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  1 / 2207 MEDLINE  
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[PMID]:28036383
[Au] Autor:Koval T; Østergaard LH; Lehmbeck J; Nørgaard A; Lipovová P; Dusková J; Skálová T; Trundová M; Kolenko P; Fejfarová K; Stránský J; Svecová L; Hasek J; Dohnálek J
[Ad] Endereço:Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology CAS, v. v. i., Biocev, Vestec, Czech Republic.
[Ti] Título:Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition.
[So] Source:PLoS One;11(12):e0168832, 2016.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The single-strand-specific S1 nuclease from Aspergillus oryzae is an archetypal enzyme of the S1-P1 family of nucleases with a widespread use for biochemical analyses of nucleic acids. We present the first X-ray structure of this nuclease along with a thorough analysis of the reaction and inhibition mechanisms and of its properties responsible for identification and binding of ligands. Seven structures of S1 nuclease, six of which are complexes with products and inhibitors, and characterization of catalytic properties of a wild type and mutants reveal unknown attributes of the S1-P1 family. The active site can bind phosphate, nucleosides, and nucleotides in several distinguished ways. The nucleoside binding site accepts bases in two binding modes-shallow and deep. It can also undergo remodeling and so adapt to different ligands. The amino acid residue Asp65 is critical for activity while Asn154 secures interaction with the sugar moiety, and Lys68 is involved in interactions with the phosphate and sugar moieties of ligands. An additional nucleobase binding site was identified on the surface, which explains the absence of the Tyr site known from P1 nuclease. For the first time ternary complexes with ligands enable modeling of ssDNA binding in the active site cleft. Interpretation of the results in the context of the whole S1-P1 nuclease family significantly broadens our knowledge regarding ligand interaction modes and the strategies of adjustment of the enzyme surface and binding sites to achieve particular specificity.
[Mh] Termos MeSH primário: Aspergillus oryzae/enzimologia
Aspergillus oryzae/metabolismo
Proteínas Fúngicas/metabolismo
Endonucleases Específicas para DNA e RNA de Cadeia Simples/metabolismo
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Aminoácidos/metabolismo
Sítios de Ligação/fisiologia
Catálise
Domínio Catalítico/fisiologia
Cinética
Alinhamento de Sequência
Especificidade por Substrato
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Amino Acids); 0 (Fungal Proteins); EC 3.1.30.1 (Endonuclease S1, Aspergillus); EC 3.1.30.1 (Single-Strand Specific DNA and RNA Endonucleases)
[Em] Mês de entrada:1706
[Cu] Atualização por classe:170630
[Lr] Data última revisão:
170630
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161231
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0168832


  2 / 2207 MEDLINE  
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[PMID]:28033325
[Au] Autor:Yang J; Sharma S; Watzinger P; Hartmann JD; Kötter P; Entian KD
[Ad] Endereço:Institute of Molecular and Cellular Microbiology Goethe University, Frankfurt am Main, Germany.
[Ti] Título:Mapping of Complete Set of Ribose and Base Modifications of Yeast rRNA by RP-HPLC and Mung Bean Nuclease Assay.
[So] Source:PLoS One;11(12):e0168873, 2016.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Ribosomes are large ribonucleoprotein complexes that are fundamental for protein synthesis. Ribosomes are ribozymes because their catalytic functions such as peptidyl transferase and peptidyl-tRNA hydrolysis depend on the rRNA. rRNA is a heterogeneous biopolymer comprising of at least 112 chemically modified residues that are believed to expand its topological potential. In the present study, we established a comprehensive modification profile of Saccharomyces cerevisiae's 18S and 25S rRNA using a high resolution Reversed-Phase High Performance Liquid Chromatography (RP-HPLC). A combination of mung bean nuclease assay, rDNA point mutants and snoRNA deletions allowed us to systematically map all ribose and base modifications on both rRNAs to a single nucleotide resolution. We also calculated approximate molar levels for each modification using their UV (254nm) molar response factors, showing sub-stoichiometric amount of modifications at certain residues. The chemical nature, their precise location and identification of partial modification will facilitate understanding the precise role of these chemical modifications, and provide further evidence for ribosome heterogeneity in eukaryotes.
