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Gemmer M, Chaillet ML, Förster F. Exploring the molecular composition of the multipass translocon in its native membrane environment. Life Sci Alliance 2024; 7:e202302496. [PMID: 38866426 PMCID: PMC11169918 DOI: 10.26508/lsa.202302496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024] Open
Abstract
Multispanning membrane proteins are inserted into the endoplasmic reticulum membrane by the ribosome-bound multipass translocon (MPT) machinery. Based on cryo-electron tomography and extensive subtomogram analysis, we reveal the composition and arrangement of ribosome-bound MPT components in their native membrane environment. The intramembrane chaperone complex PAT and the translocon-associated protein (TRAP) complex associate substoichiometrically with the MPT in a translation-dependent manner. Although PAT is preferentially part of MPTs bound to translating ribosomes, the abundance of TRAP is highest in MPTs associated with non-translating ribosomes. The subtomogram average of the TRAP-containing MPT reveals intermolecular contacts between the luminal domains of TRAP and an unknown subunit of the back-of-Sec61 complex. AlphaFold modeling suggests this protein is nodal modulator, bridging the luminal domains of nicalin and TRAPα. Collectively, our results visualize the variability of MPT factors in the native membrane environment dependent on the translational activity of the bound ribosome.
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Affiliation(s)
- Max Gemmer
- https://ror.org/04pp8hn57 Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Marten L Chaillet
- https://ror.org/04pp8hn57 Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Friedrich Förster
- https://ror.org/04pp8hn57 Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
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2
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Sawyer EM, Jensen LE, Meehl JB, Larsen KP, Petito DA, Hurley JH, Voeltz GK. SigmaR1 shapes rough endoplasmic reticulum membrane sheets. Dev Cell 2024:S1534-5807(24)00382-4. [PMID: 38971154 DOI: 10.1016/j.devcel.2024.06.005] [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: 09/25/2023] [Revised: 02/12/2024] [Accepted: 06/07/2024] [Indexed: 07/08/2024]
Abstract
Rough endoplasmic reticulum (ER) sheets are a fundamental domain of the ER and the gateway into the secretory pathway. Although reticulon proteins stabilize high-curvature ER tubules, it is unclear whether other proteins scaffold the flat membranes of rough ER sheets. Through a proteomics screen using ER sheet-localized RNA-binding proteins as bait, we identify the sigma-1 receptor (SigmaR1) as an ER sheet-shaping factor. High-resolution live cell imaging and electron tomography assign SigmaR1 as an ER sheet-localized factor whose levels determine the amount of rough ER sheets in cells. Structure-guided mutagenesis and in vitro reconstitution on giant unilamellar vesicles further support a mechanism whereby SigmaR1 oligomers use their extended arrays of amphipathic helices to bind and flatten the lumenal leaflet of ER membranes to oppose membrane curvature and stabilize rough ER sheets.
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Affiliation(s)
- Eric M Sawyer
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute
| | - Liv E Jensen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Janet B Meehl
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute
| | - Kevin P Larsen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniel A Petito
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gia K Voeltz
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute.
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den Brave F, Schulte U, Fakler B, Pfanner N, Becker T. Mitochondrial complexome and import network. Trends Cell Biol 2024; 34:578-594. [PMID: 37914576 DOI: 10.1016/j.tcb.2023.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023]
Abstract
Mitochondria perform crucial functions in cellular metabolism, protein and lipid biogenesis, quality control, and signaling. The systematic analysis of protein complexes and interaction networks provided exciting insights into the structural and functional organization of mitochondria. Most mitochondrial proteins do not act as independent units, but are interconnected by stable or dynamic protein-protein interactions. Protein translocases are responsible for importing precursor proteins into mitochondria and form central elements of several protein interaction networks. These networks include molecular chaperones and quality control factors, metabolite channels and respiratory chain complexes, and membrane and organellar contact sites. Protein translocases link the distinct networks into an overarching network, the mitochondrial import network (MitimNet), to coordinate biogenesis, membrane organization and function of mitochondria.
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Affiliation(s)
- Fabian den Brave
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany
| | - Uwe Schulte
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Bernd Fakler
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Pfanner
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany.
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4
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Hegde RS, Keenan RJ. A unifying model for membrane protein biogenesis. Nat Struct Mol Biol 2024; 31:1009-1017. [PMID: 38811793 PMCID: PMC7616256 DOI: 10.1038/s41594-024-01296-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/25/2024] [Indexed: 05/31/2024]
Abstract
α-Helical integral membrane proteins comprise approximately 25% of the proteome in all organisms. The membrane proteome is highly diverse, varying in the number, topology, spacing and properties of transmembrane domains. This diversity imposes different constraints on the insertion of different regions of a membrane protein into the lipid bilayer. Here, we present a cohesive framework to explain membrane protein biogenesis, in which different parts of a nascent substrate are triaged between Oxa1 and SecY family members for insertion. In this model, Oxa1 family proteins insert transmembrane domains flanked by short translocated segments, whereas the SecY channel is required for insertion of transmembrane domains flanked by long translocated segments. Our unifying model rationalizes evolutionary, genetic, biochemical and structural data across organisms and provides a foundation for future mechanistic studies of membrane protein biogenesis.
