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Query: UNIPROT:P06889 (Mol)
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The complete mitochondrial genome (mtDNA) of snow leopard Panthera uncia was obtained by using the polymerase chain reaction (PCR) technique based on the PCR fragments of 30 primers we designed. The entire mtDNA sequence was 16 773 base pairs (bp) in length, and the base composition was: A-5,357 bp (31.9%); C-4,444 bp (26.5%); G-2,428 bp (14.5%); T-4,544 bp (27.1%). The structural characteristics [0] of the P. uncia mitochondrial genome were highly similar to these of Felis catus, Acinonyx jubatus, Neofelis nebulosa and other mammals. However, we found several distinctive features of the mitochondrial genome of Panthera unica. First, the termination codon of COIII was TAA, which differed from those of F. catus, A. jubatus and N. nebulosa. Second, tRNA(Ser) ((AGY)), which lacked the ''DHU'' arm, could not be folded into the typical cloverleaf-shaped structure. Third, in the control region, a long repetitive sequence in RS-2 (32 bp) region was found with 2 repeats while one short repetitive segment (9 bp) was found with 15 repeats in the RS-3 region. We performed phylogenetic analysis based on a 3 816 bp concatenated sequence of 12S rRNA, 16S rRNA, ND2, ND4, ND5, Cyt b and ATP8 for P. uncia and other related species, the result indicated that P. uncia and P. leo were the sister species, which was different from the previous findings.
Mol Biol Rep 2009 May
PMID:The complete mitochondrial genome structure of snow leopard Panthera uncia. 1843 88

Objective Angiotensin II (Ang II), through the Ang II type 2 receptor (AT2R), may play some roles in the pathogenesis of glucose metabolism and diabetes mellitus (DM). The Adenine/Cytosine 3123 (A/C3123) polymorphism in the AT2R gene has reportedly been associated with metabolic conditions such as blood pressure and body mass index (BMI). The present cross-sectional study was aimed at investigating the association between the AT2R gene A/C3123 polymorphism and glycemic control parameters. Methods Among 286 community-dwelling Japanese subjects (men: women = 126:160; mean age, 65.1 years), AT2R A/C3123 polymorphism, which was detected by polymerase chain reaction methods, and metabolic parameters such as blood pressure, BMI, lipoprotein/lipid, insulin, and glycemic control parameters (fasting plasma glucose and HbA1c) were examined. Results In the whole study population, the proportion of C-allele was 67.0% and A-allele was 33.0%. The A-allele carriers had significantly lower HbA1c levels than the C/C-genotyped subjects in the group of women (5.5 +/- 0.6 vs. 5.8 +/- 1.5%, P = 0.042). The effect on HbA1c persisted to be significant with adjustments to age and BMI. In men, the associations between the polymorphism and glycemic control parameters were non-significantly noted. There were no differences between genotype-based groups in the other metabolic parameters in both sexes. Conclusion These results suggest that the AT2R A/C3123 polymorphism could be a polymorphic marker related to glycemic control, as presented in HbA1c, among general Japanese women.
Mol Biol Rep 2009 May
PMID:An association between angiotensin II type 2 receptor gene A/C3123 polymorphism and glycemic control marker in a general Japanese population. 1843 28

The heterodimeric integral membrane protein flavocytochrome b (Cyt b) is the catalytic core of the phagocyte NADPH oxidase, an enzyme complex that initiates a cascade of reactive oxygen species critical for the elimination of infectious agents. Many fundamental questions remain concerning the structure and catalytic mechanism of Cyt b, largely because of the inability to isolate this protein in quantities required for both biochemical analysis and meaningful attempts at high-resolution structure determination. In order to facilitate the direct analysis of Cyt b, the following method describes a rapid and efficient procedure for the immunoaffinity purification of Cyt b (under nondenaturing conditions) from neutrophil membrane fractions. The protocol presented here contains a number of steps that have been optimized and improved since the original description of this Cyt b isolation method. In order to address questions concerning the mechanism of superoxide generation by the NADPH oxidase complex, methods are additionally presented for analysis of conformational dynamics of immunoaffinity-purified Cyt b by resonance energy transfer.
Methods Mol Biol 2007
PMID:Immunoaffinity purification of human phagocyte flavocytochrome b and analysis of conformational dynamics. 1845 26

