Relationship between oxygen-induced proton efflux and membrane energization in cells of Escherichia coli

A protet-based model that can account for energy coupling in oxidative and photosynthetic phosphorylation

Two-stage (e.g. light-dark) phosphorylation experiments showed that there is a stored 'high-energy' intermediate linking electron transport and phosphorylation. Large, artificial electrochemical proton gradients (protonmotive forces or pmfs) can also drive phosphorylation, a fact seen as strongly supportive of the chemiosmotic coupling hypothesis that a pmf is the 'high-energy' intermediate. However, in such experiments there is an experimental threshold (pmf >170 mV, equivalent to ΔpH ∼2.8) below which no phosphorylation is in fact observed, and 220 mV are required to recreate in vivo rates. This leads to the correct question, which is then whether those values of the pmf generated by electron transport are large enough. Even the lower ones as required for any phosphorylation (leave alone those required to explain in vivo rates) are below the threshold [1, 2], whether measured directly with microelectrodes or via the use of membrane-permeant ions and/or acids/bases (which are always transporter substrates [3], so all such measurements are in fact artefactual). The single case that seemed large enough (220 mV) is now admitted to be a diffusion potential artefact [4]. Many other observables (inadequate bulk H+ in 'O2-pulse'-type experiments, alkaliphilic bacteria, dual-inhibitor titrations, uncoupler-binding proteins, etc.) are consistent with the view that values of the pmf, and especially of Δψ, are actually very low. A protet-based charge separation model [2], a protonic version analogous to how energy may be stored in devices called electrets, provides a high-energy intermediate that can explain the entire literature, including the very striking demonstration [5] that close proximity is required between electron transport and ATP synthase complexes for energy coupling between them to allow phosphorylation to occur. A chief purpose of this article is thus to summarise the extensive and self-consistent literature, much of which is of some antiquity and rarely considered by modern researchers, despite its clear message of the inadequacy of chemiosmotic coupling to explain these phenomena.

A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation

Textbooks of biochemistry will explain that the otherwise endergonic reactions of ATP synthesis can be driven by the exergonic reactions of respiratory electron transport, and that these two half-reactions are catalyzed by protein complexes embedded in the same, closed membrane. These views are correct. The textbooks also state that, according to the chemiosmotic coupling hypothesis, a (or the) kinetically and thermodynamically competent intermediate linking the two half-reactions is the electrochemical difference of protons that is in equilibrium with that between the two bulk phases that the coupling membrane serves to separate. This gradient consists of a membrane potential term Δψ and a pH gradient term ΔpH, and is known colloquially as the protonmotive force or pmf. Artificial imposition of a pmf can drive phosphorylation, but only if the pmf exceeds some 150-170mV; to achieve in vivo rates the imposed pmf must reach 200mV. The key question then is 'does the pmf generated by electron transport exceed 200mV, or even 170mV?' The possibly surprising answer, from a great many kinds of experiment and sources of evidence, including direct measurements with microelectrodes, indicates it that it does not. Observable pH changes driven by electron transport are real, and they control various processes; however, compensating ion movements restrict the Δψ component to low values. A protet-based model, that I outline here, can account for all the necessary observations, including all of those inconsistent with chemiosmotic coupling, and provides for a variety of testable hypotheses by which it might be refined.

Molecular-level understanding of biological energy coupling and transduction: Response to "Chemiosmotic misunderstandings"

In a recent paper entitled "Chemiosmotic misunderstandings", it is claimed that "enough shortcomings in Mitchell's chemiosmotic theory have not been found and that a novel paradigm that offers at least as much explanatory power as chemiosmosis is not ready." This view is refuted by a wealth of molecular-level experimental data and strong new theoretical and computational evidence. It is shown that the chemiosmotic theory was beset with a large number of major shortcomings ever since the time when it was first proposed in the 1960s. These multiple shortcomings and flaws of chemiosmosis were repeatedly pointed out in incisive critiques by biochemical authorities of the late 20th century. All the shortcomings and flaws have been shown to be rectified by a quantitative, unified molecular-level theory that leads to a deeper and far more accurate understanding of biological energy coupling and ATP synthesis. The new theory is shown to be consistent with pioneering X-ray and cryo-EM structures and validated by state-of-the-art single-molecule techniques. Several new biochemical experimental tests are proposed and constructive ways for providing a revitalizing conceptual background and theory for integration of the available experimental information are suggested.

