A phenylalanine for serine substitution in the beta subunit of Escherichia coli F1-ATPase affects dependence of its activity on divalent cations

The Mitochondrial Permeability Transition Pore: Channel Formation by F-ATP Synthase, Integration in Signal Transduction, and Role in Pathophysiology

The mitochondrial permeability transition (PT) is a permeability increase of the inner mitochondrial membrane mediated by a channel, the permeability transition pore (PTP). After a brief historical introduction, we cover the key regulatory features of the PTP and provide a critical assessment of putative protein components that have been tested by genetic analysis. The discovery that under conditions of oxidative stress the F-ATP synthases of mammals, yeast, and Drosophila can be turned into Ca(2+)-dependent channels, whose electrophysiological properties match those of the corresponding PTPs, opens new perspectives to the field. We discuss structural and functional features of F-ATP synthases that may provide clues to its transition from an energy-conserving into an energy-dissipating device as well as recent advances on signal transduction to the PTP and on its role in cellular pathophysiology.

Rotational catalysis in proton pumping ATPases: from E. coli F-ATPase to mammalian V-ATPase

We focus on the rotational catalysis of Escherichia coli F-ATPase (ATP synthase, F(O)F(1)). Using a probe with low viscous drag, we found stochastic fluctuation of the rotation rates, a flat energy pathway, and contribution of an inhibited state to the overall behavior of the enzyme. Mutational analyses revealed the importance of the interactions among β and γ subunits and the β subunit catalytic domain. We also discuss the V-ATPase, which has different physiological roles from the F-ATPase, but is structurally and mechanistically similar. We review the rotation, diversity of subunits, and the regulatory mechanism of reversible subunit dissociation/assembly of Saccharomyces cerevisiae and mammalian complexes. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).

Our research on proton pumping ATPases over three decades: their biochemistry, molecular biology and cell biology

ATP is synthesized by F-type proton-translocating ATPases (F-ATPases) coupled with an electrochemical proton gradient established by an electron transfer chain. This mechanism is ubiquitously found in mitochondria, chloroplasts and bacteria. Vacuolar-type ATPases (V-ATPases) are found in endomembrane organelles, including lysosomes, endosomes, synaptic vesicles, etc., of animal and plant cells. These two physiologically different proton pumps exhibit similarities in subunit assembly, catalysis and the coupling mechanism from chemistry to proton transport through subunit rotation. We mostly discuss our own studies on the two proton pumps over the last three decades, including ones on purification, kinetic analysis, rotational catalysis and the diverse roles of acidic luminal organelles. The diversity of organellar proton pumps and their stochastic fluctuation are the important concepts derived recently from our studies.

Proton pumping ATPases and diverse inside-acidic compartments

Proton-translocating ATPases are essential cellular energy converters that transduce the chemical energy of ATP hydrolysis into transmembrane proton electrochemical potential differences. The structures, catalytic mechanism, and cellular functions of three major classes of ATPases including the F-type, V-type, and P-type ATPase are discussed in this review. Physiological roles of the acidic organelles and compartments contained are also discussed.

ATP synthase F(1) sector rotation. Defective torque generation in the beta subunit Ser-174 to Phe mutant and its suppression by second mutations

Subunit gamma of the ATP synthase F(1) sector is located at the center of the alpha(3)beta(3) hexamer and rotates unidirectionally during ATP hydrolysis, generating the rotational torque of approximately 45 pN.nm. A mutant F(1) with the betaSer-174 to Phe substitution (betaS174F) in the beta subunit generated lower torque ( approximately 17 pN.nm), indicating that betaS174F is mechanically defective, the first such mutant reported. The defective rotation of betaS174F was suppressed by a second-site mutation, betaGly-149 to Ala, betaIle-163 to Ala, or betaIle-166 to Ala in the same subunit, but not by betaLeu-238 to Ala. These results suggest that the region between betaGly-149 and betaSer-174 plays an important role in the coupling between ATP hydrolysis and mechanical work.

