ATP Synthase Dimers Research Articles

Megacomplex organization of the oxidative phosphorylation system by structural analysis of respiratory supercomplexes from potato

The individual protein complexes of the oxidative phosphorylation system (OXPHOS complexes I to V) specifically interact and form defined supramolecular structures, the so-called “respiratory supercomplexes”. Some supercomplexes appear to associate into larger structures, or megacomplexes, such as a string of dimeric ATP synthase (complex V 2). A row-like organization of OXPHOS complexes I, III and IV into respiratory strings has also been proposed. These transient strings cannot be purified after detergent solubilization. Hence the shape and composition of the respiratory string was approached by an extensive structural characterization of all its possible building blocks, which are the supercomplexes. About 400,000 molecular projections of supercomplexes from potato mitochondria were processed by single particle electron microscopy. We obtained two-dimensional projection maps of at least five different supercomplexes, including the supercomplex I + III 2, III 2 + IV 1, V 2, I + III 2 + IV 1 and I 2 + III 2 in different types of position. From these maps the relative position of the individual complexes in the largest unit, the I 2 + III 2 + IV 2 supercomplex, could be determined in a coherent way. The maps also show that the I + III 2 + IV 1 supercomplex, or respirasome, differs from its counterpart in bovine mitochondria. The new structural features allow us to propose a consistent model of the respiratory string, composed of repeating I 2 + III 2 + IV 2 units, which is in agreement with dimensions observed in former freeze-fracture electron microscopy data.

Supramolecular organization of the yeast F1Fo‐ATP synthase

The yeast mitochondrial F(1)F(o)-ATP synthase is a large complex of 600 kDa that uses the proton electrochemical gradient generated by the respiratory chain to catalyse ATP synthesis from ADP and P(i). For a large range of organisms, it has been shown that mitochondrial ATP synthase adopts oligomeric structures. Moreover, several studies have suggested that a link exists between ATP synthase and mitochondrial morphology. In order to understand the link between ATP synthase oligomerization and mitochondrial morphology, more information is needed on the supramolecular organization of this enzyme within the inner mitochondrial membrane. We have conducted an electron microscopy study on wild-type yeast mitochondria at different levels of organization from spheroplast to isolated ATP synthase complex. Using electron tomography, freeze-fracture, negative staining and image processing, we show that cristae form a network of lamellae, on which ATP synthase dimers assemble in linear and regular arrays of oligomers. Our results shed new light on the supramolecular organization of the F(1)F(o)-ATP synthase and its potential role in mitochondrial morphology.

Regulation of Mitochondrial Structure and Function by the F 1F o-ATPase Inhibitor Protein, IF 1

When mitochondrial respiration is compromised, the F(1)F(o)-ATP synthase reverses and consumes ATP, serving to maintain the mitochondrial membrane potential (Delta psi(m)). This process is mitigated by IF(1). As little is known of the cell biology of IF(1), we have investigated the functional consequences of varying IF(1) expression. We report that, (1) during inhibition of respiration, IF(1) conserves ATP at the expense of Delta psi(m); (2) overexpression of IF(1) is protective against ischemic injury; (3) relative IF(1) expression level varies between tissues and cell types and dictates the response to inhibition of mitochondrial respiration; (4) the density of mitochondrial cristae is increased by IF(1) overexpression and decreased by IF(1) suppression; and (5) IF(1) overexpression increases the formation of dimeric ATP synthase complexes and increases F(1)F(o)-ATP synthase activity. Thus, IF(1) regulates mitochondrial function and structure under both physiological and pathological conditions.

