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J. Biol. Chem., Vol. 282, Issue 6, 3977-3988, February 9, 2007
Mutational Analysis of Cytochrome b at the Ubiquinol Oxidation Site of Yeast Complex III*![]() ![]() ![]() 1
From the
Received for publication, July 7, 2006 , and in revised form, December 4, 2006.
The cytochrome bc1 complex is a dimeric enzyme of the inner mitochondrial membrane that links electron transfer from ubiquinol to cytochrome c by a protonmotive Q cycle mechanism in which ubiquinol is oxidized at one center in the enzyme, referred to as center P, and ubiquinone is rereduced at a second center, referred to as center N. To better understand the mechanism of ubiquinol oxidation, we have examined catalytic activities and pre-steady-state reduction kinetics of yeast cytochrome bc1 complexes with mutations in cytochrome b that we expected would affect oxidation of ubiquinol. We mutated two residues thought to be involved in proton conduction linked to ubiquinol oxidation, Tyr132 and Glu272, and two residues proposed to be involved in docking ubiquinol into the center P pocket, Phe129 and Tyr279. Substitution of Phe129 by lysine or arginine yielded a respiration-deficient phenotype and lipid-dependent catalytic activity. Increased bypass reactions were detectable for both variants, with F129K showing the more severe effects. Substitution with lysine leads to a disturbed coordination of a b heme as deduced from changes in the midpoint potential and the EPR signature. Removal of the aromatic side chain in position Tyr279 lowers the catalytic activity accompanied by a low level of bypass reactions. Pre-steady-state kinetics of the enzymes modified at Glu272 and Tyr132 confirmed the importance of their functional groups for electron transfer. Altered center N kinetics and activation of ubiquinol oxidation by binding of cytochrome c in the Y132F and E272D enzymes indicate long range effects of these mutations.
The mitochondrial cytochrome bc1 complex, also termed ubiquinol:cytochrome c oxidoreductase (QCR)2 or complex III, is a central component of respiratory energy conversion. The multisubunit membrane protein complex catalyzes the transfer of electrons from the membrane-localized ubiquinol to the water-soluble cytochrome c. This redox reaction is coupled to translocation of protons across the membrane. The mechanism that links proton translocation to electron transfer, the protonmotive Q cycle (1), depends on two spatially separated binding sites for quinol and quinone, both located in subunit cytochrome b. The key step of the mechanism is the bifurcated route of the two electrons released upon ubiquinol oxidation at center P. One electron is transferred into the high potential chain, the 2Fe-2S cluster Rieske protein (ISP) and cytochrome c1, consequently being delivered to cytochrome c. The second electron is transferred via the low potential chain, heme bL and heme bH of cytochrome b, to center N, at which quinone is reduced to semiquinone. A complete turnover of the enzyme requires the oxidation of two ubiquinol molecules, resulting in reduction of the semiquinone (2-4).
Details of the molecular mechanism of QCR are under debate. Of special interest is the mechanism of ubiquinol oxidation at center P. The ubiquinol oxidation pocket has no direct access to the aqueous phase. A proton exit route that parallels electron transfer from ubiquinol toward heme bL has been proposed (5, 6). Center P is mainly formed by the mitochondrial encoded cytochrome b. Based on crystal structures with inhibitors bound to center P and mutational studies of the bacterial QCR (5-11), several well conserved amino acid residues were suggested to play a role in ubiquinol binding, proper bifurcated electron transfer, and proton release pathways (2, 5, 6, 10). The residue Glu272 is proposed to be a ligand for ubiquinol and to accept protons released during ubiquinol oxidation. The residue Tyr132 is located between Glu272 and heme bL. The hydroxyl group of this tyrosine is thought to stabilize the proton transfer pathway. The residue Tyr279 is proposed to preorient the substrate, whereas Phe129 presumably stabilizes the hydrophobic tail of the ubiquinol. To challenge the significance of these residues for quinol catalysis, we analyzed how mutations in Glu272, Tyr132, Phe129, and Tyr279 of cytochrome b influence ubiquinol-cytochrome c reductase activity and short circuit electron transfer reactions that result in superoxide anion production. We also used presteady-state reduction kinetics of cytochrome b and cytochrome c1 of the Tyr132 and Glu272 variants to analyze the role of these residues in electron transfer.
