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PubMed2001

pH-induced conformational transition in the soluble CuA domain of Paracoccus denitrificans cytochrome oxidase.

The pH-induced conformational transition in the CuA domain of subunit II of cytochrome oxidase of Paracoccus denitrificans (PdII) has been investigated using various spectroscopic and stopped-flow kinetic methods. UV-visible absorption and circular dichroism studies showed that an increase in pH from 6 to 10 leads to a conformation change with pK(a) = 8.2 associated with the CuA site of the protein. The secondary structure of the protein was, however, shown to remain unchanged in these two conformational states. Thermal and urea-induced unfolding studies showed that the "low-pH" conformation is more stable compared to the "high-pH" conformation of the protein. Moreover, the overall stability of the protein was found to decrease on reduction of the metal centers in the low-pH form, while the oxidation state of the metal centers did not have any significant effect on the overall stability of the protein in the high-pH form. Stopped-flow pH-jump kinetic studies suggested that the conformational transition is associated with a slow deprotonation step followed by fast conformational equilibrium. The results are discussed in the light of understanding the pH-induced conformational change in the beta-barrel structure of the protein and its effect on the coordination geometry of the metal site.

Binding Sites↗
PubMed1982

Novel features of animal mtDNA evolution as shown by sequences of two rat cytochrome oxidase subunit II genes.

The sequence of the region of the mitochondrial genome that encodes cytochrome oxidase subunit II (COII) has been determined for each of two closely related rat species, Rattus norvegicus and R. rattus. Comparison of the two sequences shows that 94.4% of the nucleotide substitutions are silent. The occurrence of this high proportion of silent substitutions leads us to propose that the rapid evolution of mtDNA relative to nuclear DNA is due only to silent changes and that amino acid-altering substitutions accumulate in nuclear and mtDNA at comparable rates. Other novel features of the nucleotide substitution pattern in the rat COII gene are a high transition/transversion ratio (8.0:1) and a strong bias toward C in equilibrium T transitions in the light strand. Comparison of the R. norvegicus COII sequence with the bovine and human sequences show that there may be selective constraints on some silent positions within the gene and that its rate of evolution may be different in different mammalian lineages.

Animals↗
PubMedDate not supplied

The distribution of callosal connections correlates with the pattern of cytochrome oxidase stripes in visual area V2 of macaque monkeys.

In visual area V2 of monkeys, cytochrome oxidase (CO) histochemistry reveals a system of stripe-like subregions where densely labeled thick and thin stripes and pale interstripes can be recognized. Several lines of evidence suggest that CO stripe-like subregions are associated with functional streams in the visual cortex. In the present study, the distribution of retrogradely labeled callosal cells in V2 and the pattern of CO staining were correlated using tangential sections through the flattened cortex. Spectral and coherency analyses of the callosal and CO patterns were performed to assess quantitatively the degree of spatial correlation between these two patterns. The results showed that labeled callosal cells accumulated along the V1/V2 border and in finger-like bands that protruded up to 7-8 mm into V2. These callosal bands were in register with thick and thin CO stripes, with relatively few labeled callosal cells found in interstripe regions. This finding supports the notion that the distribution of callosal connections in the visual cortex is dictated not only by the topography of visual areas, but also by the arrangement of cortical functional streams. Further, these results extend to interhemispheric pathways the notion of functional specificity currently associated mainly with some visual intrahemispheric pathways.

Animals↗
PubMed1996

Contingency tests of neutrality using intra/interspecific gene trees: the rejection of neutrality for the evolution of the mitochondrial cytochrome oxidase II gene in the hominoid primates.

Contingency tests of neutrality are performed using mitochondrial cytochrome oxidase II (COII) DNA sequences from hominoid primates, including humans. An intra-/interspecific haplotype tree is estimated, including a statistical assessment of ambiguities in tree topology and branch lengths. Four functional mutational categories are considered: silent and replacement substitutions in the transmembrane portion of the COII molecule, and silent and replacement substitutions in the cytosolic portion. Three tree topological mutational categories are used: intraspecific tips, intraspecific interiors, and interspecific fixed mutations. A full contingency analysis is performed, followed by nested contingency analyses. The analyses indicate that replacement mutations in the cytosolic portion are deleterious, and replacement mutations in the transmembrane portion and silent mutations throughout tend to be neutral. These conclusions are robust to ambiguities in tree topology and branch lengths. These inferences would have been impossible with an analysis that only contrasts silent and replacement vs. polymorphic and fixed. Also, intraspecific interior mutations have similar evolutionary dynamics to fixed mutations, so pooling tip and interior mutations into a single "polymorphic" class reduces power. Finally, the detected deleterious selection causes lowered inbreeding effective sizes, so arguments for small effective sizes in recent human evolutionary history based upon mitochondrial DNA may be invalid.