Characterization of Domain Interfaces in Monomeric and Dimeric ATP Synthase

We disassembled monomeric and dimeric yeast ATP synthase under mild conditions to identify labile proteins and transiently stable subcomplexes that had not been observed before. Specific removal of subunits alpha, beta, oligomycin sensitivity conferring protein (OSCP), and h disrupted the ATP synthase at the gamma-alpha(3)beta(3) rotor-stator interface. Loss of two F(1)-parts from dimeric ATP synthase led to the isolation of a dimeric subcomplex containing membrane and peripheral stalk proteins thus identifying the membrane/peripheral stalk sectors immediately as the dimerizing parts of ATP synthase. Almost all subunit a was found associated with a ring of 10 c-subunits in two-dimensional blue native/SDS gels. We therefore postulate that c10a1-complex is a stable structure in resting ATP synthase until the entry of protons induces a breaking of interactions and stepwise rotation of the c-ring relative to the a-subunit in the catalytic mechanism. Dimeric subunit a was identified in SDS gels in association with two c10-rings suggesting that a c10a2c10-complex may constitute an important part of the monomer-monomer interface in dimeric ATP synthase that seems to be further tightened by subunits b, i, e, g, and h. In contrast to the monomer-monomer interface, the interface between dimers in higher oligomeric structures remains largely unknown. However, we could show that the natural inhibitor protein Inh1 is not required for oligomerization.

Structural organization of mitochondrial ATP synthase

Specific modules and subcomplexes like F1 and F0-parts, F1-c subcomplexes, peripheral and central stalks, and the rotor part comprising a ring of c-subunits with attached subunits γ, δ, and ε can be identified in yeast and mammalian ATP synthase. Four subunits, α3β3, OSCP, and h, seem to form a structural entity at the extramembranous rotor/stator interface (γ/α3β3) to hold and stabilize the rotor in the holo-enzyme. The intramembranous rotor/stator interface (c-ring/a-subunit) must be dynamic to guarantee unhindered rotation. Unexpectedly, a c10a-assembly could be isolated with almost quantitive yield suggesting that an intermediate step in the rotating mechanism was frozen under the conditions used. Isolation of dimeric a-subunit and (c10)2a2-complex from dimeric ATP synthase suggested that the a-subunit stabilizes the same monomer–monomer interface that had been shown to involve also subunits e, g, b, i, and h. The natural inhibitor protein Inh1 does not favor oligomerization of yeast ATP synthase. Other candidates for the oligomerization of dimeric ATP synthase building blocks are discussed, e.g. the transporters for inorganic phosphate and ADP/ATP that had been identified as constituents of ATP synthasomes. Independent approaches are presented that support previous reports on the existence of ATP synthasomes in the mitochondrial membrane.

Enzyme shapes mitochondria

![][1] Ribbons of ATP synthase (yellow) dimers can be seen by electron tomography in curved membranes derived from mitochondria. KUHLBRANDT/EMBO ATP synthase bends the mitochondrial membrane to improve its performance, say Mike Strauss, Werner Kuhlbrandt, and colleagues (Max

Profiling Phosphoproteins of Yeast Mitochondria Reveals a Role of Phosphorylation in Assembly of the ATP Synthase

Mitochondria are crucial for numerous cellular processes, yet the regulation of mitochondrial functions is only understood in part. Recent studies indicated that the number of mitochondrial phosphoproteins is higher than expected; however, the effect of reversible phosphorylation on mitochondrial structure and function has only been defined in a few cases. It is thus crucial to determine authentic protein phosphorylation sites from highly purified mitochondria in a genetically tractable organism. The yeast Saccharomyces cerevisiae is a major model organism for the analysis of mitochondrial functions. We isolated highly pure yeast mitochondria and performed a systematic analysis of phosphorylation sites by a combination of different enrichment strategies and mass spectrometry. We identified 80 phosphorylation sites in 48 different proteins. These mitochondrial phosphoproteins are involved in critical mitochondrial functions, including energy metabolism, protein biogenesis, fatty acid metabolism, metabolite transport, and redox regulation. By combining yeast genetics and in vitro biochemical analysis, we found that phosphorylation of a serine residue in subunit g (Atp20) regulates dimerization of the mitochondrial ATP synthase. The authentic phosphoproteome of yeast mitochondria will represent a rich source to uncover novel roles of reversible protein phosphorylation.