Media and Yeast StrainsPremixed media were from For-Medium. YPGal (1% yeast extract, 2% peptone, and 3% galactose) and YPG (1% yeast extract, 2% peptone, and 3% glycerol) were used for growth of the yeast strains. The strains used in this study are described in detail elsewhere (12). Site-directed Mutagenesis, Biolistic Transformation, and Selection of Mitochondrial MutantsThe plasmid pBM5 carrying the wild-type intronless sequence of the cytochrome b gene was mutagenized using the QuikChange site-directed mutagenesis kit (Stratagene). The following primers were used: 5'-CTA TTG CTA CAG CTA AAT TAG GTT ATT GTT GTG-3' and 5'-CTC AAC AAT AAC CTA ATT TAG CAG TAG CAA TAG-3' for F129K, 5'-CTA TTG CTA CAG CTA GAT TAG GTT ATT GTT GTG-3' and 5'-CTC AAC AAT AAC CTA ATC TAG CTG TAG CAA TAG-3' for F129R, and 5'-TAC AGC TTT TTT AGG TTT TTG TTG TGT TTA TG-3' and 5'-CAT AAA CAC AAC AAA AAC CTA AAA AAG CTG TA-3' for Y132F. The mitochondrial biolistic transformation, the selection of the mitochondrial transformants, and the integration of the mutation into the mitochondrial genome was carried out as described before (12). The yeast strains carrying the Y279A/C/S mutation were previously constructed and were provided by B. Meunier (13). Purification of QCRWild-type and mutant yeast strains were grown in YPG or YPGal medium as indicated under "Results." Mitochondrial membranes were prepared as described previously (12). QCR was purified via a single DEAE Biogel column as described elsewhere applying a flow rate of 2-5 ml/min (14). Extinction coefficients of 17.5 mM-1 cm-1 for ascorbate reduced minus ferricyanide oxidized c heme (553-540 nm) and 25.6 mM-1 cm-1 for dithionite-reduced minus ferricyanide-oxidized b hemes (562-575 nm) were used for quantification of QCR. Reconstitution of Purified QCR with Phospholipids and Determination of H+/e- StoichiometryPurified QCR was reconstituted in soy asolectin in a 1:10 molar ratio of protein to lipid. Detergent was removed by dialysis for 24 h against 100 mM KCl, 3 mM Hepes-KOH, pH 7.2. The H+/e- stoichiometry of the QCR reconstituted into liposomes was determined by the oxidant pulse method as previously described (12).
Measurement of Ubiquinol-Cytochrome c Reductase ActivityUbiquinol-cytochrome c reductase activity of purified QCR was assayed in 50 mM KPi, pH 7.4, 250 mM sucrose, 1 mM KCN, 0.05% n-undecyl- To determine the apparent Km for DQH, variable concentrations of DQH (50-500 nM) were used as substrate in the activity assay with reconstituted enzyme. The concentration of the DQH stock solution was spectroscopically determined at the start of the experiment. Apparent Km values were obtained by linear regression in an Eadie-Hofstee plot. To determine the sensitivity to inhibitors, QCR was reconstituted with phospholipids as described above and was mixed with variable concentrations of inhibitor yielding different inhibitor/QCR ratios. The mixture was incubated for 15 min at room temperature before starting the activity assay. The concentration of the inhibitors was determined by their extinction coefficient (15). Dilutions of the inhibitors were done just before the titrations.
EPR Spectroscopy and Redox Titrations20-40 µM purified QCR (50 mM KPi, pH 6.9, 250 mM NaCl, 0.05% n-undecyl- The redox titrations were performed as described before at pH 7.5 (12). Typically, data were recorded at steps of 40 mV between -0.4 and 0.2 V under anaerobic conditions. The reference electrode was calibrated with the cyclovoltammogram of a buffered K4(Fe(CN)6) solution. All electrochemical titrations were reversible as controlled by comparing fully oxidized minus fully reduced visible spectra at different points of the experiments.
