The NDUFA1 gene product (MWFE protein) is essential for activity of complex I in mammalian mitochondria

The MWFE polypeptide of mammalian complex I (the proton-translocating NADH-quinone oxidoreductase) is 70 amino acids long, and it is predicted to be a membrane protein. The NDUFA1 gene encoding the MWFE polypeptide is located on the X chromosome. This polypeptide is 1 of approximately 28 "accessory proteins" identified in complex I, which is composed of 42 unlike subunits. It was considered accessory, because it is not one of the 14 polypeptides making up the core complex I; a homologous set of 14 polypeptides can make a fully functional proton-translocating NADH-quinone oxidoreductase in prokaryotes. One MWFE mutant has been identified and isolated from a collection of respiration-deficient Chinese hamster cell mutants. The CCL16-B2 mutant has suffered a deletion that would produce a truncated and abnormal MWFE protein. In these mutant cells, complex I activity is reduced severely (<10%). Complementation with hamster NDUFA1 cDNA restored the rotenone-sensitive complex I activity of these mutant cells to approximately 100% of the parent cell activity. Thus, it is established that the MWFE polypeptide is absolutely essential for an active complex I in mammals.

A mitochondrial DNA mutation cosegregates with the pathophysiological U wave

In a family with long QT syndrome (LQT2), some individuals who did not harbor the HERG mutation had a prolonged QTU interval on electrocardiograms after exercise. It may be determined or modified by other gene(s) or factor(s). The sequence analysis of mtDNA in these individuals of this family showed a candidate pathogenic mutation at 3394 in the ND1 gene. The cybrids (mutation at 3394) showed significantly reduced NADH-CoQ reductase (complex I) activity and O2 consumption to normal levels. These inhibitory effects on respiratory function may result in the depletion of ATP and could possibly produce an increase in Ca2+ concentration in cytosol, and it may lead to the prolongation of the QTU intervals on electrocardiograms. Therefore, we stated that the 3394 mutation in the ND1 gene is pathogenic and could be the cause of prolongation of the QTU intervals or modification of the phenotypes of not only congenital but also so-called "acquired drug-induced long QT syndrome."

The structure of the human NDUFV1 gene encoding the 51-kDa subunit of mitochondrial complex I

The genomic organization of the human 51-kDa subunit gene (NDUFV1) on human Chromosome (Chr) 11q13 was determined. The NDUFV1 gene consists of 10 exons. Exon 1 encodes for the 20-amino-acids-long import sequence, and exon 1 through 10 codes for the 444-amino-acids-long mature protein. The protein sequence is highly conserved between human and bovine. Northern blotting analysis showed that the NDUFV1 gene expression varies widely among tissues and that in testis a unique mRNA species is present. In comparison with the other complex I flavoproteins, the expression of the 51-kDa gene in pancreatic tissue is high.

The nuclear-encoded human NADH:ubiquinone oxidoreductase NDUFA8 subunit: cDNA cloning, chromosomal localization, tissue distribution, and mutation detection in complex-I-deficient patients

We report the cloning of the cDNA sequence of the nuclear-encoded NDUFA8 subunit of NADH: ubiquinone oxidoreductase, the first mitochondrial respiratory chain complex. The NDUFA8 open reading frame (ORF) includes 519 bp and encodes 172 amino acids (Mr=20.1 kDa). The human cDNA sequence shows 86.2% identity with the bovine sequence, whereas the human NDUFA8 amino acid sequence is 87.8% similar to its bovine PGIV protein counterpart. Both human and bovine NDUFA8 contain a conserved cysteine motif. Polymerase chain reaction analysis of rodent/human somatic cell hybrids maps the human NDUFA8 gene to chromosome 9. A multiple tissue blot has revealed the highest NDUFA8 mRNA expression in human heart, skeletal muscle, and fetal heart. Mutation analysis of the NDUFA8 fibroblast cDNA in 20 patients with an isolated enzymatic complex I deficiency in cultured skin fibroblasts has revealed two polymorphisms, one within the ORF and the other in the 3' untranslated region of the NDUFA8 cDNA sequence. The allelic frequency of both polymorphisms was similar in controls and complex-I-deficient patients.

