ATP synthase--the structure of the stator stalk

Transcriptome analysis of the bloom-forming dinoflagellate Prorocentrum donghaiense exposed to Ginkgo biloba leaf extract, with an emphasis on photosynthesis

Ginkgo biloba leaf extract (GBE) can effectively treat bloom-forming freshwater algae. However, there is limited information about the underlying suppression mechanism of the marine bloom-forming Prorocentrum donghaiense-the most dominant algal bloom species in the East China Sea. We investigated the effect of GBE on P. donghaiense in terms of its response to photosynthesis at the molecular/omic level. In total, 93,743 unigenes were annotated using six functional databases. Furthermore, 67,203 differentially expressed genes (DEGs) were identified in algae treated with 1.8 g∙L-1 GBE. Among these DEGs, we identified the genes involved in photosynthesis. PsbA, PsbB and PsbD in photosystem II, PsaA in photosystem I, and PetB and PetD in the cytochrome b6/f complex were downregulated. Other related genes, such as PsaC, PsaE, and PsaF in photosystem I; PetA in the cytochrome b6/f complex; and atpA, atpD, atpH, atpG, and atpE in the F-type H+-ATPase were upregulated. These results suggest that the structure and activity of the complexes were destroyed by GBE, thereby inhibiting the electron flow between the primary and secondary quinone electron acceptors, primary quinone electron acceptor, and oxygen-evolving complex in the PSII complex, and interrupting the electron flow between PSII and PSI, ultimately leading to a decline in algal cell photosynthesis. These findings provide a basis for understanding the molecular mechanisms underlying P. donghaiense exposure to GBE and a theoretical basis for the prevention and control of harmful algal blooms.

ATP synthase-associated coiled-coil-helix-coiled-coil-helix (CHCH) domain-containing proteins are critical for mitochondrial function in Toxoplasma gondii

IMPORTANCE

Members of the coiled-coil-helix-coiled-coil-helix (CHCH) domain protein family are transported into the mitochondrial intermembrane space, where they play important roles in the biogenesis and function of the organelle. Unexpectedly, the ATP synthase of the apicomplexan Toxoplasma gondii harbors CHCH domain-containing subunits of unknown function. As no other ATP synthase studied to date contains this class of proteins, characterizing their function will be of broad interest to the fields of molecular parasitology and mitochondrial evolution. Here, we demonstrate that that two T. gondii ATP synthase subunits containing CHCH domains are required for parasite survival and for stability and function of the ATP synthase. We also show that knockdown disrupts multiple aspects of the mitochondrial morphology of T. gondii and that mutation of key residues in the CHCH domains caused mis-localization of the proteins. This work provides insight into the unique features of the apicomplexan ATP synthase, which could help to develop therapeutic interventions against this parasite and other apicomplexans, such as the malaria-causing parasite Plasmodium falciparum.

How does a low-magnitude electric field influence anaerobic digestion in wastewater treatment? A review

Anaerobic digestion (AD) is a physio-biochemical process widely used for treating industrial or municipal wastewater with concomitant methane production. Several technologies have been tested to improve AD's efficiency, like pretreatments and co-digestion, among others. Recently the imposition of a low-magnitude electric field (LMEF) has been applied at the AD to improve methane yield. Despite the positive results of imputing an electric field, many gaps are not understood yet. Therefore, this review focuses on the biochemical aspects of AD and electric field for a better understanding of the effect of the LMEF on the metabolisms of the AD during wastewater treatment and its application in methane production enhancement.

Parasite powerhouse: A review of the Toxoplasma gondii mitochondrion

Toxoplasma gondii is a member of the apicomplexan phylum, a group of single-celled eukaryotic parasites that cause significant human morbidity and mortality around the world. T. gondii harbors two organelles of endosymbiotic origin: a non-photosynthetic plastid, known as the apicoplast, and a single mitochondrion derived from the ancient engulfment of an α-proteobacterium. Due to excitement surrounding the novelty of the apicoplast, the T. gondii mitochondrion was, to a certain extent, overlooked for about two decades. However, recent work has illustrated that the mitochondrion is an essential hub of apicomplexan-specific biology. Development of novel techniques, such as cryo-electron microscopy, complexome profiling, and next-generation sequencing have led to a renaissance in mitochondrial studies. This review will cover what is currently known about key features of the T. gondii mitochondrion, ranging from its genome to protein import machinery and biochemical pathways. Particular focus will be given to mitochondrial features that diverge significantly from the mammalian host, along with discussion of this important organelle as a drug target.