Pre-steady-state KineticsPre-steady-state reduction of QCRs was followed at room temperature by stopped flow rapid scanning spectroscopy using an OLIS rapid scanning monochromator. Reactions were started by mixing 2 µM bc1 complex in assay buffer containing either 50 mM potassium phosphate, pH 7.0, or 100 mM Tris-HCl, pH 8.8, plus 1 mM sodium azide, 1 mM EDTA, and 0.01% Tween 20 against an equal volume of the same buffer containing 40 µM DQH. A fresh solution of DQH substrate was prepared before each experiment. A spectrum of oxidized QCR was obtained by mixing the oxidized QCR against assay buffer and averaging the data sets to a single scan. For each experiment, seven or eight data sets were averaged, and the oxidized spectrum was subtracted from each scan. From the three-dimensional data set composed of wavelength, absorbance, and time, the time course and amplitude change for cytochrome b reduction at 563 nm or cytochrome c1 reduction at 553 nm was extracted using the OLIS software. For the experiment in which cytochrome c was added, reduction of cytochrome c1 plus cytochrome c was monitored at 551 nm. To obtain the maximum c1 absorbance value, the enzyme was reduced with ascorbate. To obtain the maximum bH absorbance, the enzyme was reduced with dithionite, and the absorbance change at 563 nm in the dithionite minus ascorbate-reduced difference spectrum was multiplied by 0.7, since the bH heme accounts for
The Ubiquinol Binding Pocket and the Location of Tyr132, Phe129, Glu272, and Tyr279 at Center PFig. 1 shows the crystal structure of the yeast ubiquinol oxidation pocket at center P with bound competitive inhibitors and the location of the cytochrome b residues that were mutated for this study. The hydroxyl group of the inhibitor stigmatellin is hydrogenbonded to the side chain of Glu272 (5). Hydrogen bond interaction with the Glu272 backbone stabilizes binding of the inhibitory substrate analogue hydroxydioxobenzothiazole (6). Glu272 is proposed to play an important role in ubiquinol oxidation (2, 5, 10). Recent mutagenesis studies in yeast support its relevance for accurate enzyme-substrate complex formation, prevention of electron short circuit reactions, and pH dependence of ubiquinol oxidation (12). The nearby residue Tyr132 is part of the binding pocket proximal to heme bL. It stabilizes via its hydroxyl group a water molecule of the suggested proton exit relay (5). Earlier studies in bacterial QCR suggest that the equivalent Tyr147 is required for efficient electron transfer to heme bL (16). The side chain of Phe129 is in hydrophobic interaction with the tail of stigmatellin and probably with that of the substrate. This residue is a locus of center P inhibitor resistance both in yeast and bacterial QCR (17-19). Mutational analysis of the equivalent residue in bacterial QCR (Phe144) indicated that replacement of Phe144 affects ubiquinol binding and oxidation (9). The residue Tyr279 is close to the highly conserved PEWY (Pro271-Tyr274) motif, and it has been suggested to take part in positioning ubiquinol prior to oxidation and in stabilizing the enzyme-substrate complex by weak hydrogen bonds (6). Initial mutational studies of this residue in yeast QCR also supported a role in ubiquinol binding (13). Mutations in Tyr279 have been reported in patients with exercise intolerance and multisystem disorder (20), and they confer antimalarial drug resistance in Plasmodium falciparum QCR (21). Effect of Mutations on QCR Stability and FunctionGrowth of the mutant strains was monitored in nonfermentable medium to study a possible impact on cell respiration. The doubling time of Y132F was with 3.6 h only slightly increased compared with 3.2 h of the wild-type strain. Mutations in Tyr279 had a more severe effect on the respiratory growth. The Y279C strain had a doubling time of 6.4 h, and growth of Y279S (7.1 h) and Y279A (8.3 h) was even slower. Both Phe129 mutants did not grow on the nonfermentable media, marking F129K and F129R as lethal mutations with respect to respiration-dependent growth (Table 1). For purification of the variant QCRs, the two latter strains were grown in galactose medium, whereas all other QCRs were isolated from cells grown with a mixture of glycerol and ethanol.
The effect of the mutations on QCR content was monitored by spectroscopic b heme quantification of mitochondrial membranes (Table 1). The Y132F mutant showed only a small decrease ( 13%) in QCR concentration. The mutations in Tyr279 resulted in a more pronounced decrease. The Y279C mutant contained 76% of the wild-type level, and the Y279A (68%) and the Y279S (64%) mutants were slightly more affected. For F129K and F129R, the QCR content was determined for cells grown in galactose. In this medium, cell growth is not limited by respiration, and thus the QCR content should not be affected by the respiratory capacity of the mutant. Nevertheless, the F129R mutant had a lower QCR content than the F129K mutant, which might indicate a reduced stability of the F129R variant. The variant enzymes were purified for further characterization. Y132F and the three variants of Y279 were purified by anion exchange chromatography without loss of activity or detectable loss of subunits as monitored with optical spectra and Western immunoblot analysis for the different purification steps (data not shown). For purification of F129R and F129K, the flow rate had to be lowered (0.6 ml/min) to prevent disintegration of the complex. We assume that the modified protein preparation retains more phospholipids, since the latter has been shown to increase complex integrity (6, 22).