A family of Type VI secretion system effector proteins that form ion-selective pores

Type VI secretion systems (T6SSs) are nanomachines widely used by bacteria to deliver toxic effector proteins directly into neighbouring cells. However, the modes of action of many effectors remain unknown. Here we report that Ssp6, an anti-bacterial effector delivered by a T6SS of the opportunistic pathogen Serratia marcescens, is a toxin that forms ion-selective pores. Ssp6 inhibits bacterial growth by causing depolarisation of the inner membrane in intoxicated cells, together with increased outer membrane permeability. Reconstruction of Ssp6 activity in vitro demonstrates that it forms cation-selective pores. A survey of bacterial genomes reveals that genes encoding Ssp6-like effectors are widespread in Enterobacteriaceae and often linked with T6SS genes. We conclude that Ssp6 and similar proteins represent a new family of T6SS-delivered anti-bacterial effectors.

Interaction of daptomycin with lipid bilayers: a lipid extracting effect

Daptomycin is the first approved member of a new structural class of antibiotics, the cyclic lipopeptides. The peptide interacts with the lipid matrix of cell membranes, inducing permeability of the membrane to ions, but its molecular mechanism has been a puzzle. Unlike the ubiquitous membrane-acting host-defense antimicrobial peptides, daptomycin does not induce pores in the cell membranes. Thus, how it affects the permeability of a membrane to ions is not clear. We studied its interaction with giant unilamellar vesicles (GUVs) and discovered a lipid-extracting phenomenon that correlates with the direct action of daptomycin on bacterial membranes observed in a recent fluorescence microscopy study. Lipid extraction occurred only when the GUV lipid composition included phosphatidylglycerol and in the presence of Ca(2+) ions, the same condition found to be necessary for daptomycin to be effective against bacteria. Furthermore, it occurred only when the peptide/lipid ratio exceeded a threshold value, which could be the basis of the minimal inhibitory concentration of daptomycin. In this first publication on the lipid extracting effect, we characterize its dependence on ions and lipid compositions. We also discuss possibilities for connecting the lipid extracting effect to the antibacterial activity of daptomycin.

Beyond the chemiosmotic theory: analysis of key fundamental aspects of energy coupling in oxidative phosphorylation in the light of a torsional mechanism of energy transduction and ATP synthesis--invited review part 2

The core of this second article shows how logical errors and inconsistencies in previous theories of energy coupling in oxidative phosphorylation are overcome by use of a torsional mechanism and the unified theory of ATP synthesis/hydrolysis. The torsional mechanism is shown to satisfy the pioneering and verified features of previous mechanisms. A considerable amount of data is identified that is incompatible with older theories but is now explained in a logically consistent and unified way. Key deficiencies in older theories are pinpointed and their resolution elucidated. Finally, major differences between old and new approaches are tabulated. The new theory now provides the elusive details of energy coupling and transduction, and allows several novel and experimentally verifiable predictions to be made and a considerable number of applications in nanotechnology, energy conversion, systems biology, and in health and disease are foreseen.

Colicin biology

Colicins are proteins produced by and toxic for some strains of Escherichia coli. They are produced by strains of E. coli carrying a colicinogenic plasmid that bears the genetic determinants for colicin synthesis, immunity, and release. Insights gained into each fundamental aspect of their biology are presented: their synthesis, which is under SOS regulation; their release into the extracellular medium, which involves the colicin lysis protein; and their uptake mechanisms and modes of action. Colicins are organized into three domains, each one involved in a different step of the process of killing sensitive bacteria. The structures of some colicins are known at the atomic level and are discussed. Colicins exert their lethal action by first binding to specific receptors, which are outer membrane proteins used for the entry of specific nutrients. They are then translocated through the outer membrane and transit through the periplasm by either the Tol or the TonB system. The components of each system are known, and their implication in the functioning of the system is described. Colicins then reach their lethal target and act either by forming a voltage-dependent channel into the inner membrane or by using their endonuclease activity on DNA, rRNA, or tRNA. The mechanisms of inhibition by specific and cognate immunity proteins are presented. Finally, the use of colicins as laboratory or biotechnological tools and their mode of evolution are discussed.