Conserved role of ATP synthase in mammalian cilia

We previously found that ATP synthases localize to male-specific sensory cilia and control the ciliary response by regulating polycystin signalling in Caenorhabditis elegans. Herein, we discovered that the ciliary localization of ATP synthase is evolutionarily conserved in mammals. We showed that the ATP synthase subunit F1β is colocalized with the cilia marker acetylated α-tubulin in both mammalian renal epithelial cells (MDCK) and normal mouse cholangiocytes (NMCs). Treatment with ATP synthase inhibitor oligomycin impaired ciliogenesis in MDCK cells, and F1β was co-immunoprecipitated with PKD2 in mammalian cells. Our study provides evidence for the evolutionarily conserved localization of ATP synthase in cilia from worm to mammals. Defects in ATP synthase can lead to ciliary dysfunction, which may be a potential mechanism of polycystic kidney disease.

Megadalton chromatin remodelers: common principles for versatile functions

ATP-dependent chromatin remodelers are enigmatic macromolecular machines that govern the arrangement and composition of nucleosomes across eukaryotic genomes. Here, we review the recent breakthrough provided by cryo-electron microscopy that reveal the first high-resolution insights into all four families of remodelers. We highlight the emerging structural and mechanistic principles with a particular focus on multi-subunit SWI/SNF and INO80/SWR1 complexes. A conserved architecture comprising a motor, rotor, stator and grip suggests a unifying mechanism for how stepwise DNA translocation enables large scale reconfigurations of nucleosomes. A molecular circuitry involving the nuclear actin containing module establishes a framework for understanding allosteric regulation. Remodelers emerge as programable hubs that enable differential processing of genetic and epigenetic information in response to the physiological state of a cell.

Signature of positive selection in mitochondrial DNA in Cetartiodactyla

Acceleration of the amino acid substitution rate is a good indicator of positive selection in adaptive evolutionary changes of functional genes. Genomic information about mammals has become readily available in recent years, as many researchers have attempted to clarify the adaptive evolution of mammals by examining evolutionary rate change based on multiple loci. The order Cetartiodactyla (Artiodactyla and Cetacea) is one of the most diverse orders of mammals. Species in this order are found throughout all continents and seas, except Antarctica, and they exhibit wide variation in morphology and habitat. Here, we focused on the metabolism-related genes of mitochondrial DNA (mtDNA) in species of the order Cetartiodactyla using 191 mtDNA sequences available in databases. Based on comparisons of the dN/dS ratio (ω) in 12 protein-coding genes, ATP8 was shown to have a higher ω value (ω = 0.247) throughout Cetartiodactyla than the other 11 genes (ω < 0.05). In a branch-site analysis of ATP8 sequences, a markedly higher ω value of 0.801 was observed in the ancestral lineage of the clade of Cetacea, which is indicative of adaptive evolution. Through efforts to detect positively selected amino acids, codon positions 52 and 54 of ATP8 were shown to have experienced positive selective pressure during the course of evolution; multiple substitutions have occurred at these sites throughout the cetacean lineage. At position 52, glutamic acid was replaced with asparagine, and, at position 54, lysine was replaced with non-charged amino acids. These sites are conserved in most Artiodactyla. These results imply that the ancestor of cetaceans underwent accelerated amino acid changes in ATP8 and replacements at codons 52 and 54, which adjusted metabolism to adapt to the marine environment.