The kinetic parameters of each QCR preparation were measured as described under "Experimental Procedures." The turnover numbers and Km values for DQH are given in Table 1. Y132F QCR exhibited about half as much cytochrome c reductase activity as compared with the wild-type enzyme. Y279C QCR retained
Effect of Mutations on Inhibitor BindingThe ubiquinol cytochrome c reductase activity of the purified QCR variants reconstituted in liposomes was measured in the presence of increasing concentrations of stigmatellin and myxothiazol to test whether the mutations change the sensitivity of the enzymes to these inhibitors. Stigmatellin binds to the niche distal to heme bL and is proposed to mimic an intermediate of quinol oxidation (5, 6). Myxothiazol binds proximal to heme bL (8, 15). Y132F QCR exhibits unchanged sensitivity to stigmatellin but is resistant to myxothiazol (Table 1). This agrees with results obtained for the equivalent mutation in bacterial QCR (9). Each of the substitutions in position 279 altered the sensitivity for both inhibitors. The alanine replacement caused a
Superoxide Anion ProductionSuperoxide production is a bypass reaction of the bifurcated electron transfer at center P (24). To analyze the influence of Phe129, Tyr132, and Tyr279 mutations on this process, superoxide anion formation of the QCR variants was assayed as the superoxide dismutase-sensitive rate of cytochrome c reduction (Fig. 2). The difference between the reaction rate in the absence and presence of superoxide dismutase yields the contribution of cytochrome c reduction by superoxide anion to the overall cytochrome c reductase activity. As previously described, wild-type enzyme preparations are virtually free of superoxide anion production (12). In F129K, H+/e- StoichiometryDuring turnover of QCR, two protons are released at center P per one electron transferred to cytochrome c according to the Q cycle. Uncoupling of the Q cycle is characterized by a lowered H+/e- stoichiometry. To analyze the effect of the mutations on the coupling of the Q cycle, the H+/e- stoichiometry was determined for reconstituted enzyme by the oxidant pulse method, in which the proton release at the side of center P is monitored (Table 1). As previously shown, an H+/e- ratio of 2 is measured for the wild-type enzyme (12). The Y132F and the three Tyr279 variants showed only minor deviations from that value (1.96-1.99). The F129K substitution uncoupled the Q cycle as indicated by a lowered H+/e- stoichiometry (1.45). In the F129R replacement, the stoichiometry was not affected. Apparently, arginine can at least partly replace phenylalanine in this position, leading to less drastic effects than for the lysine substitution. A similar effect was seen in the inhibitor binding, where F129K showed a higher resistance than F129R, and in the superoxide production assays, where the effect of the F129K mutation was markedly higher.
Redox PotentiometryPotentiometric redox titrations were carried out to evaluate possible effects of the side chain substitutions on the midpoint potentials of the heme groups (Table 2). No major changes were observed for the Y132F mutant. In the F129K variant, both b heme potentials were shifted by approximately -100 mV. The lowered potentials of both b hemes are likely to contribute to the limitation of the F129K turnover number. In the F129R variant, the potential of heme bL was shifted by plus 30 mV (Table 2). This is in agreement with only a slightly reduced turnover number of the isolated enzyme (Table 1). As expected, the midpoint potentials of the c1 hemes were not affected for any of the mutations.
EPR Analysis of Center PEPR spectra were recorded of the detergent-solubilized purified QCR to monitor the influence of the mutations on the signal of the dithionite-reduced Rieske [2Fe-2S] cluster. Changes in shape and position of the signals can be interpreted as alterations of the ISP interaction with center P. As described previously, the EPR spectra of E272Q and wild-type QCR are nearly identical, whereas E272D differs in line shape and position compared with both of them, whereby the gzz signal is markedly shifted to a higher magnetic field (12) (Table 3). Position and line shape of the EPR signal in F129R and Y132F QCR are also very similar compared with that of the wild-type enzyme. However, in all three variants of Tyr279, the gzz peak is again slightly shifted to higher magnetic fields. In addition, the gxx peak of Y279S shows a pronounced shift (Fig. 3 and Table 3).