Animals↗
PubMed1990

Roles for enteric d-type cytochrome oxidase in N2 fixation and microaerobiosis.

Escherichia coli strains that lacked the d-type cytochrome oxidase, the terminal oxidase with a high affinity for O2, grew anaerobically as well as the wild type did and were not impaired in the ability to evolve H2 from either glucose or formate. The anaerobic synthesis and activity of nitrogenase in transconjugants of these strains carrying Klebsiella pneumoniae nif genes were also normal. However, the behavior towards O2 of anaerobically grown bacteria lacking the d-type oxidase differed from that of the wild type in the following ways: the potential O2 uptake was lower, H2 evolution and nitrogenase activity supported by fermentation were more strongly inhibited by O2, and microaerobic O2-dependent nitrogenase activity in the absence of a fermentable carbon source did not occur. These results show that the d-type oxidase serves two functions in enteric bacteria--to conserve energy under microaerobic conditions and to protect anaerobic processes from inhibition by O2.

Aerobiosis↗
PubMed1992

Some observations upon the distribution of cytochrome oxidase activity in the globus pallidus of the rat.

The histochemical distribution of the enzyme cytochrome oxidase (CO) was explored in the globus pallidus (GP) of the rat, and it was compared with the distribution of acetylcholinesterase (AChE), another well-known enzyme of the basal ganglia in mammals. This neurochemical research illustrates two prominent findings. In the first place, a regional compartmentalization was detected in the pallidal distribution of CO, in which dorsal territories of the GP exhibited a more abundant presence of this enzyme. In addition, the distribution of this mitochondrial enzyme was not uniform all over those dorsal pallidal territories. Thus, the pallidal concentration of CO was gradually decreasing dorsoventrally and lateromedially, and, sometimes, areas highly stained for CO were intermingled with zones in which this enzyme was less conspicuous. In the second place, the pallidal distribution of AChE was the opposite of that found for CO (i.e. more abundant in ventral and medial territories of the GP). The functional significance of these findings is discussed in the light of the heterogeneous hodological neuroanatomy of the GP of rodents.

Acetylcholinesterase↗
PubMed1990

Regulation of cytochrome oxidase protein levels by functional activity in the macaque monkey visual system.

The activity of cytochrome oxidase (CO), a mitochondrial enzyme of oxidative energy metabolism, is regulated by nerve cell functional activity. The mechanism of CO activity regulation was studied using histochemical and immunohistochemical methods to show the distributions of CO activity and protein, respectively, in the macaque monkey visual system under normal and experimental conditions. In normal animals, patterns of CO activity were found to reflect underlying patterns of CO protein distribution; for example, puffs of high CO activity in cortical area 17 contained high levels of CO protein. Experimental animals were injected monocularly with TTX for 3-4 weeks; this treatment blocks retinal impulses in the injected eye and results in decreased CO activity in lateral geniculate laminae and striate cortical columns normally driven by the treated eye. The experimentally induced decreases in CO activity were also found to reflect underlying parallel decreases in CO protein levels. These results suggest that CO activity is regulated mainly at the level of the local amount rather than the turnover number of the enzyme and imply that the rates of CO synthesis and/or degradation are regulated by neural functional activity.

Animals↗
PubMed1984

Peroxide interaction with pulsed cytochrome oxidase. Optical and EPR studies.

