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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; 436:168591. [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] [MESH Headings] [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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Lewis AJO, Zhong F, Keenan RJ, Hegde RS. Structural analysis of the dynamic ribosome-translocon complex. eLife 2024; 13:RP95814. [PMID: 38896445 PMCID: PMC11186639 DOI: 10.7554/elife.95814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024] Open
Abstract
The protein translocon at the endoplasmic reticulum comprises the Sec61 translocation channel and numerous accessory factors that collectively facilitate the biogenesis of secretory and membrane proteins. Here, we leveraged recent advances in cryo-electron microscopy (cryo-EM) and structure prediction to derive insights into several novel configurations of the ribosome-translocon complex. We show how a transmembrane domain (TMD) in a looped configuration passes through the Sec61 lateral gate during membrane insertion; how a nascent chain can bind and constrain the conformation of ribosomal protein uL22; and how the translocon-associated protein (TRAP) complex can adjust its position during different stages of protein biogenesis. Most unexpectedly, we find that a large proportion of translocon complexes contains RAMP4 intercalated into Sec61's lateral gate, widening Sec61's central pore and contributing to its hydrophilic interior. These structures lead to mechanistic hypotheses for translocon function and highlight a remarkably plastic machinery whose conformations and composition adjust dynamically to its diverse range of substrates.
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Affiliation(s)
- Aaron JO Lewis
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Frank Zhong
- Department of Molecular Genetics and Cell Biology, The University of ChicagoChicagoUnited States
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
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Alzayed NT, Alzuabi AH, Alqusaimi RA, El-Anany EA, Alholle A, Aboelanine AH, Omar S, Alsafi R, Elmonairy AA, Alali FJ, Alahmad A, Alsharhan H, Albash B, Marafi D. Tribal Founder EMC1 Variant in 5 Kuwaiti Families Expands Phenotypic Spectrum of EMC1-Related Disorder. Neurol Genet 2024; 10:e200156. [PMID: 38784058 PMCID: PMC11115761 DOI: 10.1212/nxg.0000000000200156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/18/2024] [Indexed: 05/25/2024]
Abstract
Background and Objectives The endoplasmic reticulum (ER) membrane protein complex is a conserved multisubunit transmembrane complex that enables energy-independent insertion of newly synthesized membrane proteins into ER membranes, mediating protein folding, phospholipid transfer from ER to mitochondria, and elimination of misfolded proteins. The first subunit of EMC (EMC1) is encoded by EMC1. Both monoallelic de novo and biallelic EMC1 variants have been identified to cause cerebellar atrophy, visual impairment, and psychomotor retardation (CAVIPMR) [OMIM #616875]. Eight families with biallelic EMC1 variants and CAVIPMR have been reported. Here, we describe 8 individuals from 5 Kuwaiti families from the same tribe, with the previously reported homozygous pathogenic missense EMC1 variant [c.245C>T:p.(Thr82Met)] and CAVIPMR. Methods Proband exome sequencing was performed in 3 families, while targeted molecular testing for EMC1 [c.245C>T:p.(Thr82Met)] variant was performed in the other 2 families based on strong clinical suspicion and tribal origin. Sanger sequencing confirmed variant segregation with disease in all families. Results We identified 8 individuals from 5 Kuwaiti families with the homozygous pathogenic EMC1 variant [c.245C>T:p.(Thr82Met)] previously reported in a Turkish family with CAVIPMR. The variant was absent from Kuwait Medical Genetic Center database, thus unlikely to represent a population founder allelic variant. The average age at symptom onset was 11 weeks, with all families reporting either visual abnormalities, hypotonia, and/or global developmental delay (GDD) as the presenting features. Shared clinical features included GDD (8/8), microcephaly (8/8), truncal hypotonia (8/8), visual impairment (7/7), and failure to thrive (7/7). Other common features included hyperreflexia (5/6; 83%), peripheral hypertonia (3/5; 60%), dysmorphism (3/6; 50%), epilepsy (4/8; 50%), and chorea (3/8; 36%). Brain imaging showed cerebellar atrophy in 4/7 (57%) and cerebral atrophy in 3/6 (50%) individuals. Discussion The presence of exact biallelic homozygous EMC1 variant in 5 Kuwaiti families from the same tribe suggests a tribal founder allelic variant. The clinical features in this study are consistent with the phenotypic spectrum of EMC1-associated CAVIPMR in previous reports. The presence of chorea, first noted in this study, further expands the phenotypic spectrum. Our findings emphasize the importance of targeted EMC1 variant [c.245C>T:p.(Thr82Met)] testing for infants from affected tribe who present with visual impairment, GDD, and hypotonia.
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Affiliation(s)
- Nada T Alzayed
- From the College of Medicine (N.T.A., A.H. Alzuabi, R.A.A.), Health Science Center, Kuwait University; Section of Child Neurology (E.A.E.-A., D.M.), Department of Pediatrics, Adan Hospital, Ministry of Health, Hadiya; Kuwait Medical Genetics Centre (A. Alholle, A.H. Aboelanine, S.O., A.A.E., F.J.A., A. Alahmad, H.A., D.M.), Ministry of Health, Sulaibikhat; Department of Pediatrics (R.A., B.A.), Adan Hospital, Ministry of Health, Hadiya; Department of Pediatrics (H.A., D.M.), College of Medicine, Kuwait University, Safat; and Department of Pediatrics (H.A.), Farwaniya Hospital, Ministry of Health, Sabah Al-Nasser, Kuwait
| | - Abdullah H Alzuabi
- From the College of Medicine (N.T.A., A.H. Alzuabi, R.A.A.), Health Science Center, Kuwait University; Section of Child Neurology (E.A.E.-A., D.M.), Department of Pediatrics, Adan Hospital, Ministry of Health, Hadiya; Kuwait Medical Genetics Centre (A. Alholle, A.H. Aboelanine, S.O., A.A.E., F.J.A., A. Alahmad, H.A., D.M.), Ministry of Health, Sulaibikhat; Department of Pediatrics (R.A., B.A.), Adan Hospital, Ministry of Health, Hadiya; Department of Pediatrics (H.A., D.M.), College of Medicine, Kuwait University, Safat; and Department of Pediatrics (H.A.), Farwaniya Hospital, Ministry of Health, Sabah Al-Nasser, Kuwait
| | - Reem A Alqusaimi
- From the College of Medicine (N.T.A., A.H. Alzuabi, R.A.A.), Health Science Center, Kuwait University; Section of Child Neurology (E.A.E.-A., D.M.), Department of Pediatrics, Adan Hospital, Ministry of Health, Hadiya; Kuwait Medical Genetics Centre (A. Alholle, A.H. Aboelanine, S.O., A.A.E., F.J.A., A. Alahmad, H.A., D.M.), Ministry of Health, Sulaibikhat; Department of Pediatrics (R.A., B.A.), Adan Hospital, Ministry of Health, Hadiya; Department of Pediatrics (H.A., D.M.), College of Medicine, Kuwait University, Safat; and Department of Pediatrics (H.A.), Farwaniya Hospital, Ministry of Health, Sabah Al-Nasser, Kuwait
| | - Ehab A El-Anany
- From the College of Medicine (N.T.A., A.H. Alzuabi, R.A.A.), Health Science Center, Kuwait University; Section of Child Neurology (E.A.E.-A., D.M.), Department of Pediatrics, Adan Hospital, Ministry of Health, Hadiya; Kuwait Medical Genetics Centre (A. Alholle, A.H. Aboelanine, S.O., A.A.E., F.J.A., A. Alahmad, H.A., D.M.), Ministry of Health, Sulaibikhat; Department of Pediatrics (R.A., B.A.), Adan Hospital, Ministry of Health, Hadiya; Department of Pediatrics (H.A., D.M.), College of Medicine, Kuwait University, Safat; and Department of Pediatrics (H.A.), Farwaniya Hospital, Ministry of Health, Sabah Al-Nasser, Kuwait
| | - Abdullah Alholle
- From the College of Medicine (N.T.A., A.H. Alzuabi, R.A.A.), Health Science Center, Kuwait University; Section of Child Neurology (E.A.E.-A., D.M.), Department of Pediatrics, Adan Hospital, Ministry of Health, Hadiya; Kuwait Medical Genetics Centre (A. Alholle, A.H. Aboelanine, S.O., A.A.E., F.J.A., A. Alahmad, H.A., D.M.), Ministry of Health, Sulaibikhat; Department of Pediatrics (R.A., B.A.), Adan Hospital, Ministry of Health, Hadiya; Department of Pediatrics (H.A., D.M.), College of Medicine, Kuwait University, Safat; and Department of Pediatrics (H.A.), Farwaniya Hospital, Ministry of Health, Sabah Al-Nasser, Kuwait
| | - Ashraf H Aboelanine
- From the College of Medicine (N.T.A., A.H. Alzuabi, R.A.A.), Health Science Center, Kuwait University; Section of Child Neurology (E.A.E.-A., D.M.), Department of Pediatrics, Adan Hospital, Ministry of Health, Hadiya; Kuwait Medical Genetics Centre (A. Alholle, A.H. Aboelanine, S.O., A.A.E., F.J.A., A. Alahmad, H.A., D.M.), Ministry of Health, Sulaibikhat; Department of Pediatrics (R.A., B.A.), Adan Hospital, Ministry of Health, Hadiya; Department of Pediatrics (H.A., D.M.), College of Medicine, Kuwait University, Safat; and Department of Pediatrics (H.A.), Farwaniya Hospital, Ministry of Health, Sabah Al-Nasser, Kuwait
| | - Sherief Omar
- From the College of Medicine (N.T.A., A.H. Alzuabi, R.A.A.), Health Science Center, Kuwait University; Section of Child Neurology (E.A.E.-A., D.M.), Department of Pediatrics, Adan Hospital, Ministry of Health, Hadiya; Kuwait Medical Genetics Centre (A. Alholle, A.H. Aboelanine, S.O., A.A.E., F.J.A., A. Alahmad, H.A., D.M.), Ministry of Health, Sulaibikhat; Department of Pediatrics (R.A., B.A.), Adan Hospital, Ministry of Health, Hadiya; Department of Pediatrics (H.A., D.M.), College of Medicine, Kuwait University, Safat; and Department of Pediatrics (H.A.), Farwaniya Hospital, Ministry of Health, Sabah Al-Nasser, Kuwait
| | - Rasha Alsafi
- From the College of Medicine (N.T.A., A.H. Alzuabi, R.A.A.), Health Science Center, Kuwait University; Section of Child Neurology (E.A.E.-A., D.M.), Department of Pediatrics, Adan Hospital, Ministry of Health, Hadiya; Kuwait Medical Genetics Centre (A. Alholle, A.H. Aboelanine, S.O., A.A.E., F.J.A., A. Alahmad, H.A., D.M.), Ministry of Health, Sulaibikhat; Department of Pediatrics (R.A., B.A.), Adan Hospital, Ministry of Health, Hadiya; Department of Pediatrics (H.A., D.M.), College of Medicine, Kuwait University, Safat; and Department of Pediatrics (H.A.), Farwaniya Hospital, Ministry of Health, Sabah Al-Nasser, Kuwait
| | - Alaa A Elmonairy