[Mh] Termos MeSH primário: Proteínas de Plantas/metabolismo
RNA Ribossômico 18S/genética
RNA Ribossômico 18S/metabolismo
RNA Ribossômico/genética
RNA Ribossômico/metabolismo
Ribose/metabolismo
Saccharomyces cerevisiae/genética
Endonucleases Específicas para DNA e RNA de Cadeia Simples/metabolismo
[Mh] Termos MeSH secundário: Sequência de Bases
Cromatografia de Fase Reversa
Metilação
Mutação Puntual
RNA Fúngico/genética
RNA Fúngico/metabolismo
RNA Nucleolar Pequeno/genética
RNA Nucleolar Pequeno/metabolismo
Ribossomos/genética
Ribossomos/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Mung Bean Nuclease); 0 (Plant Proteins); 0 (RNA, Fungal); 0 (RNA, Ribosomal); 0 (RNA, Ribosomal, 18S); 0 (RNA, Small Nucleolar); 130527-23-0 (RNA, ribosomal, 25S); 681HV46001 (Ribose); EC 3.1.30.1 (Single-Strand Specific DNA and RNA Endonucleases)
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170713
[Lr] Data última revisão:
170713
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161230
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0168873


  3 / 2207 MEDLINE  
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[PMID]:27298336
[Au] Autor:Wahba L; Costantino L; Tan FJ; Zimmer A; Koshland D
[Ad] Endereço:Department of Cell and Molecular Biology, University of California at Berkeley, Berkeley, California 94720, USA;
[Ti] Título:S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation.
[So] Source:Genes Dev;30(11):1327-38, 2016 Jun 01.
[Is] ISSN:1549-5477
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:R loops form when transcripts hybridize to homologous DNA on chromosomes, yielding a DNA:RNA hybrid and a displaced DNA single strand. R loops impact the genome of many organisms, regulating chromosome stability, gene expression, and DNA repair. Understanding the parameters dictating R-loop formation in vivo has been hampered by the limited quantitative and spatial resolution of current genomic strategies for mapping R loops. We report a novel whole-genome method, S1-DRIP-seq (S1 nuclease DNA:RNA immunoprecipitation with deep sequencing), for mapping hybrid-prone regions in budding yeast Saccharomyces cerevisiae Using this methodology, we identified ∼800 hybrid-prone regions covering 8% of the genome. Given the pervasive transcription of the yeast genome, this result suggests that R-loop formation is dictated by characteristics of the DNA, RNA, and/or chromatin. We successfully identified two features highly predictive of hybrid formation: high transcription and long homopolymeric dA:dT tracts. These accounted for >60% of the hybrid regions found in the genome. We demonstrated that these two factors play a causal role in hybrid formation by genetic manipulation. Thus, the hybrid map generated by S1-DRIP-seq led to the identification of the first global genomic features causal for R-loop formation in yeast.
[Mh] Termos MeSH primário: Expressão Gênica
Genoma Fúngico/genética
Poli A/genética
Saccharomyces cerevisiae/genética
Saccharomyces cerevisiae/metabolismo
[Mh] Termos MeSH secundário: Mapeamento Cromossômico
DNA Fúngico/metabolismo
Genômica
Histonas/metabolismo
Poli A/química
Poli A/metabolismo
Conformação Proteica
RNA Fúngico/metabolismo
Endonucleases Específicas para DNA e RNA de Cadeia Simples/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Fungal); 0 (Histones); 0 (RNA, Fungal); 24937-83-5 (Poly A); EC 3.1.30.1 (Single-Strand Specific DNA and RNA Endonucleases)
[Em] Mês de entrada:1704
[Cu] Atualização por classe:170427
[Lr] Data última revisão:
170427
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160615
[St] Status:MEDLINE
[do] DOI:10.1101/gad.280834.116


  4 / 2207 MEDLINE  
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[PMID]:27151561
[Au] Autor:Ichishima E
[Ad] Endereço:a Department of Applied Biological Chemistry , Tohoku University , Sendai , Japan.
