[Peroxidase and b group cytochromes. On cyanide peroxidase complex in plants].
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Chemical Phenomena↗
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Assembly of the mitochondrial membrane system. MRP1 and MRP2, two yeast nuclear genes coding for mitochondrial ribosomal proteins.
Nuclear respiratory deficient mutants of Saccharomyces cerevisiae impaired in mitochondrial protein synthesis have been screened for lesions in ribosomal protein constituents. Two mutants, each representative of a separate pet complementation group, have been analyzed. One of the mutants, E795, was found to have altered mitochondrial ribosomes as evidenced by the absence of some ribosomal proteins. The second mutant studied, C167, appeared to have more grossly altered ribosomes that could not be isolated by standard preparative procedures. In addition to being defective in mitochondrial protein synthesis, the mutants exhibit an absence of "a" and "b" type cytochromes, are partially blocked in processing of intron bI4 of the apocytochrome b gene, have reduced levels of mitochondrial 15 S rRNA, and convert to rho- and rho 0 mutants at a high frequency. The wild type genes MRP1 and MRP2 were cloned by transformation of the pet mutations in E795 and C167, respectively, with a recombinant plasmid library of wild type yeast genomic DNA. MRP1 codes for a basic protein of 37 kDa with no significant homology to any known prokaryotic or eukaryotic ribosomal protein. MRP2 codes for a 14-kDa polypeptide homologous to protein S14 of the Escherichia coli small ribosomal subunit and to a chloroplast-encoded component of chloroplast ribosomes. The levels of MRP1 and MRP2 mRNAs were examined in glucose-repressed cells and in cells undergoing adaptation to aerobic metabolism of ethanol. The steady state concentrations of the mRNAs increased during the first 3 h of derepression, indicating that expression of these mitochondrial ribosomal protein genes is transcriptionally regulated by glucose in a fashion analogous to respiratory carriers such as cytochrome c.
Base Sequence↗
Dissecting and analyzing the secondary structure domains of group I introns through the use of chimeric intron constructs.
The mitochondrial genes of the yeast Saccharomyces cerevisiae are often interrupted by introns defined as either group I or group II. Some of the introns contained within the precursor RNAs of these genes will self splice in vitro. The fourth introns of apocytochrome b (bi4) and cytochrome oxidase (ai4) are group I introns that do not self splice in vitro, even though they can fold into the same RNA secondary structures that are characteristic of the self-splicing introns. They require an intron-encoded maturase protein and a nuclear-encoded protein (a tRNALeu synthetase) for splicing in vivo. We have divided these introns into several sequence or structural elements and assayed them individually for their ability to support self-splicing activity. This was done by replacing the equivalent elements from the self-splicing intron from Tetrahymena thermophila with the mitochondrial elements. These intron chimeras show that peripheral sequences and the elements that define the splice sites are adequate for self-splicing activity but that the central portions containing the catalytic cores of ai4 and bi4 are deficient; these cores are the likely targets of the splicing proteins. In addition, the catalytic activity of the Tetrahymena intron is remarkably resistant to the structural alterations that we have introduced; this suggests that this technique will be of general utility for studying the structural and functional relationships of elements contained within different RNAs.
Animals↗
Topography of the heme prosthetic group of cytochrome b-559 in the photosystem II reaction center.
The topography of the heme prosthetic group of cytochrome b-559 of the photosystem II reaction center was determined from measurement of the orientation of its alpha- and beta-polypeptides in thylakoid membranes of spinach chloroplasts and in osmotically disrupted cells of the cyanobacterium Synechocystis sp. PCC 6803. The accessibility to trypsin proteolysis of an epitope located near the solvent-exposed N-terminus of the beta-subunit was compared to that of the alpha-subunit, whose N- and C-termini had previously been localized from the trypsinolysis pattern to the stromal and lumenal sides of spinach thylakoid membranes, respectively [Tae et al. (1988) Biochemistry 27, 9075-9080; Vallon et al. (1989) Biochim. Biophys. Acta 975, 132-141]. The N-terminal epitope of the cyanobacterial beta-subunit was modified by introducing a tridecapeptide epitope, previously found to be immunoreactive, from the C-terminal region of the spinach chloroplast alpha-subunit. This epitope had no homology with the cyanobacterial alpha-subunit. The cells with the hybrid beta-subunit retained full photosynthetic activity. The intactness of membranes from osmotically shocked cyanobacteria was tested by trypsin inaccessibility to (a) the alpha-subunit C-terminus and (b) the manganese-stabilizing protein (MSP) of the oxygen-evolving complex that is on the lumenal side of the membrane. The loss after trypsinolysis of most of the beta-subunit immunoreactivity, under conditions where (i) the alpha-subunit was cleaved near the N-terminus in both spinach thylakoids and osmotically shocked cyanobacterial membranes and (ii) the MSP protein in cyanobacteria was not disrupted, implied that the orientation of the beta-subunit was parallel to that of the alpha-subunit in both kinds of membranes.(ABSTRACT TRUNCATED AT 250 WORDS)
Amino Acid Sequence↗
The mitochondrial genome of fission yeast: inability of all introns to splice autocatalytically, and construction and characterization of an intronless genome.
