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[PMID]: 29267285 [Au] Autor: Colombo DF; Burger L; Baubec T; Schübeler D [Ad] Endereço: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. [Ti] Título: Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content. [So] Source: PLoS Genet;13(12):e1007102, 2017 12. [Is] ISSN: 1553-7404 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Genomic location can inform on potential function and recruitment signals for chromatin-associated proteins. High mobility group (Hmg) proteins are of similar size as histones with Hmga1 and Hmga2 being particularly abundant in replicating normal tissues and in cancerous cells. While several roles for Hmga proteins have been proposed we lack a comprehensive description of their genomic location as a function of chromatin, DNA sequence and functional domains. Here we report such a characterization in mouse embryonic stem cells in which we introduce biotin-tagged constructs of wild-type and DNA-binding domain mutants. Comparative analysis of the genome-wide distribution of Hmga proteins reveals pervasive binding, a feature that critically depends on a functional DNA-binding domain and which is shared by both Hmga proteins. Assessment of the underlying queues instructive for this binding modality identifies AT richness, defined as high frequency of A or T bases, as the major criterion for local binding. Additionally, we show that other chromatin states such as those linked to cis-regulatory regions have little impact on Hmga binding both in stem and differentiated cells. As a consequence, Hmga proteins are preferentially found at AT-rich regions such as constitutively heterochromatic regions but are absent from enhancers and promoters arguing for a limited role in regulating individual genes. In line with this model, we show that genetic deletion of Hmga proteins in stem cells causes limited transcriptional effects and that binding is conserved in neuronal progenitors. Overall our comparative study describing the in vivo binding modality of Hmga1 and Hmga2 identifies the proteins' preference for AT-rich DNA genome-wide and argues against a suggested function of Hmga at regulatory regions. Instead we discover pervasive binding with enrichment at regions of higher AT content irrespective of local variation in chromatin modifications. [Mh] Termos MeSH primário: Sequência Rica em At Proteínas de Grupo de Alta Mobilidade/genética Proteínas de Grupo de Alta Mobilidade/metabolismo [Mh] Termos MeSH secundário: Animais Composição de Bases Sequência de Bases Cromatina/genética Cromatina/metabolismo DNA/química DNA/genética DNA/metabolismo Proteínas de Ligação a DNA/genética Proteínas de Ligação a DNA/metabolismo Células-Tronco Embrionárias/metabolismo Histonas/genética Camundongos Camundongos Endogâmicos C57BL Regiões Promotoras Genéticas Ligação Proteica Sequências Reguladoras de Ácido Nucleico [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T [Nm] Nome de substância: 0 (Chromatin); 0 (DNA-Binding Proteins); 0 (High Mobility Group Proteins); 0 (Histones); 9007-49-2 (DNA) [Em] Mês de entrada: 1802 [Cu] Atualização por classe: 180227 [Lr] Data última revisão: 180227 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 171222 [St] Status: MEDLINE [do] DOI: 10.1371/journal.pgen.1007102

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[PMID]: 28520934 [Au] Autor: Märtens B; Hou L; Amman F; Wolfinger MT; Evguenieva-Hackenberg E; Bläsi U [Ad] Endereço: Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria. [Ti] Título: The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts. [So] Source: Nucleic Acids Res;45(13):7938-7949, 2017 Jul 27. [Is] ISSN: 1362-4962 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: The conserved Sm and Sm-like proteins are involved in different aspects of RNA metabolism. Here, we explored the interactome of SmAP1 and SmAP2 of the crenarchaeon Sulfolobus solfataricus (Sso) to shed light on their physiological function(s). Both, SmAP1 and SmAP2 co-purified with several proteins involved in RNA-processing/modification, translation and protein turnover as well as with components of the exosome involved in 3΄ to 5΄ degradation of RNA. In follow-up studies a direct interaction with the poly(A) binding and accessory exosomal subunit DnaG was demonstrated. Moreover, elevated levels of both SmAPs resulted in increased abundance of the soluble exosome fraction, suggesting that they affect the subcellular localization of the exosome