Identification of the ubiquinol-binding site in the cytochrome bo3-ubiquinol oxidase of Escherichia coli

Electric wiring of bacteria using redox polymers and selective measurement of metabolic activity in the presence of surrounding planktonic bacteria

Non-electroactive bacteria (n-EAB), constituting the majority of known bacteria to date, have been underutilized in electrochemical conversion technologies due to their lack of direct electron transfer to electrodes. In this study, we established an electric wiring between n-EAB (gram-positive Bacillus subtilis and gram-negative Escherichia coli) and an extracellular electrode via a ferrocene-polyethyleneimine-based redox polymer (Fc-PEI). Chronoamperometry recordings indicated that Fc-PEI can transfer intracellular electrons to the extracellular electrode regardless of the molecular organization of PEI (linear or branched) and the membrane structure of bacteria (gram-positive or -negative). As fluorescence staining suggested, Fc-PEI improves the permeability of the bacterial cell membrane, enabling electron carriers in the cell to react with Fc. In addition, experiments with Fc-immobilized electrodes without PEI suggested the existence of an alternative electron transfer pathway from B. subtilis to the extracellular Fc adsorbed onto the cell membrane. Furthermore, we proposed for the first time that the bacteria/Fc-linear PEI modified structure enables selective measurement of immobilized bacterial activity by physically blocking contact between the electrode surface and planktonic cells co-existing in the surrounding media. Such electrodes can be a powerful analytical tool for elucidating the metabolic activities of specific bacteria wired to the electrode even within complex bacterial communities.

Cryo-EM structure of cytochrome bo3 quinol oxidase assembled in peptidiscs reveals an "open" conformation for potential ubiquinone-8 release

Cytochrome bo3 quinol oxidase belongs to the heme‑copper-oxidoreductase (HCO) superfamily, which is part of the respiratory chain and essential for cell survival. While the reaction mechanism of cyt bo3 has been studied extensively over the last decades, specific details about its substrate binding and product release have remained unelucidated due to the lack of structural information. Here, we report a 2.8 Å cryo-electron microscopy structure of cyt bo3 from Escherichia coli assembled in peptidiscs. Our structural model shows a conformation for amino acids 1-41 of subunit I different from all previously published structures while the remaining parts of this enzyme are similar. Our new conformation shows a "U-shape" assembly in contrast to the transmembrane helix, named "TM0", in other reported structural models. However, TM0 blocks ubiquinone-8 (reaction product) release, suggesting that other cyt bo3 conformations should exist. Our structural model presents experimental evidence for an "open" conformation to facilitate substrate/product exchange. This work helps further understand the reaction cycle of this oxidase, which could be a benefit for potential drug/antibiotic design for health science.

Synthesis and Biological Screening of New Lawson Derivatives as Selective Substrate-Based Inhibitors of Cytochrome bo3 Ubiquinol Oxidase from Escherichia coli

The respiratory chain of Escherichia coli contains two different types of terminal oxidase that are differentially regulated as a response to changing environmental conditions. These oxidoreductases catalyze the reduction of molecular oxygen to water and contribute to the proton motive force. The cytochrome bo3 oxidase (cyt bo3 ) acts as the primary terminal oxidase under atmospheric oxygen levels, whereas the bd-type oxidase is most abundant under microaerobic conditions. In E. coli, both types of respiratory terminal oxidase (HCO and bd-type) use ubiquinol-8 as electron donor. Here, we assess the inhibitory potential of newly designed and synthesized 3-alkylated Lawson derivatives through L-proline-catalyzed three-component reductive alkylation (TCRA). The inhibitory effects of these Lawson derivatives on the terminal oxidases of E. coli (cyt bo3 and cyt bd-I) were tested potentiometrically. Four compounds were able to reduce the oxidoreductase activity of cyt bo3 by more than 50 % without affecting the cyt bd-I activity. Moreover, two inhibitors for both cyt bo3 and cyt bd-I oxidase could be identified. Based on molecular-docking simulations, we propose binding modes of the new Lawson inhibitors. The molecular fragment benzyl enhances the inhibitory potential and selectivity for cyt bo3 , whereas heterocycles reduce this effect. This work extends the library of 3-alkylated Lawson derivatives as selective inhibitors for respiratory oxidases and provides molecular probes for detailed investigations of the mechanisms of respiratory-chain enzymes of E. coli.

Location of the Substrate Binding Site of the Cytochrome bo3 Ubiquinol Oxidase from Escherichia coli

Cytochrome bo₃ is a respiratory proton-pumping oxygen reductase that is a member of the heme-copper superfamily that utilizes ubiquinol-8 (Q₈H₂) as a substrate. The current consensus model has Q₈H₂ oxidized at a low affinity site (Q_L), passing electrons to a tightly bound quinone cofactor at a high affinity site (Q_H site) that stabilizes the one-electron reduced ubisemiquinone, facilitating the transfer of electrons to the redox active metal centers where O₂ is reduced to water. The current work shows that the Q₈ bound to the Q_H site is more dynamic than previously thought. In addition, mutations of residues at the Q_H site that do not abolish activity have been re-examined and shown to have properties expected of mutations at the substrate binding site (Q_L): an increase in the K_M of the substrate ubiquinol-1 (up to 4-fold) and an increase in the apparent K_i of the inhibitor HQNO (up to 8-fold). The data suggest that there is only one binding site for ubiquinol in cyt bo₃ and that site corresponds to the Q_H site.

Infrared spectroscopic markers of quinones in proteins from the respiratory chain

In bioenergetic systems quinones play a central part in the coupling of electron and proton transfer. The specific function of each quinone binding site is based on the protein-quinone interaction that can be described by means of reaction induced FTIR difference spectroscopy, induced for example by light or electrochemically. The identification of sites in enzymes from the respiratory chain is presented together with the analysis of the accommodation of different types of quinones to the same enzyme and the possibility to monitor the interaction with inhibitors. Reaction induced FTIR difference spectroscopy is shown to give an essential information on the general geometry of quinone binding sites, the conformation of the ring and of the substituents as well as essential structural information on the identity of the amino-acid residues lining this site. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.

