Structural organization of the rat cytochrome c oxidase subunit IV gene

Bigenomic transcriptional regulation of all thirteen cytochrome c oxidase subunit genes by specificity protein 1

Cytochrome c oxidase (COX) is one of only four known bigenomic proteins, with three mitochondria-encoded subunits and 10 nucleus-encoded ones derived from nine different chromosomes. The mechanism of regulating this multi-subunit, bigenomic enzyme is not fully understood. We hypothesize that specificity protein 1 (Sp1) functionally regulates the 10 nucleus-encoded COX subunit genes directly and the three mitochondrial COX subunit genes indirectly by regulating mitochondrial transcription factors A and B (TFAM, TFB1M and TFB2M) in neurons. By means of in silico analysis, electrophoretic mobility shift and supershift assays, chromatin immunoprecipitation, RNA interference and over-expression experiments, the present study documents that Sp1 is a critical regulator of all 13 COX subunit genes in neurons. This regulation is intimately associated with neuronal activity. Silencing of Sp1 prevented the upregulation of all COX subunits by KCl, and over-expressing Sp1 rescued all COX subunits from being downregulated by tetrodotoxin. Thus, Sp1 and our previously described nuclear respiratory factors 1 and 2 are the three key regulators of all 13 COX subunit genes in neurons. The binding sites for Sp1 on all 10 nucleus-encoded COX subunits, TFAM, TFB1M and TFB2M are highly conserved among mice, rats and humans.

Effects of aripiprazole and clozapine on the treatment of glycolytic carbon in PC12 cells

Aripiprazole is the only atypical antipsychotic drug known to cause the phosphorylation of AMP-activated protein kinase (AMPK) in PC12 cells. However, the molecular mechanisms underlying this phosphorylation in aripiprazole-treated PC12 cells have not yet been clarified. Here, using PC12 cells, we show that these cells incubated for 24 h with aripiprazole at 50 μM and 25 mM glucose underwent a decrease in their NAD⁺/NADH ratio. Aripiprazole suppressed cytochrome c oxidase (COX) activity but enhanced the activities of pyruvate dehydrogenase (PDH), citrate synthase and Complex I. The changes in enzyme activities coincided well with those in NADH, NAD⁺, and NAD⁺/NADH ratio. However, the bioenergetic peril judged by the lowered COX activity might not be accompanied by excessive occurrence of apoptotic cell death in aripiprazole-treated cells, because the mitochondrial membrane potential was not decreased, but rather increased. On the other hand, when PC12 cells were incubated for 24 h with clozapine at 50 μM and 25 mM glucose, the NAD⁺/NADH ratio did not change. Also, the COX activity was decreased; and the PDH activity was enhanced. These results suggest that aripiprazole-treated PC12 cells responded to the bioenergetic peril more effectively than the clozapine-treated ones to return the ATP biosynthesis back toward its ordinary level. This finding might be related to the fact that aripiprazole alone causes phosphorylation of AMPK in PC12 cells.

Nuclear activators and coactivators in mammalian mitochondrial biogenesis

The biogenesis of mitochondria requires the expression of a large number of genes, most of which reside in the nuclear genome. The protein-coding capacity of mtDNA is limited to 13 respiratory subunits necessitating that nuclear regulatory factors play an important role in governing nucleo-mitochondrial interactions. Two classes of nuclear transcriptional regulators implicated in mitochondrial biogenesis have emerged in recent years. The first includes DNA-binding transcription factors, typified by nuclear respiratory factor (NRF)-1, NRF-2 and others, that act on known nuclear genes that specify mitochondrial functions. A second, more recently defined class, includes nuclear coactivators typified by PGC-1 and related family members (PRC and PGC-1 beta). These molecules do not bind DNA but rather work through their interactions with DNA-bound transcription factors to regulate gene expression. An important feature of these coactivators is that their expression is responsive to physiological signals mediating thermogenesis, cell proliferation and gluconeogenesis. Thus, they have the ability to integrate the action of multiple transcription factors in orchestrating programs of gene expression essential to cellular energetics. The interplay of these nuclear factors appears to be a major determinant in regulating the biogenesis of mitochondria.