The signal of the reduced Rieske cluster of the F129K variant is less intense as compared with that of the wild type and cannot be clearly observed due to a strong spectral overlap with a signal of unknown origin with g values of 6.5, 5.3, and 2.0 (spectrum not shown). EPR signals with a similar line shape and resonance position compared with that of the latter have been reported for high spin ferric hemes, for instance in cytochrome c mutants, where the heme iron has lost one of its amino acid ligands (25). However, the signal observed here is dithionite-induced. Substitution of the aromatic residue by lysine may cause large structural rearrangements that affect not only inhibitor binding but the overall structure as well. Pre-steady-state Reduction Kinetics of QCRs with Mutations in Cytochrome b at Tyr132 and Glu272To further investigate the role of conserved residues at center P on quinol oxidation, pre-steady-state reduction kinetics were measured of Tyr132 and Glu272 variants. We recently showed that Glu272 governs efficient ubiquinol oxidation preventing bypass reactions at center P (12). To further investigate its role in electron transfer, the pre-steady-state reduction kinetics of the E272D and E272Q variants were analyzed. The instability of the F129R/K variants precluded their analysis. We also did not measure the kinetics for variants of Tyr279. These enzymes showed contaminations with several equivalents of cytochrome c, which overlaps spectroscopically with cytochrome c1 and would have resulted in multiple turnovers of the enzyme, rendering pre-steady-state kinetics difficult to analyze. Furthermore, the pre-steady-state kinetics of the Y132F variant was measured. The phenylalanine substitution should disturb the suggested coupled proton/electron transfer (5, 6). Since the midpoint potentials of the heme groups are not shifted in the Y132F, E272D, and E272Q mutants, any alteration in electron transfer must result from other changes in these enzymes.
The selected enzymes were purified, and their respective turnover numbers at pH 7 and 8.8 were determined for comparison with the pre-steady-state measurements (Table 4). As expected, E272D and E272Q are slightly more active after single-step anion exchange chromatography compared with the two-step purification described previously (12). This increased catalytic activity can be attributed to less delipidation (22). The pre-steady-state measurements were carried out at pH 7 and 8.8. At pH 7, the Em of the Rieske protein in wild-type QCR is
The pre-steady-state measurements were carried out with uninhibited enzyme and with inhibitors bound to center P or center N. By blocking center P with either stigmatellin or myxothiazol, reduction of cytochrome b via center N can be monitored. For those measurements, Y132F was inhibited with stigmatellin, since this variant is myxothiazol-resistant. The stigmatellin-resistant E272D and E272Q mutant enzymes were inhibited with myxothiazol. Alternatively, center N kinetics can also be monitored by cytochrome b reduction in the absence of any inhibitors, since the extents and rates of b reduction in this condition are very similar to those obtained in the presence of myxothiazol (center P blocked) but very different from those observed with antimycin (center N blocked). To investigate reduction of heme bH and heme c1 through center P, the enzymes were inhibited with antimycin. In the uninhibited Y132F enzyme, the extent of heme c1 reduction is diminished at both pH 7 and 8.8, and the rate of the first, faster phase of reduction at pH 7 is approximately half that of the wild-type enzyme. At pH 8.8, the amount of the first phase of reduction is so small (4%) that it cannot be accurately measured (Fig. 4). It should be noted that at pH 8.8 there is more reduction of the enzyme through center N than at pH 7, which obscures the effect of the change in Em of the Rieske protein on the relative amounts of c1 reduced at the two pH values. Partial reduction of cytochrome b through center N also results in inhibition of between 12% (pH 7) and 20% (pH 8.8) of center P sites even in the wild-type enzyme (Fig. 4). This missing c1 absorbance is due to the lack of an acceptor for the second electron from ubiquinol oxidation in that fraction of the enzyme population where the bH heme is already reduced. For the E272Q enzyme, the extent of heme c1 reduction is very similar to the wild-type enzyme, although the rate is significantly slower than that of the wild-type enzyme. For the E272D enzyme, the final extent of heme c1 reduction is very similar to that of the wild-type enzyme at both pH values, but the rate of the fast phase is slower than that of the wild type at pH 7. At pH 8.8, the rate of the fast phase of c1 reduction in the E272D mutant is similar to that of the wild type, although the percentage that undergoes rapid reduction is much less than the wild type (Fig. 5). However, the pH dependence of the cytochrome c reductase activity showed that the E272D enzyme had 28% of the wild-type turnover at pH 8.8 under steady-state conditions (Table 4). The Y132F mutant exhibits a marked decrease in extent of heme b reduction, which is also seen in the E272D enzyme, although to a lesser extent (Fig. 6). In addition, the Y132F and E272D enzymes show significant declines in the pre-steady-state rates, whereas the E272Q enzyme has faster rates than the wild type. We know that these rates reflect center N kinetics and not center P kinetics, because they are faster than the center P kinetics that are reflected in the fast phase of c1 reduction at pH 8.8 (Figs. 3 and 4 versus Fig. 6).