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Affiliation(s)
- Ramanujan S Hegde
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Robert J Keenan
- Gordon Center for Integrative Science, The University of Chicago, Chicago, IL, USA.
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5
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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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Pines O, Horwitz M, Herrmann JM. Privileged proteins with a second residence: dual targeting and conditional re-routing of mitochondrial proteins. FEBS J 2024. [PMID: 38857249 DOI: 10.1111/febs.17191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/15/2024] [Accepted: 05/22/2024] [Indexed: 06/12/2024]
Abstract
Almost all mitochondrial proteins are encoded by nuclear genes and synthesized in the cytosol as precursor proteins. Signals in the amino acid sequence of these precursors ensure their targeting and translocation into mitochondria. However, in many cases, only a certain fraction of a specific protein is transported into mitochondria, while the rest either remains in the cytosol or undergoes reverse translocation to the cytosol, and can populate other cellular compartments. This phenomenon is called dual localization which can be instigated by different mechanisms. These include alternative start or stop codons, differential transcripts, and ambiguous or competing targeting sequences. In many cases, dual localization might serve as an economic strategy to reduce the number of required genes; for example, when the same groups of enzymes are required both in mitochondria and chloroplasts or both in mitochondria and the nucleus/cytoplasm. Such cases frequently employ ambiguous targeting sequences to distribute proteins between both organelles. However, alternative localizations can also be used for signaling, for example when non-imported precursors serve as mitophagy signals or when they represent transcription factors in the nucleus to induce the mitochondrial unfolded stress response. This review provides an overview regarding the mechanisms and the physiological consequences of dual targeting.
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Affiliation(s)
- Ophry Pines
- Microbiology and Genetics, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Margalit Horwitz
- Microbiology and Genetics, Faculty of Medicine, Hebrew University of Jerusalem, Israel
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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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9
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Oh J, Kim DK, Ahn SH, Kim HM, Cho H. A dual role of the conserved PEX19 helix in safeguarding peroxisomal membrane proteins. iScience 2024; 27:109537. [PMID: 38585659 PMCID: PMC10995880 DOI: 10.1016/j.isci.2024.109537] [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: 11/25/2023] [Revised: 02/13/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024] Open
Abstract
Accurate localization of membrane proteins is essential for proper cellular functioning and the integrity of cellular membranes. Post-translational targeting of peroxisomal membrane proteins (PMPs) is mediated by the cytosolic chaperone PEX19 and its membrane receptor PEX3. However, the molecular mechanisms underlying PMP targeting are poorly understood. Here, using biochemical and mass spectrometry analysis, we find that a conserved PEX19 helix, αd, is critical to prevent improper exposure of the PEX26 transmembrane domain (TMD) to cytosolic chaperones. Furthermore, the αd helix of PEX19 interacts with the cytosolic domain of the PEX3 receptor, thereby triggering PEX26 release at the correct destination membrane. The peroxisome-deficient PEX3-G138E mutant completely abolishes this secondary interaction, leading to lack of PEX3-induced PEX26 release from PEX19. These findings elucidate a dual molecular mechanism that is essential to membrane protein protection and destination-specific release by a molecular chaperone.
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Affiliation(s)
- Jeonghyun Oh
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Do Kyung Kim
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Seung Hae Ahn
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Ho Min Kim
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyunju Cho
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
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10
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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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11
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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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12
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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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13
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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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14
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Avci D, Heidasch R, Costa M, Lüchtenborg C, Kale D, Brügger B, Lemberg MK. Intramembrane protease SPP defines a cholesterol-regulated abundance control of the mevalonate pathway enzyme squalene synthase. J Biol Chem 2024; 300:105644. [PMID: 38218226 PMCID: PMC10850959 DOI: 10.1016/j.jbc.2024.105644] [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: 05/24/2023] [Revised: 12/21/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024] Open
Abstract
Intramembrane proteolysis regulates important processes such as signaling and transcriptional and posttranslational abundance control of proteins with key functions in metabolic pathways. This includes transcriptional control of mevalonate pathway genes, thereby ensuring balanced biosynthesis of cholesterol and other isoprenoids. Our work shows that, at high cholesterol levels, signal peptide peptidase (SPP) cleaves squalene synthase (SQS), an enzyme that defines the branching point for allocation of isoprenoids to the sterol and nonsterol arms of the mevalonate pathway. This intramembrane cleavage releases SQS from the membrane and targets it for proteasomal degradation. Regulation of this mechanism is achieved by the E3 ubiquitin ligase TRC8 that, in addition to ubiquitinating SQS in response to cholesterol levels, acts as an allosteric activator of SPP-catalyzed intramembrane cleavage of SQS. Cellular cholesterol levels increase in the absence of SPP activity. We infer from these results that, SPP-TRC8 mediated abundance control of SQS acts as a regulation step within the mevalonate pathway.
