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[PMID]: 29066303 [Au] Autor: Thakur Z; Saini V; Arya P; Kumar A; Mehta PK [Ad] Endereço: Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India. [Ti] Título: Computational insights into promoter architecture of toxin-antitoxin systems of Mycobacterium tuberculosis. [So] Source: Gene;641:161-171, 2018 Jan 30. [Is] ISSN: 1879-0038 [Cp] País de publicação: Netherlands [La] Idioma: eng [Ab] Resumo: Toxin-antitoxin (TA) systems are two component genetic modules widespread in many bacterial genomes, including Mycobacterium tuberculosis (Mtb). The TA systems play a significant role in biofilm formation, antibiotic tolerance and persistence of pathogen inside the host cells. Deciphering regulatory motifs of Mtb TA systems is the first essential step to understand their transcriptional regulation. In this study, in silico approaches, that is, the knowledge based motif discovery and de novo motif discovery were used to identify the regulatory motifs of 79 Mtb TA systems. The knowledge based motif discovery approach was used to design a Perl based bio-tool Mtb-sig-miner available at (https://github.com/zoozeal/Mtb-sig-miner), which could successfully detect sigma (σ) factor specific regulatory motifs in the promoter region of Mtb TA modules. The manual curation of Mtb-sig-miner output hits revealed that the majority of them possessed σ regulatory motif in their promoter region. On the other hand, de novo approach resulted in the identification of a novel conserved motif [(T/A)(G/T)NTA(G/C)(C/A)AT(C/A)] within the promoter region of 14 Mtb TA systems. The identified conserved motif was also validated for its activity as conserved core region of operator sequence of corresponding TA system by molecular docking studies. The strong binding of respective antitoxin/toxin with the identified novel conserved motif reflected the validation of identified motif as the core region of operator sequence of respective TA systems. These findings provide computational insight to understand the transcriptional regulation of Mtb TA systems. [Mh] Termos MeSH primário: Antitoxinas/genética Genoma Bacteriano/genética Mycobacterium tuberculosis/genética Regiões Promotoras Genéticas/genética Sistemas Toxina-Antitoxina/genética [Mh] Termos MeSH secundário: Toxinas Bacterianas/genética Biofilmes/crescimento & desenvolvimento Biologia Computacional/métodos Simulação por Computador Farmacorresistência Bacteriana/genética Redes Reguladoras de Genes/genética Simulação de Acoplamento Molecular/métodos Regiões Operadoras Genéticas/genética [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Antitoxins); 0 (Bacterial Toxins) [Em] Mês de entrada: 1711 [Cu] Atualização por classe: 171128 [Lr] Data última revisão: 171128 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 171026 [St] Status: MEDLINE

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[PMID]: 28488852 [Au] Autor: Chang AT; Tran M; Nikonowicz EP [Ad] Endereço: Department of BioSciences, Rice University , Houston, Texas 77251-1892, United States. [Ti] Título: Structure and Dynamics of the Tetra-A Loop and (A-A)-U Sequence Motif within the Coliphage GA Replicase RNA Operator. [So] Source: Biochemistry;56(21):2690-2700, 2017 May 30. [Is] ISSN: 1520-4995 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: The three-dimensional structure of a RNA hairpin containing the RNA operator binding site for bacteriophage GA coat protein is presented. The phage GA operator contains the asymmetric (A-A)-U sequence motif and is capped by a four-adenine (tetra-A) loop. The uridine of the (A-A)-U motif preferentially pairs with the 5'-proximal cross-strand adenine, and the 3'-proximal adenine stacks into the helix. The tetra-A loop is well-ordered with adenine residues 2-4 forming a 3' stack. This loop conformation stands in contrast to the structure of the 5'-AUUA loop of the related phage MS2 operator in which residues 1 and 2 form a 5' stack. The context dependence of