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

Caloric Restriction and Ketogenic Diet Therapy for Epilepsy: A Molecular Approach Involving Wnt Pathway and KATP Channels

Epilepsy is a neurological disorder in which, in many cases, there is poor pharmacological control of seizures. Nevertheless, it may respond beneficially to alternative treatments such as dietary therapy, like the ketogenic diet or caloric restriction. One of the mechanisms of these diets is to produce a hyperpolarization mediated by the adenosine triphosphate (ATP)-sensitive potassium (KATP) channels (KATP channels). An extracellular increase of K+ prevents the release of Ca2+ by inhibiting the signaling of the Wnt pathway and the translocation of β-catenin to the cell nucleus. Wnt ligands hyperpolarize the cells by activating K+ current by Ca2+. Each of the diets described in this paper has in common a lower use of carbohydrates, which leads to biochemical, genetic processes presumed to be involved in the reduction of epileptic seizures. Currently, there is not much information about the genetic processes implicated as well as the possible beneficial effects of diet therapy on epilepsy. In this review, we aim to describe some of the possible genes involved in Wnt pathways, their regulation through the KATP channels which are implicated in each one of the diets, and how they can reduce epileptic seizures at the molecular level.

Regulation of mitochondrial respiratory chain biogenesis by estrogens/estrogen receptors and physiological, pathological and pharmacological implications

There has been increasing evidence pointing to the mitochondrial respiratory chain (MRC) as a novel and important target for the actions of 17beta-estradiol (E(2)) and estrogen receptors (ER) in a number of cell types and tissues that have high demands for mitochondrial energy metabolism. This novel E(2)-mediated mitochondrial pathway involves the cooperation of both nuclear and mitochondrial ERalpha and ERbeta and their co-activators on the coordinate regulation of both nuclear DNA- and mitochondrial DNA-encoded genes for MRC proteins. In this paper, we have: 1) comprehensively reviewed studies that reveal a novel role of estrogens and ERs in the regulation of MRC biogenesis; 2) discussed their physiological, pathological and pharmacological implications in the control of cell proliferation and apoptosis in relation to estrogen-mediated carcinogenesis, anti-cancer drug resistance in human breast cancer cells, neuroprotection for Alzheimer's disease and Parkinson's disease in brain, cardiovascular protection in human heart and their beneficial effects in lens physiology related to cataract in the eye; and 3) pointed out new research directions to address the key questions in this important and newly emerging area. We also suggest a novel conceptual approach that will contribute to innovative regimens for the prevention or treatment of a wide variety of medical complications based on E(2)/ER-mediated MRC biogenesis pathway.

Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs

By integrating genome-wide maps of RNA polymerase II (Polr2a) binding with gene expression data and H3ac and H3K4me3 profiles, we characterized promoters with enriched activity in mouse embryonic stem cells (mES) as well as adult brain, heart, kidney, and liver. We identified approximately 24,000 promoters across these samples, including 16,976 annotated mRNA 5' ends and 5153 additional sites validating cap-analysis of gene expression (CAGE) 5' end data. We showed that promoters with CpG islands are typically non-tissue specific, with the majority associated with Polr2a and the active chromatin modifications in nearly all the tissues examined. By contrast, the promoters without CpG islands are generally associated with Polr2a and the active chromatin marks in a tissue-dependent way. We defined 4396 tissue-specific promoters by adapting a quantitative index of tissue-specificity based on Polr2a occupancy. While there is a general correspondence between Polr2a occupancy and active chromatin modifications at the tissue-specific promoters, a subset of them appear to be persistently marked by active chromatin modifications in the absence of detectable Polr2a binding, highlighting the complexity of the functional relationship between chromatin modification and gene expression. Our results provide a resource for exploring promoter Polr2a binding and epigenetic states across pluripotent and differentiated cell types in mammals.

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.

