1
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Sánchez WN, Driessen AJM, Wilson CAM. Protein targeting to the ER membrane: multiple pathways and shared machinery. Crit Rev Biochem Mol Biol 2025:1-47. [PMID: 40377270 DOI: 10.1080/10409238.2025.2503746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2025] [Revised: 05/04/2025] [Accepted: 05/06/2025] [Indexed: 05/18/2025]
Abstract
The endoplasmic reticulum (ER) serves as a central hub for protein production and sorting in eukaryotic cells, processing approximately one-third of the cellular proteome. Protein targeting to the ER occurs through multiple pathways that operate both during and independent of translation. The classical translation-dependent pathway, mediated by cytosolic factors like signal recognition particle, recognizes signal peptides or transmembrane helices in nascent proteins, while translation-independent mechanisms utilize RNA-based targeting through specific sequence elements and RNA-binding proteins. At the core of these processes lies the Sec61 complex, which undergoes dynamic conformational changes and coordinates with numerous accessory factors to facilitate protein translocation and membrane insertion across and into the endoplasmic reticulum membrane. This review focuses on the molecular mechanisms of protein targeting to the ER, from the initial recognition of targeting signals to the dynamics of the translocation machinery, highlighting recent discoveries that have revealed unprecedented complexity in these cellular trafficking pathways.
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Affiliation(s)
- Wendy N Sánchez
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
- Biochemistry and Molecular Biology Department, Faculty of Chemistry and Pharmaceutical Sciences, Universidad de Chile, Santiago, Chile
- Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Christian A M Wilson
- Biochemistry and Molecular Biology Department, Faculty of Chemistry and Pharmaceutical Sciences, Universidad de Chile, Santiago, Chile
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2
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Hegde RS, Keenan RJ. A unifying model for membrane protein biogenesis. Nat Struct Mol Biol 2024; 31:1009-1017. [PMID: 38811793 PMCID: PMC7616256 DOI: 10.1038/s41594-024-01296-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/25/2024] [Indexed: 05/31/2024]
Abstract
α-Helical integral membrane proteins comprise approximately 25% of the proteome in all organisms. The membrane proteome is highly diverse, varying in the number, topology, spacing and properties of transmembrane domains. This diversity imposes different constraints on the insertion of different regions of a membrane protein into the lipid bilayer. Here, we present a cohesive framework to explain membrane protein biogenesis, in which different parts of a nascent substrate are triaged between Oxa1 and SecY family members for insertion. In this model, Oxa1 family proteins insert transmembrane domains flanked by short translocated segments, whereas the SecY channel is required for insertion of transmembrane domains flanked by long translocated segments. Our unifying model rationalizes evolutionary, genetic, biochemical and structural data across organisms and provides a foundation for future mechanistic studies of membrane protein biogenesis.
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Affiliation(s)
- Ramanujan S Hegde
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
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3
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Mattos D, Neves WD, Kitamura T, Pradhan R, Wan X, da Hora CC, Tranter D, Kazemi S, Yu X, Tripathy N, Paavilainen VO, McPhail KL, Oishi S, Badr CE, Ishmael JE. Diastereomers of Coibamide A Show Altered Sec61 Client Selectivity and Ligand-Dependent Activity against Patient-Derived Glioma Stem-like Cells. ACS Pharmacol Transl Sci 2024; 7:1823-1838. [PMID: 38898945 PMCID: PMC11184607 DOI: 10.1021/acsptsci.4c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 06/21/2024]
Abstract
Coibamide A (CbA) is a cyanobacterial lariat depsipeptide that selectively inhibits multiple secreted and integral membrane proteins from entering the endoplasmic reticulum secretory pathway through binding the alpha subunit of the Sec61 translocon. As a complex peptide-based macrocycle with 13 stereogenic centers, CbA is presumed to adopt a conformationally restricted orientation in the ligand-bound state, resulting in potent antitumor and antiangiogenic bioactivity. A stereochemical structure-activity relationship for CbA was previously defined based on cytotoxicity against established cancer cell lines. However, the ability of synthetic isomers to inhibit the biosynthesis of specific Sec61 substrates was unknown. Here, we report that two less toxic diastereomers of CbA, [L-Hiv2]-CbA and [L-Hiv2, L-MeAla11]-CbA, are pharmacologically active Sec61 inhibitors. Both compounds inhibited the expression of a secreted reporter (Gaussia luciferase), VEGF-A, and a Type 1 membrane protein (VCAM1), while [L-Hiv2]-CbA also decreased the expression of ICAM1 and BiP/GRP78. Analysis of 43 different chemokines in the secretome of SF-268 glioblastoma cells revealed different inhibitory profiles for the two diastereomers. When the cytotoxic potential of CbA compounds was compared against a panel of patient-derived glioblastoma stem-like cells (GSCs), Sec61 inhibitors were remarkably toxic to five of the six GSCs tested. Each ligand showed a distinct cytotoxic potency and selectivity pattern for CbA-sensitive GSCs, with IC50 values ranging from subnanomolar to low micromolar concentrations. Together, these findings highlight the extreme sensitivity of GSCs to Sec61 modulation and the importance of ligand stereochemistry in determining the spectrum of inhibited Sec61 client proteins.
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Affiliation(s)
- Daphne
R. Mattos
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Willian das Neves
- Department
of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Takashi Kitamura
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Richa Pradhan
- Department
of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Xuemei Wan
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Cintia Carla da Hora
- Department
of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Dale Tranter
- Institute
of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Soheila Kazemi
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Xinhui Yu
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Nirmalya Tripathy
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | | | - Kerry L. McPhail
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Shinya Oishi
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
- Laboratory
of Medicinal Chemistry, Kyoto Pharmaceutical
University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Christian E. Badr
- Department
of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Jane E. Ishmael
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
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4
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Owens SL, Ahmed SR, Lang RM, Stewart LE, Mori S. Natural Products That Contain Higher Homologated Amino Acids. Chembiochem 2024; 25:e202300822. [PMID: 38487927 PMCID: PMC11386549 DOI: 10.1002/cbic.202300822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/13/2024] [Indexed: 04/11/2024]
Abstract
This review focuses on discussing natural products (NPs) that contain higher homologated amino acids (homoAAs) in the structure as well as the proposed and characterized biosynthesis of these non-proteinogenic amino acids. Homologation of amino acids includes the insertion of a methylene group into its side chain. It is not a very common modification found in NP biosynthesis as approximately 450 homoAA-containing NPs have been isolated from four bacterial phyla (Cyanobacteria, Actinomycetota, Myxococcota, and Pseudomonadota), two fungal phyla (Ascomycota and Basidiomycota), and one animal phylum (Porifera), except for a few examples. Amino acids that are found to be homologated and incorporated in the NP structures include the following ten amino acids: alanine, arginine, cysteine, isoleucine, glutamic acid, leucine, phenylalanine, proline, serine, and tyrosine, where isoleucine, leucine, phenylalanine, and tyrosine share the comparable enzymatic pathway. Other amino acids have their individual homologation pathway (arginine, proline, and glutamic acid for bacteria), likely utilize the primary metabolic pathway (alanine and glutamic acid for fungi), or have not been reported (cysteine and serine). Despite its possible high potential in the drug discovery field, the biosynthesis of homologated amino acids has a large room to explore for future combinatorial biosynthesis and metabolic engineering purpose.
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Affiliation(s)
- Skyler L. Owens
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Shopno R. Ahmed
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Rebecca M. Lang
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Laura E. Stewart
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Shogo Mori
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
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5
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Suzuki R, Mattos DR, Kitamura T, Tsujioka R, Kobayashi K, Inuki S, Ohno H, Ishmael JE, McPhail KL, Oishi S. Design of Synthetic Surrogates for the Macrolactone Linker Motif in Coibamide A. ACS Med Chem Lett 2023; 14:1344-1350. [PMID: 37849553 PMCID: PMC10578308 DOI: 10.1021/acsmedchemlett.3c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/13/2023] [Indexed: 10/19/2023] Open
Abstract
A marine cyanobacterial cyclic depsipeptide, coibamide A (CbA), inhibits the mammalian protein secretory pathway by blocking the Sec61 translocon, which is an emerging drug target for cancer and other chronic diseases. In our previous structure-activity relationship study of CbA, the macrolactone ester linker was replaced with alkyl/alkenyl surrogates to provide synthetically accessible macrocyclic scaffolds. To optimize the cellular bioactivity profile of CbA analogues, novel lysine mimetics having β- and ε-methyl groups have now been designed and synthesized by a stereoselective route. A significant increase in cytotoxicity was observed upon introduction of these two methyl groups, corresponding to the d-MeAla α-methyl and MeThr β-methyl of CbA. All synthetic products retained the ability to inhibit secretion of a model Sec61 substrate. Tandem evaluation of secretory function inhibition in living cells and cytotoxicity was an effective strategy to assess the impact of structural modifications to the linker for ring closure.
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Affiliation(s)
- Rikito Suzuki
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
- Laboratory
of Medicinal Chemistry, Kyoto Pharmaceutical
University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Daphne R. Mattos
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Takashi Kitamura
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Rina Tsujioka
- Laboratory
of Medicinal Chemistry, Kyoto Pharmaceutical
University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Kazuya Kobayashi
- Laboratory
of Medicinal Chemistry, Kyoto Pharmaceutical
University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Shinsuke Inuki
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroaki Ohno
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Jane E. Ishmael
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Kerry L. McPhail
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Shinya Oishi
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
- Laboratory
of Medicinal Chemistry, Kyoto Pharmaceutical
University, Yamashina-ku, Kyoto 607-8412, Japan
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6
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Rehan S, Tranter D, Sharp PP, Craven GB, Lowe E, Anderl JL, Muchamuel T, Abrishami V, Kuivanen S, Wenzell NA, Jennings A, Kalyanaraman C, Strandin T, Javanainen M, Vapalahti O, Jacobson MP, McMinn D, Kirk CJ, Huiskonen JT, Taunton J, Paavilainen VO. Signal peptide mimicry primes Sec61 for client-selective inhibition. Nat Chem Biol 2023; 19:1054-1062. [PMID: 37169961 PMCID: PMC10449633 DOI: 10.1038/s41589-023-01326-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 04/06/2023] [Indexed: 05/13/2023]
Abstract
Preventing the biogenesis of disease-relevant proteins is an attractive therapeutic strategy, but attempts to target essential protein biogenesis factors have been hampered by excessive toxicity. Here we describe KZR-8445, a cyclic depsipeptide that targets the Sec61 translocon and selectively disrupts secretory and membrane protein biogenesis in a signal peptide-dependent manner. KZR-8445 potently inhibits the secretion of pro-inflammatory cytokines in primary immune cells and is highly efficacious in a mouse model of rheumatoid arthritis. A cryogenic electron microscopy structure reveals that KZR-8445 occupies the fully opened Se61 lateral gate and blocks access to the lumenal plug domain. KZR-8445 binding stabilizes the lateral gate helices in a manner that traps select signal peptides in the Sec61 channel and prevents their movement into the lipid bilayer. Our results establish a framework for the structure-guided discovery of novel therapeutics that selectively modulate Sec61-mediated protein biogenesis.