the (A-A)-U sequence motif conformation was examined using structures of 76 unique occurrences from the Protein Data Bank. The motif almost always has one adenine bulged and the other adenine adopting an A-U base pair. In the case in which the (A-A)-U motif is flanked by only one Watson-Crick base pair, the adenine adjacent to the flanking base pair tends to bulge; 80% of motifs with a 3' flanking pair have a 3' bulged adenine, and 84% of motifs with a 5' flanking pair have a 5' bulged adenine. The frequencies of 3'- and 5'-proximal adenines bulging are 33 and 67%, respectively, when the (A-A)-U motif is flanked by base pairs on both sides. Although a 3' flanking cytidine correlates (88%) with bulging of the 5'-proximal adenine, no strict dependence on flanking nucleotide identity was identified for the 5' side. [Mh] Termos MeSH primário: Colífagos/enzimologia Colífagos/genética Simulação de Dinâmica Molecular Conformação de Ácido Nucleico Motivos de Nucleotídeos Regiões Operadoras Genéticas/genética RNA Replicase/metabolismo RNA/química [Mh] Termos MeSH secundário: Sequência de Bases Modelos Moleculares RNA/genética [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 63231-63-0 (RNA); EC 2.7.7.48 (RNA Replicase) [Em] Mês de entrada: 1706 [Cu] Atualização por classe: 170623 [Lr] Data última revisão: 170623 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 170511 [St] Status: MEDLINE [do] DOI: 10.1021/acs.biochem.7b00123

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[PMID]: 28334797 [Au] Autor: Vandervelde A; Drobnak I; Hadzi S; Sterckx YG; Welte T; De Greve H; Charlier D; Efremov R; Loris R; Lah J [Ad] Endereço: Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium. [Ti] Título: Molecular mechanism governing ratio-dependent transcription regulation in the ccdAB operon. [So] Source: Nucleic Acids Res;45(6):2937-2950, 2017 Apr 07. [Is] ISSN: 1362-4962 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: Bacteria can become transiently tolerant to several classes of antibiotics. This phenomenon known as persistence is regulated by small genetic elements called toxin-antitoxin modules with intricate yet often poorly understood self-regulatory features. Here, we describe the structures of molecular complexes and interactions that drive the transcription regulation of the ccdAB toxin-antitoxin module. Low specificity and affinity of the antitoxin CcdA2 for individual binding sites on the operator are enhanced by the toxin CcdB2, which bridges the CcdA2 dimers. This results in a unique extended repressing complex that spirals around the operator and presents equally spaced DNA binding sites. The multivalency of binding sites induces a digital on-off switch for transcription, regulated by the toxin:antitoxin ratio. The ratio at which this switch occurs is modulated by non-specific interactions with the excess chromosomal DNA. Altogether, we present the molecular mechanisms underlying the ratio-dependent transcriptional regulation of the ccdAB operon. [Mh] Termos MeSH primário: Proteínas de Bactérias/química Toxinas Bacterianas/química Regulação Bacteriana da Expressão Gênica Óperon Proteínas Repressoras/química Transcrição Genética [Mh] Termos MeSH secundário: Proteínas de Bactérias/genética Proteínas de Bactérias/metabolismo Toxinas Bacterianas/genética Toxinas Bacterianas/metabolismo Sítios de Ligação DNA Bacteriano/química DNA Bacteriano/metabolismo Modelos Moleculares Regiões Operadoras Genéticas Ligação Proteica Domínios Proteicos Multimerização Proteica Proteínas Repressoras/metabolismo [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Bacterial Proteins); 0 (Bacterial Toxins); 0 (CcdA protein, Bacteria); 0 (DNA, Bacterial); 0 (Repressor Proteins) [Em] Mês de entrada: 1708 [Cu] Atualização por classe: 170809 [Lr] Data última revisão: 170809 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 170324 [St] Status: MEDLINE [do] DOI: 10.1093/nar/gkx108

