Stochastic versus augmented maximum parsimony method for estimating superimposed mutations in the divergent evolution of protein sequences. Methods tested on cytochrome c amino acid sequences.

Two ways of estimating superimposed fixed mutations in the divergent descent of proteins are examined. One method counts these in terms of a Poisson process operating within selective constraints. The other uses the maximum parsimony method to connect the contemporary sequences through intervening ancestral sequences in an evolutionary tree, and then, from the distribution of fixed mutations in dense regions of this genealogy, estimates how many fixations should be added to sparse regions. An algorithm is described which determines such augmented distances. The two methods yield similar estimates of genetic divergence when tested on a series of cytochrome c amino acid sequences. Within those constraints imposed by Darwinian selection, the dynamic behavior of the evolutionary divergence of proteins is described by the probabilistic pathways of the stochastic model. The parsimony model provides a valid Aufbau-Prinzip for examining which of those pathways occurred along a particular lineage. Concordance of the numerical magnitudes of genetic divergence estimates made by the two methods reveals them as logically consistent complements, not as mutually exclusive antagonists. Both methods indicate that cytochrome c has evolved in a non-uniform manner over geological time and more rapidly than previously estimated.     

Effect of crosslinking cytochrome c oxidase

Bovine heart cytochrome c oxidase and rat liver mitochondria were crosslinked in the presence and absence of cytochrome c. Biimidate treatment of purified cytochrome oxidase, which results in the crosslinkage of all of the oxidase protomers except subunit I when ? 20% of the free amines are modified, inhibits ascorbate-N,N,N′,N′-tetramethyl-p-phenylene diamine oxidase activity. Intermolecular crosslinking of cytochrome oxidase molecules, which results in the formation of large enzyme aggregates displaying rotational correlation times ? 1 ms, does not affect oxidase activity. Crosslinking of mitochondria covalently binds the cytochrome bc₁ and aa₃ complexes to cytochrome c, and inhibits steady-state oxidase activity. Addition of cytochrome c to purified cytochrome oxidase or to cytochrome c-depleted mitoplasts increases this inhibition slightly. Cytochrome c oligomers act as competitive inhibitors of native cytochrome c; however, crosslinking of cytochrome c to cytochrome c-depleted mitoplasts or purified cytochrome oxidase results in a catalytically inactive complex. These experiments indicate that cytochrome c oxidase subunit interactions are required for activity, and that cytochrome c mobility may be essential for electron transport between cytochrome c reductase and oxidase.     

The use of photoactivated hetero-bifunctional reagents to cross-link cytochrome c to proteins that bind it by electrostatic interactions.

Lysine residues of horse heart cytochrome c have been modified with N-5-azido-2-nitrobenzoyloxysuccinimide (ANB-NOS) and ethyl N-5-azido-2-nitrobenzoylaminoacetimidate (ANB-AI), reagents that attach nitroaryl azides onto the surface of proteins by amide and amidine linkages, respectively. When acting as an electron acceptor for yeast cytochrome b₂, modification of cytochrome c with ANB-NOS increases the K_m for the reaction by 2-fold, while modification with ANB-AI has little effect on the K_m. The V_max for the reduction of cytochrome c by cytochrome b₂ is reduced by the attachment of both compounds to cytochrome c. When the modified cytochromes c were illuminated with phosvitin, cytochrome b₅, and cytochrome c peroxidase, cross-linked species were formed which could be resolved by electrophoresis on polyacrylamide gels in the presence of sodium dodecyl sulfate. In each case the amidine derivatives of cytochrome c modified with ANB-AI showed more cross-linking than the amide derivatives of cytochrome c modified with ANB-NOS. When the modified cytochromes c were present in a 3-fold excess of phosvitin, cross-linked products containing 1, 2, and 3 molecules of cytochrome c covalently attached to phosvitin were observed. Photolysis of the modified cytochromes c in the presence of cytochrome b₅, resulted in the formation of a cross-linked 1:1 complex between the two cytochromes as well as higher order aggregates containing up to 5 molecules of cytochrome c plus cytochrome b₂. When cytochrome c peroxidase was illuminated with the modified cytochromes c, the predominant cross-linked product was a 1:1 complex between the two heme proteins. However, a cross-linked species was detected in small amounts with the apparent composition of 2 molecules of cytochrome c and 1 of the peroxidase. Also, a procedure is described for the synthesis of ANB-AI with ¹⁴C in the imidocarbon which is ultimately derived from ¹⁴CN.     