in the cell. The increased solubility of the exosome was accompanied by augmented levels of RNAs with A-rich tails that were further characterized using RNASeq. Hence, the observation that the Sso SmAPs impact on the activity of the exosome revealed a hitherto unrecognized function of SmAPs in archaea. [Mh] Termos MeSH primário: Proteínas Arqueais/metabolismo RNA Arqueal/metabolismo Sulfolobus solfataricus/metabolismo [Mh] Termos MeSH secundário: Sequência Rica em At Proteínas Arqueais/genética DNA Primase/genética DNA Primase/metabolismo Exossomos/genética Exossomos/metabolismo Estabilidade de RNA RNA Arqueal/química RNA Arqueal/genética Solubilidade Sulfolobus solfataricus/genética [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Archaeal Proteins); 0 (RNA, Archaeal); 0 (SmAP protein, Pyrobaculum aerophilum); EC 2.7.7.- (DNA Primase) [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: 170519 [St] Status: MEDLINE [do] DOI: 10.1093/nar/gkx437

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[PMID]: 28180307 [Au] Autor: Shen BW; Heiter DF; Lunnen KD; Wilson GG; Stoddard BL [Ad] Endereço: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, USA. [Ti] Título: DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target. [So] Source: Nucleic Acids Res;45(3):1516-1528, 2017 02 17. [Is] ISSN: 1362-4962 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: R.SwaI, a Type IIP restriction endonuclease, recognizes a palindromic eight base pair (bp) symmetric sequence, 5΄-ATTTAAAT-3΄, and cleaves that target at its center to generate blunt-ended DNA fragments. Here, we report three crystal structures of SwaI: unbound enzyme, a DNA-bound complex with calcium ions; and a DNA-bound, fully cleaved complex with magnesium ions. We compare these structures to two structurally similar 'PD-D/ExK' restriction endonucleases (EcoRV and HincII) that also generate blunt-ended products, and to a structurally distinct enzyme (the HNH endonuclease PacI) that also recognizes an 8-bp target site consisting solely of A:T base pairs. Binding by SwaI induces an extreme bend in the target sequence accompanied by un-pairing and re-ordering of its central A:T base pairs. This result is reminiscent of a more dramatic target deformation previously described for PacI, implying that long A:T-rich target sites might display structural or dynamic behaviors that play a significant role in endonuclease recognition and cleavage. [Mh] Termos MeSH primário: DNA/química DNA/metabolismo Desoxirribonucleases de Sítio Específico do Tipo II/química Desoxirribonucleases de Sítio Específico do Tipo II/metabolismo [Mh] Termos MeSH secundário: Sequência Rica em At Sequência de Aminoácidos Pareamento de Bases Sítios de Ligação Cristalografia por Raios X DNA/genética Desoxirribonucleases de Sítio Específico do Tipo II/genética Modelos Moleculares Mutagênese Sítio-Dirigida Conformação de Ácido Nucleico Conformação Proteica Estrutura Quaternária de Proteína Proteínas Recombinantes/química Proteínas Recombinantes/genética Proteínas Recombinantes/metabolismo Homologia de Sequência de Aminoácidos Eletricidade Estática Homologia Estrutural de Proteína Especificidade por Substrato [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Recombinant Proteins); 9007-49-2 (DNA); EC 3.1.21.- (endodeoxyribonuclease SwaI); EC 3.1.21.4 (Deoxyribonucleases, Type II Site-Specific); EC 3.2.21.- (endodeoxyribonuclease PacI) [Em] Mês de entrada: 1710 [Cu] Atualização por classe: 171030 [Lr] Data última revisão: 171030 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 170210 [St] Status: MEDLINE [do] DOI: 10.1093/nar/gkw1200

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[PMID]: 28095828 [Au] Autor: Kia A; Gloeckner C; Osothprarop T; Gormley N; Bomati E; Stephenson M; Goryshin I; He MM [Ad] Endereço: Department of Protein Engineering, Illumina Inc, 5200 Illumina Way, San Diego, CA, USA. [Ti] Título: Improved genome sequencing using an engineered transposase. [So] Source: BMC Biotechnol;17(1):6, 2017 Jan 17. [Is] ISSN: 1472-6750 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: BACKGROUND: Next-generation sequencing (NGS) has transformed genomic research by reducing turnaround time and cost. However, no major breakthrough has been made in the upstream library preparation methods until the transposase-based Nextera method was invented. Nextera combines DNA fragmentation and barcoding in a single tube reaction and therefore enables a very fast workflow to sequencing-ready DNA