[Ti] Título:Development of enzyme technology for Aspergillus oryzae, A. sojae, and A. luchuensis, the national microorganisms of Japan.
[So] Source:Biosci Biotechnol Biochem;80(9):1681-92, 2016 Sep.
[Is] ISSN:1347-6947
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:This paper describes the modern enzymology in Japanese bioindustries. The invention of Takadiastase by Jokiti Takamine in 1894 has revolutionized the world of industrial enzyme production by fermentation. In 1949, a new γ-amylase (glucan 1,4-α-glucosidase, EC 3.2.1.3) from A. luchuensis (formerly designated as A. awamori), was found by Kitahara. RNase T1 (guanyloribonuclease, EC 3.1.27.3) was discovered by Sato and Egami. Ando discovered Aspergillus nuclease S1 (single-stranded nucleate endonuclease, EC 3.1.30.1). Aspergillopepsin I (EC 3.4.23.18) from A. tubingensis (formerly designated as A. saitoi) activates trypsinogen to trypsin. Shintani et al. demonstrated Asp76 of aspergillopepsin I as the binding site for the basic substrate, trypsinogen. The new oligosaccharide moieties Man10GlcNAc2 and Man11GlcNAc2 were identified with α-1,2-mannosidase (EC 3.2.1.113) from A. tubingensis. A yeast mutant compatible of producing Man5GlcNAc2 human compatible sugar chains on glycoproteins was constructed. The acid activation of protyrosinase from A. oryzae at pH 3.0 was resolved. The hyper-protein production system of glucoamylase was established in a submerged culture.
[Mh] Termos MeSH primário: Aspergillus oryzae/enzimologia
Biotecnologia
Fermentação
[Mh] Termos MeSH secundário: Ácido Aspártico Endopeptidases/isolamento & purificação
Ácido Aspártico Endopeptidases/metabolismo
Aspergillus oryzae/metabolismo
Proteínas Fúngicas/isolamento & purificação
Proteínas Fúngicas/metabolismo
Glucana 1,4-alfa-Glucosidase/isolamento & purificação
Glucana 1,4-alfa-Glucosidase/metabolismo
Seres Humanos
Japão
Ribonuclease T1/isolamento & purificação
Ribonuclease T1/metabolismo
Endonucleases Específicas para DNA e RNA de Cadeia Simples/isolamento & purificação
Endonucleases Específicas para DNA e RNA de Cadeia Simples/metabolismo
Tripsinogênio/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (Fungal Proteins); 9002-08-8 (Trypsinogen); EC 3.1.27.3 (Ribonuclease T1); EC 3.1.30.1 (Endonuclease S1, Aspergillus); EC 3.1.30.1 (Single-Strand Specific DNA and RNA Endonucleases); EC 3.2.1.3 (Glucan 1,4-alpha-Glucosidase); EC 3.4.23.- (Aspartic Acid Endopeptidases); EC 3.4.23.18 (aspergillopepsin I)
[Em] Mês de entrada:1701
[Cu] Atualização por classe:170131
[Lr] Data última revisão:
170131
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160507
[St] Status:MEDLINE
[do] DOI:10.1080/09168451.2016.1177445


  5 / 2207 MEDLINE  
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[PMID]:27125839
[Au] Autor:Peng L; Fan J; Tong C; Xie Z; Zhao C; Liu X; Zhu Y; Liu B
[Ad] Endereço:College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China.
[Ti] Título:An ultrasensitive fluorescence method suitable for quantitative analysis of mung bean nuclease and inhibitor screening in vitro and vivo.
[So] Source:Biosens Bioelectron;83:169-76, 2016 Sep 15.