Rows of ATP Synthase Dimers in Native Mitochondrial Inner Membranes

The ATP synthase is a nanometric rotary machine that uses a transmembrane electrochemical gradient to form ATP. The structures of most components of the ATP synthase are known, and their organization has been elucidated. However, the supramolecular assembly of ATP synthases in biological membranes remains unknown. Here we show with submolecular resolution the organization of ATP synthases in the yeast mitochondrial inner membranes. The atomic force microscopy images we have obtained show how these molecules form dimers with characteristic 15 nm distance between the axes of their rotors through stereospecific interactions of the membrane embedded portions of their stators. A different interaction surface is responsible for the formation of rows of dimers. Such an organization elucidates the role of the ATP synthase in mitochondrial morphology. Some dimers have a different morphology with 10 nm stalk-to-stalk distance, in line with ATP synthases that are accessible to IF 1 inhibition. Rotation torque compensation within ATP synthase dimers stabilizes the ATP synthase structure, in particular the stator-rotor interaction.

New Insights into the Unique Structure of the F0F1-ATP Synthase from the Chlamydomonad Algae Polytomella sp. and Chlamydomonas reinhardtii

In this study, we investigate the structure of the mitochondrial F(0)F(1)-ATP synthase of the colorless alga Polytomella sp. with respect to the enzyme of its green close relative Chlamydomonas reinhardtii. It is demonstrated that several unique features of the ATP synthase in C. reinhardtii are also present in Polytomella sp. The alpha- and beta-subunits of the ATP synthase from both algae are highly unusual in that they exhibit extensions at their N- and C-terminal ends, respectively. Several subunits of the Polytomella ATP synthase in the range of 9 to 66 kD have homologs in the green alga but do not have known equivalents as yet in mitochondrial ATP synthases of mammals, plants, or fungi. The largest of these so-called ASA (ATP Synthase-Associated) subunits, ASA1, is shown to be an extrinsic protein. Short heat treatment of isolated Polytomella mitochondria unexpectedly dissociated the otherwise highly stable ATP synthase dimer of 1,600 kD into subcomplexes of 800 and 400 kD, assigned as the ATP synthase monomer and F(1)-ATPase, respectively. Whereas no ASA subunits were found in the F(1)-ATPase, all but two were present in the monomer. ASA6 (12 kD) and ASA9 (9 kD), predicted to be membrane bound, were not detected in the monomer and are thus proposed to be involved in the formation or stabilization of the enzyme. A hypothetical configuration of the Chlamydomonad dimeric ATP synthase portraying its unique features is provided to spur further research on this topic.

Metabolism controls dimerization of the chloroplast FoF1 ATP synthase in Chlamydomonas reinhardtii

Dimers and oligomers of F-type ATP synthases have been observed previously in mitochondria of various organisms and for the CFoF1 ATP synthase of chloroplasts of Chlamydomonas reinhardtii. In contrast to mitochondria, however, dimers of chloroplast ATP synthases dissociate at elevated phosphate concentration. This suggests a regulation by cell physiological processes.Stable isotope labeling of living cells and blue-native PAGE have been employed to quantitate changes in the ratio of monomeric to dimeric CFoF1 ATP synthase. Chlamydomonas reinhardtii cells were cultivated photoautotrophically in the presence of 15N and photomixotrophically at natural 14N abundance, respectively.As compared to photoautotrophic growth, an increased assembly of ATP synthase dimers on the expense of preexisting monomers during photomixotrophic growth was observed, demonstrating a metabolic control of the dimerization process.

ATP6 Homoplasmic Mutations Inhibit and Destabilize the Human F1F0-ATP Synthase without Preventing Enzyme Assembly and Oligomerization

The molecular pathogenic mechanism of the human mitochondrial diseases neurogenic ataxia and retinitis pigmentosa and maternally inherited Leigh syndrome was determined in cultured human cells harboring homoplasmic T8993G/T8993C point mutations in the mitochondrial ATP6 gene, which encodes subunit 6 of the F1F0-ATP synthase. Immunoprecipitation and blue native electrophoresis showed that F1F0-ATP synthase assembles correctly in homoplasmic mutant mitochondria. The mutants exhibited a tendency to have an increased sensitivity to subsaturating amounts of oligomycin; this provided further evidence for complete assembly and tight coupling between the F1 and F0 sectors. Furthermore, human ATP synthase dimers and higher homo-oligomers were observed for the first time, and it was demonstrated that the mutant enzymes retain enough structural integrity to oligomerize. A reproducible increase in the proportion of oligomeric-to-monomeric enzyme was found for the T8993G mutant suggesting that F1F0 oligomerization is regulated in vivo and that it can be modified in pathological conditions. Despite correct assembly, the T8993G mutation produced a 60% inhibition in ATP synthesis turnover. In vitro denaturing conditions showed F1F0 instability conferred by the mutations, although this instability did not produce enzyme disassembly in the conditions used for determination of ATP synthesis. Taken together, the data show that the primary molecular pathogenic mechanism of these deleterious human mitochondrial mutations is functional inhibition in a correctly assembled ATP synthase. Structural instability may play a role in the progression of the disease under potentially denaturing conditions, as discussed.

