Isolation and characterization of a cDNA clone for bovine cytochrome c oxidase subunit IV

Structural organization and transcription regulation of nuclear genes encoding the mammalian cytochrome c oxidase complex

Cytochrome c Oxidase (COX) is the terminal component of the bacterial as well as the mitochondrial respiratory chain complex that catalyzes the conversion of redox energy to ATP. In eukaryotes, the oligomeric enzyme is bound to mitochondrial innermembrane with subunits ranging from 7 to 13. Thus, its biosynthesis involves a coordinate interplay between nuclear and mitochondrial genomes. The largest subunits, I, II, and III, which represent the catalytic core of the enzyme, are encoded by the mitochondrial DNA and are synthesized within the mitochondria. The rest of the smaller subunits implicated in the regulatory function are encoded on the nuclear DNA and imported into mitochondria following their synthesis in the cytosol. Some of the nuclear coded subunits are expressed in tissue and developmental specific isologs. The ubiquitous subunits IV, Va, Vb, VIb, VIc, VIIb, VIIc, and VIII (L) are detected in all the tissues, although the mRNA levels for the individual subunits vary in different tissues. The tissue specific isologs VIa (H), VIIa (H), and VIII (H) are exclusive to heart and skeletal muscle. cDNA sequence analysis of nuclear coded subunits reveals 60 to 90% conservation among species both at the amino acid and nucleotide level, with the exception of subunit VIII, which exhibits 40 to 80% interspecies homology. Functional genes for COX subunits IV, Vb, VIa 'L' & 'H', VIIa 'L' & 'H', VIIc and VIII (H) from different mammalian species and their 5' flanking putative promoter regions have been sequenced and extensively characterized. The size of the genes range from 2 to 10 kb in length. Although the number of introns and exons are identical between different species for a given gene, the size varies across the species. A majority of COX genes investigated, with the exception of muscle-specific COXVIII(H) gene, lack the canonical 'TATAA' sequence and contain GC-rich sequences at the immediate upstream region of transcription start site(s). In this respect, the promoter structure of COX genes resemble those of many house-keeping genes. The ubiquitous COX genes show extensive 5' heterogeneity with multiple transcription initiation sites that bind to both general as well as specialized transcription factors such as YY1 and GABP (NRF2/ets). The transcription activity of the promoter in most of the ubiquitous genes is regulated by factors binding to the 5' upstream Sp1, NRF1, GABP (NRF2), and YY1 sites. Additionally, the murine COXVb promoter contains a negative regulatory region that encompasses the binding motifs with partial or full consensus to YY1, GTG, CArG, and ets. Interestingly, the muscle-specific COX genes contain a number of striated muscle-specific regulatory motifs such as E box, CArG, and MEF2 at the proximal promoter regions. While the regulation of COXVIa (H) gene involves factors binding to both MEF2 and E box in a skeletal muscle-specific fashion, the COXVIII (H) gene is regulated by factors binding to two tandomly duplicated E boxes in both skeletal and cardiac myocytes. The cardiac-specific factor has been suggested to be a novel bHLH protein. Mammalian COX genes provide a valuable system to study mechanisms of coordinated regulation of nuclear and mitochondrial genes. The presence of conserved sequence motifs common to several of the nuclear genes, which encode mitochondrial proteins, suggest a possible regulatory function by common physiological factors like heme/O2/carbon source. Thus, a well-orchestrated regulatory control and cross talks between the nuclear and mitochondrial genomes in response to changes in the mitochondrial metabolic conditions are key factors in the overall regulation of mitochondrial biogenesis.

Identification of tissue-specific isoforms for subunits Vb and VIIa of cytochrome c oxidase isolated from rainbow trout

Cytochrome c oxidase was isolated from heart and liver of rainbow trout (Salmo gairdnerii). SDS/PAGE analysis showed the presence of 11 different polypeptide subunits in the fish enzyme. The nuclear-coded subunits IV, Va, Vb, VIc, VIIa, VIIc and VIII could be identified by their N-terminal amino acid sequences. The mammalian subunits VIa and VIIb appear to be absent (or blocked at the N-terminal) in cytochrome c oxidase from trout. For subunit Vb, two polypeptides of different electrophoretic mobilities were found which differed in their N-terminal sequences, and represent a new pair of cytochrome-c-oxidase subunit isoforms, not found in mammalia. Both isoforms of subunit Vb were found in cytochrome c oxidase from heart and liver, but at different ratios. Subunit VIIa also seemed to occur in different isoforms, whereas subunit VIII had the same N-terminal amino acid sequence in cytochrome c oxidase of liver and heart, similar to the human-type subunit but different from rat, bovine and chicken.

