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[PMID]:28645172
[Au] Autor:Honda S; Kawamura T; Loher P; Morichika K; Rigoutsos I; Kirino Y
[Ad] Endereço:Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA.
[Ti] Título:The biogenesis pathway of tRNA-derived piRNAs in Bombyx germ cells.
[So] Source:Nucleic Acids Res;45(15):9108-9120, 2017 Sep 06.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Transfer RNAs (tRNAs) function in translational machinery and further serves as a source of short non-coding RNAs (ncRNAs). tRNA-derived ncRNAs show differential expression profiles and play roles in many biological processes beyond translation. Molecular mechanisms that shape and regulate their expression profiles are largely unknown. Here, we report the mechanism of biogenesis for tRNA-derived Piwi-interacting RNAs (td-piRNAs) expressed in Bombyx BmN4 cells. In the cells, two cytoplasmic tRNA species, tRNAAspGUC and tRNAHisGUG, served as major sources for td-piRNAs, which were derived from the 5'-part of the respective tRNAs. cP-RNA-seq identified the two tRNAs as major substrates for the 5'-tRNA halves as well, suggesting a previously uncharacterized link between 5'-tRNA halves and td-piRNAs. An increase in levels of the 5'-tRNA halves, induced by BmNSun2 knockdown, enhanced the td-piRNA expression levels without quantitative change in mature tRNAs, indicating that 5'-tRNA halves, not mature tRNAs, are the direct precursors for td-piRNAs. For the generation of tRNAHisGUG-derived piRNAs, BmThg1l-mediated nucleotide addition to -1 position of tRNAHisGUG was required, revealing an important function of BmThg1l in piRNA biogenesis. Our study advances the understanding of biogenesis mechanisms and the genesis of specific expression profiles for tRNA-derived ncRNAs.
[Mh] Termos MeSH primário: Proteínas Argonauta/genética
Bombyx/genética
Proteínas de Insetos/genética
RNA Interferente Pequeno/genética
RNA de Transferência de Ácido Aspártico/genética
RNA de Transferência de Histidina/genética
[Mh] Termos MeSH secundário: Animais
Proteínas Argonauta/metabolismo
Sequência de Bases
Bombyx/crescimento & desenvolvimento
Bombyx/metabolismo
Regulação da Expressão Gênica no Desenvolvimento
Células Germinativas/crescimento & desenvolvimento
Células Germinativas/metabolismo
Proteínas de Insetos/metabolismo
Conformação de Ácido Nucleico
RNA Interferente Pequeno/metabolismo
RNA de Transferência de Ácido Aspártico/metabolismo
RNA de Transferência de Histidina/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Argonaute Proteins); 0 (Insect Proteins); 0 (RNA, Small Interfering); 0 (RNA, Transfer, Asp); 0 (RNA, Transfer, His)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171012
[Lr] Data última revisão:
171012
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170625
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx537


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[PMID]:28499021
[Au] Autor:Gößringer M; Lechner M; Brillante N; Weber C; Rossmanith W; Hartmann RK
[Ad] Endereço:Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35037 Marburg, Germany.
[Ti] Título:Protein-only RNase P function in Escherichia coli: viability, processing defects and differences between PRORP isoenzymes.