[Is] ISSN:1873-4235
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Mung bean nuclease is a single stranded specific DNA and RNA endonuclease purified from mung bean sprouts. It yields 5'-phosphate terminated mono- and oligonucleotides. The activity level of this nuclease can act as a marker to monitor the developmental process of mung bean sprouts. In order to facilitate the activity and physiological analysis of this nuclease, we have developed a biosensing assay system based on the mung bean nuclease-induced single-stranded DNA scission and the affinity difference of graphene oxide for single-stranded DNA containing different numbers of bases. This end-point measurement method can detect mung bean nuclease in a range of 2×10(-4) to 4×10(-2) with a detection limit of 1×10(-4) unit/mL. In addition, we demonstrate the utility of the assay for screening chemical antibiotics and metal ions, resulting in the identification of several inhibitors of this enzyme in vitro. Furthermore, we firstly report that inhibiting mung bean nuclease by gentamycin sulfate and kanamycin in vivo can suppress mung bean sprouts growth. In summary, this method provides an alternative tool for the biochemical analysis for mung bean nuclease and indicates the feasibility of high-throughput screening specific inhibitors of this nuclease in vitro and in vivo.
[Mh] Termos MeSH primário: DNA de Cadeia Simples/metabolismo
Fabaceae/enzimologia
Proteínas de Plantas/antagonistas & inibidores
Proteínas de Plantas/análise
Endonucleases Específicas para DNA e RNA de Cadeia Simples/antagonistas & inibidores
Endonucleases Específicas para DNA e RNA de Cadeia Simples/análise
Espectrometria de Fluorescência/métodos
[Mh] Termos MeSH secundário: Técnicas Biossensoriais/métodos
Ensaios Enzimáticos/métodos
Inibidores Enzimáticos/metabolismo
Fabaceae/efeitos dos fármacos
Fabaceae/crescimento & desenvolvimento
Fluorescência
Grafite/química
Limite de Detecção
Óxidos/química
Proteínas de Plantas/metabolismo
Endonucleases Específicas para DNA e RNA de Cadeia Simples/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Single-Stranded); 0 (Enzyme Inhibitors); 0 (Mung Bean Nuclease); 0 (Oxides); 0 (Plant Proteins); 7782-42-5 (Graphite); EC 3.1.30.1 (Single-Strand Specific DNA and RNA Endonucleases)
[Em] Mês de entrada:1701
[Cu] Atualização por classe:170123
[Lr] Data última revisão:
170123
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160430
[St] Status:MEDLINE


  6 / 2207 MEDLINE  
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[PMID]:27057646
[Au] Autor:Futai K; Sumaoka J; Komiyama M
[Ad] Endereço:a University of Tsukuba , Tsukuba , Japan.
[Ti] Título:Fabrication of DNA/RNA Hybrids Through Sequence-Specific Scission of Both Strands by pcPNA-S1 Nuclease Combination.
[So] Source:Nucleosides Nucleotides Nucleic Acids;35(5):233-44, 2016 May 03.
[Is] ISSN:1532-2335
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:By combining two strands of pseudo-complementary peptide nucleic acid (pcPNA) with S1 nuclease, a tool for site-selective and dual-strand scission of DNA/RNA hybrids has been developed. Both of the DNA and the RNA strands in the hybrids are hydrolyzed at desired sites to provide unique sticky ends. The scission fragments are directly ligated with other DNA/RNA hybrids by using T4 DNA ligase, resulting in the formation of desired recombinant DNA/RNA hybrids.
[Mh] Termos MeSH primário: Ácidos Nucleicos Peptídicos/química
Endonucleases Específicas para DNA e RNA de Cadeia Simples/química
[Mh] Termos MeSH secundário: Sequência de Bases
Clivagem do DNA
DNA de Cadeia Simples/química
DNA de Cadeia Simples/genética
Seres Humanos
Células K562
RNA/química
RNA/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Single-Stranded); 0 (Peptide Nucleic Acids); 0 (RNA, recombinant); 63231-63-0 (RNA); EC 3.1.30.1 (Single-Strand Specific DNA and RNA Endonucleases)
[Em] Mês de entrada:1703
[Cu] Atualização por classe:170306
[Lr] Data última revisão:
170306
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160409
[St] Status:MEDLINE
[do] DOI:10.1080/15257770.2015.1131294


  7 / 2207 MEDLINE  
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[PMID]:26699908
[Au] Autor:Mardirosian M; Nalbandyan L; Miller AD; Phan C; Kelson EP; Fischhaber PL
[Ad] Endereço:Department of Chemistry and Biochemistry, California State University Northridge, 18111 Nordhoff St, Northridge, CA, 91330-8262, USA.