EPR and optical analysis of the 420 nm form of cytochrome oxidase (Kumar, C., Naqui, A., and Chance, B. (1984) J. Biol. Chem. 259, 2073-2076) shows that 1) the 420 nm form possesses a 605 nm band, g = 5 EPR signals, and a slightly blue shifted 655 nm band; 2) the reaction of H2O2 with the 420 nm form generates the peroxide complex (Soret band at 427 nm) with the formation of a 580 nm band and abolition of both the 655 nm band and the g = 5 EPR signal. Comparison of our results with past data shows that various forms of oxidase formed from the resting oxidase through different protocols may be identified to be either the 420 nm or the 427 nm form and leads to identification of a peroxy intermediate during oxidase turnover.

Electron Spin Resonance Spectroscopy↗
PubMed1993

Mitochondrial and nuclear gene expression for cytochrome oxidase subunits are disproportionately regulated by functional activity in neurons.

Mitochondrial respiratory complexes such as cytochrome oxidase (CO) contain both mitochondrial- and nuclear-encoded subunits. To determine whether mitochondrial and nuclear gene expression are regulated proportionately in neurons, we analyzed CO subunit mRNA and mitochondrial DNA (mtDNA) levels by in situ hybridization and grain counting in the visual system of normal and monocular TTX-treated monkeys. We compared the regulation of these molecules with the regulation of CO activity and CO protein, analyzed by histochemistry and immunohistochemistry, respectively. In normal animals, CO activity was in general related more closely to mtDNA and CO subunit I (COI) (mitochondrial-encoded) mRNA levels than to COIV or COVIII (nuclear-encoded) mRNA levels. For example, puffs (also known as blobs) of high CO activity in striate cortex were enriched in mtDNA and COI mRNA, but not COIV or COVIII mRNA. In 3-7 d TTX-treated animals, proportionate decreases in CO activity and CO protein were observed in specific visual centers; these changes were accompanied by disproportionate decreases in COI, COIV, and COVIII mRNA levels. After 7 d of TTX, COI mRNA fell by 49 +/- 3% (mean +/- SEM) in LGN neurons, while COIV and COVIII mRNAs fell by only 18 +/- 3% and 29 +/- 3%, respectively. In comparison, CO activity decreased by 23 +/- 2%, and mtDNA by 26 +/- 4%. Qualitative observations in striate cortex also indicated that COI mRNA changed more than COIV mRNA, COVIII mRNA, mtDNA, or CO activity. Our results suggest that the local distribution of CO within neurons, and acute regulatory changes in CO activity occurring over periods of days are controlled mainly by regulation of the mitochondrial genes that encode the catalytic subunits of the enzyme.

Animals↗
PubMed1986

Transient kinetics of subunit-III-depleted cytochrome c oxidase.

Cytochrome c oxidase from ox heart was depleted of subunit III and its transient kinetic properties studied by stopped-flow and flash photolysis. It was found that the overall mechanism of electron transfer is very similar for subunit-III-depleted and native oxidase, although significant differences in some kinetic parameters have been detected. These include the second-order rate constant for cytochrome c oxidation and the rate-limiting step of the overall process. Moreover, at low cytochrome c/oxidase ratios (where the number of reducing equivalents is insufficient), the rate of reoxidation of cytochrome a was found to be very slow, even in air, and in fact for the subunit-III-depleted enzyme is even slower than for the native oxidase. The stability of reduced cytochrome a excludes the likelihood that removal of subunit III leads to a new O2-binding site, and the result may be relevant to the lowered vectorial H+/e- stoichiometry. The subunit-III-depleted oxidase can be pulsed under appropriate conditions and its combination with CO is unchanged, as shown by kinetic experiments and difference spectroscopy.

Animals↗
PubMed1991

A new oxygen-regulated operon in Escherichia coli comprises the genes for a putative third cytochrome oxidase and for pH 2.5 acid phosphatase (appA)

