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  1 / 9520 MEDLINE  
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[PMID]:29320546
[Au] Autor:Krasikova YS; Rechkunova NI; Maltseva EA; Lavrik OI
[Ad] Endereço:Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.
[Ti] Título:RPA and XPA interaction with DNA structures mimicking intermediates of the late stages in nucleotide excision repair.
[So] Source:PLoS One;13(1):e0190782, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Replication protein A (RPA) and the xeroderma pigmentosum group A (XPA) protein are indispensable for both pathways of nucleotide excision repair (NER). Here we analyze the interaction of RPA and XPA with DNA containing a flap and different size gaps that imitate intermediates of the late NER stages. Using gel mobility shift assays, we found that RPA affinity for DNA decreased when DNA contained both extended gap and similar sized flap in comparison with gapped-DNA structure. Moreover, crosslinking experiments with the flap-gap DNA revealed that RPA interacts mainly with the ssDNA platform within the long gap and contacts flap in DNA with a short gap. XPA exhibits higher affinity for bubble-DNA structures than to flap-gap-containing DNA. Protein titration analysis showed that formation of the RPA-XPA-DNA ternary complex depends on the protein concentration ratio and these proteins can function as independent players or in tandem. Using fluorescently-labelled RPA, direct interaction of this protein with XPA was detected and characterized quantitatively. The data obtained allow us to suggest that XPA can be involved in the post-incision NER stages via its interaction with RPA.
[Mh] Termos MeSH primário: Reparo do DNA
DNA/metabolismo
Proteína de Replicação A/metabolismo
Proteína de Xeroderma Pigmentoso Grupo A/metabolismo
[Mh] Termos MeSH secundário: DNA/química
Ensaio de Desvio de Mobilidade Eletroforética
Seres Humanos
Marcadores de Fotoafinidade
Ligação Proteica
Proteínas Recombinantes/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Photoaffinity Labels); 0 (Recombinant Proteins); 0 (Replication Protein A); 0 (Xeroderma Pigmentosum Group A Protein); 9007-49-2 (DNA)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180221
[Lr] Data última revisão:
180221
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180111
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190782


  2 / 9520 MEDLINE  
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[PMID]:29178995
[Au] Autor:Das S; Chatterjee S; Pramanik S; Devi PS; Kumar GS
[Ad] Endereço:Sensor and Actuator Division, CSIR-Central Glass and Ceramic Research Institute, Kolkata 700032, India.
[Ti] Título:A new insight into the interaction of ZnO with calf thymus DNA through surface defects.
[So] Source:J Photochem Photobiol B;178:339-347, 2018 Jan.
[Is] ISSN:1873-2682
[Cp] País de publicação:Switzerland
[La] Idioma:eng
[Ab] Resumo:Experimental evidences on the binding interaction of ZnO and Calf Thymus (CT) DNA using several biophysical techniques are the centre of interest of the present study. The interaction of ZnO with CT DNA has been investigated in detail by absorption spectral study, fluorescence titration, Raman analysis, zeta potential measurement, viscometric experiment along with thermal melting study and microscopic analysis. Steady-state fluorescence study revealed the quenching (48%) of the surface defect related peak intensity of ZnO on interaction with DNA. The optimized concentration of ZnO and DNA to obtain this level of quenching has been found to be 0.049mM and 1.027µM, respectively. Additional fluorescence study with 8-hydroxy-5-quinoline (HQ) as a fluorescence probe for Zn ruled out the dissolution effect of ZnO under the experimental conditions. DNA conjugation on the surface of ZnO was also supported by Raman study. The quantitative variation in conductivity as well as electrophoretic mobility indicated significant interaction of ZnO with the DNA molecule. Circular dichroism (CD) and viscometry titrations provided clear evidence in support of the conformational retention of the DNA on interaction with ZnO. The binding interaction was found to be predominantly entropy driven in nature. The bio-physical studies presented in this paper exploring ZnO-CT DNA interaction could add a new horizon to understand the interaction between metal oxide and DNA.
