1
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Gemmer M, Chaillet ML, Förster F. Exploring the molecular composition of the multipass translocon in its native membrane environment. Life Sci Alliance 2024; 7:e202302496. [PMID: 38866426 PMCID: PMC11169918 DOI: 10.26508/lsa.202302496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024] Open
Abstract
Multispanning membrane proteins are inserted into the endoplasmic reticulum membrane by the ribosome-bound multipass translocon (MPT) machinery. Based on cryo-electron tomography and extensive subtomogram analysis, we reveal the composition and arrangement of ribosome-bound MPT components in their native membrane environment. The intramembrane chaperone complex PAT and the translocon-associated protein (TRAP) complex associate substoichiometrically with the MPT in a translation-dependent manner. Although PAT is preferentially part of MPTs bound to translating ribosomes, the abundance of TRAP is highest in MPTs associated with non-translating ribosomes. The subtomogram average of the TRAP-containing MPT reveals intermolecular contacts between the luminal domains of TRAP and an unknown subunit of the back-of-Sec61 complex. AlphaFold modeling suggests this protein is nodal modulator, bridging the luminal domains of nicalin and TRAPα. Collectively, our results visualize the variability of MPT factors in the native membrane environment dependent on the translational activity of the bound ribosome.
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Affiliation(s)
- Max Gemmer
- https://ror.org/04pp8hn57 Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Marten L Chaillet
- https://ror.org/04pp8hn57 Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Friedrich Förster
- https://ror.org/04pp8hn57 Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
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2
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Egly CL, Barny LA, Do T, McDonald EF, Knollmann BC, Plate L. The proteostasis interactomes of trafficking-deficient variants of the voltage-gated potassium channel K V11.1 associated with Long QT Syndrome. J Biol Chem 2024:107465. [PMID: 38876300 DOI: 10.1016/j.jbc.2024.107465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/16/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024] Open
Abstract
The voltage-gated potassium ion channel KV11.1 plays a critical role in cardiac repolarization. Genetic variants that render Kv11.1 dysfunctional cause Long QT Syndrome (LQTS), which is associated with fatal arrhythmias. Approximately 90% of LQTS-associated variants cause intracellular protein transport (trafficking) dysfunction, which pharmacological chaperones like E-4031 can rescue. Protein folding and trafficking decisions are regulated by chaperones, protein quality control factors, and trafficking machinery comprising the cellular proteostasis network. Here, we test whether trafficking dysfunction is associated with alterations in the proteostasis network of pathogenic Kv11.1 variants and whether pharmacological chaperones can normalize the proteostasis network of responsive variants. We used affinity-purification coupled with tandem mass tag-based quantitative mass spectrometry to assess protein interaction changes of wild-type (WT) KV11.1 or trafficking-deficient channel variants in the presence or absence of E4031. We identified 572 core KV11.1 protein interactors. Trafficking-deficient variants KV11.1-G601S and KV11.1-G601S-G965* had significantly increased interactions with proteins responsible for folding, trafficking, and degradation compared to WT. We confirmed previous findings that the proteasome is critical for KV11.1 degradation. Our report provides the first comprehensive characterization of protein quality control mechanisms of KV11.1. We find extensive interactome remodeling associated with trafficking-deficient KV11.1 variants, and with pharmacological chaperone rescue of KV11.1 cell surface expression. The identified protein interactions could be targeted therapeutically to improve KV11.1 trafficking and treat Long QT Syndrome.
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Affiliation(s)
| | - Lea A Barny
- Program in Chemical and Physical Biology, Vanderbilt University; Department of Chemistry, Vanderbilt University
| | - Tri Do
- Department of Medicine, Vanderbilt University Medical Center
| | | | | | - Lars Plate
- Department of Chemistry, Vanderbilt University; Department of Biological Sciences, Vanderbilt University; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center.
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3
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Duart G, Graña-Montes R, Pastor-Cantizano N, Mingarro I. Experimental and computational approaches for membrane protein insertion and topology determination. Methods 2024; 226:102-119. [PMID: 38604415 DOI: 10.1016/j.ymeth.2024.03.012] [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] [Received: 11/07/2023] [Revised: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
Membrane proteins play pivotal roles in a wide array of cellular processes and constitute approximately a quarter of the protein-coding genes across all organisms. Despite their ubiquity and biological significance, our understanding of these proteins remains notably less comprehensive compared to their soluble counterparts. This disparity in knowledge can be attributed, in part, to the inherent challenges associated with employing specialized techniques for the investigation of membrane protein insertion and topology. This review will center on a discussion of molecular biology methodologies and computational prediction tools designed to elucidate the insertion and topology of helical membrane proteins.
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Affiliation(s)
- Gerard Duart
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Ricardo Graña-Montes
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Noelia Pastor-Cantizano
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Ismael Mingarro
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain.
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4
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Chen S, Collart MA. Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression. J Mol Biol 2024; 436:168579. [PMID: 38648968 DOI: 10.1016/j.jmb.2024.168579] [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] [Received: 10/30/2023] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Gene expression is a fundamental and highly regulated process involving a series of tightly coordinated steps, including transcription, post-transcriptional processing, translation, and post-translational modifications. A growing number of studies have revealed an additional layer of complexity in gene expression through the phenomenon of mRNA subcellular localization. mRNAs can be organized into membraneless subcellular structures within both the cytoplasm and the nucleus, but they can also targeted to membranes. In this review, we will summarize in particular our knowledge on localization of mRNAs to organelles, focusing on important regulators and available techniques for studying organellar localization, and significance of this localization in the broader context of gene expression regulation.
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Affiliation(s)
- Siyu Chen
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
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5
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Hegde RS, Keenan RJ. A unifying model for membrane protein biogenesis. Nat Struct Mol Biol 2024:10.1038/s41594-024-01296-5. [PMID: 38811793 DOI: 10.1038/s41594-024-01296-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/25/2024] [Indexed: 05/31/2024]
Abstract
α-Helical integral membrane proteins comprise approximately 25% of the proteome in all organisms. The membrane proteome is highly diverse, varying in the number, topology, spacing and properties of transmembrane domains. This diversity imposes different constraints on the insertion of different regions of a membrane protein into the lipid bilayer. Here, we present a cohesive framework to explain membrane protein biogenesis, in which different parts of a nascent substrate are triaged between Oxa1 and SecY family members for insertion. In this model, Oxa1 family proteins insert transmembrane domains flanked by short translocated segments, whereas the SecY channel is required for insertion of transmembrane domains flanked by long translocated segments. Our unifying model rationalizes evolutionary, genetic, biochemical and structural data across organisms and provides a foundation for future mechanistic studies of membrane protein biogenesis.
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Affiliation(s)
- Ramanujan S Hegde
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Robert J Keenan
- Gordon Center for Integrative Science, The University of Chicago, Chicago, IL, USA.
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6
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Vismpas D, Förster F. RAMPing up knowledge of the translocon. eLife 2024; 13:e98548. [PMID: 38787756 PMCID: PMC11126307 DOI: 10.7554/elife.98548] [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: 05/26/2024] Open
Abstract
Advanced cryo-EM approaches reveal surprising insights into the molecular structure that allows nascent proteins to be inserted into the membrane of the endoplasmic reticulum.
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Affiliation(s)
- Dimitrios Vismpas
- Bijvoet Center for Biomolecular Research, Utrecht UniversityUtrechtNetherlands
| | - Friedrich Förster
- Bijvoet Center for Biomolecular Research, Utrecht UniversityUtrechtNetherlands
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7
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Hegde RS. Getting membrane proteins into shape. Mol Cell 2024; 84:1821-1823. [PMID: 38759622 DOI: 10.1016/j.molcel.2024.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2024]
Abstract
In this issue, Ji et al.1 show how a multipass membrane protein that initially inserts into the endoplasmic reticulum in a mostly inverted topology is post-translationally dislocated, re-inserted, and folded with the help of ATP13A1, a P-type ATPase.
