Interactions in cytochrome oxidase: functions and structure

Characterization of the 101-kilobase-pair megaplasmid pKB1, isolated from the rubber-degrading bacterium Gordonia westfalica Kb1

The complete sequence of the circular 101,016-bp megaplasmid pKB1 from the cis-1,4-polyisoprene-degrading bacterium Gordonia westfalica Kb1, which represents the first described extrachromosomal DNA of a member of this genus, was determined. Plasmid pKB1 harbors 105 open reading frames. The predicted products of 46 of these are significantly related to proteins of known function. Plasmid pKB1 is organized into three functional regions that are flanked by insertion sequence (IS) elements: (i) a replication and putative partitioning region, (ii) a putative metabolic region, and (iii) a large putative conjugative transfer region, which is interrupted by an additional IS element. Southern hybridization experiments revealed the presence of another copy of this conjugational transfer region on the bacterial chromosome. The origin of replication (oriV) of pKB1 was identified and used for construction of Escherichia coli-Gordonia shuttle vectors, which was also suitable for several other Gordonia species and related genera. The metabolic region included the heavy-metal resistance gene cadA, encoding a P-type ATPase. Expression of cadA in E. coli mediated resistance to cadmium, but not to zinc, and decreased the cellular content of cadmium in this host. When G. westfalica strain Kb1 was cured of plasmid pKB1, the resulting derivative strains exhibited slightly decreased cadmium resistance. Furthermore, they had lost the ability to use isoprene rubber as a sole source of carbon and energy, suggesting that genes essential for rubber degradation are encoded by pKB1.

The effect of antibodies to subunit V of cytochrome oxidase on cyanide inhibition of electron transfer

Binding of antibodies raised against subunit V of mammalian cytochrome oxidase to the intact membranous enzyme is redox-sensitive, suggesting the existence of 'open' and 'closed' protein conformers (Freedman, J.A., Cooper, C.E., Leece, B., Nicholls, P. and Chan, S.H.P. (1988) Biochem. Cell Biol. 66, 1210-1217). Similar open and closed states for the oxygen-reacting site have been proposed to explain cyanide binding kinetics (Jensen, P., Wilson, M.T., Aasa, R. and Malmström, B.G. (1984) Biochem. J. 224, 829-837). We therefore examined cyanide inhibition of oxidase activity polarographically and spectrophotometrically using soluble oxidase preincubated with and without anti-subunit V or non-immune rabbit gamma-globulin. The subunit-specific antibody decreased the cyanide 'on' rate and essentially eliminated the rapid phase of cyanide binding. We conclude that (i), bound antibody blocks HCN binding; (ii), antibody and HCN probably bind to the same conformation of the oxidase and (iii), the 'open'-'closed' conformation change that modulates binding of HCN may be similar to that which modulates antibody binding. The results are consistent with some reciprocating models of electron transfer and energy transduction by the oxidase (cf., Wikström, M.K.F., Krab, K. and Saraste, M. (1981) Cytochrome Oxidase: A Synthesis).

Intrinsic tryptophan phosphorescence as a marker of conformation and oxygen diffusion in purified cytochrome oxidase

Cytochrome oxidase exhibits phosphorescence from tryptophan in aqueous solution in the absence of oxygen. The lifetime for the resting reduced enzyme suspended in Tween-20 is around 30 ms at pH 8. The lifetime is longest between pH 7 and 8 and decreases with lowering of pH. Oxygen quenches the phosphorescence with a Stern-Volmer quenching constant of approximately 5 x 10(7) M-1.s-1 at 5 degrees C whereas cytochrome c has no effect. We interpret these results to indicate that room temperature tryptophan phosphorescence arises from tryptophan(s) in structured region(s) remote from the hemes and that the protein does not impose a significant barrier for the diffusion of oxygen.

Modulation of cytochrome oxidase kinetics by indirect antibody action

Polyclonal antibodies raised against isolated subunit V from beef heart cytochrome oxidase or against the intact enzyme increase its apparent affinity for the substrate cytochrome c at the high-affinity site while diminishing the turnover at that site. At the low-affinity site the major action of both types of antibody is to reduce the apparent affinity for cytochrome c. At high ionic strengths the kinetic effect of anti-subunit V is very small although it still binds to the enzyme. The results are interpreted in terms of a model for the enzyme in which antibodies can modulate cytochrome oxidase kinetics by affecting the binding of cytochrome c, even if the antibody-binding site is on a subunit not directly involved in substrate binding.