[Mh] Termos MeSH primário: DNA/química
Óxido de Zinco/química
[Mh] Termos MeSH secundário: Animais
Calorimetria
Bovinos
Dicroísmo Circular
Ensaio de Desvio de Mobilidade Eletroforética
Microscopia Eletrônica de Transmissão
Oxiquinolina/química
Espectrometria de Fluorescência
Análise Espectral Raman
Propriedades de Superfície
Termodinâmica
Viscosidade
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
5UTX5635HP (Oxyquinoline); 9007-49-2 (DNA); 91080-16-9 (calf thymus DNA); SOI2LOH54Z (Zinc Oxide)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180212
[Lr] Data última revisão:
180212
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171128
[St] Status:MEDLINE


  3 / 9520 MEDLINE  
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[PMID]:29206865
[Au] Autor:Dani P; Ujaoney AK; Apte SK; Basu B
[Ad] Endereço:Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.
[Ti] Título:Regulation of potassium dependent ATPase (kdp) operon of Deinococcus radiodurans.
[So] Source:PLoS One;12(12):e0188998, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The genome of D. radiodurans harbors genes for structural and regulatory proteins of Kdp ATPase, in an operon pattern, on Mega plasmid 1. Organization of its two-component regulatory genes is unique. Here we demonstrate that both, the structural as well as regulatory components of the kdp operon of D. radiodurans are expressed quickly as the cells experience potassium limitation but are not expressed upon increase in osmolarity. The cognate DNA binding response regulator (RR) effects the expression of kdp operon during potassium deficiency through specific interaction with the kdp promoter. Deletion of the gene encoding RR protein renders the mutant D. radiodurans (ΔRR) unable to express kdp operon under potassium limitation. The ΔRR D. radiodurans displays no growth defect when grown on rich media or when exposed to oxidative or heat stress but shows reduced growth following gamma irradiation. The study elucidates the functional and regulatory aspects of the novel kdp operon of this extremophile, for the first time.
[Mh] Termos MeSH primário: Adenosina Trifosfatases/metabolismo
Deinococcus/genética
Óperon
Potássio/metabolismo
[Mh] Termos MeSH secundário: Adenosina Trifosfatases/genética
Deinococcus/crescimento & desenvolvimento
Ensaio de Desvio de Mobilidade Eletroforética
Genes Bacterianos
Pressão Osmótica
Estresse Fisiológico
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
EC 3.6.1.- (Adenosine Triphosphatases); RWP5GA015D (Potassium)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:171229
[Lr] Data última revisão:
171229
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171206
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0188998


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[PMID]:29216242
[Au] Autor:Panmanee W; Charoenlap N; Atichartpongkul S; Mahavihakanont A; Whiteside MD; Winsor G; Brinkman FSL; Mongkolsuk S; Hassett DJ
[Ad] Endereço:Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH.
[Ti] Título:The OxyR-regulated phnW gene encoding 2-aminoethylphosphonate:pyruvate aminotransferase helps protect Pseudomonas aeruginosa from tert-butyl hydroperoxide.
