Base de dados : MEDLINE
Pesquisa : A11.284.430.214.190.875.811.870.750.349 [Categoria DeCS]
Referências encontradas : 7 [refinar]
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  1 / 7 MEDLINE  
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[PMID]:25898319
[Au] Autor:Kim Y; Liesack W
[Ad] Endereço:Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
[Ti] Título:Differential assemblage of functional units in paddy soil microbiomes.
[So] Source:PLoS One;10(4):e0122221, 2015.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Flooded rice fields are not only a global food source but also a major biogenic source of atmospheric methane. Using metatranscriptomics, we comparatively explored structural and functional succession of paddy soil microbiomes in the oxic surface layer and anoxic bulk soil. Cyanobacteria, Fungi, Xanthomonadales, Myxococcales, and Methylococcales were the most abundant and metabolically active groups in the oxic zone, while Clostridia, Actinobacteria, Geobacter, Anaeromyxobacter, Anaerolineae, and methanogenic archaea dominated the anoxic zone. The protein synthesis potential of these groups was about 75% and 50% of the entire community capacity, respectively. Their structure-function relationships in microbiome succession were revealed by classifying the protein-coding transcripts into core, non-core, and taxon-specific transcripts based on homologous gene distribution. The differential expression of core transcripts between the two microbiomes indicated that structural succession is primarily governed by the cellular ability to adapt to the given oxygen condition, involving oxidative stress, nitrogen/phosphorus metabolism, and fermentation. By contrast, the non-core transcripts were expressed from genes involved in the metabolism of various carbon sources. Among those, taxon-specific transcripts revealed highly specialized roles of the dominant groups in community-wide functioning. For instance, taxon-specific transcripts involved in photosynthesis and methane oxidation were a characteristic of the oxic zone, while those related to methane production and aromatic compound degradation were specific to the anoxic zone. Degradation of organic matters, antibiotics resistance, and secondary metabolite production were detected to be expressed in both the oxic and anoxic zones, but by different taxonomic groups. Cross-feeding of methanol between members of the Methylococcales and Xanthomonadales was suggested by the observation that in the oxic zone, they both exclusively expressed homologous genes encoding methanol dehydrogenase. Our metatranscriptomic analysis suggests that paddy soil microbiomes act as complex, functionally coordinated assemblages whose taxonomic composition is governed by the prevailing habitat factors and their hierarchical importance for community succession.
[Mh] Termos MeSH primário: Microbiologia do Solo
[Mh] Termos MeSH secundário: Anaerobiose
Crenarchaeota/genética
Produtos Agrícolas
Methylococcaceae/genética
Microbiota/genética
Myxococcales/genética
Oryza
RNA Arqueal/genética
RNA Bacteriano/genética
RNA Mensageiro/genética
RNA Ribossômico/genética
Subunidades Ribossômicas Menores de Arqueas/genética
Subunidades Ribossômicas Menores de Bactérias/genética
Transcriptoma
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (RNA, Archaeal); 0 (RNA, Bacterial); 0 (RNA, Messenger); 0 (RNA, Ribosomal)
[Em] Mês de entrada:1604
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150422
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0122221


