Hierarchy within human SI: supporting data from cytochrome oxidase,acetylcholinesterase and NADPH-diaphorase staining patterns

The human primary somatosensory cortex consists of four cytoarchitectonic subdivisions (3a, 3b, 1 and 2) that are likely to contain distinct somatosensory representations. The intraareal organization of these areas as well as that of the primary motor cortex (area 4) has been analyzed using histochemical stains of cytochrome oxidase, acetylcholinesterase and NADPH-diaphorase activity in normal human brains. Cytochrome oxidase activity was revealed in individual cortical neurons and neuropil. Areas 4, 3a and 3b were on average darker than areas 1 and 2. The laminar distribution of cytochrome oxidase activity varied in different areas. A prominent dark band was present in layers IV and lower III in areas 3a and 3b and in layer III in areas 1, 2 and 4. Acetylcholinesterase staining revealed fibers and pyramidal cells in layers III and V; stained layer III pyramids were rare in areas 3a and 3b and numerous in areas 1, 2 and 4. NADPH-diaphorase positive elements included Golgi-like stained non-pyramidal neurons and Nissl-like stained pyramidal neurons; the former were found, in small numbers, in layer II of areas 4, 3a, 3b and 1, and the latter in layers III and V of areas 4 and 3a and in layer V of areas 1 and 2. The dark cytochrome oxidase staining of layer IV and the paucity of acetylcholinesterase positive pyramids in areas 3a and 3b resemble the pattern found in primary visual and auditory areas, whereas the dark cytochrome oxidase staining in layer III and abundance of acetylcholinesterase positive pyramids in areas 1 and 2 that of association areas. These results suggest that the four areas included in human SI constitute hierarchical stages of cortical processing, with 3a and 3b corresponding to primary and 1 and 2 to secondary areas.     

Crystal data, molecular dimensions and molecular symmetry in cytochrome oxidase from Pseudomonas aeruginosa.

Pseudomonas aeruginosa cytochrome oxidase (nitrite reductase, cytochrome cd) has been crystallized in space group P2₁2₁2 with cell dimensions $\text{a = 122.8}\text{A}\text{?}\text{, b = 87.2}\text{A}\text{?}\text{, c = 73.4}\text{A}\text{?}$. Density measurements suggest that the asymmetric unit contains one 63,000 molecular weight subunit of the dimeric molecule. Crystal data agree well with electron microscopy of single molecules. The X-ray pattern extends beyond 2.5 Å resolution, and structure analysis is in progress.     

Properties of ubiquinol oxidase reconstituted from ubiquinol-cytochrome c reductase, cytochrome c and cytochrome c oxidase.

Ubiquinol-cytochrome c reductase (Complex III), cytochrome c and cytochrome c oxidase can be combined to reconstitute antimycin-sensitive ubiquinol oxidase activity. In 25 mM-acetate/Tris, pH 7.8, cytochrome c binds at high-affinity sites (KD = 0.1 microM) and low-affinity sites (KD approx. 10 microM). Quinol oxidase activity is 50% of maximal activity when cytochrome c is bound to only 25% of the high affinity sites. The other 50% of activity seems to be due to cytochrome c bound at low-affinity sites. Reconstitution in the presence of soya-bean phospholipids prevents aggregation of cytochrome c oxidase and gives rise to much higher rates of quinol oxidase. The cytochrome c dependence was unaltered. Antimycin curves have the same shape regardless of lipid/protein ratio, Complex III/cytochrome c oxidase ratio or cytochrome c concentration. Proposals on the nature of the interaction between Complex III, cytochrome c and cytochrome c oxidase are considered in the light of these results.     

Electron transfer rates and equilibrium within cytochrome c oxidase.

Intramolecular electron transfer (ET) between the CuA center and heme a in bovine cytochrome c oxidase was investigated by pulse radiolysis. CuA, the initial electron acceptor, was reduced by 1-methyl nicotinamide radicals in a diffusion-controlled reaction, as monitored by absorption changes at 830 nm. After the initial reduction phase, the 830 nm absorption was partially restored, corresponding to reoxidation of the CuA center. Concomitantly, the absorption at 445 nm and 605 nm increased, indicating reduction of heme a. The rate constants for heme a reduction and CuA reoxidation were identical within experimental error and independent of the enzyme concentration. This demonstrates that a fast intramolecular electron equilibration is taking place between CuA and heme a. The rate constants for CuA --> heme a ET and the reverse (heme a --> CuA) process were found to be 13 000 s-1 and 3700 s-1, respectively, at 25 degrees C and pH 7.4. This corresponds to an equilibrium constant of 3.4 under these conditions. Thermodynamic and activation parameters of the ET reactions were determined. The significance of these results, particularly the observed low activation barriers, are discussed within the framework of the known three-dimensional structure, ET pathways and reorganization energies.     

