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.

The consequence of ATP synthase dimer angle on mitochondrial morphology studied by cryo-electron tomography

“…This reveals extensive inter-dimer interactions mediated by subunits e and g (Fig, 4G, I and Fig. S12), in agreement with recent work demonstrating the key role that these subunits play a role in oligomerisation / row formation (21).…”

“…Dimers of ATP synthase assemble into oligomeric rows (or ribbons) along the curved ridges of crista membranes, observed by cryo-electron tomography (cryoET) (9, 11, 22). This oligomerisation (formation of dimer rows) is mediated by an ancestral motif in subunits e and g (20, 21) with assistance from subunit k (5, 23, 24). Formation of dimer rows is required for crista membrane curvature, and thus maintenance of lamellar or tubular shaped cristae (11, 12).…”

“…Based on biochemical and imaging experiments, subunits e and g were shown to be essential for dimer formation (7,11,(19)(20)(21). Dimers of ATP synthase assemble into oligomeric rows (or ribbons) along the curved ridges of crista membranes, observed by cryo-electron tomography (cryoET) (9,11,22).…”

The ancestral shape of the access proton path of mitochondrial ATP synthases revealed by a split subunit-a

“…The short N-terminal -helix of subunit-a is a widely conserved structural element of mitochondrial ATP synthases When examining the proton translocation elements of mitochondrial ATP synthases of two divergent eukaryotes, Saccharomyces cerevisiae (Guo, et al 2017) and Trypanosoma brucei (Gahura, et al 2022), we noticed a remarkable similarity between the N-terminal regions of subunit-a in the yeast and subunit ATPEG3 in the parasite. The N-termini of both proteins form a short single-turn -helix, hereafter referred to as hN, which is located at the layer corresponding to the lumenal surface of the membrane and interacts with the horizontal helix h5 of subunit-a in the same manner in both structures.…”

“…It is shaped by subunit-a and adjacent membrane elements, including lipids (Klusch, et al 2017). Recently, it was proposed that delivery of protons to the c-ring is facilitated by a Grotthuss mechanism through a chain of coordinated water molecules and adjacent amino acid residues in the inner part of the channel in mammalian (Spikes, et al 2020) and trypanosomal (Gahura, et al 2022) mitochondrial ATP synthases.…”