoma is an obstinate, high-grade malignancy because of its modest responses to radiotherapy and chemotherapy; the identification of effective therapeutics for this sarcoma is therefore necessary. Inhibition of Src family kinases (SFKs) suppresses the proliferation of synovial sarcoma cells in vitro, as we have previously reported. In this study, to validate the efficacy of Src inhibition in vivo, we employed SU6656, which was originally identified as a specific SFK inhibitor. SU6656 treatment significantly impaired the growth of established, existing tumours formed by synovial sarcoma cells in mice. Tumour cell invasion into the surrounding tissues was also abolished by SU6656. It is noteworthy that SU6656 but not PP2 induced a defect in cleavage furrow formation during cytokinesis, resulting in G2/M accumulation and subsequent apoptosis. Intriguingly, SU6656 abrogated the catalytic activities of Aurora kinases and led to the down-regulation of phosphorylated histone H3 coincidently with p53 accumulation, as did the Aurora kinase inhibitor VX-680. Structural comparison indicated an extensive similarity between the catalytic domains of SFKs and Aurora kinases. The structural analysis also revealed the potential binding mode of SU6656 to the ATP-binding cleft of Aurora B via four hydrogen bonds. SU6656 prevented angiogenesis within the tumours by attenuating vascular endothelial growth factor (VEGF) production by tumour cells and the subsequent chemotaxis of endothelial cells; these effects were the result of the inhibition of SFKs but not Aurora kinases. Based on these results, we hereby report a novel property of SU6656 as a dual inhibitor of SFKs and Aurora kinases, the suppression of both of which effectively abrogates tumour development and the progression of synovial sarcoma in vivo.
Collapse
Affiliation(s)
- Ryuta Arai
- Laboratory of Pathophysiology and Signal Transduction, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Kawaguchi A, Ose T, Yao M, Tanaka I. Crystallization and preliminary X-ray structure analysis of human ribosomal protein L30e. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1516-1518. [PMID: 22139155 PMCID: PMC3232128 DOI: 10.1107/s1744309111045131] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 10/27/2011] [Indexed: 05/31/2023]
Abstract
Many functions have been reported for the eukaryotic ribosomal protein L30e. L30e makes several inter-subunit and intra-subunit interactions with protein or RNA components of the 80S ribosome. Yeast L30e has been shown to bind to its own transcript to autoregulate expression at both the transcriptional and the translational levels. Furthermore, it has been reported that mammalian L30e is a component of the selenocysteine-incorporation machinery by binding to the selenocysteine-insertion sequence on mRNA. As high-resolution crystal structures of mammalian L30e are not available, the purification, crystallization and X-ray structure analysis of human L30e are presented here.
Collapse
Affiliation(s)
- Akiko Kawaguchi
- Graduate School of Life Sciences, Hokkaido University, Hokkaido, Sapporo 060-0810, Japan
| | - Toyoyuki Ose
- Faculty of Pharmaceutical Sciences, Hokkaido University, Hokkaido, Sapporo 060-0812, Japan
- Faculty of Advanced Life Sciences, Hokkaido University, Hokkaido, Sapporo 060-0810, Japan
| | - Min Yao
- Graduate School of Life Sciences, Hokkaido University, Hokkaido, Sapporo 060-0810, Japan
- Faculty of Advanced Life Sciences, Hokkaido University, Hokkaido, Sapporo 060-0810, Japan
| | - Isao Tanaka
- Graduate School of Life Sciences, Hokkaido University, Hokkaido, Sapporo 060-0810, Japan
- Faculty of Advanced Life Sciences, Hokkaido University, Hokkaido, Sapporo 060-0810, Japan
| |
Collapse
|
39
|
Hashiguchi T, Ose T, Kubota M, Maita N, Kamishikiryo J, Maenaka K, Yanagi Y. Crystallization strategy for the glycoprotein-receptor complex between measles virus hemagglutinin and its cellular receptor SLAM. Protein Pept Lett 2011; 19:468-73. [PMID: 21933116 DOI: 10.2174/092986612799789314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 08/18/2011] [Accepted: 08/20/2011] [Indexed: 11/22/2022]
Abstract
Measles virus (MV), one of the most contagious agents, infects immune cells using the signaling lymphocyte activation molecule (SLAM) on the cell surface. A complex of SLAM and the attachment protein, hemagglutinin (MVH), has remained elusive due to the intrinsic handling difficulty including glycosylation. Furthermore, crystals obtained of this complex are either nondiffracting or poorly-diffracting. To solve this problem, we designed a systematic approach using a combination of the following techniques; (1) a transient expression system in HEK293SGnTI(-) cells, (2) lysine methylation, (3) structure-guided mutagenesis directed at better crystal packing, (4) Endo H treatment, (5) single-chain formation for stable complex, and (6) floating-drop vapor diffusion. Using our approach, the receptor-binding head domain of MV-H covalently fused with SLAM was successfully crystallized and diffraction was improved from 4.5 Å to a final resolution of 3.15 Å . These combinational methods would be useful as crystallization strategies for complexes of glycoproteins and their receptors.