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Affiliation(s)
- Shahid Rehan
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Dale Tranter
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Phillip P Sharp
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Gregory B Craven
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Eric Lowe
- Kezar Life Sciences, South San Francisco, CA, USA
| | | | | | - Vahid Abrishami
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Suvi Kuivanen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicole A Wenzell
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | | | - Chakrapani Kalyanaraman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of California, San Francisco, CA, USA
| | - Tomas Strandin
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matti Javanainen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of California, San Francisco, CA, USA
| | | | | | - Juha T Huiskonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
| | - Ville O Paavilainen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland.
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7
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Itskanov S, Wang L, Junne T, Sherriff R, Xiao L, Blanchard N, Shi WQ, Forsyth C, Hoepfner D, Spiess M, Park E. A common mechanism of Sec61 translocon inhibition by small molecules. Nat Chem Biol 2023; 19:1063-1071. [PMID: 37169959 PMCID: PMC11458068 DOI: 10.1038/s41589-023-01337-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 04/12/2023] [Indexed: 05/13/2023]
Abstract
The Sec61 complex forms a protein-conducting channel in the endoplasmic reticulum membrane that is required for secretion of soluble proteins and production of many membrane proteins. Several natural and synthetic small molecules specifically inhibit Sec61, generating cellular effects that are useful for therapeutic purposes, but their inhibitory mechanisms remain unclear. Here we present near-atomic-resolution structures of human Sec61 inhibited by a comprehensive panel of structurally distinct small molecules-cotransin, decatransin, apratoxin, ipomoeassin, mycolactone, cyclotriazadisulfonamide and eeyarestatin. All inhibitors bind to a common lipid-exposed pocket formed by the partially open lateral gate and plug domain of Sec61. Mutations conferring resistance to the inhibitors are clustered at this binding pocket. The structures indicate that Sec61 inhibitors stabilize the plug domain in a closed state, thereby preventing the protein-translocation pore from opening. Our study provides the atomic details of Sec61-inhibitor interactions and the structural framework for further pharmacological studies and drug design.
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Affiliation(s)
- Samuel Itskanov
- Biophysics Graduate Program, University of California, Berkeley, Berkeley, CA, USA
| | - Laurie Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Tina Junne
- Biozentrum, University of Basel, Basel, Switzerland
| | - Rumi Sherriff
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Li Xiao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Nicolas Blanchard
- Université de Haute-Alsace, Université de Strasbourg, CNRS, LIMA, UMR 7042, Mulhouse, France
| | - Wei Q Shi
- Department of Chemistry, Ball State University, Muncie, IN, USA
| | - Craig Forsyth
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Dominic Hoepfner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, Basel, Switzerland
| | | | - Eunyong Park
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
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8
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Ding W, Tian D, Chen M, Xia Z, Tang X, Zhang S, Wei J, Li X, Yao X, Wu B, Tang J. Molecular Networking-Guided Isolation of Cyclopentapeptides from the Hydrothermal Vent Sediment Derived Fungus Aspergillus pseudoviridinutans TW58-5 and Their Anti-inflammatory Effects. JOURNAL OF NATURAL PRODUCTS 2023; 86:1919-1930. [PMID: 37368370 DOI: 10.1021/acs.jnatprod.3c00287] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Repetitive isolation of known compounds remains a major challenge in natural-product-based drug discovery. LC-MS/MS-based molecular networking has become a highly efficient strategy for the discovery of new natural products from complex mixtures. Herein, we report a molecular networking-guided isolation procedure, which resulted in the discovery of seven new cyclopentapeptides, namely, pseudoviridinutans A-F (1-7), from the marine-derived fungus Aspergillus pseudoviridinutans TW58-5. Compounds 1-7 feature a rare amino acid moiety, O,β-dimethyltyrosine, observed for the first time from a marine-derived fungus. The planar structures of 1-7 were elucidated by detailed analyses of IR, UV, HR ESI-Q-TOF MS, and 1D and 2D NMR spectroscopic data. Meanwhile, their absolute configurations were determined through a combination of Marfey's method and X-ray diffraction. Subsequent bioassay revealed the anti-inflammation potential of 1-7, especially 6, which inhibited the production of nitric oxide (NO), a vital inflammatory mediator, in LPS-induced murine macrophage RAW264.7 cells by regulating the expression level of NLRP3 and iNOS.
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Affiliation(s)
- Wenjuan Ding
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
| | - Danmei Tian
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drug Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Mei Chen
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drug Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Zixuan Xia
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drug Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Xiyang Tang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drug Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Sihao Zhang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drug Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Jihua Wei
- Ocean College, Zhejiang University, Zhoushan Campus, Zhoushan 316021, China
| | - Xunuo Li
- Ocean College, Zhejiang University, Zhoushan Campus, Zhoushan 316021, China
| | - Xinsheng Yao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
| | - Bin Wu
- Ocean College, Zhejiang University, Zhoushan Campus, Zhoushan 316021, China
| | - Jinshan Tang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drug Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
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9
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Abstract
Multipass membrane proteins contain two or more α-helical transmembrane domains (TMDs) that span the lipid bilayer. They are inserted cotranslationally into the prokaryotic plasma membrane or eukaryotic endoplasmic reticulum membrane. The Sec61 complex (SecY complex in prokaryotes) provides a ribosome docking site, houses a channel across the membrane, and contains a lateral gate that opens toward the lipid bilayer. Model multipass proteins can be stitched into the membrane by iteratively using Sec61's lateral gate for TMD insertion and its central pore for translocation of flanking domains. Native multipass proteins, with their diverse TMDs and complex topologies, often also rely on members of the Oxa1 family of translocation factors, the PAT complex chaperone, and other poorly understood factors. Here, we discuss the mechanisms of TMD insertion, highlight the limitations of an iterative insertion model, and propose a new hypothesis for multipass membrane protein biogenesis based on recent findings.
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Affiliation(s)
- Luka Smalinskaitė
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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10
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Pauwels E, Shewakramani NR, De Wijngaert B, Camps A, Provinciael B, Stroobants J, Kalies KU, Hartmann E, Maes P, Vermeire K, Das K. Structural insights into TRAP association with ribosome-Sec61 complex and translocon inhibition by a CADA derivative. SCIENCE ADVANCES 2023; 9:eadf0797. [PMID: 36867692 PMCID: PMC9984176 DOI: 10.1126/sciadv.adf0797] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/31/2023] [Indexed: 05/26/2023]
Abstract
During cotranslational translocation, the signal peptide of a nascent chain binds Sec61 translocon to initiate protein transport through the endoplasmic reticulum (ER) membrane. Our cryo-electron microscopy structure of ribosome-Sec61 shows binding of an ordered heterotetrameric translocon-associated protein (TRAP) complex, in which TRAP-γ is anchored at two adjacent positions of 28S ribosomal RNA and interacts with ribosomal protein L38 and Sec61α/γ. Four transmembrane helices (TMHs) of TRAP-γ cluster with one C-terminal helix of each α, β, and δ subunits. The seven TMH bundle helps position a crescent-shaped trimeric TRAP-α/β/δ core in the ER lumen, facing the Sec61 channel. Further, our in vitro assay establishes the cyclotriazadisulfonamide derivative CK147 as a translocon inhibitor. A structure of ribosome-Sec61-CK147 reveals CK147 binding the channel and interacting with the plug helix from the lumenal side. The CK147 resistance mutations surround the inhibitor. These structures help in understanding the TRAP functions and provide a new Sec61 site for designing translocon inhibitors.
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Affiliation(s)
- Eva Pauwels
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Neesha R. Shewakramani
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Brent De Wijngaert
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Anita Camps
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Becky Provinciael
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Joren Stroobants
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Kai-Uwe Kalies
- Centre for Structural and Cell Biology in Medicine, Institute of Biology, University of Lübeck, Lübeck 23562, Germany
| | - Enno Hartmann
- Centre for Structural and Cell Biology in Medicine, Institute of Biology, University of Lübeck, Lübeck 23562, Germany
| | - Piet Maes
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Kurt Vermeire
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Kalyan Das
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
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11
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Itskanov S, Park E. Mechanism of Protein Translocation by the Sec61 Translocon Complex. Cold Spring Harb Perspect Biol 2023; 15:a041250. [PMID: 35940906 PMCID: PMC9808579 DOI: 10.1101/cshperspect.a041250] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The endoplasmic reticulum (ER) is a major site for protein synthesis, folding, and maturation in eukaryotic cells, responsible for production of secretory proteins and most integral membrane proteins. The universally conserved protein-conducting channel Sec61 complex mediates core steps in these processes by translocating hydrophilic polypeptide segments of client proteins across the ER membrane and integrating hydrophobic transmembrane segments into the membrane. The Sec61 complex associates with several other molecular machines and enzymes to enable substrate engagement with the channel and coordination of protein translocation with translation, protein folding, and/or post-translational modifications. Recent cryo-electron microscopy and functional studies of these translocon complexes have greatly advanced our mechanistic understanding of Sec61-dependent protein biogenesis at the ER. Here, we will review the current models for how the Sec61 channel performs its functions in coordination with partner complexes.
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Affiliation(s)
- Samuel Itskanov
- Biophysics Graduate Program
- California Institute for Quantitative Biosciences
| | - Eunyong Park
- California Institute for Quantitative Biosciences
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
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12
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Ohsawa K, Fukaya S, Doi T. Total Synthesis and Structural Determination of Cyclodepsipeptide Decatransin. Org Lett 2022; 24:5552-5556. [PMID: 35867629 DOI: 10.1021/acs.orglett.2c02085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure determination of the 30-membered cyclodepsipeptide decatransin was demonstrated on the basis of total synthesis. Both (R)- and (S)-2-hydroxy-5-methylhexanoic acid derivatives were prepared via the Evans asymmetric alkylation. N-Alkyl-enriched peptide fragments were synthesized by the Cbz strategy in the solution phase without formation of diketopiperazine and epimerization. The synthesis of putative candidates was achieved by convergent peptide coupling of three peptide fragments, followed by macrocyclization under the Mitsunobu conditions.
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Affiliation(s)
- Kosuke Ohsawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Sakiko Fukaya
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Takayuki Doi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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13
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Synthesis, Biological Evaluation and Docking Studies of Ring-Opened Analogues of Ipomoeassin F. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27144419. [PMID: 35889292 PMCID: PMC9320607 DOI: 10.3390/molecules27144419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/04/2022] [Accepted: 07/07/2022] [Indexed: 11/17/2022]
Abstract
The plant-derived macrocyclic resin glycoside ipomoeassin F (Ipom-F) binds to Sec61α and significantly disrupts multiple aspects of Sec61-mediated protein biogenesis at the endoplasmic reticulum, ultimately leading to cell death. However, extensive assessment of Ipom-F as a molecular tool and a therapeutic lead is hampered by its limited production scale, largely caused by intramolecular assembly of the macrocyclic ring. Here, using in vitro and/or in cellula biological assays to explore the first series of ring-opened analogues for the ipomoeassins, and indeed all resin glycosides, we provide clear evidence that macrocyclic integrity is not required for the cytotoxic inhibition of Sec61-dependent protein translocation by Ipom-F. Furthermore, our modeling suggests that open-chain analogues of Ipom-F can interact with multiple sites on the Sec61α subunit, most likely located at a previously identified binding site for mycolactone and/or the so-called lateral gate. Subsequent in silico-aided design led to the discovery of the stereochemically simplified analogue 3 as a potent, alternative lead compound that could be synthesized much more efficiently than Ipom-F and will accelerate future ipomoeassin research in chemical biology and drug discovery. Our work may also inspire further exploration of ring-opened analogues of other resin glycosides.