- From the College of Medicine (N.T.A., A.H. Alzuabi, R.A.A.), Health Science Center, Kuwait University; Section of Child Neurology (E.A.E.-A., D.M.), Department of Pediatrics, Adan Hospital, Ministry of Health, Hadiya; Kuwait Medical Genetics Centre (A. Alholle, A.H. Aboelanine, S.O., A.A.E., F.J.A., A. Alahmad, H.A., D.M.), Ministry of Health, Sulaibikhat; Department of Pediatrics (R.A., B.A.), Adan Hospital, Ministry of Health, Hadiya; Department of Pediatrics (H.A., D.M.), College of Medicine, Kuwait University, Safat; and Department of Pediatrics (H.A.), Farwaniya Hospital, Ministry of Health, Sabah Al-Nasser, Kuwait
| | - Fatemah J Alali
- From the College of Medicine (N.T.A., A.H. Alzuabi, R.A.A.), Health Science Center, Kuwait University; Section of Child Neurology (E.A.E.-A., D.M.), Department of Pediatrics, Adan Hospital, Ministry of Health, Hadiya; Kuwait Medical Genetics Centre (A. Alholle, A.H. Aboelanine, S.O., A.A.E., F.J.A., A. Alahmad, H.A., D.M.), Ministry of Health, Sulaibikhat; Department of Pediatrics (R.A., B.A.), Adan Hospital, Ministry of Health, Hadiya; Department of Pediatrics (H.A., D.M.), College of Medicine, Kuwait University, Safat; and Department of Pediatrics (H.A.), Farwaniya Hospital, Ministry of Health, Sabah Al-Nasser, Kuwait
| | - Ahmad Alahmad
- From the College of Medicine (N.T.A., A.H. Alzuabi, R.A.A.), Health Science Center, Kuwait University; Section of Child Neurology (E.A.E.-A., D.M.), Department of Pediatrics, Adan Hospital, Ministry of Health, Hadiya; Kuwait Medical Genetics Centre (A. Alholle, A.H. Aboelanine, S.O., A.A.E., F.J.A., A. Alahmad, H.A., D.M.), Ministry of Health, Sulaibikhat; Department of Pediatrics (R.A., B.A.), Adan Hospital, Ministry of Health, Hadiya; Department of Pediatrics (H.A., D.M.), College of Medicine, Kuwait University, Safat; and Department of Pediatrics (H.A.), Farwaniya Hospital, Ministry of Health, Sabah Al-Nasser, Kuwait
| | - Hind Alsharhan
- From the College of Medicine (N.T.A., A.H. Alzuabi, R.A.A.), Health Science Center, Kuwait University; Section of Child Neurology (E.A.E.-A., D.M.), Department of Pediatrics, Adan Hospital, Ministry of Health, Hadiya; Kuwait Medical Genetics Centre (A. Alholle, A.H. Aboelanine, S.O., A.A.E., F.J.A., A. Alahmad, H.A., D.M.), Ministry of Health, Sulaibikhat; Department of Pediatrics (R.A., B.A.), Adan Hospital, Ministry of Health, Hadiya; Department of Pediatrics (H.A., D.M.), College of Medicine, Kuwait University, Safat; and Department of Pediatrics (H.A.), Farwaniya Hospital, Ministry of Health, Sabah Al-Nasser, Kuwait
| | - Buthaina Albash
- From the College of Medicine (N.T.A., A.H. Alzuabi, R.A.A.), Health Science Center, Kuwait University; Section of Child Neurology (E.A.E.-A., D.M.), Department of Pediatrics, Adan Hospital, Ministry of Health, Hadiya; Kuwait Medical Genetics Centre (A. Alholle, A.H. Aboelanine, S.O., A.A.E., F.J.A., A. Alahmad, H.A., D.M.), Ministry of Health, Sulaibikhat; Department of Pediatrics (R.A., B.A.), Adan Hospital, Ministry of Health, Hadiya; Department of Pediatrics (H.A., D.M.), College of Medicine, Kuwait University, Safat; and Department of Pediatrics (H.A.), Farwaniya Hospital, Ministry of Health, Sabah Al-Nasser, Kuwait
| | - Dana Marafi
- From the College of Medicine (N.T.A., A.H. Alzuabi, R.A.A.), Health Science Center, Kuwait University; Section of Child Neurology (E.A.E.-A., D.M.), Department of Pediatrics, Adan Hospital, Ministry of Health, Hadiya; Kuwait Medical Genetics Centre (A. Alholle, A.H. Aboelanine, S.O., A.A.E., F.J.A., A. Alahmad, H.A., D.M.), Ministry of Health, Sulaibikhat; Department of Pediatrics (R.A., B.A.), Adan Hospital, Ministry of Health, Hadiya; Department of Pediatrics (H.A., D.M.), College of Medicine, Kuwait University, Safat; and Department of Pediatrics (H.A.), Farwaniya Hospital, Ministry of Health, Sabah Al-Nasser, Kuwait
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Paul JW, Muratcioğlu S, Kuriyan J. A fluorescence-based sensor for calibrated measurement of protein kinase stability in live cells. Protein Sci 2024; 33:e5023. [PMID: 38801214 PMCID: PMC11129626 DOI: 10.1002/pro.5023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/22/2024] [Accepted: 05/02/2024] [Indexed: 05/29/2024]
Abstract
Oncogenic mutations can destabilize signaling proteins, resulting in increased or unregulated activity. Thus, there is considerable interest in mapping the relationship between mutations and the stability of signaling proteins, to better understand the consequences of oncogenic mutations and potentially inform the development of new therapeutics. Here, we develop a tool to study protein-kinase stability in live mammalian cells and the effects of the HSP90 chaperone system on the stability of these kinases. We determine the expression levels of protein kinases by monitoring the fluorescence of fluorescent proteins fused to those kinases, normalized to that of co-expressed reference fluorescent proteins. We used this tool to study the dependence of Src- and Raf-family kinases on the HSP90 system. We demonstrate that this sensor reports on destabilization induced by oncogenic mutations in these kinases. We also show that Src-homology 2 and Src-homology 3 domains, which are required for autoinhibition of Src-family kinases, stabilize these kinase domains in the cell. Our expression-calibrated sensor enables the facile characterization of the effects of mutations and small-molecule drugs on protein-kinase stability.
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Affiliation(s)
- Joseph W. Paul
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- California Institute for Quantitative Bioscience (QB3)University of CaliforniaBerkeleyCaliforniaUSA
| | - Serena Muratcioğlu
- Department of BiochemistryVanderbilt University School of MedicineNashvilleTennesseeUSA
| | - John Kuriyan
- Department of BiochemistryVanderbilt University School of MedicineNashvilleTennesseeUSA
- Department of ChemistryVanderbilt UniversityNashvilleTennesseeUSA
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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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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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Wenzell NA, Tuch BB, McMinn DL, Lyons MJ, Kirk CJ, Taunton J. Global signal peptide profiling reveals principles of selective Sec61 inhibition. Nat Chem Biol 2024:10.1038/s41589-024-01592-7. [PMID: 38519575 DOI: 10.1038/s41589-024-01592-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 02/26/2024] [Indexed: 03/25/2024]
Abstract
Cotransins target the Sec61 translocon and inhibit the biogenesis of an undefined subset of secretory and membrane proteins. Remarkably, cotransin inhibition depends on the unique signal peptide (SP) of each Sec61 client, which is required for cotranslational translocation into the endoplasmic reticulum. It remains unknown how an SP's amino acid sequence and biophysical properties confer sensitivity to structurally distinct cotransins. Here we describe a fluorescence-based, pooled-cell screening platform to interrogate nearly all human SPs in parallel. We profiled two cotransins with distinct effects on cancer cells and discovered a small subset of SPs, including the oncoprotein human epidermal growth factor receptor 3 (HER3), with increased sensitivity to the more selective cotransin, KZR-9873. By comparing divergent mouse and human orthologs, we unveiled a position-dependent effect of arginine on SP sensitivity. Our multiplexed profiling platform reveals how cotransins can exploit subtle sequence differences to achieve SP discrimination.
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Affiliation(s)
- Nicole A Wenzell
- Chemistry and Chemical Biology Program, University of California, San Francisco, San Francisco, CA, USA
| | - Brian B Tuch
- Kezar Life Sciences, South San Francisco, CA, USA
| | | | - Matthew J Lyons
- Chemistry and Chemical Biology Program, University of California, San Francisco, San Francisco, CA, USA
| | | | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
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8
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Muthukumar G, Stevens TA, Inglis AJ, Esantsi TK, Saunders RA, Schulte F, Voorhees RM, Guna A, Weissman JS. Triaging of α-helical proteins to the mitochondrial outer membrane by distinct chaperone machinery based on substrate topology. Mol Cell 2024; 84:1101-1119.e9. [PMID: 38428433 DOI: 10.1016/j.molcel.2024.01.028] [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: 07/31/2023] [Revised: 12/08/2023] [Accepted: 01/31/2024] [Indexed: 03/03/2024]
Abstract
Mitochondrial outer membrane ⍺-helical proteins play critical roles in mitochondrial-cytoplasmic communication, but the rules governing the targeting and insertion of these biophysically diverse proteins remain unknown. Here, we first defined the complement of required mammalian biogenesis machinery through genome-wide CRISPRi screens using topologically distinct membrane proteins. Systematic analysis of nine identified factors across 21 diverse ⍺-helical substrates reveals that these components are organized into distinct targeting pathways that act on substrates based on their topology. NAC is required for the efficient targeting of polytopic proteins, whereas signal-anchored proteins require TTC1, a cytosolic chaperone that physically engages substrates. Biochemical and mutational studies reveal that TTC1 employs a conserved TPR domain and a hydrophobic groove in its C-terminal domain to support substrate solubilization and insertion into mitochondria. Thus, the targeting of diverse mitochondrial membrane proteins is achieved through topological triaging in the cytosol using principles with similarities to ER membrane protein biogenesis systems.
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Affiliation(s)
- Gayathri Muthukumar
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Taylor A Stevens
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Alison J Inglis
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Theodore K Esantsi
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Reuben A Saunders
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Fabian Schulte
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Alina Guna
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA.
