Functional production of the Na+ F1FO ATP synthase from Acetobacterium woodii in Escherichia coli requires the native AtpI

The Na⁺ F₁F_O ATP synthase of the anaerobic, acetogenic bacterium Acetobacterium woodii has a unique F_OV_O hybrid rotor that contains nine copies of a F_O-like c subunit and one copy of a V_O-like c ₁ subunit with one ion binding site in four transmembrane helices whose cellular function is obscure. Since a genetic system to address the role of different c subunits is not available for this bacterium, we aimed at a heterologous expression system. Therefore, we cloned and expressed its Na⁺ F₁F_O ATP synthase operon in Escherichia coli. A Δatp mutant of E. coli produced a functional, membrane-bound Na⁺ F₁F_O ATP synthase that was purified in a single step after inserting a His₆-tag to its β subunit. The purified enzyme was competent in Na⁺ transport and contained the F_OV_O hybrid rotor in the same stoichiometry as in A. woodii. Deletion of the atpI gene from the A. woodii operon resulted in a loss of the c ring and a mis-assembled Na⁺ F₁F_O ATP synthase. AtpI from E. coli could not substitute AtpI from A. woodii. These data demonstrate for the first time a functional production of a F_OV_O hybrid rotor in E. coli and revealed that the native AtpI is required for assembly of the hybrid rotor.     

Fluid Mechanical Matching of H-ATP Synthase Subunit c-Ring with Lipid Membranes Revealed by H Solid-State NMR

The F₁F_o-ATP synthase utilizes the transmembrane H⁺ gradient for the synthesis of ATP. F_o subunit c-ring plays a key role in transporting H⁺ through F_o in the membrane. We investigated the interactions of Escherichia coli subunit c with dimyristoylphosphatidylcholine (DMPC-d₅₄) at lipid/protein ratios of 50:1 and 20:1 by means of ²H-solid-state NMR. In the liquid-crystalline state of DMPC, the ²H-NMR moment values and the order parameter (S_CD) profile were little affected by the presence of subunit c, suggesting that the bilayer thickness in the liquid-crystalline state is matched to the transmembrane hydrophobic surface of subunit c. On the other hand, hydrophobic mismatch of subunit c with the lipid bilayer was observed in the gel state of DMPC. Moreover, the viscoelasticity represented by a square-law function of the ²H-NMR relaxation was also little influenced by subunit c in the fluid phase, in contrast with flexible nonionic detergents or rigid additives. Thus, the hydrophobic matching of the lipid bilayer to subunit c involves at least two factors, the hydrophobic length and the fluid mechanical property. These findings may be important for the torque generation in the rotary catalytic mechanism of the F₁F_o-ATPse molecular motor.     

Structural model of the transmembrane Fo rotary sector of H-transporting ATP synthase derived by solution NMR and intersubunit cross-linking in situ

H⁺-transporting, F₁F_o-type ATP synthases utilize a transmembrane H⁺ potential to drive ATP formation by a rotary catalytic mechanism. ATP is formed in alternating β subunits of the extramembranous F₁ sector of the enzyme, synthesis being driven by rotation of the γ subunit in the center of the F₁ molecule between the alternating catalytic sites . The H⁺ electrochemical potential is thought to drive γ subunit rotation by first coupling H⁺ transport to rotation of an oligomeric rotor of c subunits within the transmembrane F_o sector. The γ subunit is forced to turn with the c-oligomeric rotor due to connections between subunit c and the γ and ε subunits of F₁. In this essay we will review recent studies on the Escherichia coli F_o sector. The monomeric structure of subunit c, determined by NMR, shows that subunit c folds in a helical hairpin with the proton carrying Asp⁶¹ centered in the second transmembrane helix (TMH). A model for the structural organization of the c₁₀ oligomer in F_o was deduced from extensive cross-linking studies and by molecular modeling. The model indicates that the H⁺-carrying carboxyl of subunit c is occluded between neighboring subunits of the c₁₀ oligomer and that two c subunits pack in a “front-to-back” manner to form the H⁺ (cation) binding site. In order for protons to gain access to Asp⁶¹ during the protonation/deprotonation cycle, we propose that the outer, Asp⁶¹-bearing TMH-2s of the c-ring and TMHs from subunits composing the inlet and outlet channels must turn relative to each other, and that the swiveling motion associated with Asp⁶¹ protonation/deprotonation drives the rotation of the c-ring. The NMR structures of wild-type subunit c differs according to the protonation state of Asp⁶¹. The idea that the conformational state of subunit c changes during the catalytic cycle is supported by the cross-linking evidence in situ, and two recent NMR structures of functional mutant proteins in which critical residues have been switched between TMH-1 and TMH-2. The structural information is considered in the context of the possible mechanism of rotary movement of the c₁₀ oligomer during coupled synthesis of ATP.     

