The isolated F0 of Escherichia coli aTP-synthase is reconstitutively active in H+-conduction and ATP-dependent energy-transduction

The Need for Consistency with Physical Laws and Logic in Choosing Between Competing Molecular Mechanisms in Biological Processes: A Case Study in Modeling ATP Synthesis

Traditionally, proposed molecular mechanisms of fundamental biological processes have been tested against experiment. However, owing to a plethora of reasons-difficulty in designing, carrying out, and interpreting key experiments, use of different experimental models and systems, conduct of studies under widely varying experimental conditions, fineness in distinctions between competing mechanisms, complexity of the scientific issues, and the resistance of some scientists to discoveries that are contrary to popularly held beliefs-this has not solved the problem despite decades of work in the field/s. The author would like to prescribe an alternative way: that of testing competing models/mechanisms for their adherence to scientific laws and principles, and checking for errors in logic. Such tests are fairly commonly carried out in the mathematics, physics, and engineering literature. Further, reported experimental measurements should not be smaller than minimum detectable values for the measurement technique employed and should truly reflect function of the actual system without inapplicable extrapolation. Progress in the biological fields would be greatly accelerated, and considerable scientific acrimony avoided by adopting this approach. Some examples from the fundamental field of ATP synthesis in oxidative phosphorylation (OXPHOS) have been reviewed that also serve to illustrate the approach. The approach has never let the author down in his 35-yr-long experience on biological mechanisms. This change in thinking should lead to a considerable saving of both time and resources, help channel research efforts toward solution of the right problems, and hopefully provide new vistas to a younger generation of open-minded biological scientists.

Reintegrating Biology Through the Nexus of Energy, Information, and Matter

Information, energy, and matter are fundamental properties of all levels of biological organization, and life emerges from the continuous flux of matter, energy, and information. This perspective piece defines and explains each of the three pillars of this nexus. We propose that a quantitative characterization of the complex interconversions between matter, energy, and information that comprise this nexus will help us derive biological insights that connect phenomena across different levels of biological organization. We articulate examples from multiple biological scales that highlight how this nexus approach leads to a more complete understanding of the biological system. Metrics of energy, information, and matter can provide a common currency that helps link phenomena across levels of biological organization. The propagation of energy and information through levels of biological organization can result in emergent properties and system-wide changes that impact other hierarchical levels. Deeper consideration of measured imbalances in energy, information, and matter can help researchers identify key factors that influence system function at one scale, highlighting avenues to link phenomena across levels of biological organization and develop predictive models of biological systems.

The proton-driven rotor of ATP synthase: ohmic conductance (10 fS), and absence of voltage gating

The membrane portion of F(0)F(1)-ATP synthase, F(0), translocates protons by a rotary mechanism. Proton conduction by F(0) was studied in chromatophores of the photosynthetic bacterium Rhodobacter capsulatus. The discharge of a light-induced voltage jump was monitored by electrochromic absorption transients to yield the unitary conductance of F(0). The current-voltage relationship of F(0) was linear from 7 to 70 mV. The current was extremely proton-specific (>10(7)) and varied only slightly ( approximately threefold) from pH 6 to 10. The maximum conductance was approximately 10 fS at pH 8, equivalent to 6240 H(+) s(-1) at 100-mV driving force, which is an order-of-magnitude greater than of coupled F(0)F(1). There was no voltage-gating of F(0) even at low voltage, and proton translocation could be driven by deltapH alone, without voltage. The reported voltage gating in F(0)F(1) is thus attributable to the interaction of F(0) with F(1) but not to F(0) proper. We simulated proton conduction by a minimal rotary model including the rotating c-ring and two relay groups mediating proton exchange between the ring and the respective membrane surface. The data fit attributed pK values of approximately 6 and approximately 10 to these relays, and placed them close to the membrane/electrolyte interface.

NH2-terminal sequence of the isolated yeast ATP synthase subunit 6 reveals post-translational cleavage

The three mitochondrially translated ATP synthase subunits of Saccharomyces cerevisiae were extracted from the enzyme and from whole mitochondria using an organic solvent mixture and then purified by reverse-phase HPLC. The amino acid composition of subunit 6 is close to the one predicted from the oli2 gene. The partial amino terminal sequence of subunit 6 reveals a post-translational cleavage site between the Thr-10 and Ser-11 residues of the precursor. Thus, mature subunit 6 contains 249 amino acid residues and displays a molecular mass of 27943 Da.