[So] Source:PLoS One;12(12):e0189066, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The LysR member of bacterial transactivators, OxyR, governs transcription of genes involved in the response to H2O2 and organic (alkyl) hydroperoxides (AHP) in the Gram-negative pathogen, Pseudomonas aeruginosa. We have previously shown that organisms lacking OxyR are rapidly killed by <2 or 500 mM H2O2 in planktonic and biofilm bacteria, respectively. In this study, we first employed a bioinformatic approach to elucidate the potential regulatory breadth of OxyR by scanning the entire P. aeruginosa PAO1 genome for canonical OxyR promoter recognition sequences (ATAG-N7-CTAT-N7-ATAG-N7-CTAT). Of >100 potential OxyR-controlled genes, 40 were strategically selected that were not predicted to be involved in the direct response to oxidative stress (e.g., catalase, peroxidase, etc.) and screened such genes by RT-PCR analysis for potentially positive or negative control by OxyR. Differences were found in 7 of 40 genes when comparing an oxyR mutant vs. PAO1 expression that was confirmed by ß-galactosidase reporter assays. Among these, phnW, encoding 2-aminoethylphosphonate:pyruvate aminotransferase, exhibited reduced expression in the oxyR mutant compared to wild-type bacteria. Electrophoretic mobility shift assays indicated binding of OxyR to the phnW promoter and DNase I footprinting analysis also revealed the sequences to which OxyR bound. Interestingly, a phnW mutant was more susceptible to t-butyl-hydroperoxide (t-BOOH) treatment than wild-type bacteria. Although we were unable to define the direct mechanism underlying this phenomenon, we believe that this may be due to a reduced efficiency for this strain to degrade t-BOOH relative to wild-type organisms because of modulation of AHP gene transcription in the phnW mutant.
[Mh] Termos MeSH primário: Proteínas de Bactérias/genética
Genes Bacterianos
Pseudomonas aeruginosa/efeitos dos fármacos
Pseudomonas aeruginosa/genética
terc-Butil Hidroperóxido/farmacologia
[Mh] Termos MeSH secundário: Pegada de DNA
Ensaio de Desvio de Mobilidade Eletroforética
Reação em Cadeia da Polimerase Via Transcriptase Reversa
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Bacterial Proteins); 955VYL842B (tert-Butylhydroperoxide)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:171226
[Lr] Data última revisão:
171226
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171208
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0189066


  5 / 9520 MEDLINE  
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[PMID]:29049397
[Au] Autor:Schneefeld M; Busche T; Geffers R; Kalinowski J; Bange FC
[Ad] Endereço:Department of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany.
[Ti] Título:The transcriptional regulator LysG (Rv1985c) of Mycobacterium tuberculosis activates lysE (Rv1986) in a lysine-dependent manner.
[So] Source:PLoS One;12(10):e0186505, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The Mycobacterium tuberculosis protein encoded by the Rv1986 gene is a target for memory T cells in patients with tuberculosis, and shows strong similarities to a lysine exporter LysE of Corynebacterium glutamicum. During infection, the pathogen Mycobacterium tuberculosis adapts its metabolism to environmental changes. In this study, we found that the expression of Rv1986 is controlled by Rv1985c. Rv1985c is located directly upstream of Rv1986 with an overlapping promoter region between both genes. Semiquantitative reverse transcription PCR using an isogenic mutant of Mycobacterium tuberculosis lacking Rv1985c showed that in the presence of lysine, Rv1985c protein positively upregulated the expression of Rv1986. RNA sequencing revealed the transcription start points for both transcripts and overlapping promoters. An inverted repeat in the center of the intergenic region was identified, and binding of Rv1985c protein to the intergenic region was confirmed by electrophoretic mobility shift assays. Whole transcriptome expression analysis and RNAsequencing showed downregulated transcription of ppsBCD in the Rv1985c-mutant compared to the wild type strain. Taken together, our findings characterize the regulatory network of Rv1985c in Mycobacterium tuberculosis. Due to their similarity of an orthologous gene pair in Corynebacterium glutamicum, we suggest to rename Rv1985c to lysG(Mt), and Rv1986 to lysE(Mt).