Tight nucleotide binding sites and ATPase activities of the Rhodospirillum rubrum RrF1-ATPase as compared to spinach chloroplast CF1-ATPase

Solubilized Rhodospirillum rubrum RrF1-ATPase, depleted of loosely bound nucleotides, retains 2.6 mol of tightly bound ATP and ADP/mol of enzyme. Incubation of the depleted RrF1 with Mg(2+)-ATP or Mg(2+)-AMP-PNP, followed by passage through two successive Sephadex centrifuge columns, results in retention of a maximal number of 4 mol of tightly bound nucleotides/mol of RrF1. They include 1.5 mol of nonexchangeable ATP, whereas all tightly bound ADP is fully exchangeable. A similar retention of only four out of the six nucleotide binding sites present on CF1 has been observed after its passage through one or two centrifuge columns. These results indicate that the photosynthetic, unlike the respiratory, F1-ATPases have faster koff constants for two of the Mg-dependent nucleotide binding sites. This could be the reason for the tenfold lower Mg2+ than Ca(2+)-ATPase activity observed with native RrF1, as with epsilon-depleted, activated CF1. An almost complete conversion of both RrF1 and CF1 from Ca(2+)- to Mg(2+)-dependent ATPases is obtained upon addition of octylglucoside, at concentrations below its CMC, to the ATPase assay medium. Thus, octylglucoside seems to affect directly the RrF1 and CF1 divalent cation binding site(s), in addition to its proposed role in relieving their inhibition by free Mg2+ ions. The RrF1-ATPase activity is 30-fold more sensitive than CF1 to efrapeptin, and completely resistant to either inhibition or stimulation by the CF1 effector, tentoxin. Octylglucoside decreases the inhibition by efrapeptin and tentoxin, but exposes on CF1 a low-affinity, stimulatory site for tentoxin.

Residues interacting with serine-174 and alanine-295 in the beta-subunit of Escherichia coli H(+)-ATP synthase: possible ternary structure of the center region of the subunit

The mutation of serine-174 to phenylalanine that causes a defect in the Escherichia coli F1-ATPase beta-subunit is suppressed by further mutations; Gly-149 to Ser, Ala-295 to Thr, Ala-295 to Pro, or Leu-400 to Gln (Miki, J., Fujiwara, K., Tsuda, M., Tsuchiya, T. and Kanazawa, H. (1990) J. Biol. Chem. 265, 21567-21572). We analyzed the effects of these second site mutations and of a newly identified Asn-158 to Tyr mutation on the activities of the ATPase without the original Ser-174 to Phe mutation. The beta-subunit with each amino acid replacement was expressed in the mutant strain JP17, which does not have a beta-subunit. Cells transformed with the plasmid carrying Ala-295 to Pro mutation alone did not grow on minimal medium agar supplemented with succinate as the sole carbon source, and showed 3% of the wild-type ATPase activity, suggesting that this mutation caused structural alterations affecting the catalytic function of the enzyme. Conversely transformants with other mutations grew well and had higher ATPase activities, suggesting that these mutations did not cause extensive structural alterations. From the transformants with the plasmid carrying the Ala-295 to Pro mutation, seven revertants capable of cell growth on succinate plates were isolated and reversion mutations were identified at residues 140, 159, 166, 171, 172 and 184 of the beta-subunits. The results suggested that Ser-174 and Ala-295 do not necessarily interact directly, but that the regions including these suppression mutation sites close to Ser-174, and Ala-295 interact with each other for the proper functioning of the ATPase. The ternary structure of the region surrounded by the residues which were identified as the reversion mutation sites for Ser-174 to Phe and Ala-295 to Pro mutations is important for the catalytic function of this enzyme.