Collapse
Affiliation(s)
- Takao Hashiguchi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060- 0812, Japan
| | | | | | | | | | | | | |
Collapse
|
40
|
Saitoh T, Igura M, Miyazaki Y, Ose T, Maita N, Kohda D. Crystallographic Snapshots of Tom20–Mitochondrial Presequence Interactions with Disulfide-Stabilized Peptides. Biochemistry 2011; 50:5487-96. [DOI: 10.1021/bi200470x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Takashi Saitoh
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mayumi Igura
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yusuke Miyazaki
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Toyoyuki Ose
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Nobuo Maita
- Institute for Enzyme Research, Tokushima University, 2-24, Shinkura-cho, Tokushima 770-8501, Japan
| | - Daisuke Kohda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
- Research Center for Advanced Immunology, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| |
Collapse
|
41
|
Ariyawutthiphan O, Ose T, Tsuda M, Gao Y, Yao M, Minami A, Oikawa H, Tanaka I. Crystallization and preliminary X-ray crystallographic study of a methyltransferase involved in 2-methylisoborneol biosynthesis in Streptomyces lasaliensis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:417-20. [PMID: 21393856 DOI: 10.1107/s1744309110051523] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 12/08/2010] [Indexed: 11/10/2022]
Abstract
The biosynthetic pathway of the off-flavour terpenoid alcohol 2-methylisoborneol (2-MIB) requires geranyl pyrophosphate methyltransferase (GPPMT) to methylate GPP before the cyclization reaction. GPPMT is the first example of an S-adenosyl-L-methionine-dependent methyltransferase that acts on general intermediates such as geranyl pyrophosphate and farnesyl pyrophosphate in isoprenoid biosynthetic pathways. In this study, recombinant GPPMT was overproduced, purified and crystallized in the absence and presence of cofactor, cofactor analogue and substrate. Well diffracting crystals of apo GPPMT containing one molecule in the asymmetric unit were obtained and the structure of this form was solved by the molecular-replacement method. Two crystal forms of the tertiary complex with GPP and sinefungin were also obtained. Structure analysis of these crystals is currently under way in order to understand the enzyme reaction mechanism.
