1
|
Sorout N, Helms V. Toward Understanding the Mechanism of Client-Selective Small Molecule Inhibitors of the Sec61 Translocon. J Mol Recognit 2024:e3108. [PMID: 39394908 DOI: 10.1002/jmr.3108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/28/2024] [Accepted: 09/27/2024] [Indexed: 10/14/2024]
Abstract
The Sec61 translocon mediates the translocation of numerous, newly synthesized precursor proteins into the lumen of the endoplasmic reticulum or their integration into its membrane. Recently, structural biology revealed conformations of idle or substrate-engaged Sec61, and likewise its interactions with the accessory membrane proteins Sec62, Sec63, and TRAP, respectively. Several natural and synthetic small molecules have been shown to block Sec61-mediated protein translocation. Since this is a key step in protein biogenesis, broad inhibition is generally cytotoxic, which may be problematic for a putative drug target. Interestingly, several compounds exhibit client-selective modes of action, such that only translocation of certain precursor proteins was affected. Here, we discuss recent advances of structural biology, molecular modelling, and molecular screening that aim to use Sec61 as feasible drug target.
Collapse
Affiliation(s)
- Nidhi Sorout
- Center for Bioinformatics, Saarland University, Saarbrücken, Saarland, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Saarland, Germany
| |
Collapse
|
2
|
Robeson L, Casanova‐Morales N, Burgos‐Bravo F, Alfaro‐Valdés HM, Lesch R, Ramírez‐Álvarez C, Valdivia‐Delgado M, Vega M, Matute RA, Schekman R, Wilson CAM. Characterization of the interaction between the Sec61 translocon complex and ppαF using optical tweezers. Protein Sci 2024; 33:e4996. [PMID: 38747383 PMCID: PMC11094780 DOI: 10.1002/pro.4996] [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: 10/19/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 05/19/2024]
Abstract
The Sec61 translocon allows the translocation of secretory preproteins from the cytosol to the endoplasmic reticulum lumen during polypeptide biosynthesis. These proteins possess an N-terminal signal peptide (SP) which docks at the translocon. SP mutations can abolish translocation and cause diseases, suggesting an essential role for this SP/Sec61 interaction. However, a detailed biophysical characterization of this binding is still missing. Here, optical tweezers force spectroscopy was used to characterize the kinetic parameters of the dissociation process between Sec61 and the SP of prepro-alpha-factor. The unbinding parameters including off-rate constant and distance to the transition state were obtained by fitting rupture force data to Dudko-Hummer-Szabo models. Interestingly, the translocation inhibitor mycolactone increases the off-rate and accelerates the SP/Sec61 dissociation, while also weakening the interaction. Whereas the translocation deficient mutant containing a single point mutation in the SP abolished the specificity of the SP/Sec61 binding, resulting in an unstable interaction. In conclusion, we characterize quantitatively the dissociation process between the signal peptide and the translocon, and how the unbinding parameters are modified by a translocation inhibitor.
Collapse
Affiliation(s)
- Luka Robeson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | - Nathalie Casanova‐Morales
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
- Facultad de Artes LiberalesUniversidad Adolfo IbáñezSantiagoChile
| | - Francesca Burgos‐Bravo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
- California Institute for Quantitative Biosciences, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Hilda M. Alfaro‐Valdés
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | - Robert Lesch
- Department of Molecular and Cellular Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Carolina Ramírez‐Álvarez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | - Mauricio Valdivia‐Delgado
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | - Marcela Vega
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | - Ricardo A. Matute
- Centro Integrativo de Biología y Química Aplicada (CIBQA)Universidad Bernardo O'HigginsSantiagoChile
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Randy Schekman
- Department of Molecular and Cellular Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Christian A. M. Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| |
Collapse
|
3
|
Dong J, Lv Y, Meng D, Shi R, Li F, Guo R, Wang Y, Guo J, Zhang Y. LncRNA WFDC21P interacts with SEC63 to promote gastric cancer malignant behaviors by regulating calcium homeostasis signaling pathway. Cancer Cell Int 2024; 24:111. [PMID: 38528582 DOI: 10.1186/s12935-024-03297-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/06/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Gastric cancer is currently estimated to be the fifth leading common cancer in the world, and responsible for about one million new cases and an estimated 769,000 cancer-related deaths each year. WFDC21P is long non-coding RNA and has been reported to play critical roles in serval types of cancer. Our research aims to investigate the biological effects and molecular mechanism of WFDC21P in gastric cancer. METHODS Datasets (GSE53137, GSE58828, and GSE109476) in GEO database were used to screen differential expressed lncRNAs in gastric cancer by online GEO2R analysis tool. Quantitative RT-PCR was used to verify the above prediction in ten pairs of gastric cancer and corresponding paracancerous tissues. Pan-cancer analysis was used to analyze the expression of WFDC21P in different types of cancer. Small interfering RNAs were used to WFDC21P knockdown. CCK-8 and colony formation assays were used to measure the proliferation and tumorigenesis abilities. Wound healing and Transwell assay were used to detect the migration and invasion abilities. Proteins that interact with WFDC21P were predicted by catRAPID database. RNA pull down and RNA Immunoprecipitation were used to confirm the interaction. Western blotting was used to detect the key proteins level in calcium homeostasis signaling pathway. Loss-of-function and rescue assays were used to evaluate the biological function of SEC63 at the background of WFDC21P silencing. RESULTS WFDC21P was upregulated in gastric cancer tissues and cell lines. WFDC21P downregulation suppressed proliferation, tumorigenesis, migration, invasion, and promoted apoptosis in gastric cancer. SEC63 protein had the capability to bind with WFDC21P and the expression of SEC63 was regulated by WFDC21P. SEC63 was also upregulated in gastric cancer and exerted effects during tumor growth and metastasis. CONCLUSIONS This study confirmed that lncRNA WFDC21P aggravated gastric cancer malignant behaviors by interacting with SEC63 to regulate the calcium homeostasis signaling pathway.
Collapse
Affiliation(s)
- Jinyao Dong
- Hepatobiliary Pancreatogastric Surgery, Shanxi Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University , Taiyuan, Shanxi, 030013, P. R. China
| | - Yongqiang Lv
- Scientific Research Department, Shanxi Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, 030013, P. R. China
| | - Debin Meng
- Hepatobiliary Pancreatogastric Surgery, Shanxi Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University , Taiyuan, Shanxi, 030013, P. R. China
| | - Ruyi Shi
- Department of Cell biology and Genetics, Shanxi Medical University, Taiyuan, Shanxi, 030001, P. R. China
| | - Feng Li
- Central Laboratory, Shanxi Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, 030013, P. R. China
| | - Rui Guo
- Hepatobiliary Pancreatogastric Surgery, Shanxi Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University , Taiyuan, Shanxi, 030013, P. R. China
| | - Yi Wang
- Hepatobiliary Pancreatogastric Surgery, Shanxi Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University , Taiyuan, Shanxi, 030013, P. R. China
| | - Jiansheng Guo
- Gastrointestinal Surgery Department, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P. R. China.
| | - Yanyan Zhang
- Hepatobiliary Pancreatic Surgery and Liver Transplantation Center, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P. R. China.
| |
Collapse
|
4
|
Child JR, Hofler AC, Chen Q, Yang BH, Kristofich J, Zheng T, Hannigan MM, Elles AL, Reid DW, Nicchitta CV. Examining SRP pathway function in mRNA localization to the endoplasmic reticulum. RNA (NEW YORK, N.Y.) 2023; 29:1703-1724. [PMID: 37643813 PMCID: PMC10578483 DOI: 10.1261/rna.079643.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 07/17/2023] [Indexed: 08/31/2023]
Abstract
Signal recognition particle (SRP) pathway function in protein translocation across the endoplasmic reticulum (ER) is well established; its role in RNA localization to the ER remains, however, unclear. In current models, mRNAs undergo translation- and SRP-dependent trafficking to the ER, with ER localization mediated via interactions between SRP-bound translating ribosomes and the ER-resident SRP receptor (SR), a heterodimeric complex comprising SRA, the SRP-binding subunit, and SRB, an integral membrane ER protein. To study SRP pathway function in RNA localization, SR knockout (KO) mammalian cell lines were generated and the consequences of SR KO on steady-state and dynamic mRNA localization examined. CRISPR/Cas9-mediated SRPRB KO resulted in profound destabilization of SRA. Pairing siRNA silencing of SRPRA in SRPRB KO cells yielded viable SR KO cells. Steady-state mRNA compositions and ER-localization patterns in parental and SR KO cells were determined by cell fractionation and deep sequencing. Notably, steady-state cytosol and ER mRNA compositions and partitioning patterns were largely unaltered by loss of SR expression. To examine SRP pathway function in RNA localization dynamics, the subcellular trafficking itineraries of newly exported mRNAs were determined by 4-thiouridine (4SU) pulse-labeling/4SU-seq/cell fractionation. Newly exported mRNAs were distinguished by high ER enrichment, with ER localization being SR-independent. Intriguingly, under conditions of translation initiation inhibition, the ER was the default localization site for all newly exported mRNAs. These data demonstrate that mRNA localization to the ER can be uncoupled from the SRP pathway function and reopen questions regarding the mechanism of RNA localization to the ER.
