Two bovine genes for cytochrome c oxidase subunit IV: a processed pseudogene and an expressed gene

Isolation and characterization of the functional gene encoding bovine cytochrome c oxidase subunit IV

The structure and expression of the gene (COX4) encoding bovine cytochrome c oxidase subunit IV (COX IV) was studied in order to identify conserved DNA sequence elements involved in the control of mammalian nuclear respiratory genes. The functional bovine COX4 gene consists of five exons and four introns and is similar in organization to rat and mouse COX4. The domain encoded by exon 3 is the most highly conserved among the three species, suggesting it may encode a key functional domain of COX IV. Transcription of bovine COX4 begins at multiple sites, as has been seen previously for rat and mouse COX4 and other TATA-less genes. Comparative analysis of bovine, rat and mouse COX4 promoters identified multiple binding sites for the regulatory proteins Sp1 and GABP (NRF-2). The varied arrangements of multiple Sp1 and GABP sites in mammalian COX4 promoters suggests flexibility in the positioning of regulatory factors in controlling COX4 expression.

Structure and chromosomal location of the bovine gene for the heart muscle isoform of cytochrome c oxidase subunit VIII

We have isolated the bovine COX8H gene for the heart/muscle isoform of cytochrome c oxidase (COX) subunit VIII from a library of bovine genomic DNA cloned into lambda EMBL3. Primer extension assays on bovine heart mRNA mapped the 5' ends of COX8H transcripts to a CA dinucleotide 62-bp upstream from the ATG codon. The gene thus spans 1565-bp and comprises two exons and one large intron of 1227 bp. Exon 1 encodes the 5' untranslated region, a 24-amino acid presequence, and the first 13 amino acids of the mature COX VIII-H protein. Exon 2 encodes the remainder of the cDNA: amino acids 14 to 46 plus the 66-bp 3' untranslated region. The exon-intron boundaries matched the consensus splice junction sequences. Two protein polymorphisms were seen: an Ala/Val polymorphism at position -6 in the presequence and the previously noted Lys/Arg polymorphism at residue 7 of the mature protein. A TaqI polymorphism occurs in the intron. The COX8H gene was mapped by bovine x rodent somatic cell hybrid mapping panels to bovine (BTA) Chromosome (Chr) 25 with 100% concordancy. BTA 25 is conserved relative to the long arm of human (HSA) Chr 11, which contains COX8, the gene for the single human COX VIII subunit that is homologous to the liver isoform.

Sequences of members of the human gene family for the c subunit of mitochondrial ATP synthase

Subunit c is an intrinsic membrane component of ATP synthase, and in mammals it is encoded by two expressed nuclear genes, P1 and P2. Both genes encode the same mature c subunit, but the mitochondrial import pre-sequences in the precursors of subunit c are different. The DNA sequences of the human P1 and P2 genes are described. They occupy about 3.0 and 10.9 kb respectively of the human genome, and both genes are split into five exons. The human genome also contains about 14 related spliced pseudogenes, and the sequence of one such pseudogene related to P2 is described. Sequences flanking the 5' ends of the human P1 and P2 coding sequences each contain a CpG-rich island. Potential promoter elements (TATA and CCAAT boxes) are present in the 5' sequences of the P1 gene, but not that of P2, although there is no direct experimental evidence to show the involvement of these sequences in transcription of the genes.

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.

Characterization and expression of a cDNA specifying subunit VIIc of bovine cytochrome c oxidase

We have isolated a cDNA that encodes subunit VIIc of bovine cytochrome c oxidase (COX VIIc). The 325-bp cDNA contains sequences encoding the mature 47-amino acid (aa) polypeptide and a 16-aa presequence. The deduced aa sequence of the processed polypeptide is identical to that of the heart protein determined by aa sequencing. Northern-blot analysis reveals a single 525-nucleotide (nt) transcript in all tissues examined, whose levels vary with the corresponding respiratory activities in different tissues; thus, no evidence for isoforms of COX VIIc is seen in adult tissues. Southern-blot analysis of bovine genomic DNA digested with three different restriction enzymes reveals several bands that hybridize with the cDNA. We present here the sequence of one genomic region that contains a processed gene encoding COX VIIc. The genomic and cDNA nt sequences are 99% identical throughout the 189-bp open reading frame; the deduced aa sequences are identical. The sequence of the genomic clone suggests that the cDNA terminates prematurely at an EcoRI site in the 3'-untranslated region. We have compared COX VIIc cDNAs from cow, human and mouse, and find the presequence similarity among them to be 100% at the aa level.