Collapse
|
42
|
Ose T, Kuroki K, Matsushima M, Maenaka K, Kumagai I. Importance of the Hydrogen Bonding Network Including Asp52 for Catalysis, as Revealed by Asn59 Mutant Hen Egg-white Lysozymes. J Biochem 2009; 146:651-7. [DOI: 10.1093/jb/mvp110] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
43
|
Ose T, Soler N, Rasubala L, Kuroki K, Kohda D, Fourmy D, Yoshizawa S, Maenaka K. Structural Basis for Dynamic Interdomain Movement and RNA Recognition of the Selenocysteine-Specific Elongation Factor SelB. Structure 2007; 15:577-86. [PMID: 17502103 DOI: 10.1016/j.str.2007.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [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: 01/27/2007] [Revised: 03/15/2007] [Accepted: 03/20/2007] [Indexed: 10/23/2022]
Abstract
Selenocysteine (Sec) is the "21st" amino acid and is genetically encoded by an unusual incorporation system. The stop codon UGA becomes a Sec codon when the selenocysteine insertion sequence (SECIS) exists downstream of UGA. Sec incorporation requires a specific elongation factor, SelB, which recognizes tRNA(Sec) via use of an EF-Tu-like domain and the SECIS mRNA hairpin via use of a C-terminal domain (SelB-C). SelB functions in multiple translational steps: binding to SECIS mRNA and tRNA(Sec), delivery of tRNA(Sec) onto an A site, GTP hydrolysis, and release from tRNA and mRNA. However, this dynamic mechanism remains to be revealed. Here, we report a large domain rearrangement in the structure of SelB-C complexed with RNA. Surprisingly, the interdomain region forms new interactions with the phosphate backbone of a neighboring RNA, distinct from SECIS RNA binding. This SelB-RNA interaction is sequence independent, possibly reflecting SelB-tRNA/-rRNA recognitions. Based on these data, the dynamic SelB-ribosome-mRNA-tRNA interactions will be discussed.
Collapse
Affiliation(s)
- Toyoyuki Ose
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T, Masai H, Saito M, Shirai T, Kohda D. Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA. EMBO J 2007; 26:2584-93. [PMID: 17464287 PMCID: PMC1868909 DOI: 10.1038/sj.emboj.7601697] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [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: 11/17/2006] [Accepted: 03/29/2007] [Indexed: 11/08/2022] Open
Abstract
In eubacteria, PriA helicase detects the stalled DNA replication forks. This critical role of PriA is ascribed to its ability to bind to the 3' end of a nascent leading DNA strand in the stalled replication forks. The crystal structures in complexes with oligonucleotides and the combination of fluorescence correlation spectroscopy and mutagenesis reveal that the N-terminal domain of PriA possesses a binding pocket for the 3'-terminal nucleotide residue of DNA. The interaction with the deoxyribose 3'-OH is essential for the 3'-terminal recognition. In contrast, the direct interaction with 3'-end nucleobase is unexpected, considering the same affinity for oligonucleotides carrying the four bases at the 3' end. Thus, the N-terminal domain of PriA recognizes the 3'-end base in a base-non-selective manner, in addition to the deoxyribose and 5'-side phosphodiester group, of the 3'-terminal nucleotide to acquire both sufficient affinity and non-selectivity to find all of the stalled replication forks generated during DNA duplication. This unique feature is prerequisite for the proper positioning of the helicase domain of PriA on the unreplicated double-stranded DNA.
Collapse
MESH Headings
- Amino Acid Sequence
- Base Sequence
- Binding Sites
- Buffers
- Crystallography, X-Ray
- DNA Helicases/chemistry
- DNA Helicases/genetics
- DNA Helicases/isolation & purification
- DNA Helicases/metabolism
- DNA Helicases/physiology
- DNA Replication/physiology
- DNA, Bacterial/physiology
- Databases, Protein
- Escherichia coli/physiology
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/isolation & purification
- Escherichia coli Proteins/metabolism
- Escherichia coli Proteins/physiology
- Histidine/chemistry
- Hydrogen Bonding
- Hydrogen-Ion Concentration
- Hydrophobic and Hydrophilic Interactions
- Ligands
- Models, Chemical
- Models, Molecular
- Molecular Sequence Data
- Oligonucleotides/analysis
- Oligonucleotides/chemistry
- Phosphates/chemistry
- Point Mutation
- Protein Binding
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Rhodamines/metabolism
- Sequence Homology, Amino Acid
- Spectrometry, Fluorescence
- Spectrum Analysis, Raman
- Thrombin/pharmacology
Collapse
Affiliation(s)
- Kaori Sasaki
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Toyoyuki Ose
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | | | - Katsumi Maenaka
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Taku Tanaka
- Genome Dynamics Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hisao Masai
- Genome Dynamics Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Mihoko Saito
