The molecular characterization of three transcriptional mutations in the yeast iso-2-cytochrome c gene

Three mutations, each of which causes overproduction of iso-2-cytochrome c, were characterized biochemically. Two, CYP3-4 and CYP3-15, were previously shown to be cis-dominant and map to the CYC7 locus which encodes the iso-2 protein, while the third, cyp1-16, maps to an unliked locus. All three mutations caused dramatically increased levels of transcription of the CYC7 gene, and the CYC7 mRNA in mutant cells was found to be the same size as that in wild type cells. The CYP3-4 mutation was found to be caused by the integration of a transposable element, Tyl, 269 base pairs 5' to the coding sequences. The CYP3-15 mutation was also found to alter the DNA, probably through a deletion or inversion with one endpoint 285 base pairs upstream from the coding sequence. The CYC7 gene in both wild type and mutant cells was not subject to catabolite repression.

Identity of the heme-not-containing protein in bovine heart cytochrome c1 preparation with the protein mediating c1-c complex formation--a protein with high glutamic acid content

A heme-not-containing protein was isolated from cytochrome c1 preparation by gel filtration after carboxymethylation and citraconylation. The amino acid sequence of this protein was determined by the analysis of tryptic and chymotryptic peptides as well as by solid-phase sequence analysis. It consisted of 78 amino acid residues and the molecular weight was calculated to be 9,175. This protein contained a high proportion of glutamic acid and glutamine (27% of the total residues) but no methionine, isoleucine, tyrosine, and tryptophan. The most notable feature was an acidic cluster of 8 consecutive glutamic acid residues near the amino(N)-terminus). The secondary structure was predicted to have a high proportion of helical content. The amino acid composition and N-terminal sequence of a protein independently prepared from bovine heart mitochondria, which is essential to the formation of the cytochrome c1-c complex, suggested that this colorless factor and the present heme-not-containing protein are identical. Evidence shows that another protein, called the non-heme protein, isolated from "two-band" cytochrome c1 preparation is also the same protein as that presented in this paper.

Affinity chromatography purification of cytochrome c oxidase and b-c1 complex from beef heart mitochondria. Use of thiol-sepharose-bound Saccharomyces cerevisiae cytochrome c

A method for simultaneous purification of cytochrome c reductase and cytochrome c oxidase using a cytochrome c affinity column is presented. Cytochrome c from Saccharomyces cerevisiae was linked to an activated thiol-Sepharose gel via its Cys-102 residue located far from the lysine residues on the front side of the molecule, responsible for the interaction with the reductase and oxidase. In previously reported affinity chromatography techniques these lysine residues most probably reacted with the column. Cytochrome c oxidase and reductase from bovine heart mitochondria bind specifically to the affinity column and can be recovered separately at different ionic strength in the elution buffer. The enzymes are highly pure and active.

The reaction of the trifluoromethylphenylcarbamylated lysine-13 derivative of horse cytochrome c with cytochrome oxidase

The kinetics of oxidation of horse cytochrome c and the trifluoromethylphenylcarbamylated lysine-13 derivative by cytochrome c oxidase (ferrocytochrome c: oxygen oxidoreductase, EC 1.9.3.1) were compared using both spectrophotometric and polarographic methods under different experimental conditions. The rate constants measured spectrophotometrically in 0.025 M tris-cacodylate buffers were similar with the two cytochrome at pH 7.8, but those with the derivative were slightly higher at pH 6. Rates measured with polarographic assays in these buffers were the same with the horse and the derivative cytochromes c at pH 6, but at pH 7.8 the rates with the derivative were less at cytochrome c concentrations between 0.05 and 0.5 micro M and were greater at higher concentrations. The pH optima in the polarographic assays of the derivative and the native pigments were different in 0.025 M Tris-cacodylate buffers; in spectrophotometric assays at pH 7.8 the trifluoromethylphenylcarbamylated lysine-13 cytochrome c showed a greater sensitivity to changes in ionic strength than did the native cytochrome. The variations in apparent Km and V values calculated from spectrophotometric and polarographic assays with the two cytochromes cannot be explained as due to changes in binding of cytochrome c to cytochrome oxidase. The large excess of O2 uptake seen in polarographic assays with horse cytochrome c over that expected from spectrophotometric measurements was not apparent with the trifluoromethylphenylcarbamylated lysine-13 derivative. Thus, the derivative seems to have decreased ability to form the combination of cytochrome c with the oxidase giving high turnover rates.