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Affiliation(s)
- Dönem Avci
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany.
| | - Ronny Heidasch
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Martina Costa
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | | | - Dipali Kale
- Biochemistry Center of Heidelberg University (BZH), Heidelberg, Germany
| | - Britta Brügger
- Biochemistry Center of Heidelberg University (BZH), Heidelberg, Germany
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany.
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15
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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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16
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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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17
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Cho H, Liu Y, Chung S, Chandrasekar S, Weiss S, Shan SO. Dynamic stability of Sgt2 enables selective and privileged client handover in a chaperone triad. Nat Commun 2024; 15:134. [PMID: 38167697 PMCID: PMC10761869 DOI: 10.1038/s41467-023-44260-5] [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: 03/24/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
Membrane protein biogenesis poses acute challenges to protein homeostasis, and how they are selectively escorted to the target membrane is not well understood. Here we address this question in the guided-entry-of-tail-anchored protein (GET) pathway, in which tail-anchored membrane proteins (TAs) are relayed through an Hsp70-Sgt2-Get3 chaperone triad for targeting to the endoplasmic reticulum. We show that the Hsp70 ATPase cycle and TA substrate drive dimeric Sgt2 from a wide-open conformation to a closed state, in which TAs are protected by both substrate binding domains of Sgt2. Get3 is privileged to receive TA from closed Sgt2, whereas off-pathway chaperones remove TAs from open Sgt2. Sgt2 closing is less favorable with suboptimal GET substrates, which are rejected during or after the Hsp70-to-Sgt2 handover. Our results demonstrate how fine-tuned conformational dynamics in Sgt2 enable hydrophobic TAs to be effectively funneled onto their dedicated targeting factor while also providing a mechanism for substrate selection.
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Affiliation(s)
- Hyunju Cho
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Center for Biomolecular and Cellular Structure, Institute for Basic Science, Daejeon, 34126, Republic of Korea
| | - Yumeng Liu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Biochemistry and Molecular Biotechnology Department, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - SangYoon Chung
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Sowmya Chandrasekar
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Physics, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
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18
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Makio T, Simmen T. Not So Rare: Diseases Based on Mutant Proteins Controlling Endoplasmic Reticulum-Mitochondria Contact (MERC) Tethering. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2024; 7:25152564241261228. [PMID: 39070058 PMCID: PMC11273598 DOI: 10.1177/25152564241261228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/12/2024] [Accepted: 05/27/2024] [Indexed: 07/30/2024]
Abstract
Mitochondria-endoplasmic reticulum contacts (MERCs), also called endoplasmic reticulum (ER)-mitochondria contact sites (ERMCS), are the membrane domains, where these two organelles exchange lipids, Ca2+ ions, and reactive oxygen species. This crosstalk is a major determinant of cell metabolism, since it allows the ER to control mitochondrial oxidative phosphorylation and the Krebs cycle, while conversely, it allows the mitochondria to provide sufficient ATP to control ER proteostasis. MERC metabolic signaling is under the control of tethers and a multitude of regulatory proteins. Many of these proteins have recently been discovered to give rise to rare diseases if their genes are mutated. Surprisingly, these diseases share important hallmarks and cause neurological defects, sometimes paired with, or replaced by skeletal muscle deficiency. Typical symptoms include developmental delay, intellectual disability, facial dysmorphism and ophthalmologic defects. Seizures, epilepsy, deafness, ataxia, or peripheral neuropathy can also occur upon mutation of a MERC protein. Given that most MERC tethers and regulatory proteins have secondary functions, some MERC protein-based diseases do not fit into this categorization. Typically, however, the proteins affected in those diseases have dominant functions unrelated to their roles in MERCs tethering or their regulation. We are discussing avenues to pharmacologically target genetic diseases leading to MERC defects, based on our novel insight that MERC defects lead to common characteristics in rare diseases. These shared characteristics of MERCs disorders raise the hope that they may allow for similar treatment options.