  2 / 7 MEDLINE  
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[PMID]:24697502
[Au] Autor:Mallik S; Kundu S
[Ad] Endereço:a Department of Biophysics, Molecular Biology and Bioinformatics , University of Calcutta , 92, APC Road, Kolkata 700009 , India.
[Ti] Título:Molecular interactions within the halophilic, thermophilic, and mesophilic prokaryotic ribosomal complexes: clues to environmental adaptation.
[So] Source:J Biomol Struct Dyn;33(3):639-56, 2015.
[Is] ISSN:1538-0254
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Using the available crystal structures of 50S ribosomal subunits from three prokaryotic species: Escherichia coli (mesophilic), Thermus thermophilus (thermophilic), and Haloarcula marismortui (halophilic), we have analyzed different structural features of ribosomal RNAs (rRNAs), proteins, and of their interfaces. We have correlated these structural features with the environmental adaptation strategies of the corresponding species. While dense intra-rRNA packing is observed in thermophilic, loose intra-rRNA packing is observed in halophilic (both compared to mesophilic). Interestingly, protein-rRNA interfaces of both the extremophiles are densely packed compared to that of the mesophilic. The intersubunit bridge regions are almost devoid of cavities, probably ensuring the proper formation of each bridge (by not allowing any loosely packed region nearby). During rRNA binding, the ribosomal proteins experience some structural transitions. Here, we have analyzed the intrinsically disordered and ordered regions of the ribosomal proteins, which are subjected to such transitions. The intrinsically disordered and disorder-to-order transition sites of the thermophilic and mesophilic ribosomal proteins are simultaneously (i) highly conserved and (ii) slowly evolving compared to rest of the protein structure. Although high conservation is observed at such sites of halophilic ribosomal proteins, but slow rate of evolution is absent. Such differences between thermophilic, mesophilic, and halophilic can be explained from their environmental adaptation strategy. Interestingly, a universal biophysical principle evident by a linear relationship between the free energy of interface formation, interface area, and structural changes of r-proteins during assembly is always maintained, irrespective of the environmental conditions.
[Mh] Termos MeSH primário: Escherichia coli/genética
Haloarcula marismortui/genética
Thermus thermophilus/genética
[Mh] Termos MeSH secundário: Adaptação Fisiológica
Pareamento de Bases
Sequência Conservada
Evolução Molecular
Interação Gene-Ambiente
Ligações de Hidrogênio
Proteínas Intrinsicamente Desordenadas
Modelos Moleculares
Filogenia
Dobramento de Proteína
Multimerização Proteica
Estrutura Quaternária de Proteína
RNA Arqueal/química
RNA Bacteriano/química
RNA Ribossômico/química
Subunidades Ribossômicas Maiores de Arqueas/química
Subunidades Ribossômicas Maiores de Arqueas/genética
Subunidades Ribossômicas Maiores de Bactérias/química
Subunidades Ribossômicas Maiores de Bactérias/genética
Subunidades Ribossômicas Menores de Arqueas/química
Subunidades Ribossômicas Menores de Arqueas/genética
Subunidades Ribossômicas Menores de Bactérias/química
Subunidades Ribossômicas Menores de Bactérias/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Intrinsically Disordered Proteins); 0 (RNA, Archaeal); 0 (RNA, Bacterial); 0 (RNA, Ribosomal)
[Em] Mês de entrada:1601
[Cu] Atualização por classe:141223
[Lr] Data última revisão:
141223
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:140405
[St] Status:MEDLINE
[do] DOI:10.1080/07391102.2014.900457


  3 / 7 MEDLINE  
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[PMID]:24825021
[Au] Autor:Blombach F; Launay H; Snijders AP; Zorraquino V; Wu H; de Koning B; Brouns SJ; Ettema TJ; Camilloni C; Cavalli A; Vendruscolo M; Dickman MJ; Cabrita LD; La Teana A; Benelli D; Londei P; Christodoulou J; van der Oost J
[Ad] Endereço:*Laboratory of Microbiology, Wageningen University, Wageningen 6703HB, The Netherlands.
[Ti] Título:Archaeal MBF1 binds to 30S and 70S ribosomes via its helix-turn-helix domain.
[So] Source:Biochem J;462(2):373-84, 2014 Sep 01.
[Is] ISSN:1470-8728
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:MBF1 (multi-protein bridging factor 1) is a protein containing a conserved HTH (helix-turn-helix) domain in both eukaryotes and archaea. Eukaryotic MBF1 has been reported to function as a transcriptional co-activator that physically bridges transcription regulators with the core transcription initiation machinery of RNA polymerase II. In addition, MBF1 has been found to be associated with polyadenylated mRNA in yeast as well as in mammalian cells. aMBF1 (archaeal MBF1) is very well conserved among most archaeal lineages; however, its function has so far remained elusive. To address this, we have conducted a molecular characterization of this aMBF1. Affinity purification of interacting proteins indicates that aMBF1 binds to ribosomal subunits. On sucrose density gradients, aMBF1 co-fractionates with free 30S ribosomal subunits as well as with 70S ribosomes engaged in translation. Binding of aMBF1 to ribosomes does not inhibit translation. Using NMR spectroscopy, we show that aMBF1 contains a long intrinsically disordered linker connecting the predicted N-terminal zinc-ribbon domain with the C-terminal HTH domain. The HTH domain, which is conserved in all archaeal and eukaryotic MBF1 homologues, is directly involved in the association of aMBF1 with ribosomes. The disordered linker of the ribosome-bound aMBF1 provides the N-terminal domain with high flexibility in the aMBF1-ribosome complex. Overall, our findings suggest a role for aMBF1 in the archaeal translation process.
[Mh] Termos MeSH primário: Proteínas Arqueais/metabolismo
Subunidades Ribossômicas Menores de Arqueas/metabolismo
Sulfolobus solfataricus/metabolismo
Transativadores/metabolismo
[Mh] Termos MeSH secundário: Motivos de Aminoácidos
Proteínas Arqueais/química
Ligação Proteica
Estrutura Terciária de Proteína
Proteínas Recombinantes/química
Subunidades Ribossômicas Menores de Arqueas/química
Transativadores/química
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Archaeal Proteins); 0 (Recombinant Proteins); 0 (Trans-Activators)
[Em] Mês de entrada:1410
[Cu] Atualização por classe:171110
[Lr] Data última revisão:
171110
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:140515
[St] Status:MEDLINE
[do] DOI:10.1042/BJ20131474