Kinetic parameters of cytochrome c oxidase in rat skeletal muscle: effect of endurance training

The kinetic properties of cytochrome c oxidase (EC 1.9.3.1) in skeletal muscle tissue of sedentary and endurance-trained rats were studied. The initial velocity of the cytochrome c oxidase reaction was determined polarographically over a large range of cytochrome c concentrations and the maximal velocity (Vmax) and the Michaelis constant (Km) were calculated. The catalytic activity of cytochrome c oxidase in isolated mitochondria was also investigated. The training programme consisted of treadmill running for 2 h a day, 6 days a week, at a speed of 30 m min-1 and 30 degrees elevation, for 4 weeks. Vmax of cytochrome oxidase with respect to cytochrome c increased significantly from 254 to 310 mumol O2 min-1 g-1 protein in response to training (P less than 0.001), whereas Km remained unchanged (18.9 and 18.7 microM). The turnover number (TN) increased from 11.1 S-1 in sedentary rats to 16.6 S-1 in trained rats (P less than 0.001). The results suggest a qualitative change in the enzyme molecule in addition to a true Vmax change of cytochrome c oxidase in response to endurance training.

Two monoclonal antibody lines directed against subunit IV of cytochrome oxidase: a study of opposite effects

Two monoclonal lines of antibodies were isolated with specificities against the amino half of Subunit IV of beef heart cytochrome oxidase. The lines had nonoverlapping epitopes. Both bound to the matrix face of membranous oxidase, neither bound to the cytoplasmic face. One line (QA4/C4) stimulated electron transfer in soluble or membranous oxidase, while the other (QA4) inhibited that activity by both oxidase preparations. These effects on electron transfer activity were not altered by the inclusion or omission of detergent. ATP depressed the binding of either antibody to either soluble or membranous oxidase. In the absence of ATP, QA4/C4 stimulated electron transfer only in the high affinity phase of cytochrome c oxidation (with decreased KM and increased Vmax), causing slight inhibition in the low affinity phase (with decreased KM). In the presence of ATP, QA4/C4 abolished the high affinity phase, but did not alter the ATP influence on the low affinity phase. In the absence of ATP, antibodies of line QA4 abolished the low affinity phase, leaving a high affinity phase similar to that induced by ATP. In the presence of ATP, QA4 abolished the high affinity phase, leaving a low affinity phase similar to that seen with ATP alone. This behavior is consistent with the dissection of two catalytic sites for cytochrome c and more than one ATP affector site.

Structure and function of cytochrome-c oxidase

Recent works on the structure and the function of cytochrome-c oxidase are reviewed. The subunit composition of the mitochondrial enzyme depends on the species and is comprised of between 5 and 13 subunits. It is reduced to 1 to 3 subunits in prokaryotes. The complete amino acid composition has been derived from protein sequencing. Gene sequences are partially known in several eukaryote species. Metal centers are only located in subunits I and II. The mitochondrial cytochrome-c oxidase is Y-shaped; the arms of the Y cross the inner membrane, the stalk protrudes into the intermembrane space. The bacterial enzyme has a simpler, elongated shape. A number of data have been accumulated on the subunit topology and on their location within the protein. All available spectrometric techniques have been used to investigate the environment of the metal centers as well as their interactions. From the literature, attention must be paid to what may be considered or not as an active form. The steady improvement of the instrumentation has yielded evidence for different kinds of heterogeneities which could reflect the in vivo situation. The 'pulsed' and 'resting' conformers have been well characterized. The 'oxygenated' form has been identified as a peroxide derivative of the fully oxidized cytochrome-c oxidase. The mammalian enzyme has been isolated in fully active monomeric form which does not preclude the initially suggested dimeric behavior in situ. The role of the lipids is still largely investigated, mainly through reconstitution experiments. Kinetic studies of electron transfer between cytochrome c and cytochrome-c oxidase lead to a single catalytic site model to account for the multiphasic kinetics. Results related to the low temperature investigation of the intermediate steps in the reaction between oxygen and cytochrome-c oxidase received a sound confirmation by the resolution of compound A at room temperature. It is also pointed out that the so-called mixed valence state might not be a transient state in the catalytic reduction of oxygen. The functioning of cytochrome-c oxidase as a proton pump has been supported by a number of experimental results. Subunit III would be involved in this process. The redox link to the proton pump has been suggested to be at the Fea-CuA site. The molecular mechanism responsible for the proton pumping is still unknown.

Membrane potentials in reconstituted cytochrome c oxidase proteoliposomes determined by butyltriphenyl phosphonium cation distribution

Equilibration of the butyltriphenyl phosphonium (BTPP+) cation into cytochrome c oxidase reconstituted proteoliposomes was measured potentiometrically. The maximum membrane potential (delta psi) generated by oxidase activity was estimated to lie between -65 and -90 mV, vesicle interior negative, when internal BTPP+ binding is taken into account. Formation of delta psi was completely prevented by valinomycin and carbonyl-cyanide-p-trifluoromethoxyphenylhydrazone but only 10% inhibited by levels of N',N'-dicyclohexylcarbodiimide that abolish proton pumping by the oxidase. delta psi is thus maintained by at least one charge transfer process that does not involve proton movement. A nonlinear relationship was obtained between oxidase activity and steady-state delta psi. The value of delta psi estimated by BTPP+ distribution was lower than that calculated using the optical probes safranine and a carbocyanine dye. Possible reasons for this discrepancy are discussed.