Collapse
Affiliation(s)
- Jessica R Child
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Alex C Hofler
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Qiang Chen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Brenda H Yang
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - JohnCarlo Kristofich
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Tianli Zheng
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Molly M Hannigan
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Andrew L Elles
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - David W Reid
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Christopher V Nicchitta
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
| |
Collapse
|
5
|
Jung M, Zimmermann R. Quantitative Mass Spectrometry Characterizes Client Spectra of Components for Targeting of Membrane Proteins to and Their Insertion into the Membrane of the Human ER. Int J Mol Sci 2023; 24:14166. [PMID: 37762469 PMCID: PMC10532041 DOI: 10.3390/ijms241814166] [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: 08/09/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
To elucidate the redundancy in the components for the targeting of membrane proteins to the endoplasmic reticulum (ER) and/or their insertion into the ER membrane under physiological conditions, we previously analyzed different human cells by label-free quantitative mass spectrometry. The HeLa and HEK293 cells had been depleted of a certain component by siRNA or CRISPR/Cas9 treatment or were deficient patient fibroblasts and compared to the respective control cells by differential protein abundance analysis. In addition to clients of the SRP and Sec61 complex, we identified membrane protein clients of components of the TRC/GET, SND, and PEX3 pathways for ER targeting, and Sec62, Sec63, TRAM1, and TRAP as putative auxiliary components of the Sec61 complex. Here, a comprehensive evaluation of these previously described differential protein abundance analyses, as well as similar analyses on the Sec61-co-operating EMC and the characteristics of the topogenic sequences of the various membrane protein clients, i.e., the client spectra of the components, are reported. As expected, the analysis characterized membrane protein precursors with cleavable amino-terminal signal peptides or amino-terminal transmembrane helices as predominant clients of SRP, as well as the Sec61 complex, while precursors with more central or even carboxy-terminal ones were found to dominate the client spectra of the SND and TRC/GET pathways for membrane targeting. For membrane protein insertion, the auxiliary Sec61 channel components indeed share the client spectra of the Sec61 complex to a large extent. However, we also detected some unexpected differences, particularly related to EMC, TRAP, and TRAM1. The possible mechanistic implications for membrane protein biogenesis at the human ER are discussed and can be expected to eventually advance our understanding of the mechanisms that are involved in the so-called Sec61-channelopathies, resulting from deficient ER protein import.
Collapse
Affiliation(s)
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany;
| |
Collapse
|
6
|
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: 7] [Impact Index Per Article: 7.0] [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.
Collapse
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.
| |
Collapse
|
7
|
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: 7] [Impact Index Per Article: 7.0] [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.
Collapse
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.
| |
Collapse
|
8
|
Hammond N, Snider J, Stagljar I, Mitchell K, Lagutin K, Jessulat M, Babu M, Teesdale-Spittle PH, Sheridan JP, Sturley SL, Munkacsi AB. Identification and characterization of protein interactions with the major Niemann-Pick type C disease protein in yeast reveals pathways of therapeutic potential. Genetics 2023; 225:iyad129. [PMID: 37440478 PMCID: PMC10471228 DOI: 10.1093/genetics/iyad129] [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: 01/12/2023] [Revised: 01/12/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Niemann-Pick type C (NP-C) disease is a rare lysosomal storage disease caused by mutations in NPC1 (95% cases) or NPC2 (5% cases). These proteins function together in cholesterol egress from the lysosome, whereby upon mutation, cholesterol and other lipids accumulate causing major pathologies. However, it is not fully understood how cholesterol is transported from NPC1 residing at the lysosomal membrane to the endoplasmic reticulum (ER) and plasma membrane. The yeast ortholog of NPC1, Niemann-Pick type C-related protein-1 (Ncr1), functions similarly to NPC1; when transfected into a mammalian cell lacking NPC1, Ncr1 rescues the diagnostic hallmarks of cholesterol and sphingolipid accumulation. Here, we aimed to identify and characterize protein-protein interactions (PPIs) with the yeast Ncr1 protein. A genome-wide split-ubiquitin membrane yeast two-hybrid (MYTH) protein interaction screen identified 11 ER membrane-localized, full-length proteins interacting with Ncr1 at the lysosomal/vacuolar membrane. These highlight the importance of ER-vacuole membrane interface and include PPIs with the Cyb5/Cbr1 electron transfer system, the ceramide synthase complex, and the Sec61/Sbh1 protein translocation complex. These PPIs were not detected in a sterol auxotrophy condition and thus depend on normal sterol metabolism. To provide biological context for the Ncr1-Cyb5 PPI, a yeast strain lacking this PPI (via gene deletions) exhibited altered levels of sterols and sphingolipids including increased levels of glucosylceramide that mimic NP-C disease. Overall, the results herein provide new physical and genetic interaction models to further use the yeast model of NP-C disease to better understand human NP-C disease.
Collapse
Affiliation(s)
- Natalie Hammond
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jamie Snider
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Mediterranean Institute for Life Sciences, Meštrovićevo Šetalište 45, HR-21000 Split, Croatia
| | | | | | - Matthew Jessulat
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Paul H Teesdale-Spittle
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jeffrey P Sheridan
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Stephen L Sturley
- Department of Biology, Barnard College-Columbia University, New York, NY 10027, USA
| | - Andrew B Munkacsi
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| |
Collapse
|
9
|
Tao S, Yang EJ, Zong G, Mou PK, Ren G, Pu Y, Chen L, Kwon HJ, Zhou J, Hu Z, Khosravi A, Zhang Q, Du Y, Shi WQ, Shim JS. ER translocon inhibitor ipomoeassin F inhibits triple-negative breast cancer growth via blocking ER molecular chaperones. Int J Biol Sci 2023; 19:4020-4035. [PMID: 37705743 PMCID: PMC10496495 DOI: 10.7150/ijbs.82012] [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: 12/20/2022] [Accepted: 03/27/2023] [Indexed: 09/15/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive type of breast cancer where no effective therapy has been developed. Here, we report that the natural product ER translocon inhibitor ipomoeassin F is a selective inhibitor of TNBC cell growth. A proteomic analysis of TNBC cells revealed that ipomoeassin F significantly reduced the levels of ER molecular chaperones, including PDIA6 and PDIA4, and induced ER stress, unfolded protein response (UPR) and autophagy in TNBC cells. Mechanistically, ipomoeassin F, as an inhibitor of Sec61α-containing ER translocon, blocks ER translocation of PDIA6, inducing its proteasomal degradation. Silencing of PDIA6 or PDIA4 by RNA interferences or treatment with a small molecule inhibitor of the protein disulfide isomerases in TNBC cells successfully recapitulated the ipomoeassin F phenotypes, including the induction of ER stress, UPR and autophagy, suggesting that the reduction of PDIAs is the key mediator of the pharmacological effects of ipomoeassin F. Moreover, ipomoeassin F significantly suppressed TNBC growth in a mouse tumor xenograft model, with a marked reduction in PDIA6 and PDIA4 levels in the tumor samples. Our study demonstrates that Sec61α-containing ER translocon and PDIAs are potential drug targets for TNBC and suggests that ipomoeassin F could serve as a lead for developing ER translocon-targeted therapy for TNBC.
Collapse
Affiliation(s)
- Shishi Tao
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Eun Ju Yang
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Guanghui Zong
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Pui Kei Mou
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Guowen Ren
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Yue Pu
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Liang Chen
- Shenzhen Laboratory of Tumor Cell Biology, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ho Jeong Kwon
- Chemical Genomics Leader Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jianhong Zhou
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Zhijian Hu
- Feinstein Institute for Medical Research, Northwell Health, 350 Community Dr., Manhasset, New York, 11030, USA
| | - Arman Khosravi
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, USA
| | - Qingyang Zhang
- Department of Mathematical Sciences, University of Arkansas, Arkansas 72701, USA
| | - Yuchun Du
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Wei Q. Shi
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, USA
| | - Joong Sup Shim
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
- MOE Frontiers Science Centre for Precision Oncology, University of Macau, Taipa, Macau SAR, China
| |
Collapse
|
10
|
Overduin M, Kervin TA, Klarenbach Z, Adra TRC, Bhat RK. Comprehensive classification of proteins based on structures that engage lipids by COMPOSEL. Biophys Chem 2023; 295:106971. [PMID: 36801589 DOI: 10.1016/j.bpc.2023.106971] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 02/05/2023] [Indexed: 02/11/2023]
Abstract
Structures can now be predicted for any protein using programs like AlphaFold and Rosetta, which rely on a foundation of experimentally determined structures of architecturally diverse proteins. The accuracy of such artificial intelligence and machine learning (AI/ML) approaches benefits from the specification of restraints which assist in navigating the universe of folds to converge on models most representative of a given protein's physiological structure. This is especially pertinent for membrane proteins, with structures and functions that depend on their presence in lipid bilayers. Structures of proteins in their membrane environments could conceivably be predicted from AI/ML approaches with user-specificized parameters that describe each element of the architecture of a membrane protein accompanied by its lipid environment. We propose the Classification Of Membrane Proteins based On Structures Engaging Lipids (COMPOSEL), which builds on existing nomenclature types for monotopic, bitopic, polytopic and peripheral membrane proteins as well as lipids. Functional and regulatory elements are also defined in the scripts, as shown with membrane fusing synaptotagmins, multidomain PDZD8 and Protrudin proteins that recognize phosphoinositide (PI) lipids, the intrinsically disordered MARCKS protein, caveolins, the β barrel assembly machine (BAM), an adhesion G-protein coupled receptor (aGPCR) and two lipid modifying enzymes - diacylglycerol kinase DGKε and fatty aldehyde dehydrogenase FALDH. This demonstrates how COMPOSEL communicates lipid interactivity as well as signaling mechanisms and binding of metabolites, drug molecules, polypeptides or nucleic acids to describe the operations of any protein. Moreover COMPOSEL can be scaled to express how genomes encode membrane structures and how our organs are infiltrated by pathogens such as SARS-CoV-2.
Collapse
Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
| | - Troy A Kervin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | | | - Trixie Rae C Adra
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Rakesh K Bhat
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
11
|
McKenna MJ, Shao S. The Endoplasmic Reticulum and the Fidelity of Nascent Protein Localization. Cold Spring Harb Perspect Biol 2023; 15:a041249. [PMID: 36041782 PMCID: PMC9979852 DOI: 10.1101/cshperspect.a041249] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
High-fidelity protein localization is essential to define the identities and functions of different organelles and to maintain cellular homeostasis. Accurate localization of nascent proteins requires specific protein targeting pathways as well as quality control (QC) mechanisms to remove mislocalized proteins. The endoplasmic reticulum (ER) is the first destination for approximately one-third of the eukaryotic proteome and a major site of protein biosynthesis and QC. In mammalian cells, trafficking from the ER provides nascent proteins access to the extracellular space and essentially every cellular membrane and organelle except for mitochondria and possibly peroxisomes. Here, we discuss the biosynthetic mechanisms that deliver nascent proteins to the ER and the QC mechanisms that interface with the ER to correct or degrade mislocalized proteins.