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8
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Ji J, Cui MK, Zou R, Wu MZ, Ge MX, Li J, Zhang ZR. An ATP13A1-assisted topogenesis pathway for folding multi-spanning membrane proteins. Mol Cell 2024; 84:1917-1931.e15. [PMID: 38723633 DOI: 10.1016/j.molcel.2024.04.010] [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] [Received: 06/27/2023] [Revised: 02/15/2024] [Accepted: 04/17/2024] [Indexed: 05/19/2024]
Abstract
Many multi-spanning membrane proteins contain poorly hydrophobic transmembrane domains (pTMDs) protected from phospholipid in mature structure. Nascent pTMDs are difficult for translocon to recognize and insert. How pTMDs are discerned and packed into mature, muti-spanning configuration remains unclear. Here, we report that pTMD elicits a post-translational topogenesis pathway for its recognition and integration. Using six-spanning protein adenosine triphosphate-binding cassette transporter G2 (ABCG2) and cultured human cells as models, we show that ABCG2's pTMD2 can pass through translocon into the endoplasmic reticulum (ER) lumen, yielding an intermediate with inserted yet mis-oriented downstream TMDs. After translation, the intermediate recruits P5A-ATPase ATP13A1, which facilitates TMD re-orientation, allowing further folding and the integration of the remaining lumen-exposed pTMD2. Depleting ATP13A1 or disrupting pTMD-characteristic residues arrests intermediates with mis-oriented and exposed TMDs. Our results explain how a "difficult" pTMD is co-translationally skipped for insertion and post-translationally buried into the final correct structure at the late folding stage to avoid excessive lipid exposure.
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Affiliation(s)
- Jia Ji
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Meng-Ke Cui
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Rong Zou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Ming-Zhi Wu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Man-Xi Ge
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Jiqiang Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Zai-Rong Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China.
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9
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Yao J, Hong H. Steric trapping strategy for studying the folding of helical membrane proteins. Methods 2024; 225:1-12. [PMID: 38428472 PMCID: PMC11107808 DOI: 10.1016/j.ymeth.2024.02.007] [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: 11/16/2023] [Revised: 02/11/2024] [Accepted: 02/18/2024] [Indexed: 03/03/2024] Open
Abstract
Elucidating the folding energy landscape of membrane proteins is essential to the understanding of the proteins' stabilizing forces, folding mechanisms, biogenesis, and quality control. This is not a trivial task because the reversible control of folding is inherently difficult in a lipid bilayer environment. Recently, novel methods have been developed, each of which has a unique strength in investigating specific aspects of membrane protein folding. Among such methods, steric trapping is a versatile strategy allowing a reversible control of membrane protein folding with minimal perturbation of native protein-water and protein-lipid interactions. In a nutshell, steric trapping exploits the coupling of spontaneous denaturation of a doubly biotinylated protein to the simultaneous binding of bulky monovalent streptavidin molecules. This strategy has been evolved to investigate key elements of membrane protein folding such as thermodynamic stability, spontaneous denaturation rates, conformational features of the denatured states, and cooperativity of stabilizing interactions. In this review, we describe the critical methodological advancement, limitation, and outlook of the steric trapping strategy.
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Affiliation(s)
- Jiaqi Yao
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Heedeok Hong
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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10
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van der Sluijs P, Hoelen H, Schmidt A, Braakman I. The Folding Pathway of ABC Transporter CFTR: Effective and Robust. J Mol Biol 2024:168591. [PMID: 38677493 DOI: 10.1016/j.jmb.2024.168591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 04/29/2024]
Abstract
De novo protein folding into a native three-dimensional structure is indispensable for biological function, is instructed by its amino acid sequence, and occurs along a vectorial trajectory. The human proteome contains thousands of membrane-spanning proteins, whose biosynthesis begins on endoplasmic reticulum-associated ribosomes. Nearly half of all membrane proteins traverse the membrane more than once, including therapeutically important protein families such as solute carriers, G-protein-coupled receptors, and ABC transporters. These mediate a variety of functions like signal transduction and solute transport and are often of vital importance for cell function and tissue homeostasis. Missense mutations in multispan membrane proteins can lead to misfolding and cause disease; an example is the ABC transporter Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). Even though our understanding of multispan membrane-protein folding still is rather rudimental, the cumulative knowledge of 20 years of basic research on CFTR folding has led to development of drugs that modulate the misfolded protein. This has provided the prospect of a life without CF to the vast majority of patients. In this review we describe our understanding of the folding pathway of CFTR in cells, which is modular and tolerates many defects, making it effective and robust. We address how modulator drugs affect folding and function of CFTR, and distinguish protein stability from its folding process. Since the domain architecture of (mammalian) ABC transporters are highly conserved, we anticipate that the insights we discuss here for folding of CFTR may lay the groundwork for understanding the general rules of ABC-transporter folding.
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Affiliation(s)
- Peter van der Sluijs
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands.
| | - Hanneke Hoelen
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands; Present address: GenDx, Yalelaan 48, 3584 CM Utrecht, The Netherlands
| | - Andre Schmidt
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands; 3D-Pharmxchange, Tilburg, the Netherlands
| | - Ineke Braakman
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
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11
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Li D, Rocha-Roa C, Schilling MA, Reinisch KM, Vanni S. Lipid scrambling is a general feature of protein insertases. Proc Natl Acad Sci U S A 2024; 121:e2319476121. [PMID: 38621120 PMCID: PMC11047089 DOI: 10.1073/pnas.2319476121] [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: 11/07/2023] [Accepted: 03/13/2024] [Indexed: 04/17/2024] Open
Abstract
Glycerophospholipids are synthesized primarily in the cytosolic leaflet of the endoplasmic reticulum (ER) membrane and must be equilibrated between bilayer leaflets to allow the ER and membranes derived from it to grow. Lipid equilibration is facilitated by integral membrane proteins called "scramblases." These proteins feature a hydrophilic groove allowing the polar heads of lipids to traverse the hydrophobic membrane interior, similar to a credit card moving through a reader. Nevertheless, despite their fundamental role in membrane expansion and dynamics, the identity of most scramblases has remained elusive. Here, combining biochemical reconstitution and molecular dynamics simulations, we show that lipid scrambling is a general feature of protein insertases, integral membrane proteins which insert polypeptide chains into membranes of the ER and organelles disconnected from vesicle trafficking. Our data indicate that lipid scrambling occurs in the same hydrophilic channel through which protein insertion takes place and that scrambling is abolished in the presence of nascent polypeptide chains. We propose that protein insertases could have a so-far-overlooked role in membrane dynamics as scramblases.
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Affiliation(s)
- Dazhi Li
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06520
| | - Cristian Rocha-Roa
- Department of Biology, University of Fribourg, FribourgCH-1700, Switzerland
| | - Matthew A. Schilling
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06520
| | - Karin M. Reinisch
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06520
| | - Stefano Vanni
- Department of Biology, University of Fribourg, FribourgCH-1700, Switzerland
- Swiss National Center for Competence in Research Bio-Inspired Materials, University of Fribourg, FribourgCH-1700, Switzerland
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12
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Zhu Q, Zhu X, Zhang L. ER membrane complex (EMC): Structure, functions, and roles in diseases. FASEB J 2024; 38:e23539. [PMID: 38498340 DOI: 10.1096/fj.202302266r] [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: 11/02/2023] [Revised: 01/22/2024] [Accepted: 02/21/2024] [Indexed: 03/20/2024]
Abstract
The endoplasmic reticulum (ER) is the largest membrane system in eukaryotic cells and is the primary site for the biosynthesis of lipids and carbohydrates, as well as for the folding, assembly, modification, and transport of secreted and integrated membrane proteins. The ER membrane complex (EMC) on the ER membrane is an ER multiprotein complex that affects the quality control of membrane proteins, which is abundant and widely preserved. Its disruption has been found to affect a wide range of processes, including protein and lipid synthesis, organelle communication, endoplasmic reticulum stress, and viral maturation, and may lead to neurodevelopmental disorders and cancer. Therefore, EMC has attracted the attention of many scholars and become a hot field. In this paper, we summarized the main contributions of the research of EMC in the past nearly 15 years, and reviewed the structure and function of EMC as well as its related diseases. We hope this review will promote further progress of research on EMC.
