Organization and sequences of genes for the subunits of ATP synthase in the thermophilic cyanobacterium Synechococcus 6716

Structure, Regulation, and Significance of Cyanobacterial and Chloroplast Adenosine Triphosphate Synthase in the Adaptability of Oxygenic Photosynthetic Organisms

In cyanobacteria and chloroplasts (in algae and plants), ATP synthase plays a pivotal role as a photosynthetic membrane complex responsible for producing ATP from adenosine diphosphate and inorganic phosphate, utilizing a proton motive force gradient induced by photosynthesis. These two ATP synthases exhibit similarities in gene organization, amino acid sequences of subunits, structure, and functional mechanisms, suggesting that cyanobacterial ATP synthase is probably the evolutionary precursor to chloroplast ATP synthase. In this review, we explore the precise synthesis and assembly of ATP synthase subunits to address the uneven stoichiometry within the complex during transcription, translation, and assembly processes. We also compare the regulatory strategies governing ATP synthase activity to meet varying energy demands in cyanobacteria and chloroplasts amid fluctuating natural environments. Furthermore, we delve into the role of ATP synthase in stress tolerance and photosynthetic carbon fixation efficiency in oxygenic photosynthetic organisms (OPsOs), along with the current researches on modifying ATP synthase to enhance carbon fixation efficiency under stress conditions. This review aims to offer theoretical insights and serve as a reference for understanding the functional mechanisms of ATP synthase, sparking innovative ideas for enhancing photosynthetic carbon fixation efficiency by utilizing ATP synthase as an effective module in OPsOs.

Structure of the ATP synthase from Mycobacterium smegmatis provides targets for treating tuberculosis

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.

Purification, characterization and crystallization of the F-ATPase from Paracoccus denitrificans

The structures of F-ATPases have been determined predominantly with mitochondrial enzymes, but hitherto no F-ATPase has been crystallized intact. A high-resolution model of the bovine enzyme built up from separate sub-structures determined by X-ray crystallography contains about 85% of the entire complex, but it lacks a crucial region that provides a transmembrane proton pathway involved in the generation of the rotary mechanism that drives the synthesis of ATP. Here the isolation, characterization and crystallization of an integral F-ATPase complex from the α-proteobacterium Paracoccus denitrificans are described. Unlike many eubacterial F-ATPases, which can both synthesize and hydrolyse ATP, the P. denitrificans enzyme can only carry out the synthetic reaction. The mechanism of inhibition of its ATP hydrolytic activity involves a ζ inhibitor protein, which binds to the catalytic F₁-domain of the enzyme. The complex that has been crystallized, and the crystals themselves, contain the nine core proteins of the complete F-ATPase complex plus the ζ inhibitor protein. The formation of crystals depends upon the presence of bound bacterial cardiolipin and phospholipid molecules; when they were removed, the complex failed to crystallize. The experiments open the way to an atomic structure of an F-ATPase complex.

Remarkable stability of the proton translocating F1FO-ATP synthase from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1

For functional characterization, we isolated the F1FO-ATP synthase of the thermophilic cyanobacterium Thermosynechococcus elongatus. Because of the high content of phycobilisomes, a combination of dye-ligand chromatography and anion exchange chromatography was necessary to yield highly pure ATP synthase. All nine single F1FO subunits were identified by mass spectrometry. Western blotting revealed the SDS stable oligomer of subunits c in T. elongatus. In contrast to the mass archived in the database (10,141 Da), MALDI-TOF-MS revealed a mass of the subunit c monomer of only 8238 Da. A notable feature of the ATP synthase was its ability to synthesize ATP in a wide temperature range and its stability against chaotropic reagents. After reconstitution of F1FO into liposomes, ATP synthesis energized by an applied electrochemical proton gradient demonstrated functional integrity. The highest ATP synthesis rate was determined at the natural growth temperature of 55 degrees C, but even at 95 degrees C ATP production occurred. In contrast to other prokaryotic and eukaryotic ATP synthases which can be disassembled with Coomassie dye into the membrane integral and the hydrophilic part, the F1FO-ATP synthase possessed a particular stability. Also with the chaotropic reagents sodium bromide and guanidine thiocyanate, significantly harsher conditions were required for disassembly of the thermophilic ATP synthase.