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14
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Saha N, Tomar RS. Copper inhibits protein maturation in the secretory pathway by targeting the Sec61 translocon in Saccharomyces cerevisiae. J Biol Chem 2022; 298:102170. [PMID: 35738397 PMCID: PMC9304788 DOI: 10.1016/j.jbc.2022.102170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/03/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022] Open
Abstract
In Saccharomyces cerevisiae, proteins destined for secretion utilize the post-translational translocon machinery to gain entry into the endoplasmic reticulum. These proteins then mature by undergoing a number of post-translational modifications in different compartments of the secretory pathway. While these modifications have been well established for many proteins, to date only a few studies have been conducted regarding the conditions and factors affecting maturation of these proteins before entering into the endoplasmic reticulum. Here, using immunoblotting, microscopy, and spot test assays, we show that excess copper inhibits the Sec61 translocon function and causes accumulation of two well-known post-translationally translocated proteins, Gas1 (glycophospholipid-anchored surface protein) and CPY (carboxypeptidase Y), in the cytosol. We further show that the copper-sensitive phenotype of sec61-deficient yeast cells is ameliorated by restoring the levels of SEC61 through plasmid transformation. Furthermore, screening of translocation-defective Sec61 mutants revealed that sec61-22, bearing L80M, V134I, M248V, and L342S mutations, is resistant to copper, suggesting that copper might be inflicting toxicity through one of these residues. In conclusion, these findings imply that copper-mediated accumulation of post-translationally translocated proteins is due to the inhibition of Sec61.
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Affiliation(s)
- Nitu Saha
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, 462066, Madhya Pradesh, India
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, 462066, Madhya Pradesh, India.
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15
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Kitamura T, Suzuki R, Inuki S, Ohno H, McPhail KL, Oishi S. Design of Coibamide A Mimetics with Improved Cellular Bioactivity. ACS Med Chem Lett 2022; 13:105-110. [PMID: 35059129 PMCID: PMC8762706 DOI: 10.1021/acsmedchemlett.1c00591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 11/30/2022] Open
Abstract
Coibamide A, a cyclic depsipeptide isolated from a Panamanian marine cyanobacterium, shows potent cytotoxic activity via the inhibition of the Sec61 translocon. We designed a coibamide A mimetic in which the ester linkage between MeThr and d-MeAla in coibamide A was replaced with an alkyl linker to provide a stable macrocyclic scaffold possessing a MeLys(Me) residue. Taking advantage of a facile solid-phase synthetic approach, an structure-activity relationship (SAR) study of the newly designed macrocyclic structure was performed, with a focus on altering the pattern of N-methyl substitution and amino acid configurations. Overall, the simplified macrocyclic scaffold with an alkyl linker resulted in a significantly reduced cytotoxicity. Instead, more potent coibamide A derivatives with a β-(4-biphenylyl)alanine (Bph) group were identified after the optimization of the Tyr(Me) position in the original macrocyclic scaffold of coibamide A based on the characteristic apratoxin A substructures. The similar SAR between coibamide A and apratoxin A suggests that the binding site of the Tyr(Me) side chain at the luminal end of Sec61α may be shared.
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Affiliation(s)
- Takashi Kitamura
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Rikito Suzuki
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
- Department
of Medicinal Chemistry, Kyoto Pharmaceutical
University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Shinsuke Inuki
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroaki Ohno
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kerry L. McPhail
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Shinya Oishi
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
- Department
of Medicinal Chemistry, Kyoto Pharmaceutical
University, Yamashina-ku, Kyoto 607-8412, Japan
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16
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Inhibitors of the Sec61 Complex and Novel High Throughput Screening Strategies to Target the Protein Translocation Pathway. Int J Mol Sci 2021; 22:ijms222112007. [PMID: 34769437 PMCID: PMC8585047 DOI: 10.3390/ijms222112007] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/29/2021] [Indexed: 02/08/2023] Open
Abstract
Proteins targeted to the secretory pathway start their intracellular journey by being transported across biological membranes such as the endoplasmic reticulum (ER). A central component in this protein translocation process across the ER is the Sec61 translocon complex, which is only intracellularly expressed and does not have any enzymatic activity. In addition, Sec61 translocon complexes are difficult to purify and to reconstitute. Screening for small molecule inhibitors impairing its function has thus been notoriously difficult. However, such translocation inhibitors may not only be valuable tools for cell biology, but may also represent novel anticancer drugs, given that cancer cells heavily depend on efficient protein translocation into the ER to support their fast growth. In this review, different inhibitors of protein translocation will be discussed, and their specific mode of action will be compared. In addition, recently published screening strategies for small molecule inhibitors targeting the whole SRP-Sec61 targeting/translocation pathway will be summarized. Of note, slightly modified assays may be used in the future to screen for substances affecting SecYEG, the bacterial ortholog of the Sec61 complex, in order to identify novel antibiotic drugs.
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17
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Potteth US, Upadhyay T, Saini S, Saraogi I. Novel Antibacterial Targets in Protein Biogenesis Pathways. Chembiochem 2021; 23:e202100459. [PMID: 34643994 DOI: 10.1002/cbic.202100459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/12/2021] [Indexed: 11/11/2022]
Abstract
Antibiotic resistance has emerged as a global threat due to the ability of bacteria to quickly evolve in response to the selection pressure induced by anti-infective drugs. Thus, there is an urgent need to develop new antibiotics against resistant bacteria. In this review, we discuss pathways involving bacterial protein biogenesis as attractive antibacterial targets since many of them are essential for bacterial survival and virulence. We discuss the structural understanding of various components associated with bacterial protein biogenesis, which in turn can be utilized for rational antibiotic design. We highlight efforts made towards developing inhibitors of these pathways with insights into future possibilities and challenges. We also briefly discuss other potential targets related to protein biogenesis.
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Affiliation(s)
- Upasana S Potteth
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Tulsi Upadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Snehlata Saini
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Ishu Saraogi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India.,Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal - 462066, Madhya Pradesh, India
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18
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Oswald J, Njenga R, Natriashvili A, Sarmah P, Koch HG. The Dynamic SecYEG Translocon. Front Mol Biosci 2021; 8:664241. [PMID: 33937339 PMCID: PMC8082313 DOI: 10.3389/fmolb.2021.664241] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
The spatial and temporal coordination of protein transport is an essential cornerstone of the bacterial adaptation to different environmental conditions. By adjusting the protein composition of extra-cytosolic compartments, like the inner and outer membranes or the periplasmic space, protein transport mechanisms help shaping protein homeostasis in response to various metabolic cues. The universally conserved SecYEG translocon acts at the center of bacterial protein transport and mediates the translocation of newly synthesized proteins into and across the cytoplasmic membrane. The ability of the SecYEG translocon to transport an enormous variety of different substrates is in part determined by its ability to interact with multiple targeting factors, chaperones and accessory proteins. These interactions are crucial for the assisted passage of newly synthesized proteins from the cytosol into the different bacterial compartments. In this review, we summarize the current knowledge about SecYEG-mediated protein transport, primarily in the model organism Escherichia coli, and describe the dynamic interaction of the SecYEG translocon with its multiple partner proteins. We furthermore highlight how protein transport is regulated and explore recent developments in using the SecYEG translocon as an antimicrobial target.
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Affiliation(s)
- Julia Oswald
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Robert Njenga
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Ana Natriashvili
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Pinku Sarmah
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany
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19
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Zong G, Hu Z, Duah KB, Andrews LE, Zhou J, O'Keefe S, Whisenhunt L, Shim JS, Du Y, High S, Shi WQ. Ring Expansion Leads to a More Potent Analogue of Ipomoeassin F. J Org Chem 2020; 85:16226-16235. [PMID: 33264019 PMCID: PMC7808706 DOI: 10.1021/acs.joc.0c01659] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Two
new ring-size-varying analogues (2 and 3) of ipomoeassin F were synthesized and evaluated. Improved cytotoxicity
(IC50: from 1.8 nM) and in vitro protein translocation
inhibition (IC50: 35 nM) derived from ring expansion imply
that the binding pocket of Sec61α (isoform 1) can accommodate
further structural modifications, likely in the fatty acid portion.
Streamlined preparation of the key diol intermediate 5 enabled gram-scale production, allowing us to establish that ipomoeassin
F is biologically active in vivo (MTD: ∼3 mg/kg).
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Affiliation(s)
- Guanghui Zong
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Zhijian Hu
- Angion Biomedica Corp., 51 Charles Lindbergh Boulevard, Uniondale, New York 11553, United States
| | - Kwabena Baffour Duah
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Lauren E Andrews
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Jianhong Zhou
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Sarah O'Keefe
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Lucas Whisenhunt
- Thermo Fisher Scientific, 6173 E. Old Marion Highway, Florence, South Carolina 29501, United States
| | - Joong Sup Shim
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, 999078 Taipa, Macau SAR China
| | - Yuchun Du
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Stephen High
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Wei Q Shi
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
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20
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Targeting of HER/ErbB family proteins using broad spectrum Sec61 inhibitors coibamide A and apratoxin A. Biochem Pharmacol 2020; 183:114317. [PMID: 33152346 DOI: 10.1016/j.bcp.2020.114317] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 01/17/2023]
Abstract
Coibamide A is a potent cancer cell toxin and one of a select group of natural products that inhibit protein entry into the secretory pathway via a direct inhibition of the Sec61 protein translocon. Many Sec61 client proteins are clinically relevant drug targets once trafficked to their final destination in or outside the cell, however the use of Sec61 inhibitors to block early biosynthesis of specific proteins is at a pre-clinical stage. In the present study we evaluated the action of coibamide A against human epidermal growth factor receptor (HER, ErbB) proteins in representative breast and lung cancer cell types. HERs were selected for this study as they represent a family of Sec61 clients that is frequently dysregulated in human cancers, including coibamide-sensitive cell types. Although coibamide A inhibits biogenesis of a broad range of Sec61 substrate proteins in a presumed substrate-nonselective manner, endogenous HER3 (ErbB-3) and EGFR (ErbB-1) proteins were more sensitive to coibamide A, and the related Sec61 inhibitor apratoxin A, than HER2 (ErbB-2). Despite this rank order of sensitivity (HER3 > EGFR > HER2), Sec61-dependent inhibition by coibamide A was sufficient to decrease cell surface expression of HER2. We report that coibamide A- or apratoxin A-mediated block of HER3 entry into the secretory pathway is unlikely to be mediated by the HER3 signal peptide alone. HER3 (G11L/S15L), that is fully resistant to the highly substrate-selective cotransin analogue CT8, was more resistant than wild-type HER3 but only at low coibamide A (3 nM) concentrations; HER3 (G11L/S15L) expression was inhibited by higher concentrations of either natural product. Time- and concentration-dependent decreases in HER protein expression induced a commensurate reduction in AKT/MAPK signaling in breast and lung cancer cell types and loss in cell viability. Coibamide A potentiated the cytotoxic efficacy of small molecule kinase inhibitors lapatinib and erlotinib in breast and lung cancer cell types, respectively. These data indicate that natural product modulators of Sec61 function have value as chemical probes to interrogate HER/ErbB signaling in treatment-resistant human cancers.