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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9
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Li M, Zhang C, Xu Y, Li S, Huang C, Wu J, Lei M. Structural insights into human EMC and its interaction with VDAC. Aging (Albany NY) 2024; 16:5501-5525. [PMID: 38517390 PMCID: PMC11006472 DOI: 10.18632/aging.205660] [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: 11/06/2023] [Accepted: 02/08/2024] [Indexed: 03/23/2024]
Abstract
The endoplasmic reticulum (ER) membrane protein complex (EMC) is a conserved, multi-subunit complex acting as an insertase at the ER membrane. Growing evidence shows that the EMC is also involved in stabilizing and trafficking membrane proteins. However, the structural basis and regulation of its multifunctionality remain elusive. Here, we report cryo-electron microscopy structures of human EMC in apo- and voltage-dependent anion channel (VDAC)-bound states at resolutions of 3.47 Å and 3.32 Å, respectively. We discovered a specific interaction between VDAC proteins and the EMC at mitochondria-ER contact sites, which is conserved from yeast to humans. Moreover, we identified a gating plug located inside the EMC hydrophilic vestibule, the substrate-binding pocket for client insertion. Conformation changes of this gating plug during the apo-to-VDAC-bound transition reveal that the EMC unlikely acts as an insertase in the VDAC1-bound state. Based on the data analysis, the gating plug may regulate EMC functions by modifying the hydrophilic vestibule in different states. Our discovery offers valuable insights into the structural basis of EMC's multifunctionality.
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Affiliation(s)
- Mingyue Li
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Chunli Zhang
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Yuntao Xu
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Shaobai Li
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Chenhui Huang
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Jian Wu
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Ming Lei
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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10
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Sun K, Liu L, Jiang X, Wang H, Wang L, Yang Y, Liu W, Zhang L, Zhao X, Zhu X. The endoplasmic reticulum membrane protein complex subunit Emc6 is essential for rhodopsin localization and photoreceptor cell survival. Genes Dis 2024; 11:1035-1049. [PMID: 37692493 PMCID: PMC10492031 DOI: 10.1016/j.gendis.2023.03.033] [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: 09/21/2022] [Revised: 02/17/2023] [Accepted: 03/29/2023] [Indexed: 09/12/2023] Open
Abstract
The endoplasmic reticulum (ER) membrane protein complex (EMC) is responsible for monitoring the biogenesis and synthetic quality of membrane proteins with tail-anchored or multiple transmembrane domains. The EMC subunit EMC6 is one of the core members of EMC and forms an enclosed hydrophilic vestibule in cooperation with EMC3. Despite studies demonstrating that deletion of EMC3 led to rhodopsin mislocalization in rod photoreceptors of mice, the precise mechanism leading to the failure of rhodopsin trafficking remains unclear. Here, we generated the first rod photoreceptor-specific knockout of Emc6 (RKO) and cone photoreceptor-specific knockout of Emc6 (CKO) mouse models. Deficiency of Emc6 in rod photoreceptors led to progressive shortening of outer segments (OS), impaired visual function, mislocalization and reduced expression of rhodopsin, and increased gliosis in rod photoreceptors. In addition, CKO mice displayed the progressive death of cone photoreceptors and abnormal localization of cone opsin protein. Subsequently, proteomics analysis of the RKO mouse retina illustrated that several cilium-related proteins, particularly anoctamin-2 (ANO2) and transmembrane protein 67 (TMEM67), were significantly down-regulated prior to OS degeneration. Detrimental rod photoreceptor cilia and mislocalized membrane disc proteins were evident in RKO mice. Our data revealed that in addition to monitoring the synthesis of rhodopsin-dominated membrane disc proteins, EMC6 also impacted rod photoreceptors' ciliogenesis by regulating the synthesis of membrane proteins associated with cilia, contributing to the mislocalization of membrane disc proteins.
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Affiliation(s)
- Kuanxiang Sun
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
- Key Laboratory of Tibetan Medicine Research, Chinese Academy of Sciences and Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, Qinghai 810008, China
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, China
| | - Lu Liu
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
| | - Xiaoyan Jiang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
| | - Heting Wang
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
| | - Lin Wang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
| | - Yeming Yang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
| | - Wenjing Liu
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, 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, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
| | - Xiaohui Zhao
- Key Laboratory of Tibetan Medicine Research, Chinese Academy of Sciences and Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, Qinghai 810008, China
| | - Xianjun Zhu
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
- Key Laboratory of Tibetan Medicine Research, Chinese Academy of Sciences and Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, Qinghai 810008, China
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, China
- Department of Ophthalmology, The First People's Hospital of Shangqiu, Shangqiu, Henan 476000, China
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11
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Jung SJ, Sridhara S, Ott M. Early steps in the biogenesis of mitochondrially encoded oxidative phosphorylation subunits. IUBMB Life 2024; 76:125-139. [PMID: 37712772 DOI: 10.1002/iub.2784] [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: 06/19/2023] [Accepted: 08/10/2023] [Indexed: 09/16/2023]
Abstract
The complexes mediating oxidative phosphorylation (OXPHOS) in the inner mitochondrial membrane consist of proteins encoded in the nuclear or the mitochondrial DNA. The mitochondrially encoded membrane proteins (mito-MPs) represent the catalytic core of these complexes and follow complicated pathways for biogenesis. Owing to their overall hydrophobicity, mito-MPs are co-translationally inserted into the inner membrane by the Oxa1 insertase. After insertion, OXPHOS biogenesis factors mediate the assembly of mito-MPs into complexes and participate in the regulation of mitochondrial translation, while protein quality control factors recognize and degrade faulty or excess proteins. This review summarizes the current understanding of these early steps occurring during the assembly of mito-MPs by concentrating on results obtained in the model organism baker's yeast.
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Affiliation(s)
- Sung-Jun Jung
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Sagar Sridhara
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Martin Ott
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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12
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Giolito ML, Bigliani G, Meinero R, Taubas JV. Palmitoylation of CYSTM (CYSPD) proteins in yeast. J Biol Chem 2024; 300:105609. [PMID: 38159851 PMCID: PMC10840359 DOI: 10.1016/j.jbc.2023.105609] [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: 06/22/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
A superfamily of proteins called cysteine transmembrane is widely distributed across eukaryotes. These small proteins are characterized by the presence of a conserved motif at the C-terminal region, rich in cysteines, that has been annotated as a transmembrane domain. Orthologs of these proteins have been involved in resistance to pathogens and metal detoxification. The yeast members of the family are YBR016W, YDL012C, YDR034W-B, and YDR210W. Here, we begin the characterization of these proteins at the molecular level and show that Ybr016w, Ydr034w-b, and Ydr210w are palmitoylated proteins. Protein S-acylation or palmitoylation, is a posttranslational modification that consists of the addition of long-chain fatty acids to cysteine residues. We provide evidence that Ybr016w, Ydr210w, and Ydr034w-b are localized to the plasma membrane and exhibit varying degrees of polarity toward the daughter cell, which is dependent on endocytosis and recycling. We suggest the names CPP1, CPP2, and CPP3 (C terminally palmitoylated protein) for YBR016W, YDR210W, and YDR034W-B, respectively. We show that palmitoylation is responsible for the binding of these proteins to the membrane indicating that the cysteine transmembrane on these proteins is not a transmembrane domain. We propose renaming the C-terminal cysteine-rich domain as cysteine-rich palmitoylated domain. Loss of the palmitoyltransferase Erf2 leads to partial degradation of Ybr016w (Cpp1), whereas in the absence of the palmitoyltransferase Akr1, members of this family are completely degraded. For Cpp1, we show that this degradation occurs via the proteasome in an Rsp5-dependent manner, but is not exclusively due to a lack of Cpp1 palmitoylation.
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Affiliation(s)
- María Luz Giolito
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Gonzalo Bigliani
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Rocío Meinero
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Javier Valdez Taubas
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
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13
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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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14
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Lohse MJ, Bock A, Zaccolo M. G Protein-Coupled Receptor Signaling: New Insights Define Cellular Nanodomains. Annu Rev Pharmacol Toxicol 2024; 64:387-415. [PMID: 37683278 DOI: 10.1146/annurev-pharmtox-040623-115054] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
G protein-coupled receptors are the largest and pharmacologically most important receptor family and are involved in the regulation of most cell functions. Most of them reside exclusively at the cell surface, from where they signal via heterotrimeric G proteins to control the production of second messengers such as cAMP and IP3 as well as the activity of several ion channels. However, they may also internalize upon agonist stimulation or constitutively reside in various intracellular locations. Recent evidence indicates that their function differs depending on their precise cellular localization. This is because the signals they produce, notably cAMP and Ca2+, are mostly bound to cell proteins that significantly reduce their mobility, allowing the generation of steep concentration gradients. As a result, signals generated by the receptors remain confined to nanometer-sized domains. We propose that such nanometer-sized domains represent the basic signaling units in a cell and a new type of target for drug development.
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Affiliation(s)
- Martin J Lohse
- ISAR Bioscience Institute, Planegg/Munich, Germany;
- Rudolf Boehm Institute of Pharmacology and Toxicology, Leipzig University, Leipzig, Germany
| | - Andreas Bock
- Rudolf Boehm Institute of Pharmacology and Toxicology, Leipzig University, Leipzig, Germany
| | - Manuela Zaccolo
- Department of Physiology, Anatomy and Genetics and National Institute for Health and Care Research Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom;
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15
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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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16
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Shi L, Ma H, Wang J, Ma M, Zhao H, Li Z, Wang JH, Wu S, Zhou Z, Dong MQ, Li Z. An EMC-Hpo-Yki axis maintains intestinal homeostasis under physiological and pathological conditions. Development 2023; 150:dev201958. [PMID: 38031990 DOI: 10.1242/dev.201958] [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: 05/07/2023] [Accepted: 11/08/2023] [Indexed: 12/01/2023]
Abstract
Balanced control of stem cell proliferation and differentiation underlines tissue homeostasis. Disruption of tissue homeostasis often results in many diseases. However, how endogenous factors influence the proliferation and differentiation of intestinal stem cells (ISCs) under physiological and pathological conditions remains poorly understood. Here, we find that the evolutionarily conserved endoplasmic reticulum membrane protein complex (EMC) negatively regulates ISC proliferation and intestinal homeostasis. Compromising EMC function in progenitors leads to excessive ISC proliferation and intestinal homeostasis disruption. Mechanistically, the EMC associates with and stabilizes Hippo (Hpo) protein, the key component of the Hpo signaling pathway. In the absence of EMC, Yorkie (Yki) is activated to promote ISC proliferation due to Hpo destruction. The EMC-Hpo-Yki axis also functions in enterocytes to maintain intestinal homeostasis. Importantly, the levels of the EMC are dramatically diminished in tunicamycin-treated animals, leading to Hpo destruction, thereby resulting in intestinal homeostasis disruption due to Yki activation. Thus, our study uncovers the molecular mechanism underlying the action of the EMC in intestinal homeostasis maintenance under physiological and pathological conditions and provides new insight into the pathogenesis of tunicamycin-induced tumorigenesis.