Escherichia coli glutamate- and arginine-dependent acid resistance systems increase internal pH and reverse transmembrane potential

Due to the acidic nature of the stomach, enteric organisms must withstand extreme acid stress for colonization and pathogenesis. Escherichia coli contains several acid resistance systems that protect cells to pH 2. One acid resistance system, acid resistance system 2 (AR2), requires extracellular glutamate, while another (AR3) requires extracellular arginine. Little is known about how these systems protect cells from acid stress. AR2 and AR3 are thought to consume intracellular protons through amino acid decarboxylation. Antiport mechanisms then exchange decarboxylation products for new amino acid substrates. This form of proton consumption could maintain an internal pH (pHi) conducive to cell survival. The model was tested by estimating the pHi and transmembrane potential (DeltaPsi) of cells acid stressed at pH 2.5. During acid challenge, glutamate- and arginine-dependent systems elevated pHi from 3.6 to 4.2 and 4.7, respectively. However, when pHi was manipulated to 4.0 in the presence or absence of glutamate, only cultures challenged in the presence of glutamate survived, indicating that a physiological parameter aside from pHi was also important. Measurements of DeltaPsi indicated that amino acid-dependent acid resistance systems help convert membrane potential from an inside negative to inside positive charge, an established acidophile strategy used to survive extreme acidic environments. Thus, reversing DeltaPsi may be a more important acid resistance strategy than maintaining a specific pHi value.

Cardiolipins and biomembrane function

Evidence is discussed for roles of cardiolipins in oxidative phosphorylation mechanisms that regulate State 4 respiration by returning ejected protons across and over bacterial and mitochondrial membrane phospholipids, and that regulate State 3 respiration through the relative contributions of proteins that transport protons, electrons and/or metabolites. The barrier properties of phospholipid bilayers support and regulate the slow proton leak that is the basis for State 4 respiration. Proton permeability is in the range 10(-3)-10(-4) cm s-1 in mitochondria and in protein-free membranes formed from extracted mitochondrial phospholipids or from stable synthetic phosphatidylcholines or phosphatidylethanolamines. The roles of cardiolipins in proton conductance in model phospholipid membrane systems need to be assessed in view of new findings by Hübner et al. [313]: saturated cardiolipins form bilayers whilst natural highly unsaturated cardiolipins form nonlamellar phases. Mitochondrial cardiolipins apparently participate in bilayers formed by phosphatidylcholines and phosphatidylethanolamines. It is not yet clear if cardiolipins themselves conduct protons back across the membrane according to their degree of fatty acyl saturation, and/or modulate proton conductance by phosphatidylcholines and phosphatidylethanolamines. Mitochondrial cardiolipins, especially those with high 18:2 acyl contents, strongly bind many carrier and enzyme proteins that are involved in oxidative phosphorylation, some of which contribute to regulation of State 3 respiration. The role of cardiolipins in biomembrane protein function has been examined by measuring retained phospholipids and phospholipid binding in purified proteins, and by reconstituting delipidated proteins. The reconstitution criterion for the significance of cardiolipin-protein interactions has been catalytical activity; proton-pumping and multiprotein interactions have yet to be correlated. Some proteins, e.g., cytochrome c oxidase are catalytically active when dimyristoylphosphatidylcholine replaces retained cardiolipins. Cardiolipin-protein interactions orient membrane proteins, matrix proteins, and on the outerface receptors, enzymes, and some leader peptides for import; activate enzymes or keep them inactive unless the inner membrane is disrupted; and modulate formation of nonbilayer HII-phases. The capacity of the proton-exchanging uncoupling protein to accelerate thermogenic respiration in brown adipose tissue mitochondria of cold-adapted animals is not apparently affected by the increased cardiolipin unsaturation; this protein seems to take over the protonophoric role of cardiolipins in other mitochondria. Many in vivo influences that affect proton leakage and carrier rates selectively alter cardiolipins in amount per mitochondrial phospholipids, in fatty acyl composition and perhaps in sidedness; other mitochondrial membrane phospholipids respond less or not at all.(ABSTRACT TRUNCATED AT 400 WORDS)

