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[PMID]:28189782
[Au] Autor:Gomes-Neto JC; Mantz S; Held K; Sinha R; Segura Munoz RR; Schmaltz R; Benson AK; Walter J; Ramer-Tait AE
[Ad] Endereço:Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA.
[Ti] Título:A real-time PCR assay for accurate quantification of the individual members of the Altered Schaedler Flora microbiota in gnotobiotic mice.
[So] Source:J Microbiol Methods;135:52-62, 2017 Apr.
[Is] ISSN:1872-8359
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Changes in the gastrointestinal microbial community are frequently associated with chronic diseases such as Inflammatory Bowel Diseases. However, understanding the relationship of any individual taxon within the community to host physiology is made complex due to the diversity and individuality of the gut microbiota. Defined microbial communities such as the Altered Schaedler Flora (ASF) help alleviate the challenges of a diverse microbiota by allowing one to interrogate the relationship between individual bacterial species and host responses. An important aspect of studying these relationships with defined microbial communities is the ability to measure the population abundance and dynamics of each member. Herein, we describe the development of an improved ASF species-specific and sensitive real-time quantitative polymerase chain reaction (qPCR) for use with SYBR Green chemistry to accurately assess individual ASF member abundance. This approach targets hypervariable regions V1 through V3 of the 16S rRNA gene of each ASF taxon to enhance assay specificity. We demonstrate the reproducibility, sensitivity and application of this new method by quantifying each ASF bacterium in two inbred mouse lines. We also used it to assess changes in ASF member abundance before and after acute antibiotic perturbation of the community as well as in mice fed two different diets. Additionally, we describe a nested PCR assay for the detection of lowly abundant ASF members. Altogether, this improved qPCR method will facilitate gnotobiotic research involving the ASF community by allowing for reproducible quantification of its members under various physiological conditions.
[Mh] Termos MeSH primário: Bactérias/genética
DNA Bacteriano/genética
DNA Bacteriano/isolamento & purificação
Microbioma Gastrointestinal/genética
Vida Livre de Germes
Reação em Cadeia da Polimerase em Tempo Real/métodos
[Mh] Termos MeSH secundário: Animais
Antibacterianos
Bactérias/classificação
Ceco/microbiologia
Contagem de Colônia Microbiana
Dieta
Fezes/microbiologia
Feminino
Trato Gastrointestinal/microbiologia
Genes Bacterianos
Interações Hospedeiro-Patógeno
Masculino
Camundongos
Camundongos Endogâmicos C3H
Camundongos Endogâmicos C57BL
Modelos Biológicos
Reação em Cadeia da Polimerase/métodos
RNA Ribossômico 16S/genética
Reprodutibilidade dos Testes
Sensibilidade e Especificidade
Especificidade da Espécie
Óperon de RNAr/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Anti-Bacterial Agents); 0 (DNA, Bacterial); 0 (RNA, Ribosomal, 16S)
[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:170213
[St] Status:MEDLINE


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[PMID]:27254767
[Au] Autor:Dabbagh N; Preisfeld A
[Ad] Endereço:Bergische University Wuppertal, Faculty of Mathematics and Natural Sciences, Zoology and Didactics of Biology, Wuppertal, Germany.
[Ti] Título:The Chloroplast Genome of Euglena mutabilis-Cluster Arrangement, Intron Analysis, and Intrageneric Trends.
[So] Source:J Eukaryot Microbiol;64(1):31-44, 2017 Jan.
[Is] ISSN:1550-7408
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:A comparative analysis of the chloroplast genome of Euglena mutabilis underlined a high diversity in the evolution of plastids in euglenids. Gene clusters in more derived Euglenales increased in complexity with only a few, but remarkable changes in the genus Euglena. Euglena mutabilis differed from other Euglena species in a mirror-inverted arrangement of 12 from 15 identified clusters, making it very likely that the emergence at the base of the genus Euglena, which has been considered a long branch artifact, is truly a probable position. This was corroborated by many similarities in gene arrangement and orientation with Strombomonas and Monomorphina, rendering the genome organization of E. mutabilis in certain clusters as plesiomorphic feature. By RNA analysis exact exon-intron boundaries and the type of the 77 introns identified were mostly determined unambiguously. A detailed intron study of psbC pointed at two important issues: First, the number of introns varied even between species, and no trend from few to many introns could be observed. Second, mat1 was localized in Eutreptiales exclusively in intron 1, and mat2 was not identified. With the emergence of Euglenaceae in most species, a new intron containing mat2 inserted in front of the previous intron 1 and thereby became intron 2 with mat1.