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Affiliation(s)
- Qi Zhu
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Xianjun Zhu
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Lin Zhang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
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13
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Makhlouf L, Peter JJ, Magnussen HM, Thakur R, Millrine D, Minshull TC, Harrison G, Varghese J, Lamoliatte F, Foglizzo M, Macartney T, Calabrese AN, Zeqiraj E, Kulathu Y. The UFM1 E3 ligase recognizes and releases 60S ribosomes from ER translocons. Nature 2024; 627:437-444. [PMID: 38383789 PMCID: PMC10937380 DOI: 10.1038/s41586-024-07093-w] [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: 04/03/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024]
Abstract
Stalled ribosomes at the endoplasmic reticulum (ER) are covalently modified with the ubiquitin-like protein UFM1 on the 60S ribosomal subunit protein RPL26 (also known as uL24)1,2. This modification, which is known as UFMylation, is orchestrated by the UFM1 ribosome E3 ligase (UREL) complex, comprising UFL1, UFBP1 and CDK5RAP3 (ref. 3). However, the catalytic mechanism of UREL and the functional consequences of UFMylation are unclear. Here we present cryo-electron microscopy structures of UREL bound to 60S ribosomes, revealing the basis of its substrate specificity. UREL wraps around the 60S subunit to form a C-shaped clamp architecture that blocks the tRNA-binding sites at one end, and the peptide exit tunnel at the other. A UFL1 loop inserts into and remodels the peptidyl transferase centre. These features of UREL suggest a crucial function for UFMylation in the release and recycling of stalled or terminated ribosomes from the ER membrane. In the absence of functional UREL, 60S-SEC61 translocon complexes accumulate at the ER membrane, demonstrating that UFMylation is necessary for releasing SEC61 from 60S subunits. Notably, this release is facilitated by a functional switch of UREL from a 'writer' to a 'reader' module that recognizes its product-UFMylated 60S ribosomes. Collectively, we identify a fundamental role for UREL in dissociating 60S subunits from the SEC61 translocon and the basis for UFMylation in regulating protein homeostasis at the ER.
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Affiliation(s)
- Linda Makhlouf
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Joshua J Peter
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Helge M Magnussen
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Rohan Thakur
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - David Millrine
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
- Translational Immunology, Cancer Biomarker Centre, Manchester CRUK Institute, Manchester, UK
| | - Thomas C Minshull
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Grace Harrison
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Joby Varghese
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Frederic Lamoliatte
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Martina Foglizzo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Thomas Macartney
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Elton Zeqiraj
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
| | - Yogesh Kulathu
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
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14
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DaRosa PA, Penchev I, Gumbin SC, Scavone F, Wąchalska M, Paulo JA, Ordureau A, Peter JJ, Kulathu Y, Harper JW, Becker T, Beckmann R, Kopito RR. UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER. Nature 2024; 627:445-452. [PMID: 38383785 DOI: 10.1038/s41586-024-07073-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 01/15/2024] [Indexed: 02/23/2024]
Abstract
Reversible modification of target proteins by ubiquitin and ubiquitin-like proteins (UBLs) is widely used by eukaryotic cells to control protein fate and cell behaviour1. UFM1 is a UBL that predominantly modifies a single lysine residue on a single ribosomal protein, uL24 (also called RPL26), on ribosomes at the cytoplasmic surface of the endoplasmic reticulum (ER)2,3. UFM1 conjugation (UFMylation) facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes that stall during co-translational translocation of secretory proteins into the ER3,4. Neither the molecular mechanism by which the UFMylation machinery achieves such precise target selection nor how this ribosomal modification promotes 60S rescue is known. Here we show that ribosome UFMylation in vivo occurs on free 60S and we present sequential cryo-electron microscopy snapshots of the heterotrimeric UFM1 E3 ligase (E3(UFM1)) engaging its substrate uL24. E3(UFM1) binds the L1 stalk, empty transfer RNA-binding sites and the peptidyl transferase centre through carboxy-terminal domains of UFL1, which results in uL24 modification more than 150 Å away. After catalysing UFM1 transfer, E3(UFM1) remains stably bound to its product, UFMylated 60S, forming a C-shaped clamp that extends all the way around the 60S from the transfer RNA-binding sites to the polypeptide tunnel exit. Our structural and biochemical analyses suggest a role for E3(UFM1) in post-termination release and recycling of the large ribosomal subunit from the ER membrane.
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Affiliation(s)
- Paul A DaRosa
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Ivan Penchev
- Department of Biochemistry, Gene Center, University of Munich, Munich, Germany
| | | | | | - Magda Wąchalska
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joshua J Peter
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Yogesh Kulathu
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Thomas Becker
- Department of Biochemistry, Gene Center, University of Munich, Munich, Germany
| | - Roland Beckmann
- Department of Biochemistry, Gene Center, University of Munich, Munich, Germany.
| | - Ron R Kopito
- Department of Biology, Stanford University, Stanford, CA, USA.
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15
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Lei ZC, Wang X, Yang L, Qu H, Sun Y, Yang Y, Li W, Zhang WB, Cao XY, Fan C, Li G, Wu J, Tian ZQ. What can molecular assembly learn from catalysed assembly in living organisms? Chem Soc Rev 2024; 53:1892-1914. [PMID: 38230701 DOI: 10.1039/d3cs00634d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Molecular assembly is the process of organizing individual molecules into larger structures and complex systems. The self-assembly approach is predominantly utilized in creating artificial molecular assemblies, and was believed to be the primary mode of molecular assembly in living organisms as well. However, it has been shown that the assembly of many biological complexes is "catalysed" by other molecules, rather than relying solely on self-assembly. In this review, we summarize these catalysed-assembly (catassembly) phenomena in living organisms and systematically analyse their mechanisms. We then expand on these phenomena and discuss related concepts, including catalysed-disassembly and catalysed-reassembly. Catassembly proves to be an efficient and highly selective strategy for synergistically controlling and manipulating various noncovalent interactions, especially in hierarchical molecular assemblies. Overreliance on self-assembly may, to some extent, hinder the advancement of artificial molecular assembly with powerful features. Furthermore, inspired by the biological catassembly phenomena, we propose guidelines for designing artificial catassembly systems and developing characterization and theoretical methods, and review pioneering works along this new direction. Overall, this approach may broaden and deepen our understanding of molecular assembly, enabling the construction and control of intelligent assembly systems with advanced functionality.
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Affiliation(s)
- Zhi-Chao Lei
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xinchang Wang
- School of Electronic Science and Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, P. R. China
| | - Liulin Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Hang Qu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Yibin Sun
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Yang Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Wei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Xiao-Yu Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science, Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jiarui Wu
- Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, P. R. China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, 310024, P. R. China
| | - Zhong-Qun Tian
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
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16
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Chamness LM, Kuntz CP, McKee AG, Penn WD, Hemmerich CM, Rusch DB, Woods H, Dyotima, Meiler J, Schlebach JP. Divergent Folding-Mediated Epistasis Among Unstable Membrane Protein Variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.25.554866. [PMID: 37662415 PMCID: PMC10473758 DOI: 10.1101/2023.08.25.554866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Many membrane proteins are prone to misfolding, which compromises their functional expression at the plasma membrane. This is particularly true for the mammalian gonadotropin-releasing hormone receptor GPCRs (GnRHR). We recently demonstrated that evolutionary GnRHR modifications appear to have coincided with adaptive changes in cotranslational folding efficiency. Though protein stability is known to shape evolution, it is unclear how cotranslational folding constraints modulate the synergistic, epistatic interactions between mutations. We therefore compared the pairwise interactions formed by mutations that disrupt the membrane topology (V276T) or tertiary structure (W107A) of GnRHR. Using deep mutational scanning, we evaluated how the plasma membrane expression of these variants is modified by hundreds of secondary mutations. An analysis of 251 mutants in three genetic backgrounds reveals that V276T and W107A form distinct epistatic interactions that depend on both the severity and the mechanism of destabilization. V276T forms predominantly negative epistatic interactions with destabilizing mutations in soluble loops. In contrast, W107A forms positive interactions with mutations in both loops and transmembrane domains that reflect the diminishing impacts of the destabilizing mutations in variants that are already unstable. These findings reveal how epistasis is remodeled by conformational defects in membrane proteins and in unstable proteins more generally.