Cytochrome c interaction with membranes. Formylated cytochrome c.

A single species of tryptophan-59 formylated cytochrome c with a half-reduction potential of 0.085 ± 0.01 V at pH 7.0 was used to study its catalytic and functional properties. The spectral properties of the modified cytochrome show that the 6th ligand position is open to reaction with azide, cyanide, and carbon monoxide. Formylated cytochrome c binds to cytochrome c depleted rat liver and pigeon heart mitochondria with the precise stoichiometry of two modified cytochrome c molecules per molecule of cytochrome a (K_D of approx 0.1 μm). Formylated cytochrome c was reducible by ascorbate and was readily oxidized by cytochrome c oxidase. The apparent K_m value of the oxidase for the formylated cytochrome c was six times higher than for the native cytochrome and the apparent V was smaller. Formylated cytochrome c does not restore the oxygen uptake in C-depleted mitochondria but inhibits, in a competitive manner, the oxygen uptake induced by the addition of native cytochrome c. Formylated cytochrome c was inactive in the reaction with mitochondrial NADH-cytochrome c reductase but was able to accept electrons through the microsomal NADPH-cytochrome c reductase.     

Purification, physicochemical properties, and localization of cytochrome c in energy-transducing membranes from Mycobacterium phlei.

Cytochrome c from Mycobacterium phlei has been isolated and purified to homogeneity using an isoelectric focusing technique. The purified cytochrome c has a molecular weight of 12,600 ± 400 and exhibits an isoelectric point (pI) of 4.7 ± 0.05. The amino acid composition of cytochrome c shows a higher proportion of valine and arginine residues and a greatly reduced content of lysine residues when compared to Bacillus subtilis cytochrome c. This imparts less acidic character to the cytochrome c from M. phlei. The cytochrome c from M. phlei acts as the most effective electron acceptor for M. phlei NADH-cytochrome c reductase, while yeast and horse heart cytochrome c are not as efficient electron acceptors. The absence of correlation between the oxidation-reduction potential with the observed activity of NADH-cytochrome c reductase activity indicates that the electrochemical potential is not a sufficient determinant for bacterial cytochrome c function. In order to obtain information concerning the topology of respiratory components, two membrane systems from M. phlei were used; ghost preparations in which the membrane is oriented rightside out as in whole cells and membrane vesicles in which membranes are oriented inside out. Labeling of protoplast ghosts and membrane vesicles with lactoperoxidase-catalyzed iodination reveals that cytochrome c is localized on the outer membrane of protoplast ghosts, which is similar to that observed in mammalian mitochondria. The results also show that cytochrome c from M. phlei binds preferentially to basic phospholipids and not to neutral or acidic phospholipids. Scatchard analysis of the binding of cytochrome c to phosphatidyl ethanolamine shows high affinity (K_a of 3.79 × 10⁵M^?1) and low affinity (K_a of 3.75 × 10⁴M^?1) binding.     

Subunit Composition of Cytochrome c Oxidase in Mitochondria of Zea mays

Cytochrome c oxidase has been purified from Zea mays mitochondria by a solubilization with dodecyl maltoside followed by a simple and rapid two step fast protein liquid chromatographic method involving anion exchange on Mono Q and size exclusion chromatography on Superose 12. The preparation obtained was resolved by urea sodium dodecyl sulfate-polyacrylamide gel electrophoresis and had a subunit composition comprising polypeptides of apparent molecular masses of 48, 31, and 25 kilodaltons at least one at 16 and 11 kilodaltons and three subunits below 10 kilodaltons. Comparison with a purified yeast cytochrome c oxidase revealed that the four largest subunits showed similar electrophoretic mobilities. Subunits I and II cross-reacted with antibodies raised against the yeast homologous polypeptides. Polypeptides of the plant ubiquinone:cytochrome c reductase complex have also been identified by cross-reaction with antibodies raised against yeast cytochrome b and c₁ subunits and by inference from comigration.     