Evolution of organellar proton-ATPases

Proton ATPases function in biological energy conversion in every known living cell. Their ubiquity and antiquity make them a prime source for evolutionary studies. There are two related families of H(+)-ATPases; while the family of F-ATPases function in eubacteria chloroplasts and mitochondria, the family of V-ATPases are present in archaebacteria and the vacuolar system of eukaryotic cells. Sequence analysis of several subunits of V- and F-ATPases revealed several of the important steps in their evolution. Moreover, these studies shed light on the evolution of the various organelles of eukaryotes and suggested some events in the evolution of the three kingdoms of eubacteria, archaebacteria and eukaryotes.

Calcium inhibition of the ATP in equilibrium with [32P]Pi exchange and of net ATP synthesis catalyzed by bovine submitochondrial particles

A previous communication (Fagian, M. M., Pereira da Silva, L. and Vercesi, A. E. (1986) Biochim. Biophys. Acta 852, 262-268) indicated that intramitochondrial calcium inhibits oxidative phosphorylation by decreasing the availability of adenine nucleotides to both the ADP/ATP translocase and the F0F1-ATP synthase complex. In this work we analyzed the interactions of calcium-nucleotide and magnesium-nucleotide complexes with the ATP synthase during catalysis of ATP in equilibrium with [32P]Pi exchange and net synthesis of ATP by submitochondrial particles. Concerning the ATP in equilibrium with [32P]Pi exchange reaction, calcium was ineffective as divalent cation when assayed alone. Furthermore, the addition of calcium increased the magnesium concentration required for half-maximal activation of the exchange, without changing Vmax. With respect to net ATP synthesis, the inhibition by calcium was shown to be due to formation of the CaADP- complex, which competes with MgADP- for the active site of the F0F1-ATP synthase. Moreover, ATP hydrolysis was competitively inhibited by CaATP2-, showing that calcium is able to interact with the enzyme in both forward and backward reactions in the same manner. That high calcium concentrations are required for significant inhibition of ATP synthesis indicates that this inhibition is relevant under conditions in which cytosolic calcium concentrations rise to pathological levels. Therefore, this mechanism may be responsible, in part, for the decrease in cellular ATP content that has been observed to occur when calcium accumulates in the cytosol.

Effect of the weakly acidic uncoupler 2,4-dinitrophenol and dimethyl sulfoxide on the coordination of Mg2+ with ATP. Possible mechanism of activation of the isolated F1-ATPase by 2,4-dinitrophenol

The exchange rate constants between Mg2(+)-free and Mg2(+)-bound ATP were determined under various conditions by line shape analysis of the 31P-NMR spectrum based on the exchange reaction, and the thermodynamic parameters of this exchange reaction were determined from the temperature dependence of its rate constants. Analysis of the activation enthalpy change delta H showed that Mg2+ is coordinated with the beta- and gamma-phosphoryl groups of ATP asymmetrically, being in closer proximity to the beta-phosphoryl group. The weakly acidic uncoupler 2,4-dinitrophenol increased this asymmetric coordination of Mg2+, and this effect was enhanced by the further addition of dimethyl sulfoxide. The hydrolysis of ATP in aqueous solution correlated well with the degree of asymmetry of Mg2+ coordination. Thus, this asymmetric coordination specifically weakens the O-P gamma bond at which specific cleavage of ATP catalyzed by most ATPases takes place in the presence of Mg2+. In this paper, the mechanism of activation of isolated ATPase (F1-ATPase) by 2,4-dinitrophenol, and that of ATP synthesis by isolated F1-ATPase in the presence of dimethyl sulfoxide are considered on the basis of these results. The essential role of the OH group of Ser-174 of the beta-subunit of F1-ATPase in ATP hydrolysis is also discussed.

Mechanism of F1-ATPase studied by the genetic approach

E. coli F1-ATPase has been studied mainly by the genetic approach. Mutations in either the alpha or beta subunit modified the kinetics of multisite and uni-site hydrolysis of ATP. The mechanism of F1-ATPase and the essential amino acid residues of beta subunits are discussed.