[Ti] Título:Saw1 localizes to repair sites but is not required for recruitment of Rad10 to repair intermediates bearing short non-homologous 3' flaps during single-strand annealing in S. cerevisiae.
[So] Source:Mol Cell Biochem;412(1-2):131-9, 2016 Jan.
[Is] ISSN:1573-4919
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:SAW1 is required for efficient removal by the Rad1-Rad10 nuclease of 3' non-homologous DNA ends (flaps) formed as intermediates during two modes of double-strand break (DSB) repair in S. cerevisiae, single-strand annealing (SSA) and synthesis-dependent strand annealing. Saw1 was shown in vitro to bind flaps with high affinity, but displayed diminished affinity when flaps were short (<30 deoxynucleotides [nt]), consistent with it not being required for short flap cleavage. Accordingly, this study, using in vivo fluorescence microscopy showed that SAW1 was not required for recruitment of Rad10-YFP to DNA DSBs during their repair by SSA when the flaps were ~10 nt. In contrast, recruitment of Rad10-YFP to DSBs when flaps were ~500 nt did require SAW1 in G1 phase of cell cycle. Interestingly, we observed a substantial increase in colocalization of Saw1-CFP and Rad10-YFP at DSBs when short flaps were formed during repair, especially in G1, indicating significant recruitment of Saw1 despite there being no requirement for Saw1 to recruit Rad10. Saw1-CFP was seldom observed at DSBs without Rad10-YFP. Together, these results support a model in which Saw1 and Rad1-Rad10 are recruited as a complex to short and long flaps in all phases of cell cycle, but that Saw1 is only required for recruitment of Rad1-Rad10 to DSBs when long flaps are formed in G1.
[Mh] Termos MeSH primário: Reparo do DNA
Proteínas de Ligação a DNA/metabolismo
Proteínas de Saccharomyces cerevisiae/metabolismo
Saccharomyces cerevisiae/genética
Endonucleases Específicas para DNA e RNA de Cadeia Simples/metabolismo
[Mh] Termos MeSH secundário: Quebras de DNA de Cadeia Dupla
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA-Binding Proteins); 0 (Saccharomyces cerevisiae Proteins); 0 (Saw1 protein, S cerevisiae); EC 3.1.30.1 (RAD10 protein, S cerevisiae); EC 3.1.30.1 (Single-Strand Specific DNA and RNA Endonucleases)
[Em] Mês de entrada:1610
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151225
[St] Status:MEDLINE
[do] DOI:10.1007/s11010-015-2616-7


  8 / 2207 MEDLINE  
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[PMID]:26686996
[Au] Autor:Okado N; Hasegawa K; Mizuhashi F; Lynch BS; Vo TD; Roberts AS
[Ad] Endereço:Shin Nihon Chemical Co., Ltd., 19-10 Showa-cho, Anjyo, Aichi 446-0063, Japan. Electronic address: nokado@snc-enzymes.co.jp.
[Ti] Título:Safety evaluation of nuclease P1 from Penicillium citrinum.
[So] Source:Food Chem Toxicol;88:21-31, 2016 Feb.