The Escherichia coli acid phosphatase gene appA is expressed in response to oxygen deprivation and is positively controlled by the product of appR (katF) which encodes a putative new sigma transcription-initiation factor. However, transcription of appA from its nearest promoter (P1) did not account for total pH 2.5 acid phosphatase expression and was not subject to regulation. The cloned region upstream of appA was extended and analyzed by insertions of transposon TnphoA and by fusions with lacZ. It contains two new genes, appC and appB, which both encode extracytoplasmic proteins. appC and appB are expressed from a promoter (P2) lying just upstream of appC. Both genes are regulated by oxygen, as is appA, and by appR gene product exactly as previously shown for appA. Analysis of the nucleotide sequence and of the origins of transcription have confirmed that the P2-appC-appB- (ORFX)-P1-appA region is organized on the chromosome as an operon transcribed clockwise from P2 and that P1 is a minor promoter for appA alone. Genes appC and appB encode proteins of Mr 58,133 and 42,377, respectively, which have the characteristics of integral membrane proteins. The deduced amino acid sequences of appC and appB show 60% and 57% homology, respectively, with subunits I and II of the E. coli cytochrome d oxidase (encoded by genes cydA and cydB). The notion that the AppC and AppB proteins constitute a new cytochrome oxidase or a new oxygen-detoxifying system is supported by the observation of enhanced sensitivity to oxygen of mutants lacking all three genes, cyo (cytochrome o oxidase), cyd (cytochrome d oxidase) and appB, compared to that of cyo cyd double mutants.

Acid Phosphatase↗
PubMed1996

1H NMR studies of the paramagnetic CuA center of cytochrome oxidase.

The dinuclear paramagnetic center of the soluble CuA domain of the cytochrome c oxidase from Bacillus subtilis has been studied using 1H NMR. The spectrum possesses remarkably sharp shifted resonances. Comparison with the spectrum of the CuA amicyanin variant provides the spin density distribution in the CuA site of cytochrome c oxidase. This represents the first paramagnetic NMR study of the dinuclear CuA center from the soluble domain of subunit II of cytochrome c oxidase.

Bacillus subtilis↗
PubMed1998

Saguenay Lac Saint Jean cytochrome oxidase deficiency: sequence analysis of nuclear encoded COX subunits, chromosomal localization and a sequence anomaly in subunit VIc.

A biochemically distinct form of cytochrome oxidase (COX) deficiency found in the Saguenay region of Quebec is an autosomal recessive trait. The cDNA sequences of all 10 nuclear-encoded subunits from a patient's fibroblasts showed normal coding sequence. Sequences for subunit VIc in two atypical patients showed a heterozygous base substitution. Subunit VIc was localized to chromosome 18.

Animals↗
PubMed1988

A comparison of the resonance Raman properties of the fast and slow forms of cytochrome oxidase.

Resonance Raman (RR) spectra of the "rapid" and "slow" forms (Baker et al., 1987) of resting cytochrome oxidase obtained with Soret excitation at 413.1 nm are reported. There are a number of conspicuous differences between the two forms in the high-frequency region of the RR spectrum which involve changes in Raman intensity arising from a blue shift in the Soret maximum of cytochrome a3 upon conversion to the slow form. In the low-frequency region a peak present at 223 cm-1 in the rapid form shifts to 220 cm-1 in the slow form; this peak is assigned as the cytochrome a3 Fe(III)-N(His-Im) stretch. The slow form of the enzyme possesses greater intensity in RR peaks near 1620 cm-1 which have been previously attributed by others to partial photoreduction of the enzyme. We have quantitated the amount of laser-induced photoreduction in these RR spectra by comparison with the spectra of mixed-valence derivatives of the enzyme and find that these 1620-cm-1 features are unreliable indicators of photoreduction. The spectra of the fast- and slow-reacting species in H2O and D2O have been compared. The fast-reacting form exhibits a 4-cm-1 shift, from 223 to 219 cm-1, upon transferring to D2O in a peak which we assign as the cytochrome a3 Fe(III)-N(His-Im) stretch. There is a parallel shift in the feature at 1651 cm-1 due to the C = O stretch of the formyl group of cytochrome a. These deuterium shifts are not observed in the slow form.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1996

Mitochondrial- and nuclear-encoded subunits of cytochrome oxidase in neurons: differences in compartmental distribution, correlation with enzyme activity, and regulation by neuronal activity.