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21
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Tranter D, Paatero AO, Kawaguchi S, Kazemi S, Serrill JD, Kellosalo J, Vogel WK, Richter U, Mattos DR, Wan X, Thornburg CC, Oishi S, McPhail KL, Ishmael JE, Paavilainen VO. Coibamide A Targets Sec61 to Prevent Biogenesis of Secretory and Membrane Proteins. ACS Chem Biol 2020; 15:2125-2136. [PMID: 32608972 PMCID: PMC7497630 DOI: 10.1021/acschembio.0c00325] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/01/2020] [Indexed: 01/19/2023]
Abstract
Coibamide A (CbA) is a marine natural product with potent antiproliferative activity against human cancer cells and a unique selectivity profile. Despite promising antitumor activity, the mechanism of cytotoxicity and specific cellular target of CbA remain unknown. Here, we develop an optimized synthetic CbA photoaffinity probe (photo-CbA) and use it to demonstrate that CbA directly targets the Sec61α subunit of the Sec61 protein translocon. CbA binding to Sec61 results in broad substrate-nonselective inhibition of ER protein import and potent cytotoxicity against specific cancer cell lines. CbA targets a lumenal cavity of Sec61 that is partially shared with known Sec61 inhibitors, yet profiling against resistance conferring Sec61α mutations identified from human HCT116 cells suggests a distinct binding mode for CbA. Specifically, despite conferring strong resistance to all previously known Sec61 inhibitors, the Sec61α mutant R66I remains sensitive to CbA. A further unbiased screen for Sec61α resistance mutations identified the CbA-resistant mutation S71P, which confirms nonidentical binding sites for CbA and apratoxin A and supports the susceptibility of the Sec61 plug region for channel inhibition. Remarkably, CbA, apratoxin A, and ipomoeassin F do not display comparable patterns of potency and selectivity in the NCI60 panel of human cancer cell lines. Our work connecting CbA activity with selective prevention of secretory and membrane protein biogenesis by inhibition of Sec61 opens up possibilities for developing new Sec61 inhibitors with improved drug-like properties that are based on the coibamide pharmacophore.
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Affiliation(s)
- Dale Tranter
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland
| | - Anja O. Paatero
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland
| | - Shinsaku Kawaguchi
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Soheila Kazemi
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Jeffrey D. Serrill
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Juho Kellosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland
| | - Walter K. Vogel
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Uwe Richter
- Molecular
and Integrative Biosciences Research Programme, Faculty of Biological
and Environmental Sciences, University of
Helsinki, Helsinki, 00014, Finland
| | - Daphne R. Mattos
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Xuemei Wan
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Christopher C. Thornburg
- Frederick
National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702, United States
| | - Shinya Oishi
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kerry L. McPhail
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Jane E. Ishmael
- Department
of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
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22
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Structure of the Inhibited State of the Sec Translocon. Mol Cell 2020; 79:406-415.e7. [PMID: 32692975 PMCID: PMC7427319 DOI: 10.1016/j.molcel.2020.06.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 04/30/2020] [Accepted: 06/05/2020] [Indexed: 02/06/2023]
Abstract
Protein secretion in eukaryotes and prokaryotes involves a universally conserved protein translocation channel formed by the Sec61 complex. Unrelated small-molecule natural products and synthetic compounds inhibit Sec61 with differential effects for different substrates or for Sec61 from different organisms, making this a promising target for therapeutic intervention. To understand the mode of inhibition and provide insight into the molecular mechanism of this dynamic translocon, we determined the structure of mammalian Sec61 inhibited by the Mycobacterium ulcerans exotoxin mycolactone via electron cryo-microscopy. Unexpectedly, the conformation of inhibited Sec61 is optimal for substrate engagement, with mycolactone wedging open the cytosolic side of the lateral gate. The inability of mycolactone-inhibited Sec61 to effectively transport substrate proteins implies that signal peptides and transmembrane domains pass through the site occupied by mycolactone. This provides a foundation for understanding the molecular mechanism of Sec61 inhibitors and reveals novel features of translocon function and dynamics. The inhibited Sec translocon adopts a conformation optimal for substrate engagement The inhibitor mycolactone wedges open the lateral gate of Sec61α Mycolactone blocks the path taken by the signal peptide during engagement Resistance mutations are likely to operate by modulating translocon dynamics
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23
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Fu Y, Estoppey D, Roggo S, Pistorius D, Fuchs F, Studer C, Ibrahim AS, Aust T, Grandjean F, Mihalic M, Memmert K, Prindle V, Richard E, Riedl R, Schuierer S, Weber E, Hunziker J, Petersen F, Tao J, Hoepfner D. Jawsamycin exhibits in vivo antifungal properties by inhibiting Spt14/Gpi3-mediated biosynthesis of glycosylphosphatidylinositol. Nat Commun 2020; 11:3387. [PMID: 32636417 PMCID: PMC7341893 DOI: 10.1038/s41467-020-17221-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/11/2020] [Indexed: 12/21/2022] Open
Abstract
Biosynthesis of glycosylphosphatidylinositol (GPI) is required for anchoring proteins to the plasma membrane, and is essential for the integrity of the fungal cell wall. Here, we use a reporter gene-based screen in Saccharomyces cerevisiae for the discovery of antifungal inhibitors of GPI-anchoring of proteins, and identify the oligocyclopropyl-containing natural product jawsamycin (FR-900848) as a potent hit. The compound targets the catalytic subunit Spt14 (also referred to as Gpi3) of the fungal UDP-glycosyltransferase, the first step in GPI biosynthesis, with good selectivity over the human functional homolog PIG-A. Jawsamycin displays antifungal activity in vitro against several pathogenic fungi including Mucorales, and in vivo in a mouse model of invasive pulmonary mucormycosis due to Rhyzopus delemar infection. Our results provide a starting point for the development of Spt14 inhibitors for treatment of invasive fungal infections.
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Affiliation(s)
- Yue Fu
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA
| | - David Estoppey
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056, Basel, Switzerland
| | - Silvio Roggo
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056, Basel, Switzerland
| | - Dominik Pistorius
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056, Basel, Switzerland
| | - Florian Fuchs
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056, Basel, Switzerland
| | - Christian Studer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056, Basel, Switzerland
| | - Ashraf S Ibrahim
- The Lundquist Institute for Biomedical Innovations at Harbor-University of California at Los Angeles (UCLA) Medical Center, Torrance, CA, 90502, USA
- David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Thomas Aust
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056, Basel, Switzerland
| | - Frederic Grandjean
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056, Basel, Switzerland
| | - Manuel Mihalic
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056, Basel, Switzerland
| | - Klaus Memmert
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056, Basel, Switzerland
| | - Vivian Prindle
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA
| | - Etienne Richard
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056, Basel, Switzerland
| | - Ralph Riedl
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056, Basel, Switzerland
| | - Sven Schuierer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056, Basel, Switzerland
| | - Eric Weber
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056, Basel, Switzerland
| | - Jürg Hunziker
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056, Basel, Switzerland
| | - Frank Petersen
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056, Basel, Switzerland
| | - Jianshi Tao
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA.
| | - Dominic Hoepfner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056, Basel, Switzerland.
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24
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Crossing the Vacuolar Rubicon: Structural Insights into Effector Protein Trafficking in Apicomplexan Parasites. Microorganisms 2020; 8:microorganisms8060865. [PMID: 32521667 PMCID: PMC7355975 DOI: 10.3390/microorganisms8060865] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/01/2020] [Accepted: 06/05/2020] [Indexed: 12/13/2022] Open
Abstract
Apicomplexans form a large phylum of parasitic protozoa, including the genera Plasmodium, Toxoplasma, and Cryptosporidium, the causative agents of malaria, toxoplasmosis, and cryptosporidiosis, respectively. They cause diseases not only in humans but also in animals, with dramatic consequences in agriculture. Most apicomplexans are vacuole-dwelling and obligate intracellular parasites; as they invade the host cell, they become encased in a parasitophorous vacuole (PV) derived from the host cellular membrane. This creates a parasite-host interface that acts as a protective barrier but also constitutes an obstacle through which the pathogen must import nutrients, eliminate wastes, and eventually break free upon egress. Completion of the parasitic life cycle requires intense remodeling of the infected host cell. Host cell subversion is mediated by a subset of essential effector parasitic proteins and virulence factors actively trafficked across the PV membrane. In the malaria parasite Plasmodium, a unique and highly specialized ATP-driven vacuolar secretion system, the Plasmodium translocon of exported proteins (PTEX), transports effector proteins across the vacuolar membrane. Its core is composed of the three essential proteins EXP2, PTEX150, and HSP101, and is supplemented by the two auxiliary proteins TRX2 and PTEX88. Many but not all secreted malarial effector proteins contain a vacuolar trafficking signal or Plasmodium export element (PEXEL) that requires processing by an endoplasmic reticulum protease, plasmepsin V, for proper export. Because vacuolar parasitic protein export is essential to parasite survival and virulence, this pathway is a promising target for the development of novel antimalarial therapeutics. This review summarizes the current state of structural and mechanistic knowledge on the Plasmodium parasitic vacuolar secretion and effector trafficking pathway, describing its most salient features and discussing the existing differences and commonalities with the vacuolar effector translocation MYR machinery recently described in Toxoplasma and other apicomplexans of significance to medical and veterinary sciences.
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25
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Lumangtad LA, Bell TW. The signal peptide as a new target for drug design. Bioorg Med Chem Lett 2020; 30:127115. [PMID: 32209293 PMCID: PMC7138182 DOI: 10.1016/j.bmcl.2020.127115] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/06/2020] [Accepted: 03/15/2020] [Indexed: 01/16/2023]
Abstract
Many current and potential drug targets are membrane-bound or secreted proteins that are expressed and transported via the Sec61 secretory pathway. They are targeted to translocon channels across the membrane of the endoplasmic reticulum (ER) by signal peptides (SPs), which are temporary structures on the N-termini of their nascent chains. During translation, such proteins enter the lumen and membrane of the ER by a process known as co-translational translocation. Small molecules have been found that interfere with this process, decreasing protein expression by recognizing the unique structures of the SPs of particular proteins. The SP may thus become a validated target for designing drugs for numerous disorders, including certain hereditary diseases.
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Affiliation(s)
| | - Thomas W Bell
- Department of Chemistry, University of Nevada, Reno, NV 89557-0216, USA.