Mitochondrial-genome-encoded RNAs: differential regulation by corticotropin in bovine adrenocortical cells

Differential screening of an adrenal cortex cDNA library for corticotropin (ACTH)-inducible genes led to the isolation of a group of cDNAs representing mitochondrial genes that encode subunits of cytochrome oxidase, ATPase, and NADH dehydrogenase. Northern blot analysis of RNA from cells stimulated by ACTH confirmed the induction of these genes by ACTH yet revealed major differences in the relative responses of the respective mRNAs. The levels of mRNAs for cytochrome oxidase subunit I and ATPase increased 2- to 4-fold and for NADH dehydrogenase subunit 3 increased 20-fold, whereas the levels of the mitochondrial 16S rRNA showed no change within 6 h of ACTH stimulation. These effects of ACTH on mitochondrial mRNA levels probably result from both activation of the H2 transcription unit that encodes mitochondrial mRNAs and alteration of mRNA stability. ACTH also increased the activity of cytochrome oxidase after 12 h of stimulation. Examination of the tissue specificity of expression of five mitochondrial genes showed a wide range of RNA levels among 11 tissues but high correlations between individual RNA levels, consistent with a coordinated expression of the mitochondrial genes, although at different levels in each cell type. Proportionately high levels of mitochondrial mRNAs were found in adrenal cortex, probably reflecting a stimulatory effect of ACTH in vivo. Overall, the results indicate that ACTH enhances the energy-producing capacity of adrenocortical cells.

Rapid evolution of the human gene for cytochrome c oxidase subunit IV

We have compared the DNA sequences of nine mammalian genes for cytochrome c oxidase subunit IV (COX4 genes)--four expressed genes (human, bovine, rat, and mouse) and five pseudogenes (human, chimpanzee, orangutan, squirrel monkey, and bovine)--and constructed the sequence of the ancestral mammalian COX4 gene. By analyzing these sequences to determine the pattern and rate of nucleotide substitution in each branch of the evolutionary tree, we deduced that the human gene has evolved rapidly since the origin of the primate pseudogene approximately 41 million years ago, and we discuss the suggestion that this results from coevolution of nuclear and mitochondrial genes for cytochrome c oxidase.

The distribution of charged amino acids in mitochondrial inner-membrane proteins suggests different modes of membrane integration for nuclearly and mitochondrially encoded proteins

We have analyzed the amino acid distribution in seven nuclearly encoded and five mitochondrially encoded inner membrane proteins with experimentally well characterized topologies. The mitochondrially encoded proteins conform to the 'positive inside' rule, i.e. they have many more positively charged residues in their non-translocated as compared to translocated domains. However, most of the nuclearly encoded proteins do not show such a bias but instead have a surprisingly skewed distribution of Glu residues with an almost ten times higher frequency in the intermembrane space than in the matrix domains. These findings suggest that some, but possibly not all, nuclearly encoded inner membrane proteins may insert into the membrane by a mechanism that does not depend on the distribution of positively charged amino acids.

Evolutionary analysis of the nucleus-encoded subunits of mammalian cytochrome c oxidase

The cytochrome c oxidase enzyme complex of eukaryotes is made up of three mitochondrial-coded subunits and a variable number of nuclear-coded subunits. Some nuclear-coded subunits are present in multiple forms and probably perform a tissue- or development-specific function. A detailed evolutionary analysis of the cytochrome c oxidase subunits that have been sequenced to date is reported here. We have found that gene duplication events from which the liver and heart isoforms of rat subunits VIa and subunit VIII originated can both be dated at about 240 +/- 90 million years ago, long before the radiation of mammalian lineages. Sequence divergence between the processed-type pseudogenes for the subunits IV, VIc and VIII have been estimated. Our results indicate that they arose fairly recently, thus suggesting that retroposition is a continuing process. We show that the rate of silent substitution in mitochondrial-coded subunits is 5-10 times higher than in nuclear-coded subunits; on the other hand replacement rates, although differing from gene to gene, are roughly of the same order of magnitude in both nuclear and mitochondrial genes. In the case of most of the nuclear-coded proteins we observed a slightly greater similarity between rats and cow, which agrees with the data obtained for mitochondrial-coded subunits.