A study of cytochrome bo3 in a tethered bilayer lipid membrane

An assay has been developed in which the activity of an ubiquinol oxidase from Escherichia coli, cytochrome bo(3) (cbo(3)), is determined as a function of the hydrophobic substrate ubiquinol-10 (UQ-10) in tethered bilayer lipid membranes (tBLMs). UQ-10 was added in situ, while the enzyme activity and the UQ-10 concentration in the membrane have been determined by cyclic voltammetry. Cbo(3) is inhibited by UQ-10 at concentrations above 5-10 pmol/cm(2), while product inhibition is absent. Cyclic voltammetry has also been used to characterise the effects of three inhibitors; cyanide, inhibiting oxygen reduction; 2-n-Heptyl-4-hydroxyquinoline N-oxide (HQNO), inhibiting the quinone oxidation and Zn(II), thought to block the proton channels required for oxygen reduction and proton pumping activity. The electrochemical behaviour of cbo(3) inhibited with HQNO and Zn(II) is almost identical, suggesting that Zn(II) ions inhibit the enzyme reduction by quinol, rather than oxygen reduction. This suggests that at Zn(II) concentration below 50µM the proton release of cbo(3) is inhibited, but not the proton uptake required to reduce oxygen to water.

The quinone-binding sites of the cytochrome bo3 ubiquinol oxidase from Escherichia coli

Cytochrome bo(3) is the major respiratory oxidase located in the cytoplasmic membrane of Escherichia coli when grown under high oxygen tension. The enzyme catalyzes the 2-electron oxidation of ubiquinol-8 and the 4-electron reduction of dioxygen to water. When solubilized and isolated using dodecylmaltoside, the enzyme contains one equivalent of ubiquinone-8, bound at a high affinity site (Q(H)). The quinone bound at the Q(H) site can form a stable semiquinone, and the amino acid residues which hydrogen bond to the semiquinone have been identified. In the current work, it is shown that the tightly bound ubiquinone-8 at the Q(H) site is not displaced by ubiquinol-1 even during enzyme turnover. Furthermore, the presence of high affinity inhibitors, HQNO and aurachin C1-10, does not displace ubiquinone-8 from the Q(H) site. The data clearly support the existence of a second binding site for ubiquinone, the Q(L) site, which can rapidly exchange with the substrate pool. HQNO is shown to bind to a single site on the enzyme and to prevent formation of the stable ubisemiquinone, though without displacing the bound quinone. Inhibition of the steady state kinetics of the enzyme indicates that aurachin C1-10 may compete for binding with quinol at the Q(L) site while, at the same time, preventing formation of the ubisemiquinone at the Q(H) site. It is suggested that the two quinone binding sites may be adjacent to each other or partially overlap.

Characterization of the semiquinone radical stabilized by the cytochrome aa3-600 menaquinol oxidase of Bacillus subtilis

Cytochrome aa(3)-600 is one of the principle respiratory oxidases from Bacillus subtilis and is a member of the heme-copper superfamily of oxygen reductases. This enzyme catalyzes the two-electron oxidation of menaquinol and the four-electron reduction of O(2) to 2H(2)O. Cytochrome aa(3)-600 is of interest because it is a very close homologue of the cytochrome bo(3) ubiquinol oxidase from Escherichia coli, except that it uses menaquinol instead of ubiquinol as a substrate. One question of interest is how the proteins differ in response to the differences in structure and electrochemical properties between ubiquinol and menaquinol. Cytochrome bo(3) has a high affinity binding site for ubiquinol that stabilizes a ubi-semiquinone. This has permitted the use of pulsed EPR techniques to investigate the protein interaction with the ubiquinone. The current work initiates studies to characterize the equivalent site in cytochrome aa(3)-600. Cytochrome aa(3)-600 has been cloned and expressed in a His-tagged form in B. subtilis. After isolation of the enzyme in dodecylmaltoside, it is shown that the pure enzyme contains 1 eq of menaquinone-7 and that the enzyme stabilizes a mena-semiquinone. Pulsed EPR studies have shown that there are both similarities as well as significant differences in the interactions of the mena-semiquinone with cytochrome aa(3)-600 in comparison with the ubi-semiquinone in cytochrome bo(3). Our data indicate weaker hydrogen bonds of the menaquinone in cytochrome aa(3)-600 in comparison with ubiquinone in cytochrome bo(3). In addition, the electronic structure of the semiquinone cyt aa(3)-600 is more shifted toward the anionic form from the neutral state in cyt bo(3).

Twin arginine translocase pathway and fast-folding lipoprotein biosynthesis in E. coli: interesting implications and applications

Bacterial lipoproteins, an important class of membrane proteins, are generally thought to be translocated in an unfolded state by the well-studied Sec machinery, whereas the role of TAT, meant for folded proteins, is hardly investigated. Using appropriately engineered fast-folding Enhanced Green Fluorescence Protein (EGFP), as a model, here we show that TAT is essential for not only translocating fast-folding lipoprotein but also its lipid modification. EGFP was lipid-modified and targeted to the outer membrane's outer surface with a prototypical TAT signal sequence containing lipobox but not with the lipoprotein or TAT signal sequence. Justifiably signal sequences of many substrate-binding and co-factor-containing lipoproteins contained both TAT-box and lipobox (Shruthi et al., submitted). Cytoplasmic accumulation of unmodified precursors of engineered EGFP in a tatC mutant implicated this TAT-box-recognizing component in lipid-modification. Similar observations reported earlier with Sec components and murein lipoprotein led us to propose that the translocation-competent and translocase-associated (Sec or TAT) precursor form is prerequisite to initiation of lipid-modification in vivo. The above missing links between translocation and lipid modification machineries in vivo is important to our understanding of bacterial lipoprotein biosynthesis and its utility as a protein engineering tool for potent applications in synthetic biology and nanobiotechnology like display, arrays on bacterial surfaces, vaccines and biosensors.