Mutational analysis of a conserved positive charge in the c-ring of E. coli ATP synthase

F₁F_o ATP synthase is a ubiquitous molecular motor that utilizes a rotary mechanism to synthesize adenosine triphosphate (ATP), the fundamental energy currency of life. The membrane-embedded F_o motor converts the electrochemical gradient of protons into rotation, which is then used to drive the conformational changes in the soluble F₁ motor that catalyze ATP synthesis. In E. coli, the F_o motor is composed of a c₁₀ ring (rotor) alongside subunit a (stator), which together provide two aqueous half channels that facilitate proton translocation. Previous work has suggested that Arg50 and Thr51 on the cytoplasmic side of each subunit c are involved in the proton translocation process, and positive charge is conserved in this region of subunit c. To further investigate the role of these residues and the chemical requirements for activity at these positions, we generated 13 substitution mutants and assayed their in vitro ATP synthesis, H⁺ pumping, and passive H⁺ permeability activities, as well as the ability of mutants to carry out oxidative phosphorylation in vivo. While polar and hydrophobic mutations were generally tolerated in either position, introduction of negative charge or removal of polarity caused a substantial defect. We discuss the possible effects of altered electrostatics on the interaction between the rotor and stator, water structure in the aqueous channel, and interaction of the rotor with cardiolipin.     

Active-Site Structure of the Thermophilic Foc-Subunit Ring in Membranes Elucidated by Solid-State NMR

F_oF₁-ATP synthase uses the electrochemical potential across membranes or ATP hydrolysis to rotate the F_oc-subunit ring. To elucidate the underlying mechanism, we carried out a structural analysis focused on the active site of the thermophilic c-subunit (TF_oc) ring in membranes with a solid-state NMR method developed for this purpose. We used stereo-array isotope labeling (SAIL) with a cell-free system to highlight the target. TF_oc oligomers were purified using a virtual ring His tag. The membrane-reconstituted TF_oc oligomer was confirmed to be a ring indistinguishable from that expressed in E. coli on the basis of the H⁺-translocation activity and high-speed atomic force microscopic images. For the analysis of the active site, 2D ¹³C-¹³C correlation spectra of TF_oc rings labeled with SAIL-Glu and -Asn were recorded. Complete signal assignment could be performed with the aid of the C^α_i+1-C^α_i correlation spectrum of specifically ¹³C,¹⁵N-labeled TF_oc rings. The C^δ chemical shift of Glu-56, which is essential for H⁺ translocation, and related crosspeaks revealed that its carboxyl group is protonated in the membrane, forming the H⁺-locked conformation with Asn-23. The chemical shift of Asp-61 C^γ of the E. coli c ring indicated an involvement of a water molecule in the H⁺ locking, in contrast to the involvement of Asn-23 in the TF_oc ring, suggesting two different means of proton storage in the c rings.     