libraries within a couple of hours. When compared to the traditional ligation-based methods, transposed-based Nextera has a slight insertion bias. RESULTS: Here we present the discovery of a mutant transposase (Tn5-059) with a lowered GC insertion bias through protein engineering. We demonstrate Tn5-059 reduces AT dropout and increases uniformity of genome coverage in both bacterial genomes and human genome. We also observe higher library diversity generated by Tn5-059 when compared to Nextera v2 for human exomes, which leads to less sequencing and lower cost per genome. In addition, when used for human exomes, Tn5-059 delivers consistent library insert size over a range of input DNA, allowing up to a tenfold variance from the 50 ng input recommendation. CONCLUSIONS: Enhanced DNA input tolerance of Tn5-059 can translate to flexibility and robustness of workflow. DNA input tolerance together with superior uniformity of coverage and lower AT dropouts extend the applications of transposase based library preps. We discuss possible mechanisms of improvements in Tn5-059, and potential advantages of using the new mutant in varieties of applications including microbiome sequencing and chromatin profiling. [Mh] Termos MeSH primário: Mapeamento Cromossômico/métodos DNA/genética Sequenciamento de Nucleotídeos em Larga Escala/métodos Engenharia de Proteínas Análise de Sequência de DNA/métodos Transposases/genética [Mh] Termos MeSH secundário: Sequência Rica em At/genética Reprodutibilidade dos Testes Sensibilidade e Especificidade [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 9007-49-2 (DNA); EC 2.7.7.- (Transposases) [Em] Mês de entrada: 1706 [Cu] Atualização por classe: 170613 [Lr] Data última revisão: 170613 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 170119 [St] Status: MEDLINE [do] DOI: 10.1186/s12896-016-0326-1

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[PMID]: 28053120 [Au] Autor: Stanage TH; Page AN; Cox MM [Ad] Endereço: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA. [Ti] Título: DNA flap creation by the RarA/MgsA protein of Escherichia coli. [So] Source: Nucleic Acids Res;45(5):2724-2735, 2017 Mar 17. [Is] ISSN: 1362-4962 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: We identify a novel activity of the RarA (also MgsA) protein of Escherichia coli, demonstrating that this protein functions at DNA ends to generate flaps. A AAA+ ATPase in the clamp loader clade, RarA protein is part of a highly conserved family of DNA metabolism proteins. We demonstrate that RarA binds to double-stranded DNA in its ATP-bound state and single-stranded DNA in its apo state. RarA ATPase activity is stimulated by single-stranded DNA gaps and double-stranded DNA ends. At these double-stranded DNA ends, RarA couples the energy of ATP binding and hydrolysis to separating the strands of duplex DNA, creating flaps. We hypothesize that the creation of a flap at the site of a leading strand discontinuity could, in principle, allow DnaB and the associated replisome to continue DNA synthesis without impediment, with leading strand re-priming by DnaG. Replication forks could thus be rescued in a manner that does not involve replisome disassembly or reassembly, albeit with loss of one of the two chromosomal products of a replication cycle. [Mh] Termos MeSH primário: Adenosina Trifosfatases/metabolismo DNA/metabolismo Proteínas de Escherichia coli/metabolismo [Mh] Termos MeSH secundário: Sequência Rica em At Trifosfato de Adenosina/metabolismo DNA/química DNA de Cadeia Simples/metabolismo Escherichia coli/enzimologia [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (DNA, Single-Stranded); 0 (Escherichia coli Proteins); 8L70Q75FXE (Adenosine Triphosphate); 9007-49-2 (DNA); EC 3.6.1.- (Adenosine Triphosphatases); EC 3.6.1.- (MgsA protein, E coli) [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: 170106 [St] Status: MEDLINE [do] DOI: 10.1093/nar/gkw1322

