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  1 / 2578 MEDLINE  
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[PMID]:29284038
[Au] Autor:Bauer RJ; Zhelkovsky A; Bilotti K; Crowell LE; Evans TC; McReynolds LA; Lohman GJS
[Ad] Endereço:Research Division, New England Biolabs, Inc., Ipswich, MA, United States of America.
[Ti] Título:Comparative analysis of the end-joining activity of several DNA ligases.
[So] Source:PLoS One;12(12):e0190062, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:DNA ligases catalyze the repair of phosphate backbone breaks in DNA, acting with highest activity on breaks in one strand of duplex DNA. Some DNA ligases have also been observed to ligate two DNA fragments with short complementary overhangs or blunt-ended termini. In this study, several wild-type DNA ligases (phage T3, T4, and T7 DNA ligases, Paramecium bursaria chlorella virus 1 (PBCV1) DNA ligase, human DNA ligase 3, and Escherichia coli DNA ligase) were tested for their ability to ligate DNA fragments with several difficult to ligate end structures (blunt-ended termini, 3'- and 5'- single base overhangs, and 5'-two base overhangs). This analysis revealed that T4 DNA ligase, the most common enzyme utilized for in vitro ligation, had its greatest activity on blunt- and 2-base overhangs, and poorest on 5'-single base overhangs. Other ligases had different substrate specificity: T3 DNA ligase ligated only blunt ends well; PBCV1 DNA ligase joined 3'-single base overhangs and 2-base overhangs effectively with little blunt or 5'- single base overhang activity; and human ligase 3 had highest activity on blunt ends and 5'-single base overhangs. There is no correlation of activity among ligases on blunt DNA ends with their activity on single base overhangs. In addition, DNA binding domains (Sso7d, hLig3 zinc finger, and T4 DNA ligase N-terminal domain) were fused to PBCV1 DNA ligase to explore whether modified binding to DNA would lead to greater activity on these difficult to ligate substrates. These engineered ligases showed both an increased binding affinity for DNA and increased activity, but did not alter the relative substrate preferences of PBCV1 DNA ligase, indicating active site structure plays a role in determining substrate preference.
[Mh] Termos MeSH primário: DNA Ligases/metabolismo
[Mh] Termos MeSH secundário: Quebras de DNA de Cadeia Dupla
Eletroforese Capilar
Seres Humanos
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
EC 6.5.1.- (DNA Ligases)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180215
[Lr] Data última revisão:
180215
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171229
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190062


  2 / 2578 MEDLINE  
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[PMID]:29048593
[Au] Autor:Krzywkowski T; Nilsson M
[Ad] Endereço:Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-171 65 Solna, Sweden.
[Ti] Título:Fidelity of RNA templated end-joining by chlorella virus DNA ligase and a novel iLock assay with improved direct RNA detection accuracy.
[So] Source:Nucleic Acids Res;45(18):e161, 2017 Oct 13.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Ligation-based nucleic acid detection methods are primarily limited to DNA, since they exhibit poor performance on RNA. This is attributed to reduced end-joining efficiency and/or fidelity of ligases. Interestingly, chlorella virus DNA ligase (PBCV-1 DNA ligase) has recently been shown to possess high RNA-templated DNA end-joining activity; however, its fidelity has not yet been systematically evaluated. Herein, we characterized PBCV-1 ligase for its RNA-templated end-joining fidelity at single base mismatches in 3' and 5' DNA probe termini and found an overall limited end-joining fidelity. To improve the specificity in PBCV-1 ligase-driven RNA detection assays, we utilized structure-specific 5' exonucleolytic activity of Thermus aquaticus DNA polymerase, used in the invader assay. In the iLock (invader padLock) probe assay, padlock probe molecules are activated prior ligation thus the base at the probe ligation junction is read twice in order to aid successful DNA ligation: first, during structure-specific invader cleavage and then during sequence-specific DNA ligation. We report two distinct iLock probe activation mechanisms and systematically evaluate the assay specificity, including single nucleotide polymorphisms on RNA, mRNA and miRNA. We show significant increase in PBCV-1 ligation fidelity in the iLock probe assay configuration for RNA detection.