Cytochrome c interaction with membranes. II. Comparative study of the interaction of c cytochromes with the mitochondrial membrane

A comparative study of the interaction of various cytochromes c with phospholipid vesicles and with mitochondrial membranes was undertaken. Both mammalian and yeast types of cytochrome c bind preferentially in the oxidized form as evidenced by the midpoint redox potential (E_m 7.0) becoming more negative upon binding. Cytochrome c which is reincorporated into cytochrome c-depleted mitochondria is kinetically comparable with the native cytochrome c component; rate of cytochrome b oxidation is maximally restored at ratios of c₁:c:a of 1:1:1. Comparison between the electron paramagnetic spectrum of cytochrome c labeled at methionine 65 or cysteine 103 reveals that upon binding to the mitochondrial membrane, the former is immobilized and not the latter. This result suggests that cytochrome c binds to the membrane at the side at which methionine 65 is located.     

Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase

Background

Orthology is a central tenet of comparative genomics and ortholog identification is instrumental to protein function prediction. Major advances have been made to determine orthology relations among a set of homologous proteins. However, they depend on the comparison of individual sequences and do not take into account divergent orthologs.

Results

We have developed an iterative orthology prediction method, Ortho-Profile, that uses reciprocal best hits at the level of sequence profiles to infer orthology. It increases ortholog detection by 20% compared to sequence-to-sequence comparisons. Ortho-Profile predicts 598 human orthologs of mitochondrial proteins from Saccharomyces cerevisiae and Schizosaccharomyces pombe with 94% accuracy. Of these, 181 were not known to localize to mitochondria in mammals. Among the predictions of the Ortho-Profile method are 11 human cytochrome c oxidase (COX) assembly proteins that are implicated in mitochondrial function and disease. Their co-expression patterns, experimentally verified subcellular localization, and co-purification with human COX-associated proteins support these predictions. For the human gene C12orf62, the ortholog of S. cerevisiae COX14, we specifically confirm its role in negative regulation of the translation of cytochrome c oxidase.

Conclusions

Divergent homologs can often only be detected by comparing sequence profiles and profile-based hidden Markov models. The Ortho-Profile method takes advantage of these techniques in the quest for orthologs.     

Cytochrome c interactions with membranes. A photoaffinity-labeled cytochrome c.

The aryl azide, 2,4-dinitro-5-fluorophenylazide, was reacted with horse heart cytochrome c to give a photoaffinity-labeled derivative of this heme protein. The modified cytochrome c, with one to two dinitroazidophenyl groups per mole of the enzyme, has a half-reduction potential the same (± 10 mV) as native cytochrome c. The dissociation constant for the modified cytochrome c from cytochrome c-depleted mitochondrial membranes and the apparent K_m for the reaction with cytochrome c oxidase were each five to six times greater than the values for native cytochrome c. Irradiation of cytochrome c-depleted mitochondrial membranes supplemented with an excess of photoaffinity-labeled cytochrome c resulted in covalent binding of the derivative to the mitochondrial membranes. Fractionation of the irradiated mitochondria in the presence of detergents and salts followed by chromatography on agarose, Bio-Gel A, showed that labeled cytochrome c was bound covalently to cytochrome c oxidase in a 1:1 molar complex. The covalently linked cytochrome c-cytochrome c oxidase complex was active in mediating the electron transfer between N,N,N′,N′-tetramethyl-p-phenylenediamine/ascorbate and the oxidase.     

Cytochrome c interaction with membranes. Interaction of cytochrome c with isolated membrane fragments and purified enzymes

The midpoint redox potential of cytochrome c and the electron paramagnetic resonance spectra of nitroxide labeled cytochromes c were measured as a function of binding to purified cytochrome c oxidase, cytochrome c peroxidase, cytochrome b₅ and succinate—cytochrome c reductase. The midpoint redox potential of horse heart cytochrome c is lowered in the presence of cytochrome c oxidase and succinate-cytochrome c reductase, but is unchanged in the presence of cytochrome c peroxidase or cytochrome b₅. Further evidence of binding is afforded by an increase in correlation time, T_c, of the spin-labeled cytochrome c at methionine 65 upon binding to cytochrome c peroxidase, cytochrome c oxidase and succinate—cytochrome c reductase. The changes in midpoint redox potential and electron paramagnetic resonance spectrum of the spin-labeled derivative upon binding can either be the consequence of specific interaction leading to formation of ES complexes, or it can be due to nonspecific electrostatic interaction between positively charged groups on cytochrome c and negatively charged groups on the isolated cytochrome preparations.     