Structure of the F1-binding domain of the stator of bovine F1Fo-ATPase and how it binds an alpha-subunit

The peripheral stalk of ATP synthase holds the alpha3beta3 catalytic subcomplex stationary against the torque of the rotating central stalk. In bovine mitochondria, the N-terminal domain of the oligomycin sensitivity conferral protein (OSCP-NT; residues 1-120) anchors one end of the peripheral stalk to the N-terminal tails of one or more alpha-subunits of the F1 subcomplex. Here we present the solution structure of OSCP-NT and an NMR titration study of its interaction with peptides representing N-terminal tails of F1 alpha-subunits. The structure comprises a bundle of six alpha-helices, and its interaction site contains adjoining hydrophobic surfaces of helices 1 and 5; residues in the region 1-8 of the alpha-subunit are essential for the interaction. The OSCP-NT is similar to the N-terminal domain of the delta-subunit from Escherichia coli ATP synthase (delta-NT), except that their surface charges differ (basic and acidic, respectively). As the charges of the adjacent crown regions in their alpha3beta3 complexes are similar, the OSCP-NT and delta-NT probably do not contact the crowns extensively. The N-terminal tails of alpha-subunit tails are probably alpha-helical, and so this interface, which is essential for the rotary mechanism of the enzyme, appears to consist of helix-helix interactions.

Identification of four genes of the Brucella melitensis ATP synthase operon F0 sector: relationship with the Rhodospirillaceae family

We have determined the nucleotide sequence of a cloned DNA fragment from the human and animal pathogen Brucella melitensis. Four genes were identified from a 4069 bp fragment, corresponding to the B. melitensis a, c, b', and b subunits of the ATP synthase F0 sector operon. A duplicated and divergent copy of the b-subunit gene was observed. This feature has been found only in photosynthetic bacteria and chloroplasts. In addition, the gene cluster was separated from the F1 sector, a characteristic described only for the Rhodospirillaceae family.

Sequence of subunit a of the Na(+)-translocating F1F0-ATPase of Acetobacterium woodii: proposal for residues involved in Na+ binding

Na+ transport through the F0 domain of Na(+)-F1F0-ATPases involves the combined action of subunits c and a but the residues involved in Na+ liganding in subunit a are unknown. As a first step towards the identification of these residues, we have cloned and sequenced the gene encoding subunit a of the Na(+)-F1F0-ATPase of Acetobacterium woodii. This is the second sequence available now for this subunit from Na(+)-F1F0-ATPases. A comparison of subunit a from Na(+)-F1F0-ATPases with those from H(+)-translocating enzymes unraveled structural similarity in a C-terminal segment including the ultimate and penultimate transmembrane helix. Seven residues are conserved in this region and, therefore, likely to be involved in Na+ liganding.

The ATP synthase atpHAGDC (F1) operon from Rhodobacter capsulatus

The atpHAGDC operon of Rhodobacter capsulatus, containing the five genes coding for the F1 sector of the ATP synthase, has been cloned and sequenced. The promoter region has been defined by primer extension analysis. It was not possible to obtain viable cells carrying atp deletions in the R. capsulatus chromosome, indicating that genes coding for ATP synthase are essential, at least under the growth conditions tested. We were able to circumvent this problem by combining gene transfer agent transduction with conjugation. This method represents an easy way to construct strains carrying mutations in indispensable genes.

Sulfite stimulates the ATP hydrolysis activity of but not proton translocation by the ATP synthase of Rhodobacter capsulatus and interferes with its activation by delta muH+

Sulfite stimulates the rate of ATP hydrolysis by the ATP synthase in chromatophores of Rhodobacter capsulatus. The stimulated activity is inhibited by oligomycin. The activation takes place also in uncoupled chromatophores. The activation consists in an increase of about 12-15-fold of the Vmax for the ATP hydrolysis reaction, while the Km for MgATP is unaffected at 0.16+/-0.03 mM. The dependence of Vmax on the sulfite concentration follows a hyperbolic pattern with half maximum effect at 12 mM. Sulfite affects the ability of the enzyme in translocating protons. Concomitant measurements of the rate of ATP hydrolysis and of ATP-induced protonic flows demonstrate that at sulfite concentrations of greater than 10 mM the hydrolytic reaction becomes progressively uncoupled from the process of proton translocation. This is accompanied by an inhibition of ATP synthesis, either driven by light or by artificially induced ionic gradients. ATP synthesis is totally inhibited at concentrations of at least 80 mM. Sulfite interferes with the mechanism of activation by delta muH+. Low concentrations of this anion (< or = 2 mM) prevent the activation by delta muH+. At higher concentrations a marked stimulation of the activity prevails, regardless of the occurrence of a delta muH+ across the membrane. Phosphate at millimolar concentrations can reverse the inhibition by sulfite. These experimental results can be simulated by a model assuming multiple and competitive equilibria for phosphate or sulfite binding with two binding sites for the two ligands (for sulfite K1S = 0.26 and K2S = 37 mM, and for phosphate K1P = 0.06 and K2P = 4.22 mM), and in which the state bound only to one sulfite molecule is totally inactive in hydrolysis. The competition between phosphate and sulfite is consistent with the molecular structures of the two ligands and of the enzyme.