Chemiosmotic coupling in cytochrome oxidase. Possible protonmotive O loop and O cycle mechanisms

Using the principle of specific vectorial ligand conduction, we outline directly coupled protonmotive O loop and O cycle mechanisms of cytochrome oxidase action that are analogous to protonmotive Q loop and Q cycle mechanisms of QH2 dehydrogenase action. We discuss these directly coupled mechanisms in the light of available experimental knowledge, and suggest that they may stimulate useful new research initiatives designed to elucidate the osmochemistry of protonmotive oxygen reduction in cytochrome oxidase.

Nucleotide sequence of the mitochondrial cytochrome oxidase subunit II gene in the yeast Hansenula saturnus

The gene for subunit II of cytochrome oxidase in the yeast Hansenula saturnus was previously shown to be located on a 1.7 kb HindIII-BamHI fragment of mitochondrial DNA (Lawson and Deters, accompanying paper). In this paper, we report the nucleotide sequence of a large part of this fragment, covering the coding region of the subunit II gene, designated coxII, and its 5' and 3' flanking regions. The coding region of the coxII gene consists of a continuous open reading frame, 744 nucleotides long, containing 6 in frame TGA codons. Examination of the sequence and alignment with known homologous gene sequences of other organisms indicates that TGA codes for tryptophan in H. saturnus mitochondria as it does in several other mitochondria. Despite considerable homology to subunit II of Saccharomyces cerevisiae, there are 9 codons used in coxII that are not used in the corresponding S. cerevisiae gene. CTT, which is believed to code for threonine in S. cerevisiae mitochondria, appears 3 times in coxII and probably codes for leucine. While the CGN family is rarely, if ever, used in S. cerevisiae mitochondria, CGT appears 4 times in coxII and probably codes for arginine. The deduced amino acid sequence, excluding the first ten amino acids at the N-terminus, is 81% homologous to the amino acid sequence of the S. cerevisiae subunit II protein. The first ten amino acids at the N-terminus are not homologous to the N-terminus of the S. cerevisiae protein but are highly homologous to the first ten amino acids of the deduced amino acid sequence of subunit II of Neurospora crassa. Minor variations of a transcription initiation signal and an end of message or processing signal reported in S. cerevisiae are found in the regions flanking the H. saturnus coxII gene. The subunit II gene contains numerous symmetrical elements, i.e. palindromes, inverted repeats, and direct repeats. Some of these have conserved counterparts in the S. cerevisiae subunit II gene, suggesting that they may be functionally or structurally important.

Identification and isolation of the cytochrome oxidase subunit II gene in mitochondria of the yeast Hansenula saturnus

Mitochondrial DNA from the petite negative yeast Hansenula saturnus has been isolated and sized by digestion with restriction enzymes. The size of the mitochondrial genome is approximately 47 kb. The gene for subunit II of cytochrome oxidase was localized in the genome by Southern blotting using a [32P]-labeled probe containing the subunit II gene of the yeast Saccharomyces cerevisiae. The probe hybridized to a 1.7 kb HindIII-BamHI fragment under stringent conditions (65 degrees C), indicating a high degree of homology between the S. cerevisiae and H. saturnus mitochondrial DNA fragments. The 1.7 kb fragment from H. saturnus was cloned into pBR322 and physically mapped. The map was used to obtain the nucleotide sequence of the subunit II gene (Lawson and Deters presented in the accompanying paper).

The reactivity of pulsed cytochrome c oxidase toward carbon monoxide

When pulsed cytochrome c oxidase is exposed to carbon monoxide in the absence of oxygen the enzyme is converted quickly to its CO-associated mixed valence state. The half-time for this reaction at 0 degree C is about 4 min. This is about 100 times faster than a similar reaction which begins with the resting form of the enzyme. The possible significance of this reaction in understanding the pulsed/resting phenomenon and the carbon monoxide oxygenase reactions of cytochrome oxidase is discussed.

Functional equivalence of monomeric (shark) and dimeric (bovine) cytochrome c oxidase

Cytochrome c oxidase isolated from hammerhead shark red muscle is monomeric in relation to the dimeric form of isolated bovine cytochrome c oxidase but in other ways bears a close resemblance to the enzyme isolated from mammalian tissue [1, 2]. Comparative studies of shark and bovine cytochrome c oxidase were extended to address the degree of functional similarity between the monomeric (shark) and dimeric (bovine) enzymes in the kinetics of peroxide binding and in the extent to which the catalytic action of the enzymes in vesicles can establish a proton gradient. Although the kinetics of peroxide binding and the proton pumping processes are complex, the dimeric and monomeric forms are quite similar with respect to these functional attributes. The kinetic heterogeneity of the process of peroxide binding is expressed in the shark enzyme as well as in the bovine enzyme, and both types of enzymes in vesicles can generate transmembrane proton gradients. On this basis we conclude that the dimeric state of isolated cytochrome c oxidase from mammalian sources is not essential for its function in vitro.