Half channels mediating H transport and the mechanism of gating in the Fo sector of Escherichia coli F1Fo ATP synthase

H⁺-transporting F₁F_o ATP synthase catalyzes the synthesis of ATP via coupled rotary motors within F_o and F₁. H⁺ transport at the subunit a–c interface in trans-membranous F_o drives rotation of the c-ring within the membrane, with subunit c being bound in a complex with the γ and ε subunits extending from the membrane. Finally, the rotation of subunit γ within the α₃β₃ sector of F₁ mechanically drives ATP synthesis within the catalytic sites. In this review, we propose and provide evidence supporting the route of proton transfer via half channels from one side of the membrane to the other, and the mechanism of gating H⁺ binding to and release from Asp61 of subunit c, via conformational movements of Arg210 in subunit a. We propose that protons are gated from the inside of a four-helix bundle at the periplasmic side of subunit a to drive protonation of cAsp61, and that this gating movement is facilitated by the swiveling of trans-membrane helices (TMHs) 4 and 5 at the site of interaction with cAsp61 on the periphery of the c-ring. Proton release to the cytoplasmic half channel is facilitated by the movement of aArg210 as a consequence of this proposed helical swiveling. Finally, release from the cytoplasmic half channel is mediated by residues in a complex of interacting extra-membraneous loops formed between TMHs of both subunits a and c. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.     

Active-Site Structure of the Thermophilic Foc-Subunit Ring in Membranes Elucidated by Solid-State NMR

F_oF₁-ATP synthase uses the electrochemical potential across membranes or ATP hydrolysis to rotate the F_oc-subunit ring. To elucidate the underlying mechanism, we carried out a structural analysis focused on the active site of the thermophilic c-subunit (TF_oc) ring in membranes with a solid-state NMR method developed for this purpose. We used stereo-array isotope labeling (SAIL) with a cell-free system to highlight the target. TF_oc oligomers were purified using a virtual ring His tag. The membrane-reconstituted TF_oc oligomer was confirmed to be a ring indistinguishable from that expressed in E. coli on the basis of the H⁺-translocation activity and high-speed atomic force microscopic images. For the analysis of the active site, 2D ¹³C-¹³C correlation spectra of TF_oc rings labeled with SAIL-Glu and -Asn were recorded. Complete signal assignment could be performed with the aid of the C^α_i+1-C^α_i correlation spectrum of specifically ¹³C,¹⁵N-labeled TF_oc rings. The C^δ chemical shift of Glu-56, which is essential for H⁺ translocation, and related crosspeaks revealed that its carboxyl group is protonated in the membrane, forming the H⁺-locked conformation with Asn-23. The chemical shift of Asp-61 C^γ of the E. coli c ring indicated an involvement of a water molecule in the H⁺ locking, in contrast to the involvement of Asn-23 in the TF_oc ring, suggesting two different means of proton storage in the c rings.     

Model of the c-subunit oligomer in the membrane domain of F-ATPases

A model is described of a dodecameric complex consisting of the integral membrane component subunit c of the H⁺-transporting F_o domain of Escherichia coli F-ATPase. A high-resolution partial structure of monomeric subunit c resulting from ¹H-NMR studies [1] was used for constructing the model. The validity of the proposed arrangement of protomers in the dodecameric complex was tested by amino acid substitution analysis and chemical, biochemical and genetic data on subunit c.     

Obstruction of Transmembrane Helical Movements in Subunit a Blocks Proton Pumping by F1Fo ATP Synthase

Subunit a plays a key role in promoting H⁺ transport-coupled rotary motion of the subunit c ring in F₁F_o ATP synthase. H⁺ binding and release occur at Asp-61 in the middle of the second transmembrane helix (TMH) of F_o subunit c. H⁺ are thought to reach cAsp61 via aqueous half-channels formed by TMHs 2–5 of subunit a. Movements of TMH4 and TMH5 have been proposed to facilitate protonation of cAsp61 from a half channel centered in a four helix bundle at the periplasmic side of subunit a. The possible necessity of these proposed TMH movements was investigated by assaying ATP driven H⁺ pumping function before and after cross-linking paired Cys substitutions at the center of TMHs within subunit a. The cross-linking of the Cys pairs aG218C/I248C in TMH4 and TMH5, and aL120C/H245C in TMH2 and TMH5, inhibited H⁺ pumping by 85–90%. H⁺ pumping function was largely unaffected by modification of the same Cys residues in the absence of cross-link formation. The inhibition is consistent with the proposed requirement for TMH movements during the gating of periplasmic H⁺ access to cAsp61. The cytoplasmic loops of subunit a have been implicated in gating H⁺ release to the cytoplasm, and previous cross-linking experiments suggest that the chemically reactive regions of the loops may pack as a single domain. Here we show that Cys substitutions in these domains can be cross-linked with retention of function and conclude that these domains need not undergo large conformational changes during enzyme function.     