Composition and primary structure of the F1F0 ATP synthase from the obligately anaerobic bacterium Clostridium thermoaceticum

The subunit composition and primary structure of the proton-translocating F1F0 ATP synthase have been determined in Clostridium thermoaceticum. The isolated enzyme has a subunit composition identical to that of the F1F0 ATP synthase purified from Clostridium thermoautotrophicum (A. Das, D. M. Ivey, and L. G. Ljungdahl, J. Bacteriol. 179:1714-1720, 1997), both having six different polypeptides. The molecular masses of the six subunits were 60, 50, 32, 17, 19, and 8 kDa, and they were identified as alpha, beta, gamma, delta, epsilon, and c, respectively, based on their reactivity with antibodies against the F1 ATPase purified from C. thermoautotrophicum and by comparing their N-terminal amino acid sequences with that deduced from the cloned genes of the C. thermoaceticum atp operon. The subunits a and b found in many bacterial ATP synthases could not be detected either in the purified ATP synthase or crude membranes of C. thermoaceticum. The C. thermoaceticum atp operon contained nine genes arranged in the order atpI (i), atpB (a), atpE (c), atpF (b), atpH (delta), atpA (alpha), atpG (gamma), atpD (beta), and atpC (epsilon). The deduced protein sequences of the C. thermoaceticum ATP synthase subunits were comparable with those of the corresponding subunits from Escherichia coli, thermophilic Bacillus strain PS3, Rhodospirillum rubrum, spinach chloroplasts, and the cyanobacterium Synechococcus strain PCC 6716. The analysis of total RNA by Northern hybridization experiments reveals the presence of transcripts (mRNA) of the genes i, a, and b subunits not found in the isolated enzyme. Analysis of the nucleotide sequence of the atp genes reveals overlap of the structural genes for the i and a subunits and the presence of secondary structures (in the b gene) which could influence the posttranscriptional regulation of the corresponding genes.

The ATP synthase gamma subunit provides the primary site of activation of the chloroplast enzyme: experiments with a chloroplast-like Synechocystis 6803 mutant

The activation characteristics of the F1Fo-ATP synthase (where F1 and Fo are the hydrophilic and membrane-bound parts respectively of the enzyme) from Synechocystis 6803 wild-type and a Synechocystis 6803 mutant with a chloroplast-like insertion in the gamma subunit have been studied. Activation of the ATP synthase in wild-type and mutant membrane vesicles was performed by acid-base transition-induced generation of a proton motive force (Delta mu H+). Since the mutant containing the regulatory segment of the chloroplast gamma subunit showed thiol-modulation (typical of the chloroplast enzyme), this segment is indeed involved in the regulation of enzyme activation. It is shown that the ATP synthase from Synechocystis 6803 wild type corresponds functionally to the reduced form of the chloroplast ATP synthase, in view of the low Delta mu H+ required for activation of the enzyme and the high stability of the active state. Both the cyanobacterial wild-type and mutant ATP synthases can be activated by methanol, which apparently does not require the presence of the gamma subunit regulatory segment.

The F1F0-ATPase complex from bovine heart mitochondria: the molar ratio of the subunits in the stalk region linking the F1 and F0 domains

