Structural organisation of the rat genes encoding liver- and heart-type of cytochrome c oxidase subunit VIa and a pseudogene related to the COXVIa-L cDNA

Low culture temperature inhibits myogenic differentiation through mitochondrial activity

A previous study by our group reported that mouse and human myoblasts fail to express myogenin and to fuse into multi-nucleate myotubes when cultured at low temperature, such as 30°C, but that this activity is rescued by adding IGF-I and vitamin C to the culture medium. In the present study, we examined mitochondrial activity as a target of the inhibitory effects of the low culture temperature. It has been suggested that mitochondria regulate myogenesis. By using a mouse myoblast cell line C2C12, we demonstrate that the expression of cytochrome c oxidase subunit I (COX I), which is encoded in mitochondrial genome, increases during myogenic differentiation at the normal culture temperature (38°C), but that this up-regulation is inhibited at 30°C. The mitochondrial membrane potential also decreased at 30°C compared to the culture at 38°C. However, IGF-I and vitamin C rescued both COX I expression and mitochondrial membrane potential at 30°C as promoting muscle differentiation. We also find that the rescue of mitochondrial activity by IGF-I and vitamin C at 30°C occurred after the myogenin expression, which suggests that myogenin regulates mitochondrial function during myogenesis. We suggest that our low temperature-culture system may be suitable for use in studying the detailed mechanism of myogenin-related phenomena during myogenesis.

Identification of rat lung--prominent genes by a parallel DNA microarray hybridization

Background

The comparison of organ transcriptomes is an important strategy for understanding gene functions. In the present study, we attempted to identify lung-prominent genes by comparing the normal transcriptomes of rat lung, heart, kidney, liver, spleen, and brain. To increase the efficiency and reproducibility, we first developed a novel parallel hybridization system, in which 6 samples could be hybridized onto a single slide at the same time.

Results

We identified the genes prominently expressed in the lung (147) or co-expressed in lung-heart (23), lung-liver (37), lung-spleen (203), and lung-kidney (98). The known functions of the lung-prominent genes mainly fell into 5 categories: ligand binding, signal transducer, cell communication, development, and metabolism. Real-time PCR confirmed 13 lung-prominent genes, including 5 genes that have not been investigated in the lung, vitamin D-dependent calcium binding protein (Calb3), mitogen activated protein kinase 13 (Mapk13), solute carrier family 29 transporters, member 1 (Slc29a1), corticotropin releasing hormone receptor (Crhr1), and lipocalin 2 (Lcn2).

Conclusion

The lung-prominent genes identified in this study may provide an important clue for further investigation of pulmonary functions.

Functional analysis of the rat cytochrome c oxidase subunit 6A1 promoter in primary neurons

Cytochrome c oxidase (COX) is a multimeric enzyme consisting of 13 subunits that are encoded in both mitochondrial and nuclear genomes. We analyzed the promoter of the rat gene encoding the liver isoform of COX subunit VIa. Using transiently transfected primary neuronal cultures as a model system, we found that the basal promoter activity of this gene is localized to a region between positions -244 and +58 relative to the transcriptional start site. This region contains putative binding sites for the transcription factors Sp1, NRF-1, and NRF-2. Two of the NRF-2 sites in this basal promoter are organized in a tandem repeat. A deletion that disrupted this tandem repeat reduced transcription to approximately 25% of the basal level. Additional small deletion series and point mutation experiments confirmed the presence of two functional NRF-2 sites arranged in a tandem repeat, as well as a NRF-1 site and an Sp1 site. In vivo binding of NRF-2 to the rCOX6A1 promoter was confirmed with chromatin immunoprecipitation assay (ChIP). We conclude that Sp1, NRF-1, and NRF-2 are important in activating transcription of the rat COX6A1 gene.

Characterization of the murine gene for subunit VIIaL of cytochrome c oxidase

Mammalian cytochrome c oxidase consists of thirteen subunits, ten encoded by the nuclear genome and three by the mitochondrial DNA. In several species, two isoforms have been isolated for nuclear-encoded subunits VIa, VIIa and VIII: an ubiquitous L (liver) form and a heart- and skeletal-muscle specific H form. The gene for murine cytochrome c oxidase subunit VIIa-L (Cox7aL) and its promoter region were isolated, sequenced and analysed. The coding region is split in four exons spanning 4.1 kbp and the promoter carries potential binding sites for Sp1, NRF1 and NRF2 transcription factors. Transcriptional activity of the promoter in reporter assays suggested an ubiquitous expression in mouse tissues.

