基因芯片在骨骼肌老龄化相关基因表达谱中的应用

对老龄组大鼠 (30月龄 )和年轻对照组大鼠 (3月龄 )的腓肠肌超微结构进行观察 ,可以看到前者肌肉肌纤维萎缩伴有线粒体空泡变性。并进行总RNA抽提、mRNA纯化、探针制备 ,应用基因芯片筛选老龄化相关基因 ,两组大鼠骨骼肌重复出现的差异表达基因 12 7个 ,下调基因涉及能量代谢、信号转导 ,上调基因涉及蛋白质分解、细胞凋亡     

Down-regulated energy metabolism genes associated with mitochondria oxidative phosphorylation and fatty acid metabolism in viral cardiomyopathy mouse heart

The majority of experimental and clinical studies indicates that the hypertrophied and failing myocardium are characterized by changes in energy and substrate metabolism that attributed to failing heart changes at the genomic level, in fact, heart failure is caused by various diseases, their energy metabolism and substrate are in different genetic variations, then the potential significance of the molecular mechanisms for the aetiology of heart failure is necessary to be evaluated. Persistent viral infection (especially coxsackievirus group B3) of the myocardium in viral myocarditis and viral dilated cardiomyopathy has never been neglected by experts. This study aimed to explore the role and regulatory mechanism of the altered gene expression for energy metabolism involved in mitochondrial oxidative phosphorylation, fatty acid metabolism in viral dilated cardiomyopathy. cDNA Microarray technology was used to evaluate the expression of >35,852 genes in a mice model of viral dilated cardiomyopathy. In total 1385 highly different genes expression, we analyzed 33 altered genes expression for energy metabolism involved in mitochondrial oxidative phosphorylation, fatty acid metabolism and further selected real-time-PCR for quantity one of regulatory mechanisms for energy including fatty acid metabolism—the UCP2 and assayed cytochrome C oxidase activity by Spectrophotometer to explore mitochondrial oxidative phosphorylation function. We found obviously different expression of 33 energy metabolism genes associated with mitochondria oxidative phosphorylation, fatty acid metabolism in cardiomyopathy mouse heart, the regulatory gene for energy metabolism: UCP2 was down-regulated and cytochrome C oxidase activity was decreased. Genes involved in both fatty acid metabolism and mitochondrial oxidative phosphorylation were down-regulated, mitochondrial uncoupling proteins (UCP2) expression did not increase but decrease which might be a kind of adaptive protection response to regulate energy metabolism for ATP produce.     

Comparing the performance of multiple mitochondrial genes in the analysis of Australian freshwater fishes

In this study, four mitochondrial genes (cytochrome oxidase I, ATPase, cytochrome b and control region) were amplified from most of the fish species found in the fresh waters of south-eastern Queensland, Australia. The performance of these different gene regions was compared in terms of their ability to cluster fish families together in a neighbour-joining tree, both individually by gene and in all combinations. The relative divergence rates of each of these genes were also calculated. The three coding genes (cytochrome oxidase I, ATPase and cytochrome b) recovered similar number of families and had broadly similar divergence rates. ATPase diverged a little more quickly than cytochrome oxidase I and cytochrome b slightly more slowly than cytochrome oxidase I. All two-gene combinations recovered the same number of families. Results from the control region were much more variable, and, although generally possessing more diversity than the other regions, were sometimes less variable.     

Two variants of the assembly factor Surf1 target specific terminal oxidases in Paracoccus denitrificans

Biogenesis of cytochrome c oxidase (COX) relies on a large number of assembly proteins, one of them being Surf1. In humans, the loss of Surf1 function is associated with Leigh syndrome, a fatal neurodegenerative disorder. In the soil bacterium Paracoccus denitrificans, homologous genes specifying Surf1 have been identified and located in two operons of terminal oxidases: surf1q is the last gene of the qox operon (coding for a ba(3)-type ubiquinol oxidase), and surf1c is found at the end of the cta operon (encoding subunits of the aa(3)-type cytochrome c oxidase). We introduced chromosomal single and double deletions for both surf1 genes, leading to significantly reduced oxidase activities in membrane. Our experiments on P. denitrificans surf1 single deletion strains show that both Surf1c and Surf1q are functional and act independently for the aa(3)-type cytochrome c oxidase and the ba(3)-type quinol oxidase, respectively. This is the first direct experimental evidence for the involvement of a Surf1 protein in the assembly of a quinol oxidase. Analyzing the heme content of purified cytochrome c oxidase, we conclude that Surf1, though not indispensable for oxidase assembly, is involved in an early step of cofactor insertion into subunit I.     