[Mh] Termos MeSH primário: Euglena/genética
Genoma de Cloroplastos/genética
Íntrons
[Mh] Termos MeSH secundário: Sequência de Bases
Evolução Biológica
Cloroplastos/genética
DNA de Cloroplastos/genética
DNA de Cloroplastos/isolamento & purificação
DNA de Protozoário/genética
Euglena/classificação
Evolução Molecular
Éxons
Ordem dos Genes
Família Multigênica
Fases de Leitura Aberta
Proteínas de Protozoários/genética
Análise de Sequência
Óperon de RNAr
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Chloroplast); 0 (DNA, Protozoan); 0 (Protozoan Proteins)
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170713
[Lr] Data última revisão:
170713
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160603
[St] Status:MEDLINE
[do] DOI:10.1111/jeu.12334


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[PMID]:28005933
[Au] Autor:Takada H; Shimada T; Dey D; Quyyum MZ; Nakano M; Ishiguro A; Yoshida H; Yamamoto K; Sen R; Ishihama A
[Ad] Endereço:Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan.
[Ti] Título:Differential Regulation of rRNA and tRNA Transcription from the rRNA-tRNA Composite Operon in Escherichia coli.
[So] Source:PLoS One;11(12):e0163057, 2016.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Escherichia coli contains seven rRNA operons, each consisting of the genes for three rRNAs (16S, 23S and 5S rRNA in this order) and one or two tRNA genes in the spacer between 16S and 23S rRNA genes and one or two tRNA genes in the 3' proximal region. All of these rRNA and tRNA genes are transcribed from two promoters, P1 and P2, into single large precursors that are afterward processed to individual rRNAs and tRNAs by a set of RNases. In the course of Genomic SELEX screening of promoters recognized by RNA polymerase (RNAP) holoenzyme containing RpoD sigma, a strong binding site was identified within 16S rRNA gene in each of all seven rRNA operons. The binding in vitro of RNAP RpoD holoenzyme to an internal promoter, referred to the promoter of riRNA (an internal RNA of the rRNA operon), within each 16S rRNA gene was confirmed by gel shift assay and AFM observation. Using this riRNA promoter within the rrnD operon as a representative, transcription in vitro was detected with use of the purified RpoD holoenzyme, confirming the presence of a constitutive promoter in this region. LacZ reporter assay indicated that this riRNA promoter is functional in vivo. The location of riRNA promoter in vivo as identified using a set of reporter plasmids agrees well with that identified in vitro. Based on transcription profile in vitro and Northern blot analysis in vivo, the majority of transcript initiated from this riRNA promoter was estimated to terminate near the beginning of 23S rRNA gene, indicating that riRNA leads to produce the spacer-coded tRNA. Under starved conditions, transcription of the rRNA operon is markedly repressed to reduce the intracellular level of ribosomes, but the levels of both riRNA and its processed tRNAGlu stayed unaffected, implying that riRNA plays a role in the continued steady-state synthesis of tRNAs from the spacers of rRNA operons. We then propose that the tRNA genes organized within the spacers of rRNA-tRNA composite operons are expressed independent of rRNA synthesis under specific conditions where further synthesis of ribosomes is not needed.
[Mh] Termos MeSH primário: Escherichia coli/genética
RNA Ribossômico/metabolismo
RNA de Transferência/metabolismo
Óperon de RNAr/genética
[Mh] Termos MeSH secundário: Sítios de Ligação
Northern Blotting
RNA Polimerases Dirigidas por DNA/genética
RNA Polimerases Dirigidas por DNA/metabolismo
Ensaio de Desvio de Mobilidade Eletroforética
Escherichia coli/metabolismo
Holoenzimas/genética
Holoenzimas/metabolismo
Microscopia de Força Atômica
Regiões Promotoras Genéticas
RNA Ribossômico/genética
RNA de Transferência/genética
Fator sigma/genética
Fator sigma/metabolismo
Transcrição Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Holoenzymes); 0 (RNA, Ribosomal); 0 (Sigma Factor); 9014-25-9 (RNA, Transfer); EC 2.7.7.- (RNA polymerase sigma 70); EC 2.7.7.6 (DNA-Directed RNA Polymerases)
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170703
[Lr] Data última revisão:
170703
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161223
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0163057


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[PMID]:27671073
[Au] Autor:Fluit AC; Jansen MD; Bosch T; Jansen WT; Schouls L; Jonker MJ; Boel CH
[Ad] Endereço:Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands A.C.Fluit@umcutrecht.nl.
