An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases

Abstract Mitochondrial ATP synthase forms stable dimers arranged into oligomeric assemblies that generate the inner-membrane curvature essential for efficient energy conversion. Here, we report cryo-EM structures of the intact ATP synthase dimer from Trypanosoma brucei in ten different rotational states. The model consists of 25 subunits, including nine lineage-specific, as well as 36 lipids. The rotary mechanism is influenced by the divergent peripheral stalk, conferring a greater conformational flexibility. Proton transfer in the lumenal half-channel occurs via a chain of five ordered water molecules. The dimerization interface is formed by subunit-g that is critical for interactions but not for the catalytic activity. Although overall dimer architecture varies among eukaryotes, we find that subunit-g together with subunit-e form an ancestral oligomerization motif, which is shared between the trypanosomal and mammalian lineages. Therefore, our data defines the subunit-g/e module as a structural component determining ATP synthase oligomeric assemblies.

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An ancestral interaction module promotes oligomerisation in divergent mitochondrial ATP synthases

10.1101/2021.10.10.463820 ◽

2021 ◽

Author(s):

Ondrej Gahura ◽

Alexander Muhleip ◽

Carolina Hierro-Yap ◽

Brian Panicucci ◽

Minal Jain ◽

...

Keyword(s):

Atp Synthase ◽

Conformational Flexibility ◽

Membrane Curvature ◽

Water Molecules ◽

Rotational States ◽

Efficient Energy ◽

Mitochondrial Atp Synthase ◽

Dimerization Interface ◽

A Chain ◽

Ordered Water

Mitochondrial ATP synthase forms stable dimers arranged into oligomeric assemblies that generate the inner-membrane curvature essential for efficient energy conversion. Here, we report cryo EM structures of the intact ATP synthase dimer from trypanosomes in 10 different rotational states. The model consists of 25 subunits, including 11 lineage-specific, as well as 36 lipids. The rotary mechanism is influenced by the divergent peripheral stalk, conferring a greater conformational flexibility. Proton transfer in the lumenal half-channel occurs via a chain of five ordered water molecules. The dimerization interface is formed by subunit-g that is critical for interactions but not for the catalytic activity. Although overall dimer architecture varies among eukaryotes, we find that subunit-g and -e form a common ancestral oligomerisation motif, which is shared between the trypanosomal and mammalian lineages. Therefore, our data defines the subunit-g/e module as a structural component determining ATP synthase oligomeric assemblies.

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Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F1-Fo coupling

10.1101/543108 ◽

2019 ◽

Cited By ~ 2

Author(s):

Bonnie J. Murphy ◽

Niklas Klusch ◽

Julian D. Langer ◽

Deryck J. Mills ◽

Özkan Yildiz ◽

...

Keyword(s):

Atp Synthase ◽

Metal Ion ◽

De Novo ◽

Atp Synthesis ◽

Joint Movement ◽

Access Channel ◽

Subunit Interface ◽

Ring Rotation ◽

Mitochondrial Atp Synthase ◽

Ordered Water

F1Fo-ATP synthases play a central role in cellular metabolism, making the energy of the proton-motive force across a membrane available for a large number of energy-consuming processes. We determined the single-particle cryo-EM structure of active dimeric ATP synthase from mitochondria of Polytomella sp. at 2.7- 2.8 Å resolution. Separation of 13 well-defined rotary substates by 3D classification provides a detailed picture of the molecular motions that accompany c-ring rotation and result in ATP synthesis. Crucially, the F1 head rotates along with the central stalk and c-ring rotor for the first ~30° of each 120° primary rotary step. The joint movement facilitates flexible coupling of the stoichiometrically mismatched F1 and Fo subcomplexes. Flexibility is mediated primarily by the interdomain hinge of the conserved OSCP subunit, a well-established target of physiologically important inhibitors. Our maps provide atomic detail of the c-ring/a-subunit interface in the membrane, where protonation and deprotonation of c-ring cGlu111 drives rotary catalysis. An essential histidine residue in the lumenal proton access channel binds a strong non-peptide density assigned to a metal ion that may facilitate c-ring protonation, as its coordination geometry changes with c-ring rotation. We resolve ordered water molecules in the proton access and release channels and at the gating aArg239 that is critical in all rotary ATPases. We identify the previously unknown ASA10 subunit and present complete de novo atomic models of subunits ASA1-10, which make up the two interlinked peripheral stalks that stabilize the Polytomella ATP synthase dimer.

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Structure of a mitochondrial ATP synthase with bound native cardiolipin

eLife ◽

10.7554/elife.51179 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 16

Author(s):

Alexander Mühleip ◽

Sarah E McComas ◽

Alexey Amunts

Keyword(s):

Atp Synthase ◽

Membrane Curvature ◽

Dimer Interface ◽

Functional Roles ◽

Lipid Interactions ◽

Mitochondrial Atp Synthase ◽

Distinct Subunit ◽

Insight Into ◽

Membrane Region ◽

Inhibitory Factor 1

The mitochondrial ATP synthase fuels eukaryotic cells with chemical energy. Here we report the cryo-EM structure of a divergent ATP synthase dimer from mitochondria of Euglena gracilis, a member of the phylum Euglenozoa that also includes human parasites. It features 29 different subunits, 8 of which are newly identified. The membrane region was determined to 2.8 Å resolution, enabling the identification of 37 associated lipids, including 25 cardiolipins, which provides insight into protein-lipid interactions and their functional roles. The rotor-stator interface comprises four membrane-embedded horizontal helices, including a distinct subunit a. The dimer interface is formed entirely by phylum-specific components, and a peripherally associated subcomplex contributes to the membrane curvature. The central and peripheral stalks directly interact with each other. Last, the ATPase inhibitory factor 1 (IF1) binds in a mode that is different from human, but conserved in Trypanosomatids.