Geometric somersaults of a polymer chain through cyclic twisting motions

This study explores the significance of geometric angle shifts, which we call geometric somersaults, arising from cyclic twisting motions of a polymer chain. A five-bead polymer chain serves as a concise and minimal model of a molecular shaft throughout this study. We first show that this polymer chain can change its orientation about its longitudinal axis largely, e.g., 120^{∘}, under conditions of zero total angular momentum by changing the two dihedral angles in a cyclic manner. This phenomenon is an example of the so-called "falling cat" phenomenon, where a falling cat undergoes a geometric somersault by changing its body shape under conditions of zero total angular momentum. We then extend the geometric somersault of the polymer chain to a noisy and viscous environment, where the polymer chain is steered by external driving forces. This extension shows that the polymer chain can achieve an orientation change keeping its total angular momentum and total external torque fluctuating around zero in a noisy and viscous environment. As an application, we argue that the geometric somersault of the polymer chain by 120^{∘} may serve as a prototypical and coarse-grained model for the rotary motion of the central shaft of ATP synthase (F_{O}F_{1}-ATPase). This geometric somersault is in clear contrast to the standard picture for the rotary motion of the central shaft as a rigid body, which generally incurs nonzero total angular momentum and nonzero total external torque. The power profile of the geometric somersault implies a preliminary mechanism for elastic power transmission. The results of this study may be of fundamental interest in twisting and rotary motions of biomolecules.

BIOGENESIS FACTOR REQUIRED FOR ATP SYNTHASE 3 Facilitates Assembly of the Chloroplast ATP Synthase Complex

Thylakoid membrane-localized chloroplast ATP synthases use the proton motive force generated by photosynthetic electron transport to produce ATP from ADP. Although it is well known that the chloroplast ATP synthase is composed of more than 20 proteins with α3β3γ1ε1δ1I1II1III14IV1 stoichiometry, its biogenesis process is currently unclear. To unravel the molecular mechanisms underlying the biogenesis of chloroplast ATP synthase, we performed extensive screening for isolating ATP synthase mutants in Arabidopsis (Arabidopsis thaliana). In the recently identified bfa3 (biogenesis factors required for ATP synthase 3) mutant, the levels of chloroplast ATP synthase subunits were reduced to approximately 25% of wild-type levels. In vivo labeling analysis showed that assembly of the CF1 component of chloroplast ATP synthase was less efficient in bfa3 than in the wild type, indicating that BFA3 is required for CF1 assembly. BFA3 encodes a chloroplast stromal protein that is conserved in higher plants, green algae, and a few species of other eukaryotic algae, and specifically interacts with the CF1β subunit. The BFA3 binding site was mapped to a region in the catalytic site of CF1β. Several residues highly conserved in eukaryotic CF1β are crucial for the BFA3-CF1β interaction, suggesting a coevolutionary relationship between BFA3 and CF1β. BFA3 appears to function as a molecular chaperone that transiently associates with unassembled CF1β at its catalytic site and facilitates subsequent association with CF1α during assembly of the CF1 subcomplex of chloroplast ATP synthase.

The Arabidopsis protein CONSERVED ONLY IN THE GREEN LINEAGE160 promotes the assembly of the membranous part of the chloroplast ATP synthase

The chloroplast F1Fo-ATP synthase/ATPase (cpATPase) couples ATP synthesis to the light-driven electrochemical proton gradient. The cpATPase is a multiprotein complex and consists of a membrane-spanning protein channel (comprising subunit types a, b, b', and c) and a peripheral domain (subunits α, β, γ, δ, and ε). We report the characterization of the Arabidopsis (Arabidopsis thaliana) CONSERVED ONLY IN THE GREEN LINEAGE160 (AtCGL160) protein (AtCGL160), conserved in green algae and plants. AtCGL160 is an integral thylakoid protein, and its carboxyl-terminal portion is distantly related to prokaryotic ATP SYNTHASE PROTEIN1 (Atp1/UncI) proteins that are thought to function in ATP synthase assembly. Plants without AtCGL160 display an increase in xanthophyll cycle activity and energy-dependent nonphotochemical quenching. These photosynthetic perturbations can be attributed to a severe reduction in cpATPase levels that result in increased acidification of the thylakoid lumen. AtCGL160 is not an integral cpATPase component but is specifically required for the efficient incorporation of the c-subunit into the cpATPase. AtCGL160, as well as a chimeric protein containing the amino-terminal part of AtCGL160 and Synechocystis sp. PCC6803 Atp1, physically interact with the c-subunit. We conclude that AtCGL160 and Atp1 facilitate the assembly of the membranous part of the cpATPase in their hosts, but loss of their functions provokes a unique compensatory response in each organism.