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Affiliation(s)
- Tadashi Makio
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Thomas Simmen
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
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19
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Delgado JM, Shepard LW, Lamson SW, Liu SL, Shoemaker CJ. The ER membrane protein complex restricts mitophagy by controlling BNIP3 turnover. EMBO J 2024; 43:32-60. [PMID: 38177312 PMCID: PMC10883272 DOI: 10.1038/s44318-023-00006-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 01/06/2024] Open
Abstract
Lysosomal degradation of autophagy receptors is a common proxy for selective autophagy. However, we find that two established mitophagy receptors, BNIP3 and BNIP3L/NIX, are constitutively delivered to lysosomes in an autophagy-independent manner. This alternative lysosomal delivery of BNIP3 accounts for nearly all its lysosome-mediated degradation, even upon mitophagy induction. To identify how BNIP3, a tail-anchored protein in the outer mitochondrial membrane, is delivered to lysosomes, we performed a genome-wide CRISPR screen for factors influencing BNIP3 flux. This screen revealed both known modifiers of BNIP3 stability as well as a pronounced reliance on endolysosomal components, including the ER membrane protein complex (EMC). Importantly, the endolysosomal system and the ubiquitin-proteosome system regulated BNIP3 independently. Perturbation of either mechanism is sufficient to modulate BNIP3-associated mitophagy and affect underlying cellular physiology. More broadly, these findings extend recent models for tail-anchored protein quality control and install endosomal trafficking and lysosomal degradation in the canon of pathways that tightly regulate endogenous tail-anchored protein localization.
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Affiliation(s)
- Jose M Delgado
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Logan Wallace Shepard
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Sarah W Lamson
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Samantha L Liu
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Christopher J Shoemaker
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA.
- Dartmouth Cancer Center, Lebanon, NH, USA.
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20
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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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21
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Paul JW, Muratcioğlu S, Kuriyan J. A Fluorescence-Based Sensor for Calibrated Measurement of Protein Kinase Stability in Live Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570636. [PMID: 38106090 PMCID: PMC10723428 DOI: 10.1101/2023.12.07.570636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
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 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 monitor the fluorescence of kinases fused to a fluorescent protein relative to that of a co-expressed reference fluorescent protein. 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 (SH2) and Src-homology 3 (SH3) 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 Biology, University of California, Berkeley, CA, 94720 USA
- California Institute for Quantitative Bioscience (QB3), University of California, Berkeley, CA, 94720 USA
| | - Serena Muratcioğlu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232 USA
| | - John Kuriyan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232 USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37240 USA
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22
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Hoock JGF, Rossetti C, Bilgin M, Depta L, Enemark-Rasmussen K, Christianson JC, Laraia L. Identification of non-conventional small molecule degraders and stabilizers of squalene synthase. Chem Sci 2023; 14:12973-12983. [PMID: 38023519 PMCID: PMC10664564 DOI: 10.1039/d3sc04064j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/15/2023] [Indexed: 12/01/2023] Open
Abstract
Squalene synthase (SQS) is an essential enzyme in the mevalonate pathway, which controls cholesterol biosynthesis and homeostasis. Although catalytic inhibitors of SQS have been developed, none have been approved for therapeutic use so far. Herein we sought to develop SQS degraders using targeted protein degradation (TPD) to lower overall cellular cholesterol content. We found that KY02111, a small molecule ligand of SQS, selectively causes SQS to degrade in a proteasome-dependent manner. Unexpectedly, compounds based on the same scaffold linked to E3 ligase recruiting ligands led to SQS stabilization. Proteomic analysis found KY02111 to reduce only the levels of SQS, while lipidomic analysis determined that KY02111-induced degradation lowered cellular cholesteryl ester content. Stabilizers shielded SQS from its natural turnover without recruiting their matching E3 ligase or affecting enzymatic target activity. Our work shows that degradation of SQS is possible despite a challenging biological setting and provides the first chemical tools to degrade and stabilize SQS.
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Affiliation(s)
- Joseph G F Hoock
- Department of Chemistry, Technical University of Denmark Kemitorvet 207 Kongens Lyngby 2800 Denmark
| | - Cecilia Rossetti
- Department of Chemistry, Technical University of Denmark Kemitorvet 207 Kongens Lyngby 2800 Denmark
| | - Mesut Bilgin
- Lipidomics Core Facility, Danish Cancer Institute Strandboulevarden 49 Copenhagen 2100 Denmark
| | - Laura Depta
- Department of Chemistry, Technical University of Denmark Kemitorvet 207 Kongens Lyngby 2800 Denmark
| | - Kasper Enemark-Rasmussen
- Department of Chemistry, Technical University of Denmark Kemitorvet 207 Kongens Lyngby 2800 Denmark
| | - John C Christianson
- Nuffield Department of Rheumatology, Orthopaedics, and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford Headington Oxford OX3 7LD UK
| | - Luca Laraia
- Department of Chemistry, Technical University of Denmark Kemitorvet 207 Kongens Lyngby 2800 Denmark
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23
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McDowell MA, Heimes M, Enkavi G, Farkas Á, Saar D, Wild K, Schwappach B, Vattulainen I, Sinning I. The GET insertase exhibits conformational plasticity and induces membrane thinning. Nat Commun 2023; 14:7355. [PMID: 37963916 PMCID: PMC10646013 DOI: 10.1038/s41467-023-42867-2] [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: 03/16/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023] Open
Abstract
The eukaryotic guided entry of tail-anchored proteins (GET) pathway mediates the biogenesis of tail-anchored (TA) membrane proteins at the endoplasmic reticulum. In the cytosol, the Get3 chaperone captures the TA protein substrate and delivers it to the Get1/Get2 membrane protein complex (GET insertase), which then inserts the substrate via a membrane-embedded hydrophilic groove. Here, we present structures, atomistic simulations and functional data of human and Chaetomium thermophilum Get1/Get2/Get3. The core fold of the GET insertase is conserved throughout eukaryotes, whilst thinning of the lipid bilayer occurs in the vicinity of the hydrophilic groove to presumably lower the energetic barrier of membrane insertion. We show that the gating interaction between Get2 helix α3' and Get3 drives conformational changes in both Get3 and the Get1/Get2 membrane heterotetramer. Thus, we provide a framework to understand the conformational plasticity of the GET insertase and how it remodels its membrane environment to promote substrate insertion.