Cytosine DNA methylation is a stable epigenetic mark for maintenance of gene silencing across cellular divisions, but it is a reversible modification. Genetic and biochemical studies have revealed that the Arabidopsis DNA glycosylase domain-containing proteins ROS1 (REPRESSOR OF SILENCING 1) and DME (DEMETER) initiate erasure of 5-methylcytosine through a base excision repair process. The Arabidopsis genome encodes two paralogs of ROS1 and DME, referred to as DEMETER-LIKE proteins DML2 and DML3. We have found that DML2 and DML3 are 5-methylcytosine DNA glycosylases that are expressed in a wide range of plant organs. We analyzed the distribution of methylation marks at two methylated loci in wild-type and dml mutant plants. Mutations in DML2 and/or DML3 lead to hypermethylation of cytosine residues that are unmethylated or weakly methylated in wild-type plants. In contrast, sites that are heavily methylated in wild-type plants are hypomethylated in mutants. These results suggest that DML2 and DML3 are required not only for removing DNA methylation marks from improperly-methylated cytosines, but also for maintenance of high methylation levels in properly targeted sites.
Plant Mol Biol 2008 Aug
PMID:Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks. 1849 21

To elucidate the species composition, genetic divergence, evolutionary relationships, and divergence time of Hoplobatrachus and Euphlyctis frogs (subfamily Dicroglossinae, family Ranidae) in Bangladesh and other Asian countries, we analyzed the mitochondrial Cyt b, 12S, and 16S rRNA genes of 252 specimens. Our phylogenetic analyses showed 13 major clades corresponding to several cryptic species as well as to nominal species in the two genera. The results suggested monophyly of Asian Hoplobatrachus species, but the position of African Hoplobatrachus occipitalis was not clarified. Nucleotide divergence and phylogenetic data suggested the presence of allopatric cryptic species allied to Euphlyctis hexadactylus in Sundarban, Bangladesh and several parapatric cryptic species in the Western Ghats, India. The presence of at least two allopatric cryptic species among diverged Euphlyctis cyanophlyctis in Bangladesh, India, and Sri Lanka was also suggested. In some cases, our estimated divergence times matched the paleogeological events of South and Southeast Asian regions that may have led to the divergence of Hoplobatrachus and Euphlyctis taxa. Especially, land formation at Bangladesh (15-10Ma) may have allowed the spread of these frog taxa to Southeast Asian areas, and the aridification of central India (5.1-1.6Ma) might have affected the gene flow of widely distributed species. The present study revealed prior underestimation of the richness of the amphibian fauna in this region, indicating the possible occurrence of many cryptic species among these groups.
Mol Phylogenet Evol 2008 Aug
PMID:Genetic divergence and evolutionary relationships in six species of genera Hoplobatrachus and Euphlyctis (Amphibia: Anura) from Bangladesh and other Asian countries revealed by mitochondrial gene sequences. 1851 95

Mechanisms regulating myofibroblastic differentiation of fibroblasts within fibroblastic foci in idiopathic pulmonary fibrosis (IPF) remain unclear. Epigenetic processes, including DNA methylation, produce heritable but potentially reversible changes in DNA or its associated proteins and are prominent in development and oncogenesis. We have shown that Thy-1 suppresses myofibroblastic differentiation of lung fibroblasts and that fibroblasts in fibroblastic foci are Thy-1(-). Epigenetic down-regulation of Thy-1 has been demonstrated in cellular transformation and clinical cancer. We hypothesized that epigenetic regulation of Thy-1 affects the lung fibroblast fibrogenic phenotype. RT-PCR, methylation-specific PCR (MSP), and bisulfite genomic sequencing were used to determine the methylation status of the Thy-1 promoter in Thy-1(+) and Thy-1(-) lung fibroblasts, and MSP-in situ hybridization (MSPISH) was performed on fibrotic tissue. Thy-1 gene expression is absent in Thy-1(-) human and rat fibroblasts despite intact Thy-1 genomic DNA. Cytosine-guanine islands in the Thy-1 gene promoter are hypermethylated in Thy-1(-), but not Thy-1(+), fibroblasts. RT-PCR and MSP demonstrate that, in IPF samples in which Thy-1 expression is absent, the Thy-1 promoter region is methylated, whereas in lung samples retaining Thy-1 expression, the promoter region is unmethylated. MSPISH confirms methylation of the Thy-1 promoter in fibroblastic foci in IPF. Treatment with DNA methyltransferase inhibitors restores Thy-1 expression in Thy-1(-) fibroblasts. Epigenetic regulation of Thy-1 is a novel and potentially reversible mechanism in fibrosis that may offer the possibility of new therapeutic options.
Am J Respir Cell Mol Biol 2008 Nov
PMID:Thy-1 promoter hypermethylation: a novel epigenetic pathogenic mechanism in pulmonary fibrosis. 1855 92