Collapse
Affiliation(s)
- Michael J McKenna
- Department of Cell Biology, Harvard Medical School, Blavatnik Institute, Boston, Massachusetts 02115, USA
| | - Sichen Shao
- Department of Cell Biology, Harvard Medical School, Blavatnik Institute, Boston, Massachusetts 02115, USA
| |
Collapse
|
12
|
The ER Protein Translocation Channel Subunit Sbh1 Controls Virulence of Cryptococcus neoformans. mBio 2023; 14:e0338422. [PMID: 36749043 PMCID: PMC9973365 DOI: 10.1128/mbio.03384-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The fungal pathogen Cryptococcus neoformans is distinguished by a cell-wall-anchored polysaccharide capsule that is critical for virulence. Biogenesis of both cell wall and capsule relies on the secretory pathway. Protein secretion begins with polypeptide translocation across the endoplasmic reticulum (ER) membrane through a highly conserved channel formed by three proteins: Sec61, Sbh1, and Sss1. Sbh1, the most divergent, contains multiple phosphorylation sites, which may allow it to regulate entry into the secretory pathway in a species- and protein-specific manner. Absence of SBH1 causes a cell-wall defect in both Saccharomyces cerevisiae and C. neoformans, although other phenotypes differ. Notably, proteomic analysis showed that when cryptococci are grown in conditions that mimic aspects of the mammalian host environment (tissue culture medium, 37°C, 5% CO2), a set of secretory and transmembrane proteins is upregulated in wild-type, but not in Δsbh1 mutant cells. The Sbh1-dependent proteins show specific features of their ER targeting sequences that likely cause them to transit less efficiently into the secretory pathway. Many also act in cell-wall biogenesis, while several are known virulence factors. Consistent with these observations, the C. neoformans Δsbh1 mutant is avirulent in a mouse infection model. We conclude that, in the context of conditions encountered during infection, Sbh1 controls the entry of virulence factors into the secretory pathway of C. neoformans, and thereby regulates fungal pathogenicity. IMPORTANCE Cryptococcus neoformans is a yeast that causes almost 200,000 deaths worldwide each year, mainly of immunocompromised individuals. The surface structures of this pathogen, a protective cell wall surrounded by a polysaccharide capsule, are made and maintained by proteins that are synthesized inside the cell and travel outwards through the secretory pathway. A protein called Sbh1 is part of the machinery that determines which polypeptides enter this export pathway. We found that when Sbh1 is absent, both C. neoformans and the model yeast S. cerevisiae show cell-wall defects. Lack of Sbh1 also changes the pattern of secretion of both transmembrane and soluble proteins, in a manner that depends on characteristics of their sequences. Notably, multiple proteins that are normally upregulated in conditions similar to those encountered during infection, including several needed for cryptococcal virulence, are no longer increased. Sbh1 thereby regulates the ability of this important pathogen to cause disease.
Collapse
|
13
|
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: 8] [Impact Index Per Article: 8.0] [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.
Collapse
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
| |
Collapse
|
14
|
Sun S, Li X, Mariappan M. Signal sequences encode information for protein folding in the endoplasmic reticulum. J Cell Biol 2023; 222:213733. [PMID: 36459117 PMCID: PMC9723807 DOI: 10.1083/jcb.202203070] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 09/22/2022] [Accepted: 10/26/2022] [Indexed: 12/05/2022] Open
Abstract
One-third of newly synthesized proteins in mammals are translocated into the endoplasmic reticulum (ER) through the Sec61 translocon. How protein translocation coordinates with chaperone availability in the ER to promote protein folding remains unclear. We find that marginally hydrophobic signal sequences and transmembrane domains cause transient retention at the Sec61 translocon and require the luminal BiP chaperone for efficient protein translocation. Using a substrate-trapping proteomic approach, we identify that nascent proteins bearing marginally hydrophobic signal sequences accumulate on the cytosolic side of the Sec61 translocon. Sec63 is co-translationally recruited to the translocation site and mediates BiP binding to incoming polypeptides. BiP binding not only releases translocationally paused nascent chains but also ensures protein folding in the ER. Increasing hydrophobicity of signal sequences bypasses Sec63/BiP-dependent translocation, but translocated proteins are prone to misfold and aggregate in the ER under limited BiP availability. Thus, the signal sequence-guided protein folding may explain why signal sequences are diverse and use multiple protein translocation pathways.
Collapse
Affiliation(s)
- Sha Sun
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT
| | - Xia Li
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT
| | - Malaiyalam Mariappan
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT
| |
Collapse
|
15
|
Xue S, Liu X, Pan Y, Xiao C, Feng Y, Zheng L, Zhao M, Huang M. Comprehensive Analysis of Signal Peptides in Saccharomyces cerevisiae Reveals Features for Efficient Secretion. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2203433. [PMID: 36478443 PMCID: PMC9839866 DOI: 10.1002/advs.202203433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/10/2022] [Indexed: 05/30/2023]
Abstract
Signal peptides (SPs) are N-terminus sequences on the nascent polypeptide for protein export or localization delivery, which are essential for maintaining cell function. SPs are also employed as a key element for industrial production of secreted recombinant proteins. Yet, detailed information and rules about SPs and their cellular interactions are still not well understood. Here, systematic bioinformatics analysis and secretion capacity measurement of genome-wide SPs from the model organism Saccharomyces cerevisiae is performed. Several key features of SPs, including region properties, consensus motifs, evolutionary relationships, codon bias, e.g., are successfully revealed. Diverse cell metabolism can be trigged by using different SPs for heterologous protein secretion. Influences on SPs with different properties by chaperones can cause different secretory efficiencies. Protein secretion by the SP NCW2 in SEC72 deletion strain is 10 times than the control. These findings provide insights into the properties and functions of SPs and contribute to both fundamental research and industrial application.
Collapse
Affiliation(s)
- Songlyu Xue
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Xiufang Liu
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Yuyang Pan
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Chufan Xiao
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Yunzi Feng
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Lin Zheng
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Mouming Zhao
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| | - Mingtao Huang
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510641China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research CenterGuangzhou510650China
| |
Collapse
|
16
|
Melnyk A, Lang S, Sicking M, Zimmermann R, Jung M. Co-chaperones of the Human Endoplasmic Reticulum: An Update. Subcell Biochem 2023; 101:247-291. [PMID: 36520310 DOI: 10.1007/978-3-031-14740-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In mammalian cells, the rough endoplasmic reticulum (ER) plays central roles in the biogenesis of extracellular plus organellar proteins and in various signal transduction pathways. For these reasons, the ER comprises molecular chaperones, which are involved in import, folding, assembly, export, plus degradation of polypeptides, and signal transduction components, such as calcium channels, calcium pumps, and UPR transducers plus adenine nucleotide carriers/exchangers in the ER membrane. The calcium- and ATP-dependent ER lumenal Hsp70, termed immunoglobulin heavy-chain-binding protein or BiP, is the central player in all these activities and involves up to nine different Hsp40-type co-chaperones, i.e., ER membrane integrated as well as ER lumenal J-domain proteins, termed ERj or ERdj proteins, two nucleotide exchange factors or NEFs (Grp170 and Sil1), and NEF-antagonists, such as MANF. Here we summarize the current knowledge on the ER-resident BiP/ERj chaperone network and focus on the interaction of BiP with the polypeptide-conducting and calcium-permeable Sec61 channel of the ER membrane as an example for BiP action and how its functional cycle is linked to ER protein import and various calcium-dependent signal transduction pathways.
Collapse
Affiliation(s)
- Armin Melnyk
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
| | - Sven Lang
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
| | - Mark Sicking
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
| | - Richard Zimmermann
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany.
| | - Martin Jung
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
| |
Collapse
|
17
|
Shao S. Protein biosynthesis at the ER: finding the right accessories. Mol Biol Cell 2023; 34:pe1. [PMID: 36520029 PMCID: PMC9816642 DOI: 10.1091/mbc.e21-09-0451] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 12/23/2022] Open
Abstract
More than 30% of eukaryotic proteins contain domains that must translocate across or integrate into the endoplasmic reticulum (ER) membrane. With few exceptions, protein translocation and transmembrane domain integration at the ER require the conserved Sec61 translocon. Decades of studies have established a clear mechanistic model for how the Sec61 translocon functions. The biosynthesis of distinct subsets of proteins at the ER also involves accessory factors that interact with the Sec61 translocon and translocating nascent proteins. However, assigning specific functions to many translocon accessory factors has been a persistent challenge in the field. This Perspective discusses recent insights into mechanisms that promote protein biosynthesis at the ER through accessory factors that directly regulate the Sec61 translocon or chaperone nascent proteins within the ER membrane. These translocon accessory factor functions, and more still to be discovered, are essential for producing a diverse and high-fidelity proteome at the ER.
Collapse
Affiliation(s)
- Sichen Shao
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| |
Collapse
|
18
|
Jung SJ, Yun M, Yim C, Hong S, Huh WK, Kim H. Expression level of Sec62 modulates membrane insertion of marginally hydrophobic segments. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184051. [PMID: 36122759 DOI: 10.1016/j.bbamem.2022.184051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/08/2022] [Accepted: 09/09/2022] [Indexed: 06/15/2023]
Abstract
In the endoplasmic reticulum (ER) membrane, transmembrane (TM) domain insertion occurs through the Sec61 channel with its auxiliary components, including Sec62. Sec62 interacts with the Sec61 channel and is located on the front side of the Sec61 lateral gate, an entry site for TM domains to the lipid bilayer. Overexpression of Sec62 led to a growth defect in yeast, and we investigated its effects on protein translocation and membrane insertion by pulse labeling of Sec62 client proteins. Our data show that the insertion efficiency of marginally hydrophobic TM segments is reduced upon Sec62 overexpression. This result suggests a potential regulatory role of Sec62 as a gatekeeper of the lateral gate, thereby modulating the insertion threshold of TM segments.