[So] Source:Nucleic Acids Res;45(12):7441-7454, 2017 Jul 07.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The RNase P family comprises structurally diverse endoribonucleases ranging from complex ribonucleoproteins to single polypeptides. We show that the organellar (AtPRORP1) and the two nuclear (AtPRORP2,3) single-polypeptide RNase P isoenzymes from Arabidopsis thaliana confer viability to Escherichia coli cells with a lethal knockdown of its endogenous RNA-based RNase P. RNA-Seq revealed that AtPRORP1, compared with bacterial RNase P or AtPRORP3, cleaves several precursor tRNAs (pre-tRNAs) aberrantly in E. coli. Aberrant cleavage by AtPRORP1 was mainly observed for pre-tRNAs that can form short acceptor-stem extensions involving G:C base pairs, including tRNAAsp(GUC), tRNASer(CGA) and tRNAHis. However, both AtPRORP1 and 3 were defective in processing of E. coli pre-tRNASec carrying an acceptor stem expanded by three G:C base pairs. Instead, pre-tRNASec was degraded, suggesting that tRNASec is dispensable for E. coli under laboratory conditions. AtPRORP1, 2 and 3 are also essentially unable to process the primary transcript of 4.5S RNA, a hairpin-like non-tRNA substrate processed by E. coli RNase P, indicating that PRORP enzymes have a narrower, more tRNA-centric substrate spectrum than bacterial RNA-based RNase P enzymes. The cells' viability also suggests that the essential function of the signal recognition particle can be maintained with a 5΄-extended 4.5S RNA.
[Mh] Termos MeSH primário: Proteínas de Escherichia coli/genética
Escherichia coli/genética
Regulação Bacteriana da Expressão Gênica
Precursores de RNA/genética
Ribonuclease P/genética
[Mh] Termos MeSH secundário: Arabidopsis/genética
Arabidopsis/metabolismo
Proteínas de Arabidopsis/genética
Proteínas de Arabidopsis/metabolismo
Pareamento de Bases
Sequência de Bases
Escherichia coli/metabolismo
Proteínas de Escherichia coli/metabolismo
Teste de Complementação Genética
Viabilidade Microbiana
Conformação de Ácido Nucleico
Precursores de RNA/metabolismo
RNA Bacteriano/genética
RNA Bacteriano/metabolismo
RNA de Transferência de Ácido Aspártico/genética
RNA de Transferência de Ácido Aspártico/metabolismo
RNA de Transferência de Histidina/genética
RNA de Transferência de Histidina/metabolismo
RNA de Transferência de Serina/genética
RNA de Transferência de Serina/metabolismo
Ribonuclease P/deficiência
Ribonuclease P/metabolismo
Transgenes
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (4.5S RNA); 0 (Arabidopsis Proteins); 0 (Escherichia coli Proteins); 0 (RNA Precursors); 0 (RNA, Bacterial); 0 (RNA, Transfer, Asp); 0 (RNA, Transfer, His); 0 (RNA, Transfer, Ser); EC 3.1.26.5 (PRORP1 protein, Arabidopsis); EC 3.1.26.5 (PRORP2 protein, Arabidopsis); EC 3.1.26.5 (PRORP3 protein, Arabidopsis); EC 3.1.26.5 (Ribonuclease P)
[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:170513
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx405


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[PMID]:28115596
[Au] Autor:Zhang J; Li D; Zhang J; Chen D; Murchie AI
[Ad] Endereço:Fudan University Pudong Medical Center, Pudong, Shanghai 201399, China.
[Ti] Título:Osmium tetroxide as a probe of RNA structure.
[So] Source:RNA;23(4):483-492, 2017 Apr.
[Is] ISSN:1469-9001
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Structured RNAs have a central role in cellular function. The capability of structured RNAs to adopt fixed architectural structures or undergo dynamic conformational changes contributes to their diverse role in the regulation of gene expression. Although numerous biophysical and biochemical tools have been developed to study structured RNAs, there is a continuing need for the development of new methods for the investigation of RNA structures, especially methods that allow RNA structure to be studied in solution close to its native cellular conditions. Here we use osmium tetroxide (OsO ) as a chemical probe of RNA structure. In this method, we have used fluorescence-based sequencing technologies to detect OsO modified RNA. We characterized the requirements for OsO modification of RNA by investigating three known structured RNAs: the M-box, glycine riboswitch RNAs, and tRNA Our results show that OsO predominantly modifies RNA at uracils that are conformationally exposed on the surface of the RNA. We also show that changes in OsO reactivity at flexible positions in the RNA correlate with ligand-driven conformational changes in the RNA structure. Osmium tetroxide modification of RNA will provide insights into the structural features of RNAs that are relevant to their underlying biological functions.
