1. Structural Biology and Molecular Biophysics

Cryo-EM structures of mitochondrial respiratory complex I from Drosophila melanogaster

  1. Ahmed-Noor A Agip
  2. Injae Chung
  3. Alvaro Sanchez-Martinez
  4. Alexander J Whitworth  Is a corresponding author
  5. Judy Hirst  Is a corresponding author
  1. University of Cambridge, United Kingdom
https://doi.org/10.7554/eLife.84424
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  1. Ahmed-Noor A Agip
  2. Injae Chung
  3. Alvaro Sanchez-Martinez
  4. Alexander J Whitworth
  5. Judy Hirst
(2023)
Cryo-EM structures of mitochondrial respiratory complex I from Drosophila melanogaster
eLife 12:e84424.
https://doi.org/10.7554/eLife.84424
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Abstract

Respiratory complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from NADH oxidation by ubiquinone to drive protons across an energy-transducing membrane. Drosophila melanogaster is a candidate model organism for complex I due to its high evolutionary conservation with the mammalian enzyme, well-developed genetic toolkit, and complex physiology for studies in specific cell types and tissues. Here, we isolate complex I from Drosophila and determine its structure, revealing a 43-subunit assembly with high structural homology to its 45-subunit mammalian counterpart, including a hitherto unknown homologue to subunit NDUFA3. The major conformational state of the Drosophila enzyme is the mammalian-type 'ready-to-go' active resting state, with a fully ordered and enclosed ubiquinone-binding site, but a subtly altered global conformation related to changes in subunit ND6. The mammalian-type 'deactive' pronounced resting state is not observed: in two minor states the ubiquinone-binding site is unchanged, but a deactive-type p-bulge is present in ND6-TMH3. Our detailed structural knowledge of Drosophila complex I provides a foundation for new approaches to disentangle mechanisms of complex I catalysis and regulation in bioenergetics and physiology.

Data availability

Structural data have been deposited in the EMDB and PDB databases under the following accession codes: EMD-15936 and 8B9Z (Dm1; active), EMD-15937 and 8BA0 (Dm2; twisted), and EMD-15938 (Dm3; cracked).

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Author details

  1. Ahmed-Noor A Agip

    MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3020-8262

  2. Injae Chung

    MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2902-4677

  3. Alvaro Sanchez-Martinez

    MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2728-6251

  4. Alexander J Whitworth

    MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
    For correspondence
    a.whitworth@mrc-mbu.cam.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1154-6629

  5. Judy Hirst

    MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
    For correspondence
    jh@mrc-mbu.cam.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8667-6797

Funding

Medical Research Council (MC_UU_00015/6)

  • Alexander J Whitworth

Medical Research Council (MC_UU_00028/6)

  • Alexander J Whitworth

Medical Research Council (MC_UU_00015/2)

  • Judy Hirst

Medical Research Council (MC_UU_00028/1)

  • Judy Hirst

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

Copyright

© 2023, Agip 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. Ahmed-Noor A Agip
  2. Injae Chung
  3. Alvaro Sanchez-Martinez
  4. Alexander J Whitworth
  5. Judy Hirst
(2023)
Cryo-EM structures of mitochondrial respiratory complex I from Drosophila melanogaster
eLife 12:e84424.
https://doi.org/10.7554/eLife.84424

Share this article

https://doi.org/10.7554/eLife.84424

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Further reading

    1. Structural Biology and Molecular Biophysics

    Resting mitochondrial complex I from Drosophila melanogaster adopts a helix-locked state

    Abhilash Padavannil, Anjaneyulu Murari ... James A Letts
    Research Article

    Respiratory complex I is a proton-pumping oxidoreductase key to bioenergetic metabolism. Biochemical studies have found a divide in the behavior of complex I in metazoans that aligns with the evolutionary split between Protostomia and Deuterostomia. Complex I from Deuterostomia including mammals can adopt a biochemically defined off-pathway ‘deactive’ state, whereas complex I from Protostomia cannot. The presence of off-pathway states complicates the interpretation of structural results and has led to considerable mechanistic debate. Here, we report the structure of mitochondrial complex I from the thoracic muscles of the model protostome Drosophila melanogaster. We show that although D. melanogaster complex I (Dm-CI) does not have a NEM-sensitive deactive state, it does show slow activation kinetics indicative of an off-pathway resting state. The resting-state structure of Dm-CI from the thoracic muscle reveals multiple conformations. We identify a helix-locked state in which an N-terminal α-helix on the NDUFS4 subunit wedges between the peripheral and membrane arms. Comparison of the Dm-CI structure and conformational states to those observed in bacteria, yeast, and mammals provides insight into the roles of subunits across organisms, explains why the Dm-CI off-pathway resting state is NEM insensitive, and raises questions regarding current mechanistic models of complex I turnover.