Differential expression of nuclear genes for cytochrome c oxidase during myogenesis

Recent studies of patients with mitochondrial myopathies suggest the existence of both muscle-specific and developmentally regulated isoforms of cytochrome c oxidase (COX), the terminal enzyme complex of the electron transport chain. To investigate the temporal pattern of gene expression of nuclear genes for COX in developing muscle, the steady-state levels of COX mRNA in total RNA from a satellite cell-derived mouse muscle cell line, C2C12, were analyzed and compared with COX mRNA levels in mature rat skeletal muscle. Undifferentiated myoblasts, myotubes just after fusion (early myotubes), and fully differentiated, contractile, striated myotubes (late myotubes) were analyzed for mRNA levels for four of the 10 different nuclear-encoded COX subunits: IV, Vb, Vlc and VIII-liver. Of these, IV, Vb and Vlc are identical in both bovine heart and liver, whereas subunit VIII has heart and liver isoforms. In C2C12 myoblasts, the level of mRNA for subunits IV, Vb, and VIII-liver is equal to or greater than the level in tissues such as brain, skeletal muscle, and liver. As myoblasts fuse and differentiate into myotubes, the levels of mRNA for these subunits undergo radically different changes. Transcripts for subunits IV and Vb accumulate to higher levels during myogenesis. The level of subunit VIII transcripts decreases during myogenesis, providing additional evidence that subunit VIII has tissue-specific isoforms in the rat. Little mRNA for COX Vlc was detected in either the C2C12 cell line or in primary embryonic rat myoblasts or myotubes in culture in spite of high levels in adult skeletal muscles, suggesting that subunit Vlc may have both fetal and adult isoforms in rodents.

Survey of amino-terminal proteolytic cleavage sites in mitochondrial precursor proteins: leader peptides cleaved by two matrix proteases share a three-amino acid motif

We have compiled sequences of precursor proteins for 50 mitochondrial proteins for which the mature amino terminus has been determined by amino acid sequence analysis. Included in this set are 8 precursors that have leader peptides that are cleaved in two places by mitochondrial matrix proteases. When these eight leader peptides are aligned and compared, a highly conserved three-amino acid motif is identified as being common to this class of leader peptides. This motif includes an arginine at position -10, a hydrophobic residue at position -8, and serine, threonine, or glycine at position -5 relative to the mature amino terminus. The initial cleavage of these peptides by matrix processing protease occurs within the motif, between residues at -9 and -8, such that arginine at position -10 is at position -2 relative to the cleaved bond. The rest of the motif is within the octapeptide removed by subsequent cleavage catalyzed by intermediate-specific protease. An additional 14 leader peptides in this collection (all of those that contain an arginine at -10) conform to this motif. Assuming that these 14 precursors are matured in two steps, we compared the internal cleavage sites at position -8 with the ends of the other 30 leader peptides in the collection. We find that 74% of matrix processing protease cleavage sites follow an arginine at position -2 relative to cleavage.

Domain structure of mitochondrial and chloroplast targeting peptides

Representative samples of mitochondrial and chloroplast targeting peptides have been analyzed in terms of amino acid composition, positional amino acid preferences and amphiphilic character. No highly conserved 'homology blocks' are found in either class of topogenic sequence. Mitochondrial-matrix-targeting peptides are composed of two domains with different amphiphilic properties. Arginine is frequently found either at position -10 or -2 relative to the cleavage site, suggesting that some targeting peptides may be cleaved twice in succession by two different matrix proteases. In stroma-targeting chloroplast transit peptides three distinct regions are evident: an uncharged amino-terminal domain, a central domain lacking acidic residues and a carboxy-terminal domain with the potential to form an amphiphilic beta-strand. Targeting peptides that route proteins to the mitochondrial intermembrane space or the lumen of chloroplast thylakoids have a mosaic design with an amino-terminal matrix- or stroma-targeting part attached to a carboxy-terminal extension that shares many characteristics with secretory signal peptides.