Genomic structure of the human NDUFS8 gene coding for the iron-sulfur TYKY subunit of the mitochondrial NADH:ubiquinone oxidoreductase

The structural organization of the NDUFS8 gene coding for the TYKY subunit of the human mitochondrial NADH:ubiquinone oxidoreductase (Complex I) has been determined by sequencing of a genomic fragment cloned from a cosmid library. The NDUFS8 gene is located on chromosome 11q13 immediately downstream of the ALDH7 isoform gene. It spans about 6kb and contains seven exons ranging in size from 51 to 186bp. Three CCAAT box sequence motifs are present upstream of the transcription start. Sp1 and NRF1 binding site motifs are present in the first intron. Expression of the gene is ubiquitous but predominant in heart and skeletal muscle. Immunodetection of the TYKY subunit in placental mitochondria after two-dimensional gel electrophoresis revealed that the mature protein has a molecular mass of 22kDa and a pI in the range of 4.9-5.0.

cDNA sequence and chromosomal localization of the remaining three human nuclear encoded iron sulphur protein (IP) subunits of complex I: the human IP fraction is completed

NADH:ubiquinone oxidoreductase (complex I) of the mitochondrial respiratory chain can be fragmented in a flavoprotein (FP), iron-sulfur protein (IP), and hydrophobic protein (HP) subfraction. The IP subfraction is hypothesized to be significant, since it contains important prosthetic groups highly conserved among species. We cloned the cDNA of three remaining human NADH:ubiquinone oxidoreductase subunits of this IP fraction: the NDUFS2 (49 kDa), NDUFS3 (30 kDa), and NDUFS6 (13 kDa) subunits. All presented cDNAs include the complete open reading frame (ORF), which consist of 1392, 795, and 375 base pairs, coding for 463, 264, and 124 amino acids, respectively. The latter show 96, 90, and 83% homology with the corresponding bovine translation products. The 3' untranslated regions (UTR) are complete in all three cDNAs. Polymerase chain reaction performed with DNA isolated from somatic human-rodent cell hybrids containing defined human chromosomes as template gave a human-specific signal which mapped the NDUFS2 and NDUFS3 subunits to chromosomes 1 and 11, respectively. In the case of the NDUFS6 subunit a pseudogene may be present since signals were seen in the lanes containing chromosomes 5 and 6. The NDUFS2 contains a highly conserved protein kinase C phosphorylation site and the NDUFS3 subunit contains a highly conserved casein kinase II phosphorylation site which make them strong candidates for future mutation detection studies in enzymatic complex I-deficient patients.

Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae)

We examine rate heterogeneity among evolutionary lineages of the grass family at two plasmid loci, ndhF and rbcL, and we introduce a method to determine whether patterns of rate heterogeneity are correlated between loci. We show both that rates of synonymous evolution are heterogeneous among grass lineages and that are heterogeneity is correlated between loci at synonymous sites. At nonsynonymous sites, the pattern of rate heterogeneity is not correlated between loci, primarily due to an aberrant pattern of rate heterogeneity at nonsynonymous sites of rbcL. We compare patterns of synonymous rate heterogeneity to predictors based on the generation time effect and the speciation rate hypotheses. Although there is some evidence for generation time effects, neither generation time effects nor speciation rates appear to be sufficient to explain patterns of rate heterogeneity in the grass plastid sequences.

ndhF sequence evolution and the major clades in the sunflower family

An extensive sequence comparison of the chloroplast ndhF gene from all major clades of the largest flowering plant family (Asteraceae) shows that this gene provides approximately 3 times more phylogenetic information than rbcL. This is because it is substantially longer and evolves twice as fast. The 5' region (1380 bp) of ndhF is very different from the 3' region (855 bp) and is similar to rbcL in both the rate and the pattern of sequence change. The 3' region is more A+T-rich, has higher levels of nonsynonymous base substitution, and shows greater transversion bias at all codon positions. These differences probably reflect different functional constraints on the 5' and 3' regions of ndhF. The two patterns of base substitutions of ndhF are particularly advantageous for phylogenetic reconstruction because the conserved and variable segments can be used for older and recent groups, respectively. Phylogenetic analyses of 94 ndhF sequences provided much better resolution of relationships than previous molecular and morphological phylogenies of the Asteraceae. The ndhF tree identified five major clades: (i) the Calyceraceae is the sister family of Asteraceae; (ii) the Barnadesioideae is monophyletic and is the sister group to the rest of the family; (iii) the Cichorioideae and its two basal tribes Mutisieae and Cardueae are paraphyletic; (iv) four tribes of Cichorioideae (Lactuceae, Arctoteae, Liabeae, and Vernonieae) form a monophyletic group, and these are the sister clade of the Asteroideae; and (v) the Asteroideae is monophyletic and includes three major clades.