Tracking of proton flow during transition from anaerobiosis to steady state. 1. Response of matrix pH indicators

1. The kinetics of acidification and realkalinization of the matrix after addition of nigericin to respiring and non-respiring mitochondria, recorded by intramitochondrial pH indicators such as neutral red and 2',7'-bis(carboxyethyl)-5(6)-carboxyfluorescein (BCECF), is complementary to that recorded by extramitochondrial pH indicators. The extent of acidification decreases with the logarithm of the KCl concentration and is inhibited by Pi and ammonium ions. 2. Proton translocation during respiration has been compared with proton extraction from matrix bulk water. During oxygen pulses to EGTA-untreated mitochondria, BCECF records an extraction of protons from matrix bulk water of about 2-3 nmol H+/mg, reduced to 1-2 nmol H+/mg in EGTA-treated mitochondria. Since the amount of proton translocation required to achieve steady state is of the order of 6-7 nmol H+/mg, it appears that 75-90% of the protons are not extracted from matrix bulk water. Only a slight response is recorded by neutral red. 3. The effect of permeant cations and of uncouplers on the distribution of proton extraction between membrane and matrix bulk water has been studied in presteady state. During Sr2+ uptake, proton extrusion into cytosolic bulk water, as well as proton extraction from matrix bulk water, corresponds almost to 100% of the protons translocated by the redox proton pumps. In the absence of Sr2+, parallel to the disappearance of the proton extrusion in cytosolic bulk water, the proton extraction from matrix bulk water diminishes to about 20% of the proton translocation. 4. The mechanism by which divalent cation uptake and protonophoric uncouplers affect the distribution of proton extraction between matrix bulk water and membrane domains and the nature of the membrane domains are discussed.

Tracking of proton flow during transition from anaerobiosis to steady state in rat liver mitochondria

(1) The hydrophobic pH indicator Bromthymol blue and the hydrophilic pH indicator Phenol red have been used to follow the redox-pump-linked proton flows during transition from anaerobiosis to static head. The domains monitored by the pH indicators, whether external or internal, and the localization of the dye, whether free or membrane bound, have been identified by recording the absorbance changes following addition of nigericin or valinomycin to anaerobic or aerobic mitochondria and the effects of permeant and impermeant buffers. (2) After addition of the H+/K+ exchanger, nigericin, to anaerobic mitochondria. Phenol red and Bromthymol blue record an alkalinization and an acidification, respectively, indicating that while the hydrophilic pH indicator faces an external domain, the hydrophobic pH indicator faces, at least partly, an internal domain. The latter effect is sensitive to phosphate and to phosphate carrier inhibitors. On the other hand, addition of nigericin to aerobic mitochondria leads to an increased Bromthymol blue absorbance, which reflects an alkalinization, indicating that the pH indicator faces an external domain. The reorientation of the dye from the internal to the external domain is a function of the uncoupler concentration and thus of the membrane potential (cf. Mitchell et al. (1968) Eur. J. Biochem. 4, 9-19). (3) The amount of oxygen required for the transition from anaerobiosis to static head has been determined by following in parallel the extent of oxidation of cytochrome aa3 and the rise of delta mu H+. With succinate as substrate, 50% levels of cytochrome oxidation are obtained at 0.125 ngatom oxygen/mg and 50% of Safranine response at about 0.2 ngatom oxygen/mg. These amounts of oxygen correspond to an H+ displacement of about 0.8-1.2 ngatom/mg on the basis of the H+/O stoichiometry. It is concluded that mitochondria are in presteady state below, and in static head above, displacement of 2-3 ngatom H+/mg. This figure is very close to the original calculation of Mitchell (Mitchell, P. (1966) Biol. Rev. 41, 445-502). (4) Transition, by oxygen pulses, of EGTA-supplemented mitochondria from anaerobiosis to either presteady state or static head state results in a response of the hydrophilic pH indicator, Phenol red, which is negligible in amount and/or kinetically unrelated to the delta mu H+ rise. The fact that H+ extrusion in the bulk aqueous phase is negligible also in presteady state excludes proton cycling as an explanation. Addition of oxygen pulses to Sr2(+)-supplemented anaerobic mitochondria results in an H+ extrusion whose amount and rate is proportional to the Sr2+ concentration.(ABSTRACT TRUNCATED AT 400 WORDS)