ATP synthase in mycobacteria: special features and implications for a function as drug target

ATP synthase is a ubiquitous enzyme that is largely conserved across the kingdoms of life. This conservation is in accordance with its central role in chemiosmotic energy conversion, a pathway utilized by far by most living cells. On the other hand, in particular pathogenic bacteria whilst employing ATP synthase have to deal with energetically unfavorable conditions such as low oxygen tensions in the human host, e.g. Mycobacterium tuberculosis can survive in human macrophages for an extended time. It is well conceivable that such ATP synthases may carry idiosyncratic features that contribute to efficient ATP production. In this review genetic and biochemical data on mycobacterial ATP synthase are discussed in terms of rotary catalysis, stator composition, and regulation of activity. ATP synthase in mycobacteria is of particular interest as this enzyme has been validated as a target for promising new antibacterial drugs. A deeper understanding of the working of mycobacterial ATP synthase and its atypical features can provide insight in adaptations of bacterial energy metabolism. Moreover, pinpointing and understanding critical differences as compared with human ATP synthase may provide input for the design and development of selective ATP synthase inhibitors as antibacterials. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.

Effect of structural modulation of polyphenolic compounds on the inhibition of Escherichia coli ATP synthase

In this paper we present the inhibitory effect of a variety of structurally modulated/modified polyphenolic compounds on purified F(1) or membrane bound F(1)F(o)Escherichia coli ATP synthase. Structural modulation of polyphenols with two phenolic rings inhibited ATP synthase essentially completely; one or three ringed polyphenols individually or fused together inhibited partially. We found that the position of hydroxyl and nitro groups plays critical role in the degree of binding and inhibition of ATPase activity. The extended positioning of hydroxyl groups on imino diphenolic compounds diminished the inhibition and abridged position enhanced the inhibition potency. This was contrary to the effect by simple single ringed phenolic compounds where extended positioning of hydroxyl group was found to be effective for inhibition. Also, introduction of nitro group augmented the inhibition on molar scale in comparison to the inhibition by resveratrol but addition of phosphate group did not. Similarly, aromatic diol or triol with rigid or planar ring structure and no free rotation poorly inhibited the ATPase activity. The inhibition was identical in both F(1)F(o) membrane preparations as well as in isolated purified F(1) and was reversible in all cases. Growth assays suggested that modulated compounds used in this study inhibited F(1)-ATPase as well as ATP synthesis nearly equally.

Role of Charged Residues in the Catalytic Sites of Escherichia coli ATP Synthase

Here we describe the role of charged amino acids at the catalytic sites of Escherichia coli ATP synthase. There are four positively charged and four negatively charged residues in the vicinity of of E. coli ATP synthase catalytic sites. Positive charges are contributed by three arginine and one lysine, while negative charges are contributed by two aspartic acid and two glutamic acid residues. Replacement of arginine with a neutral amino acid has been shown to abrogate phosphate binding, while restoration of phosphate binding has been accomplished by insertion of arginine at the same or a nearby location. The number and position of positive charges plays a critical role in the proper and efficient binding of phosphate. However, a cluster of many positive charges inhibits phosphate binding. Moreover, the presence of negatively charged residues seems a requisite for the proper orientation and functioning of positively charged residues in the catalytic sites. This implies that electrostatic interactions between amino acids are an important constituent of initial phosphate binding in the catalytic sites. Significant loss of function in growth and ATPase activity assays in mutants generated through charge modulations has demonstrated that precise location and stereochemical interactions are of paramount importance.