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[PMID]: 28160603 [Au] Autor: Yeo HK; Park YW; Lee JY [Ad] Endereço: Department of Life Science, Dongguk University-Seoul, 32, Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do 10326, Republic of Korea. [Ti] Título: Structural basis of operator sites recognition and effector binding in the TetR family transcription regulator FadR. [So] Source: Nucleic Acids Res;45(7):4244-4254, 2017 Apr 20. [Is] ISSN: 1362-4962 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: FadR is a fatty acyl-CoA dependent transcription factor that regulates genes encoding proteins involved in fatty-acid degradation and synthesis pathways. In this study, the crystal structures of Bacillus halodurans FadR, which belong to the TetR family, have been determined in three different forms: ligand-bound, ligand-free and DNA-bound at resolutions of 1.75, 2.05 and 2.80 Å, respectively. Structural and functional data showed that B. halodurans FadR was bound to its operator site without fatty acyl-CoAs. Structural comparisons among the three different forms of B. halodurans FadR revealed that the movement of DNA binding domains toward the operator DNA was blocked upon binding of ligand molecules. These findings suggest that the TetR family FadR negatively regulates the genes involved in fatty acid metabolism by binding cooperatively to the operator DNA as a dimer of dimers. [Mh] Termos MeSH primário: Proteínas de Bactérias/química DNA Bacteriano/química Regiões Operadoras Genéticas Proteínas Repressoras/química [Mh] Termos MeSH secundário: Bacillus/genética Proteínas de Bactérias/metabolismo DNA Bacteriano/metabolismo Modelos Moleculares Ligação Proteica Conformação Proteica Proteínas Repressoras/metabolismo [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Bacterial Proteins); 0 (DNA, Bacterial); 0 (FadR protein, Bacteria); 0 (Repressor Proteins) [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: 170205 [St] Status: MEDLINE [do] DOI: 10.1093/nar/gkx009

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[PMID]: 28073944 [Au] Autor: Rodionova IA; Vetting MW; Li X; Almo SC; Osterman AL; Rodionov DA [Ad] Endereço: Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA. [Ti] Título: A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea. [So] Source: Nucleic Acids Res;45(7):3785-3799, 2017 Apr 20. [Is] ISSN: 1362-4962 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: Riboflavin (vitamin B2) is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide, which are essential coenzymes in all free-living organisms. Riboflavin biosynthesis in many Bacteria but not in Archaea is controlled by FMN-responsive riboswitches. We identified a novel bifunctional riboflavin kinase/regulator (RbkR), which controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain. Using comparative genomics, we predicted RbkR operator sites and reconstructed RbkR regulons in 94 archaeal genomes. While the identified RbkR operators showed significant variability between archaeal lineages, the conserved core of RbkR regulons includes riboflavin biosynthesis genes, known/predicted vitamin uptake transporters and the rbkR gene. The DNA motifs and CTP-dependent riboflavin kinase activity of two RbkR proteins were experimentally validated in vitro. The DNA binding activity of RbkR was stimulated by CTP and suppressed by FMN, a product of riboflavin kinase. The crystallographic structure of RbkR from Thermoplasma acidophilum was determined in complex with CTP and its DNA operator revealing key residues for operator and ligand recognition. Overall, this study contributes to our understanding of metabolic and regulatory networks for vitamin homeostasis in Archaea. [Mh] Termos MeSH primário: Archaea/genética Proteínas Arqueais/metabolismo Fosfotransferases (Aceptor do Grupo Álcool)/metabolismo Riboflavina/metabolismo Fatores de Transcrição/metabolismo [Mh] Termos MeSH secundário: Archaea/enzimologia Archaea/metabolismo Proteínas Arqueais/química DNA Arqueal/química DNA Arqueal/metabolismo Evolução Molecular Genoma Arqueal Regiões Operadoras Genéticas Fosfotransferases (Aceptor do Grupo Álcool)/química Domínios Proteicos Regulon Fatores de Transcrição/química [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Archaeal Proteins); 0 (DNA, Archaeal); 0 (Transcription Factors); EC 2.7.1.- (Phosphotransferases (Alcohol Group Acceptor)); EC 2.7.1.26 (riboflavin kinase); TLM2976OFR (Riboflavin) [Em] Mês de entrada: 1710 [Cu] Atualização por classe: 171005 [Lr] Data última revisão: 171005 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 170112 [St] Status: MEDLINE [do] DOI: 10.1093/nar/gkw1331