ATP4, the structural gene for yeast F0F1 ATPase subunit 4

A plasmid containing the gene coding for the Saccharomyces cerevisiae F0F1 ATPase subunit 4 was isolated from a yeast genomic DNA library using the oligonucleotide probe procedure. The gene and the surrounding regions were cloned into M13 tg 130 and M13 tg 131 phage vectors. A 732-base-pair open reading frame encoding a 244-amino-acid polypeptide is described. The nucleotide sequence predicts that subunit 4 is probably derived from a precursor protein with a hydrophilic and basic 35-amino-acid leader sequence. Mature subunit 4 contains 209 amino acid residues and the predicted molecular mass is 23250 Da. This subunit presents amphiphilic behaviour with two distinct domains. A high alpha-helix content of 77% was predicted from the sequence. Subunit 4 shows homology with the b subunit of Escherichia coli ATP synthase.

F0 part of the ATP synthase from Escherichia coli. Influence of subunits a, and b, on the structure of subunit c

Four different sets of proteoliposomes were prepared from F0, subunit c, a complex of subunits a and c (ac complex) and an ac complex supplemented with subunit b. Only liposomes containing intact F0 or all subunits of F0 were active in proton translocation and F1 binding [Schneider, E. and Altendorf, K. (1985) EMBO J. 4, 515-518]. The conformation of subunit c in the different preparations was analyzed by labelling the proteoliposomes with the hydrophobic photoactivatable reagent 3-(trifluoromethyl)-3-(m-[125I]iodophenyl)diazirine ([125I]TID). Subsequent isolation and Edman degradation of this polypeptide revealed distinct radioactive labelling patterns over the entire amino acid sequence. In the F0 complex and in the ac complex subunit c retains a labelling pattern which is related to that found in TID-labelled membrane vesicles of Escherichia coli [Hoppe et al. (1984) Biochemistry 23, 5610-5616]. In the absence of subunit a, considerably more and different amino acid residues of subunit c are modified. The labelling data are discussed in relation to structural aspects of F0 and functional properties of proteoliposomes reconstituted with F0 or individual subunits.

Bacterial adenosine 5'-triphosphate synthase (F1F0): purification and reconstitution of F0 complexes and biochemical and functional characterization of their subunits

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The proton channel, CF0, in thylakoid membranes. Only a low proportion of CF1-lacking CF0 is active with a high unit conductance (169 fS)

We investigated the conductance of pea thylakoid membranes and their capacity for photophosphorylation as function of the extraction of chloroplast coupling factor CF1. The degree of extraction was varied via the incubation time in EDTA-containing hypo-osmolar medium and was measured by rocket electroimmunodiffusion. The conductance of thylakoid membranes was measured by flash kinetic spectrophotometry. The time course of extraction followed the time course of thylakoid swelling. Contrary to expectation increasing loss of CF1 did not primarily increase the velocity of proton efflux from each vesicle. Instead proton-tight vesicles were converted to leaky ones, which lost phosphorylating activity. Two subpopulations occurred, although both types of vesicles, leaky and proton-tight ones, were CF1-depleted to a similar degree. This implied that only a small fraction of CF1-lacking CF0 was functional as a proton channel. Tight vesicles had no functional channels while leaky ones had at least one. We determined the proportion of tight vesicles in three independent ways: via the residual phosphorylation activity, via measurements of proton efflux and via measurements of the electric relaxation across the membrane. The results obtained were identical. A statistical evaluation of the data led us to the following conclusions. EDTA treatment produced vesicles containing approximately 10(5) chlorophyll molecules, equivalent to a total of approximately 100 CF0CF1 per vesicle. Even at the highest degree of extraction (75% of total CF1 extracted) only 2.5 out of 75 exposed CF0 per vesicle were proton-conducting. The unit conductance of one open CF0 channel was 169 +/- 18 fS at pH 7.5 and room temperature. At an electrical driving force of 100 mV this was equivalent to the passage of approximately 10(5) protons/s. The most important consequence of this relatively high unit conductance was that a single open CF0 channel was capable of dissipating the protonmotive force of one vesicle, thereby deactivating the whole remaining catalytic capacity of this vesicle.