[Ti] Título:rRNA Operon Copy Number Can Explain the Distinct Epidemiology of Hospital-Associated Methicillin-Resistant Staphylococcus aureus.
[So] Source:Antimicrob Agents Chemother;60(12):7313-7320, 2016 Dec.
[Is] ISSN:1098-6596
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The distinct epidemiology of original hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) and early community-associated MRSA (CA-MRSA) is largely unexplained. S. aureus carries either five or six rRNA operon copies. Evidence is provided for a scenario in which MRSA has adapted to the hospital environment by rRNA operon loss (six to five copies) due to antibiotic pressure. Early CA-MRSA, in contrast, results from wild-type methicillin-susceptible S. aureus (MSSA) that acquired mecA without loss of an rRNA operon. Of the HA-MRSA isolates (n = 77), 67.5% had five rRNA operon copies, compared to 23.2% of the CA-MRSA isolates (n = 69) and 7.7% of MSSA isolates (n = 195) (P < 0.001). In addition, 105 MSSA isolates from cystic fibrosis patients were tested, because these patients are repeatedly treated with antibiotics; 32.4% of these isolates had five rRNA operon copies. For all subsets, a correlation between resistance profile and rRNA copy number was found. Furthermore, we showed that in vitro antibiotic pressure may result in rRNA operon copy loss. We also showed that without antibiotic pressure, S. aureus isolates containing six rRNA copies are more fit than isolates with five copies. We conclude that HA-MRSA and cystic fibrosis isolates most likely have adapted to an environment with high antibiotic pressure by the loss of an rRNA operon copy. This loss has facilitated resistance development, which promoted survival in these niches. However, strain fitness decreased, which explains their lack of success in the community. In contrast, CA-MRSA isolates retained six rRNA operon copies, rendering them fitter and thereby able to survive and spread in the community.
[Mh] Termos MeSH primário: Infecções Comunitárias Adquiridas/epidemiologia
Infecção Hospitalar/epidemiologia
Staphylococcus aureus Resistente à Meticilina/genética
RNA Bacteriano/genética
Infecções Estafilocócicas/epidemiologia
Óperon de RNAr/genética
[Mh] Termos MeSH secundário: Antibacterianos/uso terapêutico
Proteínas de Bactérias/genética
Técnicas de Tipagem Bacteriana
Infecções Comunitárias Adquiridas/microbiologia
Infecção Hospitalar/microbiologia
Fibrose Cística/microbiologia
Genoma Bacteriano/genética
Seres Humanos
Staphylococcus aureus Resistente à Meticilina/isolamento & purificação
Testes de Sensibilidade Microbiana
Proteínas de Ligação às Penicilinas/genética
Polimorfismo Genético/genética
Infecções Estafilocócicas/tratamento farmacológico
Infecções Estafilocócicas/microbiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Anti-Bacterial Agents); 0 (Bacterial Proteins); 0 (Penicillin-Binding Proteins); 0 (RNA, Bacterial); 0 (mecA protein, Staphylococcus aureus)
[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:160928
[St] Status:MEDLINE


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[PMID]:27542937
[Au] Autor:Amram E; Borovok I; Nachum-Biala Y; Ayling R; Lerner U; Harrus S; Lysnyansky I
[Ad] Endereço:Mycoplasma Unit, Division of Avian and Aquatic Diseases, Kimron Veterinary Institute, Beit Dagan, Israel Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel.
[Ti] Título:High Prevalence of Diverse Insertion Sequences within the rRNA Operons of Mycoplasma bovis.
[So] Source:Appl Environ Microbiol;82(21):6386-6394, 2016 Nov 01.