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[PMID]: 27998932 [Au] Autor: Bendtsen KL; Xu K; Luckmann M; Winther KS; Shah SA; Pedersen CNS; Brodersen DE [Ad] Endereço: Centre for Bacterial Stress Response and Persistence. [Ti] Título: Toxin inhibition in C. crescentus VapBC1 is mediated by a flexible pseudo-palindromic protein motif and modulated by DNA binding. [So] Source: Nucleic Acids Res;45(5):2875-2886, 2017 Mar 17. [Is] ISSN: 1362-4962 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: Expression of bacterial type II toxin-antitoxin (TA) systems is regulated at the transcriptional level through direct binding of the antitoxin to pseudo-palindromic sequences on operator DNA. In this context, the toxin functions as a co-repressor by stimulating DNA binding through direct interaction with the antitoxin. Here, we determine crystal structures of the complete 90 kDa heterooctameric VapBC1 complex from Caulobacter crescentus CB15 both in isolation and bound to its cognate DNA operator sequence at 1.6 and 2.7 Å resolution, respectively. DNA binding is associated with a dramatic architectural rearrangement of conserved TA interactions in which C-terminal extended structures of the antitoxin VapB1 swap positions to interlock the complex in the DNA-bound state. We further show that a pseudo-palindromic protein sequence in the antitoxin is responsible for this interaction and required for binding and inactivation of the VapC1 toxin dimer. Sequence analysis of 4127 orthologous VapB sequences reveals that such palindromic protein sequences are widespread and unique to bacterial and archaeal VapB antitoxins suggesting a general principle governing regulation of VapBC TA systems. Finally, a structure of C-terminally truncated VapB1 bound to VapC1 reveals discrete states of the TA interaction that suggest a structural basis for toxin activation in vivo. [Mh] Termos MeSH primário: Proteínas de Bactérias/química Toxinas Bacterianas/química Caulobacter crescentus/genética DNA Bacteriano/química Proteínas de Ligação a DNA/química Glicoproteínas de Membrana/química Regiões Operadoras Genéticas [Mh] Termos MeSH secundário: Motivos de Aminoácidos Proteínas de Bactérias/metabolismo Toxinas Bacterianas/antagonistas & inibidores Toxinas Bacterianas/metabolismo DNA Bacteriano/metabolismo Proteínas de Ligação a DNA/metabolismo Glicoproteínas de Membrana/metabolismo Modelos Moleculares Conformação de Ácido Nucleico Ligação Proteica Domínios Proteicos [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Bacterial Proteins); 0 (Bacterial Toxins); 0 (DNA, Bacterial); 0 (DNA-Binding Proteins); 0 (Membrane Glycoproteins); 147571-32-2 (VapB protein, Bacteria) [Em] Mês de entrada: 1708 [Cu] Atualização por classe: 170808 [Lr] Data última revisão: 170808 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 161222 [St] Status: MEDLINE [do] DOI: 10.1093/nar/gkw1266