Characterization of cytochrome bo3 activity in a native-like surface-tethered membrane

We have developed a simple native-like surface-tethered membrane system to investigate the activity of cbo(3) (cytochrome bo(3)), a terminal oxidase in Escherichia coli. The tethered membranes consist of E. coli inner-membrane extracts mixed with additional E. coli lipids containing various amounts of the cbo(3) substrate UQ-10 (ubiquinol-10). Tethered membranes are formed by self-assembly from vesicles on to gold electrodes functionalized with cholesterol derivatives. cbo(3) activity was monitored using CV (cyclic voltammetry) with electron transfer to cbo(3) mediated by UQ-10. The apparent K(m) for oxygen with this system is 1.1+/-0.4 microM, in good agreement with values reported in the literature for whole-cell experiments and for purified cbo(3). Increasing the concentration of lipophilic UQ-10 in the membrane leads to an increase in cbo(3) activity. The activity of cbo(3) with long-chain ubiquinones appears to be different from previous reports using short-chain substrate analogues such as UQ-1 in that typical Michaelis-Menten kinetics are not observed using UQ-10. This native-like membrane model thus provides new insights into the interaction of transmembrane enzymes with hydrophobic substrates which contrasts with studies using hydrophilic UQ analogues.

Cytochrome c oxidase: chemistry of a molecular machine

The plethora of proposed chemical models attempting to explain the proton pumping reactions catalyzed by the CcO complex, especially the number of recent models, makes it clear that the problem is far from solved. Although we have not discussed all of the models proposed to date, we have described some of the more detailed models in order to illustrate the theoretical concepts introduced at the beginning of this section on proton pumping as well as to illustrate the rich possibilities available for effecting proton pumping. It is clear that proton pumping is effected by conformational changes induced by oxidation/reduction of the various redox centers in the CcO complex. It is for this reason that the CcO complex is called a redox-linked proton pump. The conformational changes of the proton pump cycle are usually envisioned to be some sort of ligand-exchange reaction arising from unstable geometries upon oxidation/reduction of the various redox centers. However, simple geometrical rearrangements, as in the Babcock and Mitchell models are also possible. In any model, however, hydrogen bonds must be broken and reformed due to conformational changes that result from oxidation/reduction of the linkage site during enzyme turnover. Perhaps the most important point emphasized in this discussion, however, is the fact that proton pumping is a directed process and it is electron and proton gating mechanisms that drive the proton pump cycle in the forward direction. Since many of the models discussed above lack effective electron and/or proton gating, it is clear that the major difficulty in developing a viable chemical model is not formulating a cyclic set of protein conformational changes effecting proton pumping (redox linkage) but rather constructing the model with a set of physical constraints so that the proposed cycle proceeds efficiently as postulated. In our discussion of these models, we have not been too concerned about which electron of the catalytic cycle was entering the site of linkage, but merely whether an ET to the binuclear center played a role. However, redox linkage only occurs if ET to the activated binuclear center is coupled to the proton pump. Since all of the models of proton pumping presented here, with the exception of the Rousseau expanded model and the Wikström model, have a maximum stoichiometry of 1 H+/e-, they inadequately explain the 2 H+/e- ratio for the third and fourth electrons of the dioxygen reduction cycle (see Section V.B). One way of interpreting this shortfall of protons is that the remaining protons are pumped by an as yet undefined indirectly coupled mechanism. In this scenario, the site of linkage could be coupled to the pumping of one proton in a direct fashion and one proton in an indirect fashion for a given electron. For a long time, it was assumed that at least some elements of such an indirect mechanism reside in subunit III. While recent evidence argues against the involvement of subunit III in the proton pump, subunit III may still participate in a regulatory and/or structural capacity (Section II.E). Attention has now focused on subunits I and II in the search for residues intimately involved in the proton pump mechanism and/or as part of a proton channel. In particular, the role of some of the highly conserved residues of helix VIII of subunit I are currently being studied by site directed mutagenesis. In our opinion, any model that invokes heme alpha 3 or CuB as the site of linkage must propose a very effective means by which the presumedly fast uncoupling ET to the dioxygen intermediates is prevented. It is difficult to imagine that ET over the short distance from heme alpha 3 or CuB to the dioxygen intermediate requires more than 1 ns. In addition, we expect the conformational changes of the proton pump to require much more than 1 ns (see Section V.B).

Identification of a ubiquinone-binding site that affects autophosphorylation of the sensor kinase RegB

Rhodobacter capsulatus regulates many metabolic processes in response to the level of environmental oxygen and the energy state of the cell. One of the key global redox regulators of the cell's metabolic physiology is the sensor kinase RegB that controls the synthesis of numerous energy generation and utilization processes. In this study, we have succeeded in purifying full-length RegB containing six transmembrane-spanning elements. Exogenous addition of excess oxidized coenzyme Q1 is capable of inhibiting RegB autophosphorylation approximately 6-fold. However, the addition of reduced coenzyme Q1 exhibits no inhibitory effect on kinase activity. A ubiquinone-binding site, as defined by azidoquinone photo affinity cross-linking, was determined to lie within a periplasmic loop between transmembrane helices 3 and 4 that contains a fully conserved heptapeptide sequence of GGXXNPF. Mutation of the phenylalanine in this heptapeptide renders RegB constitutively active in vivo, indicating that this domain is responsible for sensing the redox state of the ubiquinone pool and subsequently controlling RegB autophosphorylation.

Mass spectrometric analysis of the ubiquinol-binding site in cytochrome bd from Escherichia coli

Cytochrome bd is a heterodimeric terminal ubiquinol oxidase in the aerobic respiratory chain of Escherichia coli. For understanding the unique catalytic mechanism of the quinol oxidation, mass spectrometry was used to identify amino acid residue(s) that can be labeled with a reduced form of 2-azido-3-methoxy-5-methyl-6-geranyl-1,4-benzoquinone or 2-methoxy-3-azido-5-methyl-6-geranyl-1,4-benzoquinone. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry demonstrated that the photo inactivation of ubiquinol-1 oxidase activity was accompanied by the labeling of subunit I with both azidoquinols. The cross-linked domain was identified by reverse-phase high performance liquid chromatography of subunit I peptides produced by in-gel double digestion with lysyl endopeptidase and endoproteinase Asp-N. Electrospray ionization quadrupole time-of-flight mass spectrometry determined the amino acid sequence of the peptide (m/z 1047.5) to be Glu(278)-Lys(283), where a photoproduct of azido-Q(2) was linked to the carboxylic side chain of I-Glu(280). This study demonstrated directly that the N-terminal region of periplasmic loop VI/VII (Q-loop) is a part of the quinol oxidation site and indicates that the 2- and 3-methoxy groups of the quinone ring are in the close vicinity of I-Glu(280).