An antibody-binding site in the native enzyme between amino acid residues 205-287 of the gamma-subunit of F1 from Escherichia coli

A monoclonal antibody was isolated specific for the isolated denatured gamma-subunit of F1 from Escherichia coli and binding to native F1. The binding site of this antibody was identified between amino acid residues 205-287 of the polypeptide chain thus being located at the surface of the F1 complex.

The beta subunit of the Escherichia coli ATP synthase exhibits a tight membrane binding property

We have developed a chromatographic procedure to analyze the association of the subunits of the Escherichia coli F1Fo-ATP synthase with the cytoplasmic membrane. Minicells containing [35S]-labeled ATP synthase subunits are treated with lysozyme, solubilized, and chromatographed on a Sepharose CL-2B column in buffer containing urea and taurodeoxycholate. ATP synthase subunits are resolved into membrane intrinsic and membrane extrinsic subunits. Interestingly, a significant amount (36%) of the F1 subunit beta fractionates with the membrane intrinsic Fo subunits. About half of this amount (19%) of beta is non-specifically bound to the membrane. Interaction of beta with the membrane is not mediated by the amino terminal portion of beta.

Subunit b of the membrane moiety (F0) of ATP synthase (F1F0) from Escherichia coli is indispensable for H+ translocation and binding of the water-soluble F1 moiety

The ATP synthase complex, designated F1F0, of Escherichia coli is composed of a water-soluble portion (F1; membrane-associated ATPase, EC 3.6.1.3) with ATP-hydrolyzing activity and a membrane-integrated part (F0) with H+-translocating activity. F0 is built up from three kinds of subunits (a, b, and c). We have isolated the F0 portion directly from membranes of an E. coli strain (KY 7485) that overproduces the enzyme several fold. Subunit b was extracted from purified F0 by two methods. One method included prolonged incubation of the F0 complex in the presence of trichloroacetate (2.5 M) and the separation of subunit b and an a-c complex by gel filtration. Alternatively, subunit b was extracted by deoxycholate and separated from the a-c complex by hydrophobic-interaction chromatography. Integrated into liposomes, the a-c complex exhibited neither H+ uptake nor binding of F1. However, a functional F0 complex was reconstituted by adding stoichiometric amounts of subunit b to the a-c complex.

Structure of the membrane-embedded F0 part of F1F0 ATP synthase from Escherichia coli as inferred from labeling with 3-(Trifluoromethyl)-3-(m-[125I]iodophenyl)diazirine

3-(Trifluoromethyl)-3-(m-[125I]iodophenyl)diazirine [( 125I]TID) is a photoactivatable carbene precursor designed to label selectively the hydrophobic core of membranes. We have used this reagent to obtain information on the topological organization of the membrane-embedded subunits of F1F0 ATP synthase from Escherichia coli. The study included [125I]TID labeling of F0 subunits in different structural (conformational) states and Edman degradations of the labeled polypeptides in order to assign the covalently bound radioactivity to individual amino acid residues. Released phenylthiohydantoin amino acids were analyzed by thin-layer chromatography, and the radioactive derivatives were visualized by autoradiography. The data suggest that labeling patterns can be correlated in a meaningful manner with reagent accessibility and hence with protein-lipid contact. Subunit b appears to be anchored to the membrane by a short N-terminal segment. As almost all of the amino acids of this part are accessible to the reagent, it is inferred that this segment has little interaction with the other subunits. In contrast, in the two segments of subunit c that were labeled with [125I]TID, only certain amino acids reacted with the label. The pattern of these labeled residues is compatible with that of tightly packed alpha-helices.

The DCCD-reactive aspartyl-residue of subunit C from the Escherichia coli ATP-synthase is important for the conformation of F0

The effect of various point mutations in subunits a and and c of the E. coli ATP-synthase was characterized. In each of the mutants there was no F0-dependent H+-conduction, but still an ATPase-activity comparable to wildtype activities. In addition, the subunit b could be extracted from the mutant's F0 but not from the F0 of wildtype. The effects are interpreted as a change in the conformation of F0 caused by the different mutations.