[Mh] Termos MeSH primário: Técnicas Biossensoriais/métodos
Reparo do DNA por Junção de Extremidades
DNA Ligases/metabolismo
Sondas de DNA/metabolismo
RNA/análise
Moldes Genéticos
Proteínas Virais/metabolismo
[Mh] Termos MeSH secundário: Pareamento Incorreto de Bases/fisiologia
Técnicas Biossensoriais/normas
Sondas de DNA/química
Limite de Detecção
MicroRNAs/genética
MicroRNAs/metabolismo
Polimorfismo de Nucleotídeo Único/fisiologia
RNA/genética
RNA/metabolismo
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
Reação em Cadeia da Polimerase em Tempo Real/métodos
Sensibilidade e Especificidade
Especificidade por Substrato
[Pt] Tipo de publicação:EVALUATION STUDIES; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA Probes); 0 (MicroRNAs); 0 (RNA, Messenger); 0 (Viral Proteins); 63231-63-0 (RNA); EC 6.5.1.- (Chlorella virus DNA ligase); EC 6.5.1.- (DNA Ligases)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171031
[Lr] Data última revisão:
171031
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171020
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx708


  3 / 2578 MEDLINE  
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[PMID]:28927538
[Au] Autor:Gibriel AA; Adel O
[Ad] Endereço:Biochemistry & Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt; Center for Drug Research & Development (CDRD), Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt. Electronic address: strsceap@googlemail.com.
[Ti] Título:Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications.
[So] Source:Mutat Res;773:66-90, 2017 Jul.
[Is] ISSN:1873-135X
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Genetic variants have been reported to cause several genetic diseases. Various genotyping assays have been developed for diagnostic and screening purposes but with certain limitations in sensitivity, specificity, cost effectiveness and/or time savings. Since the discovery of ligase chain reaction (LCR) in the late nineties, it became one of the most favored platforms for detecting these variants and also for genotyping low abundant contaminants. Recent and powerful modifications with the integration of various detection strategies such as electrochemical and magnetic biosensors, nanoparticles (NPs), quantum dots, quartz crystal and leaky surface acoustic surface biosensors, DNAzyme, rolling circle amplification (RCA), strand displacement amplification (SDA), surface enhanced raman scattering (SERS), chemiluminescence and fluorescence resonance energy transfer have been introduced to both LCR and ligation based amplifications to enable high-throughput and inexpensive multiplex genotyping with improved robustness, simplicity, sensitivity and specificity. In this article, classical and up to date modifications in LCR and ligation based amplifications are critically evaluated and compared with emphasis on points of strength and weakness, sensitivity, cost, running time, equipment needed, applications and multiplexing potential. Versatile genotyping applications such as genetic diseases detection, bacterial and viral pathogens detection are also detailed. Ligation based gold NPs biosensor, ligation based RCA and ligation mediated SDA assays enhanced detection limit tremendously with a discrimination power approaching 1.5aM, 2aM and 0.1fM respectively. MLPA (multiplexed ligation dependent probe amplification) and SNPlex assays have been commercialized for multiplex detection of at least 48 SNPs at a time. MOL-PCR (multiplex oligonucleotide ligation) has high-throughput capability with multiplex detection of 50 SNPs/well in a 96 well plate. Ligase detection reaction (LDR) is one of the most widely used LCR versions that have been successfully integrated with several detection strategies with improved sensitivity down to 0.4fM.
[Mh] Termos MeSH primário: Técnicas de Genotipagem
Reação em Cadeia da Ligase
[Mh] Termos MeSH secundário: Técnicas Biossensoriais
DNA Ligases/genética
DNA Ligases/metabolismo
Genoma Humano
Ouro/química
Seres Humanos
Nanopartículas Metálicas/química
Reação em Cadeia da Polimerase
Polimorfismo de Nucleotídeo Único
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
7440-57-5 (Gold); EC 6.5.1.- (DNA Ligases); EC 6.5.1.2 (DNA ligase (NAD))
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171002
[Lr] Data última revisão:
171002
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170921
[St] Status:MEDLINE


  4 / 2578 MEDLINE  
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[PMID]:28911122
[Au] Autor:Welch R; Chung D; Grass J; Landick R; Keles S
[Ad] Endereço:Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA.
[Ti] Título:Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments.