In this paper we report the inability of four group I introns in the gene encoding subunit I of cytochrome c oxidase (cox1) and the group II intron in the apocytochrome b gene (cob) to splice autocatalytically. Furthermore we present the characterization of the first cox1 intron in the mutator strain anar-14 and the construction and characterization of strains with intronless mitochondrial genomes. We provide evidence that removal of introns at the DNA level (termed DNA splicing) is dependent on an active RNA maturase. Finally we demonstrate that the absence of introns does not abolish homologous mitochondrial recombination.
Amino Acid Sequence↗
Resonance Raman spectroscopic identification of a histidine ligand of b595 and the nature of the ligation of chlorin d in the fully reduced Escherichia coli cytochrome bd oxidase.
Cytochrome bd oxidase is a bacterial terminal oxidase that contains three cofactors: a low-spin heme (b558), a high-spin heme (b595), and a chlorin d. The center of dioxygen reduction has been proposed to be a binuclear b595/d site, whereas b558 is mainly involved in transferring electrons from ubiquinol to the oxidase. Information on the nature of the axial ligands of the three heme centers has come from site-directed mutagenesis and spectroscopy, which have implicated a His/Met coordination for b558 (Spinner, F., Cheesman, M. R., Thomson, A. J., Kaysser, T., Gennis, R. B., Peng, Q., & Peterson, J. (1995) Biochem. J. 308, 641-644; Kaysser, T. M., Ghaim, J. B., Georgiou, C., & Gennis, R. B. (1995) Biochemistry 34, 13491-13501), but the ligands to b595 and d are not known with certainty. In this work, the three heme chromophores of the fully reduced cytochrome bd oxidase are studied individually by selective enhancement of their resonance Raman (rR) spectra at particular excitation wavelengths. The rR spectrum obtained with 413.1-nm excitation is dominated by the bands of the 5cHS b595(2+) cofactor. Excitation close to 560 nm yields a rR spectrum dominated by the 6cLS b558(2+) heme. Wavelengths between these values enhance contributions from both b595(2+) and b558(2+) chromophores. The rR bands of the ferrous chlorin become the major features with red laser excitation (595-650 nm). The rR data indicate that d2+ is a 5cHS system whose axial ligand is either a weakly coordinating protein donor or a water molecule. In the low-frequency region of the 441.6-nm spectrum, we assign a rR band at 225 cm-1 to the (b595)Fe(II)-N(His) stretching vibration, based on its 1.2-cm(-1) upshift in the 54Fe-labeled enzyme. This observation provides the first physical evidence that the proximal ligand of b595 is a histidine. Site-directed mutagenesis had suggested that His 19 is associated with either b595 or d (Fang, H., Lin, R. -J., & Gennis, R. B. (1989) J. Biol. Chem. 264, 8026-8032). On the basis of the present study, we propose that the proximal ligand of b595 is His 19. We have also studied the reaction of cyanide with the fully reduced cytochrome bd oxidase. In approximately 700-fold excess cyanide (approximately 35 mM), the 629-nm UV/vis band of d2+ is blue-shifted to 625 nm and diminished in intensity. However, the rR spectra at each of three different gamma(0) (413.1, 514.5, and 647.1 nm) are identical with or without cyanide, thus indicating that both b595 and d remain as 5cHS species in the presence of CN-. This observation leads to the proposal that a native ligand of ferrous chlorin d is replaced by CN- to form the 5cHS d2+ cyano adduct. These findings corroborate our companion study of the "as-isolated" enzyme in which we proposed a 5cHS d3+ cyano adduct (Sun, J., Osborne, J. P., Kahlow, M. A., Kaysser, T. M., Hill, J. J., Gennis, R. B., & Loehr, T. M. (1995) Biochemistry 34, 12144-12151). To further characterize the unusual and unexpected nature of these proposed high-spin cyanide adducts, we have obtained EPR spectral evidence that binding of cyanide to fully oxidized cytochrome bd oxidase perturbs a spin-state equilibrium in the chlorin d3+ to yield entirely the high-spin form of the cofactor.