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, and JST-BIRD, Siga, Japan
| | - Tsuyoshi Shirai
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, and JST-BIRD, Siga, Japan
| | - Daisuke Kohda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan. Tel.:+81 92 642 6968; Fax: +81 92 642 6764; E-mail:
| |
Collapse
|
45
|
Amano Y, Ishimura N, Furuta K, Okita K, Masaharu M, Azumi T, Ose T, Koshino K, Ishihara S, Adachi K, Kinoshita Y. Interobserver agreement on classifying endoscopic diagnoses of nonerosive esophagitis. Endoscopy 2006; 38:1032-5. [PMID: 17058170 DOI: 10.1055/s-2006-944778] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND STUDY AIMS The majority of patients with gastroesophageal reflux disease in Japan have low-grade esophagitis, including minimal changes. A modified Los Angeles classification of esophagitis, consisting of erosive esophagitis (grades A - D) and nonerosive esophagitis (grades M and N) has been proposed and is in clinical use in Japan. However, it is unclear whether nonerosive esophagitis with only undemarcated mucosal discoloration (grade M) is clinically significant, since interobserver variations in classification have not been investigated. The aim of the present study was therefore to evaluate interobserver variance and diagnostic agreement in the diagnosis of nonerosive esophagitis (grades M and N). MATERIALS AND METHODS A total of 84 endoscopists were enrolled to assess the grade of esophagitis in 30 patients by viewing endoscopic images of the gastroesophageal junction. The images were projected onto a screen, and all of the endoscopists reviewed them concurrently. The diagnosis was selected from the following three categories in the modified Los Angeles classification: grades N, M, or A. The endoscopists were grouped according to their experience, whether they had a board license, and whether they had received specialist training in esophagitis. The kappa coefficient of reliability was calculated. RESULTS The kappa coefficient of reliability for all the endoscopists in the diagnosis of cases of grade M and N nonerosive esophagitis was unacceptably low at 0.22 (95 % CI, 0.21 - 0.24). Endoscopists with a board license and those who had completed a special esophagitis diagnostic course had slightly higher kappa values (0.26; 95 % CI, 0.23 - 0.30 and 0.29; 95 % CI, 0.26 - 0.32), respectively. CONCLUSIONS Interobserver agreement on the endoscopic diagnosis of nonerosive esophagitis (grades M and N) is too low to be of clinical value.
Collapse
Affiliation(s)
- Y Amano
- Division of Gastrointestinal Endoscopy, Shimane University Hospital, Izumo, Japan.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Ose T, Kadowaki Y, Fukuhara H, Kazumori H, Ishihara S, Udagawa J, Otani H, Takasawa S, Okamoto H, Kinoshita Y. Reg I-knockout mice reveal its role in regulation of cell growth that is required in generation and maintenance of the villous structure of small intestine. Oncogene 2006; 26:349-59. [PMID: 16909126 DOI: 10.1038/sj.onc.1209799] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Reg I (regenerating gene product I) is a growth factor that plays a central role in the generation and regeneration of the gastric mucosal architecture. On the other hand, mouse Reg I mRNA is expressed at the highest levels in the small intestine among the gastrointestinal tissues. In the current study, with the aim to clarify the role of Reg I protein in the small intestine, the temporal and spatial pattern of Reg I expression and the phenotype of Reg I-knockout mice in the tissue were examined. In the wild-type mice, immunohistochemistry localized Reg I protein expression in absorptive cells located in the lower half of the intestinal villi. Reg I expression was undetectable until embryonic day 13 (E13), when the fetal intestine still lacks villous structure; however, it dramatically increased at E17 along with the formation and maturation of the fetal intestinal villi. In the small intestine of the adult Reg I-knockout mice, less densely packed, round-shaped aberrant morphology of the absorptive cells was observed light microscopically, and electron microscopical examination revealed a strikingly loose connection of these cells to the basement membrane. Antiproliferating cell nuclear antigen staining and anti-Ki67 staining demonstrated the marked decrease in the number of proliferating cells in the small intestinal mucosa of the knockout mice. The cell migration speed visualized by one shot labeling of 5-bromodeoxyuridine was significantly slower in the knockout mice. These phenotypes of Reg I-knockout mice emerged, in accordance with the temporal pattern of Reg I expression described above, from E17. Reg I was considered to be a regulator of cell growth that is required to generate and maintain the villous structure of the small intestine.