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Affiliation(s)
- Melanie A McDowell
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438, Frankfurt am Main, Germany.
| | - Michael Heimes
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Giray Enkavi
- Department of Physics, University of Helsinki, P. O. Box 64, FI-00014, Helsinki, Finland
| | - Ákos Farkas
- Department of Molecular Biology, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Daniel Saar
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Blanche Schwappach
- Department of Molecular Biology, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, P. O. Box 64, FI-00014, Helsinki, Finland
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
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24
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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: 6] [Impact Index Per Article: 6.0] [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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25
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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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26
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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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27
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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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28
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Li YP, Shen RJ, Cheng YM, Zhao Q, Jin K, Jin ZB, Zhang S. Exome sequencing in retinal dystrophy patients reveals a novel candidate gene ER membrane protein complex subunit 3. Heliyon 2023; 9:e20146. [PMID: 37809982 PMCID: PMC10559921 DOI: 10.1016/j.heliyon.2023.e20146] [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: 05/05/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Inherited retinal dystrophies (IRDs) are a heterogeneous group of visual disorders caused by different pathogenic mutations in genes and regulatory sequences. The endoplasmic reticulum (ER) membrane protein complex (EMC) subunit 3 (EMC3) is the core unit of the EMC insertase that integrates the transmembrane peptides into lipid bilayers, and the function of its cytoplasmic carboxyl terminus remains to be elucidated. In this study, an insertional mutation c.768insT in the C-terminal coding region of EMC3 was identified and associated with dominant IRDs in a five-generation family. This mutation caused a frameshift in the coding sequence and a gain of an additional 16 amino acid residues (p.L256F-fs-ext21) to form a helix structure in the C-terminus of the EMC3 protein. The mutation is heterozygous with an incomplete penetrance, and cosegregates in all patients examined. This finding indicates that the C-terminus of EMC3 is essential for EMC functions and that EMC3 may be a novel candidate gene for retinal degenerative diseases.
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Affiliation(s)
- Yan-Ping Li
- Laboratory for Stem Cell & Retinal Regeneration, The Eye Hospital, Basic Medical College, Wenzhou Medical University, Wenzhou, 325027, China
| | - Ren-Juan Shen
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, 100730, China
| | - You-Min Cheng
- Laboratory for Stem Cell & Retinal Regeneration, The Eye Hospital, Basic Medical College, Wenzhou Medical University, Wenzhou, 325027, China
| | - Qingqing Zhao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310030, China
| | - Kangxin Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, 100730, China
| | - Zi-Bing Jin
- Laboratory for Stem Cell & Retinal Regeneration, The Eye Hospital, Basic Medical College, Wenzhou Medical University, Wenzhou, 325027, China
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, 100730, China
| | - Shaodan Zhang
- The Eye Hospital of Wenzhou Medical University, National Clinical Research Center for Ocular Diseases, Glaucoma Research Institute of Wenzhou Medical University, Wenzhou, 325027, China
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29
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553624. [PMID: 37645817 PMCID: PMC10462106 DOI: 10.1101/2023.08.16.553624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Mitochondrial outer membrane α-helical proteins play critical roles in mitochondrial-cytoplasmic communication, but the rules governing the targeting and insertion of these biophysically diverse substrates 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 α-helical substrates reveals that these components are organized into distinct targeting pathways which act on substrates based on their topology. NAC is required for efficient targeting of polytopic proteins whereas signal-anchored proteins require TTC1, a novel cytosolic chaperone which 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, 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, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 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, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Reuben A. Saunders
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 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, 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, 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, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute Technology, Cambridge 02142, MA
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30
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525086. [PMID: 36711738 PMCID: PMC9882262 DOI: 10.1101/2023.01.22.525086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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
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31
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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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32
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Keele GR, Zhang JG, Szpyt J, Korstanje R, Gygi SP, Churchill GA, Schweppe DK. Global and tissue-specific aging effects on murine proteomes. Cell Rep 2023; 42:112715. [PMID: 37405913 PMCID: PMC10588767 DOI: 10.1016/j.celrep.2023.112715] [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: 09/16/2022] [Revised: 03/06/2023] [Accepted: 06/13/2023] [Indexed: 07/07/2023] Open
Abstract
Maintenance of protein homeostasis degrades with age, contributing to aging-related decline and disease. Previous studies have primarily surveyed transcriptional aging changes. To define the effects of age directly at the protein level, we perform discovery-based proteomics in 10 tissues from 20 C57BL/6J mice, representing both sexes at adult and late midlife ages (8 and 18 months). Consistent with previous studies, age-related changes in protein abundance often have no corresponding transcriptional change. Aging results in increases in immune proteins across all tissues, consistent with a global pattern of immune infiltration with age. Our protein-centric data reveal tissue-specific aging changes with functional consequences, including altered endoplasmic reticulum and protein trafficking in the spleen. We further observe changes in the stoichiometry of protein complexes with important roles in protein homeostasis, including the CCT/TriC complex and large ribosomal subunit. These data provide a foundation for understanding how proteins contribute to systemic aging across tissues.