Diverse capacities for the adaptive response to DNA alkylation in Bacillus species and strains

Our previous studies of Bacillus subtilis showed that the genes responsible for the adaptive response to DNA alkylation were organized as a divergent regulon, in contrast to scattered operons in Escherichia coli ada regulon. To study the generality and diversity of gene organization, several species and strains of Bacillus were examined for the responsiveness to DNA alkylation. B. cereus cells exhibited the highest resistance to MNNG treatment. When the cells were grown in the presence of MNNG, 3-methyladenine DNA glycosylase and two species of DNA methyltransferase were induced as in B. subtilis 168 cells. B. licheniformis 749 and B. amyloliquefaciens H cells exhibited a partial response that manifested itself as the induction of one species of DNA methyltransferase. On the other hand, B. thuringiensis var. Tohokuensis, B. megaterium KMT, and B. subtilis W23 cells were totally deficient in this response, and were hypersensitive to alkylating agents. To determine the cause of this deficiency in strain W23, we examined the genomic structure of the corresponding region where three genes (alkA, adaA, and adaB) were located in 168. No homologues for the three genes were detected in W23 DNA by Southern hybridization. Two genes (glmS and ndhF) flanking the adaptive response regulon in 168 were also present in W23. A sequence of about 2750 bp that carried the entire regulon in 168 was replaced with a sequence of about 250 bp that was unique to W23. At the ends of the conserved segments, palindromic sequences corresponding to the transcriptional termination sites of the adaB and glmS genes were observed. The regulon in 168 could be artificially replaced by the W23 sequence, and be regained through DNA-mediated transformation.

In search of butterfly origins

To determine the sister taxon to butterflies, the relationships among the macrolepidopteran superfamilies were investigated using sequence data from the ND1 gene of mitochondrial DNA. Both sequence data and translated amino acids were used. We examined how different models of amino acid evolution (nonadditive) affected the inference of tree topology. We then added previously published sequence data from the 18S and 28S subunits of ribosomal RNA. In most analyses, regardless of data type and treatment, the Hedyloidea is either the sister taxon to butterflies or derived within the butterfly clade. These molecular results are compared to a reanalysis of morphological characteristics. The reanalysis of morphology agrees with Minet's 1991 hypothesis of hedyloid relationships. Analysis of combined molecular and morphology data supports the hypothesis that hedylids are the sister group to butterflies. Scott's hypothesis that hawk moths (Sphingidae) are the sister taxon to butterflies is discounted.

Characterization of a gene responsible for the Na+/H+ antiporter system of alkalophilic Bacillus species strain C-125

An alkali-sensitive mutant, 38154, of the alkalophilic Bacillus sp. strain C-125 could not grow at an alkaline pH. The nucleotide sequence of a 3.7 kb parental DNA fragment that recovers the growth of 38154 at alkaline pH has four open reading frames (ORF1-4). By subcloning the fragment, we demonstrated that a 0.25 kb DNA region is responsible for the recovery. Direct sequencing of the mutant's corresponding region revealed a G to A substitution. The mutation resulted in an amino acid substitution from Gly-393 to Arg of the putative ORF1 product, which was deduced to be an 804-amino-acid polypeptide with a molecular weight of 89,070. The N-terminal part of the putative ORF1 product showed amino acid similarity to those of the chain-5 products of eukaryotic NADH quinone oxidoreductases. Membrane vesicles prepared from 38154 did not show membrane potential (delta psi)-driven Na+/H+ antiporter activity. Antiporter activity was resumed by introducing a parental DNA fragment which recovered the mutant's alkalophily. These results indicate that the mutation in 38154 affects, either directly or indirectly, the electrogenic Na+/H+ antiporter activity. This is the first report which shows that a gene responsible for the Na+/H+ antiporter system is important in the alkalophily of alkalophilic microorganisms.

Free radical modes of cytotoxicity of adriamycin and streptonigrin

Free radical modes of cytotoxicity of streptonigrin (STN) and Adriamycin (ADR) in Chinese hamster V79 cells under aerobic conditions were evaluated using 4-hydroxy-2,2,6,6-tetramethylpiperidine-1-oxyl (TP), a low molecular weight stable nitroxide free radical with antioxidant properties and desferrioxamine (DF), a transition metal chelator. In addition, exogenous superoxide dismutase (SOD, EC 1.15.1.1) and catalase (CAT, EC 1.11.1.6), were tested for cytoprotective effects. EPR studies showed that TP reacts with the semiquinones of both ADR and STN and also with O2- radicals generated during aerobic redox cycling of the respective semiquinone radicals. Pulsed field gel electrophoresis studies confirmed that DNA double-strand breaks (dsb) induced by STN in V79 cells were inhibited completely by TP, whereas ADR-induced DNA dsb were not affected by TP. Clonogenic cell survival studies showed that STN-induced cytotoxicity could be inhibited completely by DF or TP. Both agents were ineffective in inhibiting ADR-induced cytotoxicity. SOD and CAT were ineffective in protecting against both STN and ADR cytotoxicity. Our results are consistent with a mechanism requiring the semiquinone radical intermediate of STN for cytotoxicity and minimal free radical involvement in ADR-induced V79 cell cytotoxicity.