Sequence of the yeast iso-1-cytochrome c mRNA

The nucleotide sequence of the yeast iso-1-cytochrome c (CYC1) mRNA is presented. The mRNA was enriched by hybridization to cloned CYC1 DNA attached to a solid matrix: either nitrocellulose filters or diazobenzyloxymethyl cellulose powder. The sequence of the 5'-end of the mRNA was determined by the extension of a CYC1-specific dodecanucleotide primer; the sequence of the 3'-end was determined using a decanucleotide d(pT8-G-A) primer. The CYC1 mRNA begins 61 nucleotides 5' to the AUG initiation codon, extends through the coding sequence to 172 to 175 nucleotides 3' to the UAA termination codon, followed by the poly(A) tail. There are no intervening sequences. Some of the sequences that the CYC1 mRNA shares in common with other eukaryotic mRNAs are discussed.

Myxothiazol, a new inhibitor of the cytochrome b-c1 segment of th respiratory chain

Myxothiazol inhibited oxygen consumption of beef heart mitochondria in the presence and absence of 2,4-dinitrophenol, as well as NADH oxidation by submitochondrial particles. The doses required for 50% inhibition were 0.58 mol myxothiazol/mol cytochrome b for oxygen consumption of beef heart mitochondria, and 0.45 mol/mol cytochrome b for NADH oxidation by submitochondrial particles. Difference spectra with beef heart mitochondria and with cell suspensions of Saccharomyces cerevisiae revealed that myxothiazol blocked the electron transport within the cytochrome b-c1 segment of the respiratory chain. Myxothiazol induced a spectral change in cytochrome b which was different from and independent of the shift induced by antimycin. Myxothiazol did not give the extra reduction of cytochrome b typical for antimycin. Studies on the effect of mixtures of myxothiazol and antimycin on the inhibition of NADH oxidation indicated that the binding sites of the two inhibitors are not identical.

Guanidine hydrochloride induced unfolding of yeast iso-2 cytochrome c

The properties of the guanidine hydrochloride induced unfolding transition of iso-2 cytochrome c (iso-2) from Saccharomyces cerevisiae have been investigated by using kinetic and equilibrium techniques and have been compared with previously published studies of horse cytochrome c, which differs from iso-2 by 46% in amino acid sequence. Measurements of absorbance in the ultraviolet and visible spectral regions as a function of guanidine hydrochloride concentration give superimposable equilibrium transition curves with a midpoint of 1.15 M at pH 7.2 and 20 degrees C. A two-state analysis of the equilibrium data gives a Gibbs free energy of unfolding of 3.1 kcal/mol at 20 degrees C in the absence of denaturant. This agrees well with the predicted difference in stability between S. cerevisiae iso-2 and horse cytochrome c estimated from the free energies of transfer of buried hydrophobic groups. Three kinetic phases associated with folding can be detected throughout most of the transition zone. Two of the phases are detected by stopped-flow mixing experiments. The third phase is over within the mixing time of the flow experiments but is detectable by temperature jumps. At 20 degrees C, pH 7.2, the slowest phase (T1) is in the 20-100-s time range, the middle phase (T2) is in the 0.1-3-s range, and the fastest phase (T3) is on the order of 1 ms. For the reactions observed in the stopped flow (T1 and T2), a simplified three-state mechanism can be used to predict quantitatively the relative amplitudes of the phases and the equilibrium unfolding curve from the observed time constant data. Previously this same mechanism has been successful in describing the folding reactions of horse cytochrome c [Hagerman, P. J. (1977) Biopolymers 16, 731]. We suggest that the qualitative features of protein folding reactions may be conserved among homologous proteins.