Transient formation of ubisemiquinone radical and subsequent electron transfer process in the Escherichia coli cytochrome bo

To elucidate a unique mechanism for the quinol oxidation in the Escherichia coli cytochrome bo, we applied pulse radiolysis technique to the wild-type enzyme with or without a single bound ubiquinone-8 at the high-affinity quinone binding site (Q(H)), using N-methylnicotinamide (NMA) as an electron mediator. With the ubiquinone bound enzyme, the reduction of the oxidase occurred in two phases as judged from kinetic difference spectra. In the faster phase, the transient species with an absorption maximum at 440 nm, a characteristic of the formation of ubisemiquinone anion radical, appeared within 10 micros after pulse radiolysis. In the slower phase, a decrease of absorption at 440 nm was accompanied by an increase of absorption at 428 and 561 nm, characteristic of the reduced form. In contrast, with the bound ubiquinone-8-free wild-type enzyme, NMA radicals directly reduced hemes b and o, though the reduction yield was low. These results indicate that a pathway for an intramolecular electron transfer from ubisemiquinone anion radical at the Q(H) site to heme b exists in cytochrome bo. The first-order rate constant of this process was calculated to be 1.5 x 10(3) s(-1) and is comparable to a turnover rate for ubiquinol-1. The rate constant for the intramolecular electron transfer decreased considerably with increasing pH, though the yields of the formation of ubisemiquinone anion radical and the subsequent reduction of the hemes were not affected. The pH profile was tightly linked to the stability of the bound ubisemiquinone in cytochrome bo [Ingledew, W. J., Ohnishi, T., and Salerno, J. C. (1995) Eur. J. Biochem. 227, 903-908], indicating that electron transfer from the bound ubisemiquinone at the Q(H) site to the hemes slows down at the alkaline pH where the bound ubisemiquinone can be stabilized. These findings are consistent with our previous proposal that the bound ubiquinone at the Q(H) site mediates electron transfer from the low-affinity quinol oxidation site in subunit II to low-spin heme b in subunit I.

ENDOR spectroscopic studies of stable semiquinone radicals bound to the Escherichia coli cytochrome bo3 quinol oxidase

The putative oxidation of ubiquinol by the cytochrome bo3 terminal oxidase of Escherichia coli in sequential one-electron steps requires stabilization of the semiquinone. ENDOR spectroscopy has recently been used to study the native ubisemiquinone radical formed in the cytochrome bo3 quinone-binding site [Veselov, A.V., Osborne, J.P., Gennis, R.B. & Scholes, C.P. (2000) Biochemistry 39, 3169-3175]. Comparison of these spectra with those from the decyl-ubisemiquinone radical in vitro indicated that the protein induced large changes in the electronic structure of the ubisemiquinone radical. We have used quinone-substitution experiments to obtain ENDOR spectra of ubisemiquinone, phyllosemiquinone and plastosemiquinone anion radicals bound at the cytochrome bo3 quinone-binding site. Large changes in the electronic structures of these semiquinone anion radicals are induced on binding to the cytochrome bo3 oxidase. The changes in electronic structure are, however, independent of the electronic structures of these semiquinones in vitro. Thus it is shown to be the structure of this binding site in the protein, not the covalent structure of the bound quinone, that determines the electronic structure of the protein-bound semiquinone.

Vibrational modes of ubiquinone in cytochrome bo(3) from Escherichia coli identified by Fourier transform infrared difference spectroscopy and specific (13)C labeling

In this study we present the infrared spectroscopic characterization of the bound ubiquinone in cytochrome bo(3) from Escherichia coli. Electrochemically induced Fourier transform infrared (FTIR) difference spectra of DeltaUbiA (an oxidase devoid of bound ubiquinone) and DeltaUbiA reconstituted with ubiquinone 2 and with isotopically labeled ubiquinone 2, where (13)C was introduced either at the 1- or at the 4-position of the ring (C=O groups), have been obtained. The vibrational modes of the quinone bound to the discussed high-affinity binding site (Q(H)) are compared to those from the synthetic quinones in solution, leading to the assignment of the C=O modes to a split signal at 1658/1668 cm(-)(1), with both carbonyls similarly contributing. The FTIR spectra of DeltaUbiA reconstituted with the labeled quinones indicate an essentially symmetrical and weak hydrogen bonding of the two C=O groups from the neutral quinone with the protein and distinct conformations of the 2- and 3-methoxy groups. Perturbations of the vibrational modes of the 5-methyl side groups are discussed for a signal at 1452 cm(-)(1). Only negligible shifts of the aromatic ring modes can be reported for the reduced and the protonated form of the quinone. Alterations of the protein upon quinone binding are reflected in the electrochemically induced FTIR difference spectra. In particular, difference signals at 1640-1633 cm(-)(1) and 1700-1670 cm(-)(1) indicate variations of beta-sheet secondary structure elements and loops, bands at 1706 and 1678 cm(-)(1) are tentatively attributed to individual amino acids, and a difference signal a 1540 cm(-)(1) is discussed to reflect an influence on C=C modes of the porphyrin ring or on deprotonated propionate groups of the hemes. Further tentative assignments are presented and discussed. The (13)C labeling experiments allow the assignment of the vibrational modes of a bound ubiquinone 8 in the electrochemically induced FTIR difference spectra of wild-type bo(3).

Role of a bound ubiquinone on reactions of the Escherichia coli cytochrome bo with ubiquinol and dioxygen

To probe the functional role of a bound ubiquinone-8 in cytochrome bo-type ubiquinol oxidase from Escherichia coli, we examined reactions with ubiquinol-1 and dioxygen. Stopped-flow studies showed that anaerobic reduction of the wild-type and the bound ubiquinone-free (DeltaUbiA) enzymes with ubiquinol-1 immediately takes place with four kinetic phases. Replacement of the bound ubiquinone with 2,6-dibromo-4-cyanophenol (PC32) suppressed the anaerobic reduction of the hemes with ubiquinol-1 by eliminating the fast phase. Flow-flash studies in the reaction of the fully reduced enzyme with dioxygen showed that the heme b-to-heme o electron transfer occurs with a rate constant of approximately 1x10(4) s(-1) in all three preparations. These results support our previous proposal that the bound ubiquinone is involved in facile oxidation of substrates in subunit II and subsequent intramolecular electron transfer to low-spin heme b in subunit I.