Structure-sensitivity relationship of anthracycline antibiotics to C7-reduction by redox enzymes

About 30 antitumor anthracycline antibiotics were tested for their susceptibilities to reductive deglycosidation at C-7 catalyzed by rat liver microsomal NADPH-cytochrome P-450 reductase, xanthine oxidase, cytochrome C reductase and DT-diaphorase. Enzymatic activities to reduce the C-7 position of anthracycline antibiotics were similar among the four redox enzymes although a few exceptions were observed with DT-diaphorase. Among therapeutic use of anthracyclines, aclacinomycin A (ACM-A, aclarubicin) and daunomycin (daunorubicin) were found to be highly sensitive to the redox enzymes tested while adriamycin (ADM, doxorubicin) and THP-ADM (pirarubicin) were resistant to enzymatic reductive deglycosidation. When glycosidic and hydroxylated analogs of ACM-A were compared it was found that anthracyclines with smaller glycoside residues were more sensitive to the redox enzymes and the presence of hydroxyl groups on the aglycone moiety decreased the reductive deglycosidation activities. Thus, the aglycone, aklavinone, was most rapidly reduced to 7-deoxyaklavinone. 1-Hydroxy-, 2-hydroxy-, 11-hydroxy- and 1,11-dihydroaclacinomycins A were more resistant to the redox enzymes that ACM-A. Especially, 2-hydroxyaclacinomycins were completely insensitive to the enzymatic reduction. THP-ADM, 4'-substituted analog of ADM, was more resistant to the redox enzymes than ADM itself. These results show that the presence of a hydroxyl group, its position on aglycone, the presence of 4'-substituent on aminosugar and its length in the anthracycline molecule play important roles on the C-7 reduction by the redox enzymes. Relationship between reductive deglycosidation susceptibilities and cell-growth inhibitory activities of anthracycline antibiotics are also discussed.

Studies on the CoQH2-cytochrome c reductase segment of the respiratory chain of yeast mitochondria, using mutants of the cytochrome b split gene

Our work relating to the role of cytochrome b in the CoQH2-cytochrome c reductase segment of the respiratory chain of S. cerevisiae mitochondria is reviewed here and new results are reported. The results concerning the structure-function relationship of cytochrome b in this complex, analyzed within the framework of the eight transmembrane alpha helice cytochrome b folding model, agree with the following features of the proton motive Q cycle (or SQ cycle): i) the antimycin A and myxothiazol binding domains are located on opposite sides of the inner mitochondrial membrane; and ii) the antimycin A binding domain is associated with the b562 domain, the myxothiazol domain with the b565 domain. These results were obtained from structural data derived from amino-acid sequence studies on mit- mutants and from biochemical studies of these mutants. However, functional studies are reported here that are not in agreement with the following features of the above models: i) the serial arrangement of the two hemes of cytochrome b and ii) the isolation of cytochrome b from redox changes with the couple fumarate/succinate in the presence of antimycin A and myxothiazol.

Structure and function of the mitochondrial bc1 complex. A mutational analysis of the yeast Rieske iron-sulfur protein