Cytochrome a Group↗
Evidence for the presence of two terminal oxidases in the trypanosomatid Crithidia oncopelti.
Increasing concentrations of cyanide inhibited the respiration of whole cells of Crithidia oncopelti in a biphasic fashion. Approximately 80% inhibition was attained with 40 microM-KCN. No further inhibition occurred until the concentration of KCN reached approximately 200 microM. Thereafter inhibition rose gradually to 100% at 1500 microM-KCN. Difference spectra revealed the presence of two CO-reacting haemoproteins. These were shown to be two different functional oxidases by photochemical action spectra obtained by using laser light. One oxidase was identified as cytochrome a + a3 whilst the other had the properties of cytochrome o. Both oxidases could be detected in cells at all stages of growth by the above methods.
Animals↗
Unusual mitochondria in the hepatocytes of rats treated with a vitamin B12 analogue.
Adult male rats were administered hydroxy-cobalamin (c-lactam) (HCCL), a vitamin B12 analogue, by means of osmotic mini-pumps. The metabolic effects of HCCL are similar to those produced by simple dietary deficiency of vitamin B12 (Frenkel et al., 1976), but the morphological alterations in hepatic mitochondria are quite different in the two treatments. In HCCL-treated animals, hepatic mitochondria showed significant increases in number. In one rat, the hepatic mitochondria frequently had a single, elongated, circumferentially-oriented crista, with the inner compartment being occupied by a greatly augmented matrix. Such organelles appeared to be capable of division, as indicated by medially-partitioned forms. Numerous hooded mitochondria were present in the hepatic cells of the same animal. Almost every mitochondrion of whatever morphology was partially or completely shrouded by a cistern of rough endoplasmic reticulum. These mitochondrial morphological changes may be related to the chronic metabolic changes in this animal model of methylmalonic aciduria.
Animals↗
Femtosecond resolution of ligand-heme interactions in the high-affinity quinol oxidase bd: A di-heme active site?
Interaction of the two high-spin hemes in the oxygen reduction site of the bd-type quinol oxidase from Escherichia coli has been studied by femtosecond multicolor transient absorption spectroscopy. The previously unidentified Soret band of ferrous heme b(595) was determined to be centered around 440 nm by selective excitation of the fully reduced unliganded or CO-bound cytochrome bd in the alpha-band of heme b(595). The redox state of the b-type hemes strongly affects both the line shape and the kinetics of the absorption changes induced by photodissociation of CO from heme d. In the reduced enzyme, CO photodissociation from heme d perturbs the spectrum of ferrous cytochrome b(595) within a few ps, pointing to a direct interaction between hemes b(595) and d. Whereas in the reduced enzyme no heme d-CO geminate recombination is observed, in the mixed-valence CO-liganded complex with heme b(595) initially oxidized, a significant part of photodissociated CO does not leave the protein and recombines with heme d within a few hundred ps. This caging effect may indicate that ferrous heme b(595) provides a transient binding site for carbon monoxide within one of the routes by which the dissociated ligand leaves the protein. Taken together, the data indicate physical proximity of the hemes d and b(595) and corroborate the possibility of a functional cooperation between the two hemes in the dioxygen-reducing center of cytochrome bd.
Binding Sites↗
Self-splicing activity of the mitochondrial group-I introns from Aspergillus nidulans and related introns from other species.
The mitochondrial genome of Aspergillus nidulans contains several group-I introns. Each one has been assayed for its ability to self-splice in vitro in the absence of proteins. The intron from the apocytochrome b gene is unusual among subgroup IB4 introns in being able to self-splice, unlike a similar intron from Saccharomyces cerevisiae. The first intron in the cytochrome oxidase subunit-1 gene self-splices but only correctly completes the first step of splicing; cryptic 3' splice-sites are recognized instead and these are also used at a low frequency in vivo. The highly homologous intron from Podospora anserina completes both steps in vitro. The remaining introns do not self-splice. The correlation between subgroup category, the likely presence of specific tertiary interactions, and self-splicing activity is discussed.