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Affiliation(s)
- Lin Shi
- Laboratory of Stem Cell Biology, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Hubing Ma
- Laboratory of Stem Cell Biology, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jinjun Wang
- Laboratory of Stem Cell Biology, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Meifang Ma
- Laboratory of Stem Cell Biology, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Hang Zhao
- Laboratory of Stem Cell Biology, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Zhengran Li
- Laboratory of Stem Cell Biology, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jian-Hua Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Shian Wu
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zizhang Zhou
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Zhouhua Li
- Laboratory of Stem Cell Biology, College of Life Sciences, Capital Normal University, Beijing 100048, China
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17
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Kong Q, Zhu Z, Xu Q, Yu F, Wang Q, Gu Z, Xia K, Jiang D, Kong H. Nature-Inspired Thylakoid-Based Photosynthetic Nanoarchitectures for Biomedical Applications. SMALL METHODS 2023:e2301143. [PMID: 38040986 DOI: 10.1002/smtd.202301143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/22/2023] [Indexed: 12/03/2023]
Abstract
"Drawing inspiration from nature" offers a wealth of creative possibilities for designing cutting-edge materials with improved properties and performance. Nature-inspired thylakoid-based nanoarchitectures, seamlessly integrate the inherent structures and functions of natural components with the diverse and controllable characteristics of nanotechnology. These innovative biomaterials have garnered significant attention for their potential in various biomedical applications. Thylakoids possess fundamental traits such as light harvesting, oxygen evolution, and photosynthesis. Through the integration of artificially fabricated nanostructures with distinct physical and chemical properties, novel photosynthetic nanoarchitectures can be catalytically generated, offering versatile functionalities for diverse biomedical applications. In this article, an overview of the properties and extraction methods of thylakoids are provided. Additionally, the recent advancements in the design, preparation, functions, and biomedical applications of a range of thylakoid-based photosynthetic nanoarchitectures are reviewed. Finally, the foreseeable challenges and future prospects in this field is discussed.
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Affiliation(s)
- Qunshou Kong
- Department of Nuclear Medicine, Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Molecular Imaging, Wuhan, 430022, China
- Key Laboratory of Biological Targeted Therapy, The Ministry of Education, Wuhan, 430022, China
| | - Zhimin Zhu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qin Xu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Feng Yu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Qisheng Wang
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Zhihua Gu
- Shanghai Pudong TCM Hospital, Shanghai, 201205, China
| | - Kai Xia
- Shanghai Frontier Innovation Research Institute, Shanghai, 201108, China
- Xiangfu Laboratory, Jiashan, 314102, China
- Shanghai Stomatological Hospital, Fudan University, Shanghai, 200031, China
| | - Dawei Jiang
- Department of Nuclear Medicine, Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Molecular Imaging, Wuhan, 430022, China
- Key Laboratory of Biological Targeted Therapy, The Ministry of Education, Wuhan, 430022, China
| | - Huating Kong
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
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18
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Yang Y, Wu S, Chen Y, Ju H. Surface-enhanced Raman scattering sensing for detection and mapping of key cellular biomarkers. Chem Sci 2023; 14:12869-12882. [PMID: 38023499 PMCID: PMC10664603 DOI: 10.1039/d3sc04650h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Cellular biomarkers mainly contain proteins, nucleic acids, glycans and many small molecules including small biomolecule metabolites, reactive oxygen species and other cellular chemical entities. The detection and mapping of the key cellular biomarkers can effectively help us to understand important cellular mechanisms associated with physiological and pathological processes, which greatly promote the development of clinical diagnosis and disease treatment. Surface-enhanced Raman scattering (SERS) possesses high sensitivity and is free from the influence of strong self-fluorescence in living systems as well as the photobleaching of the dyes. It exhibits rich and narrow chemical fingerprint spectra for multiplexed detection, and has become a powerful tool to detect and map cellular biomarkers. In this review, we present an overview of recent advances in the detection and mapping of different classes of cellular biomarkers based on SERS sensing. These advances fully confirm that the SERS-based sensors and sensing methods have great potential for the exploration of biological mechanisms and clinical applications. Additionally, we also discuss the limitations of present research and the future developments of the SERS technology in this field.
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Affiliation(s)
- Yuanjiao Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Shan Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Yunlong Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
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19
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Li S, Yang M, Zhao R, Peng L, Liu W, Jiang X, He Y, Dai E, Zhang L, Yang Y, Shi Y, Zhao P, Yang Z, Zhu X. Defective EMC1 drives abnormal retinal angiogenesis via Wnt/β-catenin signaling and may be associated with the pathogenesis of familial exudative vitreoretinopathy. Genes Dis 2023; 10:2572-2585. [PMID: 37554197 PMCID: PMC10404869 DOI: 10.1016/j.gendis.2022.10.003] [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: 04/27/2022] [Revised: 09/10/2022] [Accepted: 10/01/2022] [Indexed: 11/06/2022] Open
Abstract
Endoplasmic reticulum (ER) membrane protein complex (EMC) is required for the co-translational insertion of newly synthesized multi-transmembrane proteins. Compromised EMC function in different cell types has been implicated in multiple diseases. Using inducible genetic mouse models, we revealed defects in retinal vascularization upon endothelial cell (EC) specific deletion of Emc1, the largest subunit of EMC. Loss of Emc1 in ECs led to reduced vascular progression and vascular density, diminished tip cell sprouts, and vascular leakage. We then performed an unbiased transcriptomic analysis on human retinal microvascular endothelial cells (HRECs) and revealed a pivotal role of EMC1 in the β-catenin signaling pathway. Further in-vitro and in-vivo experiments proved that loss of EMC1 led to compromised β-catenin signaling activity through reduced expression of Wnt receptor FZD4, which could be restored by lithium chloride (LiCl) treatment. Driven by these findings, we screened genomic DNA samples from familial exudative vitreoretinopathy (FEVR) patients and identified one heterozygous variant in EMC1 that co-segregated with FEVR phenotype in the family. In-vitro expression experiments revealed that this variant allele failed to facilitate the expression of FZD4 on the plasma membrane and activate the β-catenin signaling pathway, which might be a main cause of FEVR. In conclusion, our findings reveal that variants in EMC1 gene cause compromised β-catenin signaling activity, which may be associated with the pathogenesis of FEVR.
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Affiliation(s)
- Shujin Li
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
- Research Unit for Blindness Prevention of the Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, China
| | - Mu Yang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
- Research Unit for Blindness Prevention of the Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, China
| | - Rulian Zhao
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
- Research Unit for Blindness Prevention of the Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, China
| | - Li Peng
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
| | - Wenjing Liu
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
| | - Xiaoyan Jiang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
| | - Yunqi He
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
| | - Erkuan Dai
- Department of Ophthalmology, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Lin Zhang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
| | - Yeming Yang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
| | - Yi Shi
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
| | - Peiquan Zhao
- Department of Ophthalmology, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Zhenglin Yang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
- Research Unit for Blindness Prevention of the Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, China
| | - Xianjun Zhu
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
- Research Unit for Blindness Prevention of the Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, China
- Key Laboratory of Tibetan Medicine Research, Chinese Academy of Sciences and Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, Qinghai 810008, China
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20
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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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21
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Guna A, Page KR, Replogle JM, Esantsi TK, Wang ML, Weissman JS, Voorhees RM. A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens. BMC Genomics 2023; 24:651. [PMID: 37904134 PMCID: PMC10614335 DOI: 10.1186/s12864-023-09754-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: 06/20/2023] [Accepted: 10/19/2023] [Indexed: 11/01/2023] Open
Abstract
Mapping genetic interactions is essential for determining gene function and defining novel biological pathways. We report a simple to use CRISPR interference (CRISPRi) based platform, compatible with Fluorescence Activated Cell Sorting (FACS)-based reporter screens, to query epistatic relationships at scale. This is enabled by a flexible dual-sgRNA library design that allows for the simultaneous delivery and selection of a fixed sgRNA and a second randomized guide, comprised of a genome-wide library, with a single transduction. We use this approach to identify epistatic relationships for a defined biological pathway, showing both increased sensitivity and specificity than traditional growth screening approaches.
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Affiliation(s)
- Alina Guna
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave, Pasadena, CA, 91125, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Katharine R Page
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave, Pasadena, CA, 91125, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Theodore K Esantsi
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Maxine L Wang
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave, Pasadena, CA, 91125, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave, Pasadena, CA, 91125, USA.
- Howard Hughes Medical Institute Freeman Hrabowski Scholar, California Institute of Technology, Pasadena, CA, 91125, USA.
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22
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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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23
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Li X, Jiang Z, Su Y, Wang K, Jiang X, Sun K, Yang Y, Zhou Y, Zhu X, Zhang L. Deletion of Emc1 in photoreceptor cells causes retinal degeneration in mice. FEBS J 2023; 290:4356-4370. [PMID: 37098815 DOI: 10.1111/febs.16807] [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: 02/07/2023] [Revised: 03/30/2023] [Accepted: 04/25/2023] [Indexed: 04/27/2023]
Abstract
The endoplasmic reticulum membrane protein complex (EMC) plays a critical role in the synthesis of multipass membrane proteins. Genetic studies indicated that mutations in EMC1 gene were associated with retinal degeneration diseases; however, the role of EMC1 in photoreceptor has not been confirmed. Here, we show that Emc1 ablation in the photoreceptor cells of mice recapitulated the retinitis pigmentosa phenotypes, including an attenuated scotopic electroretinogram response and the progressive degeneration of rod cells and cone cells. Histopathological examination of tissues from rod-specific Emc1 knockout mice revealed mislocalized rhodopsin and irregularly arranged cone cells at the age of 2 months. Further immunoblotting analysis revealed decreased levels of membrane proteins and endoplasmic reticulum chaperones in 1-month-old rod-specific Emc1 knockout mice retinae, and this led us to speculate that the loss of membrane proteins is the main cause of the degeneration of photoreceptors. EMC1 most likely regulated the membrane protein levels at an earlier step in the biosynthetic process before the proteins translocated into the endoplasmic reticulum. The present study demonstrates the essential roles of Emc1 in photoreceptor cells, and reveals the mechanism through which EMC1 mutations are linked to retinitis pigmentosa.