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Affiliation(s)
| | | | - John Szpyt
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA.
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33
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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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34
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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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35
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Woo TT, Williams JM, Tsai B. How host ER membrane chaperones and morphogenic proteins support virus infection. J Cell Sci 2023; 136:jcs261121. [PMID: 37401530 PMCID: PMC10357032 DOI: 10.1242/jcs.261121] [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: 07/05/2023] Open
Abstract
The multi-functional endoplasmic reticulum (ER) is exploited by viruses to cause infection. Morphologically, this organelle is a highly interconnected membranous network consisting of sheets and tubules whose levels are dynamic, changing in response to cellular conditions. Functionally, the ER is responsible for protein synthesis, folding, secretion and degradation, as well as Ca2+ homeostasis and lipid biosynthesis, with each event catalyzed by defined ER factors. Strikingly, these ER host factors are hijacked by viruses to support different infection steps, including entry, translation, replication, assembly and egress. Although the full repertoire of these ER factors that are hijacked is unknown, recent studies have uncovered several ER membrane machineries that are exploited by viruses - ranging from polyomavirus to flavivirus and coronavirus - to facilitate different steps of their life cycle. These discoveries should provide better understanding of virus infection mechanisms, potentially leading to the development of more effective anti-viral therapies.
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Affiliation(s)
- Tai-Ting Woo
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, BSRB 3043, Ann Arbor, MI 48109,USA
| | - Jeffrey M. Williams
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, BSRB 3043, Ann Arbor, MI 48109,USA
| | - Billy Tsai
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, BSRB 3043, Ann Arbor, MI 48109,USA
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36
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Shiota N, Shimokawa-Chiba N, Fujiwara K, Chiba S. Identification of Bacillus subtilis YidC substrates using a MifM-instructed translation arrest-based reporter. J Mol Biol 2023:168172. [PMID: 37290739 DOI: 10.1016/j.jmb.2023.168172] [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: 04/06/2023] [Revised: 05/26/2023] [Accepted: 05/31/2023] [Indexed: 06/10/2023]
Abstract
YidC is a member of the YidC/Oxa1/Alb3 protein family that is crucial for membrane protein biogenesis in the bacterial plasma membrane. While YidC facilitates the folding and complex assembly of membrane proteins along with the Sec translocon, it also functions as a Sec-independent membrane protein insertase in the YidC-only pathway. However, little is known about how membrane proteins are recognized and sorted by these pathways, especially in Gram-positive bacteria, for which only a small number of YidC substrates have been identified to date. In this study, we aimed to identify Bacillus subtilis membrane proteins whose membrane insertion depends on SpoIIIJ, the primary YidC homolog in B. subtilis. We took advantage of the translation arrest sequence of MifM, which can monitor YidC-dependent membrane insertion. Our systematic screening identified eight membrane proteins as candidate SpoIIIJ substrates. Results of our genetic study also suggest that the conserved arginine in the hydrophilic groove of SpoIIIJ is crucial for the membrane insertion of the substrates identified here. However, in contrast to MifM, a previously identified YidC substrate, the importance of the negatively charged residue on the substrates for membrane insertion varied depending on the substrate. These results suggest that B. subtilis YidC uses substrate-specific interactions to facilitate membrane insertion.
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Affiliation(s)
- Narumi Shiota
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan
| | - Naomi Shimokawa-Chiba
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan; Institute for Protein Dynamics, Kyoto Sangyo University, Japan
| | - Keigo Fujiwara
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan; Institute for Protein Dynamics, Kyoto Sangyo University, Japan
| | - Shinobu Chiba
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan; Institute for Protein Dynamics, Kyoto Sangyo University, Japan.