Cloning and characterization of the mouse cytochrome c oxidase subunit IV gene

cDNA for mouse cytochrome c oxidase subunit IV (COXIV) was isolated by screening mouse liver and kidney cDNA libraries with a bovine COXIV cDNA probe. The 679-nucleotide nearly full length cDNA codes for a 22-amino acid presequence and a 147-amino acid mature protein which show 77 to 95% positional identity with the predicted sequences of human, bovine, and rat subunits. Screening of mouse genomic lambda EMBL3 library using the mouse cDNA probe yielded two overlapping clones. Restriction mapping and sequencing of the clones show that the mouse COXIV mRNA sequences are contained in five exons ranging from 58 to 236 base pairs, and four introns in a 7-kilobase region of the mouse genome. Southern blot analysis of restriction-digested genomic DNA indicates the presence of a single gene for COXIV in the mouse genome. Primer extension analysis using a synthetic 22-mer oligonucleotide, together with the 0.68-kilobase size of the mRNA shown by the Northern blot analysis, indicates that the major transcription start site of the COXIV gene is located 59 nucleotides upstream of the translation start site. The COXIV gene is highly GC rich and lacks TATA and CAAT elements in the immediate upstream region of the transcription start site. The putative promoter region, however, contains a number of GC boxes similar to those involved in the binding of Sp1 transcription factor. The unique features of the gene, as well as its characteristics common to other nuclear genes coding for different mitochondrial proteins, have been discussed.

Human cytochrome c oxidase subunit VIb: characterization and mapping of a multigene family

We report the isolation and sequence of a human heart cDNA coding for cytochrome c oxidase (COX) subunit VIb (COX VIb). This cDNA extends 50 bp upstream from the region coding for the mature peptide. By Northern analysis, a single transcript of approx. 550 nucleotides (nt) has been identified in six human tissues. Southern analysis of human genomic DNA demonstrates the presence of multiple loci that show high homology to the cDNA. These loci cosegregate with either five or six different human chromosomes in human-rodent somatic cell hybrids. Using the COX6b cDNA, genomic sequences representing two of these loci have been isolated and characterized. The nt sequence analysis suggests that both loci represent COX6b pseudogenes.

Identification of three human pseudogenes for subunit VIb of cytochrome c oxidase: a molecular record of gene evolution

Three pseudogenes for the nuclear-encoded subunit VIb of cytochrome c oxidase (COX) were isolated by screening a human genomic library with cloned human cDNA coding for COX subunit VIb. The nucleotide sequences of the pseudogenes, designated psi COX6b-1, psi COX6b-2 and psi COX6b-3, were determined. Pseudogene psi COX6b-1 bears all the hallmarks of a processed pseudogene and diverged from the parental gene after the divergence of man and cow. Alu repetitive elements were integrated into the structural sequences of the other two pseudogenes. Comparison with the human and bovine cDNA sequences encoding COX subunit VIb suggests that psi COX6b-2 and psi COX6b-3 were formed earlier in evolution than psi COX6b-1. Genomic Southern analysis indicated that a few more pseudogenes for COX subunit VIb are likely to be present in the human genome. Identical nt differences with respect to the human cDNA sequence in the pseudogenes provide some clues on the evolution of the ancestral gene coding for COX subunit VIb.

Structure of the human cytochrome c oxidase subunit Vb gene and chromosomal mapping of the coding gene and of seven pseudogenes

Subunit Vb of mammalian cytochrome c oxidase (COX; EC 1.9.3.1) is encoded by a nuclear gene and assembled with the other 12 COX subunits encoded in both mitochondrial and nuclear DNA. We have cloned the gene for human COX subunit Vb (COX5B) and determined the exon-intron structure by both hybridization analysis and DNA sequencing. The gene contains five exons and four introns; the four coding exons span a region of approximately 2.4 kb. The 5' end of the COX5B gene is GC-rich and contains many HpaII sites. Genomic Southern blot analysis of human DNA probed with the human COX Vb cDNA identified eight restriction fragments containing COX Vb-related sequences that were mapped to different chromosomes with panels of human x Chinese hamster somatic cell hybrids. Because only one of these fragments hybridized with a 210-bp probe from intron 4, we conclude that there is a single expressed gene for COX subunit Vb in the human genome. We have mapped this gene to chromosome 2, region cen-q13.