The absorbance coefficient of beef heart cytochrome c1

Isolated cytochrome c1 contains endogenous reducing equivalents. They can be removed by treating the protein with sodium dithionite followed by chromatography. This treatment has no effect on the reaction with cytochrome c, nor does it alter the optical spectrum, or the polypeptide or amino acid composition of the protein. Both the titration of dithionite-treated ferrocytochrome c1 with potassium ferricyanide and the anaerobic titration of dithionite-treated ferricytochrome c1 with NADH in the presence of phenazine methosulphate lead to the same value for the absorbance coefficient of cytochrome c1: 19.2 mM-1 . cm-1 at 552.4 nm for the reduced-minus-oxidised form. This value was also obtained when the haem content was determined by comparing the spectra of the reduced pyridine haemochromes of cytochrome c and cytochrome c1. Comparison of the optical spectra of cytochrome c and cytochrome c1 by integration shows equal transition moments for the transitions in the porphyrin systems of both proteins. A set of equations with which the concentration of the cytochromes aa3, b, c and c1 can be calculated from one reduced-minus-oxidised difference spectrum of a mixture of these proteins.

An extensive deletion causing overproduction of yeast iso-2-cytochrome c

CYC7-H3 is a cis-dominant regulatory mutation that causes a 20-fold overproduction of yeast iso-2-cytochrome c. The CYC7-H3 mutation is an approximately 5 kb deletion with one breakpoint located in the 5' noncoding region of the CYC7 gene, approximately 200 base from the ATG initiation codon. The deletion apparently fuses a new regulatory region to the structural portion of the CYC7 locus. The CYC7-H3 deletion encompasses the RAD23 locus, which controls UV sensitivity and the ANP1 locus, which controls osmotic sensitivity. The gene cluster CYC7-RAD23-ANP1 displays striking similarity to the gene cluster CYC1-OSM1-RAD7, which controls, respectively, iso-1-cytochrome c, osmotic sensitivity and UV sensitivity. We suggest that these gene clusters are related by an ancient transpositional event.

DNA sequence of a mutation in the leader region of the yeast iso-1-cytochrome c mRNA

We have constructed a plasmid that selectively integrates adjacent to the CYC1 locus, which determines iso-1-cytochrome c in the yeast Saccharomyces cerevisiae. Different CYC1 alleles can be conveniently recovered by digestion of total DNA from transformed strains with BgI II, a restriction endonuclease that does not cut the vector or the CYC1 gene, followed by transformation of Escherichia coli, selecting the ampicillin resistance gene carried on the original vector. This procedure was used to clone the cyc1-362 gene, which contains an alteration in front of the AUG initiation codon. The cyc1-362 mutational causes a deficiency of the iso-1-cytochrome c protein but still allows transcription of the iso-1-cytochrome c mRNA. DNA sequence analysis showed that the cyc1-362 mutation consisted of two single-base-pair substitutions, producing an A leads to G change 18 nucleotides and a G leads to A change 30 nucleotides in front of the AUG initiation codon in the mRNA. The A leads to G change at position -18 resulted in the creation of an AUG triplet, which is proximal to the normal initiation site and out of phase with the normal reading frame. The deficiency of iso-1-cytochrome c is most simply explained by assuming that translation initiates at the more proximal abnormal AUG site but not at the normal AUG site.