[Is] ISSN:1873-6351
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Nuclease P1 has been widely used in the food industry to enhance or create flavor. One commercial source of this enzyme is Penicillium citrinum, an anamorphic mesophilic fungus with a long history of safe use in Europe and Asia as a fermentation organism used in the production of ribonucleases. Given the intended use in food for human consumption, and noting its potential presence at trace levels in finished products, a series of safety studies including an in vitro Ames and chromosome aberration assay, an in vivo rat erythrocyte micronucleus assay and a 90-day oral toxicity study in rats were conducted. No mutagenic activity was observed in the Ames assay. Equivocal activity in the chromosome aberration assay was not replicated in the micronucleus assay at doses of up to 1007 mg total organic solids (TOS)/kg body weight (bw)/day. Following oral administration of nuclease P1 at dosages of 10.1, 101 or 1007 mg TOS/kg bw/day to Sprague-Dawley rats, no adverse effects on any study parameter were observed. The no-observed-adverse-effect level was considered to be 1007 mg TOS/kg bw/day. The results of the genotoxicity studies and subchronic rat study support the safe use in food production of nuclease P1 produced from P. citrinum.
[Mh] Termos MeSH primário: Proteínas Fúngicas/toxicidade
Penicillium/enzimologia
Endonucleases Específicas para DNA e RNA de Cadeia Simples/toxicidade
[Mh] Termos MeSH secundário: Animais
Dano ao DNA
Relação Dose-Resposta a Droga
Feminino
Proteínas Fúngicas/administração & dosagem
Masculino
Distribuição Aleatória
Ratos
Ratos Sprague-Dawley
Endonucleases Específicas para DNA e RNA de Cadeia Simples/administração & dosagem
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Fungal Proteins); EC 3.1.30.1 (Nuclease P1, Penicillium citrinum); EC 3.1.30.1 (Single-Strand Specific DNA and RNA Endonucleases)
[Em] Mês de entrada:1610
[Cu] Atualização por classe:161230
[Lr] Data última revisão:
161230
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151222
[St] Status:MEDLINE


  9 / 2207 MEDLINE  
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[PMID]:26548958
[Au] Autor:Ida C; Yamashita S; Tsukada M; Sato T; Eguchi T; Tanaka M; Ogata S; Fujii T; Nishi Y; Ikegami S; Moss J; Miwa M
[Ad] Endereço:Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan; Department of Applied Life Studies, College of Nagoya Women's University, Nagoya-shi, Aichi 467-8610, Japan.
[Ti] Título:An enzyme-linked immunosorbent assay-based system for determining the physiological level of poly(ADP-ribose) in cultured cells.
[So] Source:Anal Biochem;494:76-81, 2016 Feb 01.
[Is] ISSN:1096-0309
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:PolyADP-ribosylation is mediated by poly(ADP-ribose) (PAR) polymerases (PARPs) and may be involved in various cellular events, including chromosomal stability, DNA repair, transcription, cell death, and differentiation. The physiological level of PAR is difficult to determine in intact cells because of the rapid synthesis of PAR by PARPs and the breakdown of PAR by PAR-degrading enzymes, including poly(ADP-ribose) glycohydrolase (PARG) and ADP-ribosylhydrolase 3. Artifactual synthesis and/or degradation of PAR likely occurs during lysis of cells in culture. We developed a sensitive enzyme-linked immunosorbent assay (ELISA) to measure the physiological levels of PAR in cultured cells. We immediately inactivated enzymes that catalyze the synthesis and degradation of PAR. We validated that trichloroacetic acid is suitable for inactivating PARPs, PARG, and other enzymes involved in metabolizing PAR in cultured cells during cell lysis. The PAR level in cells harvested with the standard radioimmunoprecipitation assay buffer was increased by 450-fold compared with trichloroacetic acid for lysis, presumably because of activation of PARPs by DNA damage that occurred during cell lysis. This ELISA can be used to analyze the biological functions of polyADP-ribosylation under various physiological conditions in cultured cells.