The F1 globular catalytic domain and the F0 intrinsic membrane domain of the F1F0-ATPases in bacteria, chloroplasts, and mitochondria are connected by a slender stalk. In the F1F0 complex from bovine heart mitochondria, the stalk is thought to contain subunits OSCP, d, and F6, and the globular part of the membrane bound subunit b, referred to as b'. It has been shown previously that the OSCP, b', d, and F6 proteins can be assembled in vitro into a water soluble complex named the "stalk". The stalk and F1-ATPase together form another complex named F1.stalk. In this paper, the molar ratios of the OSCP, b (or b'), d, and F6 in the stalk, F.stalk, and F1F0-ATPase complexes have been investigated by three independent methods. By quantitation of radioactivity incorporated by S-carboxymethylation with iodo-2-[14C]acetic acid into a stalk complex containing a form of F6 with the mutation Glu3-Cys, it was shown that the stalk consists of equimolar quantities of its four constituent proteins. In the stalk complex containing the natural F6 sequence, this conclusion was confirmed both by quantitation of radioactivity incorporated by Nepsilon-acetimidation with ethyl [1-14C]acetimidate, and by quantitative N-terminal sequence analysis of subunits. By similar Nepsilon-acetimidation experiments, it has been demonstrated that the F1.stalk complex contains one copy per assembly of the OSCP, b', d, and F6 proteins and that the F1F0-ATPase contains one copy per enzyme complex of subunits OSCP, b, and d. The presence of one copy per complex of the OSCP, b' (or b), d, and F6 proteins in the F1.stalk and F1F0-ATPase complexes, respectively, was confirmed by quantitative sequencing.

DCCD-sensitive proton permeability of bacterial photosynthetic membranes. Cross-reconstitution studies with purified bovine heart Fo subunits

The DCCD-sensitive proton permeability of chromatophores, from a green strain of Rhodobacter Capsulatus is potentiometrically detected following the proton release induced by a transmembrane diffusion potential imposed by a valinomycin-mediated potassium influx with a procedure already used for bovine heart submitochondrial particles (ESMP) and vesicles from Escherichia coli (Zanotti et al. (1994) Eur. J. Biochem. 222, 733-741). In the photosynthetic system, addition of increasing amounts of DCCD inhibits, with a similar titre, both proton permeability and MgATP-dependent ATPase activity as detected in the dark. The titre for 50% inhibition coincides with that obtained measuring proton permeability and ATP hydrolysis in ESMP. Upon removal of F1, the passive proton permeability is much less sensitive to DCCD in chromatophores than in USMP, suggesting that in chromatophores the F1-Fo interaction shapes the DCCD-sensitive proton conducting pathway. Addition of the purified mitochondrial FoI-PVP and oligomycin sensitivity-conferring (OSCP) proteins to the F1 stripped chromatophores restored the sensitivity of proton permeability to DCCD detected in untreated chromatophores. Analysis of the binding of 14C[DCCD] on F1 stripped chromatophores shows that the increase of DCCD sensitivity of proton permeability, caused by addition of mitochondrial Fo proteins, is related to an increase of the binding of the inhibitor to subunit c of Fo sector of ATP synthase complex.

Membrane vesicles fromSynechocystis 6803 showing proton and electron transport and high ATP synthase activities

A simple procedure for the preparation of well-coupled and stable membrane vesicles from the transformable cyanobacteriumSynechocystis 6803 is described with the primary aim of producing vesicles suitable for the study of photosynthetic electron transport and phosphorylation. Spheroplasts were obtained from the cyanobacterium by lysozyme treatment and stored untill prior to measurement, thylakoid vesicles were obtained by osmotic shock. These vesicles showed very high and stable ATP synthesis rates either driven by light or by acid-base transition, and also performed light-induced ATP hydrolysis and linear electron transport. Formation of a proton gradient is studied by aminoacridines.

The H+/ATP coupling ratio of the ATP synthase from thiol-modulated chloroplasts and two cyanobacterial strains is four

In this paper the authors emphasise that the proton translocating ATP synthase from thiol-modulated chloroplasts and two cyanobacterial strains has a coupling ratio of 4 protons per ATP synthesised or hydrolysed. This ratio is determined by several thermodynamic studies at equilibrium between phosphate potential (Delta Gp) and proton gradient (Delta(mu)H+), and is confirmed by measurement of proton flux during ATP hydrolysis. Ratios lower than 4 H+/ATP that have been published in the past have predominantly been determined with the oxidised chloroplast enzyme. Errors in these measurements will be discussed.

Effects of the uncI gene on expression of uncB, the gene coding for the a subunit of the F1F0 ATPase of Escherichia coli

The eight genes coding for the subunits of the E. coli F1F0 ATPase are preceded by a gene, designated uncI. A homologous gene, or a gene coding for an analagous protein, is found preceding the ATPase genes of several microorganisms. No function for the 1 gene has been described. Using lac fusions to measure gene expression in vivo, we tested the effects of deleting uncI on the expression of the adjacent gene uncB, which codes for the a subunit of the F0 sector of the ATPase. Deleting uncI reduced the expression of three uncB'-'lacZ fusion genes in vivo, but had no effect on the expression of two uncB'-'lacZ fusion genes containing a relatively smaller amount of the uncB coding region. The uncI deletion also reduced the relative synthesis of the a subunit in vitro. The I gene therefore appears to specifically affect the expression of uncB or the synthesis of the a subunit at some step after translational initiation of uncB.