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Affiliation(s)
- Xiao Li
- 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, China
| | - Zhilin Jiang
- 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, China
| | - Yujing Su
- 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, China
| | - Kaifang Wang
- 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, China
| | - Xiaoyan Jiang
- 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, China
| | - Kuanxiang Sun
- 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, China
| | - Yeming Yang
- 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, China
| | - Yu Zhou
- 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, 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, China
- Key Laboratory of Tibetan Medicine Research, Chinese Academy of Sciences and Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, 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, China
- Key Laboratory of Tibetan Medicine Research, Chinese Academy of Sciences and Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
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24
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Marquez J, Aslam F, Khokha MK. Expanding EMC foldopathies: Topogenesis deficits alter the neural crest. Genesis 2023; 61:e23520. [PMID: 37318954 PMCID: PMC10524326 DOI: 10.1002/dvg.23520] [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: 06/23/2022] [Revised: 04/13/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023]
Abstract
The endoplasmic reticulum (ER) membrane protein complex (EMC) is essential for the insertion of a wide variety of transmembrane proteins into the plasma membrane across cell types. Each EMC is composed of Emc1-7, Emc10, and either Emc8 or Emc9. Recent human genetics studies have implicated variants in EMC genes as the basis for a group of human congenital diseases. The patient phenotypes are varied but appear to affect a subset of tissues more prominently than others. Namely, craniofacial development seems to be commonly affected. We previously developed an array of assays in Xenopus tropicalis to assess the effects of emc1 depletion on the neural crest, craniofacial cartilage, and neuromuscular function. We sought to extend this approach to additional EMC components identified in patients with congenital malformations. Through this approach, we determine that EMC9 and EMC10 are important for neural crest development and the development of craniofacial structures. The phenotypes observed in patients and our Xenopus model phenotypes similar to EMC1 loss of function likely due to a similar mechanism of dysfunction in transmembrane protein topogenesis.
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Affiliation(s)
- Jonathan Marquez
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Faiza Aslam
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Mustafa K. Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT, USA
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25
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Pleiner T, Hazu M, Pinton Tomaleri G, Nguyen VN, Januszyk K, Voorhees RM. A selectivity filter in the ER membrane protein complex limits protein misinsertion at the ER. J Cell Biol 2023; 222:e202212007. [PMID: 37199759 PMCID: PMC10200711 DOI: 10.1083/jcb.202212007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/31/2023] [Accepted: 04/20/2023] [Indexed: 05/19/2023] Open
Abstract
Tail-anchored (TA) proteins play essential roles in mammalian cells, and their accurate localization is critical for proteostasis. Biophysical similarities lead to mistargeting of mitochondrial TA proteins to the ER, where they are delivered to the insertase, the ER membrane protein complex (EMC). Leveraging an improved structural model of the human EMC, we used mutagenesis and site-specific crosslinking to map the path of a TA protein from its cytosolic capture by methionine-rich loops to its membrane insertion through a hydrophilic vestibule. Positively charged residues at the entrance to the vestibule function as a selectivity filter that uses charge-repulsion to reject mitochondrial TA proteins. Similarly, this selectivity filter retains the positively charged soluble domains of multipass substrates in the cytosol, thereby ensuring they adopt the correct topology and enforcing the "positive-inside" rule. Substrate discrimination by the EMC provides a biochemical explanation for one role of charge in TA protein sorting and protects compartment integrity by limiting protein misinsertion.
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Affiliation(s)
- Tino Pleiner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Masami Hazu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Giovani Pinton Tomaleri
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Vy N. Nguyen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kurt Januszyk
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rebecca M. Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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26
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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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27
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Yagita Y, Zavodszky E, Peak-Chew SY, Hegde RS. Mechanism of orphan subunit recognition during assembly quality control. Cell 2023; 186:3443-3459.e24. [PMID: 37480851 PMCID: PMC10501995 DOI: 10.1016/j.cell.2023.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 05/16/2023] [Accepted: 06/22/2023] [Indexed: 07/24/2023]
Abstract
Cells contain numerous abundant molecular machines assembled from multiple subunits. Imbalances in subunit production and failed assembly generate orphan subunits that are eliminated by poorly defined pathways. Here, we determined how orphan subunits of the cytosolic chaperonin CCT are recognized. Several unassembled CCT subunits recruited the E3 ubiquitin ligase HERC2 using ZNRD2 as an adaptor. Both factors were necessary for orphan CCT subunit degradation in cells, sufficient for CCT subunit ubiquitination with purified factors, and necessary for optimal cell fitness. Domain mapping and structure prediction defined the molecular features of a minimal HERC2-ZNRD2-CCT module. The structural model, whose key elements were validated in cells using point mutants, shows why ZNRD2 selectively recognizes multiple orphaned CCT subunits without engaging assembled CCT. Our findings reveal how failures during CCT assembly are monitored and provide a paradigm for the molecular recognition of orphan subunits, the largest source of quality control substrates in cells.
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Affiliation(s)
- Yuichi Yagita
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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28
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Koike Y, Takahata M, Nakajima M, Otomo N, Suetsugu H, Liu X, Endo T, Imagama S, Kobayashi K, Kaito T, Kato S, Kawaguchi Y, Kanayama M, Sakai H, Tsuji T, Miyamoto T, Inose H, Yoshii T, Kashii M, Nakashima H, Ando K, Taniguchi Y, Takeuchi K, Ito S, Tomizuka K, Hikino K, Iwasaki Y, Kamatani Y, Maeda S, Nakajima H, Mori K, Seichi A, Fujibayashi S, Kanchiku T, Watanabe K, Tanaka T, Kida K, Kobayashi S, Takahashi M, Yamada K, Takuwa H, Lu HF, Niida S, Ozaki K, Momozawa Y, Yamazaki M, Okawa A, Matsumoto M, Iwasaki N, Terao C, Ikegawa S. Genetic insights into ossification of the posterior longitudinal ligament of the spine. eLife 2023; 12:e86514. [PMID: 37461309 DOI: 10.7554/elife.86514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/22/2023] [Indexed: 07/20/2023] Open
Abstract
Ossification of the posterior longitudinal ligament of the spine (OPLL) is an intractable disease leading to severe neurological deficits. Its etiology and pathogenesis are primarily unknown. The relationship between OPLL and comorbidities, especially type 2 diabetes (T2D) and high body mass index (BMI), has been the focus of attention; however, no trait has been proven to have a causal relationship. We conducted a meta-analysis of genome-wide association studies (GWASs) using 22,016 Japanese individuals and identified 14 significant loci, 8 of which were previously unreported. We then conducted a gene-based association analysis and a transcriptome-wide Mendelian randomization approach and identified three candidate genes for each. Partitioning heritability enrichment analyses observed significant enrichment of the polygenic signals in the active enhancers of the connective/bone cell group, especially H3K27ac in chondrogenic differentiation cells, as well as the immune/hematopoietic cell group. Single-cell RNA sequencing of Achilles tendon cells from a mouse Achilles tendon ossification model confirmed the expression of genes in GWAS and post-GWAS analyses in mesenchymal and immune cells. Genetic correlations with 96 complex traits showed positive correlations with T2D and BMI and a negative correlation with cerebral aneurysm. Mendelian randomization analysis demonstrated a significant causal effect of increased BMI and high bone mineral density on OPLL. We evaluated the clinical images in detail and classified OPLL into cervical, thoracic, and the other types. GWAS subanalyses identified subtype-specific signals. A polygenic risk score for BMI demonstrated that the effect of BMI was particularly strong in thoracic OPLL. Our study provides genetic insight into the etiology and pathogenesis of OPLL and is expected to serve as a basis for future treatment development.
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Affiliation(s)
- Yoshinao Koike
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Department of Orthopedic Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Masahiko Takahata
- Department of Orthopedic Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Masahiro Nakajima
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
| | - Nao Otomo
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Department of Orthopedic Surgery, Keio University School of Medicine, Nagoya, Japan
| | - Hiroyuki Suetsugu
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Tsutomu Endo
- Department of Orthopedic Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Shiro Imagama
- Department of Orthopedics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuyoshi Kobayashi
- Department of Orthopedics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takashi Kaito
- Department of Orthopaedic Surgery, Osaka University Graduate School of Medicine, Suita, Japan
| | - Satoshi Kato
- Department of Orthopaedic Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | | | - Masahiro Kanayama
- Department of Orthopedics, Hakodate Central General Hospital, Hakodate, Japan
| | - Hiroaki Sakai
- Department of Orthopaedic Surgery, Spinal Injuries Center, Iizuka, Japan
| | - Takashi Tsuji
- Department of Orthopedic Surgery, Keio University School of Medicine, Nagoya, Japan
- Department of Spine and Spinal Cord Surgery, Fujita Health University, Toyoake, Japan
| | - Takeshi Miyamoto
- Department of Orthopedic Surgery, Keio University School of Medicine, Nagoya, Japan
- Department of Orthopedic Surgery, Kumamoto University, Kumamoto, Japan
| | - Hiroyuki Inose
- Department of Orthopaedic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Toshitaka Yoshii
- Department of Orthopaedic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masafumi Kashii
- Department of Orthopaedic Surgery, Osaka University Graduate School of Medicine, Suita, Japan
| | - Hiroaki Nakashima
- Department of Orthopedics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kei Ando
- Department of Orthopedics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuki Taniguchi
- Department of Orthopaedic Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Takeuchi
- Department of Orthopaedic Surgery, National Okayama Medical Center, Okayama, Japan
| | - Shuji Ito
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Department of Orthopedic Surgery, Shimane University Faculty of Medicine, Izumo, Japan
| | - Kohei Tomizuka
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Keiko Hikino
- Laboratory for Pharmacogenomics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Yusuke Iwasaki
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Shingo Maeda
- Department of Bone and Joint Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Hideaki Nakajima
- Department of Orthopaedics and Rehabilitation Medicine, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Kanji Mori
- Department of Orthopaedic Surgery, Shiga University of Medical Science, Otsu, Japan
| | - Atsushi Seichi
- Department of Orthopedics, Jichi Medical University, Shimotsuke, Japan
| | - Shunsuke Fujibayashi
- Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tsukasa Kanchiku
- Department of Orthopedic Surgery, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Kei Watanabe
- Department of Orthopaedic Surgery, Niigata University Medical and Dental General Hospital, Nankoku, Japan
| | - Toshihiro Tanaka
- Department of Orthopaedic Surgery, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Kazunobu Kida
- Department of Orthopaedic Surgery, Kochi Medical School, Nankoku, Japan
| | - Sho Kobayashi
- Department of Orthopaedic Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Masahito Takahashi
- Department of Orthopaedic Surgery, Kyorin University School of Medicine, Tokyo, Japan
| | - Kei Yamada
- Department of Orthopaedic Surgery, Kurume University School of Medicine, Obu, Japan
| | - Hiroshi Takuwa
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
- Department of Orthopedic Surgery, Shimane University Faculty of Medicine, Izumo, Japan
| | - Hsing-Fang Lu
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
- Million-Person Precision Medicine Initiative, China Medical University Hospital, Taichung, Taiwan
| | - Shumpei Niida
- Core Facility Administration, Research Institute, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Kouichi Ozaki
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Masashi Yamazaki
- Department of Orthopaedic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Atsushi Okawa
- Department of Orthopaedic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Morio Matsumoto
- Department of Orthopedic Surgery, Keio University School of Medicine, Nagoya, Japan
| | - Norimasa Iwasaki
- Department of Orthopedic Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
- Department of Orthopedic Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
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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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Chen Z, Mondal A, Abderemane-Ali F, Jang S, Niranjan S, Montaño JL, Zaro BW, Minor DL. EMC chaperone-Ca V structure reveals an ion channel assembly intermediate. Nature 2023; 619:410-419. [PMID: 37196677 PMCID: PMC10896479 DOI: 10.1038/s41586-023-06175-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 05/05/2023] [Indexed: 05/19/2023]
Abstract
Voltage-gated ion channels (VGICs) comprise multiple structural units, the assembly of which is required for function1,2. Structural understanding of how VGIC subunits assemble and whether chaperone proteins are required is lacking. High-voltage-activated calcium channels (CaVs)3,4 are paradigmatic multisubunit VGICs whose function and trafficking are powerfully shaped by interactions between pore-forming CaV1 or CaV2 CaVα1 (ref. 3), and the auxiliary CaVβ5 and CaVα2δ subunits6,7. Here we present cryo-electron microscopy structures of human brain and cardiac CaV1.2 bound with CaVβ3 to a chaperone-the endoplasmic reticulum membrane protein complex (EMC)8,9-and of the assembled CaV1.2-CaVβ3-CaVα2δ-1 channel. These structures provide a view of an EMC-client complex and define EMC sites-the transmembrane (TM) and cytoplasmic (Cyto) docks; interaction between these sites and the client channel causes partial extraction of a pore subunit and splays open the CaVα2δ-interaction site. The structures identify the CaVα2δ-binding site for gabapentinoid anti-pain and anti-anxiety drugs6, show that EMC and CaVα2δ interactions with the channel are mutually exclusive, and indicate that EMC-to-CaVα2δ hand-off involves a divalent ion-dependent step and CaV1.2 element ordering. Disruption of the EMC-CaV complex compromises CaV function, suggesting that the EMC functions as a channel holdase that facilitates channel assembly. Together, the structures reveal a CaV assembly intermediate and EMC client-binding sites that could have wide-ranging implications for the biogenesis of VGICs and other membrane proteins.