Essential arginine in subunit a and aspartate in subunit c of FoF1 ATP synthase: Effect of repositioning within Helix 4 of subunit a and Helix 2 of subunit c

F_oF₁ ATP synthase couples proton flow through the integral membrane portion F_o (ab₂c₁₀) to ATP-synthesis in the extrinsic F₁-part ((αβ)₃γδε) (Escherichia coli nomenclature and stoichiometry). Coupling occurs by mechanical rotation of subunits c₁₀γε relative to (αβ)₃δab₂. Two residues were found to be essential for proton flow through ab₂c_10, namely Arg₂₁₀ in subunit a (aR210) and Asp₆₁ in subunits c (cD61). Their deletion abolishes proton flow, but “horizontal” repositioning, by anchoring them in adjacent transmembrane helices, restores function. Here, we investigated the effects of “vertical” repositioning aR210, cD61, or both by one helical turn towards the N- or C-termini of their original helices. Other than in the horizontal the vertical displacement changes the positions of the side chains within the depth of the membrane. Mutant aR210A/aN214R appeared to be short-circuited in that it supported proton conduction only through EF₁-depleted EF_o, but not in EF_oEF_1, nor ATP-driven proton pumping. Mutant cD61N/cM65D grew on succinate, retained the ability to synthesize ATP and supported passive proton conduction but apparently not ATP hydrolysis-driven proton pumping.     

ATP synthases: bioinformatic based insights into how their electrochemically driven motor comprised of subunits a and c might serve as a drug target

ATP synthases, widely distributed in bacteria, eukaryotic mitochondria and chloroplasts, are highly conserved multi-subunit complexes. Although the conserved acidic residue in the transmembrane helix of the c subunit functions in H⁺ transport, the surrounding residues differ among species. Such divergence could lead to different regulatory modes since pH-dependent H⁺ transport has been demonstrated in E. coli with a c subunit carrying an additional acidic residue in the helix. There is further divergence in the number of c subunits that form the ring structure which is determined by the higher ordered structure. Recently, it was suggested that certain chemicals recognize the a and c subunits of pathogenic bacterial F₀. Since there may be structural divergence even in well-conserved ATP synthases, the c subunit-ring as well as the a subunit in F₀ could be targets for drugs for specific bacterial species.     

F0 cysteine,bCys21, in the Escherichia coli ATP synthase is involved in regulation of potassium uptake and molecular hydrogen production in anaerobic conditions

The single cysteine in the b subunit of the membranous F₀ sector and the 19 cysteines in extramembranous F₁ sector of the Escherichia coli ATP synthase were replaced by alanine. When cells were grown under anaerobic conditions on glucose, the k _cat for ATP hydrolysis of membrane vesicles containing the bCys21Ala mutant enzyme, but not enzymes with other cysteine replacements, was lower, while ATP-driven H⁺ pumping was unchanged. However, the ATP-dependent increase in the number of accessible thiol groups in membrane vesicles was negated. Furthermore, K⁺ uptake and molecular hydrogen production by whole cells and protoplasts was greatly decreased. These results indicate a role for the F₀ subunit bCys21 in the functionality of F₀F₁ and coupling to other membranous activities under fermentative conditions.     

Specific labelling of the (Ca2+ + Mg2+)-ATPase of Escherichia coli with 8-azido-ATP and 4-chloro-7-nitrobenzofurazan

1. 8-Azido-ATP is a substrate for Escherichia coli (Ca²⁺ + Mg²⁺)-ATPase (E. coli F₁).2. Illumination of E. coli F₁ in the presence of 8-azido-ATP causes inhibition of ATPase activity. The presence of ATP during illumination prevents inhibition.3. 8-Azido-ATP and 4-chloro-7-nitrobenzofurazan (NbfCl) bind predominantly to the α subunit of the enzyme, but also significantly to the β subunit.4. The α subunit of E. coli F₁ seems to have some properties that in other F₁-ATPases are associated with the β subunit.     