Scapharca inaequivalvis A and B miniglobin genes: promoter activity of the 5' flanking regions and in vivo transcription

Globin genes of the bivalve mollusk Scapharca inaequivalvis have the two intron/three exon organization typical of vertebrate and many invertebrate globins, with introns in highly conserved positions. Sequence studies on the A and B globin genes of the mollusk tetrameric hemoglobin gave evidence for the existence of 'minigenes' spanning part of the first and second intron, in-frame with the heme binding domain encoded by the central exon. Putative promoter and regulatory sequences flanking these minigenes were identified in the 3' regions of intron I. Here we report cloning and functional analysis of these regions ( approximately 400bp) and their promoter activity, which was assessed in K562 cells by transient transfection, was established. Moreover, in vitro reverse transcriptase-polymerase chain reaction (RT-PCR) on total cytoplasmatic RNA demonstrated that the A and B minigenes are transcriptionally active in the erythrocytes of S. inaequivalvis. Thus, the present results lead to the conclusion that the present-day organization of the globin genes of S. inaequivalvis tetrameric hemoglobin is still reminiscent of an ancestral globin gene before exon shuffling.

Characterization and regulation of the 5'-flanking region of the murine endothelial protein C receptor gene

The protein C pathway plays a critical role in the negative regulation of blood coagulation. The nucleotide sequence of the murine endothelial protein C receptor (mEPCR) gene was determined for 8.8 kilobase pairs of the genomic structure and 3.4 kilobase pairs of the 5'-flanking region. RNase protection assay revealed six major transcription start sites clustered at -100 to -109 upstream of the translation initiation site. A series of 5'-promoter deletion fragments were fused to a luciferase reporter gene and transiently transfected into bovine aortic endothelium. Deletion of the sequence from -220 to -180 dramatically reduced luciferase expression in bovine aortic endothelial cells. This region of the murine endothelial protein C receptor gene contains one AP4 site and one SP1 site. Mutations in the core sequence of the AP4 and SP1 sites impaired both nuclear protein binding and luciferase expression. These results suggest important roles for AP4 and SP1 in the constitutive expression of mEPCR. A thrombin response element (CCCACCCC) was found to mediate the induction of mEPCR by thrombin in cell culture. Transgenic mice were developed expressing green fluorescent protein driven by the -350 to -1 or -1080 to -1 promoter. Thrombin up-regulated mEPCR and the transgene in vivo.

Human COX6A1 gene: promoter analysis, cDNA isolation and expression in the monkey brain

The human COX6A1 gene encodes the ubiquitous isoform of cytochrome c oxidase (COX) subunit VIa (VIa-L), and is located in a CpG island on chromosome 12q24.2. We compared the COX6A1 gene with the published cDNA and several ESTs and concluded that subunit COX VIa-L is synthesized as a preprotein, as are other COX subunits. The same transcription start sites were identified by primer extension analysis of human brain and lymphoblastoid RNA. Analysis of the COX6A1 promoter revealed several conserved sequence elements found in other COX genes, namely binding sites for nuclear respiratory factor 1 (NRF-1), nuclear respiratory factor 2/GA binding protein (NRF-2/GABP), and ying-yang protein 1 (YY1). These conserved elements were shown to bind nuclear proteins from HeLa nuclear extracts. COX6A1 cDNA was isolated from a human brain cDNA library, and the sequence was identical to that of human liver. The expression of this gene was demonstrated by in-situ hybridization in monkey brain sections with our human brain cDNA. Monocular impulse blockade in adult monkeys induced a downregulation of COX6A1 expression in deprived visual neurons, suggesting that this subunit gene is regulated by neuronal activity.

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 subunit structure of cytochrome-c oxidase from tuna heart and liver

Cytochrome-c oxidase was isolated from tuna liver and heart, and the subunit composition was analysed by SDS/PAGE by two separation systems. Two additional subunits of the enzyme complex were immunoprecipitated from solubilized mitochondria with an antibody against bovine subunit IV. The N-terminal and internal amino acid sequences of all nuclear-coded subunits were determined after blotting onto poly(vinylidene difluoride) membranes or by tryptic hydrolysis of gel bands and HPLC separation of peptides, respectively. 13 subunits were identified with isoforms for subunits Va, VIc, VIIb and VIII. The isoforms for subunits Va and VIIb are found in liver and heart, isoforms for subunit VIc only in heart, and isoforms for subunit VIII only in liver. Isoforms for subunits Va, VIc and VIIb have not been described in other species. The postulated mechanism of thermogenesis in mammals, based on decreased H+/e- stoichiometry at high ATP/ADP ratios due to binding of ATP to the heart-type subunit VIa [Frank, V. & Kadenbach, B. (1996) FEBS Lett. 382, 121-124], appears not to occur in tuna, because no isoforms of subunit VIa were found.