[Mh] Termos MeSH primário: Proteínas de Bactérias/metabolismo
Lisina/metabolismo
Mycobacterium tuberculosis/metabolismo
Transativadores/metabolismo
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Proteínas de Bactérias/química
Proteínas de Bactérias/genética
Ensaio de Desvio de Mobilidade Eletroforética
Regulação Bacteriana da Expressão Gênica
Genes Bacterianos
Mycobacterium tuberculosis/genética
Regiões Promotoras Genéticas
Reação em Cadeia da Polimerase Via Transcriptase Reversa
Homologia de Sequência de Aminoácidos
Transativadores/química
Transativadores/genética
Transcriptoma
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (Trans-Activators); K3Z4F929H6 (Lysine)
[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:171020
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0186505


  6 / 9520 MEDLINE  
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[PMID]:29020107
[Au] Autor:Temprana CF; Prieto MJ; Igartúa DE; Femia AL; Amor MS; Alonso SDV
[Ad] Endereço:Laboratorio de Biomembranas (LBM), Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina.
[Ti] Título:Diacetylenic lipids in the design of stable lipopolymers able to complex and protect plasmid DNA.
[So] Source:PLoS One;12(10):e0186194, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Different viral and non-viral vectors have been designed to allow the delivery of nucleic acids in gene therapy. In general, non-viral vectors have been associated with increased safety for in vivo use; however, issues regarding their efficacy, toxicity and stability continue to drive further research. Thus, the aim of this study was to evaluate the potential use of the polymerizable diacetylenic lipid 1,2-bis(10,12-tricosadiynoyl)-sn-glycero-3-phosphocholine (DC8,9PC) as a strategy to formulate stable cationic lipopolymers in the delivery and protection of plasmid DNA. Cationic lipopolymers were prepared following two different methodologies by using DC8,9PC, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and the cationic lipids (CL) 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP), stearylamine (SA), and myristoylcholine chloride (MCL), in a molar ratio of 1:1:0.2 (DMPC:DC8,9PC:CL). The copolymerization methodology allowed obtaining cationic lipopolymers which were smaller in size than those obtained by the cationic addition methodology although both techniques presented high size stability over a 166-day incubation period at 4°C. Cationic lipopolymers containing DOTAP or MCL were more efficient in complexing DNA than those containing SA. Moreover, lipopolymers containing DOTAP were found to form highly stable complexes with DNA, able to resist serum DNAses degradation. Furthermore, neither of the cationic lipopolymers (with or without DNA) induced red blood cell hemolysis, although metabolic activity determined on the L-929 and Vero cell lines was found to be dependent on the cell line, the formulation and the presence of DNA. The high stability and DNA protection capacity as well as the reduced toxicity determined for the cationic lipopolymer containing DOTAP highlight the potential advantage of using lipopolymers when designing novel non-viral carrier systems for use in in vivo gene therapy. Thus, this work represents the first steps toward developing a cationic lipopolymer-based gene delivery system using polymerizable and cationic lipids.
[Mh] Termos MeSH primário: Acetileno/química
DNA/metabolismo
Lipídeos/química
Plasmídeos/metabolismo
Polímeros/síntese química
[Mh] Termos MeSH secundário: Animais
Bioensaio
Células COS
Cátions
Sobrevivência Celular
Cercopithecus aethiops
Desoxirribonucleases/metabolismo
Ensaio de Desvio de Mobilidade Eletroforética
Citometria de Fluxo
Hemólise
Luz
Camundongos
Peso Molecular
Polimerização
Polímeros/química
Espalhamento de Radiação
Eletricidade Estática
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Cations); 0 (Lipids); 0 (Polymers); 9007-49-2 (DNA); EC 3.1.- (Deoxyribonucleases); OC7TV75O83 (Acetylene)
[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:171012
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0186194


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[PMID]:28859169
[Au] Autor:Kushwaha NK; Bhardwaj M; Chakraborty S
[Ad] Endereço:Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
[Ti] Título:The replication initiator protein of a geminivirus interacts with host monoubiquitination machinery and stimulates transcription of the viral genome.
[So] Source:PLoS Pathog;13(8):e1006587, 2017 Aug.