Characterization of dimeric ATP synthase and cristae membrane ultrastructure from Saccharomyces and Polytomella mitochondria

There is increasing evidence now that F 1F 0 ATP synthase is arranged in dimers in the inner mitochondrial membrane of several organisms. The dimers are also considered to be the building blocks of oligomers. It was recently found that the monomers in beef and the alga Polytomella ATP synthase dimer make an angle of ∼40° and ∼70°, respectively. This arrangement is considered to induce a strong local bending of the membrane. To further understand the packing of dimers into oligomers we performed an electron microscopy analysis of ATP synthase dimers purified from Saccharomyces cerevisiae. Two types of dimers were found in which the angle between the monomers is either ∼90° or ∼35°. According to our interpretation, the wide-angle dimers (70–90°) are “true-dimers” whereas the small-angle dimers (35–40°) rather are “pseudo-dimers”, which represent breakdown products of two adjacent true dimers in the oligomer. Ultrathin sectioning of intact Polytomella mitochondria indicates that the inner mitochondrial or cristae membrane is folded into lamellae and tubuli. Oligomers of ATP synthase can arrange in a helical fashion in tubular-shaped cristae membranes. These results strongly support the hypothesized role of ATP synthase oligomers in structural determination of the mitochondrial inner membrane.

Supercomplexes and subcomplexes of mitochondrial oxidative phosphorylation

Dimerization or oligomerization of ATP synthase has been proposed to play an important role for mitochondrial cristae formation and to be involved in regulating ATP synthase activity. We found comparable oligomycin-sensitive ATPase activity for monomeric and oligomeric ATP synthase suggesting that oligomerization/monomerization dynamics are not directly involved in regulating ATP synthase activity. Binding of the natural IF 1 inhibitor protein has been shown to induce dimerization of F 1-subcomplexes. This suggested that binding of IF 1 might also dimerize holo ATP synthase, and possibly link dimerization and inhibition. Analyzing mitochondria of human rho zero cells that contain mitochondria but lack mitochondrial DNA, we identified three subcomplexes of ATP synthase: (i) F 1 catalytic domain, (ii) F 1-domain with bound IF 1, and (iii) F 1-c subcomplex with bound IF 1 and a ring of subunits c. Since both IF 1 containing subcomplexes were present in monomeric state and exhibited considerably reduced ATPase activity as compared to the third subcomplex lacking IF 1, we postulate that inhibition and induction of dimerization of F 1-subcomplexes by IF 1 are independent events. F 1-subcomplexes were also found in mitochondria of patients with specific mitochondrial disorders, and turned out to be useful for the clinical differentiation between various types of mitochondrial biosynthesis disorders. Supramolecular associations of respiratory complexes, the “respirasomes”, seem not to be the largest assemblies in the structural organization of the respiratory chain, as suggested by differential solubilization of mitochondria and electron microscopic analyses of whole mitochondria. We present a model for a higher supramolecular association of respirasomes into a “respiratory string”.