[So] Source:Nucleic Acids Res;45(15):e145, 2017 Sep 06.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:ChIP-exo/nexus experiments rely on innovative modifications of the commonly used ChIP-seq protocol for high resolution mapping of transcription factor binding sites. Although many aspects of the ChIP-exo data analysis are similar to those of ChIP-seq, these high throughput experiments pose a number of unique quality control and analysis challenges. We develop a novel statistical quality control pipeline and accompanying R/Bioconductor package, ChIPexoQual, to enable exploration and analysis of ChIP-exo and related experiments. ChIPexoQual evaluates a number of key issues including strand imbalance, library complexity, and signal enrichment of data. Assessment of these features are facilitated through diagnostic plots and summary statistics computed over regions of the genome with varying levels of coverage. We evaluated our QC pipeline with both large collections of public ChIP-exo/nexus data and multiple, new ChIP-exo datasets from Escherichia coli. ChIPexoQual analysis of these datasets resulted in guidelines for using these QC metrics across a wide range of sequencing depths and provided further insights for modelling ChIP-exo data.
[Mh] Termos MeSH primário: Imunoprecipitação da Cromatina/métodos
DNA/metabolismo
Acurácia dos Dados
Interpretação Estatística de Dados
Exodesoxirribonucleases/metabolismo
Sequenciamento de Nucleotídeos em Larga Escala/métodos
Análise de Sequência de DNA/métodos
[Mh] Termos MeSH secundário: Sítios de Ligação/genética
Imunoprecipitação da Cromatina/normas
DNA/análise
DNA Ligases/metabolismo
Conjuntos de Dados como Assunto
Escherichia coli/genética
Escherichia coli/metabolismo
Sequenciamento de Nucleotídeos em Larga Escala/normas
Análise de Sequência com Séries de Oligonucleotídeos/métodos
Análise de Sequência com Séries de Oligonucleotídeos/normas
Ligação Proteica
Controle de Qualidade
Análise de Sequência de DNA/normas
Software
Fatores de Transcrição/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; VALIDATION STUDIES
[Nm] Nome de substância:
0 (Transcription Factors); 9007-49-2 (DNA); EC 3.1.- (Exodeoxyribonucleases); EC 6.5.1.- (DNA Ligases)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171107
[Lr] Data última revisão:
171107
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170916
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx594


  5 / 2578 MEDLINE  
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[PMID]:28700629
[Au] Autor:Bodine TJ; Evangelista MA; Chang HT; Ayoub CA; Samuel BS; Sucgang R; Zechiedrich L
[Ad] Endereço:Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, United States of America.
[Ti] Título:Escherichia coli DNA ligase B may mitigate damage from oxidative stress.
[So] Source:PLoS One;12(7):e0180800, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Escherichia coli encodes two DNA ligases, ligase A, which is essential under normal laboratory growth conditions, and ligase B, which is not. Here we report potential functions of ligase B. We found that across the entire Enterobacteriaceae family, ligase B is highly conserved in both amino acid identity and synteny with genes associated with oxidative stress. Deletion of ligB sensitized E. coli to specific DNA damaging agents and antibiotics resulted in a weak mutator phenotype, and decreased biofilm formation. Overexpression of ligB caused a dramatic extension of lag phase that eventually resumed normal growth. The ligase function of ligase B was not required to mediate the extended lag phase, as overexpression of a ligase-deficient ligB mutant also blocked growth. Overexpression of ligB during logarithmic growth caused an immediate block of cell growth and DNA replication, and death of about half of cells. These data support a potential role for ligase B in the base excision repair pathway or the mismatch repair pathway.
[Mh] Termos MeSH primário: DNA Ligases/metabolismo
Escherichia coli/enzimologia
Escherichia coli/metabolismo
[Mh] Termos MeSH secundário: Dano ao DNA/genética
DNA Ligases/genética
Replicação do DNA/genética
Replicação do DNA/fisiologia
Enterobacteriaceae/genética
Enterobacteriaceae/metabolismo
Estresse Oxidativo/genética
Estresse Oxidativo/fisiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
EC 6.5.1.- (DNA Ligases)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170925
[Lr] Data última revisão:
170925
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170713
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0180800


  6 / 2578 MEDLINE  
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[PMID]:28656718
[Au] Autor:Pandey P; Verma V; Gautam G; Kumari N; Dhar SK; Gourinath S
[Ad] Endereço:School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
[Ti] Título:Targeting the ß-clamp in Helicobacter pylori with FDA-approved drugs reveals micromolar inhibition by diflunisal.
