Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients

  1. Lakshmi E Miller-Vedam
  2. Bastian Bräuning
  3. Katerina D Popova
  4. Nicole T Schirle Oakdale
  5. Jessica L Bonnar
  6. Jesuraj R Prabu
  7. Elizabeth A Boydston
  8. Natalia Sevillano
  9. Matthew J Shurtleff
  10. Robert M Stroud
  11. Charles S Craik
  12. Brenda A Schulman  Is a corresponding author
  13. Adam Frost  Is a corresponding author
  14. Jonathan S Weissman  Is a corresponding author
  1. Whitehead Institute for Biomedical Research, United States
  2. Max Plank Institute for Biochemistry, Germany
  3. University of California, San Francisco, United States
  4. Max Planck Institute of Biochemistry, Germany
  5. FairJourney Biologics, Portugal
  6. Stanford University, United States
  7. St Jude Children's Research Hospital, United States

Abstract

Membrane protein biogenesis in the endoplasmic reticulum (ER) is complex and failure-prone. The ER membrane protein complex (EMC), comprising eight conserved subunits, has emerged as a central player in this process. Yet, we have limited understanding of how EMC enables insertion and integrity of diverse clients, from tail-anchored to polytopic transmembrane proteins. Here, yeast and human EMC cryo-EM structures reveal conserved intricate assemblies and human-specific features associated with pathologies. Structure-based functional studies distinguish between two separable EMC activities, as an insertase regulating tail-anchored protein levels and a broader role in polytopic membrane protein biogenesis. These depend on mechanistically coupled yet spatially distinct regions including two lipid-accessible membrane cavities which confer client-specific regulation, and a non-insertase EMC function mediated by the EMC lumenal domain. Our studies illuminate the structural and mechanistic basis of EMC's multifunctionality and point to its role in differentially regulating the biogenesis of distinct client protein classes.

Data availability

All data generated or analyzed during this study are included in the manuscript or will have been made available in public repositories. Flow cytometry data and analysis code is available at Github (https://github.com/katerinadpopova/emcstructurefunction). Electron microscopy maps are available at the EMDB (unsharpened, sharpened, half maps, FSC file) (accession codes EMDB - 11732, 11733, 23003, 23033), models at the PDB (accession codes PDB - 7ADO, 7ADP, 7KRA, 7KTX), and raw cryo-EM data at EMPIAR. Key Resource Table is included as an appendix to the main article and is referenced throughout the Methods section with relevant reagents used or generated during the course of the study allowing for replication of these or request of specific cell lines and reagents. Supplementary file 1 contains raw mass spectrometry data. Supplementary file 4 contains un-cropped western blots. Supplementary file 5 contains plasmid sequences for mutant constructs generated for this study.

The following data sets were generated

Article and author information

Author details

  1. Lakshmi E Miller-Vedam

    Biology, Whitehead Institute for Biomedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2980-7479
  2. Bastian Bräuning

    Molecular Signaling, Max Plank Institute for Biochemistry, Martinsreid, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7194-2500
  3. Katerina D Popova

    Biology, Whitehead Institute for Biomedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Nicole T Schirle Oakdale

    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Jessica L Bonnar

    Biology, Whitehead Institute for Biomedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Jesuraj R Prabu

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Elizabeth A Boydston

    Biology, Whitehead Institute for Biomedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8365-0436
  8. Natalia Sevillano

    Antibody Engineering, FairJourney Biologics, Porto, Portugal
    Competing interests
    The authors declare that no competing interests exist.
  9. Matthew J Shurtleff

    Bioengineering, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9846-3051
  10. Robert M Stroud

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Charles S Craik

    Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7704-9185
  12. Brenda A Schulman

    Department of Structural Biology, St Jude Children's Research Hospital, Memphis, United States
    For correspondence
    schulman@biochem.mpg.de
    Competing interests
    The authors declare that no competing interests exist.
  13. Adam Frost

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    For correspondence
    adam.frost@ucsf.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2231-2577
  14. Jonathan S Weissman

    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
    For correspondence
    Jonathan.Weissman@ucsf.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2445-670X

Funding

Deutsche Forschungsgemeinschaft

  • Brenda A Schulman

Chan Zuckerberg Initiative

  • Adam Frost

Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg

  • Brenda A Schulman

National Institutes of Health (P50AI150476,1P41CA196276-01)

  • Natalia Sevillano
  • Charles S Craik

Helen Hay Whitney Foundation

  • Matthew J Shurtleff

Peter und Traudl Engelhorn Stiftung

  • Bastian Bräuning

Jane Coffin Childs Memorial Fund for Medical Research

  • Nicole T Schirle Oakdale

National Institutes of Health (1DP2OD017690-01)

  • Adam Frost

National Institutes of Health (GM24485)

  • Robert M Stroud

Howard Hughes Medical Institute

  • Jonathan S Weissman

The funders had no role in study design, data collection, data interpretation, or the decision to submit the work for publication.

Copyright

© 2020, Miller-Vedam et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Lakshmi E Miller-Vedam
  2. Bastian Bräuning
  3. Katerina D Popova
  4. Nicole T Schirle Oakdale
  5. Jessica L Bonnar
  6. Jesuraj R Prabu
  7. Elizabeth A Boydston
  8. Natalia Sevillano
  9. Matthew J Shurtleff
  10. Robert M Stroud
  11. Charles S Craik
  12. Brenda A Schulman
  13. Adam Frost
  14. Jonathan S Weissman
(2020)
Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients
eLife 9:e62611.
https://doi.org/10.7554/eLife.62611

Share this article

https://doi.org/10.7554/eLife.62611

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