[Mh] Termos MeSH primário: Sondas Moleculares/química
Tetróxido de Ósmio/química
RNA de Transferência de Ácido Aspártico/química
Riboswitch/genética
[Mh] Termos MeSH secundário: Sequência de Bases
Conformação de Ácido Nucleico
RNA de Transferência de Ácido Aspártico/genética
Coloração e Rotulagem/métodos
Uracila/química
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Molecular Probes); 0 (RNA, Transfer, Asp); 0 (Riboswitch); 56HH86ZVCT (Uracil); P40W033BGM (Osmium Tetroxide)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170906
[Lr] Data última revisão:
170906
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170125
[St] Status:MEDLINE
[do] DOI:10.1261/rna.057539.116


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[PMID]:27956500
[Au] Autor:Myka KK; Hawkins M; Syeda AH; Gupta MK; Meharg C; Dillingham MS; Savery NJ; Lloyd RG; McGlynn P
[Ad] Endereço:Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK.
[Ti] Título:Inhibiting translation elongation can aid genome duplication in Escherichia coli.
[So] Source:Nucleic Acids Res;45(5):2571-2584, 2017 Mar 17.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Conflicts between replication and transcription challenge chromosome duplication. Escherichia coli replisome movement along transcribed DNA is promoted by Rep and UvrD accessory helicases with Δrep ΔuvrD cells being inviable under rapid growth conditions. We have discovered that mutations in a tRNA gene, aspT, in an aminoacyl tRNA synthetase, AspRS, and in a translation factor needed for efficient proline-proline bond formation, EF-P, suppress Δrep ΔuvrD lethality. Thus replication-transcription conflicts can be alleviated by the partial sacrifice of a mechanism that reduces replicative barriers, namely translating ribosomes that reduce RNA polymerase backtracking. Suppression depends on RelA-directed synthesis of (p)ppGpp, a signalling molecule that reduces replication-transcription conflicts, with RelA activation requiring ribosomal pausing. Levels of (p)ppGpp in these suppressors also correlate inversely with the need for Rho activity, an RNA translocase that can bind to emerging transcripts and displace transcription complexes. These data illustrate the fine balance between different mechanisms in facilitating gene expression and genome duplication and demonstrate that accessory helicases are a major determinant of this balance. This balance is also critical for other aspects of bacterial survival: the mutations identified here increase persistence indicating that similar mutations could arise in naturally occurring bacterial populations facing antibiotic challenge.
[Mh] Termos MeSH primário: Replicação do DNA
Escherichia coli/genética
Genoma Bacteriano
Elongação Traducional da Cadeia Peptídica
[Mh] Termos MeSH secundário: DNA Helicases/genética
Escherichia coli/enzimologia
Escherichia coli/crescimento & desenvolvimento
Proteínas de Escherichia coli/genética
Proteínas de Escherichia coli/metabolismo
Mutação
RNA de Transferência de Ácido Aspártico/genética
Supressão Genética
Aminoacilação de RNA de Transferência
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Escherichia coli Proteins); 0 (RNA, Transfer, Asp); 0 (Rho protein, E coli); 0 (rep protein, E coli); EC 3.6.1.- (UvrD protein, E coli); EC 3.6.4.- (DNA Helicases)
[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:161214
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkw1254


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[PMID]:27536005
[Au] Autor:Wang M; Peng Y; Zheng J; Zheng B; Jin X; Liu H; Wang Y; Tang X; Huang T; Jiang P; Guan MX
[Ad] Endereço:Division of Clinical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
[Ti] Título:A deafness-associated tRNAAsp mutation alters the m1G37 modification, aminoacylation and stability of tRNAAsp and mitochondrial function.