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Affiliation(s)
- Laura M. Chamness
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Charles P. Kuntz
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Andrew G. McKee
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Wesley D. Penn
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | | | - Douglas B. Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, USA
| | - Hope Woods
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA
| | - Dyotima
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- Institute for Drug Discovery, Leipzig University, Leipzig, SAC, Germany
| | - Jonathan P. Schlebach
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
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17
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Ren J, Zhang Z, Geng S, Cheng Y, Han H, Fan Z, Dai W, Zhang H, Wang X, Zhang Q, He B. Molecular Mechanisms of Intracellular Delivery of Nanoparticles Monitored by an Enzyme-Induced Proximity Labeling. NANO-MICRO LETTERS 2024; 16:103. [PMID: 38300384 PMCID: PMC10834923 DOI: 10.1007/s40820-023-01313-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/05/2023] [Indexed: 02/02/2024]
Abstract
Achieving increasingly finely targeted drug delivery to organs, tissues, cells, and even to intracellular biomacromolecules is one of the core goals of nanomedicines. As the delivery destination is refined to cellular and subcellular targets, it is essential to explore the delivery of nanomedicines at the molecular level. However, due to the lack of technical methods, the molecular mechanism of the intracellular delivery of nanomedicines remains unclear to date. Here, we develop an enzyme-induced proximity labeling technology in nanoparticles (nano-EPL) for the real-time monitoring of proteins that interact with intracellular nanomedicines. Poly(lactic-co-glycolic acid) nanoparticles coupled with horseradish peroxidase (HRP) were fabricated as a model (HRP(+)-PNPs) to evaluate the molecular mechanism of nano delivery in macrophages. By adding the labeling probe biotin-phenol and the catalytic substrate H2O2 at different time points in cellular delivery, nano-EPL technology was validated for the real-time in situ labeling of proteins interacting with nanoparticles. Nano-EPL achieves the dynamic molecular profiling of 740 proteins to map the intracellular delivery of HRP (+)-PNPs in macrophages over time. Based on dynamic clustering analysis of these proteins, we further discovered that different organelles, including endosomes, lysosomes, the endoplasmic reticulum, and the Golgi apparatus, are involved in delivery with distinct participation timelines. More importantly, the engagement of these organelles differentially affects the drug delivery efficiency, reflecting the spatial-temporal heterogeneity of nano delivery in cells. In summary, these findings highlight a significant methodological advance toward understanding the molecular mechanisms involved in the intracellular delivery of nanomedicines.
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Affiliation(s)
- Junji Ren
- Department of Pharmaceutics School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, People's Republic of China
| | - Zibin Zhang
- Department of Pharmaceutics School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, People's Republic of China
| | - Shuo Geng
- Department of Pharmaceutics School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, People's Republic of China
| | - Yuxi Cheng
- Department of Pharmaceutics School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, People's Republic of China
| | - Huize Han
- Department of Pharmaceutics School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, People's Republic of China
| | - Zhipu Fan
- Department of Pharmaceutics School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, People's Republic of China
| | - Wenbing Dai
- Department of Pharmaceutics School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, People's Republic of China
| | - Hua Zhang
- Department of Pharmaceutics School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, People's Republic of China
| | - Xueqing Wang
- Department of Pharmaceutics School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, People's Republic of China
| | - Qiang Zhang
- Department of Pharmaceutics School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, People's Republic of China.
| | - Bing He
- Department of Pharmaceutics School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, People's Republic of China.
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18
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Gamerdinger M, Deuerling E. Cotranslational sorting and processing of newly synthesized proteins in eukaryotes. Trends Biochem Sci 2024; 49:105-118. [PMID: 37919225 DOI: 10.1016/j.tibs.2023.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 11/04/2023]
Abstract
Ribosomes interact with a variety of different protein biogenesis factors that guide newly synthesized proteins to their native 3D shapes and cellular localization. Depending on the type of translated substrate, a distinct set of cotranslational factors must interact with the ribosome in a timely and coordinated manner to ensure proper protein biogenesis. While cytonuclear proteins require cotranslational maturation and folding factors, secretory proteins must be maintained in an unfolded state and processed cotranslationally by transport and membrane translocation factors. Here we explore the specific cotranslational processing steps for cytonuclear, secretory, and membrane proteins in eukaryotes and then discuss how the nascent polypeptide-associated complex (NAC) cotranslationally sorts these proteins into the correct protein biogenesis pathway.
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Affiliation(s)
- Martin Gamerdinger
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany.
| | - Elke Deuerling
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany.
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19
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Poerschke S, Oeljeklaus S, Cruz-Zaragoza LD, Schenzielorz A, Dahal D, Hillen HS, Das H, Kremer LS, Valpadashi A, Breuer M, Sattmann J, Richter-Dennerlein R, Warscheid B, Dennerlein S, Rehling P. Identification of TMEM126A as OXA1L-interacting protein reveals cotranslational quality control in mitochondria. Mol Cell 2024; 84:345-358.e5. [PMID: 38199007 PMCID: PMC10805001 DOI: 10.1016/j.molcel.2023.12.013] [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] [Received: 02/23/2023] [Revised: 10/17/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
Cellular proteostasis requires transport of polypeptides across membranes. Although defective transport processes trigger cytosolic rescue and quality control mechanisms that clear translocases and membranes from unproductive cargo, proteins that are synthesized within mitochondria are not accessible to these mechanisms. Mitochondrial-encoded proteins are inserted cotranslationally into the inner membrane by the conserved insertase OXA1L. Here, we identify TMEM126A as a OXA1L-interacting protein. TMEM126A associates with mitochondrial ribosomes and translation products. Loss of TMEM126A leads to the destabilization of mitochondrial translation products, triggering an inner membrane quality control process, in which newly synthesized proteins are degraded by the mitochondrial iAAA protease. Our data reveal that TMEM126A cooperates with OXA1L in protein insertion into the membrane. Upon loss of TMEM126A, the cargo-blocked OXA1L insertase complexes undergo proteolytic clearance by the iAAA protease machinery together with its cargo.
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Affiliation(s)
- Sabine Poerschke
- Institute for Cellular Biochemistry, University of Goettingen, 37073 Goettingen, Germany
| | - Silke Oeljeklaus
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, 97074 Wuerzburg, Germany
| | | | - Alexander Schenzielorz
- Institute for Biology II, Faculty for Biology, Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany
| | - Drishan Dahal
- Institute for Cellular Biochemistry, University of Goettingen, 37073 Goettingen, Germany
| | - Hauke Sven Hillen
- Institute for Cellular Biochemistry, University of Goettingen, 37073 Goettingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany; Research Group Structure and Function of Molecular Machines, Max Planck Institute for Multidisciplinary Sciences, 37077 Goettingen, Germany
| | - Hirak Das
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, 97074 Wuerzburg, Germany
| | - Laura Sophie Kremer
- Institute for Cellular Biochemistry, University of Goettingen, 37073 Goettingen, Germany
| | - Anusha Valpadashi
- Institute for Cellular Biochemistry, University of Goettingen, 37073 Goettingen, Germany
| | - Mirjam Breuer
- Institute for Cellular Biochemistry, University of Goettingen, 37073 Goettingen, Germany
| | - Johannes Sattmann
- Institute for Cellular Biochemistry, University of Goettingen, 37073 Goettingen, Germany
| | - Ricarda Richter-Dennerlein
- Institute for Cellular Biochemistry, University of Goettingen, 37073 Goettingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany; Goettingen Center for Molecular Biosciences, University of Goettingen, 37077 Goettingen, Germany
| | - Bettina Warscheid
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, 97074 Wuerzburg, Germany; Cluster of Excellence CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Sven Dennerlein
- Institute for Cellular Biochemistry, University of Goettingen, 37073 Goettingen, Germany.
| | - Peter Rehling
- Institute for Cellular Biochemistry, University of Goettingen, 37073 Goettingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany; Goettingen Center for Molecular Biosciences, University of Goettingen, 37077 Goettingen, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy, Goettingen, Germany; Max Planck Institute for Multidisciplinary Sciences, 37077 Goettingen, Germany.