Role of a bound ubiquinone on reactions of the Escherichia coli cytochrome bo with ubiquinol and dioxygen

To probe the functional role of a bound ubiquinone-8 in cytochrome bo-type ubiquinol oxidase from Escherichia coli, we examined reactions with ubiquinol-1 and dioxygen. Stopped-flow studies showed that anaerobic reduction of the wild-type and the bound ubiquinone-free (delta UbiA) enzymes with ubiquinol-1 immediately takes place with four kinetic phases. Replacement of the bound ubiquinone with 2,6-dibromo-4-cyanophenol (PC32) suppressed the anaerobic reduction of the hemes with ubiquinol-1 by eliminating the fast phase. Flow-flash studies in the reaction of the fully reduced enzyme with dioxygen showed that the heme b to heme o electron transfer occurs with a rate constant of approximately 10(4) s-1 in all three preparations. These results support our previous proposal that the bound ubiquinone is involved in facile oxidation of substrates in subunit II and subsequent intramolecular electron transfer to low-spin heme b in subunit I.

Redox-linked transient deprotonation at the binuclear site in the aa(3)-type quinol oxidase from Acidianus ambivalens: implications for proton translocation

The hyperthermophilic archaeon Acidianus ambivalens expresses a membrane-bound aa(3)-type quinol oxidase, when grown aerobically, that we have studied by resonance Raman spectroscopy. The purified aa(3) oxidase, which does not contain bound quinol, undergoes a reversible slow conformational change at heme a(3) upon reduction, as indicated by a change in the frequency of its heme formyl stretching mode, from 1,660 cm(-1) to 1,667 cm(-1). In contrast, upon reduction of the integral membrane enzyme or the purified enzyme preincubated with decylubiquinol, this mode appears at 1,667 cm(-1) much more rapidly, suggesting a role of the bound quinol in controlling the redox-linked conformational changes. The shift of the formyl mode to higher frequency is attributed to a loss of hydrogen bonding that is associated with a group having a pKa of approximately 3.8. Based on these observations, a crucial element for proton translocation involving a redox-linked conformational change near the heme a(3) formyl group is postulated.

Role of the isoprenyl tail of ubiquinone in reaction with respiratory enzymes: studies with bovine heart mitochondrial complex I and Escherichia coli bo-type ubiquinol oxidase

The hydrophobic isoprene tail of ubiquinone-2 (Q2) exihibits binding specificity in redox reactions with bovine heart mitochondrial complex I (Ohshima, M., Miyoshi, H., Sakamoto, K., Takegami, K., Iwata, J., Kuwabara, K., Iwamura, H., and Yagi, T. (1998) Biochemistry 37, 6436-6445) and the Escherichia coli bo-type ubiquinol oxidase (Sakamoto, K., Miyoshi, H., Takegami, K., Mogi, T., Anraku, Y., and Iwamura, H. (1996) J. Biol. Chem. 271, 29897-29902). To identify the structural factor(s) of the diprenyl tail of Q2 governing the specific interaction with these enzymes, we synthesized a series of novel Q2 analogues in which only one of the structural factors of the diprenyl tail was systematically modified. In bovine complex I, the presence of the methyl branch and the pi-electron system in the first isoprene unit are responsible for high-affinity binding of Q2 to the ubiquinone reduction site, which results in a low Km and kcat values of Q2 reduction. The position of the methyl group in the tail is strictly recognized by the enzyme. In contrast to complex I, in bo-type ubiquinol oxidase, either of the two pi-electron systems in the tail is required for high-affinity binding of Q2H2 to the enzyme, while the presence of the methyl branch and the location of the pi-electron systems are not strictly recognized by the enzyme. We concluded that the role of the ubiquinone tail is not simply the enhancement of the hydrophobicity of the molecule and that molecular recognition of the tail by the quinone redox site differs among the respiratory enzymes.

Thermodynamics of electron transfer in Escherichia coli cytochrome bo3

The proton translocation mechanism of the Escherichia coli cytochrome bo3 complex is intimately tied to the electron transfers within the enzyme. Herein we evaluate two models of proton translocation in this enzyme, a cytochrome c oxidase-type ion-pump and a Q-cycle mechanism, on the basis of the thermodynamics of electron transfer. We conclude that from a thermodynamic standpoint, a Q-cycle is the more favorable mechanism for proton translocation and is likely occurring in the enzyme.

Isolation and characterizations of quinone analogue-resistant mutants of bo-type ubiquinol oxidase from Escherichia coli

Cytochrome bo is a member of the heme-copper terminal oxidase superfamily and serves as a four-subunit ubiquinol oxidase in the aerobic respiratory chain of Escherichia coli. To probe the location and structural properties of the ubiquinol oxidation site, we isolated and characterized five or 10 spontaneous mutants resistant to either 2,6-dimethyl-1,4-benzoquinone, 2,6-dichloro-4-nitrophenol, or 2,6-dichloro-4-dicyanovinylphenol, the potent competitive inhibitors for the oxidation of ubiquinol-1 [Sato-Watanabe, M., Mogi, T., Miyoshi, H., Iwamura, H., Matsushita, K., Adachi, O., and Anraku, Y. (1994) J. Biol. Chem. 269, 28899-28907]. Analyses of the growth yields and the ubiquinol-1 oxidase activities of the mutant membranes showed that the mutations increased the degree of the resistance to the selecting compounds. Notably, several mutants showed the cross-resistance. These data indicate that the binding sites for substrate and the competitive inhibitors are partially overlapped in the ubiquinol oxidation site. All the mutations were linked to the expression vector, and 23 mutations examined were all present in the C-terminal hydrophilic domain (Pro96-His315) of subunit II. Sequencing analysis revealed that seven mutations examined are localized near both ends of the cupredoxin fold. Met248Ile, Ser258Asn, Phe281Ser, and His284Pro are present in a quinol oxidase-specific (Qox) domain and proximal to low-spin heme b in subunit I and the lost CuA site in subunit II, whereas Ile129Thr, Asn198Thr, and Gln233His are rather scattered in a three-dimensional structure and closer to transmembrane helices of subunit II. Our data suggest that the Qox domain and the CuA end of the cupredoxin fold provide the quinol oxidation site and are involved in electron transfer to the metal centers in subunit I.