[Is] ISSN:1098-5336
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Insertion sequences (ISs) are widespread in the genome of Mycoplasma bovis strain PG45, but no ISs were identified within its two tandemly positioned rRNA operons (rrn1 and rrn2). However, characterization of the rrn locus in 70 M. bovis isolates revealed the presence of ISs related to the ISMbov1 (IS30 family) and ISMbov4 (IS4 family) isomers in 35 isolates. ISs were inserted into intergenic region 1 (IGR-1) or IGR-3, which are the putative promoter regions of rrn1 and rrn2, respectively, and into IGR-5, located downstream of the rrl2 gene. Seven different configurations (A to G) of the rrn locus with respect to ISs were identified, including those in five annotated genomes. The transcriptional start site for the single rrn operon in M. bovis strain 88127 was mapped within IGR-1, 60 bp upstream of the rrs gene. Notably, only 1 nucleotide separated the direct repeat (DR) for ISMbov1 and the promoter -35 element in configuration D, while in configuration F, the -35 motif was a part of the ISMbov1 DR. Relative quantitative real-time (qRT) PCR analysis and growth rate comparisons detected a significant increase (P < 0.05) in the expression of the rrs genes and in the number of viable cells during log phase growth (8, 12, and 16 h) in the strains with configuration F in comparison to strains with one or two rrn operons that did not have ISs. A high prevalence of IS elements within or close to the M. bovis rrn operon-promoter region may reflect their important role in regulation of both ribosome synthesis and function. IMPORTANCE: Data presented in this study show a high prevalence of diverse ISs within the M. bovis rrn locus resulting in intraspecies variability and diversity. Such abundance of IS elements near or within the rrn locus may offer a selective advantage to M. bovis Moreover, the fact that expression of the rrs genes as well as the number of viable cells increased in the group of strains with IS element insertion within a putative promoter -35 sequence (configuration F) in comparison to that in strains with one or two rrn operons that do not have ISs may serve as a basis for understanding the possible role of M. bovis IS elements in fundamental biological processes such as regulation of ribosome synthesis and function.
[Mh] Termos MeSH primário: Mutagênese Insercional
Mycoplasma bovis/genética
Óperon de RNAr
[Mh] Termos MeSH secundário: Elementos de DNA Transponíveis
DNA Bacteriano/genética
DNA Intergênico
Genoma Bacteriano
Mycoplasma bovis/crescimento & desenvolvimento
Regiões Promotoras Genéticas
Reação em Cadeia da Polimerase em Tempo Real
Sítio de Iniciação de Transcrição
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA Transposable Elements); 0 (DNA, Bacterial); 0 (DNA, Intergenic)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171027
[Lr] Data última revisão:
171027
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160821
[St] Status:MEDLINE


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[PMID]:27129708
[Au] Autor:Mariano DC; Sousa Tde J; Pereira FL; Aburjaile F; Barh D; Rocha F; Pinto AC; Hassan SS; Saraiva TD; Dorella FA; de Carvalho AF; Leal CA; Figueiredo HC; Silva A; Ramos RT; Azevedo VA
[Ad] Endereço:Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
[Ti] Título:Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002.
[So] Source:BMC Genomics;17:315, 2016 Apr 30.
[Is] ISSN:1471-2164
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Studies have detected mis-assemblies in genomes of the species Corynebacterium pseudotuberculosis. These new discover have been possible due to the evolution of the Next-Generation Sequencing platforms, which have provided sequencing with accuracy and reduced costs. In addition, the improving of techniques for construction of high accuracy genomic maps, for example, Whole-genome mapping (WGM) (OpGen Inc), have allow high-resolution assembly that can detect large rearrangements. RESULTS: In this work, we present the resequencing of Corynebacterium pseudotuberculosis strain 1002 (Cp1002). Cp1002 was the first strain of this species sequenced in Brazil, and its genome has been used as model for several studies in silico of caseous lymphadenitis disease. The sequencing was performed using the platform Ion PGM and fragment library (200 bp kit). A restriction map was constructed, using the technique of WGM with the enzyme KpnI. After the new assembly process, using WGM as scaffolder, we detected a large inversion with size bigger than one-half of genome. A specific analysis using BLAST and NR database shows that the inversion occurs between two homology RNA ribosomal regions. CONCLUSION: In conclusion, the results showed by WGM could be used to detect mismatches in assemblies, providing genomic maps with high resolution and allow assemblies with more accuracy and completeness. The new assembly of C. pseudotuberculosis was deposited in GenBank under the accession no. CP012837.