Sequential changes in the expression of mitochondrial protein mRNA during the development of brown adipose tissue in bovine and ovine species. Sudden occurrence of uncoupling protein mRNA during embryogenesis and its disappearance after birth

Samples of adipose tissue were obtained from different sites in bovine and ovine foetuses and newborns. RNA was isolated and analysed using bovine cDNA and ovine genomic probe for uncoupling protein (UCP), cDNA for subunits III and IV of cytochrome c oxidase and cDNA for ADP/ATP carrier. UCP mRNA was characterized for the first time in foetal bovine and ovine adipose tissue. It appeared later than mRNA of cytochrome c oxidase subunit III, and increased dramatically at birth (10-fold). ADP/ATP carrier mRNA was expressed at a lower level but also increased 10-fold at birth. It was demonstrated that UCP mRNA reached its highest level at birth in all bovine adipose tissues studied, except subcutaneous tissue. It disappeared quickly afterwards, being no longer detectable two days after birth. Similar variations were observed in newborn lambs. ADP/ATP carrier mRNA showed the same pattern of expression as UCP mRNA; although it was still lightly expressed two days after birth, it disappeared soon afterwards. Only mRNAs for cytochrome c oxidase subunits III and IV remained at the same level during the first postnatal week. On the basis of these data and of observations reported in the literature a sequence of events for the development of brown adipose cells in vivo is proposed. Soon after birth the perirenal adipose tissue of ruminants, which still contains mitochondria of typical brown adipose tissue morphology and high levels of cytochrome c oxidase mRNA, lacks UCP mRNA. Can it still be considered as brown fat? Ruminant species appear to be attractive models to study both the differentiation of brown adipose tissue and its possible conversion to white fat in large animals.

Import of rat liver mitochondrial transhydrogenase

The biosynthesis of pyridine dinucleotide transhydrogenase has been studied in isolated rat hepatocytes and in a rabbit reticulocyte-lysate translation system supplemented with either intact isolated rat liver mitochondria or the soluble matrix fraction from isolated mitochondria. In intact hepatocytes, the transhydrogenase precursor was short-lived in the cytosol and was efficiently imported into the membranous fraction. When the cell-free translation mixture was incubated with intact mitochondria, the transhydrogenase precursor was processed to the mature form, to an extent that depended on the amount of added mitochondria. Incubation of the translation mixture with the soluble mitochondria matrix fraction converted the precursor to a mature-sized protein with 75% efficiency, this being blocked by various proteinase inhibitors such as EDTA, 1,10-phenanthroline and leupeptin.

Molecular defects in cytochrome oxidase in mitochondrial diseases

Defects of cytochrome c oxidase (COX) show remarkable clinical, biochemical, and genetic heterogeneity. Clinically, there are two main groups of disorders, one dominated by muscle involvement, the other by brain dysfunction. Biochemically, the enzyme defect may be confined to one or a few tissues (reflecting the existence of tissue-specific isozymes) or affect all tissues. Immunologically reactive enzyme protein is decreased in some forms of COX deficiency but not in others. Because COX is encoded both by nuclear and by mitochondrial genes, COX deficiencies may be due to mutations of either genome and may offer useful models to study the communication between nuclei and mitochondria. We have isolated full-length cDNA clones encoding human COX subunits IV, Vb, and VIII and a partial-length clone for subunit Va. These clones are being used as probes to analyze the DNA and RNA of patients with COX deficiency.

Organization and nucleotide sequence of two chromosomal genes for rat cytochrome c oxidase subunit VIc: a structural and a processed gene

A rat genomic library was screened with a cDNA probe coding for rat liver cytochrome c oxidase subunit VIc (COX-VIc). Out of 16 clones mapped, four inserts were different and did not overlap. Two inserts that gave strong hybridization signals were characterized by sequence analysis. These data show that we have cloned two different genes for rat COX-VIc. The rat COX-VIc-2 gene contains four exons and three introns. The 5' boundary of the first exon was mapped by primer extension experiments. The nucleotide sequence of the first three exons is identical to the sequence of the rat liver cDNA probe; thus, we can conclude that this gene is expressed in rat liver. The second gene (COX-VIc-1) is 88% homologous to the rat liver cDNA and contains an open reading frame of 228 nucleotides capable of coding for a full-length COX-VIc polypeptide of 76 amino acids. This predicted translation product is 79% homologous to the rat liver peptide. The absence of introns and other factors, such as the presence of a 13-bp direct repeat and a poly(A) addition signal, indicate that this locus is a processed gene which may have evolved from spliced mRNA intermediates.