Tryptophan-136 in subunit II of cytochrome bo3 from Escherichia coli may participate in the binding of ubiquinol

In the cytochrome c oxidases, the role of subunit II is to provide the electron entry site into the enzyme. This subunit contains both the binding site for the substrate, cytochrome c, and the CuA redox center, which is initially reduced by cytochrome c. Cytochrome bo3 and other quinol oxidases that are members of the heme-copper oxidase superfamily have a homologous subunit II, but the CuA site is absent, as is the docking site for cytochrome c. Speculation that subunit II in the quinol oxidases may also be important as an electron entry site is supported by the demonstration several years ago that a photoreactive substrate analogue, azido-Q, covalently labeled subunit II in cytochrome bo3. In the current work, a sequence alignment of subunit II of heme-copper quinol oxidases is used as a guide to select conserved residues that might be important for the binding of ubiquinol to cytochrome bo3. Results are presented for point mutants in 24 different residue positions in subunit II. The membrane-bound enzymes were examined by optical spectroscopy and by determining the activity of ubiquinol-1 oxidase. In each case, the Km for ubiquinol-1 was determined as a measure of possible perturbation to a quinol binding site. The only mutant that had a noticeably altered Km for ubiquinol-1 was W136A, in which the Km was about sixfold increased. Thus, W136 may be at or close to a substrate (ubiquinol)-binding site in cytochrome bo3. In the cytochrome c oxidases, the equivalent tryptophan (W121 in Paracoccus denitrificans) has been identified as the "electron entry site".

Using matrix-assisted laser desorption ionization mass spectrometry to map the quinol binding site of cytochrome bo3 from Escherichia coli

The cytochrome bo3 ubiquinol oxidase contains at least one and possibly two binding sites for ubiquinol/ubiquinone. Previous studies used the photoreactive affinity label 3-[3H]azido-2-methyl-5-methoxy-6-geranyl-1,4-benzoquinone (azido-Q), a substrate analogue, to demonstrate that subunit II contributes to at least one of the quinol binding sites. In the current work, mass spectroscopy is used to identify a peptide within subunit II that is photolabeled by the azido-Q. Purified cytochrome bo3 was photolabeled as previously described using azido-Q that was not tritiated (i.e., not radiolabeled). Subunit II was then isolated from an SDS-PAGE gel and proteolyzed in situ with trypsin. The resulting peptides were eluted from the gel and then identified using matrix-assisted laser desorption ionization mass spectrometry. The resulting mass spectrum was compared to that obtained by analysis of subunit II that had not been exposed to the photolabel. Using the amino acid sequence, each peak in the mass spectrum of the unlabeled subunit II could be assigned to an expected trypsin fragment. Two additional peaks were observed in the mass spectrum of the photolabeled subunit with m/z 1931.9 and 2287.7. Subtraction of the mass of azido-Q from the peak at m/z 1931.9 results in a mass equivalent to that of a peptide consisting of amino acids 165-178. The assignment of the peak at m/z 2287.7 cannot be made unequivocally and may correspond either to the covalent attachment of azido-Q to peptide 254-270 or to a peptide resulting from incomplete proteolysis. The labeled peptide, 165-178, is within the water-soluble domain of subunit II, whose X-ray structure is known. This peptide is located near the site where CuA is located in the homologous cytochrome c oxidases and can be placed near the interface between subunits I and II.

Characterization and functional role of the QH site of bo-type ubiquinol oxidase from Escherichia coli

Cytochrome bo is a four-subunit terminal ubiquinol oxidase in the aerobic respiratory chain of Escherichia coli that vectorially translocates protons not only via directed protolytic reactions but also via proton pumping. Previously, we postulated that a bound quinone in the high-affinity quinone binding site (QH) mediates electron transfer from the low-affinity quinol oxidation site (QL) in subunit II to low-spin heme b in subunit I as an electron gate and a transient electron reservoir [Sato-Watanabe, M., Mogi, T., Ogura, T., Kitagawa, T., Miyoshi, H., Iwamura, H., and Anraku, Y. (1994b) J. Biol. Chem. 269, 28908-28912]. In the present study, we carried out screening of ubiquinone analogues using a bound ubiquinone-free enzyme (DeltaUbiA1) that has been isolated from a ubiquinone biosynthesis mutant, and identified PC24 (2-chloro-4, 6-dinitrophenol), PC32 (2,6-dibromo-4-cyanophenol), and PC52 (2-isopropyl-5-methyl-4,6-dinitrophenol) as potent QH site inhibitors. PC15 (2,6-dichloro-4-nitrophenol) and PC16 (2, 6-dichloro-4-dicyanovinylphenol), potent QL site inhibitors, did not exhibit such a selective inhibition of the QH site. Binding studies using the air-oxidized DeltaUbiA enzyme showed that PC32 and PC52 have 4- to 7-fold higher affinity than ubiquinone-1. Reconstitution of the QH site with PC32 and PC52 resulted in a decrease of the apparent Vmax value to 1/7 and 1/3, respectively, of the control activity. These findings suggest that structural features of the QL and QH sites are different, and provide further support for the involvement of the QH site in intramolecular electron transfer and facile oxidation of quinols at the QL site.

Substitutions of conserved aromatic amino acid residues in subunit I perturb the metal centers of the Escherichia coli bo-type ubiquinol oxidase

Cytochrome bo is a four-subunit quinol oxidase in the aerobic respiratory chain of Escherichia coli and functions as a redox-coupled proton pump. Subunit I binds all the redox metal centers, low-spin heme b, high-spin heme o, and CuB, whose axial ligands have been identified to be six invariant histidines. This work explored the possible roles of the aromatic amino acid residues conserved in the putative transmembrane helices (or at the boundary of the membrane) of subunit I. Sixteen aromatic amino acid residues were individually substituted by Leu, except for Tyr61 and Trp282 by Phe and Phe415 by Trp. Leu substitutions of Trp280 and Tyr288 in helix VI, Trp331 in loop VII-VIII, and Phe348 in helix VIII reduced the catalytic activity, whereas all other mutations did not affect the in vivo activity. Spectroscopic analyses of the purified mutant enzymes revealed that the defects were attributable to perturbations of the binuclear center. On the basis of these findings and recent crystallographic studies on cytochrome c oxidases, we discuss the possible roles of the conserved aromatic amino acid residues in subunit I of the heme-copper terminal oxidases.