Apoproteins↗
The electron transport chain of Bacterionema matruchotii.
The membrane fraction of Bacterionema matruchotii contains an electron transport chain with oxidizing activity for NADH and succinate. Respiration was inhibited by KCN, 2-heptyl-4-hydroxyquinoline-N-oxide, UV light irradiation and CO. UV light irradiation, analysis of membrane extracts, and reconstitution of respiration in UV light treated membranes suggested that respiration is mediated by a menaquinone derivative. The membranes contained cytochromes a, b, and c. Inhibition studies and the effect of KCN and CO on the cytochrome spectrum indicated the presence of an a+a3 cytochrome oxidase and cytochrome o. The membrane fraction from cells grown under O2-limiting conditions contained nitrate reductase activity. In B. matruchotii, electron transport is coupled to oxidative phosphorylation as judged by the effects of substrates and inhibitors on the intracellular ATP concentration.
Actinomycetaceae↗
A comprehensive characterization of a group IB intron and its encoded maturase reveals that protein-assisted splicing requires an almost intact intron RNA.
The group I intron (AnCOB) of the mitochondrial apocytochrome b gene from Aspergillus nidulans encodes a bi-functional maturase protein that is also a DNA endonuclease. Although the AnCOB intron self-splices, the encoded maturase protein greatly facilitates splicing, in part, by stabilizing RNA tertiary structure. To determine their role in self-splicing and in protein-assisted splicing, several peripheral RNA sub-domains in the 313 nucleotide intron were deleted (P2, P9, P9.1) or truncated (P5ab, P6a). The sequence in two helices (P2 and P9) was also inverted. Except for P9, the deleted regions are not highly conserved among group I introns and are often dispensable for catalytic activity. Nevertheless, despite the very tight binding of AnCOB RNA to the maturase and the high activity of the bimolecular complex (the rate of 5' splice-site cleavage was >20 min(-1) with guanosine as the cofactor), the intron was surprisingly sensitive to these modifications. Several mutations inactivated splicing completely and virtually all impaired splicing to varying degrees. Mutants containing comparatively small deletions in various regions of the intron significantly decreased binding affinity (generally >10(4)-fold), indicating that none of the domains that remained constitutes the primary recognition site of the maturase. The data argue that tight binding requires tertiary interactions that can be maintained by only a relatively intact intron RNA, and that the binding mechanism of the maturase differs from those of two other well-characterized group I intron splicing factors, CYT-18 and Cpb2. A model is proposed in which the protein promotes widespread cooperative folding of an RNA lacking extensive initial tertiary structure.
Apoproteins↗
[Demonstration of individual reactivity in the dynamics of changes in the concentration of mitochondrial cytochromes during the cirrhotic process].
Using repeated operative biopsies the author examined changes in the concentration of cytochromes a, b, c1 and c in mitochondrial protein of hepatocytes during the development of cirrhosis in rabbit liver. Individual responsiveness was discovered at the level of enzymatic constitution of the mitochondria, that is in the shifts in the specific weight of the respiratory chains in the protein of these organelles.
Animals↗
The cytochromes of Dictyostelium discoideum.
1. Low temperature (77 K), reduced oxidized difference spectra of "purified" mitochondria of Dictyostelium discoideum revealed the presence of b, c and a-type cytochromes. 2. The same components were also identifiable in intact organisms, the only possible discrepancies from the contribution by "microsomal" b-type cytochromes which showed major maxima at 533, 553, and 560 nm. 3. Room temperature carbon monoxide difference spectra of mitochondrial enriched fractions revealed at least three components reacting with CO. These were: cytochrome a3; another a-type cytochrome, a614; a b-type cytochrome. The latter component rapidly reacted with CO but ligand dissociation was observed over a period of about 20 min. 4. Microsomal membranes contained at least two CO-reacting components tentatively attributed to cytochromes P-450 and P-420 and it is suggested that cytochrome P-450 may be converted to cytochrome P-420 in the presence of CO and sodium dithionite. 5. The results are compared with those obtained for other protozoa.
Animals↗
Alternative respiration pathways in Schwanniomyces castellii. I. Isolation and characterization of cytochrome-deficient mutants.