Opioids stimulate sarcolemmal NAD(P)H-vanadate dehydrogenase activity

The present study demonstrates that the bovine cardiac sarcolemma possesses an NAD(P)H dehydrogenase activity which is able to oxidize both NADH and NAD(P)H in the presence of vanadate as an electron acceptor. The NADH dehydrogenase activity was significantly higher than the NAD(P)H dehydrogenase activity and both of them were almost completely inhibited by superoxide dismutase and atebrin and markedly reduced by the addition of the protonophore 2,4-dinitrophenol. The incubation of the sarcolemma in the presence of 10(-10), 10(-9), 10(-8) M methionine-enkephalin, a prevalent delta-opioid receptor agonist, or dynorphin A (1-17), a prevalent kappa-receptor agonist, produced a dose-dependent increase in the NAD(P)H dehydrogenase activity, with 10(-10) and 10(-9) M dynorphin A (1-17) more effective than the corresponding doses of methionine-enkephalin. The preincubation of the sarcolemma in the presence of superoxide-dismutase, atebrin or 2,4-dinitrophenol strongly inhibited the opioid-stimulated dehydrogenase activity. The stimulatory action elicited by 10(-8) M methionine-enkephalin or dynorphin A (1-17) was completely antagonized by 10(-8) M naloxone or Mr 1452, respectively, whilst 10(-8) M naloxone exerted only a partially antagonistic action against the effect produced by 10(-8) M dynorphin A (1-17), significantly more accentuated than the action of 10(-8) M Mr 1452 versus the same dose of methionine-enkephalin.

A minimal hypothesis for membrane-linked free-energy transduction. The role of independent, small coupling units

Experimental data are reviewed that are not in keeping with the scheme of 'delocalized' protonic coupling in membrane-linked free-energy transduction. It turns out that there are three main types of anomalies: (i) rates of electron transfer and of ATP synthesis do not solely depend on their own driving force and on delta mu H, (ii) the ('static head') ratio of delta Gp to delta mu H varies with delta mu H and (iii) inhibition of either some of the electron-transfer chains or some of the H+-ATPases, does not cause an overcapacity in the other, non-inhibited proton pumps. None of the earlier free-energy coupling schemes, alternative to delocalized protonic coupling, can account for these three anomalies. We propose to add a fifth postulate, namely that of the coupling unit, to the four existing postulates of 'delocalized protonic coupling' and show that, with this postulate, protonic coupling can again account for most experimental observations. We also discuss: (i) how experimental data that might seem to be at odds with the 'coupling unit' hypothesis can be accounted for and (ii) the problem of the spatial arrangement of the electrical field in the different free-energy coupling schemes.

On the effects of thiocyanate and venturicidin on respiration-driven proton translocation in Paracoccus denitrificans