The Oligomeric Subunit c Rotor in the Fo Sector of ATP Synthase: Unresolved Questions in Our Understanding of Function

We have proposed a model for the oligomeric c-rotor of the F_o sector of ATP synthase and its interaction with subunit a during H⁺-transport driven rotation. The model is based upon the solution structure of monomeric subunit c, determined by NMR, and an extensive series of cross-linking distance constraints between c subunits and between subunits c and a. To explain the complete set of cross-linking data, we have suggested that the second transmembrane helix rotates during its interaction with subunit a in the course of the H⁺-translocation cycle. The H⁺-transport coupled rotation of this helix is proposed to drive the stepwise movement of the c-oligomeric rotor. The model is testable and provides a useful framework for addressing questions raised by other experiments.     

Structure analysis of membrane-reconstituted subunit <Emphasis Type="Italic">c</Emphasis>-ring of <Emphasis Type="Italic">E. coli</Emphasis> H<Superscript>+</Superscript>-ATP synthase by solid-state NMR

The subunit c-ring of H⁺-ATP synthase (F_o c-ring) plays an essential role in the proton translocation across a membrane driven by the electrochemical potential. To understand its structure and function, we have carried out solid-state NMR analysis under magic-angle sample spinning. The uniformly [¹³C, ¹⁵N]-labeled F_o c from E. coli (EF_o c) was reconstituted into lipid membranes as oligomers. Its high resolution two- and three-dimensional spectra were obtained, and the ¹³C and ¹⁵N signals were assigned. The obtained chemical shifts suggested that EF_o c takes on a hairpin-type helix-loop-helix structure in membranes as in an organic solution. The results on the magnetization transfer between the EF_o c and deuterated lipids indicated that Ile55, Ala62, Gly69 and F76 were lined up on the outer surface of the oligomer. This is in good agreement with the cross-linking results previously reported by Fillingame and his colleagues. This agreement reveals that the reconstituted EF_o c oligomer takes on a ring structure similar to the intact one in vivo. On the other hand, analysis of the ¹³C nuclei distance of [3-¹³C]Ala24 and [4-¹³C]Asp61 in the F_o c-ring did not agree with the model structures proposed for the EF_o c-decamer and dodecamer. Interestingly, the carboxyl group of the essential Asp61 in the membrane-embedded EF_o c-ring turned out to be protonated as COOH even at neutral pH. The hydrophobic surface of the EF_o c-ring carries relatively short side chains in its central region, which may allow soft and smooth interactions with the hydrocarbon chains of lipids in the liquid-crystalline state.     

Mechanism of Inhibition by C-terminal α-Helices of the ? Subunit of Escherichia coli FoF1-ATP Synthase

The ϵ subunit of bacterial F_oF₁-ATP synthase (F_oF₁), a rotary motor protein, is known to inhibit the ATP hydrolysis reaction of this enzyme. The inhibitory effect is modulated by the conformation of the C-terminal α-helices of ϵ, and the “extended” but not “hairpin-folded” state is responsible for inhibition. Although the inhibition of ATP hydrolysis by the C-terminal domain of ϵ has been extensively studied, the effect on ATP synthesis is not fully understood. In this study, we generated an Escherichia coli F_oF₁ (EF_oF₁) mutant in which the ϵ subunit lacked the C-terminal domain (F_oF₁^ϵΔC), and ATP synthesis driven by acid-base transition (ΔpH) and the K⁺-valinomycin diffusion potential (ΔΨ) was compared in detail with that of the wild-type enzyme (F_oF₁^ϵWT). The turnover numbers (k_cat) of F_oF₁^ϵWT were severalfold lower than those of F_oF₁^ϵΔC. F_oF₁^ϵWT showed higher Michaelis constants (K_m). The dependence of the activities of F_oF₁^ϵWT and F_oF₁^ϵΔC on various combinations of ΔpH and ΔΨ was similar, suggesting that the rate-limiting step in ATP synthesis was unaltered by the C-terminal domain of ϵ. Solubilized F_oF₁^ϵWT also showed lower k_cat and higher K_m values for ATP hydrolysis than the corresponding values of F_oF₁^ϵΔC. These results suggest that the C-terminal domain of the ϵ subunit of EF_oF₁ slows multiple elementary steps in both the ATP synthesis/hydrolysis reactions by restricting the rotation of the γ subunit.     

