1
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Gaspar CJ, Gomes T, Martins JC, Melo MN, Adrain C, Cordeiro TN, Domingos PM. Xport-A functions as a chaperone by stabilizing the first five transmembrane domains of rhodopsin-1. iScience 2023; 26:108309. [PMID: 38025784 PMCID: PMC10663829 DOI: 10.1016/j.isci.2023.108309] [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: 08/19/2022] [Revised: 04/21/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Rhodopsin-1 (Rh1), the main photosensitive protein of Drosophila, is a seven-transmembrane domain protein, which is inserted co-translationally in the endoplasmic reticulum (ER) membrane. Biogenesis of Rh1 occurs in the ER, where various chaperones interact with Rh1 to aid in its folding and subsequent transport from the ER to the rhabdomere, the light-sensing organelle of the photoreceptors. Xport-A has been proposed as a chaperone/transport factor for Rh1, but the exact molecular mechanism for Xport-A activity upon Rh1 is unknown. Here, we propose a model where Xport-A functions as a chaperone during the biogenesis of Rh1 in the ER by stabilizing the first five transmembrane domains (TMDs) of Rh1.
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Affiliation(s)
- Catarina J. Gaspar
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB-NOVA), Av. da República, 2780-157 Oeiras, Portugal
- Membrane Traffic Lab, Instituto Gulbenkian de Ciência (IGC), 2780-156 Oeiras, Portugal
| | - Tiago Gomes
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB-NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Joana C. Martins
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB-NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB-NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Colin Adrain
- Membrane Traffic Lab, Instituto Gulbenkian de Ciência (IGC), 2780-156 Oeiras, Portugal
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, 97 Lisburn Road, BT9 7AE Belfast, UK
| | - Tiago N. Cordeiro
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB-NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Pedro M. Domingos
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB-NOVA), Av. da República, 2780-157 Oeiras, Portugal
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2
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Huang Y, Yu G, Yang Y. MIGGRI: A multi-instance graph neural network model for inferring gene regulatory networks for Drosophila from spatial expression images. PLoS Comput Biol 2023; 19:e1011623. [PMID: 37939200 PMCID: PMC10659162 DOI: 10.1371/journal.pcbi.1011623] [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: 04/02/2023] [Revised: 11/20/2023] [Accepted: 10/22/2023] [Indexed: 11/10/2023] Open
Abstract
Recent breakthrough in spatial transcriptomics has brought great opportunities for exploring gene regulatory networks (GRNs) from a brand-new perspective. Especially, the local expression patterns and spatio-temporal regulation mechanisms captured by spatial expression images allow more delicate delineation of the interplay between transcript factors and their target genes. However, the complexity and size of spatial image collections pose significant challenges to GRN inference using image-based methods. Extracting regulatory information from expression images is difficult due to the lack of supervision and the multi-instance nature of the problem, where a gene often corresponds to multiple images captured from different views. While graph models, particularly graph neural networks, have emerged as a promising method for leveraging underlying structure information from known GRNs, incorporating expression images into graphs is not straightforward. To address these challenges, we propose a two-stage approach, MIGGRI, for capturing comprehensive regulatory patterns from image collections for each gene and known interactions. Our approach involves a multi-instance graph neural network (GNN) model for GRN inference, which first extracts gene regulatory features from spatial expression images via contrastive learning, and then feeds them to a multi-instance GNN for semi-supervised learning. We apply our approach to a large set of Drosophila embryonic spatial gene expression images. MIGGRI achieves outstanding performance in the inference of GRNs for early eye development and mesoderm development of Drosophila, and shows robustness in the scenarios of missing image information. Additionally, we perform interpretable analysis on image reconstruction and functional subgraphs that may reveal potential pathways or coordinate regulations. By leveraging the power of graph neural networks and the information contained in spatial expression images, our approach has the potential to advance our understanding of gene regulation in complex biological systems.
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Affiliation(s)
- Yuyang Huang
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai, China
| | - Gufeng Yu
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai, China
| | - Yang Yang
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai, China
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3
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McKenna MJ, Shao S. The Endoplasmic Reticulum and the Fidelity of Nascent Protein Localization. Cold Spring Harb Perspect Biol 2023; 15:a041249. [PMID: 36041782 PMCID: PMC9979852 DOI: 10.1101/cshperspect.a041249] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
High-fidelity protein localization is essential to define the identities and functions of different organelles and to maintain cellular homeostasis. Accurate localization of nascent proteins requires specific protein targeting pathways as well as quality control (QC) mechanisms to remove mislocalized proteins. The endoplasmic reticulum (ER) is the first destination for approximately one-third of the eukaryotic proteome and a major site of protein biosynthesis and QC. In mammalian cells, trafficking from the ER provides nascent proteins access to the extracellular space and essentially every cellular membrane and organelle except for mitochondria and possibly peroxisomes. Here, we discuss the biosynthetic mechanisms that deliver nascent proteins to the ER and the QC mechanisms that interface with the ER to correct or degrade mislocalized proteins.