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.

The rat cytochrome c oxidase subunit IV gene family: tissue-specific and hormonal differences in subunit IV and cytochrome c mRNA expression

We have isolated three members of the rat cytochrome c oxidase subunit IV gene family: one functional gene and two processed pseudogenes. The pseudogenes appear to represent the only other closely related sequences in this family. The functional gene encodes an isoform which is expressed in all tissues examined and has features characteristic of 'housekeeping' genes. These include multiple transcription start sites mapped to within an approximately 50 bp region and a GC-rich promoter lacking typical CCAAT or TATAA sequences. Although the subunit IV gene is expressed at its highest levels in cardiac and skeletal muscle, consistent with the high energy demand in those tissues, its expression differs from that of cytochrome c in several respects. 1) Subunit IV mRNA abundance in various tissues is relatively uniform when compared to the highly variable levels of cytochrome c mRNAs. 2) Unlike cytochrome c, subunit IV mRNA is expressed at a surprisingly high level in testis. 3) While cytochrome c mRNA levels in liver are increased markedly in response to thyroid hormone treatment, subunit IV mRNA is not significantly affected. Differences in the expression of these two nuclear-encoded respiratory genes are consistent with differences in regulatory elements within their promoters. Therefore, the regulation of nuclear-encoded respiratory genes in response to tissue demands for cellular energy may not be satisfactorily explained by a set of universal regulators common to all such genes.

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.

Novel use of a chimpanzee pseudogene for chromosomal mapping of human cytochrome c oxidase subunit IV

We have isolated a chimpanzee processed pseudogene for subunit IV of cytochrome c oxidase (COX; EC 1.9.3.1) by screening a chimpanzee genomic library in lambda Charon 32 with a bovine liver cDNA encoding COX subunit IV (COX IV), and localized it to a 1.9-kb HindIII fragment. Southern-blot analysis of genomic DNA from five primates showed that DNAs from human, gorilla, and chimpanzee each contained the 1.9-kb pseudogene fragment, whereas orangutan and pigtail macaque monkey DNA did not. This result clearly indicates that the pseudogene arose before the divergence of the chimpanzee and gorilla from the primate lineage. By screening Chinese hamster x human hybrid panels with the human COX4 cDNA, we have mapped COX4 genes to two human chromosomes, 14 and 16. The 1.9-kb HindIII fragment containing the pseudogene, COX4P1, can be assigned to chromosome 14, and by means of rearranged chromosomes in somatic cell hybrids, to 14q21-qter. Similarly, the functional gene, COX4, has been mapped to 16q22-qter.

Context effects and inefficient initiation at non-AUG codons in eucaryotic cell-free translation systems

The context requirements for recognition of an initiator codon were evaluated in vitro by monitoring the relative use of two AUG codons that were strategically positioned to produce long (pre-chloramphenicol acetyl transferase [CAT]) and short versions of CAT protein. The yield of pre-CAT initiated from the 5'-proximal AUG codon increased, and synthesis of CAT from the second AUG codon decreased, as sequences flanking the first AUG codon increasingly resembled the eucaryotic consensus sequence. Thus, under prescribed conditions, the fidelity of initiation in extracts from animal as well as plant cells closely mimics what has been observed in vivo. Unexpectedly, recognition of an AUG codon in a suboptimal context was higher when the adjacent downstream sequence was capable of assuming a hairpin structure than when the downstream region was unstructured. This finding adds a new, positive dimension to regulation by mRNA secondary structure, which has been recognized previously as a negative regulator of initiation. Translation of pre-CAT from an AUG codon in a weak context was not preferentially inhibited under conditions of mRNA competition. That result is consistent with the scanning model, which predicts that recognition of the AUG codon is a late event that occurs after the competition-sensitive binding of a 40S ribosome-factor complex to the 5' end of mRNA. Initiation at non-AUG codons was evaluated in vitro and in vivo by introducing appropriate mutations in the CAT and preproinsulin genes. GUG was the most efficient of the six alternative initiator codons tested, but GUG in the optimal context for initiation functioned only 3 to 5% as efficiently as AUG. Initiation at non-AUG codons was artifactually enhanced in vitro at supraoptimal concentrations of magnesium.