On the Structure of the Proton-Binding Site in the Fo Rotor of Chloroplast ATP Synthases

The recently reported crystal structures of the membrane-embedded proton-dependent c-ring rotors of a cyanobacterial F₁F_o ATP synthase and a chloroplast F₁F_o ATP synthase have provided new insights into the mechanism of this essential enzyme. While the overall features of these c-rings are similar, a discrepancy in the structure and hydrogen-bonding interaction network of the H⁺ sites suggests two distinct binding modes, potentially reflecting a mechanistic differentiation. Importantly, the conformation of the key glutamate side chain to which the proton binds is also altered. To investigate the nature of these differences, we use molecular dynamics simulations of both c-rings embedded in a phospholipid membrane. We observe that the structure of the c₁₅ ring from Spirulina platensis is unequivocally stable within the simulation time. By contrast, the proposed structure of the H⁺ site in the chloroplast c₁₄ ring changes rapidly and consistently into that reported for the c₁₅ ring, indicating that the latter represents a common binding mode. To assess this hypothesis, we have remodeled the c₁₄ ring by molecular replacement using the published structure factors. The resulting structure provides clear evidence in support of a common binding site conformation and is also considerably improved statistically. These findings, taken together with a sequence analysis of c-subunits in the ATP synthase family, indicate that the so-called proton-locked conformation observed in the c₁₅ ring may be a common characteristic not only of light-driven systems such as chloroplasts and cyanobacteria but also of a selection of other bacterial species.     

Residues in the Polar Loop of Subunit c in Escherichia coli ATP Synthase Function in Gating Proton Transport to the Cytoplasm

Rotary catalysis in F₁F₀ ATP synthase is powered by proton translocation through the membrane-embedded F₀ sector. Proton binding and release occur in the middle of the membrane at Asp-61 on the second transmembrane helix (TMH) of subunit c, which folds in a hairpin-like structure with two TMHs. Previously, the aqueous accessibility of Cys substitutions in the transmembrane regions of subunit c was probed by testing the inhibitory effects of Ag⁺ or Cd²⁺ on function, which revealed extensive aqueous access in the region around Asp-61 and on the half of TMH2 extending to the cytoplasm. In the current study, we surveyed the Ag⁺ and Cd²⁺ sensitivity of Cys substitutions in the loop of the helical hairpin and used a variety of assays to categorize the mechanisms by which Ag⁺ or Cd²⁺ chelation with the Cys thiolates caused inhibition. We identified two distinct metal-sensitive regions in the cytoplasmic loop where function was inhibited by different mechanisms. Metal binding to Cys substitutions in the N-terminal half of the loop resulted in an uncoupling of F₁ from F₀ with release of F₁ from the membrane. In contrast, substitutions in the C-terminal half of the loop retained membrane-bound F₁ after metal treatment. In several of these cases, inhibition was shown to be due to blockage of passive H⁺ translocation through F₀ as assayed with F₀ reconstituted into liposomes. The results suggest that the C-terminal domain of the cytoplasmic loop may function in gating H⁺ translocation to the cytoplasm.     

UncI protein can mediate ring-assembly of c-subunits of FoF1-ATP synthase in vitro

In F_oF₁-ATP synthase, multimeric c-subunits are assembled to a ring (c-ring) in the membranes that rotates as protons flow across F_o. We recently reported that assembly of c-ring of Propionigenium modestum in the membranes of Escherichia coli cells required P. modestum UncI, a product of the conserved uncI gene in the F_oF₁ operon. However, cooperation with endogenous factors in E. coli remained unclear. Here, P. modestum c-subunit was synthesized in vitro in the presence of liposomes. When c-subunit alone was synthesized, it did not form c-ring. However, when c-subunit and P. modestum UncI were synthesized together, c-ring was formed. Fusion of the two kinds of liposomes, one containing only unassembled c-subunit and the other only UncI, resulted in gradual formation of c-ring. Thus, UncI alone can mediate in vitro post-translational c-ring assembly.