Cloning, characterization, and chromosomal localization of human liver form cytochrome c oxidase subunit VIa related genes

The chromosomal location of human cytochrome c oxidase (COX) subunit VIa Liver (VIa-L) isoform related sequences has been determined by a combination of in situ hybridization and analysis of human-hamster somatic cell hybrid panels. COX VIa-L related sequences were present on chromosomes 6 and 12. It has been verified that at least two COX VIa-L genes are on chromosome 6, one of which is a pseudogene. In total, four COX VIa-L related sequences have been cloned and their nucleotide sequences analyzed. At least three of the sequences represent pseudogenes; their relatedness to the COX VIa-L cDNA is discussed.

Structure of the human gene (COX6A2) for the heart/muscle isoform of cytochrome c oxidase subunit VIa and its chromosomal location in humans, mice, and cattle

We have mapped the gene for the heart/muscle isoform of cytochrome c oxidase (COX) subunit VIa in three mammalian species and isolated the human COX6AH gene (HGMW-approved symbol COX6A2). The bovine gene was mapped by somatic cell hybrid mapping panels to bovine chromosome BTA 25 with 94-95% concordance. The mouse gene (Cox6ah) was mapped using an interspecific backcross panel from the cross (C57BL/6J x Mus spretus)F1 x Mus spretus probed with the mouse COX VIa-H cDNA. Cox6ah was located on distal chromosome 7, between D7Mit8 and D7Mit13. From the regions of known gene conservation among these three species, we predicted that human COX6AH would be located on chromosome 16p. We hybridized a human x rodent mapping panel of somatic cell hybrids with the human cDNA to confirm this assignment. These data taken together indicated that the human COX6AH gene is located on the short arm of chromosome 16 and facilitated the isolation of the human gene from a chromosome 16-enriched library. The human COX6AH gene spans about 1 kb and contains three exons and two small introns. The sequences of the proximal 5' flanking regions of COX6AH genes are highly conserved between human, bovine, and rodent.

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.

Structural characterization and regulatory element analysis of the heart isoform of cytochrome c oxidase VIa

In order to investigate the mechanism(s) governing the striated muscle-specific expression of cytochrome c oxidase VIaH we have characterized the murine gene and analyzed its transcriptional regulatory elements in skeletal myogenic cell lines. The gene is single copy, spans 689 base pairs (bp), and is comprised of three exons. The 5'-ends of transcripts from the gene are heterogeneous, but the most abundant transcript includes a 5'-untranslated region of 30 nucleotides. When fused to the luciferase reporter gene, the 3.5-kilobase 5'-flanking region of the gene directed the expression of the heterologous protein selectively in differentiated Sol8 cells and transgenic mice, recapitulating the pattern of expression of the endogenous gene. Deletion analysis identified a 300-bp fragment sufficient to direct the myotube-specific expression of luciferase in Sol8 cells. The region lacks an apparent TATA element, and sequence motifs predicted to bind NRF-1, NRF-2, ox-box, or PPAR factors known to regulate other nuclear genes encoding mitochondrial proteins are not evident. Mutational analysis, however, identified two cis-elements necessary for the high level expression of the reporter protein: a MEF2 consensus element at -90 to -81 bp and an E-box element at -147 to -142 bp. Additional E-box motifs at closely located positions were mutated without loss of transcriptional activity. The dependence of transcriptional activation of cytochrome c oxidase VIaH on cis-elements similar to those found in contractile protein genes suggests that the striated muscle-specific expression is coregulated by mechanisms that control the lineage-specific expression of several contractile and cytosolic proteins.

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.