The reaction between cytochrome c1 and cytochrome c

The kinetics of electron transfer between the isolated enzymes of cytochrome c1 and cytochrome c have been investigated using the stopped-flow technique. The reaction between ferrocytochrome c1 and ferricytochrome c is fast; the second-order rate constant (k1) is 3.0 . 10(7) M-1 . s-1 at low ionic strength (I = 223 mM, 10 degrees C). The value of this rate constant decreases to 1.8 . 10(5) M-1 . s-1 upon increasing the ionic strength to 1.13 M. The ionic strength dependence of the electron transfer between cytochrome c1 and cytochrome c implies the involvement of electrostatic interactions in the reaction between both cytochromes. In addition to a general influence of ionic strength, specific anion effects are found for phosphate, chloride and morpholinosulphonate. These anions appear to inhibit the reaction between cytochrome c1 and cytochrome c by binding of these anions to the cytochrome c molecule. Such a phenomenon is not observed for cacodylate. At an ionic strength of 1.02 M, the second-order rate constants for the reaction between ferrocytochrome c1 and ferricytochrome c and the reverse reaction are k1 = 2.4 . 10(5) M-1 . s-1 and k-1 = 3.3 . 10(5) M-1 . s-1, respectively (450 mM potassium phosphate, pH 7.0, 1% Tween 20, 10 degrees C). The 'equilibrium' constant calculated from the rate constants (0.73) is equal to the constant determined from equilibrium studies. Moreover, it is shown that at this ionic strength, the concentrations of intermediary complexes are very low and that the value of the equilibrium constant is independent of ionic strength. These data can be fitted into the following simple reaction scheme: cytochrome c2+1 + cytochrome c3+ in equilibrium or formed from cytochrome c3+1 + cytochrome c2+.

Electrostatic interaction of cytochrome c with cytochrome c1 and cytochrome oxidase

The reactions of horse heart cytochrome c with succinate-cytochrome c reductase and cytochrome oxidase were studied as a function of ionic strength using both spectrophotometric and oxygen electrode assay techniques. The kinetic parameter Vmax/Km for both reactions decreased very rapidly as the ionic strength was increased, indicating that electrostatic interactions were important to the reactions. A new semiempirical relationship for the electrostatic energy of interaction between cytochrome c and its oxidation-reduction partners was developed, in which specific complementary charge-pair interactions between lysine amino groups on cytochrome c and negatively charged carboxylate groups on the other protein are assumed to dominate the interaction. The contribution of individual cytochrome c lysine amino groups to the electrostatic interaction was estimated from the decrease in reaction rate caused by specific modification of the lysine amino groups by reagents that change the charge to 0 or -1. These estimates range from -0.9 kcal/mol for lysines immediately surrounding the heme crevice of cytochrome c to 0 kcal/mol for lysines well removed from the heme crevice region. The semiempirical relationship for the total electrostatic energy of interaction was in quantitative agreement with the experimental ionic strength dependence of the reaction rates when the parameters were based on the specific lysine modification results. The electrostatic energies of interaction between cytochrome c and its reductase and oxidase were nearly the same, providing additional evidence that the two reactions take place at similar sites on cytochrome c.

Binding of arylazidocytochrome c to yeast cytochrome c peroxidase

Cytochrome c derivatives modified with a photoactivatable arylazido group in selected lysine residues were irradiated in the presence of cytochrome c peroxidase (EC 1.11.1.5). A derivative modified at lysine 13 was able to cross-link to the enzyme and inhibit electron transfer activity. Complete inhibition of cytochrome c peroxidase activity was obtained when 1 mol of cytochrome c was covalently bound per mol of cytochrome c peroxidase. Chemical cleavage of the covalent complex has been used for a preliminary characterization of the site of cross-linking of cytochrome c to cytochrome c peroxidase. This linkage site was localized to the NH2 terminal part of cytochrome c peroxidase including residues 1-51.