Calcium-induced release of cytochrome c from cardiolipin nanodisks: Implications for apoptosis

Miniature bilayer membranes comprised of phospholipid and an apolipoprotein scaffold, termed nanodisks (ND), have been used in binding studies. When ND formulated with cardiolipin (CL), but not phosphatidylcholine, were incubated with cytochrome c, FPLC gel filtration chromatography provided evidence of a stable binding interaction. Incubation of CL ND with CaCl₂ resulted in a concentration-dependent increase in sample turbidity caused by ND particle disruption. Prior incubation of CL ND with cytochrome c increased CL ND sensitivity to CaCl₂-induced effects. Centrifugation of CaCl₂-treated CL ND samples yielded pellet and supernatant fractions. Whereas the ND scaffold protein, apolipophorin III, was recovered in the pellet fraction along with CL, the majority of the cytochrome c pool was in the supernatant fraction. Moreover, when cytochrome c CL ND were incubated with CaCl₂ at concentrations below the threshold to induce ND particle disruption, FPLC analysis showed that cytochrome c was released. Pre-incubation of CL ND with CaCl₂ under conditions that do not disrupt ND particle integrity prevented cytochrome c binding to CL ND. Thus, competition between Ca²⁺ and cytochrome c for a common binding site on CL modulates cytochrome c binding and likely plays a role in its dissociation from CL-rich cristae membranes in response to apoptotic stimuli.     

Characterisation of ionisations that influence the redox potential of mitochondrial cytochrome c and photosynthetic bacterial cytochromes c2

Several cytochromes c₂ from the Rhodospirillaceae show a pH dependence of redox potential in the physiological pH range which can be described by equations involving an ionisation in the oxidised form (pK_o) and one in the reduced form (pK_r). These cytochromes fall into one of two groups according to the degree of separation of pK_o and pK_r. In group A, represented here by the Rhodomicrobium vannielii cytochrome c₂, the separation is approx. one pH unit and the ionisation is that of a haem propionic acid. Members of this group are unique among both cytochromes c₂ and mitochondrial cytochromes c in lacking the conserved residue Arg-38. We propose that the role of Arg-38 is to lower the pK of the nearby propionic acid, so that it lies out of the physiological pH range. Substitution of this residue by an uncharged amino acid leads to a raised pK for the propionic acid. In group B, represented here by Rhodopseudomonas viridis cytochrome c₂, the separation between pK_o and pK_r is approx. 0.4 pH unit and the ionisable group is a histidine at position 39. This was established by NMR spectroscopy and confirmed by chemical modification. Only a few other members of the cytochrome c₂/mitochondrial cytochrome c family have a histidine at this position and of these, both Crithidia cytochrome c-557 and yeast cytochrome c were found to have a pH-dependent redox potential similar to that of Rps. viridis cytochrome c₂. Using Coulomb's law, it was found that the energy required to separate pK_o and pK_r could be accounted for by simple electrostatic interactions between the haem iron and the ionisable group.     

Comparative study on stabilization mechanism of monomeric cytochrome c5 from deep-sea piezophilic Shewanella violacea

Monomeric cytochrome c₅ from deep-sea piezophilic Shewanella violacea (SVcytc₅) was stable against heat and denaturant compared with the homologous protein from shallow-sea piezo-sensitive Shewanella livingstonensis (SLcytc₅). Here, the SVcytc₅ crystal structure revealed that the Lys-50 side chain on the flexible loop formed a hydrogen bond with heme whereas that of corresponding hydrophobic Leu-50 could not form such a bond in SLcytc₅, which appeared to be one of possible factors responsible for the difference in stability between the two proteins. This structural insight was confirmed by a reciprocal mutagenesis study on the thermal stability of these two proteins. As SVcytc₅ was isolated from a deep-sea piezophilic bacterium, the present comparative study indicates that adaptation of monomeric SVcytc₅ to high pressure environments results in stabilization against heat.     