Functional complementation of an oxa1− yeast mutation identifies an Arabidopsis thaliana cDNA involved in the assembly of respiratory complexes

The nuclear gene OXA1 is essential for respiratory growth in yeast. It codes for a chaperon-like protein, and has pleiotropic effects on the assembly of cytochrome c oxidase and ATP synthase of the mitochondrial respiratory chain. To study respiratory complex formation in plants, we have cloned a homolog of the yeast oxa1⁻ in Arabidopsis thaliana , OXA1At , by functional complementation of a yeast oxa1⁻ mutant. OXA1At is a single copy gene and appears to be constitutively expressed in A. thaliana . Although OXA1At encodes a protein sharing only 30% amino acid identity with the yeast Oxa1 protein, hydrophobic domains likely corresponding to trans -membrane domains are strictly conserved. Cytochrome spectra and measurements of respiratory activities show that replacement of the yeast Oxa1 protein with the A. thaliana homolog leads to correct assembly and activity of cytochrome c oxidase, but to partial restoration of ATPase activity. Our results suggest that the Oxa1At protein is essential for the respiratory complex assembly in A. thaliana , and that genes involved in mitochondrial multiprotein complex formation can be conserved between plants and other organisms.     

The sequence of the cyo operon indicates substantial structural similarities between the cytochrome o ubiquinol oxidase of Escherichia coli and the aa3-type family of cytochrome c oxidases

The cytochrome o complex is one of two ubiquinol oxidases in the aerobic respiratory system of Escherichia coli. This enzyme catalyzes the two-electron oxidation of ubiquinol-8 which is located in the cytoplasmic membrane, and the four-electron reduction of molecular oxygen to water. The purified oxidase contains at least four subunits by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis and has been shown to couple electron flux to the generation of a proton motive force across the membrane. In this paper, the DNA sequence of the cyo operon, containing the structural genes for the oxidase, is reported. This operon is shown to encode five open reading frames, cyoABCDE. The gene products of three of these, cyoA, cyoB, and cyoC, are clearly related to subunits II, I, and III, respectively, of the eukaryotic and prokaryotic aa3-type cytochrome c oxidases. This family of cytochrome c oxidases contain heme a and copper as prosthetic groups, whereas the E. coli enzyme contains heme b (protoheme IX) and copper. The most striking sequence similarities relate the large subunits (I) of both the E. coli quinol oxidase and the cytochrome c oxidases. It is likely that the sequence similarities reflect a common molecular architecture of the two heme binding sites and of a copper binding site in these enzymes. In addition, the cyoE open reading frame is closely related to a gene denoted ORF1 from Paracoccus dentrificans which is located in between the genes encoding subunits II and III of the cytochrome c oxidase of this organism. The function of the ORF1 gene product is not known. These sequence relationships define a superfamily of membrane-bound respiratory oxidases which share structural features but which have different functions. The E. coli cytochrome o complex oxidizes ubiquinol but has no ability to catalyze the oxidation of reduced cytochrome c. Nevertheless, it is clear that the E. coli oxidase and the aa3-type cytochrome c oxidases must have very similar structures, at least in the vicinity of the catalytic centers, and they are very likely to have similar mechanisms for bioenergetic coupling (proton pumping).     