Principles of control over formation of structures responsible for respiratory functions of mitochondria

Topogenesis of mitochondrial proteins includes their synthesis in cytosol and mitochondria, their translocation across the outer and inner membranes, sorting to various mitochondrial compartments, and assembly of different protein complexes. These complexes are involved in transport functions, electron transfer through the respiratory chain, generation of transmembrane electrochemical potential, oxidative phosphorylation of ADP into ATP, etc. To perform these functions, a special stringent control is required over formation of submitochondrial structures and the mitochondrion as a whole. Such control is expected to rigorously eliminate not only misfolded proteins but also incorrectly incorporated subunits and is realized in mitochondria by means of numerous proteases with different functions and localizations. In the case of more complicated protein formations, e.g. supercomplexes, the protein quality is assessed by their ability to realize the integral function of the respiratory chain and, thus, ensure the stability of the whole system. Considering supercomplexes of the mitochondrial respiratory chain, the present review clearly demonstrates that this control is realized by means of various (mainly vacuolar) proteases with different functions and localizations. The contemporary experimental data also confirm the author's original idea that the general mechanism of assembly of subcellular structures is based on the "selection by performance criterion" and "stabilization by functioning".

Essentials for ATP synthesis by F1F0 ATP synthases

The majority of cellular energy in the form of adenosine triphosphate (ATP) is synthesized by the ubiquitous F(1)F(0) ATP synthase. Power for ATP synthesis derives from an electrochemical proton (or Na(+)) gradient, which drives rotation of membranous F(0) motor components. Efficient rotation not only requires a significant driving force (DeltamuH(+)), consisting of membrane potential (Deltapsi) and proton concentration gradient (DeltapH), but also a high proton concentration at the source P side. In vivo this is maintained by dynamic proton movements across and along the surface of the membrane. The torque-generating unit consists of the interface of the rotating c ring and the stator a subunit. Ion translocation through this unit involves a sophisticated interplay between the c-ring binding sites, the stator arginine, and the coupling ions on both sides of the membrane. c-ring rotation is transmitted to the eccentric shaft gamma-subunit to elicit conformational changes in the catalytic sites of F(1), leading to ATP synthesis.

Inhibition of ATPase activity of Escherichia coli ATP synthase by polyphenols

We have studied the inhibitory effect of five polyphenols namely, resveratrol, piceatannol, quercetin, quercetrin, and quercetin-3-beta-D glucoside on Escherichia coli ATP synthase. Recently published X-ray crystal structures of bovine mitochondrial ATP synthase inhibited by resveratrol, piceatannol, and quercetin, suggest that these compounds bind in a hydrophobic pocket between the gamma-subunit C-terminal tip and the hydrophobic inside of the surrounding annulus in a region critical for rotation of the gamma-subunit. Herein, we show that resveratrol, piceatannol, quercetin, quercetrin, or quercetin-3-beta-d glucoside all inhibit E. coli ATP synthase but to different degrees. Whereas piceatannol inhibited ATPase essentially completely ( approximately 0 residual activity), inhibition by other compounds was partial with approximately 20% residual activity by quercetin, approximately 50% residual activity by quercetin-3-beta-D glucoside, and approximately 60% residual activity by quercetrin or resveratrol. Piceatannol was the most potent inhibitor (IC(50) approximately 14 microM) followed by quercetin (IC(50) approximately 33 microM), quercetin-3-beta-D glucoside (IC(50) approximately 71 microM), resveratrol (IC(50) approximately 94 microM), quercitrin (IC(50) approximately 120 microM). Inhibition was identical in both F(1)F(o) membrane preparations as well as in isolated purified F(1). In all cases inhibition was reversible. Interestingly, resveratrol and piceatannol inhibited both ATPase and ATP synthesis whereas quercetin, quercetrin or quercetin-3-beta-d glucoside inhibited only ATPase activity and not ATP synthesis.