[Is] ISSN:1553-7374
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Geminiviruses constitute a group of plant viruses, with a ssDNA genome, whose replication in the nucleus of an infected cell requires the function of geminivirus-encoded replication initiator protein (Rep). Our results suggest that monoubiquitinated histone 2B (H2B-ub) promotes tri-methylation of histone 3 at lysine 4 (H3-K4me3) on the promoter of Chilli leaf curl virus (ChiLCV). We isolated homologues of two major components of the monoubiquitination machinery: UBIQUITIN-CONJUGATING ENZYME2 (NbUBC2) and HISTONE MONOUBIQUITINATION1 (NbHUB1) from N. benthamiana. ChiLCV failed to cause disease in NbUBC2-, and NbHUB1-silenced plants, at the same time, H2B-ub and H3-K4me3 modifications were decreased, and the occupancy of RNA polymerase II on the viral promoter was reduced as well. In further investigations, Rep protein of ChiLCV was found to re-localize NbUBC2 from the cytoplasm to the nucleoplasm, like NbHUB1, the cognate partner of NbUBC2. Rep was observed to interact and co-localize with NbHUB1 and NbUBC2 in the nuclei of the infected cells. In summary, the current study reveals that the ChiLCV Rep protein binds the viral genome and interacts with NbUBC2 and NbHUB1 for the monoubiquitination of histone 2B that subsequently promotes trimethylation of histone 3 at lysine 4 on ChiLCV mini-chromosomes and enhances transcription of the viral genes.
[Mh] Termos MeSH primário: Begomovirus/genética
Regulação Viral da Expressão Gênica/genética
Interações Hospedeiro-Parasita/genética
Proteínas Virais/metabolismo
Replicação Viral/genética
[Mh] Termos MeSH secundário: Animais
DNA Helicases/genética
Proteínas de Ligação a DNA/metabolismo
Ensaio de Desvio de Mobilidade Eletroforética
Transferência Ressonante de Energia de Fluorescência
Genoma Viral/genética
Immunoblotting
Imunoprecipitação
Proteínas de Plantas/metabolismo
Reação em Cadeia da Polimerase
Tabaco/virologia
Transativadores/genética
Transcrição Genética/genética
Técnicas do Sistema de Duplo-Híbrido
Ubiquitinação
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA-Binding Proteins); 0 (Plant Proteins); 0 (Trans-Activators); 0 (Viral Proteins); 0 (replication initiator protein); EC 3.6.4.- (DNA Helicases)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171003
[Lr] Data última revisão:
171003
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170901
[St] Status:MEDLINE
[do] DOI:10.1371/journal.ppat.1006587


  8 / 9520 MEDLINE  
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[PMID]:28829844
[Au] Autor:Vu KT; Zhang F; Hulleman JD
[Ad] Endereço:Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States.
[Ti] Título:Conditional, Genetically Encoded, Small Molecule-Regulated Inhibition of NFκB Signaling in RPE Cells.
[So] Source:Invest Ophthalmol Vis Sci;58(10):4126-4137, 2017 Aug 01.
[Is] ISSN:1552-5783
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Purpose: Nuclear factor κB (NFκB) is a ubiquitously expressed, proinflammatory transcription factor that controls the expression of genes involved in cell survival, angiogenesis, complement activation, and inflammation. Studies have implicated NFκB-dependent cytokines or complement-related factors as being detrimentally involved in retinal diseases, thus making inhibition of NFκB signaling a potential therapeutic target. We sought to develop a conditional and reversible method that could regulate pathogenic NFκB signaling by the addition of a small molecule. Methods: We developed a genetically based, trimethoprim (TMP)-regulated approach that conditionally inhibits NFκB signaling by fusing a destabilized dihydrofolate reductase (DHFR) domain to an inhibitor of NFκB, IκBα, in ARPE-19 cells. We then challenged ARPE-19 cells with a number of stimuli that have been demonstrated to trigger NFκB signaling, including LPS, TNFα, IL-1α, and A2E. Western blotting, electrophoretic mobility shift assay, quantitative PCR, ELISA, and NFκB reporter assays were used to evaluate the effectiveness of this DHFR-IκBα approach. Results: This destabilized domain approach, coupled with doxycycline-inducibility, allowed for accurate control over the abundance of DHFR-IκBα. Stabilization of DHFR-IκBα with TMP prevented IL-1α-, A2E-, LPS-, and TNFα-induced NFκB-mediated upregulation and release of the proinflammatory cytokines IL-1ß and IL-6 from ARPE-19 cells (by as much as 93%). This strategy is dosable, completely reversible, and can be cycled "on" or "off" within the same cell population repeatedly to confer protection at desired time points. Conclusions: These studies lay the groundwork for the use of destabilized domains in retinal pigment epithelium (RPE) cells in vivo and in this context, demonstrate their utility for preventing inflammatory signaling.