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26
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Tranter D, Filipuzzi I, Lochmann T, Knapp B, Kellosalo J, Estoppey D, Pistorius D, Meissner A, Paavilainen VO, Hoepfner D. Kendomycin Cytotoxicity against Bacterial, Fungal, and Mammalian Cells Is Due to Cation Chelation. JOURNAL OF NATURAL PRODUCTS 2020; 83:965-971. [PMID: 32182062 PMCID: PMC7497661 DOI: 10.1021/acs.jnatprod.9b00826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Indexed: 06/10/2023]
Abstract
Kendomycin is a small-molecule natural product that has gained significant attention due to reported cytotoxicity against pathogenic bacteria and fungi as well as a number of cancer cell lines. Despite significant biomedical interest and attempts to reveal its mechanism of action, the cellular target of kendomycin remains disputed. Herein it is shown that kendomycin induces cellular responses indicative of cation stress comparable to the effects of established iron chelators. Furthermore, addition of excess iron and copper attenuated kendomycin cytotoxicity in bacteria, yeast, and mammalian cells. Finally, NMR analysis demonstrated a direct interaction with cations, corroborating a close link between the observed kendomycin polypharmacology across different species and modulation of iron and/or copper levels.
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Affiliation(s)
- Dale Tranter
- Institute
of Biotechnology, University of Helsinki, Helsinki, 00014, Finland
| | - Ireos Filipuzzi
- Novartis
Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Thomas Lochmann
- Novartis
Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Britta Knapp
- Novartis
Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Juho Kellosalo
- Institute
of Biotechnology, University of Helsinki, Helsinki, 00014, Finland
| | - David Estoppey
- Novartis
Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Dominik Pistorius
- Novartis
Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Axel Meissner
- Novartis
Institutes for BioMedical Research, 4056 Basel, Switzerland
| | | | - Dominic Hoepfner
- Novartis
Institutes for BioMedical Research, 4056 Basel, Switzerland
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27
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Luesch H, Paavilainen VO. Natural products as modulators of eukaryotic protein secretion. Nat Prod Rep 2020; 37:717-736. [PMID: 32067014 DOI: 10.1039/c9np00066f] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Covering: up to the end of 2019Diverse natural product small molecules have allowed critical insights into processes that govern eukaryotic cells' ability to secrete cytosolically synthesized secretory proteins into their surroundings or to insert newly synthesized integral membrane proteins into the lipid bilayer of the endoplasmic reticulum. In addition, many components of the endoplasmic reticulum, required for protein homeostasis or other processes such as lipid metabolism or maintenance of calcium homeostasis, are being investigated for their potential in modulating human disease conditions such as cancer, neurodegenerative conditions and diabetes. In this review, we cover recent findings up to the end of 2019 on natural products that influence protein secretion or impact ER protein homeostasis, and serve as powerful chemical tools to understand protein flux through the mammalian secretory pathway and as leads for the discovery of new therapeutics.
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Affiliation(s)
- Hendrik Luesch
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, P.O. Box 100485, Gainesville, Florida 32610, USA.
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28
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Van Puyenbroeck V, Pauwels E, Provinciael B, Bell TW, Schols D, Kalies KU, Hartmann E, Vermeire K. Preprotein signature for full susceptibility to the co-translational translocation inhibitor cyclotriazadisulfonamide. Traffic 2019; 21:250-264. [PMID: 31675144 DOI: 10.1111/tra.12713] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/24/2019] [Accepted: 10/26/2019] [Indexed: 01/13/2023]
Abstract
Cyclotriazadisulfonamide (CADA) inhibits the co-translational translocation of human CD4 (huCD4) into the endoplasmic reticulum lumen in a signal peptide (SP)-dependent way. We propose that CADA binds the nascent huCD4 SP in a folded conformation within the translocon resembling a normally transitory state during translocation. Here, we used alanine scanning on the huCD4 SP to identify the signature for full susceptibility to CADA. In accordance with our previous work, we demonstrate that residues in the vicinity of the hydrophobic h-region are critical for sensitivity to CADA. In particular, exchanging Gln-15, Val-17 or Pro-20 in the huCD4 SP for Ala resulted in a resistant phenotype. Together with positively charged residues at the N-terminal portion of the mature protein, these residues mediate full susceptibility to the co-translational translocation inhibitory activity of CADA towards huCD4. In addition, sensitivity to CADA is inversely related to hydrophobicity in the huCD4 SP. In vitro translocation experiments confirmed that the general hydrophobicity of the h-domain and positive charges in the mature protein are key elements that affect both the translocation efficiency of huCD4 and the sensitivity towards CADA. Besides these two general SP parameters that determine the functionality of the signal sequence, unique amino acid pairs (L14/Q15 and L19/P20) in the SP hydrophobic core add specificity to the sensitivity signature for a co-translational translocation inhibitor.
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Affiliation(s)
- Victor Van Puyenbroeck
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Eva Pauwels
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Becky Provinciael
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Thomas W Bell
- Department of Chemistry, University of Nevada, Reno, Nevada
| | - Dominique Schols
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Kai-Uwe Kalies
- Centre for Structural and Cell Biology in Medicine, Institute of Biology, University of Lübeck, Lübeck, Germany
| | - Enno Hartmann
- Centre for Structural and Cell Biology in Medicine, Institute of Biology, University of Lübeck, Lübeck, Germany
| | - Kurt Vermeire
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
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29
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Steinberg R, Knüpffer L, Origi A, Asti R, Koch HG. Co-translational protein targeting in bacteria. FEMS Microbiol Lett 2019; 365:4966980. [PMID: 29790984 DOI: 10.1093/femsle/fny095] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/09/2018] [Indexed: 01/16/2023] Open
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and have to be transported into or across the cytoplasmic membrane. Bacteria use multiple protein transport systems in parallel, but the majority of proteins engage two distinct targeting systems. One is the co-translational targeting by two universally conserved GTPases, the signal recognition particle (SRP) and its receptor FtsY, which deliver inner membrane proteins to either the SecYEG translocon or the YidC insertase for membrane insertion. The other targeting system depends on the ATPase SecA, which targets secretory proteins, i.e. periplasmic and outer membrane proteins, to SecYEG for their subsequent ATP-dependent translocation. While SRP selects its substrates already very early during their synthesis, the recognition of secretory proteins by SecA is believed to occur primarily after translation termination, i.e. post-translationally. In this review we highlight recent progress on how SRP recognizes its substrates at the ribosome and how the fidelity of the targeting reaction to SecYEG is maintained. We furthermore discuss similarities and differences in the SRP-dependent targeting to either SecYEG or YidC and summarize recent results that suggest that some membrane proteins are co-translationally targeted by SecA.
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Affiliation(s)
- Ruth Steinberg
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| | - Lara Knüpffer
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| | - Andrea Origi
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany.,Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestr. 1, Freiburg D-79104, Germany
| | - Rossella Asti
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
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30
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Spiess M, Junne T, Janoschke M. Membrane Protein Integration and Topogenesis at the ER. Protein J 2019; 38:306-316. [DOI: 10.1007/s10930-019-09827-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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31
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Ojha R, Leli NM, Onorati A, Piao S, Verginadis II, Tameire F, Rebecca VW, Chude CI, Murugan S, Fennelly C, Noguera-Ortega E, Chu CT, Liu S, Xu X, Krepler C, Xiao M, Xu W, Wei Z, Frederick DT, Boland G, Mitchell TC, Karakousis GC, Schuchter LM, Flaherty KT, Zhang G, Herlyn M, Koumenis C, Amaravadi RK. ER Translocation of the MAPK Pathway Drives Therapy Resistance in BRAF-Mutant Melanoma. Cancer Discov 2018; 9:396-415. [PMID: 30563872 DOI: 10.1158/2159-8290.cd-18-0348] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 09/01/2018] [Accepted: 12/07/2018] [Indexed: 12/11/2022]
Abstract
Resistance to BRAF and MEK inhibitors (BRAFi + MEKi) in BRAF-mutant tumors occurs through heterogeneous mechanisms, including ERK reactivation and autophagy. Little is known about the mechanisms by which ERK reactivation or autophagy is induced by BRAFi + MEKi. Here, we report that in BRAF-mutant melanoma cells, BRAFi + MEKi induced SEC61-dependent endoplasmic reticulum (ER) translocation of the MAPK pathway via GRP78 and KSR2. Inhibition of ER translocation prevented ERK reactivation and autophagy. Following ER translocation, ERK exited the ER and was rephosphorylated by PERK. Reactivated ERK phosphorylated ATF4, which activated cytoprotective autophagy. Upregulation of GRP78 and phosphorylation of ATF4 were detected in tumors of patients resistant to BRAFi + MEKi. ER translocation of the MAPK pathway was demonstrated in therapy-resistant patient-derived xenografts. Expression of a dominant-negative ATF4 mutant conferred sensitivity to BRAFi + MEKi in vivo. This mechanism reconciles two major targeted therapy resistance pathways and identifies druggable targets, whose inhibition would likely enhance the response to BRAFi + MEKi. SIGNIFICANCE: ERK reactivation and autophagy are considered distinct resistance pathways to BRAF + MEK inhibition (BRAFi + MEKi) in BRAF V600E cancers. Here, we report BRAFi + MEKi-induced ER translocation of the MAPK pathway is necessary for ERK reactivation, which drives autophagy. The ER translocation mechanism is a major druggable driver of resistance to targeted therapy.This article is highlighted in the In This Issue feature, p. 305.
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Affiliation(s)
- Rani Ojha
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nektaria M Leli
- Department of Radiation Oncology, Smilow Center for Translational Research, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Angelique Onorati
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Shengfu Piao
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ioannis I Verginadis
- Department of Radiation Oncology, Smilow Center for Translational Research, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Feven Tameire
- Department of Radiation Oncology, Smilow Center for Translational Research, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Vito W Rebecca
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Cynthia I Chude
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sengottuvelan Murugan
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Colin Fennelly
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Estela Noguera-Ortega
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Charleen T Chu
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Shujing Liu
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Xiaowei Xu
- Department of Pathology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Clemens Krepler
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, Wistar Institute, Philadelphia, Pennsylvania
| | - Min Xiao
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, Wistar Institute, Philadelphia, Pennsylvania
| | - Wei Xu
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey
| | - Dennie T Frederick
- Massachusetts General Hospital, Harvard University, Boston, Massachusetts
| | - Genevieve Boland
- Massachusetts General Hospital, Harvard University, Boston, Massachusetts
| | - Tara C Mitchell
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Lynn M Schuchter
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Keith T Flaherty
- Massachusetts General Hospital, Harvard University, Boston, Massachusetts
| | - Gao Zhang
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, Wistar Institute, Philadelphia, Pennsylvania
| | - Meenhard Herlyn
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, Wistar Institute, Philadelphia, Pennsylvania
| | - Constantinos Koumenis
- Department of Radiation Oncology, Smilow Center for Translational Research, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ravi K Amaravadi
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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32
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Klein W, Rutz C, Eckhard J, Provinciael B, Specker E, Neuenschwander M, Kleinau G, Scheerer P, von Kries JP, Nazaré M, Vermeire K, Schülein R. Use of a sequential high throughput screening assay to identify novel inhibitors of the eukaryotic SRP-Sec61 targeting/translocation pathway. PLoS One 2018; 13:e0208641. [PMID: 30543669 PMCID: PMC6292634 DOI: 10.1371/journal.pone.0208641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/20/2018] [Indexed: 11/22/2022] Open
Abstract
The SRP-Sec61 targeting/translocation pathway of eukaryotic cells targets nascent protein chains to the membrane of the endoplasmic reticulum. Using this machinery, secretory proteins are translocated across this membrane whereas membrane proteins are integrated into the lipid bilayer. One of the key players of the pathway is the protein-conducting Sec61 (translocon) complex of the endoplasmic reticulum. The Sec61 complex has no enzymatic activity, is expressed only intracellularly and is difficult to purify and to reconstitute. Screening for small molecule inhibitors impairing its functions is thus notoriously difficult. Such inhibitors may not only be valuable tools for cell biology, they may also represent novel anti-tumor drugs. Here we have developed a two-step, sequential screening assay for inhibitors of the whole SRP-Sec61 targeting/translocation pathway which might include molecules affecting Sec61 complex functions. The resulting hit compounds were analyzed using a whole cell biosynthesis assay and a cell free transcription/translation/translocation assay. Using this methodology, we identified novel compounds inhibiting this pathway. Following structure-based back screening, one of these substances was analyzed in more detail and we could show that it indeed impairs translocation at the level of the Sec61 complex. A slightly modified methodology may be used in the future to screen for substances affecting SecYEG, the bacterial ortholog of the Sec61 complex in order to derive novel antibiotic drugs.