The b subunits in the peripheral stalk of F1F0 ATP synthase preferentially adopt an offset relationship

The peripheral stalk of F1F0 ATP synthase is essential for the binding of F1 to FO and for proper transfer of energy between the two sectors of the enzyme. The peripheral stalk of Escherichia coli is composed of a dimer of identical b subunits. In contrast, photosynthetic organisms express two b-like genes that form a heterodimeric peripheral stalk. Previously we generated chimeric peripheral stalks in which a portion of the tether and dimerization domains of the E. coli b subunits were replaced with homologous sequences from the b and b' subunits of Thermosynechococcus elongatus (Claggett, S. B., Grabar, T. B., Dunn, S. D., and Cain, B. D. (2007) J. Bacteriol. 189, 5463-5471). The spatial arrangement of the chimeric b and b' subunits, abbreviated Tb and Tb', has been investigated by Cu2+-mediated disulfide cross-link formation. Disulfide formation was studied both in soluble model polypeptides and between full-length subunits within intact functional F1F0 ATP synthase complexes. In both cases, disulfides were preferentially formed between TbA83C and Tb'A90C, indicating the existence of a staggered relationship between helices of the two chimeric subunits. Even under stringent conditions rapid formation of disulfides between these positions occurred. Importantly, formation of this cross-link had no detectable effect on ATP-driven proton pumping, indicating that the staggered conformation is compatible with normal enzymatic activity. Under less stringent reaction conditions, it was also possible to detect b subunits cross-linked through identical positions, suggesting that an in-register, nonstaggered parallel conformation may also exist.

From protons to OXPHOS supercomplexes and Alzheimer's disease: structure-dynamics-function relationships of energy-transducing membranes

By the elucidation of high-resolution structures the view of the bioenergetic processes has become more precise. But in the face of these fundamental advances, many problems are still unresolved. We have examined a variety of aspects of energy-transducing membranes from large protein complexes down to the level of protons and functional relevant picosecond protein dynamics. Based on the central role of the ATP synthase for supplying the biological fuel ATP, one main emphasis was put on this protein complex from both chloroplast and mitochondria. In particular the stoichiometry of protons required for the synthesis of one ATP molecule and the supramolecular organisation of ATP synthases were examined. Since formation of supercomplexes also concerns other complexes of the respiratory chain, our work was directed to unravel this kind of organisation, e.g. of the OXPHOS supercomplex I(1)III(2)IV(1), in terms of structure and function. Not only the large protein complexes or supercomplexes work as key players for biological energy conversion, but also small components as quinones which facilitate the transfer of electrons and protons. Therefore, their location in the membrane profile was determined by neutron diffraction. Physico-chemical features of the path of protons from the generators of the electrochemical gradient to the ATP synthase, as well as of their interaction with the membrane surface, could be elucidated by time-resolved absorption spectroscopy in combination with optical pH indicators. Diseases such as Alzheimer's dementia (AD) are triggered by perturbation of membranes and bioenergetics as demonstrated by our neutron scattering studies.

Role of {alpha}-subunit VISIT-DG sequence residues Ser-347 and Gly-351 in the catalytic sites of Escherichia coli ATP synthase

This paper describes the role of alpha-subunit VISIT-DG sequence residues alphaSer-347 and alphaGly-351 in catalytic sites of Escherichia coli F(1)F(o) ATP synthase. X-ray structures show the very highly conserved alpha-subunit VISIT-DG sequence in close proximity to the conserved phosphate-binding residues alphaArg-376, betaArg-182, betaLys-155, and betaArg-246 in the phosphate-binding subdomain. Mutations alphaS347Q and alphaG351Q caused loss of oxidative phosphorylation and reduced ATPase activity of F(1)F(o) in membranes by 100- and 150-fold, respectively, whereas alphaS347A mutation showed only a 13-fold loss of activity and also retained some oxidative phosphorylation activity. The ATPase of alphaS347Q mutant was not inhibited, and the alphaS347A mutant was slightly inhibited by MgADP-azide, MgADP-fluoroaluminate, or MgADP-fluoroscandium, in contrast to wild type and alphaG351Q mutant. Whereas 7-chloro-4-nitrobenzo-2-oxa-1, 3-diazole (NBD-Cl) inhibited wild type and alphaG351Q mutant ATPase essentially completely, ATPase in alphaS347A or alphaS347Q mutant was inhibited maximally by approximately 80-90%, although reaction still occurred at residue betaTyr-297, proximal to the alpha-subunit VISIT-DG sequence, near the phosphate-binding pocket. Inhibition characteristics supported the conclusion that NBD-Cl reacts inbetaE (empty) catalytic sites, as shown previously by x-ray structure analysis. Phosphate protected against NBD-Cl inhibition in wild type and alphaG351Q mutant but not in alphaS347Q or alphaS347A mutant. The results demonstrate that alphaSer-347 is an additional residue involved in phosphate-binding and transition state stabilization in ATP synthase catalytic sites. In contrast, alphaGly-351, although strongly conserved and clearly important for function, appears not to play a direct role.