Molecular cloning and further characterization of cDNAs for rat nuclear-encoded cytochrome c oxidase subunits VIc and VIII

A cDNA library was constructed from poly(A)-rich RNA of H35 rat hepatoma cells by insertion into lambda gt11. Screening with an antiserum to rat liver holocytochrome-c oxidase yielded fifteen different recombinant clones. Eight clones were identified using monospecific antisera to individual subunits of the rat liver enzyme. The cDNA clones coding for subunits VIc and VIII were further characterized by DNA sequence analysis after subcloning in pUC8 and M13 mp9. The deduced amino acid sequences show 80% and 60% homology to the corresponding bovine heart subunits, respectively. From the nucleotide sequences we can conclude that subunit VIc is not synthesized as a larger precursor molecule like most other mitochondrial proteins. The size of the mRNAs coding for subunits VIc and VIII is about 450 nucleotides, as revealed by Northern blot analysis with RNAs from different tissues. The clones were further used as probes for Southern blotting. Restricted high-molecular-mass DNA showed a complex pattern of bands indicating multigene families for both subunits in the rat genome.

Artificial mitochondrial presequences

Synthetic oligonucleotides were used to construct artificial mitochondrial presequences that contained, besides the initiator methionine, only arginine, serine, and leucine. The ratio of these three amino acids was adjusted to match that of basic, hydroxylated, and hydrophobic residues in natural mitochondrial presequences. When these sequences were fused to the N terminus of yeast cytochrome oxidase subunit IV lacking its own presequence, they directed the attached subunit IV to its correct intramitochondrial location in vivo. They also mediated import of subunit IV into isolated yeast mitochondria. In contrast, artificial sequences containing glutamine, arginine, and serine residues following the initiator methionine were inactive. Thus, the targeting function of mitochondrial presequences does not depend on specific amino acid sequences but may instead depend on the overall balance between basic, hydrophobic, and hydroxylated amino acids.

Isolation and nucleotide sequence of a cDNA clone encoding rat mitochondrial malate dehydrogenase

We have determined the complete sequence of the rat mitochondrial malate dehydrogenase (mMDH) precursor derived from nucleotide sequence of the cDNA. A single synthetic oligodeoxynucleotide probe was used to screen a rat atrial cDNA library constructed in lambda gt10. A 1.2 kb full-length cDNA clone provided the first complete amino acid sequence of pre-mMDH. The 1014 nucleotide-long open reading frame encodes the 314 residue long mature mMDH protein and a 24 amino acid NH2-terminal extension which directs mitochondrial import and is cleaved from the precursor after import to generate mature mMDH. The amino acid composition of the transit peptide is polar and basic. The pre-mMDH transit peptide shows marked homology with those of two other enzymes targeted to the rat mitochondrial matrix.

Molecular cloning of cDNA for rat mitochondrial 3-hydroxyacyl-CoA dehydrogenase

Messenger RNA for 3-hydroxyacyl-CoA dehydrogenase, a mitochondrial matrix enzyme of fatty acid beta-oxidation, was purified from livers of di(2-ethylhexyl)phthalate-treated rats by immunoadsorption of hepatic free polysomes to fixed cells of Staphylococcus aureus and enrichment for poly(A)-rich RNA by oligo(dT)-cellulose chromatography. Plasmid cDNA was constructed from this poly(A)-rich RNA by a modification of the method of Okayama and Berg and was transformed into the Escherichia coli DH1 strain. Plasmids containing cDNA sequences coding for 3-hydroxyacyl-CoA dehydrogenase were screened by differential colony hybridization, and were identified by hybrid-arrested translation and hybrid-selected translation. Plasmid pHADH-1, which contains a 1400-base-pair insert, hybridized to rat 3-hydroxyacyl-CoA dehydrogenase mRNA with a length of 1700 bases. Determination of the dehydrogenase mRNA by in vitro translation and dot-blot analysis with the cDNA probe showed that the induction of the enzyme in rat liver by di(2-ethylhexyl)phthalate could be attributed to an increase in the mRNA concentration.