The Peripheral Stalk Participates in the Yeast ATP Synthase Dimerization Independently of e and g Subunits

It is now clearly established that dimerization of the F(1)F(o) ATP synthase takes place in the mitochondrial inner membrane. Interestingly, oligomerization of this enzyme seems to be involved in cristae morphogenesis. As they were able to form homodimers, subunits 4, e, and g have been proposed as potential ATP synthase dimerization subunits. In this paper, we provide evidence that subunit h, a peripheral stalk component, is located either at or near the ATP synthase dimerization interface. Subunit h homodimers were formed in mitochondria and were found to be associated to ATP synthase dimers. Moreover, homodimerization of subunit h and of subunit i turned out to be independent of subunits e and g, confirming the existence of an ATP synthase dimer in the mitochondrial inner membrane in the absence of subunits e and g. For the first time, this dimer has been observed by BN-PAGE. Finally, from these results we are now able to update our model for the supramolecular organization of the ATP synthase in the membrane and propose a role for subunits e and g, which stabilize the ATP synthase dimers and are involved in the oligomerization of the complex.

Analysis of the role(s) and molecular organization of Subunit g in yeast F1Fo‐ATP synthase

F1Fo-ATP synthase is a molecular machine responsible for the synthesis of ATP. The F1Fo-ATP synthase consists of two oligomeric parts, the catalytic F1 sector and the membrane-embedded Fo sector. Recently it has been demonstrated that F1Fo-ATP synthase complexes exist as dimers via a physical association of two neighboring Fo-sectors. In yeast, two Fo-sector subunits, subunit g (Su g) and subunit e (Su e) play a key role in ATP synthase dimerization. Su g and Su e are not essential proteins in S. cerevisiae but play an important role in ATP synthase dimerization and in the development of cristae morphology. Su g and Su e are small hydrophobic proteins and each contains a conserved dimerization motif called GXXXG motif in their single transmembrane(TM) segment. Our previous studies were focused on the conserved GXXXG motif of Su g. We have demonstrated the importance of the GXXXG motif for the stability of Su g within the ATP synthase complex and also for the stable formation of ATP synthase dimers. We have also shown a close physical proximity between Su g and Su e; however, our data suggested that an intact GXXXG motif is not required for this interaction. We propose that both Su g and Su e may interact with other mitochondrial protein(s) via GXXXG motif. Our present work focuses on a partially conserved C-terminal region of Su g present in the mitochondrial intermembrane space. To study the potential role of Su g C-terminal region for the function(s) of Su g we have created Su g C-terminal deletion mutants in yeast. We are currently investigating the ability of these mutants to support ATP synthase dimerization and their ability to recruit a putative morphology factor important for mitochondrial morphology. Support: United States Public Health Service Grant RO1GM61573 to R. A. S.

Structure of dimeric ATP synthase from mitochondria: An angular association of monomers induces the strong curvature of the inner membrane

Respiration in all cells depends upon synthesis of ATP by the ATP synthase complex, a rotary motor enzyme. The structure of the catalytic moiety of ATP synthase, the so-called F 1 headpiece, is well established. F 1 is connected to the membrane-bound and ion translocating F 0 subcomplex by a central stalk. A peripheral stalk, or stator, prevents futile rotation of the headpiece during catalysis. Although the enzyme functions as a monomer, several lines of evidence have recently suggested that monomeric ATP synthase complexes might interact to form a dimeric supercomplex in mitochondria. However, due to its fragility, the structure of ATP synthase dimers has so far not been precisely defined for any organism. Here we report the purification of a stable dimeric ATP synthase supercomplex, using mitochondria of the alga Polytomella. Structural analysis by electron microscopy and single particle analysis revealed that dimer formation is based on specific interaction of the F 0 parts, not the F 1 headpieces which are not at all in close proximity. Remarkably, the angle between the two F 0 part is about 70°, which induces a strong local bending of the membrane. Hence, the function of ATP synthase dimerisation is to control the unique architecture of the mitochondrial inner membrane.

Structure of dimeric mitochondrial ATP synthase: novel F0 bridging features and the structural basis of mitochondrial cristae biogenesis.

The F1F0-ATP synthase exists as a dimer in mitochondria, where it is essential for the biogenesis of the inner membrane cristae. How two ATP synthase complexes dimerize to promote cristae formation is unknown. Here we resolved the structure of the dimeric F1F0 ATP synthase complex isolated from bovine heart mitochondria by transmission electron microscopy. The structure of the ATP synthase dimer has an overall conic appearance that is consistent with the proposed role of the dimeric enzyme in mitochondrial cristae biogenesis. The ATP synthase dimer interface is formed by contacts on both the F0 and F1 domains. A cross-bridging protein density was resolved which connects the two F0 domains on the intermembrane space side of the membrane. On the matrix side of the complex, the two F1 moieties are connected by a protein bridge, which is attributable to the IF1 inhibitor protein.