Collapse
Affiliation(s)
- Sung-Jun Jung
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea
| | - Mekang Yun
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea
| | - Chewon Yim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea
| | - Sujin Hong
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea
| | - Won-Ki Huh
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea
| | - Hyun Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea.
| |
Collapse
|
19
|
Bhadra P, Römisch K, Helms V. Effect of Sec62 on the conformation of the Sec61 channel in yeast. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184050. [PMID: 36116515 DOI: 10.1016/j.bbamem.2022.184050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/22/2022] [Accepted: 09/09/2022] [Indexed: 06/15/2023]
Abstract
Most eukaryotic secretory and membrane proteins are funneled by the Sec61 complex into the secretory pathway. Furthermore, some substrate peptides rely on two essential accessory proteins, Sec62 and Sec63, being present to assist with their translocation via the Sec61 channel in post-translational translocation. Cryo-electron microscopy (cryo-EM) recently succeeded in determining atomistic structures of unbound and signal sequence-engaged Sec complexes from Saccharomyces cerevisiae, involving the Sec61 channel and the proteins Sec62, Sec63, Sec71 and Sec72. In this study, we investigated the conformational effects of Sec62 on Sec61. Indeed, we observed in molecular dynamics simulations that the conformational dynamics of lateral gate, plug and pore region of Sec61 are altered by the presence/absence of Sec62. In molecular dynamics simulations that were started from the cryo-EM structures of Sec61 coordinated to Sec62 or of apo Sec61, we observed that the luminal side of the lateral gate gradually adopts a closed conformation similar to the apo state during unbound state simulations. In contrast, it adopts a wider conformation in the bound state. Furthermore, we demonstrate that the conformation of the active (substrate-bound) state of the Sec61 channel shifts toward an alternative conformation in the absence of the substrate. We suggest that the signal peptide holds/stabilizes the active state conformation of Sec61 during post-translational translocation. Thus, our study explains the effect of Sec62 on the conformation of the Sec61 channel and describes the conformational transitions of Sec61 channel.
Collapse
Affiliation(s)
- Pratiti Bhadra
- Center for Bioinformatics, Saarland University, Saarland Informatics Campus, Saarbrücken, Saarland, Germany
| | - Karin Römisch
- Faculty of Natural Sciences and Technology, Saarland University, Saarbrücken, Saarland, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarland Informatics Campus, Saarbrücken, Saarland, Germany.
| |
Collapse
|
20
|
O'Keefe S, Pool MR, High S. Membrane protein biogenesis at the ER: the highways and byways. FEBS J 2022; 289:6835-6862. [PMID: 33960686 DOI: 10.1111/febs.15905] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/19/2021] [Accepted: 04/28/2021] [Indexed: 01/13/2023]
Abstract
The Sec61 complex is the major protein translocation channel of the endoplasmic reticulum (ER), where it plays a central role in the biogenesis of membrane and secretory proteins. Whilst Sec61-mediated protein translocation is typically coupled to polypeptide synthesis, suggestive of significant complexity, an obvious characteristic of this core translocation machinery is its surprising simplicity. Over thirty years after its initial discovery, we now understand that the Sec61 complex is in fact the central piece of an elaborate jigsaw puzzle, which can be partly solved using new research findings. We propose that the Sec61 complex acts as a dynamic hub for co-translational protein translocation at the ER, proactively recruiting a range of accessory complexes that enhance and regulate its function in response to different protein clients. It is now clear that the Sec61 complex does not have a monopoly on co-translational insertion, with some transmembrane proteins preferentially utilising the ER membrane complex instead. We also have a better understanding of post-insertion events, where at least one membrane-embedded chaperone complex can capture the newly inserted transmembrane domains of multi-span proteins and co-ordinate their assembly into a native structure. Having discovered this array of Sec61-associated components and competitors, our next challenge is to understand how they act together in order to expand the range and complexity of the membrane proteins that can be synthesised at the ER. Furthermore, this diversity of components and pathways may open up new opportunities for targeted therapeutic interventions designed to selectively modulate protein biogenesis at the ER.
Collapse
Affiliation(s)
- Sarah O'Keefe
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Martin R Pool
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Stephen High
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| |
Collapse
|
21
|
Lang S, Nguyen D, Bhadra P, Jung M, Helms V, Zimmermann R. Signal Peptide Features Determining the Substrate Specificities of Targeting and Translocation Components in Human ER Protein Import. Front Physiol 2022; 13:833540. [PMID: 35899032 PMCID: PMC9309488 DOI: 10.3389/fphys.2022.833540] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 05/17/2022] [Indexed: 12/11/2022] Open
Abstract
In human cells, approximately 30% of all polypeptides enter the secretory pathway at the level of the endoplasmic reticulum (ER). This process involves cleavable amino-terminal signal peptides (SPs) or more or less amino-terminal transmembrane helices (TMHs), which serve as targeting determinants, at the level of the precursor polypeptides and a multitude of cytosolic and ER proteins, which facilitate their ER import. Alone or in combination SPs and TMHs guarantee the initial ER targeting as well as the subsequent membrane integration or translocation. Cytosolic SRP and SR, its receptor in the ER membrane, mediate cotranslational targeting of most nascent precursor polypeptide chains to the polypeptide-conducting Sec61 complex in the ER membrane. Alternatively, fully-synthesized precursor polypeptides and certain nascent precursor polypeptides are targeted to the ER membrane by either the PEX-, SND-, or TRC-pathway. Although these targeting pathways may have overlapping functions, the question arises how relevant this is under cellular conditions and which features of SPs and precursor polypeptides determine preference for a certain pathway. Irrespective of their targeting pathway(s), most precursor polypeptides are integrated into or translocated across the ER membrane via the Sec61 channel. For some precursor polypeptides specific Sec61 interaction partners have to support the gating of the channel to the open state, again raising the question why and when this is the case. Recent progress shed light on the client spectrum and specificities of some auxiliary components, including Sec62/Sec63, TRAM1 protein, and TRAP. To address the question which precursors use a certain pathway or component in intact human cells, i.e., under conditions of fast translation rates and molecular crowding, in the presence of competing precursors, different targeting organelles, and relevant stoichiometries of the involved components, siRNA-mediated depletion of single targeting or transport components in HeLa cells was combined with label-free quantitative proteomics and differential protein abundance analysis. Here, we present a summary of the experimental approach as well as the resulting differential protein abundance analyses and discuss their mechanistic implications in light of the available structural data.
Collapse
Affiliation(s)
- Sven Lang
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Duy Nguyen
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Pratiti Bhadra
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Martin Jung
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| |
Collapse
|
22
|
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: 0.5] [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.
Collapse
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.
| |
Collapse
|
23
|
Pang AP, Luo Y, Hu X, Zhang F, Wang H, Gao Y, Durrani S, Li C, Shi X, Wu FG, Li BZ, Lu Z, Lin F. Transmembrane transport process and endoplasmic reticulum function facilitate the role of gene cel1b in cellulase production of Trichoderma reesei. Microb Cell Fact 2022; 21:90. [PMID: 35590356 PMCID: PMC9118834 DOI: 10.1186/s12934-022-01809-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 04/30/2022] [Indexed: 11/16/2022] Open
Abstract
Background A total of 11 β-glucosidases are predicted in the genome of Trichoderma reesei, which are of great importance for regulating cellulase biosynthesis. Nevertheless, the relevant function and regulation mechanism of each β-glucosidase remained unknown. Results We evidenced that overexpression of cel1b dramatically decreased cellulase synthesis in T. reesei RUT-C30 both at the protein level and the mRNA level. In contrast, the deletion of cel1b did not noticeably affect cellulase production. Protein CEL1B was identified to be intracellular, being located in vacuole and cell membrane. The overexpression of cel1b reduced the intracellular pNPGase activity and intracellular/extracellular glucose concentration without inducing carbon catabolite repression. On the other hand, RNA-sequencing analysis showed the transmembrane transport process and endoplasmic reticulum function were affected noticeably by overexpressing cel1b. In particular, some important sugar transporters were notably downregulated, leading to a compromised cellular uptake of sugars including glucose and cellobiose. Conclusions Our data suggests that the cellulase inhibition by cel1b overexpression was not due to the β-glucosidase activity, but probably the dysfunction of the cellular transport process (particularly sugar transport) and endoplasmic reticulum (ER). These findings advance the knowledge of regulation mechanism of cellulase synthesis in filamentous fungi, which is the basis for rationally engineering T. reesei strains to improve cellulase production in industry. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01809-1.
Collapse
Affiliation(s)
- Ai-Ping Pang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yongsheng Luo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xin Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Funing Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Haiyan Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yichen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Samran Durrani
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Chengcheng Li
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiaotong Shi
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Fu-Gen Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Bing-Zhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
| | - Fengming Lin
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
| |
Collapse
|
24
|
Ramírez AS, Nosol K, Locher KP. Production of Human ABC Transporters and Oligosaccharyltransferase Complexes for Structural Studies. Methods Mol Biol 2022; 2507:273-294. [PMID: 35773587 DOI: 10.1007/978-1-0716-2368-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Structural studies of membrane proteins require high-quality samples. The target proteins should not only be pure and homogeneous but should also be active and allow the capture of a functionally relevant state. Here we present optimized methods for the expression and purification of human ABC transporters and oligosaccharyltransferase (OST) complexes that can be used for high-resolution structure determination using single-particle cryo-electron microscopy (cryo-EM). The protocols are based on the generation of stable cell lines that enable tetracycline-inducible expression of the target proteins. For the multidrug exporter ABCB1, we describe a protocol for reconstitution into nanodiscs and evaluation of the ATPase activity in the presence of drugs. For human OST, we describe a strategy for the purification of OST-A and OST-B complexes, including techniques to evaluate their integrity and activity using in vitro glycosylation assays. These protocols can be adapted for the production of other human ABC transporters and multimeric membrane protein complexes.