[Mh] Termos MeSH primário: Técnicas de Química Analítica/métodos
Ensaio de Imunoadsorção Enzimática
Poli Adenosina Difosfato Ribose/análise
[Mh] Termos MeSH secundário: Anticorpos/imunologia
Dano ao DNA
Desoxirribonuclease I/metabolismo
Glicosídeo Hidrolases/metabolismo
Células HEK293
Células HeLa
Seres Humanos
Poli Adenosina Difosfato Ribose/imunologia
Poli(ADP-Ribose) Polimerases/metabolismo
Ensaio de Radioimunoprecipitação
Endonucleases Específicas para DNA e RNA de Cadeia Simples/metabolismo
Ácido Tricloroacético/química
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., INTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Antibodies); 26656-46-2 (Poly Adenosine Diphosphate Ribose); 5V2JDO056X (Trichloroacetic Acid); EC 2.4.2.30 (Poly(ADP-ribose) Polymerases); EC 3.1.21.1 (Deoxyribonuclease I); EC 3.1.30.1 (Single-Strand Specific DNA and RNA Endonucleases); EC 3.2.1.- (Glycoside Hydrolases); EC 3.2.1.143 (poly ADP-ribose glycohydrolase)
[Em] Mês de entrada:1609
[Cu] Atualização por classe:151228
[Lr] Data última revisão:
151228
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151110
[St] Status:MEDLINE


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[PMID]:26124052
[Au] Autor:Tomic B; Kusic-Tisma J
[Ti] Título:HsOrc4-Dependent Dna Remodeling of the ori-ß Dhfr Replicator.
[So] Source:Cell Mol Biol Lett;20(4):549-61, 2015 Dec.
[Is] ISSN:1689-1392
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Replication of DNA in multicellular organisms initiates from origin of replication (ori) sequences, which significantly differ in length and complexity. One of the best characterized is hamster dihydrofolate reductase (DHFR), which contains the ori-ß sequence with several functionally relevant domains, such as an AT-rich region, dinucleotide repeat element (DNR), sequence-induced bend DNA (BEND) and a RIP60 protein-binding site (RIP60). Prior to initiation, ori sequences are recognized by origin recognition complex (ORC), which is a hetero hexamer complex that serves as the landing pad for proteins of the pre-replication complex. The function of each ORC subunit is still unclear. In this study, we analyze the function of subunit 4 of the human ORC complex (HsOrc4) in interaction with a plasmid bearing the ori-ß DHFR sequence. We show that the topologically closed DHFR ori-ß replicator contains a bubble-like structure within its AT-rich region and that it is reversibly modified in the interaction with HsOrc4. The non-canonical structure of the AT-rich region in the topologically closed ori sequence is recognized and changed by HsOrc4 using the energy of supercoiled DNA. These findings could help to further elucidate DNA replication and its possible association with human genetic diseases.
[Mh] Termos MeSH primário: Proteínas de Ciclo Celular/metabolismo
Conformação de Ácido Nucleico
Complexo de Reconhecimento de Origem/metabolismo
Origem de Replicação
Tetra-Hidrofolato Desidrogenase/genética
[Mh] Termos MeSH secundário: Sequência Rica em At
Animais
Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos/metabolismo
Sítios de Ligação
Proteínas de Ciclo Celular/química
Proteínas de Ciclo Celular/genética
Cricetulus
Replicação do DNA
Complexo de Reconhecimento de Origem/química
Complexo de Reconhecimento de Origem/genética
Proteínas de Plantas/química
Proteínas de Plantas/metabolismo
Plasmídeos/química
Plasmídeos/genética
Endonucleases Específicas para DNA e RNA de Cadeia Simples/química
Endonucleases Específicas para DNA e RNA de Cadeia Simples/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Basic Helix-Loop-Helix Leucine Zipper Transcription Factors); 0 (Cell Cycle Proteins); 0 (Mung Bean Nuclease); 0 (ORC4 protein, human); 0 (Origin Recognition Complex); 0 (Plant Proteins); 0 (REPIN1 protein, human); EC 1.5.1.3 (Tetrahydrofolate Dehydrogenase); EC 3.1.30.1 (Single-Strand Specific DNA and RNA Endonucleases)
[Em] Mês de entrada:1608
[Cu] Atualização por classe:151017
[Lr] Data última revisão:
151017
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150701
[St] Status:MEDLINE



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