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Affiliation(s)
- Zhou Chen
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Abhisek Mondal
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Fayal Abderemane-Ali
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Seil Jang
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Sangeeta Niranjan
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - José L Montaño
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Balyn W Zaro
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Daniel L Minor
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA, USA.
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA, USA.
- Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
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31
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Liu N, Huang M, Liang X, Cao M, Lun Z, Zhang Y, Yang J, Bhadauria V, Zhao W, Yan J, Peng YL, Lu X. Magnaporthe oryzae endoplasmic reticulum membrane complex regulates the biogenesis of membrane proteins for pathogenicity. THE NEW PHYTOLOGIST 2023; 238:1163-1181. [PMID: 36772852 DOI: 10.1111/nph.18810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
In eukaryotes, the majority of newly synthesized integral membrane proteins are inserted into the endoplasmic reticulum (ER) membrane before transferred to their functional sites. The conserved ER membrane complex (EMC) takes part in the insertion process for tail-anchored membrane proteins. However, the function of EMC in phytopathogenic fungi has not been characterized. Here, we report the identification and functional characterization of two EMC subunits MoEmc5 and MoEmc2 in Magnaporthe oryzae. The knockout mutants ΔMoemc5 and ΔMoemc2 exhibit substantial defect in autophagy, pathogenicity, cell wall integrity, and magnesium ion sensitivity. We demonstrate that the autophagy process was severely impaired in the ΔMoemc5 and ΔMoemc2 mutants because of the low-protein steady-state level of Atg9, the sole membrane-associated autophagy protein. Furthermore, the protein level of membrane proteins Chs4, Fks1, and MoMnr2 is also significantly reduced in the ΔMoemc5 and ΔMoemc2 strains, leading to their supersensitivity to Calcofluor white, Congo red, and magnesium. In addition, MoEmc5, but not MoEmc2, acts as a magnesium transporter independent of its EMC function. Magnaporthe oryzae EMC regulates the biogenesis of membrane proteins for autophagy and virulence; therefore, EMC subunits could be potential targets for fungicide design in the future.
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Affiliation(s)
- Ning Liu
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Manna Huang
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Xinyuan Liang
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Miao Cao
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Zhiqin Lun
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Yan Zhang
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Jun Yang
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Vijai Bhadauria
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Wensheng Zhao
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Jiye Yan
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - You-Liang Peng
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Xunli Lu
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
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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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Hsiao JM, Penalva YCM, Wu HYL, Xiao B, Jansen G, Dejgaard K, Young JC, Munter LM. Putative Protein Interactome of the Rhomboid Protease RHBDL4. Biochemistry 2023; 62:1209-1218. [PMID: 36857408 DOI: 10.1021/acs.biochem.2c00680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The physiological functions of the rhomboid-related protein 4 (RHBDL4) are emerging, but their molecular details remain unclear. Because increased expression of RHBDL4 has been clinically linked to poorer outcomes in cancer patients, this association urgently demands a better understanding of RHBDL4. To elucidate the molecular interactions and pathways that RHBDL4 may be involved in, we conducted proximity-dependent biotin identification (BioID) assays. Our analyses corroborated several of the expected protein interactors such as the transitional endoplasmic reticulum (ER) ATPase VCP/p97 (TERA), but they also described novel putative interactors including IRS4, PGAM5, and GORS2. Using proximity-ligation assays, we validated VCP/p97, COPB, and VRK2 as proteins that are in proximity to RHBDL4. Overall, our results support the emerging functions of RHBDL4 in ER quality control and also point toward putative RHBDL4 functions in protein membrane insertion and membrane organization and trafficking.
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Affiliation(s)
| | - Ylauna Christine Mégane Penalva
- Department of Pharmacology & Therapeutics, McGill University, Montreal H3G 0B1, Québec, Canada
- Integrated Program in Neuroscience, McGill University, Montreal H3A 2B4, Québec, Canada
- Cell Information Systems Group, Bellini Life Sciences Complex, McGill University, Montreal H3G 0B1, Québec, Canada
| | - Helen Yee-Li Wu
- Department of Pharmacology & Therapeutics, McGill University, Montreal H3G 0B1, Québec, Canada
- Cell Information Systems Group, Bellini Life Sciences Complex, McGill University, Montreal H3G 0B1, Québec, Canada
| | - Bin Xiao
- Department of Pharmacology & Therapeutics, McGill University, Montreal H3G 0B1, Québec, Canada
- Cell Information Systems Group, Bellini Life Sciences Complex, McGill University, Montreal H3G 0B1, Québec, Canada
| | - Gregor Jansen
- Department of Biochemistry, McGill University, Montreal H3G 0B1, Québec, Canada
| | - Kurt Dejgaard
- Department of Biochemistry, McGill University, Montreal H3G 0B1, Québec, Canada
| | - Jason C Young
- Department of Biochemistry, McGill University, Montreal H3G 0B1, Québec, Canada
| | - Lisa Marie Munter
- Department of Pharmacology & Therapeutics, McGill University, Montreal H3G 0B1, Québec, Canada
- Cell Information Systems Group, Bellini Life Sciences Complex, McGill University, Montreal H3G 0B1, Québec, Canada
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Wu H, Hegde RS. Mechanism of signal-anchor triage during early steps of membrane protein insertion. Mol Cell 2023; 83:961-973.e7. [PMID: 36764302 PMCID: PMC10155758 DOI: 10.1016/j.molcel.2023.01.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/08/2022] [Accepted: 01/18/2023] [Indexed: 02/11/2023]
Abstract
Most membrane proteins use their first transmembrane domain, known as a signal anchor (SA), for co-translational targeting to the endoplasmic reticulum (ER) via the signal recognition particle (SRP). The SA then inserts into the membrane using either the Sec61 translocation channel or the ER membrane protein complex (EMC) insertase. How EMC and Sec61 collaborate to ensure SA insertion in the correct topology is not understood. Using site-specific crosslinking, we detect a pre-insertion SA intermediate adjacent to EMC. This intermediate forms after SA release from SRP but before ribosome transfer to Sec61. The polypeptide's N-terminal tail samples a cytosolic vestibule bordered by EMC3, from where it can translocate across the membrane concomitant with SA insertion. The ribosome then docks on Sec61, which has an opportunity to insert those SAs skipped by EMC. These results suggest that EMC acts between SRP and Sec61 to triage SAs for insertion during membrane protein biogenesis.
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Affiliation(s)
- Haoxi Wu
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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35
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Raza A, Diehl SA, Krementsov DN, Case LK, Li D, Kost J, Ball RL, Chesler EJ, Philip VM, Huang R, Chen Y, Ma R, Tyler AL, Mahoney JM, Blankenhorn EP, Teuscher C. A genetic locus complements resistance to Bordetella pertussis-induced histamine sensitization. Commun Biol 2023; 6:244. [PMID: 36879097 PMCID: PMC9988836 DOI: 10.1038/s42003-023-04603-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
Histamine plays pivotal role in normal physiology and dysregulated production of histamine or signaling through histamine receptors (HRH) can promote pathology. Previously, we showed that Bordetella pertussis or pertussis toxin can induce histamine sensitization in laboratory inbred mice and is genetically controlled by Hrh1/HRH1. HRH1 allotypes differ at three amino acid residues with P263-V313-L331 and L263-M313-S331, imparting sensitization and resistance respectively. Unexpectedly, we found several wild-derived inbred strains that carry the resistant HRH1 allotype (L263-M313-S331) but exhibit histamine sensitization. This suggests the existence of a locus modifying pertussis-dependent histamine sensitization. Congenic mapping identified the location of this modifier locus on mouse chromosome 6 within a functional linkage disequilibrium domain encoding multiple loci controlling sensitization to histamine. We utilized interval-specific single-nucleotide polymorphism (SNP) based association testing across laboratory and wild-derived inbred mouse strains and functional prioritization analyses to identify candidate genes for this modifier locus. Atg7, Plxnd1, Tmcc1, Mkrn2, Il17re, Pparg, Lhfpl4, Vgll4, Rho and Syn2 are candidate genes within this modifier locus, which we named Bphse, enhancer of Bordetella pertussis induced histamine sensitization. Taken together, these results identify, using the evolutionarily significant diversity of wild-derived inbred mice, additional genetic mechanisms controlling histamine sensitization.