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20
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Svedberg D, Winiger RR, Berg A, Sharma H, Tellgren-Roth C, Debrunner-Vossbrinck BA, Vossbrinck CR, Barandun J. Functional annotation of a divergent genome using sequence and structure-based similarity. BMC Genomics 2024; 25:6. [PMID: 38166563 PMCID: PMC10759460 DOI: 10.1186/s12864-023-09924-y] [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: 08/27/2023] [Accepted: 12/18/2023] [Indexed: 01/04/2024] Open
Abstract
BACKGROUND Microsporidia are a large taxon of intracellular pathogens characterized by extraordinarily streamlined genomes with unusually high sequence divergence and many species-specific adaptations. These unique factors pose challenges for traditional genome annotation methods based on sequence similarity. As a result, many of the microsporidian genomes sequenced to date contain numerous genes of unknown function. Recent innovations in rapid and accurate structure prediction and comparison, together with the growing amount of data in structural databases, provide new opportunities to assist in the functional annotation of newly sequenced genomes. RESULTS In this study, we established a workflow that combines sequence and structure-based functional gene annotation approaches employing a ChimeraX plugin named ANNOTEX (Annotation Extension for ChimeraX), allowing for visual inspection and manual curation. We employed this workflow on a high-quality telomere-to-telomere sequenced tetraploid genome of Vairimorpha necatrix. First, the 3080 predicted protein-coding DNA sequences, of which 89% were confirmed with RNA sequencing data, were used as input. Next, ColabFold was used to create protein structure predictions, followed by a Foldseek search for structural matching to the PDB and AlphaFold databases. The subsequent manual curation, using sequence and structure-based hits, increased the accuracy and quality of the functional genome annotation compared to results using only traditional annotation tools. Our workflow resulted in a comprehensive description of the V. necatrix genome, along with a structural summary of the most prevalent protein groups, such as the ricin B lectin family. In addition, and to test our tool, we identified the functions of several previously uncharacterized Encephalitozoon cuniculi genes. CONCLUSION We provide a new functional annotation tool for divergent organisms and employ it on a newly sequenced, high-quality microsporidian genome to shed light on this uncharacterized intracellular pathogen of Lepidoptera. The addition of a structure-based annotation approach can serve as a valuable template for studying other microsporidian or similarly divergent species.
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Affiliation(s)
- Dennis Svedberg
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 90736, Sweden
| | - Rahel R Winiger
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
| | - Alexandra Berg
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 90736, Sweden
| | - Himanshu Sharma
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 90736, Sweden
| | - Christian Tellgren-Roth
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Charles R Vossbrinck
- Department of Environmental Science, Connecticut Agricultural Experiment Station, New Haven, CT, 06504, USA
| | - Jonas Barandun
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden.
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21
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Wu H, Smalinskaitė L, Hegde RS. EMC rectifies the topology of multipass membrane proteins. Nat Struct Mol Biol 2024; 31:32-41. [PMID: 37957425 PMCID: PMC10803268 DOI: 10.1038/s41594-023-01120-6] [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: 04/25/2023] [Accepted: 09/08/2023] [Indexed: 11/15/2023]
Abstract
Most eukaryotic multipass membrane proteins are inserted into the membrane of the endoplasmic reticulum. Their transmembrane domains (TMDs) are thought to be inserted co-translationally as they emerge from a membrane-bound ribosome. Here we find that TMDs near the carboxyl terminus of mammalian multipass proteins are inserted post-translationally by the endoplasmic reticulum membrane protein complex (EMC). Site-specific crosslinking shows that the EMC's cytosol-facing hydrophilic vestibule is adjacent to a pre-translocated C-terminal tail. EMC-mediated insertion is mostly agnostic to TMD hydrophobicity, favored for short uncharged C-tails and stimulated by a preceding unassembled TMD bundle. Thus, multipass membrane proteins can be released by the ribosome-translocon complex in an incompletely inserted state, requiring a separate EMC-mediated post-translational insertion step to rectify their topology, complete biogenesis and evade quality control. This sequential co-translational and post-translational mechanism may apply to ~250 diverse multipass proteins, including subunits of the pentameric ion channel family that are crucial for neurotransmission.
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Affiliation(s)
- Haoxi Wu
- MRC Laboratory of Molecular Biology, Cambridge, UK
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22
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Knyazev DG, Winter L, Vogt A, Posch S, Öztürk Y, Siligan C, Goessweiner-Mohr N, Hagleitner-Ertugrul N, Koch HG, Pohl P. YidC from Escherichia coli Forms an Ion-Conducting Pore upon Activation by Ribosomes. Biomolecules 2023; 13:1774. [PMID: 38136645 PMCID: PMC10741985 DOI: 10.3390/biom13121774] [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: 11/05/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
The universally conserved protein YidC aids in the insertion and folding of transmembrane polypeptides. Supposedly, a charged arginine faces its hydrophobic lipid core, facilitating polypeptide sliding along YidC's surface. How the membrane barrier to other molecules may be maintained is unclear. Here, we show that the purified and reconstituted E. coli YidC forms an ion-conducting transmembrane pore upon ribosome or ribosome-nascent chain complex (RNC) binding. In contrast to monomeric YidC structures, an AlphaFold parallel YidC dimer model harbors a pore. Experimental evidence for a dimeric assembly comes from our BN-PAGE analysis of native vesicles, fluorescence correlation spectroscopy studies, single-molecule fluorescence photobleaching observations, and crosslinking experiments. In the dimeric model, the conserved arginine and other residues interacting with nascent chains point into the putative pore. This result suggests the possibility of a YidC-assisted insertion mode alternative to the insertase mechanism.
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Affiliation(s)
- Denis G. Knyazev
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Lukas Winter
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Andreas Vogt
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany (Y.Ö.); (H.-G.K.)
- Spemann-Graduate School of Biology and Medicine (SGBM), Albert Ludwig University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany
| | - Sandra Posch
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Yavuz Öztürk
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany (Y.Ö.); (H.-G.K.)
| | - Christine Siligan
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Nikolaus Goessweiner-Mohr
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Nora Hagleitner-Ertugrul
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany (Y.Ö.); (H.-G.K.)
- Spemann-Graduate School of Biology and Medicine (SGBM), Albert Ludwig University of Freiburg, 79104 Freiburg, Germany
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
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23
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Karki S, Javanainen M, Rehan S, Tranter D, Kellosalo J, Huiskonen JT, Happonen L, Paavilainen V. Molecular view of ER membrane remodeling by the Sec61/TRAP translocon. EMBO Rep 2023; 24:e57910. [PMID: 37983950 DOI: 10.15252/embr.202357910] [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: 08/01/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
Protein translocation across the endoplasmic reticulum (ER) membrane is an essential step during protein entry into the secretory pathway. The conserved Sec61 protein-conducting channel facilitates polypeptide translocation and coordinates cotranslational polypeptide-processing events. In cells, the majority of Sec61 is stably associated with a heterotetrameric membrane protein complex, the translocon-associated protein complex (TRAP), yet the mechanism by which TRAP assists in polypeptide translocation remains unknown. Here, we present the structure of the core Sec61/TRAP complex bound to a mammalian ribosome by cryogenic electron microscopy (cryo-EM). Ribosome interactions anchor the Sec61/TRAP complex in a conformation that renders the ER membrane locally thinner by significantly curving its lumenal leaflet. We propose that TRAP stabilizes the ribosome exit tunnel to assist nascent polypeptide insertion through Sec61 and provides a ratcheting mechanism into the ER lumen mediated by direct polypeptide interactions.
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Affiliation(s)
- Sudeep Karki
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Matti Javanainen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Shahid Rehan
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Protein Biochemistry and Structural Biology, Omass Therapeutics Ltd, Oxford, UK
| | - Dale Tranter
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Juho Kellosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Juha T Huiskonen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Lotta Happonen
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Ville Paavilainen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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24
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Zhou X, Yang Y, Wang G, Wang S, Sun D, Ou X, Lian Y, Li L. Molecular pathway of mitochondrial preprotein import through the TOM-TIM23 supercomplex. Nat Struct Mol Biol 2023; 30:1996-2008. [PMID: 37696957 DOI: 10.1038/s41594-023-01103-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/18/2023] [Indexed: 09/13/2023]
Abstract
Over half of mitochondrial proteins are imported from the cytosol via the pre-sequence pathway, controlled by the TOM complex in the outer membrane and the TIM23 complex in the inner membrane. The mechanisms through which proteins are translocated via the TOM and TIM23 complexes remain unclear. Here we report the assembly of the active TOM-TIM23 supercomplex of Saccharomyces cerevisiae with translocating polypeptide substrates. Electron cryo-microscopy analyses reveal that the polypeptide substrates pass the TOM complex through the center of a Tom40 subunit, interacting with a glutamine-rich region. Structural and biochemical analyses show that the TIM23 complex contains a heterotrimer of the subunits Tim23, Tim17 and Mgr2. The polypeptide substrates are shielded from lipids by Mgr2 and Tim17, which creates a translocation pathway characterized by a negatively charged entrance and a central hydrophobic region. These findings reveal an unexpected pre-sequence pathway through the TOM-TIM23 supercomplex spanning the double membranes of mitochondria.