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37
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Bryen SJ, Zhang K, Dziaduch G, Bommireddipalli S, Naseri T, Reupena MS, Viali S, Minster RL, Waddell LB, Charlton A, O’Grady GL, Evesson FJ, Cooper ST. Compound heterozygous splicing variants expand the genotypic spectrum of EMC1-related disorders. Clin Genet 2023; 103:553-559. [PMID: 36799557 PMCID: PMC10101692 DOI: 10.1111/cge.14311] [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: 08/31/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023]
Abstract
EMC1 encodes subunit 1 of the endoplasmic reticulum (ER) membrane protein complex (EMC), a transmembrane domain insertase involved in membrane protein biosynthesis. Variants in EMC1 are described as a cause of global developmental delay, hypotonia, cortical visual impairment, and commonly, cerebral atrophy on MRI scan. We report an individual with severe global developmental delay and progressive cerebellar atrophy in whom exome sequencing identified a heterozygous essential splice-site variant in intron-3 of EMC1 (NM_015047.3:c.287-1G>A). Whole genome sequencing (WGS) identified a deep intronic variant in intron-20 of EMC1 (NM_015047.3:c.2588-771C>G) that was poorly predicted by in silico programs to disrupt pre-mRNA splicing. Reverse Transcription-PCR (RT-PCR) revealed stochastic activation of a pseudo-exon associated with the c.2588-771C>G variant and mis-splicing arising from the c.287-1G>A variant. This case highlights the utility of WGS and RNA studies to identify and assess likely pathogenicity of deep intronic variants and expands the genotypic and phenotypic spectrum of EMC1-related disorders.
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Affiliation(s)
- Samantha J. Bryen
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Katharine Zhang
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, NSW, Australia
- Functional Neuromics, Children’s Medical Research Institute, Westmead, NSW, Australia
| | - Gregory Dziaduch
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, NSW, Australia
- Functional Neuromics, Children’s Medical Research Institute, Westmead, NSW, Australia
| | - Shobhana Bommireddipalli
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Take Naseri
- Ministry of Health, Apia, Samoa
- International Health Institute, School of Public Health, Brown University, Providence, RI, USA
| | | | | | | | - Leigh B. Waddell
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | | | - Gina L. O’Grady
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia
- Paediatric Neuroservices, Starship Child Health, Auckland, New Zealand
| | - Frances J. Evesson
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, NSW, Australia
- Functional Neuromics, Children’s Medical Research Institute, Westmead, NSW, Australia
| | - Sandra T. Cooper
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia
- Functional Neuromics, Children’s Medical Research Institute, Westmead, NSW, Australia
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38
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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: 2] [Impact Index Per Article: 2.0] [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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39
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Delgado JM, Wallace Shepard L, Lamson SW, Liu SL, Shoemaker CJ. The ER membrane protein complex governs lysosomal turnover of a mitochondrial tail-anchored protein, BNIP3, to restrict mitophagy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.22.533681. [PMID: 36993512 PMCID: PMC10055395 DOI: 10.1101/2023.03.22.533681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Lysosomal degradation of autophagy receptors is a common proxy for selective autophagy. However, we find that two established mitophagy receptors, BNIP3 and BNIP3L/NIX, violate this assumption. Rather, BNIP3 and NIX are constitutively delivered to lysosomes in an autophagy-independent manner. This alternative lysosomal delivery of BNIP3 accounts for nearly all of its lysosome-mediated degradation, even upon mitophagy induction. To identify how BNIP3, a tail-anchored protein in the outer mitochondrial membrane, is delivered to lysosomes, we performed a genome-wide CRISPR screen for factors influencing BNIP3 flux. By this approach, we revealed both known modifiers of BNIP3 stability as well as a pronounced reliance on endolysosomal components, including the ER membrane protein complex (EMC). Importantly, the endolysosomal system regulates BNIP3 alongside, but independent of, the ubiquitin-proteosome system (UPS). Perturbation of either mechanism is sufficient to modulate BNIP3-associated mitophagy and affect underlying cellular physiology. In short, while BNIP3 can be cleared by parallel and partially compensatory quality control pathways, non-autophagic lysosomal degradation of BNIP3 is a strong post-translational modifier of BNIP3 function. More broadly, these data reveal an unanticipated connection between mitophagy and TA protein quality control, wherein the endolysosomal system provides a critical axis for regulating cellular metabolism. Moreover, these findings extend recent models for tail-anchored protein quality control and install endosomal trafficking and lysosomal degradation in the canon of pathways that ensure tight regulation of endogenous TA protein localization.