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Affiliation(s)
- Abbas Raza
- Department of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Sean A Diehl
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, 05405, USA
| | - Dimitry N Krementsov
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, 05405, USA
| | - Laure K Case
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Dawei Li
- Department of Biomedical Science, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Jason Kost
- Catalytic Data Science, Charleston, SC, 29403, USA
| | - Robyn L Ball
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | | | | | - Rui Huang
- School of Life Sciences, University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yan Chen
- School of Life Sciences, University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Runlin Ma
- School of Life Sciences, University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Anna L Tyler
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, 05405, USA
| | - J Matthew Mahoney
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
- Department of Neurological Sciences, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Elizabeth P Blankenhorn
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - Cory Teuscher
- Department of Medicine, University of Vermont, Burlington, VT, 05405, USA.
- Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, 05405, USA.
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36
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Fenech EJ, Cohen N, Kupervaser M, Gazi Z, Schuldiner M. A toolbox for systematic discovery of stable and transient protein interactors in baker's yeast. Mol Syst Biol 2023; 19:e11084. [PMID: 36651308 PMCID: PMC9912024 DOI: 10.15252/msb.202211084] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 01/19/2023] Open
Abstract
Identification of both stable and transient interactions is essential for understanding protein function and regulation. While assessing stable interactions is more straightforward, capturing transient ones is challenging. In recent years, sophisticated tools have emerged to improve transient interactor discovery, with many harnessing the power of evolved biotin ligases for proximity labelling. However, biotinylation-based methods have lagged behind in the model eukaryote, Saccharomyces cerevisiae, possibly due to the presence of several abundant, endogenously biotinylated proteins. In this study, we optimised robust biotin-ligation methodologies in yeast and increased their sensitivity by creating a bespoke technique for downregulating endogenous biotinylation, which we term ABOLISH (Auxin-induced BiOtin LIgase diminiSHing). We used the endoplasmic reticulum insertase complex (EMC) to demonstrate our approaches and uncover new substrates. To make these tools available for systematic probing of both stable and transient interactions, we generated five full-genome collections of strains in which every yeast protein is tagged with each of the tested biotinylation machineries, some on the background of the ABOLISH system. This comprehensive toolkit enables functional interactomics of the entire yeast proteome.
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Affiliation(s)
- Emma J Fenech
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Nir Cohen
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Meital Kupervaser
- The de Botton Protein Profiling Institute of the Nancy and Stephen Grand Israel National Centre for Personalized MedicineWeizmann Institute of ScienceRehovotIsrael
| | - Zohar Gazi
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Maya Schuldiner
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
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37
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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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38
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Sun S, Li X, Mariappan M. Signal sequences encode information for protein folding in the endoplasmic reticulum. J Cell Biol 2023; 222:213733. [PMID: 36459117 PMCID: PMC9723807 DOI: 10.1083/jcb.202203070] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 09/22/2022] [Accepted: 10/26/2022] [Indexed: 12/05/2022] Open
Abstract
One-third of newly synthesized proteins in mammals are translocated into the endoplasmic reticulum (ER) through the Sec61 translocon. How protein translocation coordinates with chaperone availability in the ER to promote protein folding remains unclear. We find that marginally hydrophobic signal sequences and transmembrane domains cause transient retention at the Sec61 translocon and require the luminal BiP chaperone for efficient protein translocation. Using a substrate-trapping proteomic approach, we identify that nascent proteins bearing marginally hydrophobic signal sequences accumulate on the cytosolic side of the Sec61 translocon. Sec63 is co-translationally recruited to the translocation site and mediates BiP binding to incoming polypeptides. BiP binding not only releases translocationally paused nascent chains but also ensures protein folding in the ER. Increasing hydrophobicity of signal sequences bypasses Sec63/BiP-dependent translocation, but translocated proteins are prone to misfold and aggregate in the ER under limited BiP availability. Thus, the signal sequence-guided protein folding may explain why signal sequences are diverse and use multiple protein translocation pathways.
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Affiliation(s)
- Sha Sun
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT
| | - Xia Li
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT
| | - Malaiyalam Mariappan
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale West Campus, West Haven, CT
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39
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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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40
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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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41
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Tang X, Wei W, Snowball JM, Nakayasu ES, Bell SM, Ansong C, Lin X, Whitsett JA. EMC3 regulates mesenchymal cell survival via control of the mitotic spindle assembly. iScience 2022; 26:105667. [PMID: 36624844 PMCID: PMC9823123 DOI: 10.1016/j.isci.2022.105667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 08/15/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
Eukaryotic cells transit through the cell cycle to produce two daughter cells. Dysregulation of the cell cycle leads to cell death or tumorigenesis. Herein, we found a subunit of the ER membrane complex, EMC3, as a key regulator of cell cycle. Conditional deletion of Emc3 in mouse embryonic mesoderm led to reduced size and patterning defects of multiple organs. Emc3 deficiency impaired cell proliferation, causing spindle assembly defects, chromosome mis-segregation, cell cycle arrest at G2/M, and apoptosis. Upon entry into mitosis, mesenchymal cells upregulate EMC3 protein levels and localize EMC3 to the mitotic centrosomes. Further analysis indicated that EMC3 works together with VCP to tightly regulate the levels and activity of Aurora A, an essential factor for centrosome function and mitotic spindle assembly: while overexpression of EMC3 or VCP degraded Aurora A, their loss led to increased Aurora A stability but reduced Aurora A phosphorylation in mitosis.
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Affiliation(s)
- Xiaofang Tang
- Perinatal Institute, Divisions of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 7029, Cincinnati, OH 45229, USA,Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, 2nd Nanjiang Rd, Nansha District, Guangzhou 511458, China
| | - Wei Wei
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, No. 2005 Songhu Rd, Shanghai 200438, China
| | - John M. Snowball
- Perinatal Institute, Divisions of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 7029, Cincinnati, OH 45229, USA
| | - Ernesto S. Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, USA
| | - Sheila M. Bell
- Perinatal Institute, Divisions of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 7029, Cincinnati, OH 45229, USA
| | - Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, USA
| | - Xinhua Lin
- Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, 2nd Nanjiang Rd, Nansha District, Guangzhou 511458, China,State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, No. 2005 Songhu Rd, Shanghai 200438, China,Corresponding author
| | - Jeffrey A. Whitsett
- Perinatal Institute, Divisions of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 7029, Cincinnati, OH 45229, USA,Corresponding author
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42
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McKenna MJ, Adams BM, Chu V, Paulo JA, Shao S. ATP13A1 prevents ERAD of folding-competent mislocalized and misoriented proteins. Mol Cell 2022; 82:4277-4289.e10. [PMID: 36283413 PMCID: PMC9675726 DOI: 10.1016/j.molcel.2022.09.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/18/2022] [Accepted: 09/26/2022] [Indexed: 11/18/2022]
Abstract
The biosynthesis of thousands of proteins requires targeting a signal sequence or transmembrane segment (TM) to the endoplasmic reticulum (ER). These hydrophobic ɑ helices must localize to the appropriate cellular membrane and integrate in the correct topology to maintain a high-fidelity proteome. Here, we show that the P5A-ATPase ATP13A1 prevents the accumulation of mislocalized and misoriented proteins, which are eliminated by different ER-associated degradation (ERAD) pathways in mammalian cells. Without ATP13A1, mitochondrial tail-anchored proteins mislocalize to the ER through the ER membrane protein complex and are cleaved by signal peptide peptidase for ERAD. ATP13A1 also facilitates the topogenesis of a subset of proteins with an N-terminal TM or signal sequence that should insert into the ER membrane with a cytosolic N terminus. Without ATP13A1, such proteins accumulate in the wrong orientation and are targeted for ERAD by distinct ubiquitin ligases. Thus, ATP13A1 prevents ERAD of diverse proteins capable of proper folding.
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Affiliation(s)
- Michael J McKenna
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115, USA
| | - Benjamin M Adams
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115, USA
| | - Vincent Chu
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115, USA
| | - Sichen Shao
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115, USA.
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43
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Smalinskaitė L, Kim MK, Lewis AJO, Keenan RJ, Hegde RS. Mechanism of an intramembrane chaperone for multipass membrane proteins. Nature 2022; 611:161-166. [PMID: 36261528 PMCID: PMC7614104 DOI: 10.1038/s41586-022-05336-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 09/12/2022] [Indexed: 01/29/2023]
Abstract
Multipass membrane proteins play numerous roles in biology and include receptors, transporters, ion channels and enzymes1,2. How multipass proteins are co-translationally inserted and folded at the endoplasmic reticulum is not well understood2. The prevailing model posits that each transmembrane domain (TMD) of a multipass protein successively passes into the lipid bilayer through a front-side lateral gate of the Sec61 protein translocation channel3-9. The PAT complex, an intramembrane chaperone comprising Asterix and CCDC47, engages early TMDs of multipass proteins to promote their biogenesis by an unknown mechanism10. Here, biochemical and structural analysis of intermediates during multipass protein biogenesis showed that the nascent chain is not engaged with Sec61, which is occluded and latched closed by CCDC47. Instead, Asterix binds to and redirects the substrate to a location behind Sec61, where the PAT complex contributes to a multipass translocon surrounding a semi-enclosed, lipid-filled cavity11. Detection of multiple TMDs in this cavity after their emergence from the ribosome suggests that multipass proteins insert and fold behind Sec61. Accordingly, biogenesis of several multipass proteins was unimpeded by inhibitors of the Sec61 lateral gate. These findings elucidate the mechanism of an intramembrane chaperone and suggest a new framework for multipass membrane protein biogenesis at the endoplasmic reticulum.
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Affiliation(s)
- Luka Smalinskaitė
- MRC Laboratory of Molecular Biology, Cell Biology Division, Cambridge, UK
| | - Min Kyung Kim
- MRC Laboratory of Molecular Biology, Cell Biology Division, Cambridge, UK
| | - Aaron J O Lewis
- MRC Laboratory of Molecular Biology, Cell Biology Division, Cambridge, UK
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Cell Biology Division, Cambridge, UK.