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Affiliation(s)
- Wolfgang Klein
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Claudia Rutz
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Jamina Eckhard
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Becky Provinciael
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Edgar Specker
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | | | - Gunnar Kleinau
- Charité—Universitätsmedizin Berlin, Campus Charité Mitte, Charité Centrum Grundlagenmedizin CC2, Institut für Medizinische Physik und Biophysik, Group Protein X-ray Crystallography & Signal Transduction, Berlin, Germany
| | - Patrick Scheerer
- Charité—Universitätsmedizin Berlin, Campus Charité Mitte, Charité Centrum Grundlagenmedizin CC2, Institut für Medizinische Physik und Biophysik, Group Protein X-ray Crystallography & Signal Transduction, Berlin, Germany
| | | | - Marc Nazaré
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Kurt Vermeire
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Ralf Schülein
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
- * E-mail:
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33
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Demangel C, High S. Sec61 blockade by mycolactone: A central mechanism in Buruli ulcer disease. Biol Cell 2018; 110:237-248. [PMID: 30055020 DOI: 10.1111/boc.201800030] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/19/2018] [Indexed: 12/14/2022]
Abstract
Infection with Mycobacterium ulcerans results in a necrotising skin disease known as a Buruli ulcer, the pathology of which is directly linked to the bacterial production of the toxin mycolactone. Recent studies have identified the protein translocation machinery of the endoplasmic reticulum (ER) membrane as the primary cellular target of mycolactone, and shown that the toxin binds to the core subunit of the Sec61 complex. Mycolactone binding strongly inhibits the capacity of the Sec61 translocon to transport newly synthesised membrane and secretory proteins into and across the ER membrane. Since the ER acts as the entry point for the mammalian secretory pathway, and hence regulates initial access to the entire endomembrane system, mycolactone-treated cells have a reduced ability to produce a range of proteins including secretory cytokines and plasma membrane receptors. The global effect of this molecular blockade of protein translocation at the ER is that the host is unable to mount an effective immune response to the underlying mycobacterial infection. Prolonged exposure to mycolactone is normally cytotoxic, since it triggers stress responses activating the transcription factor ATF4 and ultimately inducing apoptosis.
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Affiliation(s)
- Caroline Demangel
- Immunobiology of Infection Unit, Institut Pasteur, Paris, France.,INSERM, U1221, Paris, France
| | - Stephen High
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
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34
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Jin J, Hsieh YH, Chaudhary AS, Cui J, Houghton JE, Sui SF, Wang B, Tai PC. SecA inhibitors as potential antimicrobial agents: differential actions on SecA-only and SecA-SecYEG protein-conducting channels. FEMS Microbiol Lett 2018; 365:5037921. [PMID: 30007321 PMCID: PMC7190897 DOI: 10.1093/femsle/fny145] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/13/2018] [Indexed: 12/13/2022] Open
Abstract
Sec-dependent protein translocation is an essential process in bacteria. SecA is a key component of the translocation machinery and has multiple domains that interact with various ligands. SecA acts as an ATPase motor to drive the precursor protein/peptide through the SecYEG protein translocation channels. As SecA is unique to bacteria and there is no mammalian counterpart, it is an ideal target for the development of new antimicrobials. Several reviews detail the assays for ATPase and protein translocation, as well as the search for SecA inhibitors. Recent studies have shown that, in addition to the SecA-SecYEG translocation channels, there are SecA-only channels in the lipid bilayers, which function independently from the SecYEG machinery. This mini-review focuses on recent advances on the newly developed SecA inhibitors that allow the evaluation of their potential as antimicrobial agents, as well as a fundamental understanding of mechanisms of SecA function(s). These SecA inhibitors abrogate the effects of efflux pumps in both Gram-positive and Gram-negative bacteria. We also discuss recent findings that SecA binds to ribosomes and nascent peptides, which suggest other roles of SecA. A model for the multiple roles of SecA is presented.
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Affiliation(s)
- Jinshan Jin
- Department of Biology, Center for Biotechnology and Drug Design and Georgia State University, Atlanta, GA 30303, USA
| | - Ying-Hsin Hsieh
- Department of Biology, Center for Biotechnology and Drug Design and Georgia State University, Atlanta, GA 30303, USA
| | - Arpana S Chaudhary
- Department of Chemistry, Center for Biotechnology and Drug Design and Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA
| | - Jianmei Cui
- Department of Chemistry, Center for Biotechnology and Drug Design and Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA
| | - John E Houghton
- Department of Biology, Center for Biotechnology and Drug Design and Georgia State University, Atlanta, GA 30303, USA
| | - Sen-fang Sui
- State Key Laboratory of Membrane Biology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Binghe Wang
- Department of Chemistry, Center for Biotechnology and Drug Design and Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA
| | - Phang C Tai
- Department of Biology, Center for Biotechnology and Drug Design and Georgia State University, Atlanta, GA 30303, USA
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Knyazev DG, Kuttner R, Zimmermann M, Sobakinskaya E, Pohl P. Driving Forces of Translocation Through Bacterial Translocon SecYEG. J Membr Biol 2018; 251:329-343. [PMID: 29330604 PMCID: PMC6028853 DOI: 10.1007/s00232-017-0012-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 12/22/2017] [Indexed: 11/09/2022]
Abstract
This review focusses on the energetics of protein translocation via the Sec translocation machinery. First we complement structural data about SecYEG's conformational rearrangements by insight obtained from functional assays. These include measurements of SecYEG permeability that allow assessment of channel gating by ligand binding and membrane voltage. Second we will discuss the power stroke and Brownian ratcheting models of substrate translocation and the role that the two models assign to the putative driving forces: (i) ATP (SecA) and GTP (ribosome) hydrolysis, (ii) interaction with accessory proteins, (iii) membrane partitioning and folding, (iv) proton motive force (PMF), and (v) entropic contributions. Our analysis underlines how important energized membranes are for unravelling the translocation mechanism in future experiments.
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Affiliation(s)
- Denis G Knyazev
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria.
| | - Roland Kuttner
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria
| | - Mirjam Zimmermann
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria
| | | | - Peter Pohl
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria
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Van Puyenbroeck V, Vermeire K. Inhibitors of protein translocation across membranes of the secretory pathway: novel antimicrobial and anticancer agents. Cell Mol Life Sci 2018; 75:1541-1558. [PMID: 29305616 PMCID: PMC5897483 DOI: 10.1007/s00018-017-2743-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/15/2017] [Accepted: 12/27/2017] [Indexed: 12/22/2022]
Abstract
Proteins routed to the secretory pathway start their journey by being transported across biological membranes, such as the endoplasmic reticulum. The essential nature of this protein translocation process has led to the evolution of several factors that specifically target the translocon and block translocation. In this review, various translocation pathways are discussed together with known inhibitors of translocation. Properties of signal peptide-specific systems are highlighted for the development of new therapeutic and antimicrobial applications, as compounds can target signal peptides from either host cells or pathogens and thereby selectively prevent translocation of those specific proteins. Broad inhibition of translocation is also an interesting target for the development of new anticancer drugs because cancer cells heavily depend on efficient protein translocation into the endoplasmic reticulum to support their fast growth.
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Affiliation(s)
- Victor Van Puyenbroeck
- Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, 3000, Leuven, Belgium
| | - Kurt Vermeire
- Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, 3000, Leuven, Belgium.
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38
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Ogbechi J, Hall BS, Sbarrato T, Taunton J, Willis AE, Wek RC, Simmonds RE. Inhibition of Sec61-dependent translocation by mycolactone uncouples the integrated stress response from ER stress, driving cytotoxicity via translational activation of ATF4. Cell Death Dis 2018. [PMID: 29540678 PMCID: PMC5852046 DOI: 10.1038/s41419-018-0427-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mycolactone is the exotoxin virulence factor of Mycobacterium ulcerans that causes the neglected tropical disease Buruli ulcer. We recently showed it to be a broad spectrum inhibitor of Sec61-dependent co-translational translocation of proteins into the endoplasmic reticulum (ER). An outstanding question is the molecular pathway linking this to its known cytotoxicity. We have now used translational profiling to better understand the reprogramming that occurs in cells exposed to mycolactone. Gene ontology identified enrichment in genes involved in cellular response to stress, and apoptosis signalling among those showing enhanced translation. Validation of these results supports a mechanism by which mycolactone activates an integrated stress response meditated by phosphorylation of eIF2α via multiple kinases (PERK, GCN, PKR) without activation of the ER stress sensors IRE1 or ATF6. The response therefore uncouples the integrated stress response from ER stress, and features translational and transcriptional modes of genes expression that feature the key regulatory transcription factor ATF4. Emphasising the importance of this uncoupled response in cytotoxicity, downstream activation of this pathway is abolished in cells expressing mycolactone-resistant Sec61α variants. Using multiple genetic and biochemical approaches, we demonstrate that eIF2α phosphorylation is responsible for mycolactone-dependent translation attenuation, which initially protects cells from cell death. However, chronic activation without stress remediation enhances autophagy and apoptosis of cells by a pathway facilitated by ATF4 and CHOP. Our findings demonstrate that priming events at the ER can result in the sensing of stress within different cellular compartments.
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Affiliation(s)
- Joy Ogbechi
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Belinda S Hall
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | | | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Anne E Willis
- MRC Toxicology Unit, Lancaster Rd, Leicester, LE1 9HN, UK
| | - Ronald C Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202-5126, USA
| | - Rachel E Simmonds
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, GU2 7XH, UK.
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Son S, Hong YS, Jang M, Heo KT, Lee B, Jang JP, Kim JW, Ryoo IJ, Kim WG, Ko SK, Kim BY, Jang JH, Ahn JS. Genomics-Driven Discovery of Chlorinated Cyclic Hexapeptides Ulleungmycins A and B from a Streptomyces Species. JOURNAL OF NATURAL PRODUCTS 2017; 80:3025-3031. [PMID: 29083895 DOI: 10.1021/acs.jnatprod.7b00660] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Analysis of the genome sequence of Streptomyces sp. KCB13F003 showed the presence of a cryptic gene cluster encoding flavin-dependent halogenase and nonribosomal peptide synthetase. Pleiotropic approaches using multiple culture media followed by LC-MS-guided isolation and spectroscopic analysis enabled the identification of two new chlorinated cyclic hexapeptides, ulleungmycins A and B (1 and 2). Their structures, including absolute configurations, were determined by 1D and 2D NMR techniques, advanced Marfey's analysis, and GITC derivatization. The new peptides, featuring unusual amino acids 5-chloro-l-tryptophan and d-homoleucine, exhibited moderate antibacterial activities against Gram-positive pathogenic bacteria including methicillin-resistant and quinolone-resistant Staphylococcus aureus.