The complete inhibition of heme b reduction by stigmatellin in the QCR from the Y132F mutant as shown in Fig. 7 is a further indication of a defect at center N in this enzyme. This suggests that the center P Y132F mutation causes a long range structural effect. It also appears that the presence of stigmatellin at center P has a slowing effect on the rate of b reduction through center N in the wild-type enzyme (Fig. 7 versus Fig. 6).
In the presence of antimycin at pH 8.8, center P in only one monomer is active during pre-steady-state reduction of the wild-type enzyme, and
The pronounced decline in the pre-steady-state rate of c1 reduction in the Y132F enzyme seemed inconsistent with the catalytic activity of this enzyme (Table 1). We thus tested the effect of added cytochrome c on the pre-steady-state reduction of this enzyme. As shown in Fig. 9, the addition of one cytochrome c per dimer fully restores the extent of c1 reduction that was lost in the Y132F mutant in the absence (Fig. 4) or presence (Fig. 8) of antimycin and increases by
In this work, we analyzed the effect of mutations at the ubiquinol oxidation site of the yeast mitochondrial QCR. We focused on mutations in the residues Phe129, Tyr132, Glu272, and Tyr279 of cytochrome b. These residues with proposed functional implications are highly conserved in mitochondrial and bacterial QCRs (27, 28). The residue Phe129 lines the hydrophobic substrate channel at center P, the side chain directed toward the hydrophobic cavity that facilitates substrate access to center P as well as to center N of the other monomer (Fig. 1). Phe129 is involved in binding of the hydrophobic tail of the inhibitor stigmatellin and presumably that of ubiquinol (5, 8). Substitution of the phenylalanine by lysine or arginine resulted in a lethal growth phenotype on nonfermentable carbon sources, clearly indicating a major limitation of QCR catalysis. Accordingly, the cytochrome c reductase activity of the F129K QCR was lowered to 27% of the wild-type rate. A similar decrease was observed for the bacterial mutant in the equivalent residue Phe144 (9, 29). The purified QCR from the F129R mutant retained 84% of the wild-type turnover. It is surprising that this relative high catalytic rate does not sustain respiratory growth. The decreased QCR content in mitochondrial membranes obtained from cells grown in galactose medium suggests instability of this enzyme in the membrane. Accordingly, the F129R QCR had lower turnover numbers in the membrane, indicating that a part of the enzyme is inactive, which is then lost during purification. Furthermore, the variant enzyme was less stable during purification. The method had to be adapted by lowering the buffer flow to prevent disintegration of the multisubunit complex and concomitant loss of activity. Most likely, a higher lipid content improved stability and activity of the complex (6, 22).
The F129K QCR was insensitive to both stigmatellin and myxothiazol. Simultaneous resistance toward inhibitors of both center P domains was seen also in bacterial QCR, when the equivalent residue Phe144 was substituted by neutral residues as valine, glycine, leucine, and cysteine. This indicates that this residue forms a common surface of both inhibitor binding domains (9, 27, 30). Substitution of Phe129 by a charged residue will obviously abolish the observed nonpolar interaction with the hydrophobic tail of the inhibitor. This hinders not only binding of the inhibitors, as deduced from the resistance of F129K, but affects as well binding of the substrate, as indicated by the 5-fold increased Km value for DQH (see Table 1). In agreement, replacement mutations with nonaromatic residues in the equivalent position Phe144 in bacterial QCR caused a major loss in affinity for the substrate, resulting in a partially depleted center P binding pocket (29). The F129R enzyme had decreased sensitivity for stigmatellin and myxothiazol as shown by increased IC50 values relative to the wild-type QCR. In contrast to the lysine substitution, the cytochrome c reductase activity could still be inhibited. Phe129 is part of a nonpolar patch at the cavity surface with the cytochrome b residues Leu130, Phe179, and Ile147 as direct neighbors. Introduction of lysine may lead to local structural changes. Arginine may be less disturbing, since its side chain is larger, and the guanidino group can form planar stacking interactions with aromatic residues and is more likely than lysine to participate in stabilizing cation- interactions.