Context effects and inefficient initiation at non-AUG codons in eucaryotic cell-free translation systems

The context requirements for recognition of an initiator codon were evaluated in vitro by monitoring the relative use of two AUG codons that were strategically positioned to produce long (pre-chloramphenicol acetyl transferase [CAT]) and short versions of CAT protein. The yield of pre-CAT initiated from the 5'-proximal AUG codon increased, and synthesis of CAT from the second AUG codon decreased, as sequences flanking the first AUG codon increasingly resembled the eucaryotic consensus sequence. Thus, under prescribed conditions, the fidelity of initiation in extracts from animal as well as plant cells closely mimics what has been observed in vivo. Unexpectedly, recognition of an AUG codon in a suboptimal context was higher when the adjacent downstream sequence was capable of assuming a hairpin structure than when the downstream region was unstructured. This finding adds a new, positive dimension to regulation by mRNA secondary structure, which has been recognized previously as a negative regulator of initiation. Translation of pre-CAT from an AUG codon in a weak context was not preferentially inhibited under conditions of mRNA competition. That result is consistent with the scanning model, which predicts that recognition of the AUG codon is a late event that occurs after the competition-sensitive binding of a 40S ribosome-factor complex to the 5' end of mRNA. Initiation at non-AUG codons was evaluated in vitro and in vivo by introducing appropriate mutations in the CAT and preproinsulin genes. GUG was the most efficient of the six alternative initiator codons tested, but GUG in the optimal context for initiation functioned only 3 to 5% as efficiently as AUG. Initiation at non-AUG codons was artifactually enhanced in vitro at supraoptimal concentrations of magnesium.

Cytochrome oxidase subunit V gene of Neurospora crassa: DNA sequences, chromosomal mapping, and evidence that the cya-4 locus specifies the structural gene for subunit V

The sequences of cDNA and genomic DNA clones for Neurospora cytochrome oxidase subunit V show that the protein is synthesized as a 171-amino-acid precursor containing a 27-amino-acid N-terminal extension. The subunit V protein sequence is 34% identical to that of Saccharomyces cerevisiae subunit V; these proteins, as well as the corresponding bovine subunit, subunit IV, contain a single hydrophobic domain which most likely spans the inner mitochondrial membrane. The Neurospora crassa subunit V gene (cox5) contains two introns, 398 and 68 nucleotides long, which share the conserved intron boundaries 5'GTRNGT...CAG3' and the internal consensus sequence ACTRACA. Two short sequences, YGCCAG and YCCGTTY, are repeated four times each in the cox5 gene upstream of the mRNA 5' termini. The cox5 mRNA 5' ends are heterogeneous, with the major mRNA 5' end located 144 to 147 nucleotides upstream from the translational start site. The mRNA contains a 3'-untranslated region of 186 to 187 nucleotides. Using restriction-fragment-length polymorphism, we mapped the cox5 gene to linkage group IIR, close to the arg-5 locus. Since one of the mutations causing cytochrome oxidase deficiency in N. crassa, cya-4-23, also maps there, we transformed the cya-4-23 strain with the wild-type cox5 gene. In contrast to cya-4-23 cells, which grow slowly, cox5 transformants grew quickly, contained cytochrome oxidase, and had 8- to 11-fold-higher levels of subunit V in their mitochondria. These data suggest (i) that the cya-4 locus in N. crassa specifies structural information for cytochrome oxidase subunit V and (ii) that, in N. crassa, as in S. cerevisiae, deficiencies in the production of nuclearly encoded cytochrome oxidase subunits result in deficiency in cytochrome oxidase activity. Finally, we show that the lower levels of subunit V in cya-4-23 cells are most likely due to substantially reduced levels of translatable subunit V mRNA.