Collapse
Affiliation(s)
- Ana S Ramírez
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Kamil Nosol
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Kaspar P Locher
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland.
| |
Collapse
|
25
|
Tirincsi A, Sicking M, Hadzibeganovic D, Haßdenteufel S, Lang S. The Molecular Biodiversity of Protein Targeting and Protein Transport Related to the Endoplasmic Reticulum. Int J Mol Sci 2021; 23:143. [PMID: 35008565 PMCID: PMC8745461 DOI: 10.3390/ijms23010143] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
Looking at the variety of the thousands of different polypeptides that have been focused on in the research on the endoplasmic reticulum from the last five decades taught us one humble lesson: no one size fits all. Cells use an impressive array of components to enable the safe transport of protein cargo from the cytosolic ribosomes to the endoplasmic reticulum. Safety during the transit is warranted by the interplay of cytosolic chaperones, membrane receptors, and protein translocases that together form functional networks and serve as protein targeting and translocation routes. While two targeting routes to the endoplasmic reticulum, SRP (signal recognition particle) and GET (guided entry of tail-anchored proteins), prefer targeting determinants at the N- and C-terminus of the cargo polypeptide, respectively, the recently discovered SND (SRP-independent) route seems to preferentially cater for cargos with non-generic targeting signals that are less hydrophobic or more distant from the termini. With an emphasis on targeting routes and protein translocases, we will discuss those functional networks that drive efficient protein topogenesis and shed light on their redundant and dynamic nature in health and disease.
Collapse
Affiliation(s)
- Andrea Tirincsi
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Mark Sicking
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Drazena Hadzibeganovic
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Sarah Haßdenteufel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| |
Collapse
|
26
|
Mycolactone enhances the Ca2+ leak from endoplasmic reticulum by trapping Sec61 translocons in a Ca2+ permeable state. Biochem J 2021; 478:4005-4024. [PMID: 34726690 PMCID: PMC8650850 DOI: 10.1042/bcj20210345] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 10/19/2021] [Accepted: 11/02/2021] [Indexed: 01/17/2023]
Abstract
The Mycobacterium ulcerans exotoxin, mycolactone, is an inhibitor of co-translational translocation via the Sec61 complex. Mycolactone has previously been shown to bind to, and alter the structure of the major translocon subunit Sec61α, and change its interaction with ribosome nascent chain complexes. In addition to its function in protein translocation into the ER, Sec61 also plays a key role in cellular Ca2+ homeostasis, acting as a leak channel between the endoplasmic reticulum (ER) and cytosol. Here, we have analysed the effect of mycolactone on cytosolic and ER Ca2+ levels using compartment-specific sensors. We also used molecular docking analysis to explore potential interaction sites for mycolactone on translocons in various states. These results show that mycolactone enhances the leak of Ca2+ ions via the Sec61 translocon, resulting in a slow but substantial depletion of ER Ca2+. This leak was dependent on mycolactone binding to Sec61α because resistance mutations in this protein completely ablated the increase. Molecular docking supports the existence of a mycolactone-binding transient inhibited state preceding translocation and suggests mycolactone may also bind Sec61α in its idle state. We propose that delayed ribosomal release after translation termination and/or translocon ‘breathing' during rapid transitions between the idle and intermediate-inhibited states allow for transient Ca2+ leak, and mycolactone's stabilisation of the latter underpins the phenotype observed.
Collapse
|
27
|
Jung SJ, Kim H. Emerging View on the Molecular Functions of Sec62 and Sec63 in Protein Translocation. Int J Mol Sci 2021; 22:ijms222312757. [PMID: 34884562 PMCID: PMC8657602 DOI: 10.3390/ijms222312757] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 12/18/2022] Open
Abstract
Most secreted and membrane proteins are targeted to and translocated across the endoplasmic reticulum (ER) membrane through the Sec61 protein-conducting channel. Evolutionarily conserved Sec62 and Sec63 associate with the Sec61 channel, forming the Sec complex and mediating translocation of a subset of proteins. For the last three decades, it has been thought that ER protein targeting and translocation occur via two distinct pathways: signal recognition particle (SRP)-dependent co-translational or SRP-independent, Sec62/Sec63 dependent post-translational translocation pathway. However, recent studies have suggested that ER protein targeting and translocation through the Sec translocon are more intricate than previously thought. This review summarizes the current understanding of the molecular functions of Sec62/Sec63 in ER protein translocation.
Collapse
Affiliation(s)
| | - Hyun Kim
- Correspondence: ; Tel.: +82-2-880-4440; Fax: +82-2-872-1993
| |
Collapse
|
28
|
Take Me Home, Protein Roads: Structural Insights into Signal Peptide Interactions during ER Translocation. Int J Mol Sci 2021; 22:ijms222111871. [PMID: 34769302 PMCID: PMC8584900 DOI: 10.3390/ijms222111871] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/14/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
Cleavable endoplasmic reticulum (ER) signal peptides (SPs) and other non-cleavable signal sequences target roughly a quarter of the human proteome to the ER. These short peptides, mostly located at the N-termini of proteins, are highly diverse. For most proteins targeted to the ER, it is the interactions between the signal sequences and the various ER targeting and translocation machineries such as the signal recognition particle (SRP), the protein-conducting channel Sec61, and the signal peptidase complex (SPC) that determine the proteins’ target location and provide translocation fidelity. In this review, we follow the signal peptide into the ER and discuss the recent insights that structural biology has provided on the governing principles of those interactions.
Collapse
|
29
|
Srinivasan K, Banerjee A, Baid P, Dhur A, Sengupta J. Ribosome-membrane crosstalk: Co-translational targeting pathways of proteins across membranes in prokaryotes and eukaryotes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:163-198. [PMID: 35034718 DOI: 10.1016/bs.apcsb.2021.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ribosomes are the molecular machine of living cells designed for decoding mRNA-encoded genetic information into protein. Being sophisticated machinery, both in design and function, the ribosome not only carries out protein synthesis, but also coordinates several other ribosome-associated cellular processes. One such process is the translocation of proteins across or into the membrane depending on their secretory or membrane-associated nature. These proteins comprise a large portion of a cell's proteome and act as key factors for cellular survival as well as several crucial functional pathways. Protein transport to extra- and intra-cytosolic compartments (across the eukaryotic endoplasmic reticulum (ER) or across the prokaryotic plasma membrane) or insertion into membranes majorly occurs through an evolutionarily conserved protein-conducting channel called translocon (eukaryotic Sec61 or prokaryotic SecYEG channels). Targeting proteins to the membrane-bound translocon may occur via post-translational or co-translational modes and it is often mediated by recognition of an N-terminal signal sequence in the newly synthesizes polypeptide chain. Co-translational translocation is coupled to protein synthesis where the ribosome-nascent chain complex (RNC) itself is targeted to the translocon. Here, in the light of recent advances in structural and functional studies, we discuss our current understanding of the mechanistic models of co-translational translocation, coordinated by the actively translating ribosomes, in prokaryotes and eukaryotes.
Collapse
Affiliation(s)
- Krishnamoorthi Srinivasan
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aneek Banerjee
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priya Baid
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Ankit Dhur
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Jayati Sengupta
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
| |
Collapse
|
30
|
Bhadra P, Helms V. Molecular Modeling of Signal Peptide Recognition by Eukaryotic Sec Complexes. Int J Mol Sci 2021; 22:10705. [PMID: 34639046 PMCID: PMC8509349 DOI: 10.3390/ijms221910705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/17/2021] [Accepted: 09/27/2021] [Indexed: 12/23/2022] Open
Abstract
Here, we review recent molecular modelling and simulation studies of the Sec translocon, the primary component/channel of protein translocation into the endoplasmic reticulum (ER) and bacterial periplasm, respectively. Our focus is placed on the eukaryotic Sec61, but we also mention modelling studies on prokaryotic SecY since both systems operate in related ways. Cryo-EM structures are now available for different conformational states of the Sec61 complex, ranging from the idle or closed state over an inhibited state with the inhibitor mycolactone bound near the lateral gate, up to a translocating state with bound substrate peptide in the translocation pore. For all these states, computational studies have addressed the conformational dynamics of the translocon with respect to the pore ring, the plug region, and the lateral gate. Also, molecular simulations are addressing mechanistic issues of insertion into the ER membrane vs. translocation into the ER, how signal-peptides are recognised at all in the translocation pore, and how accessory proteins affect the Sec61 conformation in the co- and post-translational pathways.
Collapse
Affiliation(s)
| | - Volkhard Helms
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Postfach 15 11 50, 66041 Saarbruecken, Germany;
| |
Collapse
|
31
|
Sicking M, Jung M, Lang S. Lights, Camera, Interaction: Studying Protein-Protein Interactions of the ER Protein Translocase in Living Cells. Int J Mol Sci 2021; 22:10358. [PMID: 34638699 PMCID: PMC8508666 DOI: 10.3390/ijms221910358] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 12/12/2022] Open
Abstract
Various landmark studies have revealed structures and functions of the Sec61/SecY complex in all domains of live demonstrating the conserved nature of this ancestral protein translocase. While the bacterial homolog of the Sec61 complex resides in the plasma membrane, the eukaryotic counterpart manages the transfer of precursor proteins into or across the membrane of the endoplasmic reticulum (ER). Sec61 complexes are accompanied by a set of dynamically recruited auxiliary proteins assisting the transport of certain precursor polypeptides. TRAP and Sec62/Sec63 are two auxiliary protein complexes in mammalian cells that have been characterized by structural and biochemical methods. Using these ER membrane protein complexes for our proof-of-concept study, we aimed to detect interactions of membrane proteins in living mammalian cells under physiological conditions. Bimolecular luminescence complementation and competition was used to demonstrate multiple protein-protein interactions of different topological layouts. In addition to the interaction of the soluble catalytic and regulatory subunits of the cytosolic protein kinase A, we detected interactions of ER membrane proteins that either belong to the same multimeric protein complex (intra-complex interactions: Sec61α-Sec61β, TRAPα-TRAPβ) or protein complexes in juxtaposition (inter-complex interactions: Sec61α-TRAPα, Sec61α-Sec63, and Sec61β-Sec63). In the process, we established further control elements like synthetic peptide complementation for expression profiling of fusion constructs and protease-mediated reporter degradation demonstrating the cytosolic localization of a reporter complementation. Ease of use and flexibility of the approach presented here will spur further research regarding the dynamics of protein-protein interactions in response to changing cellular conditions in living cells.