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[PMID]: 28013045 [Au] Autor: Shin M [Ad] Endereço: Department of Microbiology, Kyungpook National University School of Medicine, 680 Gukchaebosang-Ro, Jung-gu, Daegu, 41944, South Korea. Electronic address: shinms@knu.ac.kr. [Ti] Título: The mechanism underlying Ler-mediated alleviation of gene repression by H-NS. [So] Source: Biochem Biophys Res Commun;483(1):392-396, 2017 Jan 29. [Is] ISSN: 1090-2104 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Secretion of effector proteins in Enteropathogeneic Escherichia coli (EPEC) and Enterohemorrhagic Escherichia coli (EHEC) is mediated by a specialized type III secretion system, components of which are encoded in the LEE operons 1 to 5. H-NS, a global repressor in E. coli, silences the expression of LEE operons. Ler, a master regulator in LEE operons, shares 24% amnio acid identity and 44% amino acid similarity to H-NS. Interestingly, rather than a gene silencer, its main role has been characterized as an antagonizing protein that relieves H-NS-mediated transcriptional silencing. In the previous study we reported molecular mechanism for the repression of LEE5 promoter in EPEC and EHEC by H-NS as a protein interaction between upstream DNA-bound H-NS and the αCTD of promoter-bound RNA polymerase. The mechanism underlying Ler-mediated alleviation of the genes repression by H-NS is largely unknown. We examined regulatory effect of these proteins on LEE5p activity using various in vitro tools. Our results revealed that binding affinity of Ler to the LEE5p DNA is about 40 folds greater than that of H-NS as determined by surface plasmon resonance. We verified that Ler binding removed H-NS bound to the same stretch of DNA on LEE5 promoter resulting in a derepression. [Mh] Termos MeSH primário: Proteínas de Escherichia coli/genética Escherichia coli/genética Proteínas de Fímbrias/genética Transativadores/genética [Mh] Termos MeSH secundário: Sequência Rica em At Proteínas de Escherichia coli/metabolismo Proteínas de Fímbrias/metabolismo Regulação Bacteriana da Expressão Gênica Regiões Promotoras Genéticas Ressonância de Plasmônio de Superfície Transativadores/metabolismo Transcrição Genética [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Escherichia coli Proteins); 0 (FimG protein, E coli); 0 (Ler protein, E coli); 0 (Trans-Activators); 147680-16-8 (Fimbriae Proteins) [Em] Mês de entrada: 1706 [Cu] Atualização por classe: 170613 [Lr] Data última revisão: 170613 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 161226 [St] Status: MEDLINE

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[PMID]: 27932420 [Au] Autor: Figueroa-Martinez F; Nedelcu AM; Smith DR; Reyes-Prieto A [Ad] Endereço: Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada E3B 5A3 (F.F.-M., A.M.N., A.R.-P.). [Ti] Título: The Plastid Genome of Polytoma uvella Is the Largest Known among Colorless Algae and Plants and Reflects Contrasting Evolutionary Paths to Nonphotosynthetic Lifestyles. [So] Source: Plant Physiol;173(2):932-943, 2017 Feb. [Is] ISSN: 1532-2548 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: The loss of photosynthesis is frequently associated with parasitic or pathogenic lifestyles, but it also can occur in free-living, plastid-bearing lineages. A common consequence of becoming nonphotosynthetic is the reduction in size and gene content of the plastid genome. In exceptional circumstances, it can even result in the complete loss of the plastid DNA (ptDNA) and its associated gene expression system, as reported recently in several lineages, including the nonphotosynthetic green algal genus Polytomella Closely related to Polytomella is the polyphyletic genus Polytoma, the members of which lost photosynthesis independently of Polytomella Species from both genera are free-living organisms that contain nonphotosynthetic plastids, but unlike Polytomella, Polytoma members have retained a genome in their colorless plastid. Here, we present the plastid genome of Polytoma uvella: to our knowledge, the first report of ptDNA from a nonphotosynthetic chlamydomonadalean alga. The P. uvella ptDNA contains 25 protein-coding genes, most of which are related to gene expression and none are connected to photosynthesis. However, despite its reduced coding capacity, the P. uvella ptDNA is inflated with short repeats and is tens of kilobases larger than the ptDNAs of its closest known photosynthetic relatives, Chlamydomonas leiostraca and Chlamydomonas applanata In fact, at approximately 230 kb, the ptDNA of P. uvella represents the largest plastid genome currently reported from a nonphotosynthetic alga or plant. Overall, the P. uvella and Polytomella plastid genomes reveal two very different evolutionary paths following the loss of photosynthesis: expansion and complete deletion, respectively. We hypothesize that recombination-based DNA-repair mechanisms are at least partially responsible for the different evolutionary outcomes observed in such closely related nonphotosynthetic algae. [Mh] Termos MeSH primário: Evolução Biológica Clorófitas/genética Genomas de Plastídeos Fotossíntese/genética [Mh] Termos MeSH secundário: Sequência Rica em At/genética Sequência de Bases Sequência Conservada/genética DNA de Cloroplastos/genética Funções Verossimilhança Filogenia [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (DNA, Chloroplast) [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: 161210 [St] Status: MEDLINE [do] DOI: 10.1104/pp.16.01628