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44
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O'Keefe S, Pool MR, High S. Membrane protein biogenesis at the ER: the highways and byways. FEBS J 2022; 289:6835-6862. [PMID: 33960686 DOI: 10.1111/febs.15905] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/19/2021] [Accepted: 04/28/2021] [Indexed: 01/13/2023]
Abstract
The Sec61 complex is the major protein translocation channel of the endoplasmic reticulum (ER), where it plays a central role in the biogenesis of membrane and secretory proteins. Whilst Sec61-mediated protein translocation is typically coupled to polypeptide synthesis, suggestive of significant complexity, an obvious characteristic of this core translocation machinery is its surprising simplicity. Over thirty years after its initial discovery, we now understand that the Sec61 complex is in fact the central piece of an elaborate jigsaw puzzle, which can be partly solved using new research findings. We propose that the Sec61 complex acts as a dynamic hub for co-translational protein translocation at the ER, proactively recruiting a range of accessory complexes that enhance and regulate its function in response to different protein clients. It is now clear that the Sec61 complex does not have a monopoly on co-translational insertion, with some transmembrane proteins preferentially utilising the ER membrane complex instead. We also have a better understanding of post-insertion events, where at least one membrane-embedded chaperone complex can capture the newly inserted transmembrane domains of multi-span proteins and co-ordinate their assembly into a native structure. Having discovered this array of Sec61-associated components and competitors, our next challenge is to understand how they act together in order to expand the range and complexity of the membrane proteins that can be synthesised at the ER. Furthermore, this diversity of components and pathways may open up new opportunities for targeted therapeutic interventions designed to selectively modulate protein biogenesis at the ER.
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Affiliation(s)
- Sarah O'Keefe
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Martin R Pool
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Stephen High
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
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45
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Bloemeke N, Meighen‐Berger K, Hitzenberger M, Bach NC, Parr M, Coelho JPL, Frishman D, Zacharias M, Sieber SA, Feige MJ. Intramembrane client recognition potentiates the chaperone functions of calnexin. EMBO J 2022; 41:e110959. [PMID: 36314723 PMCID: PMC9753464 DOI: 10.15252/embj.2022110959] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
One-third of the human proteome is comprised of membrane proteins, which are particularly vulnerable to misfolding and often require folding assistance by molecular chaperones. Calnexin (CNX), which engages client proteins via its sugar-binding lectin domain, is one of the most abundant ER chaperones, and plays an important role in membrane protein biogenesis. Based on mass spectrometric analyses, we here show that calnexin interacts with a large number of nonglycosylated membrane proteins, indicative of additional nonlectin binding modes. We find that calnexin preferentially bind misfolded membrane proteins and that it uses its single transmembrane domain (TMD) for client recognition. Combining experimental and computational approaches, we systematically dissect signatures for intramembrane client recognition by calnexin, and identify sequence motifs within the calnexin TMD region that mediate client binding. Building on this, we show that intramembrane client binding potentiates the chaperone functions of calnexin. Together, these data reveal a widespread role of calnexin client recognition in the lipid bilayer, which synergizes with its established lectin-based substrate binding. Molecular chaperones thus can combine different interaction modes to support the biogenesis of the diverse eukaryotic membrane proteome.
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Affiliation(s)
- Nicolas Bloemeke
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Kevin Meighen‐Berger
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Manuel Hitzenberger
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Nina C Bach
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Marina Parr
- Department of Bioinformatics, TUM School of Life SciencesTechnical University of MunichFreisingGermany
| | - Joao PL Coelho
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Dmitrij Frishman
- Department of Bioinformatics, TUM School of Life SciencesTechnical University of MunichFreisingGermany
| | - Martin Zacharias
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Stephan A Sieber
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Matthias J Feige
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
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46
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Guna A, Stevens TA, Inglis AJ, Replogle JM, Esantsi TK, Muthukumar G, Shaffer KCL, Wang ML, Pogson AN, Jones JJ, Lomenick B, Chou TF, Weissman JS, Voorhees RM. MTCH2 is a mitochondrial outer membrane protein insertase. Science 2022; 378:317-322. [PMID: 36264797 PMCID: PMC9674023 DOI: 10.1126/science.add1856] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In the mitochondrial outer membrane, α-helical transmembrane proteins play critical roles in cytoplasmic-mitochondrial communication. Using genome-wide CRISPR screens, we identified MTCH2, and its paralog MTCH1, and showed that it is required for insertion of biophysically diverse tail-anchored (TA), signal-anchored, and multipass proteins, but not outer membrane β-barrel proteins. Purified MTCH2 was sufficient to mediate insertion into reconstituted proteoliposomes. Functional and mutational studies suggested that MTCH2 has evolved from a solute carrier transporter. MTCH2 uses membrane-embedded hydrophilic residues to function as a gatekeeper for the outer membrane, controlling mislocalization of TAs into the endoplasmic reticulum and modulating the sensitivity of leukemia cells to apoptosis. Our identification of MTCH2 as an insertase provided a mechanistic explanation for the diverse phenotypes and disease states associated with MTCH2 dysfunction. We showed that MTCH2 was both necessary and sufficient for insertion of diverse α-helical proteins into the mitochondrial outer membrane, and was the defining member of a family of insertases that have co-opted the SLC25 transporter fold.
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Affiliation(s)
- Alina Guna
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Taylor A Stevens
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Alison J Inglis
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA.,Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Theodore K Esantsi
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Gayathri Muthukumar
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Kelly C L Shaffer
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Maxine L Wang
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Angela N Pogson
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jeff J Jones
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Brett Lomenick
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
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47
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Berks BC. Assembly surprise for membrane proteins. Nature 2022; 611:40-41. [PMID: 36261716 DOI: 10.1038/d41586-022-03221-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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48
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Substrate-driven assembly of a translocon for multipass membrane proteins. Nature 2022; 611:167-172. [PMID: 36261522 PMCID: PMC9630114 DOI: 10.1038/s41586-022-05330-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 09/07/2022] [Indexed: 11/19/2022]
Abstract
Most membrane proteins are synthesized on endoplasmic reticulum (ER)-bound ribosomes docked at the translocon, a heterogeneous ensemble of transmembrane factors operating on the nascent chain1,2. How the translocon coordinates the actions of these factors to accommodate its different substrates is not well understood. Here we define the composition, function and assembly of a translocon specialized for multipass membrane protein biogenesis3. This ‘multipass translocon’ is distinguished by three components that selectively bind the ribosome–Sec61 complex during multipass protein synthesis: the GET- and EMC-like (GEL), protein associated with translocon (PAT) and back of Sec61 (BOS) complexes. Analysis of insertion intermediates reveals how features of the nascent chain trigger multipass translocon assembly. Reconstitution studies demonstrate a role for multipass translocon components in protein topogenesis, and cells lacking these components show reduced multipass protein stability. These results establish the mechanism by which nascent multipass proteins selectively recruit the multipass translocon to facilitate their biogenesis. More broadly, they define the ER translocon as a dynamic assembly whose subunit composition adjusts co-translationally to accommodate the biosynthetic needs of its diverse range of substrates. Biochemical reconstitution and functional analysis reveal how newly synthesized multipass membrane proteins dynamically remodel the translocon to facilitate their successful biogenesis.
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49
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Wang YJ, Di XJ, Mu TW. Quantitative interactome proteomics identifies a proteostasis network for GABA A receptors. J Biol Chem 2022; 298:102423. [PMID: 36030824 PMCID: PMC9493394 DOI: 10.1016/j.jbc.2022.102423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/29/2022] Open
Abstract
Gamma-aminobutyric acid type A (GABAA) receptors are the primary inhibitory neurotransmitter-gated ion channels in the mammalian central nervous system. Maintenance of GABAA receptor protein homeostasis (proteostasis) in cells utilizing its interacting proteins is essential for the function of GABAA receptors. However, how the proteostasis network orchestrates GABAA receptor biogenesis in the endoplasmic reticulum is not well understood. Here, we employed a proteomics-based approach to systematically identify the interactomes of GABAA receptors. We carried out a quantitative immunoprecipitation-tandem mass spectrometry analysis utilizing stable isotope labeling by amino acids in cell culture. Furthermore, we performed comparative proteomics by using both WT α1 subunit and a misfolding-prone α1 subunit carrying the A322D variant as the bait proteins. We identified 125 interactors for WT α1-containing receptors, 105 proteins for α1(A322D)-containing receptors, and 54 overlapping proteins within these two interactomes. Our bioinformatics analysis identified potential GABAA receptor proteostasis network components, including chaperones, folding enzymes, trafficking factors, and degradation factors, and we assembled a model of their potential involvement in the cellular folding, degradation, and trafficking pathways for GABAA receptors. In addition, we verified endogenous interactions between α1 subunits and selected interactors by using coimmunoprecipitation in mouse brain homogenates. Moreover, we showed that TRIM21 (tripartite motif containing-21), an E3 ubiquitin ligase, positively regulated the degradation of misfolding-prone α1(A322D) subunits selectively. This study paves the way for understanding the molecular mechanisms as well as fine-tuning of GABAA receptor proteostasis to ameliorate related neurological diseases such as epilepsy.
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Affiliation(s)
- Ya-Juan Wang
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA; Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.
| | - Xiao-Jing Di
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Ting-Wei Mu
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.
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50
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Dong C, Fang X, Xiong J, Zhang J, Gan H, Song C, Wang L. Simultaneous Visualization of Dual Intercellular Signal Transductions via SERS Imaging of Membrane Proteins Dimerization on Single Cells. ACS NANO 2022; 16:14055-14065. [PMID: 35969886 DOI: 10.1021/acsnano.2c03914] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The visualization of protein dimerization on live cells is an urgent need and of vital importance for facile monitoring the signal transduction during intercellular communication. Herein, a highly sensitive and specific SERS strategy for simultaneously imaging dual homodimerizations of membrane proteins on single live cells was proposed by networking of AuNPs-based dual-recognition probes (dual-RPs) and SERS tags via proximity ligation-assisted catalytic hairpin assembly (CHA). The dual-RPs were prepared by comodifying hairpin-structured ssDNAs H1-Met and H1-TβRII on 50 nm AuNPs and two SERS tags for membrane proteins Met and TβRII were prepared respectively by labeling their corresponding Raman molecules and hairpin-structured single-stranded DNAs H2-Met or H2-TβRII on 15 nm AuNPs. The membrane proteins were ligated proximally by specific aptamers, and the dimerizations of proteins resulted in the proximity ligation-assisted CHA-based networking of dual-RPs and SERS tags to form 15Au-50Au network nanostructures with significantly enhanced SERS effect. The SERS strategy for visualizing the membrane protein dimerization was established and the good performance on simultaneously SERS imaging dual dimerizations of membrane proteins (i.e., Met-Met and TβRII-TβRII) was confirmed. Furthermore, the membrane protein dimerization-based signaling pathways between cancer cells and stromal cells or stem cells were observed by SERS, which indicates that the proposed SERS strategy is a good method for high-sensitivity monitoring of membrane proteins dimerizations-based multiple intercellular signal transductions in a natural and complex cellular microenvironment.
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Affiliation(s)
- Chen Dong
- State Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Xinyue Fang
- State Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Jingrong Xiong
- State Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Jingjing Zhang
- State Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Hongyu Gan
- State Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Chunyuan Song
- State Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Lianhui Wang
- State Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
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