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The structure has been determined by electron cryomicroscopy of the adenosine triphosphate (ATP) synthase from Mycobacterium smegmatis. This analysis confirms features in a prior description of the structure of the enzyme, but it also describes other highly significant attributes not recognized before that are crucial for understanding the mechanism and regulation of the mycobacterial enzyme. First, we resolved not only the three main states in the catalytic cycle described before but also eight substates that portray structural and mechanistic changes occurring during a 360° catalytic cycle. Second, a mechanism of auto-inhibition of ATP hydrolysis involves not only the engagement of the C-terminal region of an α-subunit in a loop in the γ-subunit, as proposed before, but also a “fail-safe” mechanism involving the b′-subunit in the peripheral stalk that enhances engagement. A third unreported characteristic is that the fused bδ-subunit contains a duplicated domain in its N-terminal region where the two copies of the domain participate in similar modes of attachment of the two of three N-terminal regions of the α-subunits. The auto-inhibitory plus the associated “fail-safe” mechanisms and the modes of attachment of the α-subunits provide targets for development of innovative antitubercular drugs. The structure also provides support for an observation made in the bovine ATP synthase that the transmembrane proton-motive force that provides the energy to drive the rotary mechanism is delivered directly and tangentially to the rotor via a Grotthuss water chain in a polar L-shaped tunnel.

Bedaquiline (BDQ), a first-in-class diarylquinoline anti-tuberculosis drug, and its analogue, TBAJ-587, prevent the growth and proliferation of Mycobacterium tuberculosis by inhibiting ATP synthase 1 , 2 . However, BDQ also inhibits human ATP synthase 3 . At present, how these compounds interact with either M. tuberculosis ATP synthase or human ATP synthase is unclear. Here we present cryogenic electron microscopy structures of M. tuberculosis ATP synthase with and without BDQ and TBAJ-587 bound, and human ATP synthase bound to BDQ. The two inhibitors interact with subunit a and the c-ring at the leading site, c-only sites and lagging site in M. tuberculosis ATP synthase, showing that BDQ and TBAJ-587 have similar modes of action. The quinolinyl and dimethylamino units of the compounds make extensive contacts with the protein. The structure of human ATP synthase in complex with BDQ reveals that the BDQ-binding site is similar to that observed for the leading site in M. tuberculosis ATP synthase, and that the quinolinyl unit also interacts extensively with the human enzyme. This study will improve researchers’ understanding of the similarities and differences between human ATP synthase and M. tuberculosis ATP synthase in terms of the mode of BDQ binding, and will allow the rational design of novel diarylquinolines as anti-tuberculosis drugs. Cryogenic electron microscopy structures of Mycobacterium tuberculosis ATP synthase and human ATP synthase bound to the anti-tuberculosis drug bedaquiline or its analogue TBAJ-587 shed light on drug binding and could lead to new treatments for tuberculosis.

The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial matrix via the proton inlet half channel proceeds via a Grotthus mechanism, and a similar mechanism may operate in the exit half channel. The structure has given information about the architecture and mechanical constitution and properties of the peripheral stalk, part of the membrane extrinsic region of the stator, and how the action of the peripheral stalk damps the side-to-side rocking motions that occur in the enzyme complex during the catalytic cycle. It also describes wedge structures in the membrane domains of each monomer, where the skeleton of each wedge is provided by three α-helices in the membrane domains of the b-subunit to which the supernumerary subunits e, f, and g and the membrane domain of subunit A6L are bound. Protein voids in the wedge are filled by three specifically bound cardiolipin molecules and two other phospholipids. The external surfaces of the wedges link the monomeric complexes together into the dimeric structures and provide a pivot to allow the monomer–monomer interfaces to change during catalysis and to accommodate other changes not related directly to catalysis in the monomer–monomer interface that occur in mitochondrial cristae. The structure of the bovine dimer also demonstrates that the structures of dimeric ATP synthases in a tetrameric porcine enzyme have been seriously misinterpreted in the membrane domains.

Background The ATP synthase F1 subunit α ( ATP5F1A ) gene encodes a critical structural subunit of mitochondrial complex V. ATP5F1A mutations are linked to mitochondrial complex V deficiency diseases. Although only 14 cases have been reported globally, the genotype-phenotype correlations and underlying molecular mechanisms remain poorly understood. Objective To investigate the pathogenic mechanisms of ATP5F1A deficiency through functional analysis of a recurrent missense variant. Method A Han Chinese family with developmental delay and motor dysfunction was studied. Whole-exome sequencing and trio analysis identified the causative variant. Pathogenicity was evaluated using bioinformatic predictions and structural modeling. HEK293T cells were transfected with wild-type or mutant-type ATP5F1A plasmids for Western blot and immunofluorescence analysis. Morpholino (MO) oligonucleotides were microinjected into zebrafish embryos for gene knockdown. Motor neuron development was observed in Tg( mnx1 :eGFP) zebrafish, with accompanying behavioral assessments. RNA sequencing was conducted to explore the underlying molecular pathways. Results A de novo missense variant (c.1252G > A, p.Gly418Arg) in ATP5F1A was identified and shown to segregate with the disease phenotype. The mutation reduced protein stability and expression. In HEK293T cells, the mutant protein exhibited reduced expression without affecting mitochondrial localization. In zebrafish, atp5fa1 knockdown caused growth retardation, motor dysfunction, and impaired motor neuron axon development. Rescue experiments with human wild-type ATP5F1A mRNA partially restored motor neuron morphology. Transcriptomic analysis identified 2,261 differentially expressed genes, enriched in neurotransmission and apelin signaling pathways. qPCR confirmed downregulation of autophagy-related genes ( apln , becn1 , map1lc3b ) in knockdown larvae. Western blot showed that atp5fa1 knockdown increased P62 and decreased Lc3b-II expression in zebrafish models. Conclusion This study is the first to report pathogenic ATP5F1A mutations in the Chinese population. Atp5fa1 dysfunction leads to multi-system defects and disease phenotypes in a zebrafish model, possibly mediated through inhibiting autophagy activation mechanisms.