Cytochrome oxidase subunit V gene of Neurospora crassa: DNA sequences, chromosomal mapping, and evidence that the cya-4 locus specifies the structural gene for subunit V

The sequences of cDNA and genomic DNA clones for Neurospora cytochrome oxidase subunit V show that the protein is synthesized as a 171-amino-acid precursor containing a 27-amino-acid N-terminal extension. The subunit V protein sequence is 34% identical to that of Saccharomyces cerevisiae subunit V; these proteins, as well as the corresponding bovine subunit, subunit IV, contain a single hydrophobic domain which most likely spans the inner mitochondrial membrane. The Neurospora crassa subunit V gene (cox5) contains two introns, 398 and 68 nucleotides long, which share the conserved intron boundaries 5'GTRNGT...CAG3' and the internal consensus sequence ACTRACA. Two short sequences, YGCCAG and YCCGTTY, are repeated four times each in the cox5 gene upstream of the mRNA 5' termini. The cox5 mRNA 5' ends are heterogeneous, with the major mRNA 5' end located 144 to 147 nucleotides upstream from the translational start site. The mRNA contains a 3'-untranslated region of 186 to 187 nucleotides. Using restriction-fragment-length polymorphism, we mapped the cox5 gene to linkage group IIR, close to the arg-5 locus. Since one of the mutations causing cytochrome oxidase deficiency in N. crassa, cya-4-23, also maps there, we transformed the cya-4-23 strain with the wild-type cox5 gene. In contrast to cya-4-23 cells, which grow slowly, cox5 transformants grew quickly, contained cytochrome oxidase, and had 8- to 11-fold-higher levels of subunit V in their mitochondria. These data suggest (i) that the cya-4 locus in N. crassa specifies structural information for cytochrome oxidase subunit V and (ii) that, in N. crassa, as in S. cerevisiae, deficiencies in the production of nuclearly encoded cytochrome oxidase subunits result in deficiency in cytochrome oxidase activity. Finally, we show that the lower levels of subunit V in cya-4-23 cells are most likely due to substantially reduced levels of translatable subunit V mRNA.

Subunit Va of human and bovine cytochrome c oxidase is highly conserved

We have isolated a full-length cDNA clone specifying the nuclear-encoded subunit Va of the human mitochondrial respiratory enzyme cytochrome c oxidase (COX; EC 1.9.3.1.). The deduced sequence of the polypeptide is 95% identical to that of the corresponding subunit of bovine COX, which makes it the most conserved polypeptide among the known bovine/human pairs of COX subunits. This polypeptide contains an N-terminal presequence which is rich in basic and hydroxylated residues, but differs from the deduced presequences of all other previously isolated COX subunits in that it also contains a negatively charged residue. We find no evidence of tissue-specific isoforms of subunit Va, as Northern analysis showed a single, identically-sized transcript in RNA from human muscle, liver, and brain, while coxVa cDNAs isolated from both endothelial and fetal muscle cDNA libraries had identical nucleotide sequences.

Tissue-specific differences between heart and liver cytochrome c oxidase

Bovine liver cytochrome c oxidase has been isolated and the subunit structure of this preparation compared with that of the bovine heart enzyme. Of the 10 nuclear-coded subunits, 3 were different in the 2 tissue forms, having different migrations in sodium dodecyl sulfate-polyacrylamide gel electrophoresis, different antigenicities to antibodies made against the heart subunits, and different N-terminal amino acid sequences. Subunit ASA of heart begins with the N-terminal sequence of SSG in liver and is different in 17 of the first 33 residues including a deletion of 2 residues in the liver isoform of this subunit. Subunit CVII of liver differs from its heart counterpart in 6 of the first 37 residues while subunit CIX from liver differs from the heart isoform in 15 of the first 25 residues. No differences between tissue types were observed in partial sequencing of the remaining nuclear-coded subunits. Recently, the major portion of the sequence of subunit CIX from rat liver has been obtained by cloning and sequencing of the cDNA for this polypeptide [Suske, G., Mengel, T., Cordingley, M., & Kadenbach, B. (1987) Eur. J. Biochem. 168, 233-237]. There is a greater sequence homology of the rat and bovine liver forms of CIX than there is between the bovine heart and liver isoforms.

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.

Isolation of a cDNA clone encoding subunit IV of human cytochrome c oxidase

We have isolated a full-length human liver cDNA clone specifying the nuclear-encoded subunit IV of the human mitochondrial respiratory chain enzyme, cytochrome c oxidase (COX; EC 1.9.3.1). The human cDNA clone is highly homologous to its bovine counterpart in the coding regions for both the mature polypeptide and the presequence, and the gene is evolving more slowly than that of any of the three mitochondrially encoded COX subunit genes. We find no preliminary evidence for tissue-specific isoforms of COX subunit IV, as Northern analysis of muscle, liver, and HeLa cell RNA shows an identically sized transcript in each cell type.