Membrane-bound and water-soluble cytochrome c1 from Neurospora mitochondria

Cytochrome c1 is a subunit of ubiquinol--cytochrome c reductase (EC 1.10.2.2). In Neurospora crassa wild type 74A grown in the presence of chloramphenicol, the subunit is inserted only into the bilayer of the mitochondrial inner membranes without associating with other proteins. From these modified membranes a monodisperse (cytochrome c1)-Triton complex was isolated by subjecting the Triton-solubilized membranes to affinity chromatography on immobilized cytochrome c. A water-soluble pentamer of cytochrome c1 was prepared from the (cytochrome c1)-Triton complex by removing the detergent. By limited proteolytic digestion of the cytochrome c1-Triton complex with chymotrypsin, a water-soluble monomeric cytochrome c1 was prepared which has a molecular weight of only 24 000 as compared to 31 000 of the membrane-bound cytochrome c1. The 24 000-Mr cytochrome c1 and the 31 000-Mr cytochrome c1 have same light absorption spectra and cytochrome-c-binding properties. These results are used to propose the following model. Cytochrome c1 consists of a large hydrophilic part and a small hydrophobic part. The hydrophilic part extends from the mitochondrial inner membrane into the intermembrane space. This part carries the heme and interacts with cytochrome c. The hydrophobic part anchors the cytochrome c1 to the bilayer.

Isolation of the cytochrome-bc1 complex from rat-liver mitochondria

The cytochrome bc1 complex has been isolated from rat-liver mitochondria by two different procedures. The enzyme isolated by either procedure exhibits a specific cytochrome b and cytochrome c1 heme content of approximately 8 and 4 nmol/mg protein respectively. Both preparations contain only seven polypeptides on sodium dodecylsulfate gel electrophoresis, with the following apparent molecular weights: I, 50000; II, 46000; III, 33000; IV, 25000; V, 12500; VI, 10000; VII, 5600. The polypeptide composition is identical to that of the beef-heart enzyme isolated by cholate/ammonium sulfate fractionation. Furthermore, with the exception of subunit II (core protein 2), the apparent molecular weights of the subunits are identical in the rat-liver and beef-heart enzymes.

Deletion mapping of sequences essential for in vivo transcription of the iso-1-cytochrome c gene

The 5' termini of yeast CYC1 RNA molecules have been mapped, by nuclease S1 digestion of mRNA . DNA duplexes, to seven locations from 29 to 93 base pairs upstream from the initiating ATG codon. When the CYC1 gene is introduced into yeast in plasmid YEp13, substantially the same transcripts are made. Using this system to study in vivo gene expression, we measured the capacity of enzymatically produced DNA deletions to form the normal set of RNAs. Four regions of 5'-flanking DNA were identified as functional. Sequences within the region -242 to -139 are required for maximal CYC1 transcript formation; their deletion reduces transcription by a factor of 15 but does not change the pattern of 5' ends observed. Deletion of the sequence between -242 and -99 does not further change the overall transcript level but does affect the specificity of CYC1 mRNA starting. A deletion that extends from -242 to -75 causes both an additional shift in the pattern of 5' ends observed and a further large decrease (factor of 10--20) in CYC1 RNA level. Deletions that extend from -242 to -43, and particularly two deletions that extend still closer to the initiating ATG, cause the appearance of an abundant transcript which starts upstream of position -1078 and of minor transcripts starting in the region -325 to -245.

Rapid reduction of cytochrome c1 in the presence of antimycin and its implication for the mechanism of electron transfer in the cytochrome b-c1 segment of the mitochondrial respiratory chain

Antimycin, a specific and highly potent inhibitor of electron transfer in the cytochrome b-c1 segment of the mitochondrial respiratory chain, does not inhibit reduction of cytochrome c1 by succinate in isolated succinate-cytochrome c reductase complex under conditions where the respiratory chain complex undergoes one oxidation-reduction turnover. If a slight molar excess of cytochrome c is added to the isolated reductase complex in the presence of antimycin, there is rapid reduction of one equivalent of c type cytochrome by succinate, after which reduction of the remaining c type cytochrome is inhibited. Antimycin fully inhibits succinate-cytochrome c reductase activity of isolated succinate-cytochrome c reductase complex in which the b-c1 complex undergoes multiple turnovers in a catalytic fashion. In addition, when antimycin is added to isolated reductase complex in the presence of cytochrome c plus cytochrome c oxidase, the inhibitor causes a "crossover" in the steady state level of reduction of the cytochromes b and c1 comparable to this classical effect in mitochondria. On the basis of these results, it is suggested that linear schemes of electron transfer are not adequate to account for the site of antimycin inhibition and the mechanism of electron transfer in the cytochrome b-c1 segment of the respiratory chain. The effects of antimycin are consistent with cyclic electron transfer mechanisms such as the protonmotive Q cycle.