Molecular cloning of cDNA for rat mitochondrial 3-oxoacyl-CoA thiolase

Messenger RNA of rat 3-oxoacyl-CoA thiolase (acetyl-CoA acyltransferase), a mitochondrial matrix enzyme involved in fatty acid beta-oxidation, was enriched by immunoprecipitation of rat liver free polysomes and recombinant plasmids were prepared from the enriched mRNA by a modification of the vector-primer method of Okayama and Berg. The transformants were initially screened for 3-oxoacyl-CoA thiolase cDNA sequences by differential colony hybridization with [32P]cDNAs, synthesized from the immunopurified and unpurified mRNAs. The cDNA clones for 3-oxoacyl-CoA thiolase were identified by hybrid-arrested translation and hybrid-selected translation. One of the clones, designated pT1-1, contained a 700-base insert and hybridized to a mRNA species of 1.6 X 10(3) bases in rat liver. The transformants were rescreened using the cDNA insert of pT1-1 as a hybridization probe and a clone (pT1-19) with a 1.5 X 10(3)-base insert was obtained. Activity and concentration of 3-oxoacyl-CoA thiolase mRNA were quantified by in vitro translation and dot-blot analysis using the cDNA insert as a hybridization probe. The level of translatable and hybridizable mRNA in rat liver was increased about 5.1-fold and 4.6-fold, respectively, after administration of di-(2-ethylhexyl)phthalate, a potent inducer of the enzyme. The 3-oxoacyl-CoA thiolase mRNA levels thus determined correlated closely with levels of the activity and amount of this enzyme.

Cloning and sequence analysis of a cDNA encoding porcine mitochondrial aspartate aminotransferase precursor

The primary structure of pig mitochondrial aspartate aminotransferase (mAspATase; L-aspartate:2-oxoglutarate aminotransferase, EC 2.6.1.1) precursor was deduced from its cDNA sequence. A library of cDNA clones was constructed from pig liver poly(A)+ RNA by applying the vector/primer method of Okayama and Berg [Okayama, H. & Berg, P. (1982) Mol. Cell. Biol. 2, 161-170]. The library was screened for pig mAspATase sequences by using a mixture of eight oligodeoxyribonucleotides as a probe. The sequences of the probe were deduced from the known amino acid sequence of pig mAspATase residues 196-201. Two recombinant plasmids containing inserts of about 2500 and 2600 base pairs were selected for sequence analysis. The amino acid sequence predicted from the cDNA sequence shows that the pig mAspATase precursor consists of the mature enzyme of 401 amino acid residues and an amino-terminal segment of 29 amino acid residues called the "presequence" that contains four basic amino acid residues, no acidic residues, and no hydrophobic amino acid stretch. The sequence of this 29-amino acid mAspATase precursor segment was compared with the presequences of other mitochondrial enzymes.

Primary structure of a gene for subunit V of the cytochrome c oxidase from Saccharomyces cerevisiae

We have isolated a gene coding for cytochrome c oxidase subunit V by genetic complementation in yeast. This protein is made as a 153 amino acid long precursor; its amino-terminal extension of 20 amino acids contains four basic residues and no acidic one, a feature common to most pre-sequences of imported mitochondrial proteins.

Mitochondrial myopathies

Mitochondrial myopathies are clinically heterogeneous disorders that can affect multiple systems besides skeletal muscle (mitochondrial encephalomyopathies or cytopathies) and are usually defined by morphological abnormalities of muscle mitochondria. There are a few distinctive syndromes, such as the Kearns-Sayre syndrome; myoclonus epilepsy with ragged-red fibers; and mitochondrial myopathy, encephalopathy, lactic acidosis, and strokelike episodes. Biochemically, mitochondrial myopathies can be divided into defects of substrate utilization, oxidation-phosphorylation coupling, and the respiratory chain. Because mitochondria have their own DNA and their own translation and transcription apparatuses, mitochondrial myopathies can be due to defects of either a nuclear or mitochondrial genome and can be transmitted by mendelian or maternal inheritance.