The mitochondrial adenosine triphosphate (ATP) synthase produces most of the ATP required by mammalian cells. We isolated porcine tetrameric ATP synthase and solved its structure at 6.2-angstrom resolution using a single-particle cryo–electron microscopy method. Two classical V-shaped ATP synthase dimers lie antiparallel to each other to form an H-shaped ATP synthase tetramer, as viewed from the matrix. ATP synthase inhibitory factor subunit 1 (IF1) is a well-known in vivo inhibitor of mammalian ATP synthase at low pH. Two IF1 dimers link two ATP synthase dimers, which is consistent with the ATP synthase tetramer adopting an inhibited state. Within the tetramer, we refined structures of intact ATP synthase in two different rotational conformations at 3.34- and 3.45-Å resolution.

This study aims to evaluate the effect of melatonin supplementation on the outcomes of in vitro fertilization (IVF) and mitochondrial adenosine triphosphate production (MT-ATP6) gene expression in Iranian infertile couples. A single-blind nonrandomized controlled trial was conducted, recruiting 90 infertile couples who underwent IVF at an infertility center in Tehran, Iran. Patients who were assigned to the intervention group received melatonin as a supplementation to the standard controlled ovarian stimulation (COS). The control group received a COS protocol only. Primary outcome was the mRNA level of the MT-ATP6 gene in cumulus cells of ovarian follicles. Secondary outcomes were the mean number of mature oocytes retrieved, the embryo quality, and biochemical and clinical pregnancy rates. The mRNA level of the MT-ATP6 gene in cumulus cells between intervention and control groups was not statistically different (0.931 vs.1; P  ˃ 0.05). The mean number of poor-quality embryos was significantly lower in the intervention group than that in the control group (0.27 vs. 0.80; P  = 0.028). The biochemical and clinical pregnancy rates were higher in the intervention group (24% vs. 14%, P  = 0.089, and 14% vs. 7%, P  = 0.302, respectively); however, the difference was not significant. Melatonin supplementation did not increase the odds of clinical pregnancy and the number of mature oocytes retrieved, but significantly reduced the number of low-quality embryos. More extensive studies focusing on the level of MT-ATP6 gene expression in the oocyte or blastomere cells may further elucidate the effect of supplementation with melatonin in infertile couples who have poor clinical outcomes. Trial registration: Current Controlled Trials: IRCT2015042912307N4.

The opening of the permeability transition pore, a nonspecific channel in inner mitochondrial membranes, is triggered by an elevated total concentration of calcium ions in the mitochondrial matrix, leading to disruption of the inner membrane and necrotic cell death. Cyclosporin A inhibits pore opening by binding to cyclophilin D, which interacts with the pore. It has been proposed that the pore is associated with the ATP synthase complex. Previously, we confirmed an earlier observation that the pore survives in cells lacking membrane subunits ATP6 and ATP8 of ATP synthase, and in other cells lacking the enzyme’s c₈ rotor ring or, separately, its peripheral stalk subunits b and oligomycin sensitive conferral protein. Here, we investigated whether the pore is associated with the remaining membrane subunits of the enzyme. Individual deletion of subunits e, f, g, and 6.8-kDa proteolipid disrupts dimerization of the complex, and deletion of DAPIT (diabetes-associated protein in insulin sensitive tissue) possibly influences oligomerization of dimers, but removal of each subunit had no effect on the pore. Also, we removed together the enzyme’s membrane bound c₈ ring and the δ-subunit from the catalytic domain. The resulting cells assemble only a subcomplex derived from the peripheral stalk and membrane-associated proteins. Despite diminished levels of respiratory complexes, these cells generate a membrane potential to support uptake of calcium into the mitochondria, leading to pore opening, and retention of its characteristic properties. It is most unlikely that the ATP synthase, dimer or monomer, or any component, provides the permeability transition pore.