[Mh] Termos MeSH primário: Mapeamento Cromossômico/métodos
Corynebacterium pseudotuberculosis/genética
Genoma Bacteriano
Genômica/métodos
Óperon de RNAr/genética
[Mh] Termos MeSH secundário: DNA Bacteriano/genética
Biblioteca Gênica
Sequenciamento de Nucleotídeos em Larga Escala
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, Bacterial)
[Em] Mês de entrada:1611
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160501
[St] Status:MEDLINE
[do] DOI:10.1186/s12864-016-2673-7


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[PMID]:26976590
[Au] Autor:Winkelman JT; Chandrangsu P; Ross W; Gourse RL
[Ad] Endereço:Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706.
[Ti] Título:Open complex scrunching before nucleotide addition accounts for the unusual transcription start site of E. coli ribosomal RNA promoters.
[So] Source:Proc Natl Acad Sci U S A;113(13):E1787-95, 2016 Mar 29.
[Is] ISSN:1091-6490
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Most Escherichia coli promoters initiate transcription with a purine 7 or 8 nt downstream from the -10 hexamer, but some promoters, including the ribosomal RNA promoter rrnB P1, start 9 nt from the -10 element. We identified promoter and RNA polymerase determinants of this noncanonical rrnB P1 start site using biochemical and genetic approaches including mutational analysis of the promoter, Fe(2+) cleavage assays to monitor template strand positions near the active-site, and Bpa cross-linking to map the path of open complex DNA at amino acid and nucleotide resolution. We find that mutations in several promoter regions affect transcription start site (TSS) selection. In particular, we show that the absence of strong interactions between the discriminator region and σ region 1.2 and between the extended -10 element and σ region 3.0, identified previously as a determinant of proper regulation of rRNA promoters, is also required for the unusual TSS. We find that the DNA in the single-stranded transcription bubble of the rrnB P1 promoter complex expands and is "scrunched" into the active site channel of RNA polymerase, similar to the situation in initial transcribing complexes. However, in the rrnB P1 open complex, scrunching occurs before RNA synthesis begins. We find that the scrunched open complex exhibits reduced abortive product synthesis, suggesting that scrunching and unusual TSS selection contribute to the extraordinary transcriptional activity of rRNA promoters by increasing promoter escape, helping to offset the reduction in promoter activity that would result from the weak interactions with σ.
[Mh] Termos MeSH primário: Escherichia coli/genética
Regiões Promotoras Genéticas/genética
Sítio de Iniciação de Transcrição
[Mh] Termos MeSH secundário: RNA Polimerases Dirigidas por DNA/genética
RNA Polimerases Dirigidas por DNA/metabolismo
Evolução Molecular
Regulação Bacteriana da Expressão Gênica
Mutação
Conformação de Ácido Nucleico
Nucleotídeos/genética
Nucleotídeos/metabolismo
Transcrição Genética
Óperon de RNAr/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Nm] Nome de substância:
0 (Nucleotides); EC 2.7.7.6 (DNA-Directed RNA Polymerases)
[Em] Mês de entrada:1609
[Cu] Atualização por classe:161116
[Lr] Data última revisão:
161116
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160316
[St] Status:MEDLINE
[do] DOI:10.1073/pnas.1522159113


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[PMID]:26872975
[Au] Autor:Qayyum MZ; Dey D; Sen R
[Ad] Endereço:From the Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Tuljaguda Complex, 4-1-714 Mozamjahi Road, Nampally, Hyderabad 500 001, India and Graduate Studies, Manipal University, Manipal, Karnataka 576104 India.
[Ti] Título:Transcription Elongation Factor NusA Is a General Antagonist of Rho-dependent Termination in Escherichia coli.
[So] Source:J Biol Chem;291(15):8090-108, 2016 Apr 08.