[So] Source:Nucleic Acids Res;44(22):10974-10985, 2016 Dec 15.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:In this report, we investigated the pathogenic mechanism underlying the deafness-associated mitochondrial(mt) tRNA 7551A > G mutation. The m.7551A > G mutation is localized at a highly conserved nucleotide(A37), adjacent (3') to the anticodon, which is important for the fidelity of codon recognition and stabilization in functional tRNAs. It was anticipated that the m.7551A > G mutation altered the structure and function of mt-tRNA The primer extension assay demonstrated that the m.7551A > G mutation created the m G37 modification of mt-tRNA Using cybrid cell lines generated by transferring mitochondria from lymphoblastoid cell lines derived from a Chinese family into mitochondrial DNA(mtDNA)-less (ρ ) cells, we demonstrated the significant decreases in the efficiency of aminoacylation and steady-state level of mt-tRNA in mutant cybrids, compared with control cybrids. A failure in metabolism of mt-tRNA caused the variable reductions in mtDNA-encoded polypeptides in mutant cybrids. Impaired mitochondrial translation led to the respiratory phenotype in mutant cybrids. The respiratory deficiency lowed mitochondrial adenosine triphosphate production and increased the production of oxidative reactive species in mutant cybrids. Our data demonstrated that mitochondrial dysfunctions caused by the m.7551A > G mutation are associated with deafness. Our findings may provide new insights into the pathophysiology of maternally transmitted deafness that was manifested by altered nucleotide modification of mitochondrial tRNA.
[Mh] Termos MeSH primário: Surdez/genética
Mitocôndrias/genética
RNA de Transferência de Ácido Aspártico/genética
[Mh] Termos MeSH secundário: Linhagem Celular
Estudos de Associação Genética
Seres Humanos
Masculino
Potencial da Membrana Mitocondrial
Linhagem
Mutação Puntual
Estabilidade de RNA
Espécies Reativas de Oxigênio/metabolismo
Adulto Jovem
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Transfer, Asp); 0 (Reactive Oxygen Species)
[Em] Mês de entrada:1706
[Cu] Atualização por classe:170728
[Lr] Data última revisão:
170728
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160819
[St] Status:MEDLINE


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[PMID]:26424849
[Au] Autor:Müller M; Hartmann M; Schuster I; Bender S; Thüring KL; Helm M; Katze JR; Nellen W; Lyko F; Ehrenhofer-Murray AE
[Ad] Endereço:Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
[Ti] Título:Dynamic modulation of Dnmt2-dependent tRNA methylation by the micronutrient queuine.
[So] Source:Nucleic Acids Res;43(22):10952-62, 2015 Dec 15.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Dnmt2 enzymes are cytosine-5 methyltransferases that methylate C38 of several tRNAs. We report here that the activities of two Dnmt2 homologs, Pmt1 from Schizosaccharomyces pombe and DnmA from Dictyostelium discoideum, are strongly stimulated by prior queuosine (Q) modification of the substrate tRNA. In vivo tRNA methylation levels were stimulated by growth of cells in queuine-containing medium; in vitro Pmt1 activity was enhanced on Q-containing RNA; and queuine-stimulated in vivo methylation was abrogated by the absence of the enzyme that inserts queuine into tRNA, eukaryotic tRNA-guanine transglycosylase. Global analysis of tRNA methylation in S. pombe showed a striking selectivity of Pmt1 for tRNA(Asp) methylation, which distinguishes Pmt1 from other Dnmt2 homologs. The present analysis also revealed a novel Pmt1- and Q-independent tRNA methylation site in S. pombe, C34 of tRNA(Pro). Notably, queuine is a micronutrient that is scavenged by higher eukaryotes from the diet and gut microflora. This work therefore reveals an unanticipated route by which the environment can modulate tRNA modification in an organism.