Collapse
Affiliation(s)
| | | | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (M.S.); (M.J.)
| |
Collapse
|
32
|
Rapid inactivation of the yeast Sec complex selectively blocks transport of post-translationally translocated proteins. J Biol Chem 2021; 297:101171. [PMID: 34492269 PMCID: PMC8503631 DOI: 10.1016/j.jbc.2021.101171] [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: 06/21/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 11/29/2022] Open
Abstract
The yeast endoplasmic reticulum has three distinct protein translocation channels. The heterotrimeric Sec61 and Ssh1 complexes, which bind translating ribosomes, mediate cotranslational translocation of proteins targeted to the endoplasmic reticulum by the signal recognition particle (SRP) and SRP receptor targeting pathway, whereas the heptameric Sec complex has been proposed to mediate ribosome-independent post-translational translocation of proteins with less hydrophobic signal sequences that escape recognition by the SRP. However, multiple reports have proposed that the Sec complex may function cotranslationally and be involved in translocation or integration of SRP-dependent protein translocation substrates. To provide insight into these conflicting views, we induced expression of the tobacco etch virus protease to achieve rapid inactivation of the Sec complex by protease-mediated cleavage within the cytoplasmic domain of the Sec63 protein. Protein translocation assays conducted after tobacco etch virus protease induction revealed a complete block in translocation of two well-characterized substrates of the Sec complex, carboxypeptidase Y (CPY) and Gas1p, when the protease cleavage sites were located at structural domain boundaries in Sec63. However, integration of SRP-dependent membrane protein substrates was not detectably impacted. Moreover, redirecting CPY to the cotranslational pathway by increasing the hydrophobicity of the signal sequence rendered translocation of CPY insensitive to inactivation of the Sec complex. We conclude that the Sec complex is primarily responsible for the translocation of yeast secretome proteins with marginally hydrophobic signal sequences.
Collapse
|
33
|
Cancer associated mutations in Sec61γ alter the permeability of the ER translocase. PLoS Genet 2021; 17:e1009780. [PMID: 34460824 PMCID: PMC8439465 DOI: 10.1371/journal.pgen.1009780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 09/14/2021] [Accepted: 08/16/2021] [Indexed: 11/19/2022] Open
Abstract
Translocation of secretory and integral membrane proteins across or into the ER membrane occurs via the Sec61 complex, a heterotrimeric protein complex possessing two essential sub-units, Sec61p/Sec61α and Sss1p/Sec61γ and the non-essential Sbh1p/Sec61β subunit. In addition to forming a protein conducting channel, the Sec61 complex maintains the ER permeability barrier, preventing flow of molecules and ions. Loss of Sec61 integrity is detrimental and implicated in the progression of disease. The Sss1p/Sec61γ C-terminus is juxtaposed to the key gating module of Sec61p/Sec61α and is important for gating the translocon. Inspection of the cancer genome database identifies six mutations in highly conserved amino acids of Sec61γ/Sss1p. We identify that five out of the six mutations identified affect gating of the ER translocon, albeit with varying strength. Together, we find that mutations in Sec61γ that arise in malignant cells result in altered translocon gating dynamics, this offers the potential for the translocon to represent a target in co-therapy for cancer treatment.
Collapse
|
34
|
Davis MM, Lamichhane R, Bruce BD. Elucidating Protein Translocon Dynamics with Single-Molecule Precision. Trends Cell Biol 2021; 31:569-583. [PMID: 33865650 DOI: 10.1016/j.tcb.2021.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 01/28/2023]
Abstract
Translocons are protein assemblies that facilitate the targeting and transport of proteins into and across biological membranes. Our understanding of these systems has been advanced using genetics, biochemistry, and structural biology. Despite these classic advances, until recently we have still largely lacked a detailed understanding of how translocons recognize and facilitate protein translocation. With the advent and improvements of cryogenic electron microscopy (cryo-EM) single-particle analysis and single-molecule fluorescence microscopy, the details of how translocons function are finally emerging. Here, we introduce these methods and evaluate their importance in understanding translocon structure, function, and dynamics.
Collapse
Affiliation(s)
- Madeline M Davis
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
| | - Rajan Lamichhane
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
| | - Barry D Bruce
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; Department of Microbiology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; Graduate Program in Genome Science and Technology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; Chemical and Biomolecular Engineering, University of Tennessee at Knoxville, Knoxville, TN 37996, USA.
| |
Collapse
|
35
|
Jung SJ, Kim JEH, Junne T, Spiess M, Kim H. Cotranslational Targeting and Posttranslational Translocation can Cooperate in Spc3 Topogenesis. J Mol Biol 2021; 433:167109. [PMID: 34153287 DOI: 10.1016/j.jmb.2021.167109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 11/19/2022]
Abstract
Secretory and membrane proteins follow either the signal recognition particle (SRP)-dependent cotranslational translocation pathway or the SRP-independent Sec62/Sec63-dependent posttranslational pathway for their translocation across the endoplasmic reticulum (ER). However, increasing evidence suggests that most proteins are cotranslationally targeted to the ER, suggesting mixed mechanisms. It remains unclear how these two pathways cooperate. Previous studies have shown that Spc3, a signal-anchored protein, requires SRP and Sec62 for its biogenesis. This study investigated the targeting and topogenesis of Spc3 and the step at which SRP and Sec62 act using in vivo and in vitro translocation assays and co-immunoprecipitation. Our data suggest that Spc3 reaches its final topology in two steps: it enters the ER lumen head-first and then inverts its orientation. The first step is partially dependent on SRP, although independent of the Sec62/Sec63 complex. The second step is mediated by the Sec62/Sec63 complex. These data suggest that SRP and Sec62 act on a distinct step in the topogenesis of Spc3.
Collapse
Affiliation(s)
- Sung-Jun Jung
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea
| | - Ji Eun Hani Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea
| | - Tina Junne
- Biozentrum, University of Basel, Basel, Switzerland
| | | | - Hyun Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea.
| |
Collapse
|
36
|
Sicking M, Lang S, Bochen F, Roos A, Drenth JPH, Zakaria M, Zimmermann R, Linxweiler M. Complexity and Specificity of Sec61-Channelopathies: Human Diseases Affecting Gating of the Sec61 Complex. Cells 2021; 10:1036. [PMID: 33925740 PMCID: PMC8147068 DOI: 10.3390/cells10051036] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 12/14/2022] Open
Abstract
The rough endoplasmic reticulum (ER) of nucleated human cells has crucial functions in protein biogenesis, calcium (Ca2+) homeostasis, and signal transduction. Among the roughly one hundred components, which are involved in protein import and protein folding or assembly, two components stand out: The Sec61 complex and BiP. The Sec61 complex in the ER membrane represents the major entry point for precursor polypeptides into the membrane or lumen of the ER and provides a conduit for Ca2+ ions from the ER lumen to the cytosol. The second component, the Hsp70-type molecular chaperone immunoglobulin heavy chain binding protein, short BiP, plays central roles in protein folding and assembly (hence its name), protein import, cellular Ca2+ homeostasis, and various intracellular signal transduction pathways. For the purpose of this review, we focus on these two components, their relevant allosteric effectors and on the question of how their respective functional cycles are linked in order to reconcile the apparently contradictory features of the ER membrane, selective permeability for precursor polypeptides, and impermeability for Ca2+. The key issues are that the Sec61 complex exists in two conformations: An open and a closed state that are in a dynamic equilibrium with each other, and that BiP contributes to its gating in both directions in cooperation with different co-chaperones. While the open Sec61 complex forms an aqueous polypeptide-conducting- and transiently Ca2+-permeable channel, the closed complex is impermeable even to Ca2+. Therefore, we discuss the human hereditary and tumor diseases that are linked to Sec61 channel gating, termed Sec61-channelopathies, as disturbances of selective polypeptide-impermeability and/or aberrant Ca2+-permeability.
Collapse
Affiliation(s)
- Mark Sicking
- Department of Medical Biochemistry & Molecular Biology, Saarland University, D-66421 Homburg, Germany;
| | - Sven Lang
- Department of Medical Biochemistry & Molecular Biology, Saarland University, D-66421 Homburg, Germany;
| | - Florian Bochen
- Department of Otorhinolaryngology, Head and Neck Surgery, Saarland University Medical Center, D-66421 Homburg, Germany; (F.B.); (M.L.)
| | - Andreas Roos
- Department of Neuropediatrics, Essen University Hospital, D-45147 Essen, Germany;
| | - Joost P. H. Drenth
- Department of Molecular Gastroenterology and Hepatology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Muhammad Zakaria
- Department of Genetics, Hazara University, Mansehra 21300, Pakistan;
| | - Richard Zimmermann
- Department of Medical Biochemistry & Molecular Biology, Saarland University, D-66421 Homburg, Germany;
| | - Maximilian Linxweiler
- Department of Otorhinolaryngology, Head and Neck Surgery, Saarland University Medical Center, D-66421 Homburg, Germany; (F.B.); (M.L.)
| |
Collapse
|
37
|
Amphipathic environments for determining the structure of membrane proteins by single-particle electron cryo-microscopy. Q Rev Biophys 2021; 54:e6. [PMID: 33785082 DOI: 10.1017/s0033583521000044] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past decade, the structural biology of membrane proteins (MPs) has taken a new turn thanks to epoch-making technical progress in single-particle electron cryo-microscopy (cryo-EM) as well as to improvements in sample preparation. The present analysis provides an overview of the extent and modes of usage of the various types of surfactants for cryo-EM studies. Digitonin, dodecylmaltoside, protein-based nanodiscs, lauryl maltoside-neopentyl glycol, glyco-diosgenin, and amphipols (APols) are the most popular surfactants at the vitrification step. Surfactant exchange is frequently used between MP purification and grid preparation, requiring extensive optimization each time the study of a new MP is undertaken. The variety of both the surfactants and experimental approaches used over the past few years bears witness to the need to continue developing innovative surfactants and optimizing conditions for sample preparation. The possibilities offered by novel APols for EM applications are discussed.