Collapse
Affiliation(s)
- T Ose
- Department of Gastroenterology and Hepatology, School of Medicine (Formerly Second Department of Internal Medicine and Anatomy, Shimane Medical University), Shimane University, Izumo, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Shiroishi M, Kajikawa M, Kuroki K, Ose T, Kohda D, Maenaka K. Crystal structure of the human monocyte-activating receptor, "Group 2" leukocyte Ig-like receptor A5 (LILRA5/LIR9/ILT11). J Biol Chem 2006; 281:19536-44. [PMID: 16675463 DOI: 10.1074/jbc.m603076200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human leukocyte Ig-like receptor B1 (LILRB1) and B2 (LILRB2) belong to "Group 1" receptors and recognize a broad range of major histocompatibility complex class I molecules (MHCIs). In contrast, "Group 2" receptors show low similarity with LILRB1/B2, and their ligands remain to be identified. To date, the structural and functional characteristics of Group 2 LILRs are poorly understood. Here we report the crystal structure of the extracellular domain of LILRA5, which is an activating Group 2 LILR expressed on monocytes and neutrophils. Unexpectedly, the structure showed large changes in structural conformation and charge distribution in the region corresponding to the MHCI binding site of LILRB1/B2, which are also distinct from killer cell Ig-like receptors and Fc alpha receptors. These changes probably confer the structural hindrance for the MHCI binding, and their key amino acid substitutions are well conserved in Group 2 LILRs. Consistently, the surface plasmon resonance and flow cytometric analyses demonstrated that LILRA5 exhibited no affinities to all tested MHCIs. These results raised the possibility that LILRA5 as well as Group 2 LILRs do not play a role in any MHCI recognition but could possibly bind to non-MHCI ligand(s) on the target cells to provide a novel immune regulation mechanism.
Collapse
Affiliation(s)
- Mitsunori Shiroishi
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | | | | | | | | | | |
Collapse
|
48
|
Yuki T, Amano Y, Kushiyama Y, Takahashi Y, Ose T, Moriyama I, Fukuhara H, Ishimura N, Koshino K, Furuta K, Ishihara S, Adachi K, Kinoshita Y. Evaluation of modified crystal violet chromoendoscopy procedure using new mucosal pit pattern classification for detection of Barrett's dysplastic lesions. Dig Liver Dis 2006; 38:296-300. [PMID: 16542886 DOI: 10.1016/j.dld.2006.01.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Revised: 01/30/2006] [Accepted: 01/31/2006] [Indexed: 12/11/2022]
Abstract
BACKGROUND Pit pattern diagnosis is important for endoscopic detection of dysplastic Barrett's lesions, though using magnification endoscopy can be difficult and laborious. We investigated the usefulness of a modified crystal violet chromoendoscopy procedure and utilised a new pit pattern classification for diagnosis of dysplastic Barrett's lesions. METHODS A total of 1,030 patients suspected of having a columnar lined oesophagus were examined, of whom 816 demonstrated a crystal violet-stained columnar lined oesophagus. The early group of patients underwent 0.05% crystal violet chromoendoscopy, while the later group was examined using 0.03% crystal violet with 3.0% acetate. A targeted biopsy of the columnar lined oesophagus was performed using crystal violet staining after making a diagnosis of closed or open type pit pattern with a newly proposed system of classification. The relationship between type of pit pattern and histologically identified dysplastic Barrett's lesions was evaluated. RESULTS Dysplastic Barrett's lesions were identified in biopsy samples with an open type pit pattern with a sensitivity of 96.0%. Further, Barrett's mucosa with the intestinal predominant mucin phenotype was closely associated with the open type pit pattern (sensitivity 81.9%, specificity 95.6%). CONCLUSIONS The new pit pattern classification for diagnosis of Barrett's mucosa was found to be useful for identification of cases with dysplastic lesions and possible malignant potential using a crystal violet chromoendoscopic procedure.