[Mh] Termos MeSH primário: DNA (Citosina-5-)-Metiltransferases/metabolismo
Guanina/análogos & derivados
Micronutrientes/metabolismo
RNA de Transferência/metabolismo
Proteínas de Schizosaccharomyces pombe/metabolismo
[Mh] Termos MeSH secundário: Dictyostelium/enzimologia
Guanina/metabolismo
Metilação
Pentosiltransferases/metabolismo
RNA de Transferência de Ácido Aspártico/metabolismo
Schizosaccharomyces/genética
Schizosaccharomyces/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Micronutrients); 0 (RNA, Transfer, Asp); 0 (Schizosaccharomyces pombe Proteins); 5Z93L87A1R (Guanine); 72496-59-4 (queuine); 9014-25-9 (RNA, Transfer); EC 2.1.1.37 (DNA (Cytosine-5-)-Methyltransferases); EC 2.1.1.37 (Pmt1 protein, S pombe); EC 2.4.2.- (Pentosyltransferases); EC 2.4.2.29 (queuine tRNA-ribosyltransferase)
[Em] Mês de entrada:1606
[Cu] Atualização por classe:171116
[Lr] Data última revisão:
171116
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151002
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkv980


  7 / 251 MEDLINE  
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[PMID]:25747896
[Au] Autor:Elhardt W; Shanmugam R; Jurkowski TP; Jeltsch A
[Ad] Endereço:Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany.
[Ti] Título:Somatic cancer mutations in the DNMT2 tRNA methyltransferase alter its catalytic properties.
[So] Source:Biochimie;112:66-72, 2015 May.
[Is] ISSN:1638-6183
[Cp] País de publicação:France
[La] Idioma:eng
[Ab] Resumo:Methylation of tRNA is an important post-transcriptional modification and aberrations in tRNA modification has been implicated in cancer. The DNMT2 protein methylates C38 of tRNA-Asp and it has a role in cellular physiology and stress response and its expression levels are altered in cancer tissues. Here we studied whether DNMT2 somatic mutations found in cancer tissues affect the activity of the enzyme. We have generated 13 DNMT2 variants and purified the corresponding proteins. All proteins were properly folded as determined by circular dichroism spectroscopy. We tested their RNA methylation activity using in vitro generated tRNA-Asp. One of the mutations (E63K) caused a twofold increase in activity, while two of them led to a strong (over fourfold) decrease in activity (G155S and L257V). Two additional mutant proteins were almost inactive (R371H and G155V). The strong effect of some of the somatic cancer mutations on DNMT2 activity suggests that these mutations have a functional role in tumorigenesis.
[Mh] Termos MeSH primário: DNA (Citosina-5-)-Metiltransferases/química
Mutação de Sentido Incorreto
Proteínas de Neoplasias/química
Neoplasias/enzimologia
Processamento Pós-Transcricional do RNA
RNA de Transferência de Ácido Aspártico/química
[Mh] Termos MeSH secundário: Substituição de Aminoácidos
Animais
Catálise
DNA (Citosina-5-)-Metiltransferases/genética
DNA (Citosina-5-)-Metiltransferases/metabolismo
Seres Humanos
Metilação
Camundongos
Proteínas de Neoplasias/genética
Proteínas de Neoplasias/metabolismo
Neoplasias/genética
RNA de Transferência de Ácido Aspártico/genética
RNA de Transferência de Ácido Aspártico/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Neoplasm Proteins); 0 (RNA, Transfer, Asp); EC 2.1.1.37 (DNA (Cytosine-5-)-Methyltransferases); EC 2.1.1.37 (TRDMT1 protein, human)
[Em] Mês de entrada:1601
[Cu] Atualização por classe:171116
[Lr] Data última revisão:
171116
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150310
[St] Status:MEDLINE


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[PMID]:25447692
[Au] Autor:Lehmann D; Schubert K; Joshi PR; Baty K; Blakely EL; Zierz S; Taylor RW; Deschauer M
[Ad] Endereço:Department of Neurology, University of Halle-Wittenberg, Ernst-Grube-Str. 40, Halle/Saale 06097, Germany.
[Ti] Título:A novel m.7539C>T point mutation in the mt-tRNA(Asp) gene associated with multisystemic mitochondrial disease.
[So] Source:Neuromuscul Disord;25(1):81-4, 2015 Jan.