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[PMID]: 27670714 [Au] Autor: Lewis DEA; Gussin GN; Adhya S [Ad] Endereço: Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA. [Ti] Título: New Insights into the Phage Genetic Switch: Effects of Bacteriophage Lambda Operator Mutations on DNA Looping and Regulation of P , P , and P . [So] Source: J Mol Biol;428(22):4438-4456, 2016 Nov 06. [Is] ISSN: 1089-8638 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: One of the best understood systems in genetic regulatory biology is the so-called "genetic switch" that determines the choice the phage-encoded CI repressor binds cooperatively to tripartite operators, O and O , in a defined pattern, thus blocking the transcription at two lytic promoters, P and P , and auto-regulating the promoter, P , which directs CI synthesis by the prophage. Fine-tuning of the maintenance of lysogeny is facilitated by interactions between CI dimers bound to O and O through the formation of a loop by the intervening DNA segment. By using a purified in vitro transcription system, we have genetically dissected the roles of individual operator sites in the formation of the DNA loop and thus have gained several new and unexpected insights into the system. First, although both O and O are tripartite, the presence of only a single active CI binding site in one of the two operators is sufficient for DNA loop formation. Second, in P , unlike in P , the promoter distal operator site, O 3, is sufficient to directly repress P . Third, DNA looping mediated by the formation of CI octamers arising through the interaction of pairs of dimers bound to adjacent operator sites in O and O does not require O and O to be aligned "in register", that is, CI bound to "out-of-register" sub-operators, for example, O 1~O 2 and O 2~O 3, can also mediate loop formation. Finally, based on an examination of the mechanism of activation of P when only O 1 or O 2 are wild type, we hypothesize that RNA polymerase bound at P interferes with DNA loop formation. Thus, the formation of DNA loops involves potential interactions between proteins bound at numerous cis-acting sites, which therefore very subtly contribute to the regulation of the "switch". [Mh] Termos MeSH primário: Bacteriófago lambda/genética DNA Viral/genética Regulação Viral da Expressão Gênica Conformação de Ácido Nucleico Regiões Operadoras Genéticas Regiões Promotoras Genéticas [Mh] Termos MeSH secundário: Bacteriófago lambda/fisiologia DNA Viral/metabolismo Lisogenia Mutação Ligação Proteica Proteínas Repressoras/metabolismo Transcrição Genética Ativação Viral [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (DNA, Viral); 0 (Repressor Proteins) [Em] Mês de entrada: 1706 [Cu] Atualização por classe: 170917 [Lr] Data última revisão: 170917 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 160928 [St] Status: MEDLINE

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[PMID]: 27601326 [Au] Autor: Yang J; Zhou K; Liu P; Dong Y; Gao Z; Zhang J; Liu Q [Ad] Endereço: School of Life Sciences, University of Dalian Science and Technology, Dalian, Liaolin Province, 230027, People's Republic of China. [Ti] Título: Structural insight into the E. coli HigBA complex. [So] Source: Biochem Biophys Res Commun;478(4):1521-7, 2016 09 30. [Is] ISSN: 1090-2104 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: The toxin-antitoxin system is ubiquitously existed in bacteria and archaea, performing a wide variety of functions modulating cell fitness in response to environmental cues. In this report, we solved the crystal structure of the toxin-antitoxin HigBA complex from E. coli K-12 to 2.7 Å resolution. The crystal structure of the HigBA complex displays a hetero-tetramer (HigBA)2 form comprised by two HigB and two HigA subunits. Each toxin HigB resumes a microbial RNase T1 fold, characteristic of a three antiparallel ß-sheet core shielded by a few α-helices at either side. Each antitoxin HigA composed of all α-helices resembles a "C"-shaped clamp nicely encompassing a HigB in the (HigBA)2 complex. Two HigA monomers dimerize at their N-terminal domain. We showed that HigA helix α1 was essential for HigA dimerization and the hetero-tetramer (HigBA)2 formation, but not for a hetero-dimeric HigBA formation. HigA dimerization mediated by helix α1 was dispensable for DNA-binding, as a heterodimeric HigBA complex still bound to the higBA operator in vitro. The HigA C-terminal domain with a helix-turn-helix fold was essential for DNA