  4 / 7 MEDLINE  
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[PMID]:23326205
[Au] Autor:Gebetsberger J; Zywicki M; Künzi A; Polacek N
[Ad] Endereço:Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
[Ti] Título:tRNA-derived fragments target the ribosome and function as regulatory non-coding RNA in Haloferax volcanii.
[So] Source:Archaea;2012:260909, 2012.
[Is] ISSN:1472-3654
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Nonprotein coding RNA (ncRNA) molecules have been recognized recently as major contributors to regulatory networks in controlling gene expression in a highly efficient manner. These RNAs either originate from their individual transcription units or are processing products from longer precursor RNAs. For example, tRNA-derived fragments (tRFs) have been identified in all domains of life and represent a growing, yet functionally poorly understood, class of ncRNA candidates. Here we present evidence that tRFs from the halophilic archaeon Haloferax volcanii directly bind to ribosomes. In the presented genomic screen of the ribosome-associated RNome, a 26-residue-long fragment originating from the 5' part of valine tRNA was by far the most abundant tRF. The Val-tRF is processed in a stress-dependent manner and was found to primarily target the small ribosomal subunit in vitro and in vivo. As a consequence of ribosome binding, Val-tRF reduces protein synthesis by interfering with peptidyl transferase activity. Therefore this tRF functions as ribosome-bound small ncRNA capable of regulating gene expression in H. volcanii under environmental stress conditions probably by fine tuning the rate of protein production.
[Mh] Termos MeSH primário: Haloferax volcanii/genética
RNA Arqueal/genética
RNA de Transferência/genética
[Mh] Termos MeSH secundário: Sequência de Bases
Regulação da Expressão Gênica em Archaea
Redes Reguladoras de Genes
Haloferax volcanii/metabolismo
Conformação de Ácido Nucleico
Processamento Pós-Transcricional do RNA
RNA Arqueal/química
RNA Arqueal/metabolismo
RNA de Transferência/química
RNA de Transferência/metabolismo
RNA de Transferência de Valina/química
RNA de Transferência de Valina/genética
RNA de Transferência de Valina/metabolismo
RNA não Traduzido/química
RNA não Traduzido/genética
RNA não Traduzido/metabolismo
Subunidades Ribossômicas Menores de Arqueas/genética
Subunidades Ribossômicas Menores de Arqueas/metabolismo
Ribossomos/genética
Ribossomos/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (RNA, Archaeal); 0 (RNA, Transfer, Val); 0 (RNA, Untranslated); 9014-25-9 (RNA, Transfer)
[Em] Mês de entrada:1306
[Cu] Atualização por classe:150219
[Lr] Data última revisão:
150219
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:130118
[St] Status:MEDLINE
[do] DOI:10.1155/2012/260909


  5 / 7 MEDLINE  
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[PMID]:22561061
[Au] Autor:Horz HP; Seyfarth I; Conrads G
[Ad] Endereço:Division of Oral Microbiology and Immunology, Department of Medical Microbiology, RWTH Aachen University Hospital, Germany. hhorz@ukaachen.de
[Ti] Título:McrA and 16S rRNA gene analysis suggests a novel lineage of Archaea phylogenetically affiliated with Thermoplasmatales in human subgingival plaque.
[So] Source:Anaerobe;18(3):373-7, 2012 Jun.
[Is] ISSN:1095-8274
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Based on the molecular analysis of human subgingival plaque samples from 30 periodontitis patients a novel lineage of Archaea within the phylogenetic radiation of Thermoplasmatales was identified in 10% of cases. Co-occurrence of unique 16S rRNA gene and mcrA gene sequences suggests that this lineage corresponds to a hitherto unknown group of methanogens.
[Mh] Termos MeSH primário: Proteínas Arqueais/genética
Placa Dentária/microbiologia
RNA Ribossômico 16S/genética
Subunidades Ribossômicas Menores de Arqueas/genética
Thermoplasmales/genética
[Mh] Termos MeSH secundário: Idoso
Sequência de Aminoácidos
Archaea/genética
Archaea/isolamento & purificação
Sequência Conservada
Evolução Molecular
Feminino
Seres Humanos
Funções Verossimilhança
Masculino
Meia-Idade
Dados de Sequência Molecular
Tipagem Molecular
Periodontite/microbiologia
Filogenia
Análise de Sequência de DNA
Thermoplasmales/isolamento & purificação
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Archaeal Proteins); 0 (RNA, Ribosomal, 16S)
[Em] Mês de entrada:1210
[Cu] Atualização por classe:120611
[Lr] Data última revisão:
120611
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:120508
[St] Status:MEDLINE
[do] DOI:10.1016/j.anaerobe.2012.04.006