Use of monoclonal antibodies in immuno-electron microscopy for the determination of subunit stoichiometry in oligomeric enzymes. There are three alpha-subunits in the F1-ATPase of Escherichia coli

The subunit stoichiometry of oligomeric enzymes can be determined by immuno-electron microscopy using monoclonal antibodies against the individual subunits. Monoclonal antibodies against native F1-ATPase of Escherichia coli were prepared that were specific for the alpha-subunit. The immune complexes of F1 and monoclonal antibodies were isolated. Electron microscopy revealed the presence of three immunoglobulins per molecule of F1-ATPase. This unequivocally demonstrates an alpha 3 stoichiometry for the F1-ATPase of E. coli.

Chemical modification of the F0 part of the ATP synthase (F1F0) from Escherichia coli. Effects on proton conduction and F1 binding

The purified F0 part of the ATP synthase complex from Escherichia coli was incorporated into liposomes and chemically modified by various reagents. The modified F0-liposomes were assayed for H+ uptake and, after reconstitution with F1, for total and dicyclohexylcarbodiimide-sensitive ATPase activity. The water-soluble carbodiimide, 1-ethyl-3-(-3-dimethylaminopropyl)carbodiimide methiodide, (1.2 mM), inhibited H+ uptake to a great extent. Binding of F1 was almost unaffected, but the hydrolysis of ATP was uncoupled from H+ transport. This is reflected by the inhibition of dicyclohexylcarbodiimide-sensitive ATPase activity. Woodward's reagent K, N-ethyl-5-phenylisoxazolium-3'-sulfonate, inhibited both H+ uptake and total ATPase activity. Modification of arginine residues by phenylglyoxal (20 mM) was followed by inhibition of the F1 binding activity by 80% of the control. H+ translocation was reduced to 70%. Diethylpyrocarbonate (3 mM) exhibited a strong inhibiting effect on H+ uptake but not on F1 binding. Modification of tyrosine (by tetranitromethane) as well as lysine residues (by succinic anhydride) did not affect F0 functions. From the data presented we conclude that carboxyl-groups, different from the dicyclohexylcarbodiimide-binding site, are involved in H+ translocation through F0 and, in part, in the functional binding of F1. Furthermore, for the latter function, also arginine residues seem to be important. The role of histidine residues remains unclear at present.

Use of lambda unc transducing bacteriophages in genetic and biochemical characterization of H+-ATPase mutants of Escherichia coli

The eight subunits of the H+-ATPase of Escherichia coli are coded by the genes of the unc operon, which maps between bglB and asnA. A collection of unc mutations were transferred via P1 transduction into a strain in which lambda cI857 S7 was inserted into bglB. The lambda phage was induced, and asnA+ transducing phage that carried unc were selected. Transducing phage carrying mutations in the uncA, B, D, E, and F genes were used for complementation analysis with a collection of unc mutants, including mutants which had been reported previously but not genetically characterized. Some mutations gave a simple complementation pattern, indicating a single defective gene, whereas other mutations gave more complex patterns. Two mutants (uncE105 and uncE107) altered in the proteolipid (omega) subunit of F0 were not complemented by any of the lambda unc phage, even though both mutants had a fully functional F1 ATPase and therefore normal A and D genes. Hence, only limited conclusions can be drawn from genetic complementation alone, since it cannot distinguish normal from abnormal genes in certain classes of unc mutants. The lambda unc phage proved to be essential in characterizing several mutants defective in F0-mediated H+ translocation. The unc gene products were overproduced by heat induction of the lysogenized lambda unc phage to determine whether all the F0 subunits were in the membrane. Two mutants that gave a simple complementation pattern, indicative of one defective gene, did not assemble a three-subunit F0. The uncB108 mutant was shown to lack the chi subunit of F0 but to retain psi and omega. Trace amounts of an altered omega subunit and normal amounts of chi and psi were found in the uncE106 mutant. A substitution of aspartate for glycine at residue 58 of the protein was determined by DNA sequence analysis of the uncE gene cloned from the lambda uncE106 phage DNA. One of the omega-defective, noncomplementing mutants (uncE107) was shown to retain all three F0 subunits. The uncE gene from this mutant was also sequenced to confirm an asparagine-for-aspartate substitution at position 61 (the dicyclohexylcarbodiimide-binding site) of the omega subunit.