[So] Source:FEBS Lett;591(15):2311-2322, 2017 Aug.
[Is] ISSN:1873-3468
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The ß-clamp is the processivity-promoting factor for most of the enzymes in prokaryotic DNA replication; hence, it is a crucial drug target. In the present study, we investigated the ß-clamp from Helicobacter pylori, aiming to seek potential drug molecules against this gastric-cancer-causing bacterium. An in silico screening of Food and Drug Administration (FDA) approved drugs against the H. pylori ß-clamp, followed by its in vitro inhibition using a surface competition approach, yielded the drug diflunisal as a positive initial hit. Diflunisal inhibits the growth of H. pylori in the micromolar range. We determined the structure of diflunisal in complex with the ß-clamp to show that the drug binds at subsite I, which is a protein-protein interaction site. Successful identification of FDA-approved molecules against H. pylori may lead to better and faster drug development.
[Mh] Termos MeSH primário: Antibacterianos/farmacologia
DNA Polimerase III/antagonistas & inibidores
DNA Polimerase III/química
Diflunisal/farmacologia
Helicobacter pylori/efeitos dos fármacos
[Mh] Termos MeSH secundário: Antibacterianos/química
Sítios de Ligação
Cristalografia por Raios X
DNA Ligases/metabolismo
DNA Polimerase III/metabolismo
Diflunisal/química
Aprovação de Drogas
Avaliação Pré-Clínica de Medicamentos/métodos
Inibidores Enzimáticos/química
Inibidores Enzimáticos/farmacologia
Helicobacter pylori/enzimologia
Concentração Inibidora 50
Simulação de Acoplamento Molecular
Conformação Proteica
Estados Unidos
United States Food and Drug Administration
[Pt] Tipo de publicação:LETTER
[Nm] Nome de substância:
0 (Anti-Bacterial Agents); 0 (Enzyme Inhibitors); 7C546U4DEN (Diflunisal); EC 2.7.7.- (DNA Polymerase III); EC 6.5.1.- (DNA Ligases)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171010
[Lr] Data última revisão:
171010
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170629
[St] Status:MEDLINE
[do] DOI:10.1002/1873-3468.12734


  7 / 2578 MEDLINE  
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[PMID]:28655200
[Au] Autor:An R; Li Q; Fan Y; Li J; Pan X; Komiyama M; Liang X
[Ad] Endereço:College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
[Ti] Título:Highly efficient preparation of single-stranded DNA rings by T4 ligase at abnormally low Mg(II) concentration.
[So] Source:Nucleic Acids Res;45(15):e139, 2017 Sep 06.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Preparation of large amount of single-stranded circular DNA in high selectivity is crucial for further developments of nanotechnology and other DNA sciences. Herein, a simple but practically useful methodology to prepare DNA rings has been presented. One of the essential factors is to use highly diluted T4 ligase buffer for ligase reactions. This strategy is based on our unexpected finding that, in diluted T4 buffers, intermolecular polymerization of DNA fragments is greatly suppressed with respect to their intramolecular cyclization. This promotion of cyclization is attributable to abnormally low concentration of Mg2+ ion (0.5-1.0 mM) but not ATP in the media for T4 ligase reactions. The second essential factor is to add DNA substrate intermittently to the mixture and maintain its temporal concentration low. By combining these two factors, single-stranded DNA rings of various sizes (31-74 nt) were obtained in high selectivity (89 mol% for 66-nt DNA) and in satisfactorily high productivity (∼0.2 mg/ml). A linear 72-nt DNA was converted to the corresponding DNA ring in nearly 100% selectivity. The superiority of this new method was further substantiated by the fact that small-sized DNA rings (31-42 nt), which were otherwise hardly obtainable, were successfully prepared in reasonable yields.