Respiratory-defective mutants of Saccharomyces cerevisiae assigned to a single complementation group (G12) have been determined to have lesions in the iron-sulfur protein (Rieske protein) of ubiquinol: cytochrome c reductase. Mutants capable of expressing the protein were chosen for further studies. The genes from 13 independent isolates were cloned and their mutations sequenced. Twelve mutations were ascertained to cause single amino acid substitutions in the carboxyl-terminal regions of the protein between residues 127 and 173. This region is proposed to be part of the catalytic domain with the ligands responsible for co-ordinating the two irons of the 2Fe-2S cluster. Based on the catalytic properties of the ubiquinol: cytochrome c reductase complex and the electron paramagnetic resonance (e.p.r.) signals of the iron-sulfur protein, the mutants describe two different phenotypes. A subset of mutants have no detectable iron-sulfur cluster and are completely deficient in ubiquinol: cytochrome c reductase activity. These strains identify mutations in residues considered to be essential for binding of the iron or for maintaining a proper tertiary structure of the catalytic domain. A second group of mutants have reduced levels of enzymatic activity and exhibit e.p.r. spectra characteristic of the Rieske iron-sulfur cluster. The mutations in the latter strains have been ascribed to residues that influence the redox properties of the cluster by distorting the iron-binding pocket. A secondary and tertiary structure model is presented of the carboxyl-terminal 65 residues constituting the catalytic domain of the iron-sulfur protein. It is postulated that the two irons of the cluster are co-ordinated by three cysteine and a single histidine residue located in a loop structure. The catalytic domain also contains two short alpha-helices and three beta-strands that form a partial beta-barrel. Most of the hydrophilic amino acids are present in turns that map to one pole of the domain. When viewed in the context of the model, mutations that abolish the iron-sulfur cluster are mostly in residues defining the boundaries of the alpha-helices and beta-strands. The notable exception is a cysteine residue that has been assigned to the loop with the iron ligands. This cysteine residue is proposed to co-ordinate one iron of the cluster. Mutations that reduce ubiquinol: cytochrome c reductase activity and alter the redox potential of the cluster occur in residues located in the loop that contains the ligands of the cluster.

Effect of different detergent systems on the molecular size of UDP glucuronosyltransferase and other microsomal drug-metabolizing enzymes

Mouse liver microsomes were solubilized in various detergent systems, and the resulting aggregate structures associated with cytochrome P-450, cytochrome c reductase, and UDP glucuronosyltransferase were sized by gel filtration chromatography. Cholate or its derivative, CHAPS, in combination with Emulgen 911 or Lubrol 12A9 were necessary to generate a particle of about 140 k daltons, the smallest structure associated with cytochrome P-450. Cholate or CHAPS alone was sufficient to generate a minimally sized aggregate of 200 k daltons associated with NADPH cytochrome c reductase activity. Cholate in combination with Emulgen 911 or Lubrol 12A9 generated particles of about 280 k daltons associated with UDP glucuronosyltransferase activity. CHAPS alone also generated similarly sized particles under conditions in which UDP glucuronosyltransferase activity toward 1-naphthol and morphine was two to about twenty times greater, respectively, than with the combination of detergents. This finding suggests that the zwitterionic CHAPS is superior to other detergent systems for studies concerned with the purification of transferase enzymes, a microsomal system in which investigation of the number of different forms has been hampered by the instability of the enzyme upon solubilization and subsequent manipulation.

A sensitive spectrophotometric assay for pyruvate dehydrogenase and oxoglutarate dehydrogenase complexes

The activities of pyruvate dehydrogenase and oxoglutarate dehydrogenase can be reliably measured by coupling the production of NADH to the reduction of added cytochrome c. Maximum activities required the addition of NADH-cytochrome c reductase activity prepared from rat heart mitochondria. Compared to other spectrophotometric assays this method provides an eight-fold increase in sensitivity and is particularly suitable for use with small tissue samples such as needle-biopsy samples of human skeletal muscle. Measurements of activities in rat tissues showed them to be in the order skeletal muscle less than liver less than heart less than or equal to brown adipose tissue. Activities in normal human skeletal muscle were similar to those of rat muscle. In the rat tissues specific differences were seen in the relative activities of the two complexes and cytochrome c oxidase suggesting tissue-specific differences in the activities of the dehydrogenases and components of the electron-transport chain.

Ion-exchange chromatography in the presence of the non-ionic dissociating agent chloral hydrate. Application to a membrane protein, bovine heart cytochrome c oxidase

In previous work we have shown that aq. 100% (w/v) chloral hydrate (2,2,2-trichloroethane-1,1-diol) is a potent non-ionic protein dissociating agent. We have employed it in systems of polyacrylamide-gel electrophoresis and have demonstrated the presence of 15 components in a preparation of bovine heart cytochrome c oxidase [Griffin & Landon (1981) Biochem. J. 197, 333-344]. Here we describe the use of solutions containing aq. 100% (w/v) chloral hydrate in the ion-exchange column chromatographic separation on CM-cellulose of the alpha- and beta-chains of human haemoglobin, which we have employed as a model protein of known structure. We also describe the use of similar procedures in order to fractionate the polypeptide components of bovine heart cytochrome c oxidase. An effective separation has been obtained and we suggest that chloral hydrate-containing solutions could have general application in the ion-exchange-chromatographic analysis of membrane proteins, a procedure that has had restricted use owing to the inadequacy of non-ionic dissociating agents available previously.