ATP in current biotechnology: regulation, applications and perspectives

Adenosine tri-phosphate (ATP), the most important energy source for metabolic reactions and pathways, plays a vital role in the growth of industrial strain and the production of target metabolites. In this review, current advances in manipulating ATP in industrial strains, including altering NADH availability, and regulating NADH oxidation pathway, oxygen supply, proton gradient, the electron transfer chain activity and the F(0)F(1)-ATPase activity, are summarized and discussed. By applying these strategies, optimal product concentrations, yields and productivity in industrial biotechnology have been achieved. Furthermore, the mechanisms by which ATP extends the substrate utilization spectra and enhances the ability to challenge harsh environmental stress have been elucidated. Finally, three critical issues related to ATP manipulation have been addressed.

Crystallization of the c14-rotor of the chloroplast ATP synthase reveals that it contains pigments

The ATP synthase is one of the most important enzymes on earth as it couples the transmembrane electrochemical potential of protons to the synthesis of ATP from ADP and inorganic phosphate, providing the main ATP source of almost all higher life on earth. During ATP synthesis, stepwise protonation of a conserved carboxylate on each protein subunit of an oligomeric ring of 10-15 c-subunits is commonly thought to drive rotation of the rotor moiety (c(10-14)gammaepsilon) relative to stator moiety (alpha(3)beta(3)deltaab(2)). Here we report the isolation and crystallization of the c(14)-ring of subunit c from the spinach chloroplast enzyme diffracting as far as 2.8 A. Though ATP synthase was not previously known to contain any pigments, the crystals of the c-subunit possessed a strong yellow color. The pigment analysis revealed that they contain 1 chlorophyll and 2 carotenoids, thereby showing for the first time that the chloroplast ATP synthase contains cofactors, leading to the question of the possible roles of the functions of the pigments in the chloroplast ATP synthase.

Evolutionary primacy of sodium bioenergetics

Background

The F- and V-type ATPases are rotary molecular machines that couple translocation of protons or sodium ions across the membrane to the synthesis or hydrolysis of ATP. Both the F-type (found in most bacteria and eukaryotic mitochondria and chloroplasts) and V-type (found in archaea, some bacteria, and eukaryotic vacuoles) ATPases can translocate either protons or sodium ions. The prevalent proton-dependent ATPases are generally viewed as the primary form of the enzyme whereas the sodium-translocating ATPases of some prokaryotes are usually construed as an exotic adaptation to survival in extreme environments.

Results

We combine structural and phylogenetic analyses to clarify the evolutionary relation between the proton- and sodium-translocating ATPases. A comparison of the structures of the membrane-embedded oligomeric proteolipid rings of sodium-dependent F- and V-ATPases reveals nearly identical sets of amino acids involved in sodium binding. We show that the sodium-dependent ATPases are scattered among proton-dependent ATPases in both the F- and the V-branches of the phylogenetic tree.

Conclusion

Barring convergent emergence of the same set of ligands in several lineages, these findings indicate that the use of sodium gradient for ATP synthesis is the ancestral modality of membrane bioenergetics. Thus, a primitive, sodium-impermeable but proton-permeable cell membrane that harboured a set of sodium-transporting enzymes appears to have been the evolutionary predecessor of the more structurally demanding proton-tight membranes. The use of proton as the coupling ion appears to be a later innovation that emerged on several independent occasions.

Reviewers

This article was reviewed by J. Peter Gogarten, Martijn A. Huynen, and Igor B. Zhulin. For the full reviews, please go to the Reviewers' comments section.