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Affiliation(s)
- Jose M Delgado
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH
| | - Logan Wallace Shepard
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH
| | - Sarah W Lamson
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH
| | - Samantha L Liu
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH
| | - Christopher J Shoemaker
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH
- Dartmouth Cancer Center, Lebanon, NH, USA
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40
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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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41
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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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42
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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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43
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Kozono T, Jogano C, Okumura W, Sato H, Matsui H, Takagi T, Okumura N, Takao T, Tonozuka T, Nishikawa A. Cleavage of the Jaw1 C-terminal region enhances its augmentative effect on the Ca2+ release via IP3 receptors. J Cell Sci 2023; 136:287037. [PMID: 36789796 DOI: 10.1242/jcs.260439] [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: 08/11/2022] [Accepted: 01/17/2023] [Indexed: 02/16/2023] Open
Abstract
Jaw1 (also known as IRAG2), a tail-anchored protein with 39 carboxyl (C)-terminal amino acids, is oriented to the lumen of the endoplasmic reticulum and outer nuclear membrane. We previously reported that Jaw1, as a member of the KASH protein family, plays a role in maintaining nuclear shape via its C-terminal region. Furthermore, we recently reported that Jaw1 functions as an augmentative effector of Ca2+ release from the endoplasmic reticulum by interacting with the inositol 1,4,5-trisphosphate receptors (IP3Rs). Intriguingly, the C-terminal region is partially cleaved, meaning that Jaw1 exists in the cell in at least two forms - uncleaved and cleaved. However, the mechanism of the cleavage event and its physiological significance remain to be determined. In this study, we demonstrate that the C-terminal region of Jaw1 is cleaved after its insertion by the signal peptidase complex (SPC). Particularly, our results indicate that the SPC with the catalytic subunit SEC11A, but not SEC11C, specifically cleaves Jaw1. Furthermore, using a mutant with a defect in the cleavage event, we demonstrate that the cleavage event enhances the augmentative effect of Jaw1 on the Ca2+ release ability of IP3Rs.
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Affiliation(s)
- Takuma Kozono
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Chifuyu Jogano
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Wataru Okumura
- Department of Food and Energy Systems Science, Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Hiroyuki Sato
- Cooperative Major in Advanced Health Science, Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Hitomi Matsui
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Tsubasa Takagi
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Nobuaki Okumura
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Toshifumi Takao
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Takashi Tonozuka
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Atsushi Nishikawa
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan.,Department of Food and Energy Systems Science, Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan.,Cooperative Major in Advanced Health Science, Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
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44
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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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45
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Shan SO. Role of Hsp70 in Post-Translational Protein Targeting: Tail-Anchored Membrane Proteins and Beyond. Int J Mol Sci 2023; 24:1170. [PMID: 36674686 PMCID: PMC9866221 DOI: 10.3390/ijms24021170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The Hsp70 family of molecular chaperones acts as a central 'hub' in the cell that interacts with numerous newly synthesized proteins to assist in their biogenesis. Apart from its central and well-established role in facilitating protein folding, Hsp70s also act as key decision points in the cellular chaperone network that direct client proteins to distinct biogenesis and quality control pathways. In this paper, we review accumulating data that illustrate a new branch in the Hsp70 network: the post-translational targeting of nascent membrane and organellar proteins to diverse cellular organelles. Work in multiple pathways suggests that Hsp70, via its ability to interact with components of protein targeting and translocation machineries, can initiate elaborate substrate relays in a sophisticated cascade of chaperones, cochaperones, and receptor proteins, and thus provide a mechanism to safeguard and deliver nascent membrane proteins to the correct cellular membrane. We discuss the mechanistic principles gleaned from better-studied Hsp70-dependent targeting pathways and outline the observations and outstanding questions in less well-studied systems.
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Affiliation(s)
- Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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46
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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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47
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Itskanov S, Park E. Mechanism of Protein Translocation by the Sec61 Translocon Complex. Cold Spring Harb Perspect Biol 2023; 15:a041250. [PMID: 35940906 PMCID: PMC9808579 DOI: 10.1101/cshperspect.a041250] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The endoplasmic reticulum (ER) is a major site for protein synthesis, folding, and maturation in eukaryotic cells, responsible for production of secretory proteins and most integral membrane proteins. The universally conserved protein-conducting channel Sec61 complex mediates core steps in these processes by translocating hydrophilic polypeptide segments of client proteins across the ER membrane and integrating hydrophobic transmembrane segments into the membrane. The Sec61 complex associates with several other molecular machines and enzymes to enable substrate engagement with the channel and coordination of protein translocation with translation, protein folding, and/or post-translational modifications. Recent cryo-electron microscopy and functional studies of these translocon complexes have greatly advanced our mechanistic understanding of Sec61-dependent protein biogenesis at the ER. Here, we will review the current models for how the Sec61 channel performs its functions in coordination with partner complexes.
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Affiliation(s)
- Samuel Itskanov
- Biophysics Graduate Program
- California Institute for Quantitative Biosciences
| | - Eunyong Park
- California Institute for Quantitative Biosciences
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
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48
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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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49
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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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50
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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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