One-step purification of histidine-tagged cytochrome bo3 from Escherichia coli and demonstration that associated quinone is not required for the structural integrity of the oxidase

The cytochrome bo3 ubiquinol oxidase from Escherichia coli is a member of the heme-copper superfamily of proton-pumping respiratory oxidases. An improved preparative protocol was desired that would minimize the potential damage during protein isolation of labile mutants of the oxidase. Variants of the oxidase containing a histidine tag at the carboxy-terminus of either subunit I, II or III were constructed. The constructs with the histidine tag on either subunit I or II successfully allowed the enzyme to be isolated with high purity in one step using Ni2+ affinity chromatography. The enzyme with the histidine tag on subunit II is particularly useful insofar as the enzyme isolated in this manner has little, if any, heterogeneity resulting from the presence of heme O in the low spin heme-binding site, i.e., cytochrome oo3 is minimized. The enzyme can be prepared in virtually any quantity very rapidly and is suitable for biophysical characterization. Cytochrome bo3 was prepared in either Triton X-100, sucrose monolaurate, or dodecyl maltoside. The enzyme isolated in the presence of either sucrose monolaurate or dodecyl maltoside contains approximately one equivalent of associated ubiquinone, whereas this is absent when Triton X-100 is used. However, the UV/vis absorbance and steady-state kinetic properties of the enzyme are virtually identical regardless of which detergent is used. These data are consistent with previous reports that cytochrome bo3 contains an equivalent of 'tightly associated' ubiquinone, but clearly demonstrate that this quinone can be removed without damaging the enzyme and is not critical to the maintenance of the native structure of the oxidase.

Exploring subunit-subunit interactions in the Escherichia coli bo-type ubiquinol oxidase by extragenic suppressor mutation analysis

Cytochrome bo-type ubiquinol oxidase is a four-subunit heme-copper terminal oxidase and functions as a redox-coupled proton pump in the aerobic respiratory chain of Escherichia coli. On the basis of deletion and chemical cross-linking analyses on subunit IV, we proposed that subunit IV is essential for CuB binding to subunit I and that it is present in a cleft between subunits I and III (Saiki, K., Nakamura, H., Mogi, T., and Anraku, Y. (1996) J. Biol. Chem. 271, 15336-15340). To extend previous studies, we carried out alanine-scanning mutagenesis for selected 16-amino acid residues in subunit IV to explore subunit-subunit interactions in bo-type ubiquinol oxidase. We found that only the replacement of Phe83 in helix III resulted in the reduction of the catalytic activity but that this did not significantly affect the UV-visible spectroscopic properties and the copper content. This suggests that individual amino acid substitutions, including the six invariant residues, are not enough to alter such properties of the metal centers. Extragenic suppressor mutations were isolated for the Phe83 --> Ala mutation of subunit IV and identified as missense mutations in helices VII and VIII in subunit I. These observations provide further support for specific interactions of subunit IV with helix VII and/or VIII, the CuB binding domain, of subunit I and suggest that subunit IV functions as a domain-specific molecular chaperon in the oxidase complex.

Oxidation of ubiquinol by cytochrome bo3 from Escherichia coli: kinetics of electron and proton transfer

In this study we have used the so-called flow-flash technique to investigate electron and proton transfer during the reaction between cytochrome bo3 with bound ubiquinol (QH2) and dioxygen. The results are compared to those from the well-characterized mitochondrial cytochrome alpha alpha3. Qualitatively, the same type of absorbance changes associated with electron transfer were observed in both enzymes whereas the protonation reactions were markedly different. In the bacterial QH2-bound enzyme, three kinetic phases with time constants of approximately 45 micros, approximately 700 micros, and approximately 4 ms associated with electron-transfer reactions were observed. The first phase is attributed to oxidation of hemes b and o3 and formation of the "peroxy" intermediate. The second and third phases were not observed after addition of the herbicide HQNO, which displaces QH2 from its binding site. They are attributed to electron transfer from QH2 to heme b and from heme b to the binuclear center, respectively. In both enzymes, the initial electron transfer was followed by a slower uptake of 0.9 +/- 0.3 proton per enzyme molecule (tau approximately 90 micros), previously attributed to protonation of a group near the binuclear center. Only in the bacterial enzyme, the second electron-transfer reaction was accompanied by a net release of 1.1 +/- 0.3 H+, which is attributed to proton release during oxidation of QH2. It was followed by a slower uptake of 1.2 +/- 0.4 H+ during transfer of the fourth electron to the binuclear center. The two slowest protonation reactions were not observed in the presence of HQNO.

The archaeal SoxABCD complex is a proton pump in Sulfolobus acidocaldarius

The thermoacidophilic archaeon Sulfolobus acidocaldarius expresses a very unusual quinol oxidase, which contains four heme a redox centers and one copper atom. The enzyme was solubilized with dodecyl maltoside and purified to homogeneity by a combination of hydrophobic interaction and anion exchange chromatography. The oxidase complex consists of four polypeptide subunits with apparent molecular masses of 64, 39, 27, and 14 kDa that are encoded by the soxABCD operon (Lübben, M., Kolmerer, B., and Saraste, M. (1992) EMBO J. 11, 805-812). The optical spectra and redox potentials of the SoxABCD complex have been characterized, and the absorption coefficients of the contributing cytochromes a587 and aa3 were determined. The EPR spectra indicate the presence of three low spin and one high spin heme species, the latter associated with the binuclear heme CuB site. Standard midpoint potentials of the cytochrome a587 heme centers were determined as +210 and +270 mV, respectively. The maximum turnover of the complex (1300 s-1 at 65 degrees C) was found to be about three times greater than that of the previously studied isolated cytochrome aa3 subunit alone (Gleissner, M., Elferink, M. G., Driessen, A. J., Konings, W. N., Anemüller, S., and Schäfer, G. (1994) Eur. J. Biochem. 224, 983-990). With N,N,N',N'-tetramethyl-1,4-phenylenediamine as a reductant, the SoxABCD complex reconstituted into liposomes generates a proton motive force. A new method is described by co-reconstitution of SoxABCD with a Sulfolobus Rieske FeS-protein (SoxL), allowing energization by cytochrome c. It is based on the finding that this Rieske protein can equilibrate electrons between cytochrome c and quinones reversibly (Schmidt, C. L., Anemüller, S., Teixeira, M., and Schäfer, G. (1995) FEBS Lett. 359, 239-243). With this system, generating no scalar protons, the stoichiometry of proton translocation could be determined. A net H+/e- ratio >1 was determined, identifying the SoxABCD complex as a proton-pumping quinol oxidase. According to structural analysis, the cytochrome aa3 moiety of the complex does not contain the signature of a H+ pumping channel as identified in Rhodobacter sphaeroides or Paracoccus denitrificans. Therefore, for H+ translocation, a mechanism different from that in typical heme-copper oxidases of the aa3 or bo3 type is discussed.