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Affiliation(s)
- Xueyin Zhou
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yuqi Yang
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Guopeng Wang
- School of Life Sciences, Peking University, Beijing, China
| | - Shanshan Wang
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Dongjie Sun
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Xiaomin Ou
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Yuke Lian
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Long Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China.
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25
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Ansell TB, Song W, Coupland CE, Carrique L, Corey RA, Duncan AL, Cassidy CK, Geurts MMG, Rasmussen T, Ward AB, Siebold C, Stansfeld PJ, Sansom MSP. LipIDens: simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins. Nat Commun 2023; 14:7774. [PMID: 38012131 PMCID: PMC10682427 DOI: 10.1038/s41467-023-43392-y] [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: 07/08/2022] [Accepted: 11/07/2023] [Indexed: 11/29/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) enables the determination of membrane protein structures in native-like environments. Characterising how membrane proteins interact with the surrounding membrane lipid environment is assisted by resolution of lipid-like densities visible in cryo-EM maps. Nevertheless, establishing the molecular identity of putative lipid and/or detergent densities remains challenging. Here we present LipIDens, a pipeline for molecular dynamics (MD) simulation-assisted interpretation of lipid and lipid-like densities in cryo-EM structures. The pipeline integrates the implementation and analysis of multi-scale MD simulations for identification, ranking and refinement of lipid binding poses which superpose onto cryo-EM map densities. Thus, LipIDens enables direct integration of experimental and computational structural approaches to facilitate the interpretation of lipid-like cryo-EM densities and to reveal the molecular identities of protein-lipid interactions within a bilayer environment. We demonstrate this by application of our open-source LipIDens code to ten diverse membrane protein structures which exhibit lipid-like densities.
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Affiliation(s)
- T Bertie Ansell
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Wanling Song
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- MSD R&D Innovation Centre, 120 Moorgate, London, EC2M 6UR, UK
| | - Claire E Coupland
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Loic Carrique
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, BS8 1TD, UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Department of Chemistry, Aarhus University, Lagelsandsgade 140, 8000, Aarhus C, Denmark
| | - C Keith Cassidy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Maxwell M G Geurts
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Tim Rasmussen
- Biocenter and Rudolf-Virchow-Zentrum, Universität Würzburg, Haus D15, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Phillip J Stansfeld
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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26
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Kleizen B, de Mattos E, Papaioannou O, Monti M, Tartaglia GG, van der Sluijs P, Braakman I. Transmembrane Helices 7 and 8 Confer Aggregation Sensitivity to the Cystic Fibrosis Transmembrane Conductance Regulator. Int J Mol Sci 2023; 24:15741. [PMID: 37958724 PMCID: PMC10648718 DOI: 10.3390/ijms242115741] [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: 09/04/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023] Open
Abstract
The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a large multi-spanning membrane protein that is susceptible to misfolding and aggregation. We have identified here the region responsible for this instability. Temperature-induced aggregation of C-terminally truncated versions of CFTR demonstrated that all truncations up to the second transmembrane domain (TMD2), including the R region, largely resisted aggregation. Limited proteolysis identified a folded structure that was prone to aggregation and consisted of TMD2 and at least part of the Regulatory Region R. Only when both TM7 (TransMembrane helix 7) and TM8 were present, TMD2 fragments became as aggregation-sensitive as wild-type CFTR, in line with increased thermo-instability of late CFTR nascent chains and in silico prediction of aggregation propensity. In accord, isolated TMD2 was degraded faster in cells than isolated TMD1. We conclude that TMD2 extended at its N-terminus with part of the R region forms a protease-resistant structure that induces heat instability in CFTR and may be responsible for its limited intracellular stability.
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Affiliation(s)
- Bertrand Kleizen
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; (B.K.); (E.d.M.); (O.P.); (P.v.d.S.)
| | - Eduardo de Mattos
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; (B.K.); (E.d.M.); (O.P.); (P.v.d.S.)
| | - Olga Papaioannou
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; (B.K.); (E.d.M.); (O.P.); (P.v.d.S.)
| | - Michele Monti
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy; (M.M.); (G.G.T.)
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genoa, Italy
| | - Gian Gaetano Tartaglia
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy; (M.M.); (G.G.T.)
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genoa, Italy
| | - Peter van der Sluijs
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; (B.K.); (E.d.M.); (O.P.); (P.v.d.S.)
| | - Ineke Braakman
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; (B.K.); (E.d.M.); (O.P.); (P.v.d.S.)
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27
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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.
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Affiliation(s)
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany;
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28
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Njenga R, Boele J, Öztürk Y, Koch HG. Coping with stress: How bacteria fine-tune protein synthesis and protein transport. J Biol Chem 2023; 299:105163. [PMID: 37586589 PMCID: PMC10502375 DOI: 10.1016/j.jbc.2023.105163] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Maintaining a functional proteome under different environmental conditions is challenging for every organism, in particular for unicellular organisms, such as bacteria. In order to cope with changing environments and stress conditions, bacteria depend on strictly coordinated proteostasis networks that control protein production, folding, trafficking, and degradation. Regulation of ribosome biogenesis and protein synthesis are cornerstones of this cellular adaptation in all domains of life, which is rationalized by the high energy demand of both processes and the increased resistance of translationally silent cells against internal or external poisons. Reduced protein synthesis ultimately also reduces the substrate load for protein transport systems, which are required for maintaining the periplasmic, inner, and outer membrane subproteomes. Consequences of impaired protein transport have been analyzed in several studies and generally induce a multifaceted response that includes the upregulation of chaperones and proteases and the simultaneous downregulation of protein synthesis. In contrast, generally less is known on how bacteria adjust the protein targeting and transport machineries to reduced protein synthesis, e.g., when cells encounter stress conditions or face nutrient deprivation. In the current review, which is mainly focused on studies using Escherichia coli as a model organism, we summarize basic concepts on how ribosome biogenesis and activity are regulated under stress conditions. In addition, we highlight some recent developments on how stress conditions directly impair protein targeting to the bacterial membrane. Finally, we describe mechanisms that allow bacteria to maintain the transport of stress-responsive proteins under conditions when the canonical protein targeting pathways are impaired.
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Affiliation(s)
- Robert Njenga
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Julian Boele
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Yavuz Öztürk
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany.
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29
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Li D, Rocha-Roa C, Schilling MA, Reinisch KM, Vanni S. Lipid scrambling is a general feature of protein insertases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555937. [PMID: 37693532 PMCID: PMC10491306 DOI: 10.1101/2023.09.01.555937] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Glycerophospholipids are synthesized primarily in the cytosolic leaflet of the endoplasmic reticulum (ER) membrane and must be equilibrated between bilayer leaflets to allow the ER and membranes derived from it to grow. Lipid equilibration is facilitated by integral membrane proteins called "scramblases". These proteins feature a hydrophilic groove allowing the polar heads of lipids to traverse the hydrophobic membrane interior, similar to a credit-card moving through a reader. Nevertheless, despite their fundamental role in membrane expansion and dynamics, the identity of most scramblases has remained elusive. Here, combining biochemical reconstitution and molecular dynamics simulations, we show that lipid scrambling is a general feature of protein insertases, integral membrane proteins which insert polypeptide chains into membranes of the ER and organelles disconnected from vesicle trafficking. Our data indicate that lipid scrambling occurs in the same hydrophilic channel through which protein insertion takes place, and that scrambling is abolished in the presence of nascent polypeptide chains. We propose that protein insertases could have a so-far overlooked role in membrane dynamics as scramblases.