[Mh] Termos MeSH primário: Inibidores do Citocromo P-450 CYP2C8/farmacologia
NF-kappa B/antagonistas & inibidores
Epitélio Pigmentado da Retina/metabolismo
Tetra-Hidrofolato Desidrogenase/farmacologia
Trimetoprima/farmacologia
[Mh] Termos MeSH secundário: Western Blotting
Sobrevivência Celular/efeitos dos fármacos
Células Cultivadas
Inibidores do Citocromo P-450 CYP2C8/química
Ensaio de Desvio de Mobilidade Eletroforética
Ensaio de Imunoadsorção Enzimática
Regulação da Expressão Gênica/efeitos dos fármacos
Seres Humanos
NF-kappa B/metabolismo
Domínios Proteicos/efeitos dos fármacos
Transdução de Sinais/efeitos dos fármacos
Tetra-Hidrofolato Desidrogenase/química
Trimetoprima/química
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Cytochrome P-450 CYP2C8 Inhibitors); 0 (NF-kappa B); AN164J8Y0X (Trimethoprim); EC 1.5.1.3 (Tetrahydrofolate Dehydrogenase)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170828
[Lr] Data última revisão:
170828
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170823
[St] Status:MEDLINE
[do] DOI:10.1167/iovs.17-22133


  9 / 9520 MEDLINE  
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[PMID]:28829576
[Au] Autor:Kranawetter C; Brady S; Sun L; Schroeder M; Chen SJ; Heng X
[Ad] Endereço:Department of Biochemistry, University of Missouri , Columbia, Missouri 65211, United States.
[Ti] Título:Nuclear Magnetic Resonance Study of RNA Structures at the 3'-End of the Hepatitis C Virus Genome.
[So] Source:Biochemistry;56(37):4972-4984, 2017 Sep 19.
[Is] ISSN:1520-4995
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The 3'-end of the genomic RNA of the hepatitis C virus (HCV) embeds conserved elements that regulate viral RNA synthesis and protein translation by mechanisms that have yet to be elucidated. Previous studies with oligo-RNA fragments have led to multiple, mutually exclusive secondary structure predictions, indicating that HCV RNA structure may be context-dependent. Here we employed a nuclear magnetic resonance (NMR) approach that involves long-range adenosine interaction detection, coupled with site-specific H labeling, to probe the structure of the intact 3'-end of the HCV genome (385 nucleotides). Our data reveal that the 3'-end exists as an equilibrium mixture of two conformations: an open conformation in which the 98 nucleotides of the 3'-tail (3'X) form a two-stem-loop structure with the kissing-loop residues sequestered and a closed conformation in which the 3'X rearranges its structure and forms a long-range kissing-loop interaction with an upstream cis-acting element 5BSL3.2. The long-range kissing species is favored under high-Mg conditions, and the intervening sequences do not affect the equilibrium as their secondary structures remain unchanged. The open and closed conformations are consistent with the reported function regulation of viral RNA synthesis and protein translation, respectively. Our NMR detection of these RNA conformations and the structural equilibrium in the 3'-end of the HCV genome support its roles in coordinating various steps of HCV replication.