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Affiliation(s)
- Michael J McKenna
- Department of Cell Biology, Harvard Medical School, Blavatnik Institute, Boston, Massachusetts 02115, USA
| | - Sichen Shao
- Department of Cell Biology, Harvard Medical School, Blavatnik Institute, Boston, Massachusetts 02115, USA
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4
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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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5
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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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6
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Gaspar CJ, Vieira LC, Santos CC, Christianson JC, Jakubec D, Strisovsky K, Adrain C, Domingos PM. EMC is required for biogenesis of Xport-A, an essential chaperone of Rhodopsin-1 and the TRP channel. EMBO Rep 2022; 23:e53210. [PMID: 34918864 PMCID: PMC8728618 DOI: 10.15252/embr.202153210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 10/26/2021] [Accepted: 11/10/2021] [Indexed: 01/07/2023] Open
Abstract
The ER membrane protein complex (EMC) is required for the biogenesis of a subset of tail anchored (TA) and polytopic membrane proteins, including Rhodopsin-1 (Rh1) and the TRP channel. To understand the physiological implications of EMC-dependent membrane protein biogenesis, we perform a bioinformatic identification of Drosophila TA proteins. From 254 predicted TA proteins, screening in larval eye discs identified two proteins that require EMC for their biogenesis: fan and Xport-A. Fan is required for male fertility in Drosophila and we show that EMC is also required for this process. Xport-A is essential for the biogenesis of both Rh1 and TRP, raising the possibility that disruption of Rh1 and TRP biogenesis in EMC mutants is secondary to the Xport-A defect. We show that EMC is required for Xport-A TMD membrane insertion and that EMC-independent Xport-A mutants rescue Rh1 and TRP biogenesis in EMC mutants. Finally, our work also reveals a role for Xport-A in a glycosylation-dependent triage mechanism during Rh1 biogenesis in the endoplasmic reticulum.
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Affiliation(s)
- Catarina J Gaspar
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB‐NOVA)OeirasPortugal
- Membrane Traffic LabInstituto Gulbenkian de Ciência (IGC)OeirasPortugal
| | - Lígia C Vieira
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB‐NOVA)OeirasPortugal
- Present address:
Center for Genomics and Systems BiologyNew York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Cristiana C Santos
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB‐NOVA)OeirasPortugal
| | - John C Christianson
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesBotnar Research CentreUniversity of OxfordOxfordUK
| | - David Jakubec
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesPragueCzech Republic
| | - Kvido Strisovsky
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesPragueCzech Republic
| | - Colin Adrain
- Membrane Traffic LabInstituto Gulbenkian de Ciência (IGC)OeirasPortugal
- Patrick G Johnston Centre for Cancer ResearchQueen’s UniversityBelfastUK
| | - Pedro M Domingos
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB‐NOVA)OeirasPortugal
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7
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Phillips BP, Miller EA. Ribosome-associated quality control of membrane proteins at the endoplasmic reticulum. J Cell Sci 2020; 133:133/22/jcs251983. [PMID: 33247003 PMCID: PMC7116877 DOI: 10.1242/jcs.251983] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Protein synthesis is an energetically costly, complex and risky process. Aberrant protein biogenesis can result in cellular toxicity and disease, with membrane-embedded proteins being particularly challenging for the cell. In order to protect the cell from consequences of defects in membrane proteins, quality control systems act to maintain protein homeostasis. The majority of these pathways act post-translationally; however, recent evidence reveals that membrane proteins are also subject to co-translational quality control during their synthesis in the endoplasmic reticulum (ER). This newly identified quality control pathway employs components of the cytosolic ribosome-associated quality control (RQC) machinery but differs from canonical RQC in that it responds to biogenesis state of the substrate rather than mRNA aberrations. This ER-associated RQC (ER-RQC) is sensitive to membrane protein misfolding and malfunctions in the ER insertion machinery. In this Review, we discuss the advantages of co-translational quality control of membrane proteins, as well as potential mechanisms of substrate recognition and degradation. Finally, we discuss some outstanding questions concerning future studies of ER-RQC of membrane proteins.
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Affiliation(s)
- Ben P Phillips
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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8
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Miller-Vedam LE, Bräuning B, Popova KD, Schirle Oakdale NT, Bonnar JL, Prabu JR, Boydston EA, Sevillano N, Shurtleff MJ, Stroud RM, Craik CS, Schulman BA, Frost A, Weissman JS. Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients. eLife 2020; 9:e62611. [PMID: 33236988 PMCID: PMC7785296 DOI: 10.7554/elife.62611] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
Membrane protein biogenesis in the endoplasmic reticulum (ER) is complex and failure-prone. The ER membrane protein complex (EMC), comprising eight conserved subunits, has emerged as a central player in this process. Yet, we have limited understanding of how EMC enables insertion and integrity of diverse clients, from tail-anchored to polytopic transmembrane proteins. Here, yeast and human EMC cryo-EM structures reveal conserved intricate assemblies and human-specific features associated with pathologies. Structure-based functional studies distinguish between two separable EMC activities, as an insertase regulating tail-anchored protein levels and a broader role in polytopic membrane protein biogenesis. These depend on mechanistically coupled yet spatially distinct regions including two lipid-accessible membrane cavities which confer client-specific regulation, and a non-insertase EMC function mediated by the EMC lumenal domain. Our studies illuminate the structural and mechanistic basis of EMC's multifunctionality and point to its role in differentially regulating the biogenesis of distinct client protein classes.