Membrane topology of ATP synthase from bovine heart mitochondria and Escherichia coli

The polypeptides exposed to lipids in the membranous F0 sector of the mitochondrial and Escherichia coli ATP synthases were labelled with radioactive photoreactive lipids. Highly resolving gel electrophoretic conditions were used in order to separate all the eighteen components forming the bovine heart mitochondrial enzyme. The hydrophobic labelling was performed on fully active and inhibitor-sensitive ATP synthases. In the mitochondrial enzyme prepared according to Serrano et al. (1976) [J. Biol. Chem. 251, 2453-2461] seven polypeptides of Mr 30500; 11500; 10500; 10000; 9500; 8500 and 4500 were labelled. The major amount of radioactivity was associated with the 30500-Mr component, which is thought to be the adenine nucleotide carrier. In the preparation of Galante et al., (1979) which almost completely lacks this component [J. Biol. Chem. 254, 12372-12378] nine polypeptides of Mr 25000; 21000; 11500; 10500; 10000; 9500; 9200; 8500 and 4500 were labelled. In the ATPase synthase from E. coli the major amount of labelling was associated with subunit b and only a minor portion with subunit c.

In vitro membrane association of the F0 polypeptides of the Escherichia coli proton translocating ATPase

The F0 polypeptides a, b, and c of the H+-translocating ATPase associated with membranes when synthesized in vitro. This association occurred when the membranes were present either cotranslationally or post-translationally. In addition, the F0 polypeptides associated with liposomes. The membrane association seemed to be an insertion process since there was protection of polypeptides a and c from proteolysis. The in vitro insertion of the F0 polypeptides a, b, and c was independent of the synthesis of each polypeptide and of the F1 polypeptides.

Differential polypeptide synthesis of the proton-translocating ATPase of Escherichia coli

We investigated the regulation of the synthesis of the eight polypeptides of the Escherichia coli proton-translocating ATPase. A plasmid carrying the eight genes of the unc operon was used to direct in vivo and in vitro protein synthesis of the eight polypeptides. Analysis of these data indicates that the ATPase polypeptides are synthesized in unequal amounts both in vitro and in vivo. We identified several regions within the unc operon at which expression of a gene is either increased or decreased from that of the preceding gene. Since genetic information indicates a single polycistronic mRNA for all eight genes of this operon, the observed differential synthesis of the polypeptides is most likely the result of translational regulation. The effect of varying the temperature suggests that the secondary structure in the mRNA may affect the rate of translation initiation in the region between uncE and uncF.

Topological and functional aspects of the proton conductor, F0, of the Escherichia coli ATP-synthase

The isolated H+ conductor, F0, of the Escherichia coli ATP-synthase consists of three subunits, a, b, and c. H+-permeable liposomes can be reconstituted with F0 and lipids; addition of F1-ATPase reconstitutes a functional ATP-synthase. Mutants with altered or missing F0 subunits are defective in H+ conduction. Thus, all three subunits are necessary for the expression of H+ conduction. The subunits a and b contain binding sites for F1. Computer calculations, cross-links, membrane-permeating photo-reactive labels, and proteases were used to develop tentative structural models for the individual F0 subunits.

ATP synthetase (F1F0) of Escherichia coli K-12. High-yield preparation of functional F0 by hydrophobic affinity chromatography

1. The purified ATP synthetase complex (F1F0) from Escherichia coli was adsorbed to immobilized poly-(L-lysine)-deoxycholic acid. About 0.7 mg F1F0 were bound per ml of settled gel. The hydrophilic F1 part was dissociated from the complex by treatment with 7 M urea. F0 was eluted in high yield either with deoxycholate (6 mM) or taurodeoxycholate (10 mM). About 14% of the total protein bound to the column was eluted as F0, which corresponds to 64% of the total F0 in the F1F0 complex. 2. The purified F0 preparation obtained was composed of three different kinds of subunits with apparent molecular weights of 24000 (a), 19000 (b) and 8300 (c), respectively as determined by sodium dodecyl sulfate gel electrophoresis. 3. After incorporation into liposomes and the generation of a potassium diffusion potential by valinomycin, the F0 preparation mediated H+ translocation. This H+ uptake is inhibited by either dicyclohexylcarbodiimide or purified F1 ATPase. 4. Incubation of F0-containing liposomes with F1 led to the reconstitution of an ATP-driven quenching of acridine-dye fluorescence. The quenching was abolished by uncoupler and prevented by dicyclohexylcarbodiimide.