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Dimers of mitochondrial ATP synthase induce membrane curvature and self-assemble into rows

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1816556116 ◽

2019 ◽

Vol 116 (10) ◽

pp. 4250-4255 ◽

Cited By ~ 54

Author(s):

Thorsten B. Blum ◽

Alexander Hahn ◽

Thomas Meier ◽

Karen M. Davies ◽

Werner Kühlbrandt

Keyword(s):

Lipid Bilayer ◽

Yarrowia Lipolytica ◽

Atp Synthase ◽

Membrane Curvature ◽

Specific Lipids ◽

Inner Membrane ◽

Mitochondrial Atp Synthase ◽

Mitochondrial Morphogenesis ◽

Electron Cryotomography ◽

Main Factor

Mitochondrial ATP synthases form dimers, which assemble into long ribbons at the rims of the inner membrane cristae. We reconstituted detergent-purified mitochondrial ATP synthase dimers from the green algaePolytomellasp. and the yeastYarrowia lipolyticainto liposomes and examined them by electron cryotomography. Tomographic volumes revealed that ATP synthase dimers from both species self-assemble into rows and bend the lipid bilayer locally. The dimer rows and the induced degree of membrane curvature closely resemble those in the inner membrane cristae. Monomers of mitochondrial ATP synthase reconstituted into liposomes do not bend membrane visibly and do not form rows. No specific lipids or proteins other than ATP synthase dimers are required for row formation and membrane remodelling. Long rows of ATP synthase dimers are a conserved feature of mitochondrial inner membranes. They are required for cristae formation and a main factor in mitochondrial morphogenesis.

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Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization

Nature Communications ◽

10.1038/s41467-020-18993-6 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Rasmus Kock Flygaard ◽

Alexander Mühleip ◽

Victor Tobiasson ◽

Alexey Amunts

Keyword(s):

Atp Synthase ◽

Single Copy ◽

Membrane Curvature ◽

Universal Property ◽

Membrane Anchor ◽

Unique Type ◽

Type Iii ◽

Mitochondrial Atp Synthase ◽

Fundamental Phenomenon ◽

Tetrameric Form

Abstract Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we characterized the unique type III mitochondrial ATP synthase in its dimeric and tetrameric form. The cryo-EM structure of a ciliate ATP synthase dimer reveals an unusual U-shaped assembly of 81 proteins, including a substoichiometrically bound ATPTT2, 40 lipids, and co-factors NAD and CoQ. A single copy of subunit ATPTT2 functions as a membrane anchor for the dimeric inhibitor IF1. Type III specific linker proteins stably tie the ATP synthase monomers in parallel to each other. The intricate dimer architecture is scaffolded by an extended subunit-a that provides a template for both intra- and inter-dimer interactions. The latter results in the formation of tetramer assemblies, the membrane part of which we determined to 3.1 Å resolution. The structure of the type III ATP synthase tetramer and its associated lipids suggests that it is the intact unit propagating the membrane curvature.

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ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria

Nature Communications ◽

10.1038/s41467-020-20381-z ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Alexander Mühleip ◽

Rasmus Kock Flygaard ◽

Jana Ovciarikova ◽

Alice Lacombe ◽

Paula Fernandes ◽

...

Keyword(s):

Atp Synthase ◽

Apical Membrane ◽

Membrane Curvature ◽

Structural Basis ◽

Dimer Interface ◽

Mitochondrial Atp Synthase ◽

Subtomogram Averaging

AbstractMitochondrial ATP synthase plays a key role in inducing membrane curvature to establish cristae. In Apicomplexa causing diseases such as malaria and toxoplasmosis, an unusual cristae morphology has been observed, but its structural basis is unknown. Here, we report that the apicomplexan ATP synthase assembles into cyclic hexamers, essential to shape their distinct cristae. Cryo-EM was used to determine the structure of the hexamer, which is held together by interactions between parasite-specific subunits in the lumenal region. Overall, we identified 17 apicomplexan-specific subunits, and a minimal and nuclear-encoded subunit-a. The hexamer consists of three dimers with an extensive dimer interface that includes bound cardiolipins and the inhibitor IF1. Cryo-ET and subtomogram averaging revealed that hexamers arrange into ~20-megadalton pentagonal pyramids in the curved apical membrane regions. Knockout of the linker protein ATPTG11 resulted in the loss of pentagonal pyramids with concomitant aberrantly shaped cristae. Together, this demonstrates that the unique macromolecular arrangement is critical for the maintenance of cristae morphology in Apicomplexa.

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