Structure of the cytosolic part of the subunit b-dimer of Escherichia coli F0F1-ATP synthase

The structure of the external stalk and its function in the catalytic mechanism of the F(0)F(1)-ATP synthase remains one of the important questions in bioenergetics. The external stalk has been proposed to be either a rigid stator that binds F(1) or an elastic structural element that transmits energy from the small rotational steps of subunits c to the F(1) sector during catalysis. We employed proteomics, sequence-based structure prediction, molecular modeling, and electron spin resonance spectroscopy using site-directed spin labeling to understand the structure and interfacial packing of the Escherichia coli b-subunit homodimer external stalk. Comparisons of bacterial, cyanobacterial, and plant b-subunits demonstrated little sequence similarity. Supersecondary structure predictions, however, show that all compared b-sequences have extensive heptad repeats, suggesting that the proteins all are capable of packing as left-handed coiled-coils. Molecular modeling subsequently indicated that b(2) from the E. coli ATP synthase could pack into stable left-handed coiled-coils. Thirty-eight substitutions to cysteine in soluble b-constructs allowed the introduction of spin labels and the determination of intersubunit distances by ESR. These distances correlated well with molecular modeling results and strongly suggest that the E. coli subunit b-dimer can stably exist as a left-handed coiled-coil.

Role of alphaPhe-291 residue in the phosphate-binding subdomain of catalytic sites of Escherichia coli ATP synthase

The role of alphaPhe-291 residue in phosphate binding by Escherichia coli F1F0-ATP synthase was examined. X-ray structures of bovine mitochondrial enzyme suggest that this residue resides in close proximity to the conserved betaR246 residue. Herein, we show that mutations alphaF291D and alphaF291E in E. coli reduce the ATPase activity of F1F0 membranes by 350-fold. Yet, significant oxidative phosphorylation activity is retained. In contrast to wild-type, ATPase activities of mutants were not inhibited by MgADP-azide, MgADP-fluoroaluminate, or MgADP-fluoroscandium. Whereas, 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl) inhibited wild-type ATPase essentially completely, ATPase in mutants was inhibited maximally by approximately 75%, although reaction still occurred at residue betaTyr-297, proximal to alphaPhe-291 in the phosphate-binding pocket. Inhibition characteristics supported the conclusion that NBD-Cl reacts in betaE (empty) catalytic sites, as shown previously by X-ray structure analysis. Phosphate protected against NBD-Cl inhibition in wild-type but not in mutants. In addition, our data suggest that the interaction of alphaPhe-291 with phosphate during ATP hydrolysis or synthesis may be distinct.

Role of the Asymmetry of the Homodimeric b2 Stator Stalk in the Interaction with the F1 Sector of Escherichia coli ATP Synthase

The b subunit dimer in the peripheral stator stalk of Escherichia coli ATP synthase is essential for enzyme assembly and the rotational catalytic mechanism. Recent protein chemical evidence revealed the dimerization domain of b to contain a novel two-stranded right-handed coiled coil with offset helices. Here, the existence of this structure in more complete constructs of b containing the C-terminal domain, and therefore capable of binding to the peripheral F1-ATPase, was supported by the more efficient formation of intersubunit disulfide bonds between cysteine residues that are proximal only in the offset arrangement and by the greater thermal stabilities of cross-linked heterodimers trapped in the offset configuration as opposed to homodimers with the helices trapped in-register. F1-ATPase binding analyses revealed the offset heterodimers to bind F1 more tightly than in-register homodimers. Mutations near the C terminus of b were incorporated specifically into either the N-terminally or the C-terminally shifted polypeptide, bN or bC, respectively, to determine the contribution of each position to F1 binding. Deletion of the last four residues of bN substantially weakened F1 binding, whereas the effect of the deletion in bC was modest. Similarly, benzophenone maleimide introduced at the C terminus of bN, but not bC, mediated cross-linking to the delta subunit of F1. These results imply that the polypeptide in the bN position is more important for F1 binding than the one in the bC position and illustrate the significance of the asymmetry of the b dimer in the enzyme.