Probing substrate binding site of the Escherichia coli quinol oxidases using synthetic ubiquinol analogues

Substrate binding sites of the Escherichia coli bo- and bd-type quinol oxidases were probed with systematically synthesized ubiquinol analogues. The apparent Km values of ubiquinol-2 derivatives to the bo-type enzyme were much lower than that of the corresponding 6-n-decyl derivatives. The isoprenoid structure is less hydrophobic than the saturated n-alkyl group with the same carbon number; therefore, the native isoprenoid side chain appears to play a specific role in quinol binding besides simply increasing hydrophobicity of the molecule. The Vmax values of 2-methoxy-3-ethoxy analogues were greater than that of 2-ethoxy-3-methoxy analogues irrespective of the side chain structure. This result indicates not only that a methoxy group in the 2-position is recognized more strictly than the 3-position by the binding site but also that the side chain structure does not affect binding of the quinol ring moiety. Systematic analysis of the electron-donating activities of the analogues with different substituents in the 5-position revealed that the 5-methyl group is important for the activity. In the parallel studies with the bd-type enzyme, we obtained similar observations except that almost all quinol analogues, but not ubiquinol-1, elicited a remarkable substrate inhibition at higher concentrations. These results indicate that the two structurally unrelated terminal oxidases share common structural properties for the quinol-oxidation site.

Biochemical and spectroscopic properties of the four-subunit quinol oxidase (cytochrome ba3) from Paracoccus denitrificans

The ba3 quinol oxidase from Paracoccus denitrificans has been purified by a new protocol leading to significantly higher yields than previously reported (Richter et al. (1994) J. Biol. Chem. 269, 23079-23086). In an SDS PAG an additional protein band compared with the previous preparation appears, which can be identified as the major form of subunit II. All protein bands can be assigned to genes of the qox operon by N-terminal sequencing, indicating that the oxidase consists of four subunits. In addition to one heme A, one heme B, and one copper atom, the preparation contains two ubiquinone molecules per enzyme. The oxidase is further characterized by electron paramagnetic resonance (EPR), circular dichroism (CD) and magnetic circular dichroism (MCD) spectroscopy.

Probing a role of subunit IV of the Escherichia coli bo-type ubiquinol oxidase by deletion and cross-linking analyses

Subunit IV of the Escherichia coli bo-type ubiquinol oxidase is a 12-kDa membrane protein encoded by the cyoD gene and is conserved in the bacterial heme-copper terminal oxidases. To probe the functional role of subunit IV, we carried out deletion analysis and chemical cross-linking experiments with a homobifunctional and cleavable reagent. Spectroscopic properties of the mutant oxidases suggest that the C-terminal two-third (Val45 to His109) containing helices II and III is essential for the functional expression of the oxidase complex and for the CuB binding to the heme-copper binuclear center in subunit I. Cross-linking studies indicate that subunit IV is in close vicinity to subunit III. Based on these observations, we propose that subunit IV is present in a cleft formed by subunits I and III and assists the CuB binding to subunit I during biosynthesis or assembly of the oxidase complex.

Comparison of the structural features of ubiquinone reduction sites between glucose dehydrogenase in Escherichia coli and bovine heart mitochondrial complex I

To characterize the structural features of the ubiquinone reduction site of glucose dehydrogenase (GlcDH) in Escherichia coli, we performed structure/activity studies of a systematic set of synthetic ubiquinone analogues and specific inhibitors (synthetic capsaicins) of this site. Considering the proposed similarity of the quinone binding domain motif between GlcDH and one subunit of mitochondrial complex I [Friedrich, T., Strohdeicher, M., Hofhaus, G., Preis, D., Sahm, H. & Weiss, H. (1990) FEBS Lett. 265, 37-40], we compared the structure/activity profiles of the substrates and inhibitors for GlcDH with those for bovine heart mitochondrial complex i. With respect to GlcDH, replacement of one or both methoxy groups in the 2 and 3 positions of benzoquinone ring by ethoxy group(s) resulted in a drastic decrease in the electron accepting activity. The presence of a 5-methyl group and the conformational property of the 6-alkyl side chain did not significantly contribute to the activity. These results suggested that only half of the benzoquinone ring (the moiety corresponding to the 2 and 3 positions) is recognized by the quinone reduction site in a strict sense. In contrast, quinone analogues with structural modifications at all positions in the benzoquinone ring retained the activity with mitochondrial complex I. This finding indicated that the catalytic site of complex I is spacious enough to accommodate a variety of structurally different quinone derivatives. The correlation of the inhibitory potencies of a series of synthetic capsaicins between the two enzymes was very poor. These findings indicated that the binding environment of ubiquinone in GlcDH is very specific and differs from that in mitochondrial complex I.

Stabilization of a semiquinone radical at the high-affinity quinone-binding site (QH) of the Escherichia coli bo-type ubiquinol oxidase

Reaction of ubiquinone in the high-affinity quinone-binding site (QH) in bo-type ubiquinol oxidase from Escherichia coli was revealed by EPR and optical studies. In the QH site, ubiquinol was shown to be oxidized to ubisemiquinone and to ubiquinone, while no semiquinone signal was detected in the oxidase isolated from mutant cells that cannot synthesize ubiquinone. The QH site highly stabilized ubisemiquinone radical with a stability constant of 1-4 at pH 8.5 and the stability became lower at the lower pH. Midpoint potential of QH2/Q couple was -2 mV at pH 8.5 and showed -60 mV/pH dependence indicative of 2H+/2e- reaction. The Em was more negative than that of low-spin heme b above pH 7.0. We conclude that the QH mediates intramolecular electron transfer from ubiquinol in the low-affinity quinol oxidation site (QL) to low-spin heme b. Unique roles of the quinone-binding sites in the bacterial ubiquinol oxidase are discussed.