The midpoint potentials of both b hemes in the F129K variant were lowered by
The F129R mutation provoked less marked effects than the lysine substitution at this position. For F129R, the midpotential of heme bL was only slightly increased by 20-30 mV, and the turnover was lowered to 84%. The EPR spectrum of the reduced F129R QCR is comparable with that of the wild-type enzyme, and the variant QCR exhibited an unchanged H+/e- stoichiometry. As discussed above, the arginine side chain with its capacity to interact with -electron systems might be better suited to preserve the local architecture. However, the mutation affects the bifurcated electron transfer at center P, since superoxide production was increased to 25% of the total cytochrome c reductase activity. This is nearly as high as for E272D, for which 30% of the activity can be attributed to oxygen radical-producing bypass reactions (12).
Tyr279 has been postulated to participate in the positioning of the substrate ubiquinol (6). Alanine, serine, and cysteine replacements resulted in a distinct decrease of catalytic turnover (18, 25, and 55% of wild-type turnover, respectively). Apparently, the mutations make QCR a limiting step in respiratory growth, since the doubling times of the mutants increased
To further investigate the role of center P residues in catalysis, we analyzed pre-steady-state reduction kinetics of the cytochromes in enzymes with mutations in Glu272 and Tyr132. Both residues are located between the ubiquinol oxidation pocket and heme bL. Glu272 was recently shown to govern efficient ubiquinol oxidation (12). The residue is highly but not fully conserved in cytochrome b, which might question its suggested role as proton acceptor for ubiquinol oxidation. We recently pointed out that in - and -proteobacteria, in which this PEWY glutamate is replaced by valine or proline, at the position equivalent to His253 in yeast a glutamate is conserved. Based on structural considerations, we suggested that it can take over the proton transfer reaction (12). Tyr132 is one of the very few fully conserved cytochrome b residues (27, 29). Variants of these two residues exhibited decreased catalytic rates as compared with that of the wild-type enzyme (13% E272Q and 49% E272D (12); 48% Y132F (Table 1)) and increased superoxide production ( 50% E272Q and 30% E272D (12); 20% Y132F). Furthermore, the Km for DQH is increased by 8.4-fold for Y132F, the largest increase observed among the mutants described here as well as previously (12). The midpoint potentials of b and c1 hemes were not affected in any of these mutants. The Y132F enzyme exhibited disturbed electron transfer into the high potential chain as evident from diminished extent of cytochrome c1 reduction upon ubiquinol addition at both pH 7.0 and 8.8. The disturbed reduction of the high potential chain is most evident at pH 8.8 (Fig. 4), where only 25% of the maximal reduction can be reached, whereas the cytochrome c1 in the wild-type enzyme can be reduced to over 80%. A similar but less drastically disturbed reduction of cytochrome c1 is observed for enzyme with the E272D mutation. In the E272D enzyme, the extent of cytochrome c1 reduction was comparable with that in the wild-type enzyme, but the rate of reduction was decreased (Figs. 5 and 8). Very pronounced decreased reduction extent and disturbed kinetics were observed for the reduction of the b hemes in the presence of antimycin for both the Y132F and E272D variants. This result highlights a disturbed electron transfer to both high potential and low potential chains. In agreement, an increased superoxide production is observed for both of these mutations. It should be noted that the Y132F mutation, which has more pronounced effects on electron transfer at center P, shows less superoxide production than for the E272D substitution. Surprisingly, the pre-steady-state c1 reduction extent of E272Q was not affected with respect to the wild-type enzyme, despite showing the lowest turnover numbers for cytochrome c reduction and the highest level of superoxide production. Yet, the rates were slowed down by a factor of 2-5. The observation that ubiquinol oxidation can still occur in the E272Q enzyme indicates that the second proton donated by ubiquinol oxidation is able to find a slower, less efficient pathway out of center P. Still, the significantly decreased center P rate highlights the relevance of Glu272 in the rate-limiting step of ubiquinol oxidation.
