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

TSGA10 is a novel candidate gene associated with acephalic spermatozoa

Acephalic spermatozoa is a rare teratozoospermia associated with male infertility. However, the pathogenesis of this disorder remains unclear. Here, we report a 27 years old infertile male from a consanguineous family, who presented with 99% headless sperm in his ejaculate. Electron microscopic and immunofluorescence analysis suggested breakage at the midpiece of the patient's sperm cells. Subsequent whole-exome sequencing analysis identified a homozygous deletion within TSGA10 (c.211delG; p.A71Hfs*12), which resulted in the production of truncated TSGA10 protein. TSGA10 is a testis-specific protein that localized to the midpiece in the spermatozoa of a normal control; however, immunostaining failed to detect TSGA10 protein in the patient's sperm. Western blot analysis also showed complete absence of TSGA10 protein in the patient. One cycle of in vitro fertilization-assisted reproduction was conducted, but pregnancy was not achieved after embryo transfer, possibly due to poor embryo quality. Therefore, we speculate that the presence of rare sequence variants within TSGA10 may be associated with acephalic spermatozoa in humans.

Three nucleus-encoded subunits of mitochondrial cytochrome c oxidase of the whiteleg shrimp Litopenaeus vannamei: cDNA characterization, phylogeny and mRNA expression during hypoxia and reoxygenation

The mitochondrial cytochrome c oxidase (COX) catalyzes the reduction of oxygen to water playing a key role in the respiratory chain and ATP synthesis. The nucleus-encoded COX subunits do not participate in catalysis, but some are known to play a role in the expression, assembly and activity of the enzyme. Since hypoxia continuously affects the shrimp environment, it is important to study COX to understand their ability to deal with low oxygen levels. The goal of this research was to characterize the complementary DNA (cDNA) sequences of three nucleus-encoded subunits -coxIV, coxVa, and coxVb- and to evaluate the shrimp COX response to hypoxia by measuring their gene expression. The cDNA sequence of coxIV consisted of 532bp, which encodes a 17.47kDa protein, while coxVa cDNA consisted of 460bp and coded a protein of 17.11kDa, and the coxVb coding sequence consisted of 364bp encoding a 13.74kDa protein. Shrimp subunits do not have isoforms, and they are not differentially expressed during hypoxia, as observed in mammals. Coordinated changes were detected in the mRNA amounts of nuclear and mitochondrial subnits; these changes, at the transcriptional level, are suggested to be controlled through transcriptional factors Sp1 and NRF2.

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.

Genetic ecotoxicology of asbestos pollution in the house mouse Mus musculus domesticus

PURPOSE

We tested the genetic diversity in wild mice (Mus musculus domesticus) inhabiting the asbestos-polluted area as a model for the long-term mutagenic effect of asbestos. Hazardous effects of deposited asbestos persist in the environment because of low rate of fiber disintegration. The upper layers of the soil in the vicinity of a former asbestos factory are nearly "saturated" with asbestos fibers and dust. Natural populations of mice dwell in this area and are constantly exposed to asbestos fibers.

METHODS

We measured the microsatellites genetic diversity of wild mice (Mus musculus domesticus) inhabiting the asbestos-polluted area as a model for the long-term mutagenic effect of this environmental toxin.

RESULTS

The six tested microsatellites were highly polymorphic, revealing 111 different alleles for the two sampled populations. Effective number of alleles was slightly higher in the polluted population relative to the control population, while observed heterozygosity was lower. The chromatographic profile of the polluted population exhibited a significantly higher number of bands, probably resulting from somatic mutations, in addition to the ordinary microsatellite band profiles.

CONCLUSIONS

Long-term exposure to asbestos fibers significantly elevates the level of somatic mutations. It also leads to a relatively high level of observed homozygosity, a phenomenon that may be associated with loss of heterozygosity. Based on the mice population, our data suggest elevated health risks for humans living in an asbestos-polluted area.