Characterization and expression of the co-transcribed cyc1 and cyc2 genes encoding the cytochrome c4 (c552) and a high-molecular-mass cytochrome c from Thiobacillus ferrooxidans ATCC 33020

The sequence of the cyc1 gene encoding the Thiobacillus ferrooxidans ATCC 33020 c₅₅₂ cytochrome, shows that this cytochrome is a 21-kDa periplasmic c₄-type cytochrome containing two similar monohaem domains. The kinetics of reduction and the fact that cytochromes c₄ are considered to be physiological electron donors of cytochrome oxidases suggest that the last steps of the iron respiratory chain are: rusticyanin→cytochrome c₄→cytochrome oxidase. In Thiobacillus ferrooxidans, cyc1 is co-transcribed with the cyc2 gene, encoding a high-molecular-mass monohaem cytochrome c. This suggests that the cytochromes encoded by these genes belong to the same electron transfer chain.     

Purification and characterization of low potential c cytochromes from Desulfovibrio desulfuricans membranes

Desulfovibrio desulfuricans grown in a lactate-sulfate medium produces, in addition to soluble cytochromes, c-type cytochromes which appear to be integral membrane proteins. Two cytochromes can be separated, an abundant 15 kDa cytochrome and a 22 kDa cytochrome. Both have optical spectra characteristics of c-type cytochromes. The 15 kDa cytochrome shows two n = 1 components in potentiometric redox titrations with midpoint potentials at −130 and −270 mV in the membrane; both were slightly lower in detergent-solubilized preparations. We suggest a designation of cytochrome cc_m for this species. Its properties suggest a function as a transmembrane electron carrier between hydrogen and sulfate.     

Nonredundant Roles for Cytochrome c2 and Two High-Potential Iron-Sulfur Proteins in the Photoferrotroph Rhodopseudomonas palustris TIE-1

The purple bacterium Rhodopseudomonas palustris TIE-1 expresses multiple small high-potential redox proteins during photoautotrophic growth, including two high-potential iron-sulfur proteins (HiPIPs) (PioC and Rpal_4085) and a cytochrome c₂. We evaluated the role of these proteins in TIE-1 through genetic, physiological, and biochemical analyses. Deleting the gene encoding cytochrome c₂ resulted in a loss of photosynthetic ability by TIE-1, indicating that this protein cannot be replaced by either HiPIP in cyclic electron flow. PioC was previously implicated in photoferrotrophy, an unusual form of photosynthesis in which reducing power is provided through ferrous iron oxidation. Using cyclic voltammetry (CV), electron paramagnetic resonance (EPR) spectroscopy, and flash-induced spectrometry, we show that PioC has a midpoint potential of 450 mV, contains all the typical features of a HiPIP, and can reduce the reaction centers of membrane suspensions in a light-dependent manner at a much lower rate than cytochrome c₂. These data support the hypothesis that PioC linearly transfers electrons from iron, while cytochrome c₂ is required for cyclic electron flow. Rpal_4085, despite having spectroscopic characteristics and a reduction potential similar to those of PioC, is unable to reduce the reaction center. Rpal_4085 is upregulated by the divalent metals Fe(II), Ni(II), and Co(II), suggesting that it might play a role in sensing or oxidizing metals in the periplasm. Taken together, our results suggest that these three small electron transfer proteins perform different functions in the cell.     

Ligand Binding to cytochrome c and other related haem proteins and peptides. Part II. Kinetic studies

The kinetics of ligand binding to native cytochrome c and myoglobin seem to suggest that both proteins bind exogenous ligands by an S_N2 mechanism, while the form of cytochrome c which lacks the 695 nm absorption band binds ligands by a limiting S_N1 mechanism. It is suggested that the rate-limiting step in the S_N2 mechanism is different from that in the S_N1 mechanism.     

An Unconventional Copper Protein Required for Cytochrome c Oxidase Respiratory Function under Extreme Acidic Conditions

Very little is known about the processes used by acidophile organisms to preserve stability and function of respiratory pathways. Here, we reveal a potential strategy of these organisms for protecting and keeping functional key enzymes under extreme conditions. Using Acidithiobacillus ferrooxidans, we have identified a protein belonging to a new cupredoxin subfamily, AcoP, for “acidophile CcO partner,” which is required for the cytochrome c oxidase (CcO) function. We show that it is a multifunctional copper protein with at least two roles as follows: (i) as a chaperone-like protein involved in the protection of the Cu_A center of the CcO complex and (ii) as a linker between the periplasmic cytochrome c and the inner membrane cytochrome c oxidase. It could represent an interesting model for investigating the multifunctionality of proteins known to be crucial in pathways of energy metabolism.