Duchenne Muscular Dystrophy (DMD) is a lethal muscle disorder, caused by mutations in the DMD gene and affects approximately 1:5000–6000 male births. In this report, we identified dysregulation of members of the Dlk1-Dio3 miRNA cluster in muscle biopsies of the GRMD dog model. Of these, we selected miR-379 for a detailed investigation because its expression is high in the muscle, and is known to be responsive to glucocorticoid, a class of anti-inflammatory drugs commonly used in DMD patients. Bioinformatics analysis predicts that miR-379 targets EIF4G2, a translational factor, which is involved in the control of mitochondrial metabolic maturation. We confirmed in myoblasts that EIF4G2 is a direct target of miR-379, and identified the DAPIT mitochondrial protein as a translational target of EIF4G2. Knocking down DAPIT in skeletal myotubes resulted in reduced ATP synthesis and myogenic differentiation. We also demonstrated that this pathway is GC-responsive since treating mice with dexamethasone resulted in reduced muscle expression of miR-379 and increased expression of EIF4G2 and DAPIT. Furthermore, miR-379 seric level, which is also elevated in the plasma of DMD patients in comparison with age-matched controls, is reduced by GC treatment. Thus, this newly identified pathway may link GC treatment to a mitochondrial response in DMD.

We have used a combination of electron cryo-tomography, subtomogram averaging, and electron crystallographic image processing to analyse the structure of intact bovine F1Fo ATP synthase in 2D membrane crystals. ATPase assays and mass spectrometry analysis of the 2D crystals confirmed that the enzyme complex was complete and active. The structure of the matrix-exposed region was determined at 24 Å resolution by subtomogram averaging and repositioned into the tomographic volume to reveal the crystal packing. F1Fo ATP synthase complexes are inclined by 16° relative to the crystal plane, resulting in a zigzag topology of the membrane and indicating that monomeric bovine heart F1Fo ATP synthase by itself is sufficient to deform lipid bilayers. This local membrane curvature is likely to be instrumental in the formation of ATP synthase dimers and dimer rows, and thus for the shaping of mitochondrial cristae. Cells use a molecule called adenosine triphosphate (or ATP for short) to power many processes that are vital for life. Animals, plants, and fungi primarily make their ATP in a specialised compartment called the mitochondrion, which is found inside their cells. The mitochondrion is often referred to as the powerhouse of cells as it captures and stores the energy that animals gain from eating food in the molecule ATP. Other enzymes in the cell break apart ATP to release the stored energy, which they use to power various cellular processes. The interior architecture of the mitochondrion includes a highly folded inner membrane where electrical energy is transformed into chemical energy. The tight folding of the inner membrane is thought to make this process more efficient. An enzyme named ATP synthase performs the final steps of the energy transformation process by producing ATP (ATP synthase literally means ‘ATP maker’). This enzyme sits in pairs along the edges of the inner membrane folds. This raises the question: does the ATP synthase cause the membrane to fold or does this enzyme just ‘prefer’ these folded edges (which are instead caused by something else inside the mitochondrion)? To investigate this question, Jiko, Davies et al. extracted ATP synthase from the mitochondria of cow hearts and mixed them with modified fat molecules to form a ‘2D membrane crystal’: a membrane containing an ordered pattern of enzymes. An electron microscope was used to generate a three-dimensional volume of the 2D membrane crystal via a process similar to a MRI or CAT scan that one might have in hospital. In the three-dimensional volume of the membrane crystal, Jiko, Davies et al. discovered that instead of being flat as expected, the membrane of the 2D membrane crystal was rippled and that this ripple was caused by the membrane-embedded part of the ATP synthase. The geometry of the ripple exactly matched half of the bend at the edge of the membrane folds in the mitochondrion. Therefore, Jiko, Davies et al. concluded that a pair of ATP synthases, as found in mitochondria, was responsible for defining the tight folds of the inner mitochondrial membrane.

IF 1 is a natural inhibitor protein for mitochondrial F o F 1 ATP synthase that blocks catalysis and rotation of the F 1 by deeply inserting its N-terminal helices into F 1 . A unique feature of IF 1 is condition-dependent inhibition; although IF 1 inhibits ATP hydrolysis by F 1 , IF 1 inhibition is relieved under ATP synthesis conditions. To elucidate this condition-dependent inhibition mechanism, we have performed single-molecule manipulation experiments on IF 1 -inhibited bovine mitochondrial F 1 ( b MF 1 ). The results show that IF 1 -inhibited F 1 is efficiently activated only when F 1 is rotated in the clockwise (ATP synthesis) direction, but not in the counterclockwise direction. The observed rotational-direction-dependent activation explains the condition-dependent mechanism of IF 1 inhibition. Investigation of mutant IF 1 with N-terminal truncations shows that the interaction with the γ subunit at the N-terminal regions is crucial for rotational-direction-dependent ejection, and the middle long helix is responsible for the inhibition of F 1 . IF 1 is a natural inhibitor of mitochondrial F o F 1 -ATP synthase, which blocks catalysis and rotation of the F 1 motor. Here, the authors show the rotational-direction-dependence of activation from IF 1 inhibition, with IF 1 being readily dissociated when F 1 rotates to the clockwise direction.