The dynamic of the t-haplotype in wild populations of the house mouse Mus musculus domesticus in Israel

The t-haplotype, a variant of the proximal part of the mouse chromosome 17, is composed of at least four inversions and is inherited as a single genetic unit. The haplotype causes embryonic mortality or male sterility when homozygous. Genes within the complex are responsible for distortion of Mendelian transmission ratio in males. Thus, the t-haplotype in heterozygous males is transferred to over 95% of the progeny. We examined the dynamic and behavior of the t-haplotype in wild populations of the house mouse in Israel. The Israeli populations show high frequency (15%-20%) of both partial and complete t-carrying mice, supporting the suggestion that the t-complex evolved in the M. domesticus line in the Israeli region. In one population that had the highest frequency of t-carrying individuals, we compared the level of gene diversity between t-carrying and normal mice in the marker's loci: H-2 locus of the major histocompatibility complex (MHC) on the t-haplotype of chromosome 17, three microsatellites on other chromosomes, and the mitochondrial D-loop. Genetic variability was high in all tested loci in both t and (+) mice. All t mice carried the same chromosome and showed the same H-2 haplotype. While t-carrying mice showed significant H-2 heterozygotes access, (+) mice expressed significant H-2 heterozygote deficiency. There were no differences in the level of gene diversity between t and (+) mice in the other loci. Heterozygosity level at the MHC may be an additional factor in the selective forces balancing the t-haplotype polymorphism.

E2F-1 Regulates the Expression of a Subset of Target Genes during Skeletal Myoblast Hypertrophy

Cellular hypertrophy, or growth without division, is an adaptive response to various physiological and pathological stimuli in postmitotic muscle. We demonstrated previously that angiotensin II stimulates hypertrophy in C2C12 myoblasts by transient activation of the cyclin-dependent kinase 4 complex, subsequent phosphorylation of retinoblastoma protein, release of histone deacetylase 1 from the retinoblastoma protein inhibitory complex, and partial activation of the transcription factor E2F-1. These observations led us to propose a model in which partial inactivation of the retinoblastoma protein complex leads to the derepression of a subset of E2F-1 targets necessary for cell growth without division during hypertrophy. We now present data that support this model and suggest the mechanism by which E2F-1 regulates hypertrophy. We examined expression profiles of angiotensin II-stimulated myoblasts and identified a subset of E2F-1 target genes that are specifically regulated during the hypertrophic response. We showed that the expression of E2F-1 targets involved in G1/S transit, DNA replication, and mitosis is not altered during the hypertrophic response, while the expression of E2F-1-regulated genes controlling early G1 progression, cytoskeletal organization, protein synthesis, mitochondrial function, and programmed cell death is up-regulated. Furthermore, we demonstrated that activation of cytochrome c oxidase genes occurs during the development of hypertrophy and that cytochrome c oxidase IV is a direct transcriptional target of E2F-1. These studies demonstrated that E2F-1 activity at specific promoters is dependent on physiological circumstances and that E2F-1 should be considered a potential target in the treatment of pathologic hypertrophy.

Regulation of murine cytochrome c oxidase Vb gene expression during myogenesis: YY-1 and heterogeneous nuclear ribonucleoprotein D-like protein (JKTBP1) reciprocally regulate transcription activity by physical interaction with the BERF-1/ZBP-89 factor