Genomic organization and promoter regulation of human cytochrome c oxidase subunit VII heart/muscle isoform (COX7AH)

We have isolated and characterized the human gene (COX7AH) for the contractile muscle isoform of cytochrome c oxidase (COX) subunit VIIa. This subunit is one of the 10 nuclear encoded subunits of the 13-subunit holoenzyme that carries out the terminal step in the electron transport chain. Using transient transfection assays, we have located a 5'-flanking region sufficient to direct high level, skeletal myotube-specific reporter gene expression. This 792 bp basal promoter, which contains the single transcription start but no canonical TATA or CCAAT boxes, contains one MEF2 site, three E boxes, and an Sp1 site that show binding to their cognate factors, and are all required for full expression. Mutation and transactivation analysis suggest that there is functional interaction between these binding sites.

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.

The role of an E box binding basic helix loop helix protein in the cardiac muscle-specific expression of the rat cytochrome oxidase subunit VIII gene

We have characterized the rat gene for muscle-specific cytochrome oxidase VIII (COX VIII(H)) and mapped the distal promoter region responsible for transcription activation in C2C12 skeletal myocytes and H9C2 cardiomyocytes. In both cell types, the promoter elements responding to the induced differentiation of myocytes map to two E boxes, designated as E1 and E2 boxes with a core sequence of CAGCTG. Gel mobility shift analysis showed that both E1 and E2 box motifs form complexes with nuclear extracts from H9C2 cardiomyocytes that were supershifted with monoclonal antibody to E2A but not with antibody to myo-D. Extracts from induced and uninduced H9C2 cardiomyocytes yielded different gel mobility patterns and also different E2A antibody supershifts suggesting a difference in the DNA-bound protein complexes cross-reacting with the E2A antibody. Transcriptional activity of the promoter construct containing intact E boxes was inhibited by coexpression with Id in differentiated H9C2 cardiomyocytes. Our results show the involvement of an E box binding basic helix loop helix protein in the cardiac muscle-specific regulation of the COX VIII(H) promoter.

Dexamethasone enhances expression of mitochondrial oxidative phosphorylation genes in rat distal colon

Dexamethasone and aldosterone are major activators of Na+ reabsorption in tight epithelia. The genes whose expression mediates the steroid actions are mostly unknown. To identify such genes, we performed differential screening of a rat colon cDNA library with total 32P-labeled cDNA probes reverse transcribed from steroid-stimulated and steroid-depleted poly(A)+ RNA. Several cDNAs whose corresponding mRNA is enhanced two- to threefold after dexamethasone injection were identified. Partial sequencing indicated that four of them code for subunits of cytochrome-c oxidase and 16S mitochondrial mRNA. The dexamethasone-induced increase in mitochondrial RNA abundance could not be mimicked by a low-salt diet, found to increase plasma aldosterone from 1.0 +/- 0.1 to 12.8 +/- 1.4 nM. Induction of mitochondrial genes by adrenal steroids may serve to prevent limitation of transport by the ATP supply to the Na(+)-K+ pump under conditions of maximal stimulation of Na+ transport.

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.

Disproportionate regulation of nuclear- and mitochondrial-encoded cytochrome oxidase subunit proteins by functional activity in neurons

Cytochrome oxidase is the terminal enzyme in the mitochondrial respiratory chain engaged in oxidative metabolism and energy production. In mammals, the holoenzyme is composed of 13 subunits encoded by both nuclear and mitochondrial genomes. The goal of the present study was to compare the effect of afferent impulse blockade on the expression of these two genomes at the subunit protein level. It also aimed to determine the correlation between the level of cytochrome oxidase activity and the relative amount of subunit proteins. Relative enzyme activity was analysed histochemically, and relative amounts of subunits IV (nuclear-encoded) and II/III (mitochondrial-derived) proteins were obtained immunohistochemically by anti-subunit IV and anti-subunit II/III antibodies in the lateral geniculate nucleus and the primary visual cortex of adult monkeys. In the normal visual centers, similar staining patterns were found for all three markers. After three and seven days of tetrodotoxin treatment, levels of enzyme activity and subunit proteins declined disproportionately in the deprived laminae of the visual center. Densitometric analysis indicates that changes in enzyme activity and subunit IV proteins were significantly greater than those of subunit II/III proteins (P < 0.01). The finding that nuclear and mitochondrial genomes are disproportionately regulated at subunit protein levels by neuronal activity implies that the two genomes operate under different regulatory mechanisms. Changes in subunit IV paralleled most closely those of cytochrome oxidase activity (coefficient of determination r2 = 0.95). This suggests that nuclear-derived subunit IV protein may play a pivotal role in controlling cytochrome oxidase holoenzyme activity.