Kinetic evidence for the re-definition of electron transfer pathways from cytochrome c to O2 within cytochrome oxidase

The reaction with O2 of equimolar mixtures of cytochrome c and cytochrome c oxidase in high and low ionic strength buffers has been examined by flow-flash spectrophotometry at room temperature. In low ionic strength media where cytochrome c and the oxidase are bound in an electrostatic, 1:1 complex some of the cytochrome c is oxidised at a faster rate than a metal centre of the oxidase. In contrast, when cytochrome c and cytochrome c oxidase are predominantly dissociated at high ionic strength cytochrome c oxidation occurs only slowly (t1/2 = 5 s) following the complete oxidation of the oxidase. These results demonstrate that maximal rates of electron transfer from cytochrome c to O2 occur when both substrates are present on the enzyme. The heterogeneous oxidation of cytochrome c observed in the complex implies more than one route for electron transfer within the enzyme. Possibilities for new electron transfer pathways from cytochrome c to O2 are proposed.     

Neuronal and endothelial nitric oxide synthase immunoreactivity and NADPH-diaphorase staining in rat and human pancreas: influence of fixation

In this study, we wished to clarify the distribution and co-localization of nitric oxide synthase and NADPH-diaphorase (NADPH-d) in nerve cells, nerve fibres and parenchymal cells in exocrine and endocrine pancreas, and to assess the influence of fixation on the staining pattern obtained. For this purpose, we applied nitric oxide synthase immunocytochemistry and NADPH-d histochemistry to rat and human pancreas under different fixation conditions. Antibodies to neuronal and endothelial nitric oxide synthase were similarly applied. We found complete co-localization of neuronal nitric oxide synthase and NADPH-d in ganglion cells, and in nerve fibres around acini, excretory ducts, blood vessels and in islets of Langerhans of rat and human pancreas. Immunoreactivity for endothelial nitric oxide synthase was co-localized with NADPH-d in endothelial cells. However, in NADPH-d reactive islet and ductal epithelial cells we could detect neither brain nor endothelial nitric oxide synthase immunoreactivity with any fixation protocol applied. There were marked differences in NADPH-d staining of both neurons and parenchymal cells under different fixation conditions. These results indicate the existence of different types of NADPH-d, which are associated or not associated with nitric oxide synthase(s), and which are differently influenced by various fixation procedures in rat and human pancreas.     

Presence of cytochrome b-245 in NADPH oxidase preparations from human neutrophils

The composition of NADPH oxidase purified by Red Sepharose chromatography of extracts from human neutrophil membranes was investigated. In contrast to that was recently reported by others, the enzyme isolated according to this procedure contained a high concentration of cytochrome b-245 and little FAD. The results reinforce the belief that cytochrome b-245 is a major component of the NADPH oxidase and plays a fundamental role in the formation of O2-by neutrophils.     

Copper chaperones for cytochrome c oxidase and human disease

Biological processes in living cells are compartmentalized between lipid membranes. Integral membrane proteins often confer specific functions to these compartments and as such have a critical role in cellular metabolism and function. Cytochrome c oxidase is a macromolecular metalloprotein complex essential for the respiratory function of the cell. Elucidating the mechanisms of assembly of cytochrome c oxidase within the inner mitochondrial membrane represents a unique challenge for understanding metalloprotein biosynthesis. Elegant genetic experiments in yeast have defined several proteins required for copper delivery to cytochrome c oxidase. While the precise role of each of these proteins in copper incorporation remains unclear, recent studies have revealed that inherited mutations in two of these proteins can result in severe pathology in human infants in association with cytochrome c oxidase deficiency. Characterization of the molecular pathogenesis of these disorders offers new insights into the mechanisms of cellular copper metabolism and the role of these cytochrome c oxidase copper chaperones in human disease.     