A transcription suppressor element (sequence -481 to -320) containing a G-rich motif (designated GTG) and a newly identified CAT-rich motif (designated CATR) was previously shown to modulate expression of the mouse cytochrome c oxidase Vb gene during myogenesis. Here, we show that the GTG element is critical for transcription activation in both undifferentiated and differentiated myocytes. Mutations of the CATR motif abolished transcription repression in myoblasts while limiting transcription activation in differentiated myotubes, suggesting contrasting functional attributes of this DNA motif at different stages of myogenesis. Results show that the activity of the transcription suppressor motif is modulated by an orchestrated interplay between ubiquitous transcription factors: ZBP-89, YY-1, and a member of the heterogeneous nuclear ribonucleoprotein D-like protein (also known as JKTBP1) family. In undifferentiated muscle cells, GTG motif-bound ZBP-89 physically and functionally interacted with CATR motif-bound YY-1 to mediate transcription repression. In differentiated myotubes, heterogeneous nuclear ribonucleoprotein D-like protein/JKTBP1 bound to the CATR motif exclusive of YY-1 and interacted with ZBP-89 in attenuating repressor activity, leading to transcription activation. Our results show a novel mechanism of protein factor switching in transcription regulation of the cytochrome c oxidase Vb gene during myogenesis.

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.

Differential expression of mitochondria-encoded genes in a hibernating mammal

A cDNA library constructed from kidney of the thirteen-lined squirrel, Spermophilus tridecemlineatus, was differentially screened for genes that were upregulated during hibernation. A clone encoding cytochrome c oxidase subunit 1 was found and confirmed to have been upregulated by northern blotting. Differential expression of Cox1 mRNA occurred in multiple organs during hibernation; in hibernating animals transcript levels were twofold higher in kidney and fourfold higher in heart and brown adipose tissue than in euthermic animals, but were unchanged in skeletal muscle. Transcript levels of mitochondrial-encoded ATP synthase 6/8 were similarly upregulated in these tissues whereas transcript levels of the nuclear encoded subunits Cox4 and ATP synthase α did not change during hibernation. Immunoblot analysis revealed a 2.4-fold increase in Cox 1 protein and a slight decrease in Cox 4 protein in kidney of hibernating squirrels, compared with euthermic controls. Hibernating mammals may increase the expression of the mitochondrial genome in general, and Cox1specifically, to prevent or minimize the damage to the electron transport chain caused by the cold and ischemia experienced during a hibernation bout.

The translation state of differentially expressed mRNAs in the hibernating 13-lined ground squirrel (Spermophilus tridecemlineatus)

The translation state of differentially expressed mRNAs were compared in kidney and brown adipose tissue of the hibernating ground squirrel, Spermophilus tridecemlineatus. Polysome analysis revealed a striking disaggregation of polyribosomes during hibernation and the redistribution of Cox4 (cytochrome c oxidase subunit 4) and Oct2 (organic cation transporter type 2) transcripts into monosome and mRNP fractions of kidney cytoplasmic extracts. Additionally, OCT2 protein levels decreased in kidney of hibernating animals in line with a strong decrease (85%) in translation rate compared with euthermic kidney. There was no translational depression in brown adipose tissue during hibernation and the H isoform of fatty-acid-binding protein (H-FABP), that is up-regulated during hibernation, was increasingly abundant in the heavy polyribosome fraction isolated from the brown adipose of hibernators. This may indicate the existence of a tissue-specific mechanism for the translational control of a subset of genes that are physiologically relevant to the survival of hibernation.

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.

Regulation of murine cytochrome oxidase Vb gene expression in different tissues and during myogenesis. Role of a YY-1 factor-binding negative enhancer

The mouse cytochrome oxidase (COX) Vb promoter contains three sequence motifs with partial or full consensus for YY-1 and GTG factor binding and a CArG box, located between positions -480 and -390. Individually, all three motifs stimulated transcription of the TKCAT promoter, and bound distinctly different proteins from the liver and differentiated C2C12 nuclear extracts. Collectively, these motifs, together with the downstream flanking sequence, -378 to -320, suppressed the transcription activity of heterologous promoters, thymidine kinase-chloramphenicol acetyltransferase (TKCAT) and COXIV/CAT. The transcription activities of both TKCAT and COXIV/CAT constructs were induced 3-4-fold during induced myogenesis of C2C12 cells. The downstream CArG-like motif binds transcription factor YY-1, while the upstream YY-1-like motif binds to a yet unidentified factor. Co-expression with intact YY-1, but not that lacking the DNA binding domain suppressed the transcriptional activity. Mutations targeted to the CArG-like motif abolished the suppressive effect of the negative enhancer and the inducibility of the promoter during myogenic differentiation. Our results suggest that the activity of the negative enhancer may determine the level of expression of the COX Vb gene in different tissues.