Cytochrome oxidase (CO), a mitochondrial energy-generating enzyme, contains both mitochondrial- and nuclear-encoded subunits. In neurons, local levels of CO activity vary among different neuronal compartments, reflecting local demands for energy. The goals of the present study were to determine if compartmental distribution of CO subunit proteins from the two genomes was correlated with local CO activity, and if their expression was regulated proportionately in neurons. The subcellular distributions of mitochondrial-encoded CO III and nuclear-encoded CO Vb proteins were quantitatively analyzed in mouse cerebellar sections subjected to postembedding immunocytochemistry. Local levels of subunit proteins were also compared to local CO activity, as revealed by CO cytochemistry. In order to study the regulation of subunit protein expression, we assessed changes in immunoreactivity of the two CO subunits as well as changes in CO activity in mouse superior colliculus after 1 to 7 days of monocular enucleation. We found that immunoreaction product for both CO III and CO Vb existed almost exclusively in mitochondria, but their compartmental distributions were different. CO III was nonhomogeneously distributed among different neuronal compartments, where its local level was positively correlated with that of CO activity. In contrast, the subcellular distribution of CO Vb was relatively uniform and did not bear a direct relationship with that of CO activity. Moreover, the two subunit proteins were disproportionately regulated by neuronal activity. CO III and CO activity exhibited parallel decreases after the deprivation of afferent input, and their changes were earlier and to a greater degree than that of CO Vb proteins. Thus, the present findings indicate that the local expression and/or distribution of CO subunit proteins from the two genomes may involve different regulatory mechanisms in neurons. Our data also suggest that the activity-dependent regulation of mitochondrial-encoded CO subunits is likely to play a major role in controlling the local levels of CO content and its activity.

Amino Acid Sequence↗
PubMed1993

Intrinsic connections of layer III of striate cortex in squirrel monkey and bush baby: correlations with patterns of cytochrome oxidase.

This study used biocytin and horseradish peroxidase (HRP) to examine the intrinsic connections of the cytochrome oxidase (CO) rich blob and CO poor nonblob zones within layer III of striate cortex in two primate species, nocturnal prosimian bush babies (Galago crassicaudatus) and diurnal simian squirrel monkeys (Saimiri sciureus). Our main objective was to determine whether separate classes of lateral geniculate nucleus (LGN) cells projected to separate superficial layer zones or layers in either species. There were three significant findings. First, we confirm that layer III consists of three sublayers, IIIA, IIIB, and IIIC in both species. Layer IIIA receives input from layers IIIB, IIIC, and V, with little or no input from LGN recipient layers IV and VI. Layer IIIB receives its input from nearly every cortical layer. Layer IIIC, receives input principally from layers IV alpha [which receives its input from magnocellular (M) LGN cells] and from layers V and VI. Taken together with other findings on the extrinsic connections of these layers, our data suggest that IIIA and IIIC provide output to separate hierarchies of visual areas and IIIB acts as a set of interneurons. Second, we find that, as in macaque monkeys, cells in both IV beta and IV alpha of bush babies and squirrel monkeys project to layer IIIB, converging within the blobs. These results suggest that information from all LGN cell classes [parvocellular (P), M, and the Koniocellular (K) or their equivalents] may be integrated within the blobs. Thus, blobs in all of these primates may perform a function that transcends visual niche differences. Third, our data show a species specific difference in the connections of the IIIB nonblobs; nonblobs receive indirect input via IV alpha from the LGN M pathway in bush babies but receive indirect input via IV beta from the LGN parvocellular (P) pathway in squirrel monkeys. These findings indicate that the role of nonblob zones within striate cortex differs from that of blob zones and takes into account visual niche differences.

Animals↗
PubMed1996

A phylogenetic analysis of cuckoo bumblebees (Psithyrus, Lepeletier) and bumblebees (Bombus, Latreille) inferred from sequences of the mitochondrial gene cytochrome oxidase I.

PCR amplification and direct sequencing of a 532-bp region of the mt CO-1 (cytochrome oxidase I) gene from five true bumblebee species and six cuckoo bumblebee species were performed. The sequences were then aligned to the corresponding sequence in the honey bee. Phylogenetic analyses based on parsimony and maximum likelihood indicate that the cuckoo bumblebees form a monophyletic group within the true bumblebees. The Bombus lucorum group (subgenus Bombus) falls out as the sister group to a clade comprising the cuckoo bumblebees and the remaining true bumblebees. A strong A + T bias (A + T = 75%) was recorded. Comparisons of all the sequences show a high-transversion bias (A<-->T) even among closely related species. The bias is most pronounced in third positions.

Animals↗