The Modification of the Conserved GXXXG Motif of the Membrane-spanning Segment of Subunit g Destabilizes the Supramolecular Species of Yeast ATP Synthase

The supernumerary subunit g is found in all mitochondrial ATP synthases. Most of the conserved amino acid residues are present in the membrane C-terminal part of the protein that contains a dimerization motif GXXXG. In yeast, alteration of this motif leads to the loss of subunit g and of supramolecular structures of the ATP synthase with concomitant appearance of anomalous mitochondrial morphologies. Disulfide bond formation involving an engineered cysteine in position 109 of subunit g and the endogenous cysteine 28 of subunit e promoted g + g, e + g, and e + e adducts, thus revealing the proximity in the mitochondrial membrane of several subunits e and g. Disulfide bond formation between two subunits g in mitochondria increased the stability of an oligomeric structure of the ATP synthase in digitonin extracts. These data suggest the participation of the dimerization motif of subunit g in the formation of supramolecular structures and is in favor of the existence of ATP synthase associations, in the inner mitochondrial membrane, whose masses are higher than those of ATP synthase dimers.

The Yeast F1F0-ATP Synthase: ANALYSIS OF THE MOLECULAR ORGANIZATION OF SUBUNIT g AND THE IMPORTANCE OF A CONSERVED GXXXG MOTIF

The F(1)F(0)-ATP synthase enzyme is located in the inner mitochondrial membrane, where it forms dimeric complexes. Dimerization of the ATP synthase involves the physical association of the neighboring membrane-embedded F(0)-sectors. In yeast, the F(0)-sector subunits g and e (Su g and Su e, respectively) play a key role in supporting the formation of ATP synthase dimers. In this study we have focused on Su g to gain a better understanding of the function and the molecular organization of this subunit within the ATP synthase complex. Su g proteins contain a GXXXG motif (G is glycine, and X is any amino acid) in their single transmembrane segment. GXXXG can be a dimerization motif that supports helix-helix interactions between neighboring transmembrane segments. We demonstrate here that the GXXXG motif is important for the function and in particular for the stability of Su g within the ATP synthase. Using site-directed mutagenesis and cross-linking approaches, we demonstrate that Su g and Su e interact, and our findings emphasize the importance of the membrane anchor regions of these proteins for their interaction. Su e also contains a conserved GXXXG motif in its membrane anchor. However, data presented here would suggest that an intact GXXXG motif in Su g is not essential for the Su g-Su e interaction. We suggest that the GXXXG motif may not be the sole basis for a Su g-Su e interaction, and possibly these dimerization motifs may enable both Su g and Su e to interact with another mitochondrial protein.

Active oligomeric ATP synthases in mammalian mitochondria

Recently, by analysis of mildly solubilized mitochondrial membranes new biochemical evidences were obtained for the occurrence of ATP synthase dimers in mitochondria of different eukaryotes from yeast to mammals. In the case of yeast even higher ATP synthase oligomers could be found. Here, we analysed by BN- and CN-PAGE mammalian (bovine and rat) mitochondria from five different tissues, which were efficiently but very mildly solubilized with digitonin. In mitochondria from all investigated tissues besides ATP synthase monomers (V 1) not only dimeric ATP synthase (V 2) but for the first time also higher oligomers, at least trimers (V 3) and tetramers (V 4), were separated. Compared with BN-PAGE, by CN-PAGE analysis the yields of preserved respiratory supercomplexes as well as of oligomeric ATP synthases (V 2–4) were significantly increased. The latter represent the majority of total ATP synthases in all cases. Importantly, all different ATP synthase species from the five tissues displayed in-gel ATP hydrolase activity, suggesting that homooligomeric ATP synthases are the constitutive, enzymatically competent organization of mammalian ATP synthases in the inner mitochondrial membrane.