Isolation and sequence of the human cytochrome c oxidase subunit VIIaL gene

The gene for human cytochrome c oxidase subunit VIIa liver isoform (COX7AL) was isolated and its sequence determined and analyzed. The three introns of the gene are considerably larger than those of the heart isoform of subunit VIIa (COX7AH), but the position of the introns relative to the cDNA sequences is homologous between the two genes. Comparison with other isolated COX7AL genes suggests that the promoter region binding motifs for transcription factors have evolved along with the coding region. In fibroblasts cultured originally from a Leigh's disease patient, a shortened COX7AL cDNA was identified by RT-PCR, consisting of exon I joined to exon IV, omitting exons II and III. No mutation could be identified in COX7AL of the patient, suggesting that the shortened cDNA is due to an alteration of the genome during cell culture. A surprising transcription of COX7AH was observed in cultured fibroblasts, suggesting a potential utility of these cells for study of its gene expression.

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.

Turkey cytochrome c oxidase contains subunit VIa of the liver type associated with low efficiency of energy transduction

Cytochrome c oxidase was isolated from turkey liver, heart and breast skeletal muscle and separated by SDS/PAGE. The N-terminal amino-acid sequence of subunit VIa from all tissues and internal sequences from the skeletal muscle enzyme show homology to the mammalian liver-type subunit VIaL, which was verified by isolation and sequencing of the cDNA of turkey subunit VIa. No cDNA corresponding to subunit VIaH (mammalian heart-type) could be found by RACE-PCR with mRNA from all turkey tissues. Measurement of proton translocation with the reconstituted enzymes from turkey liver and heart revealed H+/e- ratios below 0.5 that were independent of the intraliposomal ATP/ADP ratio, as previously found with the bovine liver enzyme. Under identical conditions, the bovine heart enzyme revealed H+/e- ratios of 0.85 at low and 0.48 at high intraliposomal ATP/ADP ratios. The results suggest that in birds the lower H+/e-ratio of cytochrome c oxidase participates in elevated resting metabolic rate and thermogenesis.

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.

Influence of thyroid hormone on the tissue-specific expression of cytochrome c oxidase isoforms during cardiac development

In mammals, cytochrome c oxidase (COX) is composed of 13 different protein subunits. In the rat, two nuclear-encoded subunits, COX VIa and VIII, exist as tissue-specific isoforms: heart and liver. Using Northern-blot analysis, the levels of transcripts for the heart and liver isoforms of VIa and VIII were examined in developing rat hearts. The liver isoform was found to be the predominant form of subunit VIa and the exclusive form of VIII in the 18-day fetal hearts. The mRNA levels of the heart isoform of both subunits increased dramatically to reach adult levels by 14 days. Although the levels of the VIa- and VIII-liver isoform mRNAs remained stable throughout early development, their levels decreased by 40 and 36% respectively between the 18-day fetal stage and 18-day neonatal stage. Therefore the up-regulation of the heart isoforms and down-regulation of the liver isoforms appear to be regulated in a co-ordinated manner during development. To determine if thyroid hormone influences the expression of these developmentally regulated isoforms, the RNA was also extracted from the hearts of 2-week-old hypothyroid rats. The results showed that the levels of VIII-heart and VIa-liver COX mRNAs were approx. 40% lower in the hypothyroid hearts, while VIII-liver and VIa-heart COX isoform expression remained unchanged. These data demonstrate that the isoforms of COX subunits VIa and VIII are not co-ordinately regulated by changes in thyroid hormone levels. Therefore we conclude that, although thyroid hormone influences the expression of isoforms, it appears to do so via a different mechanism from that which regulates the developmental transition.

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.

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.

Species-specific expression of cytochrome c oxidase isozymes

Cytochrome c oxidase was isolated from livers and hearts of sheep, dog and rabbit, and the polypeptide composition was analyzed by two different SDS-PAGE separation systems. The gels were blotted on PVDF-membranes and the N-terminal amino acid sequences of the tissue-specific subunits VIa, VIIa and VIII were determined in a protein sequencer. Except for subunit VIIa from rat, subunits VIa and VIIa from all investigated mammals are tissue-specific expressed in liver and heart. In contrast, subunit VIII is clearly different in liver and heart of bovine, dog and rat, but identical in liver and heart of human (liver-type), sheep, rabbit and also in rainbow trout (heart-type). The data suggest a strong species-specific variation of the regulatory properties of cytochrome c oxidase in different tissues.

Cloning, sequence analysis, and expression of a mouse cDNA encoding cytochrome c oxidase subunit VIa liver isoform

A cDNA encoding cytochrome c oxidase (COX) subunit VIa liver isoform (COX6aL) was isolated from a Mus musculus library and sequenced. The protein translated from the nucleotide sequence contains a presequence and is 91% identical to the human cognate sequence over the processed polypeptide region. Northern analysis shows the expression of COX6aL is developmentally regulated in heart, being about equally transcribed with the heart isoform (COX6aH) in 18-day embryos but consisting of less than 25% in adult heart.