[Mh] Termos MeSH primário: Regiões 3´ não Traduzidas
Hepacivirus/química
Modelos Moleculares
RNA Viral/química
[Mh] Termos MeSH secundário: Pareamento de Bases
Ensaio de Desvio de Mobilidade Eletroforética
Genoma Viral
Hepacivirus/genética
Hepacivirus/metabolismo
Magnésio/química
Método de Monte Carlo
Ressonância Magnética Nuclear Biomolecular
Conformação de Ácido Nucleico
Concentração Osmolar
Estabilidade de RNA
RNA Viral/metabolismo
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE; VALIDATION STUDIES
[Nm] Nome de substância:
0 (3' Untranslated Regions); 0 (RNA, Viral); I38ZP9992A (Magnesium)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171018
[Lr] Data última revisão:
171018
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170823
[St] Status:MEDLINE
[do] DOI:10.1021/acs.biochem.7b00573


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[PMID]:28806780
[Au] Autor:Santiago AE; Yan MB; Hazen TH; Sauder B; Meza-Segura M; Rasko DA; Kendall MM; Ruiz-Perez F; Nataro JP
[Ad] Endereço:Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America.
[Ti] Título:The AraC Negative Regulator family modulates the activity of histone-like proteins in pathogenic bacteria.
[So] Source:PLoS Pathog;13(8):e1006545, 2017 Aug.
[Is] ISSN:1553-7374
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The AraC Negative Regulators (ANR) comprise a large family of virulence regulators distributed among diverse clinically important Gram-negative pathogens, including Vibrio spp., Salmonella spp., Shigella spp., Yersinia spp., Citrobacter spp., and pathogenic E. coli strains. We have previously reported broad effects of the ANR members on regulators of the AraC/XylS family. Here, we interrogate possible broader effects of the ANR members on the bacterial transcriptome. Our studies focused on Aar (AggR-activated regulator), an ANR family archetype in enteroaggregative E. coli (EAEC) isolate 042. Transcriptome analysis of EAEC strain 042, 042aar and 042aar(pAar) identified more than 200 genes that were differentially expressed (+/- 1.5 fold, p<0.05). Most of those genes are located on the bacterial chromosome (195 genes, 92.85%), and are associated with regulation, transport, metabolism, and pathogenesis, based on the predicted annotation; a considerable number of Aar-regulated genes encoded for hypothetical proteins (46 genes, 21.9%) and regulatory proteins (25, 11.9%). Notably, the transcriptional expression of three histone-like regulators, H-NS (orf1292), H-NS homolog (orf2834) and StpA, was down-regulated in the absence of aar and may explain some of the effects of Aar on gene expression. By employing a bacterial two-hybrid system, LacZ reporter assays, pull-down and electrophoretic mobility shift assay (EMSA) analysis, we demonstrated that Aar binds directly to H-NS and modulates H-NS-induced gene silencing. Importantly, Aar was highly expressed in the mouse intestinal tract and was found to be necessary for maximal H-NS expression. In conclusion, this work further extends our knowledge of genes under the control of Aar and its biological relevance in vivo.
[Mh] Termos MeSH primário: Fator de Transcrição AraC/metabolismo
Escherichia coli Enteropatogênica/metabolismo
Infecções por Escherichia coli/metabolismo
Regulação Bacteriana da Expressão Gênica/fisiologia
Virulência/fisiologia
[Mh] Termos MeSH secundário: Animais
Ensaio de Desvio de Mobilidade Eletroforética
Escherichia coli Enteropatogênica/patogenicidade
Proteínas de Escherichia coli/metabolismo
Histonas/metabolismo
Camundongos
Camundongos Endogâmicos BALB C
Reação em Cadeia da Polimerase
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (AraC Transcription Factor); 0 (Escherichia coli Proteins); 0 (Histones)
[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:170815
[St] Status:MEDLINE
[do] DOI:10.1371/journal.ppat.1006545



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