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[PMID]: 27721016 [Au] Autor: Porquier A; Morgant G; Moraga J; Dalmais B; Luyten I; Simon A; Pradier JM; Amselem J; Collado IG; Viaud M [Ad] Endereço: Université Paris-Sud, 91405 Orsay, France; UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France. [Ti] Título: The botrydial biosynthetic gene cluster of Botrytis cinerea displays a bipartite genomic structure and is positively regulated by the putative Zn(II) Cys transcription factor BcBot6. [So] Source: Fungal Genet Biol;96:33-46, 2016 Nov. [Is] ISSN: 1096-0937 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Botrydial (BOT) is a non-host specific phytotoxin produced by the polyphagous phytopathogenic fungus Botrytis cinerea. The genomic region of the BOT biosynthetic gene cluster was investigated and revealed two additional genes named Bcbot6 and Bcbot7. Analysis revealed that the G+C/A+T-equilibrated regions that contain the Bcbot genes alternate with A+T-rich regions made of relics of transposable elements that have undergone repeat-induced point mutations (RIP). Furthermore, BcBot6, a Zn(II) Cys putative transcription factor was identified as a nuclear protein and the major positive regulator of BOT biosynthesis. In addition, the phenotype of the ΔBcbot6 mutant indicated that BcBot6 and therefore BOT are dispensable for the development, pathogenicity and response to abiotic stresses in the B. cinerea strain B05.10. Finally, our data revealed that B. pseudocinerea, that is also polyphagous and lives in sympatry with B. cinerea, lacks the ability to produce BOT. Identification of BcBot6 as the major regulator of BOT synthesis is the first step towards a comprehensive understanding of the complete regulation network of BOT synthesis and of its ecological role in the B. cinerea life cycle. [Mh] Termos MeSH primário: Aldeídos/metabolismo Botrytis/genética Compostos Bicíclicos com Pontes/metabolismo Proteínas Fúngicas/metabolismo Regulação Fúngica da Expressão Gênica Família Multigênica Fatores de Transcrição/metabolismo [Mh] Termos MeSH secundário: Sequência Rica em At Botrytis/metabolismo Botrytis/patogenicidade Elementos de DNA Transponíveis DNA Fúngico Proteínas Fúngicas/genética Proteínas Nucleares/genética Proteínas Nucleares/metabolismo Virulência [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Aldehydes); 0 (Bridged Bicyclo Compounds); 0 (DNA Transposable Elements); 0 (DNA, Fungal); 0 (Fungal Proteins); 0 (Nuclear Proteins); 0 (Transcription Factors); 0 (botrydial) [Em] Mês de entrada: 1710 [Cu] Atualização por classe: 171017 [Lr] Data última revisão: 171017 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 161011 [St] Status: MEDLINE

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[PMID]: 27720010 [Au] Autor: Navarre WW [Ad] Endereço: University of Toronto, Toronto, ON, Canada. Electronic address: william.navarre@utoronto.ca. [Ti] Título: The Impact of Gene Silencing on Horizontal Gene Transfer and Bacterial Evolution. [So] Source: Adv Microb Physiol;69:157-186, 2016. [Is] ISSN: 2162-5468 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: The H-NS family of DNA-binding proteins is the subject of intense study due to its important roles in the regulation of horizontally acquired genes critical for virulence, antibiotic resistance, and metabolism. Xenogeneic silencing proteins, typified by the H-NS protein of Escherichia coli, specifically target and downregulate expression from AT-rich genes by selectively recognizing specific structural features unique to the AT-rich minor groove. In doing so, these proteins facilitate bacterial evolution; enabling these cells to engage in horizontal gene transfer while buffering potential any detrimental fitness consequences that may result from it. Xenogeneic silencing and counter-silencing explain how bacterial cells can evolve effective gene regulatory strategies in the face of rampant gene gain and loss and it has extended our understanding of bacterial gene regulation beyond the classic operon model. Here we review the structures