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Affiliation(s)
- Lakshmi E Miller-Vedam
- Molecular, Cellular, and Computational Biophysics Graduate Program, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Bastian Bräuning
- Department of Molecular Machines and Signaling, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Katerina D Popova
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Biomedical Sciences Graduate Program, University of California, San FranciscoSan FranciscoUnited States
| | - Nicole T Schirle Oakdale
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Jessica L Bonnar
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Jesuraj R Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Elizabeth A Boydston
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Natalia Sevillano
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
| | - Matthew J Shurtleff
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Jonathan S Weissman
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
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9
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Borgese N. Searching for remote homologs of CAML among eukaryotes. Traffic 2020; 21:647-658. [PMID: 32715580 DOI: 10.1111/tra.12758] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 12/30/2022]
Abstract
The tryptophan rich basic protein/calcium signal-modulating cyclophilin ligand (WRB/CAML) and Get1p/Get2p complexes, in vertebrates and yeast, respectively, mediate the final step of tail-anchored protein insertion into the endoplasmic reticulum membrane via the Get pathway. While WRB appears to exist in all eukaryotes, CAML homologs were previously recognized only among chordates, raising the question as to how CAML's function is performed in other phyla. Furthermore, whereas WRB was recognized as the metazoan homolog of Get1, CAML and Get2, although functionally equivalent, were not considered to be homologous. CAML contains an N-terminal basic, TRC40/Get3-interacting, region, three transmembrane segments near the C-terminus, and a poorly conserved region between these domains. Here, I searched the NCBI protein database for remote CAML homologs in all eukaryotes, using position-specific iterated-basic local alignment search tool, with the C-terminal, the N-terminal or the full-length sequence of human CAML as query. The N-terminal basic region and full-length CAML retrieved homologs among metazoa, plants and fungi. In the latter group several hits were annotated as GET2. The C-terminal query did not return entries outside of the animal kingdom, but did retrieve over one hundred invertebrate metazoan CAML-like proteins, which all conserved the N-terminal TRC40-binding domain. The results indicate that CAML homologs exist throughout the eukaryotic domain of life, and suggest that metazoan CAML and yeast GET2 share a common evolutionary origin. They further reveal a tight link between the particular features of the metazoan membrane-anchoring domain and the TRC40-interacting region. The list of sequences presented here should provide a useful resource for future studies addressing structure-function relationships in CAML proteins.
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Affiliation(s)
- Nica Borgese
- Neuroscience Institute, CNR (Consiglio Nazionale delle Ricerche), Milan, Italy
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10
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Bai L, You Q, Feng X, Kovach A, Li H. Structure of the ER membrane complex, a transmembrane-domain insertase. Nature 2020; 584:475-478. [PMID: 32494008 PMCID: PMC7442705 DOI: 10.1038/s41586-020-2389-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/07/2020] [Indexed: 11/24/2022]
Abstract
The ER membrane complex (EMC) cooperates with the Sec61 translocon to co-translationally insert a transmembrane helix (TMH) of many multi-pass integral membrane proteins into the ER membrane, and it is also responsible for inserting the TMH of some tail-anchored proteins 1–3. How EMC accomplishes this feat has been unclear. Here we report the first cryo-EM structure of the eukaryotic EMC. We found that the Saccharomyces cerevisiae EMC contains eight subunits (Emc1–6, 7, and 10); has a large lumenal region and a smaller cytosolic region; and has a transmembrane region formed by Emc4, 5, and 6 plus the transmembrane domains (TMDs) of Emc1 and 3. We identified a 5-TMH fold centered around Emc3 that resembles the prokaryotic insertase YidC and that delineates a largely hydrophilic client pocket. The TMD of Emc4 tilts away from the main transmembrane region of EMC and is partially mobile. Mutational studies demonstrated that Emc4 flexibility and the hydrophilicity of the client pocket are required for EMC function. The EMC structure reveals a remarkable evolutionary conservation with the prokaryotic insertases 4,5; suggests a similar mechanism of TMH insertion; and provides a framework for detailed understanding of membrane insertion for numerous eukaryotic integral membrane proteins and tail-anchored proteins.
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Affiliation(s)
- Lin Bai
- Structural Biology Program, Van Andel Institute, Grand Rapids, MI, USA.
| | - Qinglong You
- Structural Biology Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Xiang Feng
- Structural Biology Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Amanda Kovach
- Structural Biology Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Huilin Li
- Structural Biology Program, Van Andel Institute, Grand Rapids, MI, USA.
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