Autoinhibition and regulation by phosphoinositides of ATP8B1, a human lipid flippase associated with intrahepatic cholestatic disorders

  1. Thibaud Dieudonné
  2. Sara Abad Herrera
  3. Michelle Juknaviciute Laursen
  4. Maylis Lejeune
  5. Charlott Stock
  6. Kahina Slimani
  7. Christine Jaxel
  8. Joseph A Lyons
  9. Cédric Montigny
  10. Thomas Günther Pomorski  Is a corresponding author
  11. Poul Nissen  Is a corresponding author
  12. Guillaume Lenoir  Is a corresponding author
  1. Université Paris-Saclay, CEA, CNRS, France
  2. Ruhr University Bochum, Germany
  3. Aarhus University, Denmark

Abstract

P4-ATPases flip lipids from the exoplasmic to the cytosolic leaflet, thus maintaining lipid asymmetry in eukaryotic cell membranes. Mutations in several human P4-ATPase genes are associated with severe diseases, e.g. in ATP8B1 causing progressive familial intrahepatic cholestasis, a rare inherited disorder progressing toward liver failure. ATP8B1 forms a binary complex with CDC50A and displays a broad specificity to glycerophospholipids, but regulatory mechanisms are unknown. Here, we report functional studies and the cryo-EM structure of the human lipid flippase ATP8B1-CDC50A at 3.1 Å resolution. We find that ATP8B1 is autoinhibited by its N- and C-terminal tails, which form extensive interactions with the catalytic sites and flexible domain interfaces. Consistently, ATP hydrolysis is unleashed by truncation of the C-terminus, but also requires phosphoinositides, most markedly phosphatidylinositol-3,4,5-phosphate (PI(3,4,5)P3), and removal of both N- and C-termini results in full activation. Restored inhibition of ATP8B1 truncation constructs with a synthetic peptide mimicking the C-terminal segment further suggests molecular communication between N- and C-termini in the autoinhibition and demonstrates that the regulatory mechanism can be interfered with by exogenous compounds. A recurring (G/A)(Y/F)AFS motif of the C-terminal segment suggests that this mechanism is employed widely across P4-ATPase lipid flippases in plasma membrane and endomembranes.

Data availability

Refined coordinates for the atomic model of the autoinhibited state of ATP8B1 have been deposited in PDB under the accession code 7PY4.The cryo-EM map of autoinhibited ATP8B1 has been deposited in EMDB under the accession code EMD-13711.

The following data sets were generated

Article and author information

Author details

  1. Thibaud Dieudonné

    Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6988-4121
  2. Sara Abad Herrera

    Department of Molecular Biochemistry, Ruhr University Bochum, Bochum, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Michelle Juknaviciute Laursen

    Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
    Competing interests
    The authors declare that no competing interests exist.
  4. Maylis Lejeune

    Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
    Competing interests
    The authors declare that no competing interests exist.
  5. Charlott Stock

    Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5471-3696
  6. Kahina Slimani

    Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
    Competing interests
    The authors declare that no competing interests exist.
  7. Christine Jaxel

    Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1387-4458
  8. Joseph A Lyons

    Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
    Competing interests
    The authors declare that no competing interests exist.
  9. Cédric Montigny

    Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0905-9861
  10. Thomas Günther Pomorski

    Department of Molecular Biochemistry, Ruhr University Bochum, Bochum, Germany
    For correspondence
    thomas.guenther-pomorski@ruhr-uni-bochum.de
    Competing interests
    The authors declare that no competing interests exist.
  11. Poul Nissen

    Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
    For correspondence
    pn@mbg.au.dk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0948-6628
  12. Guillaume Lenoir

    Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
    For correspondence
    guillaume.lenoir@i2bc.paris-saclay.fr
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8759-5179

Funding

EMBO (Short-term fellowship,7881)

  • Thibaud Dieudonné

French Infrastructure for Integrated Structural Biology (FRISBI,ANR-10-INSB-05)

  • Christine Jaxel
  • Cédric Montigny
  • Guillaume Lenoir

French ministry for higher education (PhD fellowship)

  • Thibaud Dieudonné

European Commission (Marie Sklodowska-Curie individual fellowship)

  • Thibaud Dieudonné

Agence Nationale de la Recherche (Young investigator grant,ANR-14-CE09-0022)

  • Guillaume Lenoir

Lundbeckfonden (Professorship grant)

  • Poul Nissen

Deutsche Forschungsgemeinschaft (GU 1133/11-1)

  • Thomas Günther Pomorski

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

Reviewing Editor

  1. Merritt Maduke, Stanford University School of Medicine, United States

Publication history

  1. Preprint posted: November 4, 2021 (view preprint)
  2. Received: November 4, 2021
  3. Accepted: April 12, 2022
  4. Accepted Manuscript published: April 13, 2022 (version 1)
  5. Version of Record published: April 27, 2022 (version 2)
  6. Version of Record updated: May 5, 2022 (version 3)

Copyright

© 2022, Dieudonné 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. Thibaud Dieudonné
  2. Sara Abad Herrera
  3. Michelle Juknaviciute Laursen
  4. Maylis Lejeune
  5. Charlott Stock
  6. Kahina Slimani
  7. Christine Jaxel
  8. Joseph A Lyons
  9. Cédric Montigny
  10. Thomas Günther Pomorski
  11. Poul Nissen
  12. Guillaume Lenoir
(2022)
Autoinhibition and regulation by phosphoinositides of ATP8B1, a human lipid flippase associated with intrahepatic cholestatic disorders
eLife 11:e75272.
https://doi.org/10.7554/eLife.75272
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