The Cyt family of proteins consists of delta-endotoxins expressed during sporulation of several subspecies of Bacillus thuringiensis. Its members possess insecticidal, hemolytic, and cytolytic activities through pore formation and attract attention due to their potential use as vehicles for targeted membrane destruction. The delta-endotoxins of subsp. israelensis include three Cyt species: a major Cyt1Aa and two minor proteins, Cyt2Ba and Cyt1Ca. A cleaved Cyt protein that lacks the N- and C-terminal segments forms a toxic monomer. Here, we describe the crystal structure of Cyt2Ba, cleaved at its amino and carboxy termini by bacterial endogenous protease(s). Overall, its fold resembles that of the previously described volvatoxin A2 and the nontoxic form of Cyt2Aa. The structural similarity between these three proteins may provide information regarding the mechanism(s) of membrane-perforating toxins.
J Mol Biol 2008 Jul 25
PMID:High-resolution crystal structure of activated Cyt2Ba monomer from Bacillus thuringiensis subsp. israelensis. 1857 67

Understanding the origin and evolution of cellular processes is fundamental to understand how biological activity has shaped the history of our planet. Among these, aerobic respiration is probably one of the most debated. We have applied a phylogenomics approach to investigate the origin and evolution of dioxygen reductases (O(2)Red), the key enzymes of aerobic respiratory chains. The distribution and phylogenetic analysis of the four types of O(2)Red (Cyt-bd and the A, B, and C families of heme-copper O(2)Red) from 673 complete bacterial and archaeal genomes show that these enzymes have very different evolutionary histories: Cyt-bd are of bacterial origin and were transferred to a few archaea; C-O(2)Red are of proteobacterial origin and were transferred to a few other bacteria; B-O(2)Red are of archaeal origin and were transferred to a few bacteria; and A-O(2)Red are the most ancient O(2)Red and were already present prior to the divergence of major present-day bacterial and archaeal phyla, thus before the emergence of Cyanobacteria and oxygenic photosynthesis. Implications for the origin and the evolution of aerobic respiration are discussed.
Mol Biol Evol 2009 Feb
PMID:The multiple evolutionary histories of dioxygen reductases: Implications for the origin and evolution of aerobic respiration. 1897 88

Cytosine deaminase-uracil phosphoribosyl transferase (CD-UPRT) fusion gene is known to exhibit therapeutic effect by inducing apoptosis in vitro. However, bystander effects of 5-flurocytosine (5-FC)/CD-UPRT and the molecular mechanism for apoptosis are yet to be established. In the present study, we have generated BHK21 cell line expressing both CD-UPRT and green fluorescent protein (GFP) from two separate transcripts, where GFP was used as a noninvasive probe to monitor the therapeutic effect of CD-UPRT. Enzyme activity of CD-UPRT in the stable cell line was measured by the reverse phase high-performance liquid chromatography analysis. Inhibition of cell growth and strong bystander effects of 5-FC/CD-UPRT were established, whereas characteristic surface morphology of apoptotic cell death was identified by AFM analysis. Involvement of various apoptotic signaling genes using semi-quantitative RT-PCR has been explored to substantiate the potential application of 5-FC/CD-UPRT suicide gene in therapy.
Mol Cell Biochem 2009 Apr
PMID:Understanding apoptotic signaling pathways in cytosine deaminase-uracil phosphoribosyl transferase-mediated suicide gene therapy in vitro. 1908 16

Electrochemiluminescent (ECL) arrays containing polymer ([Ru(bpy)(2)(PVP)(10)](2+), PVP = polyvinylpyridine), DNA, and selected enzymes were employed to elucidate cytochrome (cyt) P450 dependent metabolism of the tobacco specific carcinogen, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). Bioactivated NNK metabolites formed upon H(2)O(2)-enzymatic activation were captured as DNA adducts and detected simultaneously from 36 spot arrays by capturing and quantifying emitted ECL with an overhead CCD camera. Increased ECL emission was dependent on NNK exposure time. Of the enzymes tested, the activity toward NNK bioactivation was cyt P450 1A2 > 2E1 > 1B1 approximately chloroperoxidase (CPO) > myoglobin (Mb) in accordance with reported in vivo studies. Cyt P450/polyion films were also immobilized on 500 nm diameter silica nanospheres for product analysis by LC-MS. Analysis of the nanosphere film reaction media provided ECL array validation and quantitation of the bioactivated NNK hydrolysis product 4-hydroxy-1-(3-pyridyl)-1-butanone (HPB) confirming production of reactive metabolites in the films. Chemical screening in this fashion allows rapid clarification of enzymes responsible for genotoxic activation as well as offering insight into cyt P450-related toxicity and mechanisms.
Mol Biosyst 2009 Feb
PMID:Human cyt P450 mediated metabolic toxicity of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) evaluated using electrochemiluminescent arrays. 1915 62


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