Structural organization of the bovine gene for the heart/muscle isoform of cytochrome c oxidase subunit VIa

The bovine gene for the nuclear-encoded heart/muscle isoform of cytochrome c oxidase subunit VIa (COX6A1) was isolated from a library of bovine genomic DNA in lambda EMBL3 and sequenced. The gene spans 760 bp and comprises three exons and two small introns. Exon 1 encodes a 193 bp 5' untranslated region, a 12 amino acid presequence, and the first 12 amino acids of the mature COX VIa protein. Exon 2 encodes amino acids 13 to 58, and exon 3 amino acids 59 to 85 plus the 35 bp 3' untranslated region. Exons 2 and 3 are separated by a small intron of only 96 bp. All exon-intron boundaries matched the consensus splice junction sequences. COX6A1 transcripts are present in RNA from bovine heart but not brain. Primer extension and ribonuclease protection assays were used to map the 5' ends of COX6A1 transcripts in heart; both methods identified several clusters of transcription initiation sites, indicating that COX6A1 mRNA is heterogeneous at the 5' end. The proximal 5' flanking region is AT-rich and contains potential basal promoter elements, such as TATA and CCAAT boxes, associated with tissue-specific genes. A single consensus binding site for the muscle-specific transcription factor, MyoD1, was also located within this AT-rich region. The distal promoter region contained a perfect AP4 site plus potential binding sites for enhancer elements (NRF-1, Mt1, Mt3, and Mt4) proposed to regulate expression of genes for mitochondrial proteins.

Structure of the promoter region of the gene encoding cytochrome c oxidase subunit V in Dictyostelium

A cDNA for the nuclear-encoded subunit V of Dictyostelium discoideum cytochrome-c oxidase was used as a probe to screen a genomic library and isolate the complete gene. Primer-extension analysis revealed two transcription start sites located 32 and 39 nucleotides upstream of the translation initiation codon. The chloramphenicol acetyltransferase assay in transient and stable Dictyostelium transformants indicated that the 400-bp dT-rich segment 5' to the transcription start sites retained promoter activity. This region contains an octanucleotide sequence similar to the yeast HAP2/3/4 responsive element.

Transcriptional activity of a mutant thyroid hormone receptor beta in a family with generalized resistance to thyroid hormone

We previously reported a family with generalized resistance to thyroid hormone (GRTH) which had a point mutation with codon 448 CCT (proline) being converted to ACT (threonine) in the thyroid hormone receptor (TR) beta. To characterize functional properties of the mutant TR beta, transient expression studies were performed in COS cells. A double stranded oligonucleotide encompassing thyroid hormone response element (TRE) derived from the rat GH gene was synthesized. We constructed chloramphenicol acetyl transferase (CAT) plasmid containing the thymidine kinase promoter under the control of the rat GH TRE. T3 induction of CAT activity by the mutant TR beta was significantly reduced as compared with that of the normal TR beta. This was observed in the presence of 0.5-50 nM T3, but not at 500 nM T3. When the normal and mutant TR beta were cotransfected, the mutant TR beta inhibited gene activation regulated by the normal TR beta. However, a high molar excess was necessary to significantly inhibit the function of the normal receptor. Additionally, the binding of in vitro synthesized mutant TR beta to TRE was preserved.

Structural organization of a nuclear gene for the alpha-subunit of the bovine mitochondrial ATP synthase complex

The structural organization of an expressed bovine gene (ATPA1) that encodes an isoform of the alpha-subunit of the mitochondrial F0F1 ATP synthase was determined. The gene extends over 10 kilobase-pairs and is divided into 12 exons. The first exon encodes the 5' untranslated region and approximately one-half of the presequence that targets this protein to the mitochondrion. The remainder of the presequence, together with three amino acids of the mature protein, are encoded by exon 2. Primer extension and nuclease protection analyses revealed multiple sites of transcription initiation. The 5' flanking region of the ATPA1 gene can drive the transcription of a reporter gene in an orientation-dependent manner. This promoter region contains several sequence elements which might play an important role in regulating the expression of this gene, including possible TATA and CCAAT boxes, putative Sp1-binding sites, and sequences resembling AP-1, AP-2, AP-4 and cAMP-responsive elements. The ATPA1 gene also contains sequences homologous to several motifs that are shared among some nuclear genes encoding mitochondrial proteins. These include Mt1, Mt3, Mt4, a respiratory enhancer, and NRF-2 sites. Tissue-specific differences in the ATPA1 mRNA levels were observed with high levels found in skeletal muscle and heart, and lower levels in other tissues.

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.

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.