Isolation, subunit composition, and site of synthesis of human cytochrome c oxidase

Cytochrome c oxidase (ferrocytochrome c:oxygen oxidoreductase, EC 1.9.3.1), the terminal oxidase of the respiratory chain in eucaryotic cells, has been purified from human placenta mitochondria. Seven polypeptides have been identified reproducibly by high-resolution electrophoresis of the enzyme complex through sodium dodecyl sulfate (Na-DodSO4)--urea polyacrylamide gels; these correspond closely in size to the subunits of beef heart cytochrome c oxidase. When HeLa cells, grown in suspension culture, were pulse-labeled with [35S]methionine in the presence of cycloheximide to inhibit cytoplasmic protein synthesis and chased with an excess of unlabeled methionine in the absence of the drug, the mitochondrially synthesized polypeptides were resolved into at least 17 components by NaDodSO4--urea polyacrylamide gel electrophoresis. After labeled HeLa mitochondria were mixed with human placenta mitochondria and the cytochrome c oxidase was isolated, three of the labeled components were found to copurify with the three largest subunits of the complex. We conclude that human cytochrome c oxidase contains seven subunits, the three largest of which are synthesized on mitochondrial ribosomes, while the other four are synthesized in the cytoplasm.     

Protons,pumps, and potentials: Control of cytochrome oxidase

Cytochromec oxidase oxidizes cytochromec and reduces molecular oxygen to water. When the enzyme is embedded across a membrane, this process generates electrical and pH gradients, and these gradients inhibit enzyme turnover. This respiratory control process is seen both in intact mitochondria and in reconstituted proteoliposomes. Generation of pH gradients and their role in respiratory control are described. Both electron and proton movement seem to be implicated. A topochemical arrangement of redox centers, like that in the photosynthetic reaction center and the cytochromebc ₁ complex, ensures charge separation as a result of electron movement. Proton translocation does not require such a topology, although it does require alternating access to the two sides of the membrane by proton-donating and accepting groups. The sites of respiratory control within the enzyme are discussed and a model presented for electron transfer and proton pumping by the oxidase in the light of current knowledge of the transmembranous location of the redox centers involved.     

An evaluation of support for order-level monophyly and interrelationships within the class Demospongiae using partial data from the large subunit rDNA and cytochrome oxidase subunit I

Large subunit ribosomal DNA (LSU rDNA) sequence data from 120 taxa and cytochrome oxidase subunit 1(COI) sequence data from 27 taxa are analyzed separately and together to estimate the internal phylogeny of the class Demospongiae and to evaluate how consistent these data are with pre-existing hypotheses of relationship concerning order-level monophyly and relationships. The monophyly of Porifera is only slightly inconsistent with LSU data, which do not support the monophyly of the class Demospongiae regardless of the inclusion or exclusion of Homoscleromopha (this result is likely due to the placement of a single hexactinellid taxon within the Demospongiae), however, no LSU support is found for the monophyly of Silicea (Demospongiae+Hexactinellida) unless homoscleromorphs are excluded. Neither the subclasses Ceractinomorpha and Tetractinomorpha, nor the orders Halichondrida, Hadromerida, and Haplosclerida are supported as monophyletic under any data partition. The haplosclerid suborders Haplosclerina and Petrosina are supported as monophyletic to the exclusion of the suborder Spongillina, and the orders Dictyoceratida, Verongida, Poecilosclerida, Astrophorida, Spirophorida, Homosclerophorida, and Agelasida are largely reconstructed as monophyletic, with the exception of few anomalously placed taxa. Few inter-order relationships are strongly supported by any data partition, but there is moderate support for a verongid+chondrosid clade and a tetractinellid+halichondrid clade. Furthermore, LSU data strongly support the existence of two novel clades that do not correspond to the existing classification and that show no morphological uniformity. Finally, every data partition supports the monophyly of a clade that includes the order Agelasida, some members of the genus Axinella, and two taxa tentatively identified as belonging to the orders Hadromerida and Halichondrida.     

Redox-cycled oxidase. One of the reaction products of reduced cytochrome c, cytochrome c oxidase, and dioxygen

Pulsed and oxygenated forms of cytochrome c oxidase are believed to be variants of the oxidized enzyme. They were produced as a consequence of one or more reduction-oxidation cycles of the resting form and are characterized by an increase of the alpha band intensity and a red-shift of the Soret absorption band to 428 nm. The rate of decay of these species back to the resting enzyme varies appreciably and appears to depend on the nature of the reductant and/or oxidant used in their preparation. Here we report that if resting oxidase is incubated with either reduced or oxidized cytochrome c and then exposed to dioxygen, an activated form is rapidly produced which appears to be more oxidized than the starting material. This finding suggest some degree of partial reduction of the resting enzyme, but this by itself cannot explain the extent of activation. Our results further question the significance of the optical spectral "signature" of the oxygenated (Okunuki, K., and Sekuzu, I. (1954) Seitaino Kagaka 5, 265-272), pulsed (Antonini, E., Brunori, M., Colosimo, A., Greenwood, C., and Wilson, M. T. (1977) Proc. Natl. Acad. Sci. U.S.A. 74, 3128-3132), and "420 nm" species (Kumar, C., Naqui, A., and Chance, B. (1984) J. Biol. Chem. 259, 2073-2076, 11668-11671), which are thought to be activated forms of oxidized cytochrome c oxidase.     