To analyze the influence of the center P mutations on center N kinetics, ubiquinol oxidation through center P was blocked with inhibitors. Electron transfer at center N was completely inhibited by the Y132F mutation when electron transfer through center P was inhibited with stigmatellin. The Y132F mutation also caused a decrease in the extent of reduction of the b hemes via center N. Thus, the mutation at center P apparently prevents electron transfer at the quinone reduction site, indicating long range interactions within the protein. The same result was seen for the enzyme with the E272D mutation. Since no changes in the heme midpoint potentials of the Y132F and E272D enzymes were observed, the disturbed electron transfer either indicates that the substituted residues are not functionally equivalent or that the structure is perturbed. Our previous study indicates an altered environment of the Rieske protein in the E272D enzyme, as evident from shifted signals in the EPR spectrum of the reduced [2Fe-2S] cluster (12). This result indicates a modified binding mode of the ubiquinol, which might influence its oxidation and the electron transfer. In addition, the observed effects on pre-steady-state kinetics might be related to malfunction of the proposed parallel proton/electron transfer route from center P to heme bL that involves rotational displacement of Glu272 (5, 6). The shorter aspartate side chain could disrupt the proton relay. Similarly, the loss of the hydroxyl group by the Y132F mutation will destabilize the position of a water molecule, which is part of the suggested pathway and thereby affect coupled electron/proton transfer. Interestingly, the addition of one molecule cytochrome c per QCR dimer accelerated the reduction of the c1 heme in both the Y132F and E272D enzymes so that the pre-steady-state rates were consistent with the rates observed in the steady-state experiments. Apparently, cytochrome c binding activates the complex and enhances electron transfer, suggesting that structural alterations occur at center P in the mutated enzymes upon binding of the cytochrome c. In conclusion, in the present study, we could show that lysine substitution of Phe129, which is exposed in the hydrophobic substrate channel, leads to a negative respiratory growth phenotype with increased bypass reactions, uncoupling of the Q cycle, disturbed substrate binding, and shifted b heme midpoint potentials. The F129R mutant is less severely affected, suggesting that the structural integrity is better preserved. We could also show that substitutions of Tyr279, where mutations cause human mitochondrial disease, affect quinol binding and oxidation with little influence on electron transfer bypass reactions. Mutations in Glu272 and Tyr132 markedly affect center P catalysis, lowering the catalytic activity and elevating bypass reactions. Interestingly, mutations at center P that disturb ubiquinol oxidation, such as the Y132F and E272D, also strongly influence electron transfer kinetics at center N. This suggests a long range structural interaction between center P and center N. Another novel finding was that cytochrome c binding restores electron transfer in center P mutants that showed disturbed reduction of both high potential and low potential chains. This suggests that cytochrome c binding can elicit structural changes at center P. Crystallographic studies of yeast QCR with cytochrome c bound previously suggested a correlation of cytochrome c binding with center N quinone occupancy (23). The detailed characterization of the mutations supports the importance of all targeted residues for correct center P catalysis and discriminates the individual properties of the residues with respect to substrate binding and oxidation, bifurcated electron transfer, bypass reactions, and structural integrity. X-ray structure analysis of selected variants is in progress. The catalysis of ubiquinol oxidation is a robust process. Residual enzyme activity is observed in all cases, even with severe effects that abolish respiratory growth or disrupt heme ligation. However, all analyzed mutations provoke superoxide production, indicating that these residues are required for efficient catalysis to prevent bypass reactions deleterious for the organism.
* This work was supported by Deutsche Forschungsgemeinschaft Grant SFB 472 (to C. H., P. H., and F. M.), Boehringer Ingelheim Fonds (to T. W.), the Centre for Membrane Proteomics (to F. M.), and National Institutes of Health Grant GM 20379 (to B. L. T.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. 1 To whom correspondence should be addressed: Max-Planck-Institute of Biophysics, Dept. Molecular Membrane Biology, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany. Tel.: 49-69-6303-1062; Fax: 49-69-6303-1002; E-mail: Carola.Hunte{at}mpibp-frankfurt.mpg.de.
2 The abbreviations used are: QCR, ubiquinol:cytochrome c oxidoreductase; ISP, Rieske iron sulfur protein; DQH, decylubiquinol.
We thank Philipp Harbach and Lukas Hubener for practical assistance with the EPR studies.
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