binding. We also defined two palindromes in higBA operator specifically recognized by HigA and HigBA in vitro. [Mh] Termos MeSH primário: Proteínas de Escherichia coli/química Escherichia coli/metabolismo [Mh] Termos MeSH secundário: Sequência de Bases Domínio Catalítico Cristalografia por Raios X DNA Bacteriano/metabolismo Ensaio de Desvio de Mobilidade Eletroforética Modelos Moleculares Peso Molecular Regiões Operadoras Genéticas/genética Regiões Promotoras Genéticas Ligação Proteica Domínios Proteicos Multimerização Proteica Estrutura Secundária de Proteína [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T [Nm] Nome de substância: 0 (DNA, Bacterial); 0 (Escherichia coli Proteins); 0 (HigA protein, E coli); 0 (HigB protein, E coli) [Em] Mês de entrada: 1705 [Cu] Atualização por classe: 171127 [Lr] Data última revisão: 171127 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 160908 [St] Status: MEDLINE

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[PMID]: 27527206 [Au] Autor: Hammerl JA; Jäckel C; Lanka E; Roschanski N; Hertwig S [Ad] Endereço: Bundesinstitut für Risikobewertung (Federal Institute for Risk Assessment), Department of Biological Safety, Diedersdorfer Weg 1, D-12277 Berlin, Germany. jens-andre.hammerl@bfr.bund.de. [Ti] Título: Binding Specificities of the Telomere Phage Ï•KO2 Prophage Repressor CB and Lytic Repressor Cro. [So] Source: Viruses;8(8), 2016 Aug 03. [Is] ISSN: 1999-4915 [Cp] País de publicação: Switzerland [La] Idioma: eng [Ab] Resumo: Temperate bacteriophages possess a genetic switch which regulates the lytic and lysogenic cycle. The genomes of the temperate telomere phages N15, PY54, and Ï•KO2 harbor a primary immunity region (immB) comprising genes for the prophage repressor (cI or cB), the lytic repressor (cro) and a putative antiterminator (q). The roles of these products are thought to be similar to those of the lambda proteins CI (CI prophage repressor), Cro (Cro repressor), and Q (antiterminator Q), respectively. Moreover, the gene order and the location of several operator sites in the prototype telomere phage N15 and in Ï•KO2 are reminiscent of lambda-like phages. We determined binding sites of the Ï•KO2 prophage repressor CB and lytic repressor Cro on the Ï•KO2 genome in detail by electrophoretic mobility shift assay (EMSA) studies. Unexpectedly, Ï•KO2 CB and Cro revealed different binding specificities. CB was bound to three OR operators in the intergenic region between cB and cro, two OL operators between cB and the replication gene repA and even to operators of N15. Cro bound exclusively to the 16 bp operator site OR3 upstream of the Ï•KO2 prophage repressor gene. The Ï•KO2 genes cB and cro are regulated by several strong promoters overlapping with the OR operators. The data suggest that Cro represses cB transcription but not its own synthesis, as already reported for PY54 Cro. Thus, not only PY54, but also phage Ï•KO2 possesses a genetic switch that diverges significantly from the switch of lambda-like phages. [Mh] Termos MeSH primário: Bacteriófagos/enzimologia DNA Viral/metabolismo Proteínas Repressoras/metabolismo Proteínas Virais/metabolismo [Mh] Termos MeSH secundário: Bacteriófagos/genética Sítios de Ligação Ensaio de Desvio de Mobilidade Eletroforética Ordem dos Genes Genes Virais Regiões Operadoras Genéticas Regiões Promotoras Genéticas Ligação Proteica Especificidade por Substrato Sintenia [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (DNA, Viral); 0 (Repressor Proteins); 0 (Viral Proteins) [Em] Mês de entrada: 1709 [Cu] Atualização por classe: 170926 [Lr] Data última revisão: 170926 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 160817 [St] Status: MEDLINE