The genes for the eight subunits of the membrane bound ATP synthase of Escherichia coli

The genes for the eight subunits of the membrane bound ATP synthase of Escherichia coli (Ca++, Mg++ dependent ATPase, EC 3.6.1.3) were mapped through genetic, physical and functional analysis of specialized transducing phages lambda asn (von Meyenburg et al. 1978). The ATP synthase genes, designated atp1, are located at 83.2 min in a segment of the chromosome between 3.5 and 11.3 kb left (counterclockwise) of the origin of replication oriC. The counterclockwise order of the genes for the eight subunits, the expression of which starts from a control region at 3.5 kb-L, was found to be: a, (c, b, delta), alpha, gamma, (epsilon, beta) which in the notation of Downie el al. (1981) reads atp B (EFH) A G (C D). The analysis was in part based on the isolation of new types of atp (unc, Suc-) mutations. We made use of the fact that specialized transducing phages lambda asn carrying oriC can establish themselves as minichromosomes rendering asnA cells Asn+, and that the resulting Asn+ cells grow slowly if the lambda asn carries part or all of the atp operon. Selecting for fast growing strains mutations were isolated on the lambda asn which either eliminated atp genes or affected their expression ("promoter" mutations). The relationship between these atp mutations and the cop mutations of Ogura et al. (1980), which also appear to map in front of or within the atp genes, is discussed.

The nucleotide sequence of the atp genes coding for the F0 subunits a, b, c and the F1 subunit delta of the membrane bound ATP synthase of Escherichia coli

The nucleotide sequence has been determined of a 2,500 base pair segment of the E. coli chromosome located between 3.75 and 6.25 kb counterclockwise of the origin of replication at 83.5 min. The sequence contains the atp genes coding for subunits a-, b-, c-, delta- and part of the alpha-subunit of the membrane bound ATP synthase. The precise start positions of the atpE (c), atpF (b), atpH (delta) and atpA (alpha) genes have been defined by comparison of the potential coding sequences with the known amino acid sequence of the c-subunit and the determined N-terminal amino acid sequences of the respective subunits. The genes are expressed in the counterclockwise direction. Their order (counterclockwise) is: atpB (a), atpE (c), atpF (b), atpH (delta) and atpA(alpha). The coding sequences for subunits b and delta yield polypeptides of 156 and 177 amino acids, respectively, in accordance with the established sizes of these subunits; the one for the c-subunit, the DCCD binding protein, fits perfectly with its known sequence of 79 amino acids. The a-subunit is comprised within a coding sequence yielding a polypeptide of 271 amino acids. It is suggested, however, that the a-subunit (atpB) contains only 201 amino acids, in accordance with its known size, starting from a translation initiation site within the larger coding sequence. The stoichiometry of the F0 sector subunits is discussed and a model is proposed for the functioning of the highly charged b-subunit of the F0 sector as the actual proton conductor.

The dicyclohexylcarbodiimide-binding protein c of ATP synthase from Escherichia coli is not sufficient to express an efficient H+ conduction

Bacteriophage Mu was inserted into the unc genes of Escherichia coli. The resulting mutation AS12 had a polar effect on the unc operon: membranes of the mutant AS12 contained the dicyclohexylcarbodiimide-binding protein c and the protein a as sole subunits of the ATP synthase. It was shown by peptide mapping and amino acid analysis of the fragments that protein c from mutant AS12 was identical with the wild-type protein c. The absence of subunit b in mutant AS12 drastically lowered the H+ conduction dependent on the membrane-integrated moiety (F0) of the ATP synthase. This suggests that both subunits b and c are necessary for an efficient expression of H+ conduction.