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Affiliation(s)
- Dazhi Li
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Matthew A Schilling
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Karin M Reinisch
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Switzerland
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30
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Tipper DJ, Harley CA. Spf1 and Ste24: quality controllers of transmembrane protein topology in the eukaryotic cell. Front Cell Dev Biol 2023; 11:1220441. [PMID: 37635876 PMCID: PMC10456885 DOI: 10.3389/fcell.2023.1220441] [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] [Received: 05/10/2023] [Accepted: 07/14/2023] [Indexed: 08/29/2023] Open
Abstract
DNA replication, transcription, and translation in eukaryotic cells occur with decreasing but still high fidelity. In contrast, for the estimated 33% of the human proteome that is inserted as transmembrane (TM) proteins, insertion with a non-functional inverted topology is frequent. Correct topology is essential for function and trafficking to appropriate cellular compartments and is controlled principally by responses to charged residues within 15 residues of the inserted TM domain (TMD); the flank with the higher positive charge remains in the cytosol (inside), following the positive inside rule (PIR). Yeast (Saccharomyces cerevisiae) mutants that increase insertion contrary to the PIR were selected. Mutants with strong phenotypes were found only in SPF1 and STE24 (human cell orthologs are ATP13A1 and ZMPSte24) with, at the time, no known relevant functions. Spf1/Atp13A1 is now known to dislocate to the cytosol TM proteins inserted contrary to the PIR, allowing energy-conserving reinsertion. We hypothesize that Spf1 and Ste24 both recognize the short, positively charged ER luminal peptides of TM proteins inserted contrary to the PIR, accepting these peptides into their large membrane-spanning, water-filled cavities through interaction with their many interior surface negative charges. While entry was demonstrated for Spf1, no published evidence directly demonstrates substrate entry to the Ste24 cavity, internal access to its zinc metalloprotease (ZMP) site, or active withdrawal of fragments, which may be essential for function. Spf1 and Ste24 comprise a PIR quality control system that is conserved in all eukaryotes and presumably evolved in prokaryotic progenitors as they gained differentiated membrane functions. About 75% of the PIR is imposed by this quality control system, which joins the UPR, ERAD, and autophagy (ER-phagy) in coordinated, overlapping quality control of ER protein function.
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Affiliation(s)
- Donald J. Tipper
- University of Massachusetts Medical School, Worcester, MA, United States
| | - Carol A. Harley
- i3S-Instituto de Investigação e Inovação em Saude, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
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31
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Kizmaz B, Herrmann JM. Membrane insertases at a glance. J Cell Sci 2023; 136:jcs261219. [PMID: 37417332 DOI: 10.1242/jcs.261219] [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] [Indexed: 07/08/2023] Open
Abstract
Protein translocases, such as the bacterial SecY complex, the Sec61 complex of the endoplasmic reticulum (ER) and the mitochondrial translocases, facilitate the transport of proteins across membranes. In addition, they catalyze the insertion of integral membrane proteins into the lipid bilayer. Several membrane insertases cooperate with these translocases, thereby promoting the topogenesis, folding and assembly of membrane proteins. Oxa1 and BamA family members serve as core components in the two major classes of membrane insertases. They facilitate the integration of proteins with α-helical transmembrane domains and of β-barrel proteins into lipid bilayers, respectively. Members of the Oxa1 family were initially found in the internal membranes of bacteria, mitochondria and chloroplasts. Recent studies, however, also identified several Oxa1-type insertases in the ER, where they serve as catalytically active core subunits in the ER membrane protein complex (EMC), the guided entry of tail-anchored (GET) and the GET- and EMC-like (GEL) complex. The outer membrane of bacteria, mitochondria and chloroplasts contain β-barrel proteins, which are inserted by members of the BamA family. In this Cell Science at a Glance article and the accompanying poster, we provide an overview of these different types of membrane insertases and discuss their function.
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Affiliation(s)
- Büsra Kizmaz
- Cell Biology, University of Kaiserslautern, Kaiserslautern 67663, Germany
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32
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Gamerdinger M, Jia M, Schloemer R, Rabl L, Jaskolowski M, Khakzar KM, Ulusoy Z, Wallisch A, Jomaa A, Hunaeus G, Scaiola A, Diederichs K, Ban N, Deuerling E. NAC controls cotranslational N-terminal methionine excision in eukaryotes. Science 2023; 380:1238-1243. [PMID: 37347872 DOI: 10.1126/science.adg3297] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/18/2023] [Indexed: 06/24/2023]
Abstract
N-terminal methionine excision from newly synthesized proteins, catalyzed cotranslationally by methionine aminopeptidases (METAPs), is an essential and universally conserved process that plays a key role in cell homeostasis and protein biogenesis. However, how METAPs interact with ribosomes and how their cleavage specificity is ensured is unknown. We discovered that in eukaryotes the nascent polypeptide-associated complex (NAC) controls ribosome binding of METAP1. NAC recruits METAP1 using a long, flexible tail and provides a platform for the formation of an active methionine excision complex at the ribosomal tunnel exit. This mode of interaction ensures the efficient excision of methionine from cytosolic proteins, whereas proteins targeted to the endoplasmic reticulum are spared. Our results suggest a broader mechanism for how access of protein biogenesis factors to translating ribosomes is controlled.
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Affiliation(s)
- Martin Gamerdinger
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany
| | - Min Jia
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Renate Schloemer
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany
| | - Laurenz Rabl
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany
| | - Mateusz Jaskolowski
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Katrin M Khakzar
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany
| | - Zeynel Ulusoy
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany
| | - Annalena Wallisch
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany
| | - Ahmad Jomaa
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Gundula Hunaeus
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany
| | - Alain Scaiola
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Kay Diederichs
- Department of Biology, Molecular Bioinformatics, University of Konstanz, 78457 Konstanz, Germany
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Elke Deuerling
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany
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33
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Müller MBD, Kasturi P, Jayaraj GG, Hartl FU. Mechanisms of readthrough mitigation reveal principles of GCN1-mediated translational quality control. Cell 2023:S0092-8674(23)00587-1. [PMID: 37339632 PMCID: PMC10364623 DOI: 10.1016/j.cell.2023.05.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023]
Abstract
Readthrough into the 3' untranslated region (3' UTR) of the mRNA results in the production of aberrant proteins. Metazoans efficiently clear readthrough proteins, but the underlying mechanisms remain unknown. Here, we show in Caenorhabditis elegans and mammalian cells that readthrough proteins are targeted by a coupled, two-level quality control pathway involving the BAG6 chaperone complex and the ribosome-collision-sensing protein GCN1. Readthrough proteins with hydrophobic C-terminal extensions (CTEs) are recognized by SGTA-BAG6 and ubiquitylated by RNF126 for proteasomal degradation. Additionally, cotranslational mRNA decay initiated by GCN1 and CCR4/NOT limits the accumulation of readthrough products. Unexpectedly, selective ribosome profiling uncovered a general role of GCN1 in regulating translation dynamics when ribosomes collide at nonoptimal codons, enriched in 3' UTRs, transmembrane proteins, and collagens. GCN1 dysfunction increasingly perturbs these protein classes during aging, resulting in mRNA and proteome imbalance. Our results define GCN1 as a key factor acting during translation in maintaining protein homeostasis.
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Affiliation(s)
- Martin B D Müller
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Prasad Kasturi
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Gopal G Jayaraj
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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Wang J, Han S, Ye J. Topological regulation of a transmembrane protein by luminal-to-cytosolic retrotranslocation of glycosylated sequence. Cell Rep 2023; 42:112311. [PMID: 36972171 PMCID: PMC10520219 DOI: 10.1016/j.celrep.2023.112311] [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: 10/03/2022] [Revised: 02/02/2023] [Accepted: 03/11/2023] [Indexed: 03/28/2023] Open
Abstract
Transmembrane proteins must adopt proper topology to perform their functions. We previously demonstrated that ceramide regulates TM4SF20 (transmembrane 4 L6 family 20) by altering the topology of the transmembrane protein, but the underlying mechanism remains obscure. Here we report that TM4SF20 is synthesized in the endoplasmic reticulum (ER) with a cytosolic C terminus and a luminal loop before the last transmembrane helix where N132, N148, and N163 are glycosylated. In the absence of ceramide, the sequence surrounding glycosylated N163 but not N132 is retrotranslocated from lumen to cytosol independent of ER-associated degradation. Accompanying this retrotranslocation, the C terminus of the protein is relocated from cytosol to lumen. Ceramide delays the retrotranslocation process, causing accumulation of the protein that is originally synthesized. Our findings suggest that N-linked glycans, although synthesized in the lumens, may be exposed to cytosol through retrotranslocation, a reaction that may play a crucial role in topological regulation of transmembrane proteins.