and mechanisms of xenogeneic silencers as well as their impact on bacterial evolution. Several H-NS-like proteins appear to play a role in facilitating gene transfer by other mechanisms including by regulating transposition, conjugation, and participating in the activation of virulence loci like the locus of enterocyte effacement pathogenicity island of pathogenic strains of E. coli. Evidence suggests that the critical determinants that dictate whether an H-NS-like protein will be a silencer or will perform a different function do not lie in the DNA-binding domain but, rather, in the domains that control oligomerization. This suggests that H-NS-like proteins are transcription factors that both recognize and alter the shape of DNA to exert specific effects that include but are not limited to gene silencing. [Mh] Termos MeSH primário: Escherichia coli/genética Evolução Molecular Regulação Bacteriana da Expressão Gênica/genética Inativação Gênica/fisiologia Transferência Genética Horizontal/genética [Mh] Termos MeSH secundário: Sequência Rica em At/genética Proteínas de Bactérias/genética Proteínas de Ligação a DNA/genética Escherichia coli/patogenicidade Proteínas de Escherichia coli/genética Redes Reguladoras de Genes/genética Estrutura Terciária de Proteína/genética Proteínas Repressoras/genética Transativadores/genética Virulência/genética [Pt] Tipo de publicação: JOURNAL ARTICLE; REVIEW [Nm] Nome de substância: 0 (Bacterial Proteins); 0 (DNA-Binding Proteins); 0 (Escherichia coli Proteins); 0 (H-NS protein, bacteria); 0 (Ler protein, E coli); 0 (Repressor Proteins); 0 (Trans-Activators); 0 (YdgT protein, E coli); 0 (hha protein, E coli) [Em] Mês de entrada: 1703 [Cu] Atualização por classe: 170313 [Lr] Data última revisão: 170313 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 161011 [St] Status: MEDLINE

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[PMID]: 27492287 [Au] Autor: Pfeifer E; Hünnefeld M; Popa O; Polen T; Kohlheyer D; Baumgart M; Frunzke J [Ad] Endereço: Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany. [Ti] Título: Silencing of cryptic prophages in Corynebacterium glutamicum. [So] Source: Nucleic Acids Res;44(21):10117-10131, 2016 Dec 01. [Is] ISSN: 1362-4962 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: DNA of viral origin represents a ubiquitous element of bacterial genomes. Its integration into host regulatory circuits is a pivotal driver of microbial evolution but requires the stringent regulation of phage gene activity. In this study, we describe the nucleoid-associated protein CgpS, which represents an essential protein functioning as a xenogeneic silencer in the Gram-positive Corynebacterium glutamicum CgpS is encoded by the cryptic prophage CGP3 of the C. glutamicum strain ATCC 13032 and was first identified by DNA affinity chromatography using an early phage promoter of CGP3. Genome-wide profiling of CgpS binding using chromatin affinity purification and sequencing (ChAP-Seq) revealed its association with AT-rich DNA elements, including the entire CGP3 prophage region (187 kbp), as well as several other elements acquired by horizontal gene transfer. Countersilencing of CgpS resulted in a significantly increased induction frequency of the CGP3 prophage. In contrast, a strain lacking the CGP3 prophage was not affected and displayed stable growth. In a bioinformatics approach, cgpS orthologs were identified primarily in actinobacterial genomes as well as several phage and prophage genomes. Sequence analysis of 618 orthologous proteins revealed a strong conservation of the secondary structure, supporting an ancient function of these xenogeneic silencers in phage-host interaction. [Mh] Termos MeSH primário: Corynebacterium glutamicum/genética Prófagos/genética Proteínas Virais/metabolismo [Mh] Termos MeSH secundário: Sequência Rica em At Actinobacteria/genética DNA Viral/metabolismo Inativação Gênica Transferência Genética Horizontal Genoma Bacteriano Estudo de Associação Genômica Ampla Prófagos/fisiologia Homologia de Sequência de Aminoácidos Proteínas Virais/genética [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (DNA, Viral); 0 (Viral Proteins) [Em] Mês de entrada: 1706 [Cu] Atualização por classe: 170613 [Lr] Data última revisão: 170613 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 160806 [St] Status: MEDLINE

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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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