Comparison of the data, analysis, and results of X-ray absorption studies of cytochrome c oxidase

Differences in the methods of analysis of X-ray absorption data used by Powers et al. [Powers, L., Blumberg, W. E., Chance, B., Barlow, C., Leigh, J., Jr., Smith, J., Yonetani, T., Vik, S., & Peisach, J. (1979) Biochim. Biophys. Acta 547, 520-538; Powers, L., Chance, B., Ching, Y., & Angiolillo, P. (1981) Biophys. J. 34, 465-498] and Scott et al. [Scott, R., Schwartz, J., & Cramer S. (1986) Biochemistry 25, 5546-5555] are clarified. In addition, we compare the X-ray absorption data and results for resting cytochrome c oxidase reported by both groups using the same analysis method and conclude apart from any assumptions that the data are not identical.     

Subunit IV of human cytochrome c oxidase, polymorphism and a putative isoform.

As part of our study of isoenzyme forms of human cytochrome c oxidase, we purified subunit IV from human heart and skeletal muscle with reversed-phase HPLC and determined the N-terminal amino acid sequences and the electrophoretic mobility. The N-terminus of human heart subunit IV proved to be ragged with 30% of the protein lacking the first three residues. Also a Tyr/Phe polymorphism was observed at residue 16. No differences in N-terminal sequence and electrophoretic mobility were observed between subunit IV of cytochrome c oxidase from human heart and skeletal muscle. Therefore, our results suggest that identical subunits IV are present in cytochrome c oxidase from human heart and skeletal muscle. A putative isoform of subunit IV with a blocked N-terminus was purified from human heart cytochrome c oxidase, which proved to have a different retention time on a reversed-phase column and also a slightly higher electrophoretic mobility on an SDS-polyacrylamide gel compared to the native subunit IV. We could not demonstrate the existence of isoforms of subunit IV in human skeletal muscle.     

Proton pumping by cytochrome oxidase: progress, problems and postulates

The current status of our knowledge about the mechanism of proton pumping by cytochrome oxidase is discussed. Significant progress has resulted from the study of site-directed mutants within the proton-conducting pathways of the bacterial oxidases. There appear to be two channels to facilitate proton translocation within the enzyme and they are important at different parts of the catalytic cycle. The use of hydrogen peroxide as an alternative substrate provides a very useful experimental tool to explore the enzymology of this system, and insights gained from this approach are described. Proton transfer is coupled to and appears to regulate the rate of electron transfer steps during turnover. It is proposed that the initial step in the reaction involves a proton transfer to the active site that is important to convert metal-ligated hydroxide to water, which can more rapidly dissociate from the metals and allow the reaction with dioxygen which, we propose, can bind the one-electron reduced heme-copper center. Coordinated movement of protons and electrons over both short and long distances within the enzyme appear to be important at different parts of the catalytic cycle. During the initial reduction of dioxygen, direct hydrogen transfer to form a tyrosyl radical at the active site seems likely. Subsequent steps can be effectively blocked by mutation of a residue at the surface of the protein, apparently preventing the entry of protons.     

A comparative kinetic analysis of the reactivity of plant, horse, and human respiratory cytochrome c towards cytochrome c oxidase

Two synthetic genes coding for human and Arabidopsis cytochrome c, respectively, have been designed and constructed, and the recombinant proteins have been over-expressed in Escherichia coli cells. Thus a comparative analysis of the two heme proteins, including horse cytochrome c as a reference, has been performed. In addition to their physico-chemical properties, the redox behavior of the three proteins has been analyzed by following the kinetics of both their reduction by flavin semiquinones (lumiflavin, riboflavin, and FMN) and oxidation by cytochrome c oxidase. The resulting data indicate that the accessibility and electrostatic charge of the active site do not differ in a significant way among the three proteins, but human cytochrome c exhibits some intriguing differences when interacting with cytochrome c oxidase that could be related to the amino acid changes underwent by the latter along evolution.