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Affiliation(s)
- Jingcheng Wang
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sungwon Han
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jin Ye
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Bai L, Li H. Structural insights into the membrane chaperones for multi-pass membrane protein biogenesis. Curr Opin Struct Biol 2023; 79:102563. [PMID: 36863267 DOI: 10.1016/j.sbi.2023.102563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/22/2023] [Accepted: 01/28/2023] [Indexed: 03/04/2023]
Abstract
Certain transmembrane α-helices of multi-pass membrane proteins line substrate transport paths or catalytic pockets and, therefore, are partially hydrophilic. Sec61 alone is insufficient to insert these less hydrophobic segments into the membrane and needs to work with dedicated membrane chaperones. Three such membrane chaperones have been described in the literature-the endoplasmic reticulum membrane protein complex (EMC), the TMCO1 complex, and the PAT complex. Recent structural studies on these membrane chaperones have revealed their overall architecture, multi-subunit assembly, putative substrate transmembrane helix-binding pockets, and cooperative mechanisms with the ribosome and Sec61 translocon. These structures are providing initial insights into the poorly understood processes of multi-pass membrane protein biogenesis.
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Affiliation(s)
- Lin Bai
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, 100083, China.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, 49503, United States.
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36
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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: 0] [Impact Index Per Article: 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.
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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
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Hsieh LTH, Hall BS, Newcombe J, Mendum TA, Umrania Y, Deery MJ, Shi WQ, Salguero FJ, Simmonds RE. Mycolactone causes catastrophic Sec61-dependent loss of the endothelial glycocalyx and basement membrane: a new indirect mechanism driving tissue necrosis in Mycobacterium ulcerans infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.21.529382. [PMID: 36865118 PMCID: PMC9980099 DOI: 10.1101/2023.02.21.529382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The drivers of tissue necrosis in Mycobacterium ulcerans infection (Buruli ulcer disease) have historically been ascribed solely to the directly cytotoxic action of the diffusible exotoxin, mycolactone. However, its role in the clinically-evident vascular component of disease aetiology remains poorly explained. We have now dissected mycolactone's effects on primary vascular endothelial cells in vitro and in vivo. We show that mycolactone-induced changes in endothelial morphology, adhesion, migration, and permeability are dependent on its action at the Sec61 translocon. Unbiased quantitative proteomics identified a profound effect on proteoglycans, driven by rapid loss of type II transmembrane proteins of the Golgi, including enzymes required for glycosaminoglycan (GAG) synthesis, combined with a reduction in the core proteins themselves. Loss of the glycocalyx is likely to be of particular mechanistic importance, since knockdown of galactosyltransferase II (beta-1,3-galactotransferase 6; B3Galt6), the GAG linker-building enzyme, phenocopied the permeability and phenotypic changes induced by mycolactone. Additionally, mycolactone depleted many secreted basement membrane components and microvascular basement membranes were disrupted in vivo. Remarkably, exogenous addition of laminin-511 reduced endothelial cell rounding, restored cell attachment and reversed the defective migration caused by mycolactone. Hence supplementing mycolactone-depleted extracellular matrix may be a future therapeutic avenue, to improve wound healing rates.
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Affiliation(s)
| | - Belinda S Hall
- Dept of Microbial Sciences, School of Bioscience and Medicine, University of Surrey
| | - Jane Newcombe
- Dept of Microbial Sciences, School of Bioscience and Medicine, University of Surrey
| | - Tom A Mendum
- Dept of Microbial Sciences, School of Bioscience and Medicine, University of Surrey
| | - Yagnesh Umrania
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | - Michael J Deery
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | - Wei Q Shi
- Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | | | - Rachel E Simmonds
- Dept of Microbial Sciences, School of Bioscience and Medicine, University of Surrey
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Eisenack TJ, Trentini DB. Ending a bad start: Triggers and mechanisms of co-translational protein degradation. Front Mol Biosci 2023; 9:1089825. [PMID: 36660423 PMCID: PMC9846516 DOI: 10.3389/fmolb.2022.1089825] [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] [Received: 11/04/2022] [Accepted: 12/15/2022] [Indexed: 01/05/2023] Open
Abstract
Proteins are versatile molecular machines that control and execute virtually all cellular processes. They are synthesized in a multilayered process requiring transfer of information from DNA to RNA and finally into polypeptide, with many opportunities for error. In addition, nascent proteins must successfully navigate a complex folding-energy landscape, in which their functional native state represents one of many possible outcomes. Consequently, newly synthesized proteins are at increased risk of misfolding and toxic aggregation. To maintain proteostasis-the state of proteome balance-cells employ a plethora of molecular chaperones that guide proteins along a productive folding pathway and quality control factors that direct misfolded species for degradation. Achieving the correct balance between folding and degradation therefore represents a fundamental task for the proteostasis network. While many chaperones act co-translationally, protein quality control is generally considered to be a post-translational process, as the majority of proteins will only achieve their final native state once translation is completed. Nevertheless, it has been observed that proteins can be ubiquitinated during synthesis. The extent and the relevance of co-translational protein degradation, as well as the underlying molecular mechanisms, remain areas of open investigation. Recent studies made seminal advances in elucidating ribosome-associated quality control processes, and how their loss of function can lead to proteostasis failure and disease. Here, we discuss current understanding of the situations leading to the marking of nascent proteins for degradation before synthesis is completed, and the emerging quality controls pathways engaged in this task in eukaryotic cells. We also highlight the methods used to study co-translational quality control.
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Affiliation(s)
- Tom Joshua Eisenack
- University of Cologne, Faculty of Medicine, University Hospital of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Débora Broch Trentini
- University of Cologne, Faculty of Medicine, University Hospital of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany,*Correspondence: Débora Broch Trentini,
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39
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Visualization of translation and protein biogenesis at the ER membrane. Nature 2023; 614:160-167. [PMID: 36697828 PMCID: PMC9892003 DOI: 10.1038/s41586-022-05638-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 12/07/2022] [Indexed: 01/26/2023]
Abstract
The dynamic ribosome-translocon complex, which resides at the endoplasmic reticulum (ER) membrane, produces a major fraction of the human proteome1,2. It governs the synthesis, translocation, membrane insertion, N-glycosylation, folding and disulfide-bond formation of nascent proteins. Although individual components of this machinery have been studied at high resolution in isolation3-7, insights into their interplay in the native membrane remain limited. Here we use cryo-electron tomography, extensive classification and molecular modelling to capture snapshots of mRNA translation and protein maturation at the ER membrane at molecular resolution. We identify a highly abundant classical pre-translocation intermediate with eukaryotic elongation factor 1a (eEF1a) in an extended conformation, suggesting that eEF1a may remain associated with the ribosome after GTP hydrolysis during proofreading. At the ER membrane, distinct polysomes bind to different ER translocons specialized in the synthesis of proteins with signal peptides or multipass transmembrane proteins with the translocon-associated protein complex (TRAP) present in both. The near-complete atomic model of the most abundant ER translocon variant comprising the protein-conducting channel SEC61, TRAP and the oligosaccharyltransferase complex A (OSTA) reveals specific interactions of TRAP with other translocon components. We observe stoichiometric and sub-stoichiometric cofactors associated with OSTA, which are likely to include protein isomerases. In sum, we visualize ER-bound polysomes with their coordinated downstream machinery.
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40
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Guay KP, Williams RV, Hebert DN. Calnexin reveals a sugar-free taste within the lipid bilayer. EMBO J 2022; 41:e113003. [PMID: 36377534 PMCID: PMC9753440 DOI: 10.15252/embj.2022113003] [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: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Maturation of membrane proteins is complicated by the need to fold in three distinct environments. While much is known about folding in the two aqueous milieus constituted by cytoplasm and ER lumen, our knowledge of the folding, arrangement, and quality control of transmembrane regions within the lipid bilayer, and its facilitation by molecular chaperones, is limited. New work by Bloemeke et al now reveals an expanded role of the ER chaperone calnexin acting within the lipid bilayer in a carbohydrate-independent manner.
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Affiliation(s)
- Kevin P Guay
- Department of Biochemistry and Molecular BiologyUniversity of MassachusettsAmherstMAUSA
- Program in Molecular and Cellular BiologyUniversity of MassachusettsAmherstMAUSA
| | - Robert V Williams
- Department of Biochemistry and Molecular BiologyUniversity of MassachusettsAmherstMAUSA
| | - Daniel N Hebert
- Department of Biochemistry and Molecular BiologyUniversity of MassachusettsAmherstMAUSA
- Program in Molecular and Cellular BiologyUniversity of MassachusettsAmherstMAUSA
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41
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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.
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Affiliation(s)
- Sichen Shao
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115,*Address correspondence to: Sichen Shao ()
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