Exploring the molecular mechanism of acute heat stress exposure in broiler chickens using gene expression profiling

The process of heat regulation is complex and its exact molecular mechanism is not fully understood. In this study, to investigate the global gene regulation response to acute heat exposure, gene microarrays were exploited to analyze the effects of heat stress on three tissues (brain, liver, leg muscle) of the yellow broiler chicken (Gallus gallus). We detected 166 differentially expressed genes (DEGs) in the brain, 219 in the leg muscle and 317 in the liver. Six of these genes were differentially expressed in all three tissues and were validated by qRT-PCR, and included heat shock protein genes (HSPH1, HSP25), apoptosis-related genes (RB1CC1, BAG3), a cell proliferation and differentiation-related gene (ID1) and the hunger and energy metabolism related gene (PDK). All these genes might be important factors in chickens suffering from heat stress. We constructed gene co-expression networks using the DEGs of the brain, leg muscle and liver and two, four and two gene co-expression modules were identified in these tissues, respectively. Functional enrichment of these gene modules revealed that various functional clusters were related to the effects of heat stress, including those for cytoskeleton, extracellular space, ion binding and energy metabolism. We concluded that these genes and functional clusters might be important factors in chickens under acute heat stress. Further in-depth research on the newly discovered heat-related genes and functional clusters is required to fully understand their molecular functions in thermoregulation.     

Molecular characterization of skeletal muscle atrophy in the R6/2 mouse model of Huntington's disease

Huntington's disease (HD), a neurodegenerative disorder caused by mutant huntingtin, is characterized by a catabolic phenotype. To determine the mechanisms underlying muscle wasting, we examined key signal transduction pathways governing muscle protein metabolism, apoptosis, and autophagy in R6/2 mice, a well-characterized transgenic model of HD. R6/2 mice exhibited increased adiposity, elevated energy expenditure, and decreased body weight and lean mass without altered food intake. Severe skeletal muscle wasting accounted for a majority of the weight loss. Protein synthesis was unexpectedly increased 19% in gastrocnemius muscle, which was associated with overactivation of basal and refeeding-stimulated mammalian target of rapamycin (mTOR) signaling, elevated Akt expression and Ser(473) phosphorylation, and decreased AMPK Thr(172) phosphorylation. Moreover, mRNA abundance of atrogenes muscle ring finger-1 and atrophy F-box, was markedly attenuated during fasting and refeeding, and the urinary excretion of 3-methylhistidine was decreased, arguing against a role for the ubiquitin proteasome-mediated proteolysis in the atrophy. In contrast, mRNA expression of several caspase genes and genes involved in the extrinsic or intrinsic apoptotic pathway, caspase-3/7, -8, and -9 activity, protein abundance of caspase-3 and -9, Fas, and Fadd, and cytochrome c release were elevated. Protein expressions of LC3B-I and -II, beclin-I, and atg5 and -7 in muscle were upregulated. Thus, mutant huntingtin in skeletal muscle results in increased protein synthesis and mTOR signaling, which is countered by activation of the apoptotic and autophagic pathways, contributing to an overall catabolic phenotype and the severe muscle wasting.     

Normal gene expression in male F344 rat nasal transitional and respiratory epithelium

The nasal epithelium is an important target site for chemically-induced toxicity and carcinogenicity in rodents. Gene expression profiles were determined in order to provide normal baseline data for nasal transitional/respiratory epithelium from healthy rats. Cells lining the rat nasal passages were collected and gene expression analysis was performed using Clontech cDNA Rat Atlas 1.2 arrays (1185 genes). The percentages of genes within specific average expression ranges were 4.2% at 45,000-1000, 14.8% at 1000-200, 25.0% at 200-68, and 56.0% below 68. Nine out of a subset of ten genes were confirmed for relative signal intensity using quantitative real-time RT-PCR. The most highly expressed genes included those involved in phase I (e.g. cytochrome P450s) and phase II (e.g. glutathione S-transferases) xenobiotic metabolism, bioenergetics (e.g. cytochrome oxidase), osmotic balance (e.g. Na(+)/K(+) ATPase) and epithelial ionic homeostasis (e.g. ion channels). Such baseline data will contribute to further understanding the normal physiology of these cells and facilitate the interpretation of responses by the nasal epithelial cells to xenobiotic treatment or disease.     