[Is] ISSN:1873-2364
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Mitochondrial transfer RNA (mt-tRNA) mutations are the commonest sub-type of mitochondrial (mtDNA) mutations associated with human disease. We report a patient with multisytemic disease characterised by myopathy, spinal ataxia, sensorineural hearing loss, cataract and cognitive impairment in whom a novel m.7539C>T mt-tRNA(Asp) transition was identified. Muscle biopsy revealed extensive histopathological findings including cytochrome c oxidase (COX)-deficient fibres. Pyrosequencing confirmed mtDNA heteroplasmy for the mutation whilst single muscle fibre segregation studies revealed statistically significant higher mutation loads in COX-deficient fibres than in COX-positive fibres. Absence from control databases, hierarchical mt-tRNA mutation segregation within tissues, and occurrence at conserved sequence positions, further confirm this novel mt-tRNA mutation to be pathogenic. To date only three mt-tRNA(Asp) gene mutations have been described with clear evidence of pathogenicity. The novel m.7539C>T mt-tRNA(Asp) gene mutation extends the spectrum of pathogenic mutations in this gene, further supporting the notion that mt-tRNA(Asp) gene mutations are associated with multisystemic disease presentations.
[Mh] Termos MeSH primário: DNA Mitocondrial/genética
Doenças Mitocondriais/diagnóstico
Doenças Mitocondriais/genética
Mutação Puntual
RNA de Transferência de Ácido Aspártico/genética
RNA/genética
[Mh] Termos MeSH secundário: Encéfalo/patologia
Complexo IV da Cadeia de Transporte de Elétrons/metabolismo
Feminino
Seres Humanos
Meia-Idade
Mitocôndrias/metabolismo
Músculo Esquelético/enzimologia
Músculo Esquelético/patologia
[Pt] Tipo de publicação:CASE REPORTS; JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, Mitochondrial); 0 (RNA, Transfer, Asp); 0 (RNA, mitochondrial); 63231-63-0 (RNA); EC 1.9.3.1 (Electron Transport Complex IV)
[Em] Mês de entrada:1508
[Cu] Atualização por classe:170922
[Lr] Data última revisão:
170922
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:141203
[St] Status:MEDLINE


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[PMID]:25217588
[Au] Autor:Hamdane D; Guelorget A; Guérineau V; Golinelli-Pimpaneau B
[Ad] Endereço:Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France djemel.hamdane@college-de-f
[Ti] Título:Dynamics of RNA modification by a multi-site-specific tRNA methyltransferase.
[So] Source:Nucleic Acids Res;42(18):11697-706, 2014 Oct.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:In most organisms, the widely conserved 1-methyl-adenosine58 (m1A58) tRNA modification is catalyzed by an S-adenosyl-L-methionine (SAM)-dependent, site-specific enzyme TrmI. In archaea, TrmI also methylates the adjacent adenine 57, m1A57 being an obligatory intermediate of 1-methyl-inosine57 formation. To study this multi-site specificity, we used three oligoribonucleotide substrates of Pyrococcus abyssi TrmI (PabTrmI) containing a fluorescent 2-aminopurine (2-AP) at the two target positions and followed the RNA binding kinetics and methylation reactions by stopped-flow and mass spectrometry. PabTrmI did not modify 2-AP but methylated the adjacent target adenine. 2-AP seriously impaired the methylation of A57 but not A58, confirming that PabTrmI methylates efficiently the first adenine of the A57A58A59 sequence. PabTrmI binding provoked a rapid increase of fluorescence, attributed to base unstacking in the environment of 2-AP. Then, a slow decrease was observed only with 2-AP at position 57 and SAM, suggesting that m1A58 formation triggers RNA release. A model of the protein-tRNA complex shows both target adenines in proximity of SAM and emphasizes no major tRNA conformational change except base flipping during the reaction. The solvent accessibility of the SAM pocket is not affected by the tRNA, thereby enabling S-adenosyl-L-homocysteine to be replaced by SAM without prior release of monomethylated tRNA.