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[PMID]: 27307602 [Au] Autor: Couñago RM; Chen NH; Chang CW; Djoko KY; McEwan AG; Kobe B [Ad] Endereço: School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld 4072, Australia Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld 4072, Australia Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia r [Ti] Título: Structural basis of thiol-based regulation of formaldehyde detoxification in H. influenzae by a MerR regulator with no sensor region. [So] Source: Nucleic Acids Res;44(14):6981-93, 2016 Aug 19. [Is] ISSN: 1362-4962 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: Pathogenic bacteria such as Haemophilus influenzae, a major cause of lower respiratory tract diseases, must cope with a range of electrophiles generated in the host or by endogenous metabolism. Formaldehyde is one such compound that can irreversibly damage proteins and DNA through alkylation and cross-linking and interfere with redox homeostasis. Its detoxification operates under the control of HiNmlR, a protein from the MerR family that lacks a specific sensor region and does not bind metal ions. We demonstrate that HiNmlR is a thiol-dependent transcription factor that modulates H. influenzae response to formaldehyde, with two cysteine residues (Cys54 and Cys71) identified to be important for its response against a formaldehyde challenge. We obtained crystal structures of HiNmlR in both the DNA-free and two DNA-bound forms, which suggest that HiNmlR enhances target gene transcription by twisting of operator DNA sequences in a two-gene operon containing overlapping promoters. Our work provides the first structural insights into the mechanism of action of MerR regulators that lack sensor regions. [Mh] Termos MeSH primário: Proteínas de Bactérias/metabolismo Proteínas de Ligação a DNA/metabolismo Formaldeído/metabolismo Haemophilus influenzae/metabolismo Compostos de Sulfidrila/metabolismo [Mh] Termos MeSH secundário: Proteínas de Bactérias/química Cristalografia por Raios X DNA Bacteriano/química DNA Bacteriano/metabolismo Proteínas de Ligação a DNA/química RNA Polimerases Dirigidas por DNA/metabolismo Regulação Bacteriana da Expressão Gênica Haemophilus influenzae/genética Inativação Metabólica/genética Cinética Modelos Moleculares Regiões Operadoras Genéticas/genética Regiões Promotoras Genéticas Ligação Proteica Relação Estrutura-Atividade Fatores de Transcrição/metabolismo Transcrição Genética [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Bacterial Proteins); 0 (DNA, Bacterial); 0 (DNA-Binding Proteins); 0 (MerR protein, Bacteria); 0 (Sulfhydryl Compounds); 0 (Transcription Factors); 1HG84L3525 (Formaldehyde); EC 2.7.7.6 (DNA-Directed RNA Polymerases) [Em] Mês de entrada: 1706 [Cu] Atualização por classe: 170605 [Lr] Data última revisão: 170605 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 160617 [St] Status: MEDLINE [do] DOI: 10.1093/nar/gkw543

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1			PalavrasDescritor de assuntoDescritor de assunto primárioLimitesAutorPalavras do títuloPalavras do resumoIdiomaPaís de publicaçãoNome de substânciaNome de pessoa como assuntoRevistaAssunto de RevistaISSNTipo de publicaçãoIdentificador únicoMês de entradaAno de publicaçãoTexto completoAtualização por classeCategoria DeCSCategoria DeCS explodidaCategoria CID-10SubSetsPais de AfiliaçãoAfiliaçãoAfiliação 2
2	and or and not		PalavrasDescritor de assuntoDescritor de assunto primárioLimitesAutorPalavras do títuloPalavras do resumoIdiomaPaís de publicaçãoNome de substânciaNome de pessoa como assuntoRevistaAssunto de RevistaISSNTipo de publicaçãoIdentificador únicoMês de entradaAno de publicaçãoTexto completoAtualização por classeCategoria DeCSCategoria DeCS explodidaCategoria CID-10SubSetsPais de AfiliaçãoAfiliaçãoAfiliação 2
3	and or and not		PalavrasDescritor de assuntoDescritor de assunto primárioLimitesAutorPalavras do títuloPalavras do resumoIdiomaPaís de publicaçãoNome de substânciaNome de pessoa como assuntoRevistaAssunto de RevistaISSNTipo de publicaçãoIdentificador únicoMês de entradaAno de publicaçãoTexto completoAtualização por classeCategoria DeCSCategoria DeCS explodidaCategoria CID-10SubSetsPais de AfiliaçãoAfiliaçãoAfiliação 2

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