Collapse
|
38
|
Bhadra P, Yadhanapudi L, Römisch K, Helms V. How does Sec63 affect the conformation of Sec61 in yeast? PLoS Comput Biol 2021; 17:e1008855. [PMID: 33780447 PMCID: PMC8031780 DOI: 10.1371/journal.pcbi.1008855] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/08/2021] [Accepted: 03/05/2021] [Indexed: 12/31/2022] Open
Abstract
The Sec complex catalyzes the translocation of proteins of the secretory pathway into the endoplasmic reticulum and the integration of membrane proteins into the endoplasmic reticulum membrane. Some substrate peptides require the presence and involvement of accessory proteins such as Sec63. Recently, a structure of the Sec complex from Saccharomyces cerevisiae, consisting of the Sec61 channel and the Sec62, Sec63, Sec71 and Sec72 proteins was determined by cryo-electron microscopy (cryo-EM). Here, we show by co-precipitation that the Sec61 channel subunit Sbh1 is not required for formation of stable Sec63-Sec61 contacts. Molecular dynamics simulations started from the cryo-EM conformation of Sec61 bound to Sec63 and of unbound Sec61 revealed how Sec63 affects the conformation of Sec61 lateral gate, plug, pore region and pore ring diameter via three intermolecular contact regions. Molecular docking of SRP-dependent vs. SRP-independent signal peptide chains into the Sec61 channel showed that the pore regions affected by presence/absence of Sec63 play a crucial role in positioning the signal anchors of SRP-dependent substrates nearby the lateral gate.
Collapse
Affiliation(s)
- Pratiti Bhadra
- Center for Bioinformatics, Saarland University, Saarbrücken, Saarland, Germany
| | - Lalitha Yadhanapudi
- Faculty of Natural Sciences and Technology, Saarland University, Saarbrücken, Saarland, Germany
| | - Karin Römisch
- Faculty of Natural Sciences and Technology, Saarland University, Saarbrücken, Saarland, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Saarland, Germany
| |
Collapse
|
39
|
Endoplasmic reticulum composition and form: Proteins in and out. Curr Opin Cell Biol 2021; 71:1-6. [PMID: 33611096 DOI: 10.1016/j.ceb.2021.01.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 02/07/2023]
Abstract
The endoplasmic reticulum (ER) is the main harbor for newly synthesized proteins in eukaryotic cells. Through a continuous membrane network of sheets and tubules, the ER hosts secretory proteins, integral membrane proteins, and luminal proteins of the endomembrane system. These proteins are translated by ribosomes outside the ER and require subsequent integration into or translocation across the lipid bilayer of the ER. They are then modified post-translationally and folded in the ER. Some of these proteins are packaged into coat protein complex II-coated vesicles for export. Here, we review recent advances in understanding the mechanism of protein translocation and transmembrane domain insertion in the ER, summarize new insights into selective cargo packaging, and discuss the roles of ER morphological dynamics in these processes.
Collapse
|
40
|
Alva TR, Riera M, Chartron JW. Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaffii. Microb Cell Fact 2021; 20:19. [PMID: 33472617 PMCID: PMC7816318 DOI: 10.1186/s12934-020-01489-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/29/2020] [Indexed: 11/24/2022] Open
Abstract
Background Eukaryotes use distinct networks of biogenesis factors to synthesize, fold, monitor, traffic, and secrete proteins. During heterologous expression, saturation of any of these networks may bottleneck titer and yield. To understand the flux through various routes into the early secretory pathway, we quantified the global and membrane-associated translatomes of Komagataella phaffii. Results By coupling Ribo-seq with long-read mRNA sequencing, we generated a new annotation of protein-encoding genes. By using Ribo-seq with subcellular fractionation, we quantified demands on co- and posttranslational translocation pathways. During exponential growth in rich media, protein components of the cell-wall represent the greatest number of nascent chains entering the ER. Transcripts encoding the transmembrane protein PMA1 sequester more ribosomes at the ER membrane than any others. Comparison to Saccharomyces cerevisiae reveals conservation in the resources allocated by gene ontology, but variation in the diversity of gene products entering the secretory pathway. Conclusion A subset of host proteins, particularly cell-wall components, impose the greatest biosynthetic demands in the early secretory pathway. These proteins are potential targets in strain engineering aimed at alleviating bottlenecks during heterologous protein production.
Collapse
Affiliation(s)
- Troy R Alva
- Department of Bioengineering, University of California, Riverside, 92521, United States of America.
| | - Melanie Riera
- Department of Bioengineering, University of California, Riverside, 92521, United States of America
| | - Justin W Chartron
- Department of Bioengineering, University of California, Riverside, 92521, United States of America.,Protabit LLC, 1010 E Union St Suite 110, Pasadena, California, 91106, United States of America
| |
Collapse
|
41
|
Wang L, Ye Y. Clearing Traffic Jams During Protein Translocation Across Membranes. Front Cell Dev Biol 2021; 8:610689. [PMID: 33490075 PMCID: PMC7820333 DOI: 10.3389/fcell.2020.610689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
Protein translocation across membranes is a critical facet of protein biogenesis in compartmentalized cells as proteins synthesized in the cytoplasm often need to traverse across lipid bilayers via proteinaceous channels to reach their final destinations. It is well established that protein biogenesis is tightly linked to various protein quality control processes, which monitor errors in protein folding, modification, and localization. However, little is known about how cells cope with translocation defective polypeptides that clog translocation channels (translocons) during protein translocation. This review summarizes recent studies, which collectively reveal a set of translocon-associated quality control strategies for eliminating polypeptides stuck in protein-conducting channels in the endoplasmic reticulum and mitochondria.
Collapse
Affiliation(s)
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
42
|
Itskanov S, Kuo KM, Gumbart JC, Park E. Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62. Nat Struct Mol Biol 2021; 28:162-172. [PMID: 33398175 PMCID: PMC8236211 DOI: 10.1038/s41594-020-00541-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 11/12/2020] [Indexed: 12/12/2022]
Abstract
Many proteins are transported into the endoplasmic reticulum by the universally conserved Sec61 channel. Post-translational transport requires two additional proteins, Sec62 and Sec63, but their functions are poorly defined. Here, we determined cryo-EM structures of several variants of Sec61–Sec62–Sec63 complexes from Saccharomyces cerevisiae and Thermomyces lanuginosus and show that Sec62 and Sec63 induce opening of the Sec61 channel. Without Sec62, the translocation pore of Sec61 remains closed by the plug domain, rendering the channel inactive. We further show that the lateral gate of Sec61 must first be partially opened by interactions between Sec61 and Sec63 in cytosolic and lumenal domains, a simultaneous disruption of which completely closes the channel. The structures and molecular dynamics simulations suggest that Sec62 may also prevent lipids from invading the channel through the open lateral gate. Our study shows how Sec63 and Sec62 work together in a hierarchical manner to activate Sec61 for post-translational protein translocation.
Collapse
Affiliation(s)
- Samuel Itskanov
- Biophysics Graduate Program, University of California, Berkeley, CA, USA
| | - Katie M Kuo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - James C Gumbart
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.,School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Eunyong Park
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. .,California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
| |
Collapse
|
43
|
Li X, Sun S, Appathurai S, Sundaram A, Plumb R, Mariappan M. A Molecular Mechanism for Turning Off IRE1α Signaling during Endoplasmic Reticulum Stress. Cell Rep 2020; 33:108563. [PMID: 33378667 PMCID: PMC7809255 DOI: 10.1016/j.celrep.2020.108563] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/14/2020] [Accepted: 12/06/2020] [Indexed: 12/15/2022] Open
Abstract
Misfolded proteins in the endoplasmic reticulum (ER) activate IRE1α endoribonuclease in mammalian cells, which mediates XBP1 mRNA splicing to produce an active transcription factor. This promotes the expression of specific genes to alleviate ER stress, thereby attenuating IRE1α. Although sustained activation of IRE1α is linked to human diseases, it is not clear how IRE1α is attenuated during ER stress. Here, we identify that Sec63 is a subunit of the previously identified IRE1α/Sec61 translocon complex. We find that Sec63 recruits and activates BiP ATPase through its luminal J-domain to bind onto IRE1α. This leads to inhibition of higher-order oligomerization and attenuation of IRE1α RNase activity during prolonged ER stress. In Sec63-deficient cells, IRE1α remains activated for a long period of time despite the presence of excess BiP in the ER. Thus, our data suggest that the Sec61 translocon bridges IRE1α with Sec63/BiP to regulate the dynamics of IRE1α signaling in cells. The stress sensor IRE1α is attenuated during prolonged ER stress by a poorly understood mechanism. Li et al. show that IRE1α forms a complex with the Sec61/Sec63 translocon in cells. Sec63 mediates BiP binding to IRE1α and thereby inhibits IRE1α oligomerization and attenuates IRE1α signaling during prolonged ER stress.
Collapse
Affiliation(s)
- Xia Li
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT 06516, USA
| | - Sha Sun
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT 06516, USA
| | - Suhila Appathurai
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT 06516, USA
| | - Arunkumar Sundaram
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT 06516, USA
| | - Rachel Plumb
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT 06516, USA
| | - Malaiyalam Mariappan
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT 06516, USA.
| |
Collapse
|
44
|
Weng TH, Steinchen W, Beatrix B, Berninghausen O, Becker T, Bange G, Cheng J, Beckmann R. Architecture of the active post-translational Sec translocon. EMBO J 2020; 40:e105643. [PMID: 33305433 PMCID: PMC7849165 DOI: 10.15252/embj.2020105643] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 01/19/2023] Open
Abstract
In eukaryotes, most secretory and membrane proteins are targeted by an N‐terminal signal sequence to the endoplasmic reticulum, where the trimeric Sec61 complex serves as protein‐conducting channel (PCC). In the post‐translational mode, fully synthesized proteins are recognized by a specialized channel additionally containing the Sec62, Sec63, Sec71, and Sec72 subunits. Recent structures of this Sec complex in the idle state revealed the overall architecture in a pre‐opened state. Here, we present a cryo‐EM structure of the yeast Sec complex bound to a substrate, and a crystal structure of the Sec62 cytosolic domain. The signal sequence is inserted into the lateral gate of Sec61α similar to previous structures, yet, with the gate adopting an even more open conformation. The signal sequence is flanked by two Sec62 transmembrane helices, the cytoplasmic N‐terminal domain of Sec62 is more rigidly positioned, and the plug domain is relocated. We crystallized the Sec62 domain and mapped its interaction with the C‐terminus of Sec63. Together, we obtained a near‐complete and integrated model of the active Sec complex.