Collapse
Affiliation(s)
- T Yuki
- Department of Gastroenterology and Hepatology, Shimane University, School of Medicine, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Shiroishi M, Kuroki K, Ose T, Rasubala L, Shiratori I, Arase H, Tsumoto K, Kumagai I, Kohda D, Maenaka K. Efficient leukocyte Ig-like receptor signaling and crystal structure of disulfide-linked HLA-G dimer. J Biol Chem 2006; 281:10439-47. [PMID: 16455647 DOI: 10.1074/jbc.m512305200] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
HLA-G is a nonclassical major histocompatibility complex class I (MHCI) molecule, which is expressed in trophoblasts and confers immunological tolerance in the maternal-fetal interface by binding to leukocyte Ig-like receptors (LILRs, also called as LIR/ILT/CD85) and CD8. HLA-G is expressed in disulfide-linked dimer form both in solution and at the cell surface. Interestingly, MHCI dimer formations have been involved in pathogenesis and T cell activation. The structure and receptor binding characteristics of MHCI dimers have never been evaluated. Here we performed binding studies showing that the HLA-G dimer exhibited higher overall affinity to LILRB1/2 than the monomer by significant avidity effects. Furthermore, the cell reporter assay demonstrated that the dimer formation remarkably enhanced the LILRB1-mediated signaling at the cellular level. We further determined the crystal structure of the wild-type dimer of HLA-G with the intermolecular Cys(42)-Cys(42) disulfide bond. This dimer structure showed the oblique configuration to expose two LILR/CD8-binding sites upward from the membrane easily accessible for receptors, providing plausible 1:2 (HLA-G dimer:receptors) complex models. These results indicated that the HLA-G dimer conferred increased avidity in a proper structural orientation to induce efficient LILR signaling, resulting in the dominant immunosuppressive effects. Moreover, structural and functional implications for other MHCI dimers observed in activated T cells and the pathogenic allele, HLA-B27, are discussed.
Collapse
Affiliation(s)
- Mitsunori Shiroishi
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Yagi J, Adachi K, Arima N, Tanaka S, Ose T, Azumi T, Sasaki H, Sato M, Kinoshita Y. A prospective randomized comparative study on the safety and tolerability of transnasal esophagogastroduodenoscopy. Endoscopy 2005; 37:1226-31. [PMID: 16329022 DOI: 10.1055/s-2005-921037] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND STUDY AIM Transnasal esophagogastroduodenoscopy (EGD) with a small-caliber endoscope is well tolerated by patients. However, the effect of this procedure on cardiopulmonary function has not been fully investigated. The aim of this prospective, randomized study was to investigate the effect of transnasal EGD in comparison with transoral EGD on cardiopulmonary function. PATIENTS AND METHODS The study involved 450 patients referred for diagnostic EGD. Patients were randomly assigned to one of three types of unsedated EGD (150 patients per group): transnasal EGD using a small-caliber endoscope (the "XP-N" group), transoral EGD using the same small-caliber endoscope ("XP-O" group), and transoral EGD using a conventional endoscope ("XQ" group). Systolic and diastolic blood pressure, pulse rate, and arterial oxygen saturation were monitored before, and 2, 4 and 6 minutes after intubation, and just after endoscope extubation. Gagging episodes were also counted, to determine tolerance. RESULTS It was not possible to perform transnasal EGD in 12 patients (8.0%). A small amount of epistaxis was observed in eight (5.8%) of 138 patients who were examined successfully by transnasal EGD. Systolic and diastolic blood pressure, pulse rate, rate-pressure product (pulse rate x systolic blood pressure/100), and the drop in arterial oxygen saturation in the XQ group were significantly greater than in the XP-N and XP-O groups at each time point. In the XP-N group, these parameters were significantly lower than those in the XP-O group at 2 minutes after intubation. Of the tree groups the number of gagging episodes was significantly lower in the XP-N group. CONCLUSION Transnasal EGD is safer than transoral EGD as it is associated with fewer adverse effects on cardiopulmonary function and is better tolerated by patients.
Collapse
Affiliation(s)
- J Yagi
- Shimane Environment and Health Public Corporation, Matsue, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|