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Affiliation(s)
- Sangkeun Son
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST) , Daejeon 34141, Korea
| | - Young-Soo Hong
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST) , Daejeon 34141, Korea
| | - Mina Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST) , Daejeon 34141, Korea
| | - Kyung Taek Heo
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST) , Daejeon 34141, Korea
| | - Byeongsan Lee
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116, Korea
| | - Jun-Pil Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116, Korea
| | - Jong-Won Kim
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116, Korea
| | - In-Ja Ryoo
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116, Korea
| | - Won-Gon Kim
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST) , Daejeon 34141, Korea
- Superbacteria Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Daejeon 34141, Korea
| | - Sung-Kyun Ko
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST) , Daejeon 34141, Korea
| | - Bo Yeon Kim
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST) , Daejeon 34141, Korea
| | - Jae-Hyuk Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST) , Daejeon 34141, Korea
| | - Jong Seog Ahn
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST) , Daejeon 34141, Korea
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Paatero AO, Kellosalo J, Dunyak BM, Almaliti J, Gestwicki JE, Gerwick WH, Taunton J, Paavilainen VO. Apratoxin Kills Cells by Direct Blockade of the Sec61 Protein Translocation Channel. Cell Chem Biol 2017; 23:561-566. [PMID: 27203376 DOI: 10.1016/j.chembiol.2016.04.008] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 04/04/2016] [Accepted: 04/07/2016] [Indexed: 12/17/2022]
Abstract
Apratoxin A is a cytotoxic natural product that prevents the biogenesis of secretory and membrane proteins. Biochemically, apratoxin A inhibits cotranslational translocation into the ER, but its cellular target and mechanism of action have remained controversial. Here, we demonstrate that apratoxin A prevents protein translocation by directly targeting Sec61α, the central subunit of the protein translocation channel. Mutagenesis and competitive photo-crosslinking studies indicate that apratoxin A binds to the Sec61 lateral gate in a manner that differs from cotransin, a substrate-selective Sec61 inhibitor. In contrast to cotransin, apratoxin A does not exhibit a substrate-selective inhibitory mechanism, but blocks ER translocation of all tested Sec61 clients with similar potency. Our results suggest that multiple structurally unrelated natural products have evolved to target overlapping but non-identical binding sites on Sec61, thereby producing distinct biological outcomes.
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Affiliation(s)
- Anja O Paatero
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, Biocenter 3, Helsinki 00014, Finland
| | - Juho Kellosalo
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, Biocenter 3, Helsinki 00014, Finland
| | - Bryan M Dunyak
- Department of Pharmaceutical Chemistry, Institute for Neurodegenerative Disease, University of California at San Francisco, San Francisco, CA 94038, USA
| | - Jehad Almaliti
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, Institute for Neurodegenerative Disease, University of California at San Francisco, San Francisco, CA 94038, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ville O Paavilainen
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, Biocenter 3, Helsinki 00014, Finland.
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Schuierer S, Carbone W, Knehr J, Petitjean V, Fernandez A, Sultan M, Roma G. A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples. BMC Genomics 2017; 18:442. [PMID: 28583074 PMCID: PMC5460543 DOI: 10.1186/s12864-017-3827-y] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/29/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND RNA-sequencing (RNA-seq) has emerged as one of the most sensitive tool for gene expression analysis. Among the library preparation methods available, the standard poly(A) + enrichment provides a comprehensive, detailed, and accurate view of polyadenylated RNAs. However, on samples of suboptimal quality ribosomal RNA depletion and exon capture methods have recently been reported as better alternatives. METHODS We compared for the first time three commercial Illumina library preparation kits (TruSeq Stranded mRNA, TruSeq Ribo-Zero rRNA Removal, and TruSeq RNA Access) as representatives of these three different approaches using well-established human reference RNA samples from the MAQC/SEQC consortium on a wide range of input amounts (from 100 ng down to 1 ng) and degradation levels (intact, degraded, and highly degraded). RESULTS We assessed the accuracy of the generated expression values by comparison to gold standard TaqMan qPCR measurements and gained unprecedented insight into the limits of applicability in terms of input quantity and sample quality of each protocol. We found that each protocol generates highly reproducible results (R 2 > 0.92) on intact RNA samples down to input amounts of 10 ng. For degraded RNA samples, Ribo-Zero showed clear performance advantages over the other two protocols as it generated more accurate and better reproducible gene expression results even at very low input amounts such as 1 ng and 2 ng. For highly degraded RNA samples, RNA Access performed best generating reliable data down to 5 ng input. CONCLUSIONS We found that the ribosomal RNA depletion protocol from Illumina works very well at amounts far below recommendation and over a good range of intact and degraded material. We also infer that the exome-capture protocol (RNA Access, Illumina) performs better than other methods on highly degraded and low amount samples.
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Affiliation(s)
- Sven Schuierer
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland.
| | - Walter Carbone
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Judith Knehr
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Virginie Petitjean
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Anita Fernandez
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Marc Sultan
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland.
| | - Guglielmo Roma
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland.
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42
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Estoppey D, Lee CM, Janoschke M, Lee BH, Wan KF, Dong H, Mathys P, Filipuzzi I, Schuhmann T, Riedl R, Aust T, Galuba O, McAllister G, Russ C, Spiess M, Bouwmeester T, Bonamy GM, Hoepfner D. The Natural Product Cavinafungin Selectively Interferes with Zika and Dengue Virus Replication by Inhibition of the Host Signal Peptidase. Cell Rep 2017; 19:451-460. [DOI: 10.1016/j.celrep.2017.03.071] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 03/06/2017] [Accepted: 03/24/2017] [Indexed: 12/31/2022] Open
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McKenna M, Simmonds RE, High S. Mycolactone reveals the substrate-driven complexity of Sec61-dependent transmembrane protein biogenesis. J Cell Sci 2017; 130:1307-1320. [PMID: 28219954 PMCID: PMC5399781 DOI: 10.1242/jcs.198655] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/02/2017] [Indexed: 12/22/2022] Open
Abstract
Mycolactone is the exotoxin virulence factor produced by Mycobacterium ulcerans, the pathogen responsible for Buruli ulcer. The skin lesions and immunosuppression that are characteristic of this disease result from the action of mycolactone, which targets the Sec61 complex and inhibits the co-translational translocation of secretory proteins into the endoplasmic reticulum. In this study, we investigate the effect of mycolactone on the Sec61-dependent biogenesis of different classes of transmembrane protein (TMP). Our data suggest that the effect of mycolactone on TMP biogenesis depends on how the nascent chain initially engages the Sec61 complex. For example, the translocation of TMP lumenal domains driven by an N-terminal cleavable signal sequence is efficiently inhibited by mycolactone. In contrast, the effect of mycolactone on protein translocation that is driven solely by a non-cleavable signal anchor/transmembrane domain depends on which flanking region is translocated. For example, while translocation of the region N-terminal to a signal anchor/transmembrane domain is refractive to mycolactone, C-terminal translocation is efficiently inhibited. Our findings highlight the diversity of Sec61-dependent translocation and provide a molecular basis for understanding the effect of mycolactone on the biogenesis of different TMPs. Highlighted Article: The exotoxin mycolactone interferes with the biogenesis of the majority of transmembrane proteins and its actions highlight differences in how distinct classes of these proteins initially engage the Sec61 translocon.
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Affiliation(s)
- Michael McKenna
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Manchester M13 9PT, UK
| | - Rachel E Simmonds
- Department of Microbial Sciences, School of Bioscience and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Stephen High
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Manchester M13 9PT, UK
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44
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Van Puyenbroeck V, Claeys E, Schols D, Bell TW, Vermeire K. A Proteomic Survey Indicates Sortilin as a Secondary Substrate of the ER Translocation Inhibitor Cyclotriazadisulfonamide (CADA). Mol Cell Proteomics 2016; 16:157-167. [PMID: 27998951 DOI: 10.1074/mcp.m116.061051] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 11/04/2016] [Indexed: 11/06/2022] Open
Abstract
The small molecule CADA was shown to down-modulate the expression of human CD4 in a signal peptide-dependent way through inhibition of its cotranslational translocation across the ER membrane. Previous studies characterizing general glycoprotein levels and the expression of 14 different cell surface receptors showed selectivity of CADA for human CD4. Here, a PowerBlot Western Array was used as a screen to analyze the proteome of CADA-treated SUP-T1 human CD4+ T lymphocytes. This high-throughput monoclonal antibody panel-based immunoblotting assay of cellular signaling proteins revealed that only a small subset of the 444 detected proteins was differentially expressed after treatment with CADA. Validation of these proteomic data with optimized immunoblot analysis confirmed the CADA-induced change in expression of the cell cycle progression regulator pRb2 and the transcription factor c-Jun. However, the up-regulation of pRb2 or down-modulation of c-Jun by CADA had no impact on cell cycle transition. Also, the reduced protein level of human CD4 did not inhibit T cell receptor signaling. Interestingly, the signal peptide-containing membrane protein sortilin was identified as a new substrate for CADA. Both cellular expression and in vitro cotranslational translocation of sortilin were significantly reduced by CADA, although to a lesser extent as compared with human CD4. Our data demonstrate that a small signal peptide-binding drug is able to down-modulate the expression of human CD4 and sortilin, apparently with low impact on the cellular proteome.
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Affiliation(s)
- Victor Van Puyenbroeck
- From the ‡KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Elisa Claeys
- From the ‡KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Dominique Schols
- From the ‡KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Thomas W Bell
- §Department of Chemistry, University of Nevada, Reno, NV, USA
| | - Kurt Vermeire
- From the ‡KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium;
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45
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Baron L, Paatero AO, Morel JD, Impens F, Guenin-Macé L, Saint-Auret S, Blanchard N, Dillmann R, Niang F, Pellegrini S, Taunton J, Paavilainen VO, Demangel C. Mycolactone subverts immunity by selectively blocking the Sec61 translocon. J Exp Med 2016; 213:2885-2896. [PMID: 27821549 PMCID: PMC5154940 DOI: 10.1084/jem.20160662] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/26/2016] [Accepted: 10/17/2016] [Indexed: 12/29/2022] Open
Abstract
Mycolactone, an immunosuppressive macrolide released by the human pathogen Mycobacterium ulcerans, was previously shown to impair Sec61-dependent protein translocation, but the underlying molecular mechanism was not identified. In this study, we show that mycolactone directly targets the α subunit of the Sec61 translocon to block the production of secreted and integral membrane proteins with high potency. We identify a single-amino acid mutation conferring resistance to mycolactone, which localizes its interaction site near the lumenal plug of Sec61α. Quantitative proteomics reveals that during T cell activation, mycolactone-mediated Sec61 blockade affects a selective subset of secretory proteins including key signal-transmitting receptors and adhesion molecules. Expression of mutant Sec61α in mycolactone-treated T cells rescued their homing potential and effector functions. Furthermore, when expressed in macrophages, the mycolactone-resistant mutant restored IFN-γ receptor-mediated antimicrobial responses. Thus, our data provide definitive genetic evidence that Sec61 is the host receptor mediating the diverse immunomodulatory effects of mycolactone and identify Sec61 as a novel regulator of immune cell functions.