[Is] ISSN:1083-351X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:NusA is an essential protein that binds to RNA polymerase and also to the nascent RNA and influences transcription by inducing pausing and facilitating the process of transcription termination/antitermination. Its participation in Rho-dependent transcription termination has been perceived, but the molecular nature of this involvement is not known. We hypothesized that, because both Rho and NusA are RNA-binding proteins and have the potential to target the same RNA, the latter is likely to influence the global pattern of the Rho-dependent termination. Analyses of the nascent RNA binding properties and consequent effects on the Rho-dependent termination functions of specific NusA-RNA binding domain mutants revealed an existence of Rho-NusA direct competition for the overlappingnut(NusA-binding site) andrut(Rho-binding site) sites on the RNA. This leads to delayed entry of Rho at therutsite that inhibits the latter's RNA release process. High density tiling microarray profiles of these NusA mutants revealed that a significant number of genes, together with transcripts from intergenic regions, are up-regulated. Interestingly, the majority of these genes were also up-regulated when the Rho function was compromised. These results provide strong evidence for the existence of NusA-binding sites in different operons that are also the targets of Rho-dependent terminations. Our data strongly argue in favor of a direct competition between NusA and Rho for the access of specific sites on the nascent transcripts in different parts of the genome. We propose that this competition enables NusA to function as a global antagonist of the Rho function, which is unlike its role as a facilitator of hairpin-dependent termination.
[Mh] Termos MeSH primário: Proteínas de Escherichia coli/metabolismo
Escherichia coli/metabolismo
Regulação Bacteriana da Expressão Gênica
RNA Bacteriano/metabolismo
Fator Rho/metabolismo
Fatores de Elongação da Transcrição/metabolismo
[Mh] Termos MeSH secundário: Sequência de Bases
Sítios de Ligação
RNA Polimerases Dirigidas por DNA/metabolismo
Escherichia coli/química
Escherichia coli/genética
Proteínas de Escherichia coli/química
Proteínas de Escherichia coli/genética
Modelos Moleculares
Dados de Sequência Molecular
Mutação
Estrutura Terciária de Proteína
RNA Bacteriano/química
RNA Bacteriano/genética
Transcrição Genética
Fatores de Elongação da Transcrição/química
Fatores de Elongação da Transcrição/genética
Óperon de RNAr
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Escherichia coli Proteins); 0 (RNA, Bacterial); 0 (Rho Factor); 0 (Transcriptional Elongation Factors); 0 (nusA protein, E coli); EC 2.7.7.6 (DNA-Directed RNA Polymerases)
[Em] Mês de entrada:1608
[Cu] Atualização por classe:170408
[Lr] Data última revisão:
170408
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160214
[St] Status:MEDLINE
[do] DOI:10.1074/jbc.M115.701268


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[PMID]:26565722
[Au] Autor:Nemergut DR; Knelman JE; Ferrenberg S; Bilinski T; Melbourne B; Jiang L; Violle C; Darcy JL; Prest T; Schmidt SK; Townsend AR
[Ad] Endereço:Department of Biology, Duke University, Durham, NC, USA.
[Ti] Título:Decreases in average bacterial community rRNA operon copy number during succession.
[So] Source:ISME J;10(5):1147-56, 2016 May.
[Is] ISSN:1751-7370
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Trait-based studies can help clarify the mechanisms driving patterns of microbial community assembly and coexistence. Here, we use a trait-based approach to explore the importance of rRNA operon copy number in microbial succession, building on prior evidence that organisms with higher copy numbers respond more rapidly to nutrient inputs. We set flasks of heterotrophic media into the environment and examined bacterial community assembly at seven time points. Communities were arrayed along a geographic gradient to introduce stochasticity via dispersal processes and were analyzed using 16 S rRNA gene pyrosequencing, and rRNA operon copy number was modeled using ancestral trait reconstruction. We found that taxonomic composition was similar between communities at the beginning of the experiment and then diverged through time; as well, phylogenetic clustering within communities decreased over time. The average rRNA operon copy number decreased over the experiment, and variance in rRNA operon copy number was lowest both early and late in succession. We then analyzed bacterial community data from other soil and sediment primary and secondary successional sequences from three markedly different ecosystem types. Our results demonstrate that decreases in average copy number are a consistent feature of communities across various drivers of ecological succession. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, ranging from cells to populations and communities, with implications for both microbial ecology and evolution.