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.

The sequence of a small subunit of cytochrome c oxidase from Crithidia fasciculata which is homologous to mammalian subunit IV

The sequence of subunit 8 of cytochrome c oxidase from Crithidia fasciculata was determined by sequencing cDNA and N-terminus of the mature protein (Mr = 15.7 kDA). The (inferred) protein is homologous to mammalian cox IV and the corresponding cox subunits from yeast, Neurospora crassa and Dictyostelium discoideum, which is reflected in a very similar hydropathy profile. Elements that are conserved in the C. fasciculata sequence include (i) an N-terminal (D/E)-(K/R)-X-K-(X2)-W-(X2)-(I/L) motif, (ii) a putative membrane-spanning region in the middle portion of the protein, and (iii) a C-terminal W-(X13)-(N/D)-P motif. The C. fasciculata protein is synthesized with a cleavable presequence.

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.

Mitochondrial biogenesis in early mouse embryos: expression of the mRNAs for subunits IV, Vb, and VIIc of cytochrome c oxidase and subunit 9 (P1) of H(+)-ATP synthase

The mouse egg contains about 90,000 mitochondria which undergo a buildup of mitochondrial cristae and increase in respiratory activity during cleavage. The mitochondrial DNA does not replicate during preimplantation development but is transcribed actively from the two-cell stage onward (Pikó and Taylor, 1987: Dev Biol 123:364-374). To gain further insight into mitochondrial biogenesis, we have now determined the steady state amounts of the mRNAs for the cytochrome c oxidase (COX) subunits IV, Vb and VIIc and the H(+)-ATPase subunit 9 (P1) (all encoded by nuclear genes) in slot hybridization experiments of total RNA from oocytes and early embryos. All four mRNAs showed a similar developmental pattern of prevalence, characterized by a steady decline in mRNA copy numbers from the late growth-phase oocyte through the two-cell embryo, and an about 30-fold rise during cleavage through the blastocyst stage. However, the ATPase subunit 9 (P1) mRNA was about three times more prevalent in cleavage-stage embryos than the COX mRNAs. A similar pattern was obtained previously for the mitochondrial-encoded COX I and II mRNAs, but the latter accumulate at a 30-50-fold excess over the nuclear-encoded COX subunit mRNAs during the cleavage stages. The results suggest a coordinated activation and transcription of the mitochondrial and nuclear genes for the components of the respiratory apparatus beginning with the two-cell stage. It is estimated that new respiratory chains are produced at a rate of 50-100 chains hr-1/mitochondrion in the early blastocyst, accounting for 3.5-7% of the total protein synthetic activity at this stage.(ABSTRACT TRUNCATED AT 250 WORDS)

Human interferon regulatory factor 1: intron-exon organization

Interferon (IFN) regulatory factor 1 (IRF-1) is a transcriptional regulatory protein that mediates the transcriptional activation of the IFN-alpha and IFN-beta genes by viruses and IFNs. To characterize the mechanisms that govern the level of IRF-1 in cells, we isolated the IRF-1 gene and characterized the structure of its intronic and exonic domains and of its regulatory promoter region. A human placental genomic library was screened with an IRF-1 cDNA probe, and two clones that contained the IRF-1 gene and its 5' regulatory region were obtained. We used these clones to determine the complete nucleotide sequence for the IRF-1 gene, finding that the IRF-1 gene spanned 7.72 kb of DNA and included 10 exons and 9 introns. When the deduced amino acid sequences were compared among different species, the most conserved exons were exons 2, 3, and 4, in which the putative DNA binding domain for the IRF-1 protein is located.