We have isolated and studied cytochromic-deficient mutants of the amylolytic yeast Schwanniomyces castellii in order to study the possible contribution of cytochromes to alternative pathways. Three mutants were found, lacking cytochrome b, a + a3, or b and a + a3. All strains presented two alternative pathways, which were induced in the wild strain when cytochromic respiration was suppressed by growth in the presence of inhibitors, or without copper. If cytochromic respiration was absent, the Yxs yields in aerobiosis were higher than in anaerobiosis. This shows that the alternative pathways play a part in energy conservation. Cytochrome a + a3 did not appear to be directly involved in the alternative pathways.
Culture Media↗
Mosaic structure of the cox2 gene in the petite negative yeast Schizosaccharomyces pombe: a group II intron is inserted at the same location as the otherwise unrelated group II introns in the mitochondria of higher plants.
In contrast to homologous genes in other fungal mitochondrial genomes, the gene encoding subunit 2 of cytochrome oxidase (cox2) in several Schizosaccharomyces pombe strains contains a large group II intron. Its 2436 nucleotides can be folded into a typical group II intron secondary structure, possessing all the expected sequence motifs for subgroup IIA1 (Michel et al., 1989). This intron is remarkable for the following reasons: (i) Five nucleotide changes were observed compared with the continuous form of the cox2 gene in the reference strain 50 at the 3'-exon sequence, but not in the 5'-exon. (ii) One of these changes occurred at the splice point leading to a serine instead of a threonine residue in the deduced cox2 polypeptide. In all cases, the alterations resulted in the replacement of more frequently used codons by rare ones. (iii) Although the intron is able to undergo splicing, the sequence motifs thought to be necessary for interaction between the 5'-exon and the intron during the splicing process (the EBS1/IBS1 as well as the EBS2/IBS2 pairings) are unusual. (iv) The intron is inserted at the same location in the cox2 gene as the otherwise unrelated intron from higher plants.
Alleles↗
Electron transport components involved in hydrogen oxidation in free-living Rhizobium japonicum.
Membranes from free-living Rhizobium japonicum were isolated to study electron transport components involved in H2 oxidation. The H2/O2 uptake rate ratio in membranes was approximately 2. The electron transport inhibitors antimycin A, cyanide, azide, hydroxylamine, and 2-n-heptyl-4-hydroxyquinoline-N-oxide (HQNO) inhibited H2 uptake and H2-dependent O2 uptake significantly. H2-reduced minus O2-oxidized absorption difference spectra revealed peaks at 551.5, 560, and 603 nm, indicating the involvement of cytochromes c, b, and a-a3, respectively. H2-dependent cytochrome reduction was completely inhibited in the presence of 0.15 mM HQNO. This inhibition was relieved by the addition of 0.1 mM menadione. Evidence is presented for the involvement of two b-type cytochromes in H2 oxidation. One b-type cytochrome was not reduced by ascorbate and had an absorption peak at 560 nm. The reduction of this cytochrome by H2 was not inhibited by cyanide. A second b-type cytochrome, cytochrome b', was not reduced by H2 in the presence of cyanide. This cytochrome had an absorption peak at 558 nm. Carbon monoxide difference spectra with H2 as reductant provided evidence for the involvement of cytochrome o as well as cytochrome a3 in H2 oxidation. H2 uptake activity in cell-free extracts was inhibited by UV light irradiation. Most of the activity of the UV-treated extracts was restored with the addition of ubiquinone. The restored activity was inhibited by cyanide. A branched electron transport pathway from H2 to O2 is proposed.
Cyanides↗
Oxidation-reduction potentials of respiratory chain components in Thiobacillus A2.
(1) Cells of Thiobacillus A2 grown chemoautotrophically on thiosulfate or heterotrophically on succinate with oxygen contained b-, c-, o-, a- and a3-type cytochromes. The amount of cytochrome per mg of cell protein was much greater in thiosulfate-grown cells and differences in the relative concentrations of cytochromes were observed for the different growth conditions. (2) The half-reduction potentials at pH 7.0 (Em,7.0) and spectral maxima of c-, b-, a- and a3-type cytochromes were similar in cells grown aerobically with thiosulfate or with succinate as the growth substrate. (3) The half-reduction potential of the 'invisible', or high-potential copper, as determined from the potentiometric behavior of the carbon monoxide-reduced cytochrome a3 complex at pH 8.0, was 365 mV. (4) Reducing equivalents from thiosulfate appear to enter the respiratory chain at the cytochrome c level; however, studies in cell-free extracts were limited due to a loss in respiratory activity with thiosulfate as a substrate upon cell disruption.
Carbon Monoxide↗