[Mh] Termos MeSH primário: DNA Ligases/metabolismo
DNA Circular/metabolismo
DNA de Cadeia Simples/metabolismo
Magnésio/farmacologia
[Mh] Termos MeSH secundário: Sequência de Bases
Clonagem Molecular/métodos
Ciclização/efeitos dos fármacos
DNA Circular/efeitos dos fármacos
DNA de Cadeia Simples/efeitos dos fármacos
Técnicas In Vitro
Concentração Osmolar
Polimerização/efeitos dos fármacos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Circular); 0 (DNA, Single-Stranded); EC 6.5.1.- (DNA Ligases); I38ZP9992A (Magnesium)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171107
[Lr] Data última revisão:
171107
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170629
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx553


  8 / 2578 MEDLINE  
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[PMID]:28432850
[Au] Autor:Sakowski S; Krasinski T; Sarnik J; Blasiak J; Waldmajer J; Poplawski T
[Ad] Endereço:.
[Ti] Título:A detailed experimental study of a DNA computer with two endonucleases.
[So] Source:Z Naturforsch C;72(7-8):303-313, 2017 Jul 14.
[Is] ISSN:0939-5075
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:Great advances in biotechnology have allowed the construction of a computer from DNA. One of the proposed solutions is a biomolecular finite automaton, a simple two-state DNA computer without memory, which was presented by Ehud Shapiro's group at the Weizmann Institute of Science. The main problem with this computer, in which biomolecules carry out logical operations, is its complexity - increasing the number of states of biomolecular automata. In this study, we constructed (in laboratory conditions) a six-state DNA computer that uses two endonucleases (e.g. AcuI and BbvI) and a ligase. We have presented a detailed experimental verification of its feasibility. We described the effect of the number of states, the length of input data, and the nondeterminism on the computing process. We also tested different automata (with three, four, and six states) running on various accepted input words of different lengths such as ab, aab, aaab, ababa, and of an unaccepted word ba. Moreover, this article presents the reaction optimization and the methods of eliminating certain biochemical problems occurring in the implementation of a biomolecular DNA automaton based on two endonucleases.
[Mh] Termos MeSH primário: Automação/métodos
Computadores Moleculares
DNA/metabolismo
Endonucleases/metabolismo
[Mh] Termos MeSH secundário: Sequência de Bases
DNA/genética
DNA Ligases/metabolismo
Desoxirribonucleases de Sítio Específico do Tipo II/metabolismo
Modelos Teóricos
Oligonucleotídeos/genética
Oligonucleotídeos/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Oligonucleotides); 9007-49-2 (DNA); EC 3.1.- (Endonucleases); EC 3.1.21.- (endodexoyribonuclease BbvI); EC 3.1.21.4 (Deoxyribonucleases, Type II Site-Specific); EC 6.5.1.- (DNA Ligases)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170927
[Lr] Data última revisão:
170927
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170423
[St] Status:MEDLINE


  9 / 2578 MEDLINE  
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[PMID]:28373277
[Au] Autor:Heider MR; Burkhart BW; Santangelo TJ; Gardner AF
[Ad] Endereço:From New England Biolabs, Inc., Ipswich, Massachusetts 01938 and.
[Ti] Título:Defining the RNaseH2 enzyme-initiated ribonucleotide excision repair pathway in Archaea.
[So] Source:J Biol Chem;292(21):8835-8845, 2017 May 26.
[Is] ISSN:1083-351X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Incorporation of ribonucleotides during DNA replication has severe consequences for genome stability. Although eukaryotes possess a number of redundancies for initiating and completing repair of misincorporated ribonucleotides, archaea such as rely only upon RNaseH2 to initiate the pathway. Because DNA polymerases incorporate as many as 1,000 ribonucleotides per genome, RNaseH2 must be efficient at recognizing and nicking at embedded ribonucleotides to ensure genome integrity. Here, we show that ribonucleotides are incorporated by the hyperthermophilic archaeon both and and a robust ribonucleotide excision repair pathway is critical to keeping incorporation levels low in wild-type cells. Using pre-steady-state and steady-state kinetics experiments, we also show that archaeal RNaseH2 rapidly cleaves at embedded ribonucleotides (200-450 s ), but exhibits an ∼1,000-fold slower turnover rate (0.06-0.17 s ), suggesting a potential role for RNaseH2 in protecting or marking nicked sites for further processing. We found that following RNaseH2 cleavage, the combined activities of polymerase B (PolB), flap endonuclease (Fen1), and DNA ligase are required to complete ribonucleotide processing. PolB formed a ribonucleotide-containing flap by strand displacement synthesis that was cleaved by Fen1, and DNA ligase sealed the nick for complete repair. Our study reveals conservation of the overall mechanism of ribonucleotide excision repair across domains of life. The lack of redundancies in ribonucleotide repair in archaea perhaps suggests a more ancestral form of ribonucleotide excision repair compared with the eukaryotic pathway.