A fast-responding O2 electrode has been used to confirm and extend observations of a significant kinetic discrepancy between O2 reduction and consequent proton translocation in 'O2-pulse' experiments in intact cells of P. denitrificans. The permeant, chaotropic SCN- ion abolishes this discrepancy, and greatly increases the observable----H+/O ratio, to a value approaching its accepted, true, limiting stoichiometry. The observable H+ decay rates are very slow, particularly in the absence of SCN-. The submaximal----H+/O ratios observed in the absence of SCN- are essentially independent of the size of the O2 pulse, in a manner not easily explained by a delocalised chemiosmotic energy-coupling scheme. Osmotically active protoplasts of P. denitrificans do not show a significant kinetic discrepancy between O2 reduction and H+ translocation, even in the the absence of SCN-. However, the submaximal----H+/O ratios observed in the absence of SCN- are again essentially independent of the size of the O2 pulse. As in intact cells, the observable H+ decay rates are very slow. The energy-transfer inhibitor venturicidin causes a significant increase in the----H+/O ratio observed in protoplasts of P. denitrificans in the absence of SCN-; the decay kinetics of the H+ translocation process are also somewhat modified. Nevertheless, the----H+/O ratio observed in the presence of venturicidin is also independent of the size of the O2 pulse. This observation militates further against arguments in which (a) a non-ohmic leak of protons from the bulk aqueous phase might alone be the cause of the low----H+/O ratios observed in the absence of SCN-, and (b) in which there might be a delta p-dependent change ('redox slip') in the actual----H+/O ratio. It is concluded that the observable protonmotive activity of the respiratory chain of P. denitrificans in the absence of SCN- is directly influenced by the state of the H+-ATP synthetase in the cytoplasmic membrane of this organism. We are unable to explain the data in terms of a model in which the putative protonmotive force may be acting to affect the----H+/O ratio. The possibility is considered that the delocalised bulk-to-bulk phase membrane potential set up in response to protonmotive activity is energetically insignificant.

Bacteriorhodopsin in liposomes. I. A description using irreversible thermodynamics

A comprehensive description of light-induced ion transport in bacteriorhodopsin liposomes is presented. Linear irreversible thermodynamics and the chemiosmotic theory serve as theoretical bases for the formulation of a limited number of fundamental equations. In these equations mechanistic parameters characterize the dependence of ion movement and flux through the photochemical cycle of bacteriorhodopsin on electrochemical potential differences and a so-called light affinity. By making appropriate steady-state assummptions and carrying out mathematical reduction experimentally testable expressions, still containing the mechanistic parameters, are obtained. In the accompanying article rigid trials to falsify these expressions are shown to be unsuccessful.

Respiration-linked proton transport, changes in external pH, and membrane energization in cells of Escherichia coli

The kinetics of respiration-dependent proton efflux and membrane energization have been studied in intact cells of logarithmic-phase Escherichia coli. Parallel measurements of the rate and extent of proton efflux into the external medium (half-time, about 10 s; ratio of H(+) to O, about 0.5) and the oxidation of E. coli cytochrome b (half-time, </=1 s; about 6% oxidized) after a pulse of 5.5 ng-atoms of O indicate that the rate of proton efflux is at least 10 times slower than expected from the time required for the cells to reduce the oxygen added in the pulse. The kinetics of formation and dissipation of the transmembrane electric potential (deltapsi) after an O(2) pulse were estimated from changes in the fluorescence properties of the cell envelope-bound probe N-phenyl-1-naphthylamine. Under anaerobic conditions, a small pulse of oxygen induced a rapid (half-time, </=1 s) partial decrease in the fluorescence intensity of the probe, followed by a slower relaxation of the fluorescence change to the original intensity. The extent of the initial rapid decrease was linearly dependent upon the amount of oxygen added in the pulse (0 to 11 ng-atoms of O per pulse), whereas the rate of the subsequent relaxation was accelerated by the uncoupler p-trifluoromethoxycarbonylcyanidephenylhydrazone and the K(+) ionophore colicin E1. This suggests that the initial fluorescence decrease after an O(2) pulse reflects the energization of the membrane, whereas the relaxation of the fluorescence decrease reflects the subsequent deenergization of the membrane arising from counterion redistributions. The fact that the efflux of H(+) into the external medium after an O(2) pulse was inefficient and much slower (half-time, about 10 s) than the reduction of the added O(2) (half-time, </=1 s) and the energization of the membrane (half-time </=1 s) suggests that some of the protons translocated across the cytoplasmic membrane during a brief pulse of respiratory activity are accumulated in a region of the cell which is not in rapid equilibrium with the external medium.