  6 / 7 MEDLINE  
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[PMID]:19861425
[Au] Autor:Hasenöhrl D; Fabbretti A; Londei P; Gualerzi CO; Bläsi U
[Ad] Endereço:Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, 1030 Vienna, Austria. david.hasenoehrl@univie.ac.at
[Ti] Título:Translation initiation complex formation in the crenarchaeon Sulfolobus solfataricus.
[So] Source:RNA;15(12):2288-98, 2009 Dec.
[Is] ISSN:1469-9001
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The function of initiation factors in and the sequence of events during translation initiation have been intensively studied in Bacteria and Eukaryotes, whereas in Archaea knowledge on these functions/processes is limited. By employing chemical probing, we show that translation initiation factor aIF1 of the model crenarchaeon Sulfolobus solfataricus binds to the same area on the ribosome as the bacterial and eukaryal orthologs. Fluorescence energy transfer assays (FRET) showed that aIF1, like its eukaryotic and bacterial orthologs, has a fidelity function in translation initiation complex formation, and that both aIF1 and aIF1A exert a synergistic effect in stimulating ribosomal association of the Met-tRNAi(Met) binding factor a/eIF2. However, as in Eukaryotes their effect on a/eIF2 binding appears to be indirect. Moreover, FRET was used to analyze for the first time the sequence of events toward translation initiation complex formation in an archaeal model system. These studies suggested that a/eIF2-GTP binds first to the ribosome and then recruits Met-tRNAi(Met), which appears to comply with the operational mode of bacterial IF2, and deviates from the shuttle function of the eukaryotic counterpart eIF2. Thus, despite the resemblance of eIF2 and a/eIF2, recruitment of initiator tRNA to the ribosome is mechanistically different in Pro- and Eukaryotes.
[Mh] Termos MeSH primário: Proteínas Arqueais/metabolismo
Fatores de Iniciação de Peptídeos/metabolismo
Biossíntese de Proteínas
RNA Arqueal/metabolismo
Sulfolobus solfataricus/metabolismo
[Mh] Termos MeSH secundário: Sequência de Bases
Códon de Iniciação/genética
Proteínas de Ligação a DNA/metabolismo
Conformação de Ácido Nucleico
Ligação Proteica
RNA Arqueal/química
RNA Arqueal/genética
Subunidades Ribossômicas Menores de Arqueas/metabolismo
Sulfolobus solfataricus/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Archaeal Proteins); 0 (Codon, Initiator); 0 (DNA-Binding Proteins); 0 (Peptide Initiation Factors); 0 (RNA, Archaeal)
[Em] Mês de entrada:0912
[Cu] Atualização por classe:141207
[Lr] Data última revisão:
141207
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:091029
[St] Status:MEDLINE
[do] DOI:10.1261/rna.1662609


  7 / 7 MEDLINE  
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[PMID]:19054741
[Au] Autor:Ciammaruconi A; Gorini S; Londei P
[Ad] Endereço:Dpt. Biotecnologie Cellulari ed Ematologia, Università di Roma La Sapienza (Policlinico) Viale Regina Elena 324, 00161 Rome, Italy.
[Ti] Título:A bifunctional archaeal protein that is a component of 30S ribosomal subunits and interacts with C/D box small RNAs.
[So] Source:Archaea;2(3):151-8, 2008 Dec.
[Is] ISSN:1472-3646
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:We have identified a novel archaeal protein that apparently plays two distinct roles in ribosome metabolism. It is a polypeptide of about 18 kDa (termed Rbp18) that binds free cytosolic C/D box sRNAs in vivo and in vitro and behaves as a structural ribosomal protein, specifically a component of the 30S ribosomal subunit. As Rbp18 is selectively present in Crenarcheota and highly thermophilic Euryarchaeota, we propose that it serves to protect C/D box sRNAs from degradation and perhaps to stabilize thermophilic 30S subunits.
[Mh] Termos MeSH primário: Proteínas Arqueais/metabolismo
RNA Arqueal/metabolismo
Proteínas de Ligação a RNA/metabolismo
Subunidades Ribossômicas Menores de Arqueas/química
Sulfolobus solfataricus/metabolismo
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Proteínas Arqueais/química
Proteínas Arqueais/genética
Proteínas Arqueais/isolamento & purificação
Clonagem Molecular
Imunoprecipitação
Dados de Sequência Molecular
Proteínas de Ligação a RNA/química
Proteínas de Ligação a RNA/genética
Proteínas de Ligação a RNA/isolamento & purificação
Subunidades Ribossômicas Menores de Arqueas/metabolismo
Sulfolobus solfataricus/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Archaeal Proteins); 0 (RNA, Archaeal); 0 (RNA-Binding Proteins)
[Em] Mês de entrada:0903
[Cu] Atualização por classe:140901
[Lr] Data última revisão:
140901
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:081205
[St] Status:MEDLINE



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