[Mh] Termos MeSH primário: Proteínas Arqueais/metabolismo
Quebras de DNA de Cadeia Simples
Reparo do DNA/fisiologia
DNA Arqueal/metabolismo
Ribonuclease H/metabolismo
Thermococcus/metabolismo
[Mh] Termos MeSH secundário: Proteínas Arqueais/genética
DNA Ligases/genética
DNA Ligases/metabolismo
DNA Polimerase beta/genética
DNA Polimerase beta/metabolismo
DNA Arqueal/genética
Ribonuclease H/genética
Thermococcus/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Archaeal Proteins); 0 (DNA, Archaeal); EC 2.7.7.- (DNA Polymerase beta); EC 3.1.26.4 (Ribonuclease H); EC 6.5.1.- (DNA Ligases)
[Em] Mês de entrada:1706
[Cu] Atualização por classe:170609
[Lr] Data última revisão:
170609
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170405
[St] Status:MEDLINE
[do] DOI:10.1074/jbc.M117.783472


  10 / 2578 MEDLINE  
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[PMID]:28334877
[Au] Autor:Okafor CD; Lanier KA; Petrov AS; Athavale SS; Bowman JC; Hud NV; Williams LD
[Ad] Endereço:School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 0400, USA.
[Ti] Título:Iron mediates catalysis of nucleic acid processing enzymes: support for Fe(II) as a cofactor before the great oxidation event.
[So] Source:Nucleic Acids Res;45(7):3634-3642, 2017 Apr 20.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Life originated in an anoxic, Fe2+-rich environment. We hypothesize that on early Earth, Fe2+ was a ubiquitous cofactor for nucleic acids, with roles in RNA folding and catalysis as well as in processing of nucleic acids by protein enzymes. In this model, Mg2+ replaced Fe2+ as the primary cofactor for nucleic acids in parallel with known metal substitutions of metalloproteins, driven by the Great Oxidation Event. To test predictions of this model, we assay the ability of nucleic acid processing enzymes, including a DNA polymerase, an RNA polymerase and a DNA ligase, to use Fe2+ in place of Mg2+ as a cofactor during catalysis. Results show that Fe2+ can indeed substitute for Mg2+ in catalytic function of these enzymes. Additionally, we use calculations to unravel differences in energetics, structures and reactivities of relevant Mg2+ and Fe2+ complexes. Computation explains why Fe2+ can be a more potent cofactor than Mg2+ in a variety of folding and catalytic functions. We propose that the rise of O2 on Earth drove a Fe2+ to Mg2+ substitution in proteins and nucleic acids, a hypothesis consistent with a general model in which some modern biochemical systems retain latent abilities to revert to primordial Fe2+-based states when exposed to pre-GOE conditions.
[Mh] Termos MeSH primário: Coenzimas/química
Ferro/química
[Mh] Termos MeSH secundário: Catálise
DNA Ligases/metabolismo
DNA Polimerase Dirigida por DNA/metabolismo
RNA Polimerases Dirigidas por DNA/metabolismo
Magnésio/química
Oxirredução
Proteínas Virais/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Coenzymes); 0 (Viral Proteins); E1UOL152H7 (Iron); EC 2.7.7.- (Deep Vent DNA polymerase); EC 2.7.7.- (bacteriophage T7 RNA polymerase); EC 2.7.7.6 (DNA-Directed RNA Polymerases); EC 2.7.7.7 (DNA-Directed DNA Polymerase); EC 6.5.1.- (DNA Ligases); I38ZP9992A (Magnesium)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170825
[Lr] Data última revisão:
170825
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170324
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx171



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