Collapse
Affiliation(s)
- Tsai-Hsuan Weng
- Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Wieland Steinchen
- Department of Chemistry, SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Birgitta Beatrix
- Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Otto Berninghausen
- Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Thomas Becker
- Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Gert Bange
- Department of Chemistry, SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Jingdong Cheng
- Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Roland Beckmann
- Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany
| |
Collapse
|
45
|
Cohen MJ, Chirico WJ, Lipke PN. Through the back door: Unconventional protein secretion. Cell Surf 2020; 6:100045. [PMID: 33225116 PMCID: PMC7666356 DOI: 10.1016/j.tcsw.2020.100045] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/08/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022] Open
Abstract
Proteins are secreted from eukaryotic cells by several mechanisms besides the well-characterized classical secretory system. Proteins destined to enter the classical secretory system contain a signal peptide for translocation into the endoplasmic reticulum. However, many proteins lacking a signal peptide are secreted nonetheless. Contrary to conventional belief, these proteins are not just released as a result of membrane damage leading to cell leakage, but are actively packaged for secretion in alternative pathways. They are called unconventionally secreted proteins, and the best-characterized are from fungi and mammals. These proteins have extracellular functions including cell signaling, immune modulation, as well as moonlighting activities different from their well-described intracellular functions. Among the pathways for unconventional secretion are direct transfer across the plasma membrane, release within plasma membrane-derived microvesicles, use of elements of autophagy, or secretion from endosomal/multivesicular body-related components. We review the fungal and metazoan unconventional secretory pathways and their regulation, and propose experimental criteria to identify their mode of secretion.
Collapse
Affiliation(s)
- Michael J. Cohen
- The Graduate Center of the City University of New York, United States
- Biology Department, Brooklyn College of the City University of New York, United States
| | - William J. Chirico
- Department of Cell Biology, Molecular and Cellular Biology Program, SUNY Downstate Medical Center, United States
| | - Peter N. Lipke
- The Graduate Center of the City University of New York, United States
- Biology Department, Brooklyn College of the City University of New York, United States
| |
Collapse
|
46
|
Sun S, Mariappan M. C-terminal tail length guides insertion and assembly of membrane proteins. J Biol Chem 2020; 295:15498-15510. [PMID: 32878985 DOI: 10.1074/jbc.ra120.012992] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 08/27/2020] [Indexed: 11/06/2022] Open
Abstract
A large number of newly synthesized membrane proteins in the endoplasmic reticulum (ER) are assembled into multiprotein complexes, but little is known about the mechanisms required for assembly membrane proteins. It has been suggested that membrane chaperones might exist, akin to the molecular chaperones that stabilize and direct the assembly of soluble protein complexes, but the mechanisms by which these proteins would bring together membrane protein components is unclear. Here, we have identified that the tail length of the C-terminal transmembrane domains (C-TMDs) determines efficient insertion and assembly of membrane proteins in the ER. We found that membrane proteins with C-TMD tails shorter than ∼60 amino acids are poorly inserted into the ER membrane, which suggests that translation is terminated before they are recognized by the Sec61 translocon for insertion. These C-TMDs with insufficient hydrophobicity are post-translationally recognized and retained by the Sec61 translocon complex, providing a time window for efficient assembly with TMDs from partner proteins. Retained TMDs that fail to assemble with their cognate TMDs are slowly translocated into the ER lumen and are recognized by the ER-associated degradation (ERAD) pathway for removal. In contrast, C-TMDs with sufficient hydrophobicity or tails longer than ∼80 residues are quickly released from the Sec61 translocon into the membrane or the ER lumen, resulting in inefficient assembly with partner TMDs. Thus, our data suggest that C-terminal tails harbor crucial signals for both the insertion and assembly of membrane proteins.
Collapse
Affiliation(s)
- Sha Sun
- Frome the Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, Connecticut, USA
| | - Malaiyalam Mariappan
- Frome the Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, Connecticut, USA.
| |
Collapse
|
47
|
Xia D. Structural snapshots of the cellular folded protein translocation machinery Bcs1. FEBS J 2020; 288:2870-2883. [PMID: 32979284 PMCID: PMC7994207 DOI: 10.1111/febs.15576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/05/2020] [Accepted: 09/22/2020] [Indexed: 11/29/2022]
Abstract
Proteins destined to various intra‐ and extra‐cellular locations must traverse membranes most frequently in an unfolded form. When the proteins being translocated need to remain in a folded state, specialized cellular transport machinery is used. One such machine is the membrane‐bound AAA protein Bcs1 (Bcs1), which assists the iron‐sulfur protein, an essential subunit of the respiratory Complex III, across the mitochondrial inner membrane. Recent structure determinations of mouse and yeast Bcs1 in three different nucleotide states reveal its homo‐heptameric association and at least two dramatically different conformations. The apo and ADP‐bound structures are similar, both containing a large substrate‐binding cavity accessible to the mitochondrial matrix space, which contracts by concerted motion of the ATPase domains upon ATP binding, suggesting that bound substrate could then be pushed across the membrane. ATP hydrolysis drives substrate release and resets Bcs1 conformation back to the apo/ADP form. These structures shed new light on the mechanism of folded protein translocation across a membrane, provide better understanding on the assembly process of the respiratory Complex III, and correlate clinical presentations of disease‐associated mutations with their locations in the 3D structure.
Collapse
Affiliation(s)
- Di Xia
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
48
|
Runnebohm AM, Richards KA, Irelan CB, Turk SM, Vitali HE, Indovina CJ, Rubenstein EM. Overlapping function of Hrd1 and Ste24 in translocon quality control provides robust channel surveillance. J Biol Chem 2020; 295:16113-16120. [PMID: 33033070 DOI: 10.1074/jbc.ac120.016191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/06/2020] [Indexed: 12/20/2022] Open
Abstract
Translocation of proteins across biological membranes is essential for life. Proteins that clog the endoplasmic reticulum (ER) translocon prevent the movement of other proteins into the ER. Eukaryotes have multiple translocon quality control (TQC) mechanisms to detect and destroy proteins that persistently engage the translocon. TQC mechanisms have been defined using a limited panel of substrates that aberrantly occupy the channel. The extent of substrate overlap among TQC pathways is unknown. In this study, we found that two TQC enzymes, the ER-associated degradation ubiquitin ligase Hrd1 and zinc metalloprotease Ste24, promote degradation of characterized translocon-associated substrates of the other enzyme in Saccharomyces cerevisiae Although both enzymes contribute to substrate turnover, our results suggest a prominent role for Hrd1 in TQC. Yeast lacking both Hrd1 and Ste24 exhibit a profound growth defect, consistent with overlapping function. Remarkably, two mutations that mildly perturb post-translational translocation and reduce the extent of aberrant translocon engagement by a model substrate diminish cellular dependence on TQC enzymes. Our data reveal previously unappreciated mechanistic complexity in TQC substrate detection and suggest that a robust translocon surveillance infrastructure maintains functional and efficient translocation machinery.
Collapse
Affiliation(s)
| | - Kyle A Richards
- Department of Biology, Ball State University, Muncie, Indiana, USA
| | | | - Samantha M Turk
- Department of Biology, Ball State University, Muncie, Indiana, USA
| | - Halie E Vitali
- Department of Biology, Ball State University, Muncie, Indiana, USA
| | | | | |
Collapse
|
49
|
Wu M, Lander GC. How low can we go? Structure determination of small biological complexes using single-particle cryo-EM. Curr Opin Struct Biol 2020; 64:9-16. [PMID: 32599507 PMCID: PMC7666008 DOI: 10.1016/j.sbi.2020.05.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 05/07/2020] [Accepted: 05/19/2020] [Indexed: 12/26/2022]
Abstract
For decades, high-resolution structural studies of biological macromolecules with masses of <200kDa by cryo-EM single-particle analysis were considered infeasible. It was not until several years after the advent of direct detectors that the overlooked potential of cryo-EM for studying small complexes was first realized. Subsequent advances in sample preparation, imaging, and data processing algorithms have improved our ability to visualize small biological targets. In the past two years alone, nearly two hundred high-resolution structures have been determined of small (<200kDa) macromolecules, the smallest being approximately 39kDa in molecular weight. Here we summarize some salient lessons and strategies for cryo-EM studies of small biological complexes, and also consider future prospects for routine structure determination.
Collapse
Affiliation(s)
- Mengyu Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States.
| |
Collapse
|
50
|
Kriegler T, Lang S, Notari L, Hessa T. Prion Protein Translocation Mechanism Revealed by Pulling Force Studies. J Mol Biol 2020; 432:4447-4465. [PMID: 32502491 DOI: 10.1016/j.jmb.2020.05.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/10/2020] [Accepted: 05/28/2020] [Indexed: 11/26/2022]
Abstract
The mammalian prion protein (PrP) engages with the ribosome-Sec61 translocation channel complex to generate different topological variants that are either physiological, or involved in neurodegenerative diseases. Here, we describe cotranslational folding and translocation mechanisms of PrP coupled to an Xbp1-based arrest peptide as folding sensor, to measure forces acting on PrP nascent chain. Our data reveal two main pulling events followed by a minor third one exerted on the nascent chains during their translocation. Using those force landscapes, we show that a specific sequence within an intrinsically disordered region, containing a polybasic and glycine-proline rich residues, modulates the second pulling event by interacting with TRAP complex. This work also delineates the sequence of events involved in generation of PrP toxic transmembrane topologies during its synthesis. Our results shed new insight into the folding of such a topological complex protein, where marginal pulling by the signal sequence, together with the flanking downstream sequence in the mature domain, primarily drives an overall inefficient translocation resulting in the nascent chain to adopt alternative topologies.
Collapse
Affiliation(s)
- Theresa Kriegler
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, Svante Arrhenius väg 16C, SE-10691 Stockholm, Sweden
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Luigi Notari
- Department of Clinical Neuroscience, Therapeutic Immune Design Unit, CMM, L8:02, Karolinska Institutet, Sweden
| | - Tara Hessa
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, Svante Arrhenius väg 16C, SE-10691 Stockholm, Sweden.
| |
Collapse
|