Molecular genetics of F1-ATPase from Escherichia coli

We have reviewed recent molecular biological studies on F1-ATPase of Escherichia coli and emphasized the advantages of using the bacterium in studies on this important enzyme. All subunits had homologies of varied degrees with those from other organisms. Mutations of F1 subunits caused defects in catalysis and assembly. Defects of the mutant enzymes were studied extensively together with the determination of the amino acid substitutions. Extensive molecular biological studies may help greatly in understanding the normal mechanism and assembly of the complex.

Beta-subunit of Escherichia coli F1-ATPase. An amino acid replacement within a conserved sequence (G-X-X-X-X-G-K-T/S) of nucleotide-binding proteins

A mutant strain KF87 of E. coli with a defective beta-subunit (Ala-151----Val) of F1-ATPase was isolated. The mutation is within the conserved sequence (G-X-X-X-X-G-K-T/S) of nucleotide-binding proteins. The mutant F1-ATPase had a much higher rate of uni-site hydrolysis of ATP than the wild type, and about 6% of the wild-type multi-site activity. The mutant enzyme showed defective transmission of conformational change(s) between the ligand- and aurovertin-binding sites.

Escherichia coli H+-ATPase: loss of the carboxyl terminal region of the gamma subunit causes defective assembly of the F1 portion

Mutant genes for the gamma subunit of H+-translocating ATPase (H+-ATPase) were cloned from eight different strains of Escherichia coli isolated in this laboratory. Determination of their nucleotide sequences revealed that they are amber nonsense mutations: a Gln codon at position 15, 158, 227, 262, and 270, respectively, was replaced by a termination codon in these strains. As terminal Met is missing in the gamma subunit, these results indicate that these strains are capable of synthesizing fragments of gamma subunits of 13, 156, 225, 260, and 268 amino acid residues, respectively. Studies on the properties of membranes of these strains suggested the importance of the region between Gln 269 and the carboxyl terminus (residue 286) for forming a stable F1 complex with ATPase activity and the region between Gln 226 and Gln 261 for normal interaction of F1 with F0. The sequence from Gln 261 to Gln 269 also seemed to be important for stability of F1 assembly on the membranes. The high frequency of the nonsense mutations suggested that the number of essential residues is limited in this subunit. Comparison of the homologies of the amino acid sequences of the gamma subunits from four different sources confirmed this notion: 19% of amino acid residues are identically conserved in these four strains, and the conserved regions are the amino terminal and carboxyl terminal regions.

Structure of the nucleotide-binding domain in the beta-subunit of Escherichia coli F1-ATPase

We propose a working model for the tertiary structure of the nucleotide-binding domain of the beta-subunit of E. coli F1-ATPase, derived from secondary structure prediction and from comparison of the amino acid sequence with the sequences of other nucleotide-binding proteins of known three-dimensional structure. The model is consistent with previously published results of specific chemical modification studies and of analyses of mutations in the beta-subunit and its implications for subunit interactions and catalytic mechanism in F1-ATPases are discussed.

Deletion of seven amino acid residues from the gamma subunit of Escherichia coli H+-ATPase causes total loss of F1 assembly on membranes

A mutant gene for the gamma subunit of H+-translocating ATPase was cloned from Escherichia coli mutant NR70 isolated by B. P. Rosen [J. Bacteriol. 116, 1124-1129 (1973)]. Determination of its nucleotide sequence revealed a deletion of 21 base pairs between nucleotide residues 64 and 84, resulting in a deletion of seven amino acid residues (LysAlaMetGluMetValAla) from the amino-terminal portion. This deletion resulted in the loss of a hydrophobic domain of the subunit estimated by an analysis of its hydropathic character. Since F1 subunits are reported not to be assembled on the normal F0 portion of NR70, it is concluded that the hydrophobic domain deleted in the mutant subunit is important for assembly of the F1 portion. Introduction of a plasmid pNR70 carrying the mutant allele of NR70 into a wild-type strain gave no recombinants resistant to neomycin. This result suggested that the neomycin-resistant phenotype is not directly related to the defect in the gamma subunit of NR70.