The regulation of catalysis in ATP synthase

ATP synthase is regulated so as to prevent futile hydrolysis of ATP when the transmembrane proton electrochemical gradient, delta mu H+, falls. Mitochondria and chloroplasts have different mechanisms for inhibition of ATP synthase: by binding an inhibitor protein, and by stabilization of the ADP-inhibited state by making an intramolecular disulphide bond, respectively. The recently determined structure of bovine F1-ATPase is locked in a conformation that probably represents the ADP-inhibited state of the enzyme.

Bacillus subtilis F0F1 ATPase: DNA sequence of the atp operon and characterization of atp mutants

We cloned and sequenced an operon of nine genes coding for the subunits of the Bacillus subtilis F0F1 ATP synthase. The arrangement of these genes in the operon is identical to that of the atp operon from Escherichia coli and from three other Bacillus species. The deduced amino acid sequences of the nine subunits are very similar to their counterparts from other organisms. We constructed two B. subtilis strains from which different parts of the atp operon were deleted. These B. subtilis atp mutants were unable to grow with succinate as the sole carbon and energy source. ATP was synthesized in these strains only by substrate-level phosphorylation. The two mutants had a decreased growth yield (43 and 56% of the wild-type level) and a decreased growth rate (61 and 66% of the wild-type level), correlating with a twofold decrease of the intracellular ATP/ADP ratio. In the absence of oxidative phosphorylation, B. subtilis increased ATP synthesis through substrate-level phosphorylation, as shown by the twofold increase of by-product formation (mainly acetate). The increased turnover of glycolysis in the mutant strain presumably led to increased synthesis of NADH, which would account for the observed stimulation of the respiration rate associated with an increase in the expression of genes coding for respiratory enzymes. It therefore appears that B. subtilis and E. coli respond in similar ways to the absence of oxidative phosphorylation.

The role of the stalk in the coupling mechanism of F1F0-ATPases

The extrinsic and intrinsic membrane sectors of F1F0-ATPases are linked by a slender stalk 40-50 A in length. The stalk transmits the energy produced by oxidative or photosynthetic phosphorylation from the intrinsic sector, F0, to the catalytic sites in the extrinsic F1 sector. How this is achieved is unknown, but long-range conformational changes linked to transmembrane proton transport may be involved. In bacterial and chloroplast F1F0-ATPases, the stalk is probably a composite of subunits delta and epsilon, part of the gamma-subunit, and the extrinsic membrane domains of 2 subunits (identical or non-identical according to the species) that are bound to the membrane by their N-terminal regions. The stalk in the bovine mitochondrial enzyme appears to be more complex, and the gamma, delta, epsilon, OSCP, F6, b and d subunits all contribute to it. A bovine stalk complex has been assembled in vitro from bacterially expressed OSCP, F6, b and d, both in the presence and in the absence of F1-ATPase. One molecule of each of these subunits is present in the assembled complex, as there is also in each native F1F0-ATPase assembly. Providing that suitable crystals can be obtained, the stalk complex and the F1.stalk complex may permit the high resolution structure of bovine F1-ATPase to be extended into the stalk domain.

Modulation of the proton-translocation stoichiometry of H(+)-ATP synthases in two phototrophic prokaryotes by external pH

The stoichiometry between proton translocation and ATP synthesis/hydrolysis was studied in two different photosynthetic prokaryotes, the thermophilic cyanobacterium Synechococcus 6716 and the purple bacterium Rhodospirillum rubrum. The H+/ATP ratio was determined by acid-base transitions as a function of the external pH. The H+/ATP ratio of the Synechococcus 6716 ATP synthase was found to increase with increasing pH. In contrast, in R. rubrum this ratio decreased with increasing pH. These results were qualitatively supported by experiments using the fluorescence probe 9-aminoacridine. The degree of coupling between the H+ flux and the ATP synthesis/hydrolysis reaction is apparently modulated by the conditions under which the proton pump has to work. Such modulation of the H+/ATP ratio may be of physiological significance for an organism, for example when ATP synthesis is necessary at low proton-electrochemical potential difference (delta mu H+ levels). The different pH dependencies of the H+/ATP ratios in these organisms are considered in relation to the differences in the charged amino acids that are present in the F0 subunits a and c.