N.m.r. and e.p.r. characterization of [4-carboxy-2,6-dinitrophenyl-lysine]cytochromes c

Monosubstituted [4-carboxy-2,6-dinitrophenyl-lysine]cytochromes c were investigated by n.m.r. and e.p.r. Modification of Lys-13 or Lys-72 in ferricytochrome c by 4-chloro-3,5-dinitrobenzoate yields either of two different conformers that are rapidly exchanging in the native form. The equilibrium involves small local changes in the conformation of Met-80 (the sixth ligand) and Phe-82, as a result of whether Lys-13 is the 'on' or 'off' position in the Lys-13--Glu-90 salt bridge.

High-potential iron-sulfur proteins and their possible site of electron transfer

The electron-transfer mechanism of the Fe4S4 high-potential iron-sulfur proteins (HiPIP's) was explored via a stopped-flow spectrophotometric kinetic study of the reduction of Chromatium vinosum and Rhodopseudomonas gelatinosa HiPIP's by both native and trinitrophenyllysine-13 horse cytochrome c. The influence of electrostatic effects was also effectively partitioned from the redox process per se. The corrected rates were 12.3 X 10(4) and 3.8 X 10(4) M-1 s-1 for native with C. vinosum and R. gelatinosa HiPIP, respectively, and 17.5 X 10(4) and 5.46 X 10(4) M-1 s-1 for TNP-cytochrome c with the two HiPIP's, respectively. The faster rates of TNP-cytochrome c with the HiPIP's are unexpected in terms of possible steric interaction since lysine-13 is at the top of the heme crevice. In understanding the somewhat faster rates of the TNP-cytochrome c over native cytochrome c it is possible that (1) TNP-cytochrome c reacts more quickly since modification of the lysine-13 residue destabilizes somewhat the heme crevice or (2) in light of the hydrophobic nature of the trinitrophenyl group and the X-ray crystallographic structure of HiPIP, the TNP group facilitates electron transfer by interacting with a hydrophobic region on the HiPIP molecular surface. The region about the S4 sulfur atom is the most exposed and accessible hydrophobic region on the HiPIP surface, in addition to being the point of closest approach of the S4 to the external environment.

Interaction of cytochrome c with cytochrome bc1 complex of the mitochondrial respiratory chain

The binding of cytochrome c to the cytochrome bc1 complex of bovine heart mitochondria was studied. Cytochrome c derivatives, arylazido-labeled at lysine 13 or lysine 22, were prepared and their properties as electron acceptors from the bc1 complex were measured. Mixtures of bc1 complex with cytochrome c derivatives were illuminated with ultraviolet light and afterwards subjected to polyacrylamide gel electrophoresis. The gels were analysed using dual-wavelength scanning at 280 minus 300 and 400 minus 430 nm. It was found that illumination with ultraviolet light in the presence of the lysine 12 derivative produced a diminution of the polypeptide of the bc1 coplex having molecular weight 30 000 (band IV) and formation of a new polypeptide composed of band IV and cytochrome c. Band IV was identified as cytochrome c1, and it was concluded that this hemoprotein interacts with cytochrome c and contains its binding site in complex III of the mitochondrial respiratory chain. Illumination of the bc1 complex in presence of the lysine 22 derivative did not produce changes of the polypeptide pattern.