Biogenesis of mitochondria. Two-dimensional electrophoretic analysis of mitochondrial translation products in yeast

1. Mitochondrial translation products of yeast Saccharomyces cerevisiae were separated according to charge as well as molecular weight by a highly resolving two dimensional electorphoretic technique (isoelectric focusing in the first dimension ana SDS-electrophoresis in the second dimension). 2. The major protein components (the oligomeric form of subunit 9 of mitochondrial ATPase, var 1, cytochrome oxidase subunits I, II and III, subunit 6 of mitochondrial ATPase and cytochrome b apoprotein) were identified either from their mobility in SDS-electrophoresis or by using mit- mutants defective in certain mitochondrially made polypeptides. 3. This method allowed the separation of subunit III of cytochrome oxidase and subunit 6 of mitochondrial ATPase which cannot be resolved by conventional SDS-polyacrylamide gel electrophoresis. 4. Subunit II of cytochrome oxiodase resolves in two spots of similar pI values and subunit 6 of mitochondrial ATPase resolves in two spots of similar molecular weight. In both cases the double spots disappear simultaneously following a single mutation in the coresponding structural gene. 5. Total mitochondrial proteins were also resolved two-dimensionally revealing over 100 components. The mitochondrial translation products, with the exception of subunit 9 of mitochondrial ATPase, could be easily recognized among the other mitochondrial proteins.     

An archaebacterial terminal oxidase combines core structures of two mitochondrial respiratory complexes.

The operon coding for a respiratory quinol oxidase was cloned from thermoacidophilic archaebacterium Sulfolobus acidocaldarius. It contains three genes, soxA, soxB and soxC. The first two genes code for proteins related to the cytochrome c oxidase subunits II and I, respectively. soxC encodes a protein homologous to cytochrome b, which is a subunit of the mitochondrial and bacterial cytochrome c reductases and the chloroplast cytochrome b6f complex. soxA is preceded by a promoter and the genes are cotranscribed into a 4 kb mRNA. Their protein products form a complex which has been partially purified and has quinol oxidase activity. The reduced minus oxidized absorption spectrum of the complex has two maxima at 586 and 606 nm. The latter is typical of cytochrome c oxidase. The complex contains four haems A. Two haems belong to the 'cytochrome oxidase' part of the complex and two are probably bound to be apocytochrome b (SoxC) and responsible for the 586 nm absorption peak. The homology between the sox gene products and their mitochondrial counterparts suggests that energy conservation coupled to the quinol oxidation catalysed either by the Sulfolobus oxidase or two mitochondrial respiratory enzymes may have a similar mechanism.     

家鸭细胞色素C氧化酶Ⅲ（COⅢ）基因的克隆及序列分析

线粒体是存在于绝大多数真核细胞内的一种基本的、重要的细胞器,是细胞进行氧化磷酸化的场所。不同脊椎动物同源基因序列的比较显示,细胞色素b(Cytb)、细胞色素C氧化酶Ⅰ（COⅠ）、细胞色素C氧化酶Ⅱ（COⅡ）、细胞色素C氧化酶Ⅲ（COⅢ） 基因最保守,同源性最高,ATPase6、ATPase8基因、ND基因变异比较大。本试验以家鸭（家鸭起源于绿头鸭：Anas platyrhynchos）肝脏的线粒体DNA为模板,按照GenBank已经公布的潜鸭族（AF090337）的全序列及其绿头鸭的mtDNA部分序列（L22476、L16770、L22477）设计合成特异引物进行PCR扩增,克隆并测定了线粒体细胞色素C氧化酶Ⅲ亚基（COⅢ）的全序列784bp以及ATPase6基因的3'端和tRNA-Gly基因的5'端序列共934bp。 用DNAStar分析软件对家鸭与GenBank中7种禽类的COⅢ序列进行比较分析,显示家鸭与这些动物的COⅢ基因具有较高的同源性,与同科潜鸭属中的Aythya Americana的相似性 最高为90.6 %,与同目不同科的加拿大雁、小天鹅、白额雁的相似性分别为89%、88.6%、88.6%。根据家鸭与其他7种禽类的COⅢ基因序列相似性所建立的进化树,与传统的分类地位基本吻合。