[Mh] Termos MeSH primário: Bactérias/genética
Microbiologia do Solo
Óperon de RNAr/genética
[Mh] Termos MeSH secundário: Colorado
Ecossistema
Dosagem de Genes
Óperon
Filogenia
RNA Ribossômico 16S/genética
Análise de Sequência de RNA
Solo
Processos Estocásticos
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (RNA, Ribosomal, 16S); 0 (Soil)
[Em] Mês de entrada:1612
[Cu] Atualização por classe:171116
[Lr] Data última revisão:
171116
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151114
[St] Status:MEDLINE
[do] DOI:10.1038/ismej.2015.191


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[PMID]:26482806
[Au] Autor:Patrick M; Dennis PP; Ehrenberg M; Bremer H
[Ad] Endereço:Department of Medical Genetics, University of Wisconsin-Madison, USA. Electronic address: mpatrick@wisc.edu.
[Ti] Título:Free RNA polymerase in Escherichia coli.
[So] Source:Biochimie;119:80-91, 2015 Dec.
[Is] ISSN:1638-6183
[Cp] País de publicação:France
[La] Idioma:eng
[Ab] Resumo:The frequencies of transcription initiation of regulated and constitutive genes depend on the concentration of free RNA polymerase holoenzyme [Rf] near their promoters. Although RNA polymerase is largely confined to the nucleoid, it is difficult to determine absolute concentrations of [Rf] at particular locations within the nucleoid structure. However, relative concentrations of free RNA polymerase at different growth rates, [Rf]rel, can be estimated from the activities of constitutive promoters. Previous studies indicated that the rrnB P2 promoter is constitutive and that [Rf]rel in the vicinity of rrnB P2 increases with increasing growth rate. Recently it has become possible to directly visualize Rf in growing Escherichia coli cells. Here we examine some of the important issues relating to gene expression based on these new observations. We conclude that: (i) At a growth rate of 2 doublings/h, there are about 1000 free and 2350 non-specifically DNA-bound RNA polymerase molecules per average cell (12 and 28%, respectively, of 8400 total) which are in rapid equilibrium. (ii) The reversibility of the non-specific binding generates more than 1000 free RNA polymerase molecules every second in the immediate vicinity of the DNA. Of these, most rebind non-specifically to the DNA within a few ms; the frequency of non-specific binding is at least two orders of magnitude greater than specific binding and transcript initiation. (iii) At a given amount of RNA polymerase per cell, [Rf] and the density of non-specifically DNA-bound RNA polymerase molecules along the DNA both vary reciprocally with the amount of DNA in the cell. (iv) At 2 doublings/h an E. coli cell contains, on the average, about 1 non-specifically bound RNA polymerase per 9 kbp of DNA and 1 free RNA polymerase per 20 kbp of DNA. However some DNA regions (i.e. near active rRNA operons) may have significantly higher than average [Rf].
[Mh] Termos MeSH primário: DNA Bacteriano/metabolismo
RNA Polimerases Dirigidas por DNA/metabolismo
Proteínas de Escherichia coli/metabolismo
Escherichia coli/enzimologia
Regulação Bacteriana da Expressão Gênica
Modelos Biológicos
Regiões Promotoras Genéticas
[Mh] Termos MeSH secundário: Algoritmos
Proteínas de Bactérias/química
Proteínas de Bactérias/genética
Proteínas de Bactérias/metabolismo
Citoplasma/enzimologia
Citoplasma/metabolismo
Proteínas de Ligação a DNA/química
Proteínas de Ligação a DNA/genética
Proteínas de Ligação a DNA/metabolismo
RNA Polimerases Dirigidas por DNA/química
RNA Polimerases Dirigidas por DNA/genética
Difusão
Ativação Enzimática
Precursores Enzimáticos/química
Precursores Enzimáticos/genética
Precursores Enzimáticos/metabolismo
Escherichia coli/crescimento & desenvolvimento
Escherichia coli/metabolismo
Proteínas de Escherichia coli/química
Proteínas de Escherichia coli/genética
Holoenzimas/química
Holoenzimas/genética
Holoenzimas/metabolismo
Cinética
Mutação
Transporte Proteico
Solubilidade
Transcrição Genética
Óperon de RNAr
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (DNA, Bacterial); 0 (DNA-Binding Proteins); 0 (DnaA protein, Bacteria); 0 (Enzyme Precursors); 0 (Escherichia coli Proteins); 0 (Holoenzymes); EC 2.7.7.6 (DNA-Directed RNA Polymerases)
[Em] Mês de entrada:1612
[Cu] Atualização por classe:161230
[Lr] Data última revisão:
161230
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151021
[St] Status:MEDLINE



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