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Affiliation(s)
- Ludivine Baron
- Unité d’Immunobiologie de l’Infection, Institut Pasteur, Institut National de la Santé et de la Recherche Médicale U1221, 75015 Paris, France
| | | | - Jean-David Morel
- Unité d’Immunobiologie de l’Infection, Institut Pasteur, Institut National de la Santé et de la Recherche Médicale U1221, 75015 Paris, France
| | - Francis Impens
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Institut National de la Santé et de la Recherche Médicale U604, Institut National de la Recherche Agronomique, Unité sous-contrat 2020, 75015 Paris, France
| | - Laure Guenin-Macé
- Unité d’Immunobiologie de l’Infection, Institut Pasteur, Institut National de la Santé et de la Recherche Médicale U1221, 75015 Paris, France
| | - Sarah Saint-Auret
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7509, École européenne de Chimie, Polymères et Matériaux, Université de Strasbourg, 67087 Strasbourg, France
| | - Nicolas Blanchard
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7509, École européenne de Chimie, Polymères et Matériaux, Université de Strasbourg, 67087 Strasbourg, France
| | - Rabea Dillmann
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Fatoumata Niang
- Unité d’Immunobiologie de l’Infection, Institut Pasteur, Institut National de la Santé et de la Recherche Médicale U1221, 75015 Paris, France
| | - Sandra Pellegrini
- Unité de Signalisation des Cytokines, Institut Pasteur, Institut National de la Santé et de la Recherche Médicale U1221, 75015 Paris, France
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158
| | | | - Caroline Demangel
- Unité d’Immunobiologie de l’Infection, Institut Pasteur, Institut National de la Santé et de la Recherche Médicale U1221, 75015 Paris, France
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Dubnikov T, Ben-Gedalya T, Reiner R, Hoepfner D, Cabral WA, Marini JC, Cohen E. PrP-containing aggresomes are cytosolic components of an ER quality control mechanism. J Cell Sci 2016; 129:3635-3647. [PMID: 27550517 DOI: 10.1242/jcs.186981] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 08/13/2016] [Indexed: 11/20/2022] Open
Abstract
Limited detoxification capacity often directs aggregation-prone, potentially hazardous, misfolded proteins to be deposited in designated cytosolic compartments known as 'aggresomes'. The roles of aggresomes as cellular quality control centers, and the cellular origin of the deposits contained within these structures, remain to be characterized. Here, we utilized the observation that the prion protein (PrP, also known as PRNP) accumulates in aggresomes following the inhibition of folding chaperones, members of the cyclophilin family, to address these questions. We found that misfolded PrP molecules must pass through the endoplasmic reticulum (ER) in order to be deposited in aggresomes, that the Golgi plays no role in this process and that cytosolic PrP species are not deposited in pre-existing aggresomes. Prior to their deposition in the aggresome, PrP molecules lose the ER localization signal and have to acquire a GPI anchor. Our discoveries indicate that PrP aggresomes are cytosolic overflow deposition centers for the ER quality control mechanisms and highlight the importance of these structures for the maintenance of protein homeostasis within the ER.
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Affiliation(s)
- Tatyana Dubnikov
- Biochemistry and Molecular Biology, the Institute for Medical Research Israel - Canada (IMRIC), the School of Medicine of the Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Tziona Ben-Gedalya
- Biochemistry and Molecular Biology, the Institute for Medical Research Israel - Canada (IMRIC), the School of Medicine of the Hebrew University of Jerusalem, Jerusalem 91120, Israel Department of Obstetrics and Gynecology, Hadassah University Hospital, Ein Kerem, Jerusalem, 91120, Israel
| | - Robert Reiner
- Biochemistry and Molecular Biology, the Institute for Medical Research Israel - Canada (IMRIC), the School of Medicine of the Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Dominic Hoepfner
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel 4056, Switzerland
| | - Wayne A Cabral
- Bone and Extracellular Matrix Branch, NICHD, NIH, Bethesda, MD 20892, USA
| | - Joan C Marini
- Bone and Extracellular Matrix Branch, NICHD, NIH, Bethesda, MD 20892, USA
| | - Ehud Cohen
- Biochemistry and Molecular Biology, the Institute for Medical Research Israel - Canada (IMRIC), the School of Medicine of the Hebrew University of Jerusalem, Jerusalem 91120, Israel
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McKenna M, Simmonds RE, High S. Mechanistic insights into the inhibition of Sec61-dependent co- and post-translational translocation by mycolactone. J Cell Sci 2016; 129:1404-15. [PMID: 26869228 PMCID: PMC4852723 DOI: 10.1242/jcs.182352] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/03/2016] [Indexed: 12/17/2022] Open
Abstract
The virulence factor mycolactone is responsible for the immunosuppression and tissue necrosis that characterise Buruli ulcer, a disease caused by infection with Mycobacterium ulcerans In this study, we confirm that Sec61, the protein-conducting channel that coordinates entry of secretory proteins into the endoplasmic reticulum, is a primary target of mycolactone, and characterise the nature of its inhibitory effect. We conclude that mycolactone constrains the ribosome-nascent-chain-Sec61 complex, consistent with its broad-ranging perturbation of the co-translational translocation of classical secretory proteins. In contrast, the effect of mycolactone on the post-translational ribosome-independent translocation of short secretory proteins through the Sec61 complex is dependent on both signal sequence hydrophobicity and the translocation competence of the mature domain. Changes to protease sensitivity strongly suggest that mycolactone acts by inducing a conformational change in the pore-forming Sec61α subunit. These findings establish that mycolactone inhibits Sec61-mediated protein translocation and highlight differences between the co- and post-translational routes that the Sec61 complex mediates. We propose that mycolactone also provides a useful tool for further delineating the molecular mechanisms of Sec61-dependent protein translocation.
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Affiliation(s)
- Michael McKenna
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester M13 9PT, UK
| | - Rachel E Simmonds
- Department of Microbial Sciences, School of Bioscience and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Stephen High
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester M13 9PT, UK
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Abstract
Secreted and integral membrane proteins compose up to one-third of the biological proteome. These proteins contain hydrophobic signals that direct their translocation across or insertion into the lipid bilayer by the Sec61 protein-conducting channel. The molecular basis of how hydrophobic signals within a nascent polypeptide trigger channel opening is not understood. Here, we used cryo-electron microscopy to determine the structure of an active Sec61 channel that has been opened by a signal sequence. The signal supplants helix 2 of Sec61α, which triggers a rotation that opens the central pore both axially across the membrane and laterally toward the lipid bilayer. Comparisons with structures of Sec61 in other states suggest a pathway for how hydrophobic signals engage the channel to gain access to the lipid bilayer.
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Affiliation(s)
- Rebecca M Voorhees
- MRC Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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Carelli JD, Sethofer SG, Smith GA, Miller HR, Simard JL, Merrick WC, Jain RK, Ross NT, Taunton J. Ternatin and improved synthetic variants kill cancer cells by targeting the elongation factor-1A ternary complex. eLife 2015; 4. [PMID: 26651998 PMCID: PMC4786417 DOI: 10.7554/elife.10222] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/26/2015] [Indexed: 01/09/2023] Open
Abstract
Cyclic peptide natural products have evolved to exploit diverse protein targets, many of which control essential cellular processes. Inspired by a series of cyclic peptides with partially elucidated structures, we designed synthetic variants of ternatin, a cytotoxic and anti-adipogenic natural product whose molecular mode of action was unknown. The new ternatin variants are cytotoxic toward cancer cells, with up to 500-fold greater potency than ternatin itself. Using a ternatin photo-affinity probe, we identify the translation elongation factor-1A ternary complex (eEF1A·GTP·aminoacyl-tRNA) as a specific target and demonstrate competitive binding by the unrelated natural products, didemnin and cytotrienin. Mutations in domain III of eEF1A prevent ternatin binding and confer resistance to its cytotoxic effects, implicating the adjacent hydrophobic surface as a functional hot spot for eEF1A modulation. We conclude that the eukaryotic elongation factor-1A and its ternary complex with GTP and aminoacyl-tRNA are common targets for the evolution of cytotoxic natural products. DOI:http://dx.doi.org/10.7554/eLife.10222.001 Many plants, fungi, and bacteria have evolved to produce small molecules that have powerful effects on the cells of other living organisms, and can even kill them. These naturally produced compounds are often used as starting points for developing new drugs. One such class of compounds are the cyclic peptides, which can be relatively easily produced in the laboratory and are able to penetrate cells. Some cyclic peptides have also proved to be useful for treating cancer and immune diseases, so researchers are keen to identify others that have similar effects. One promising prospect, called ternatin, is produced by several species of fungi. In high doses, ternatin can kill mammalian cells, but it was not clear how it does so. To learn more, Carelli et al. searched a chemical database for cyclic peptides related to ternatin and identified several similar compounds that were reported to kill cancer cells. Inspired by the structures of these cyclic peptides, Carelli et al. synthesized modified versions of ternatin. One of these was 500 times more potent than ternatin, which means a much lower dose of the compound is still able to kill cancer cells. Further experiments showed that ternatin blocks the production of new proteins in cells. Specifically, ternatin binds to a complex that includes a protein called elongation factor-1A (eEF1A). Mutations in a particular region of eEF1A prevent ternatin from killing cells, suggesting a potential binding site for ternatin. The next challenge is to dissect the mechanism by which compounds binding to this site on eEF1A block protein synthesis and kill cells. A related challenge is to understand why certain cancer cells are hypersensitive to ternatin and other eEF1A inhibitors, while other cancer cells are relatively resistant. These questions are relevant to the development of eEF1A inhibitors as cancer treatments. DOI:http://dx.doi.org/10.7554/eLife.10222.002
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Affiliation(s)
- Jordan D Carelli
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Steven G Sethofer
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Geoffrey A Smith
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Howard R Miller
- Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Jillian L Simard
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - William C Merrick
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, United States
| | - Rishi K Jain
- Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Nathan T Ross
- Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
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50
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Natural products as probes in pharmaceutical research. J Ind Microbiol Biotechnol 2015; 43:249-60. [PMID: 26438431 DOI: 10.1007/s10295-015-1691-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/16/2015] [Indexed: 10/23/2022]
Abstract
From the start of the pharmaceutical research natural products played a key role in drug discovery and development. Over time many discoveries of fundamental new biology were triggered by the unique biological activity of natural products. Unprecedented chemical structures, novel chemotypes, often pave the way to investigate new biology and to explore new pathways and targets. This review summarizes the recent results in the area with a focus on research done in the laboratories of Novartis Institutes for BioMedical Research. We aim to put the technological advances in target identification techniques in the context to the current revival of phenotypic screening and the increasingly complex biological questions related to drug discovery.
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