[Mh] Termos MeSH primário: Adenina/metabolismo
Proteínas Arqueais/metabolismo
RNA de Transferência de Ácido Aspártico/metabolismo
tRNA Metiltransferases/metabolismo
[Mh] Termos MeSH secundário: 2-Aminopurina/metabolismo
Proteínas Arqueais/química
Sequência de Bases
Modelos Moleculares
Pyrococcus abyssi/enzimologia
RNA de Transferência de Ácido Aspártico/química
S-Adenosilmetionina/metabolismo
Especificidade por Substrato
tRNA Metiltransferases/química
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Archaeal Proteins); 0 (RNA, Transfer, Asp); 452-06-2 (2-Aminopurine); 7LP2MPO46S (S-Adenosylmethionine); EC 2.1.1.- (tRNA Methyltransferases); JAC85A2161 (Adenine)
[Em] Mês de entrada:1501
[Cu] Atualização por classe:150804
[Lr] Data última revisão:
150804
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:140914
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gku820


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[PMID]:24711368
[Au] Autor:Shanmugam R; Aklujkar M; Schäfer M; Reinhardt R; Nickel O; Reuter G; Lovley DR; Ehrenhofer-Murray A; Nellen W; Ankri S; Helm M; Jurkowski TP; Jeltsch A
[Ad] Endereço:Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany.
[Ti] Título:The Dnmt2 RNA methyltransferase homolog of Geobacter sulfurreducens specifically methylates tRNA-Glu.
[So] Source:Nucleic Acids Res;42(10):6487-96, 2014 Jun.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Dnmt2 enzymes are conserved in eukaryotes, where they methylate C38 of tRNA-Asp with high activity. Here, the activity of one of the very few prokaryotic Dnmt2 homologs from Geobacter species (GsDnmt2) was investigated. GsDnmt2 was observed to methylate tRNA-Asp from flies and mice. Unexpectedly, it had only a weak activity toward its matching Geobacter tRNA-Asp, but methylated Geobacter tRNA-Glu with good activity. In agreement with this result, we show that tRNA-Glu is methylated in Geobacter while the methylation is absent in tRNA-Asp. The activities of Dnmt2 enzymes from Homo sapiens, Drosophila melanogaster, Schizosaccharomyces pombe and Dictyostelium discoideum for methylation of the Geobacter tRNA-Asp and tRNA-Glu were determined showing that all these Dnmt2s preferentially methylate tRNA-Asp. Hence, the GsDnmt2 enzyme has a swapped transfer ribonucleic acid (tRNA) specificity. By comparing the different tRNAs, a characteristic sequence pattern was identified in the variable loop of all preferred tRNA substrates. An exchange of two nucleotides in the variable loop of murine tRNA-Asp converted it to the corresponding variable loop of tRNA-Glu and led to a strong reduction of GsDnmt2 activity. Interestingly, the same loss of activity was observed with human DNMT2, indicating that the variable loop functions as a specificity determinant in tRNA recognition of Dnmt2 enzymes.
[Mh] Termos MeSH primário: Proteínas de Bactérias/metabolismo
Geobacter/enzimologia
RNA de Transferência de Ácido Glutâmico/metabolismo
tRNA Metiltransferases/metabolismo
[Mh] Termos MeSH secundário: Animais
Seres Humanos
Metilação
Camundongos
Conformação de Ácido Nucleico
RNA de Transferência de Ácido Aspártico/química
RNA de Transferência de Ácido Aspártico/metabolismo
RNA de Transferência de Ácido Glutâmico/química
Especificidade por Substrato
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (RNA, Transfer, Asp); 0 (RNA, Transfer, Glu); EC 2.1.1.- (tRNA Methyltransferases)
[Em] Mês de entrada:1408
[Cu] Atualização por classe:150806
[Lr] Data última revisão:
150806
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:140409
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gku256



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