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Pesquisa : G02.111.570.820.709.275.500.869 [Categoria DeCS]
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  1 / 17 MEDLINE  
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[PMID]:29212661
[Au] Autor:Berry S; Rosa S; Howard M; Bühler M; Dean C
[Ad] Endereço:John Innes Centre, Norwich NR4 7UH, United Kingdom.
[Ti] Título:Disruption of an RNA-binding hinge region abolishes LHP1-mediated epigenetic repression.
[So] Source:Genes Dev;31(21):2115-2120, 2017 11 01.
[Is] ISSN:1549-5477
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Epigenetic maintenance of gene repression is essential for development. Polycomb complexes are central to this memory, but many aspects of the underlying mechanism remain unclear. LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) binds Polycomb-deposited H3K27me3 and is required for repression of many Polycomb target genes in Here we show that LHP1 binds RNA in vitro through the intrinsically disordered hinge region. By independently perturbing the RNA-binding hinge region and H3K27me3 (trimethylation of histone H3 at Lys27) recognition, we found that both facilitate LHP1 localization and H3K27me3 maintenance. Disruption of the RNA-binding hinge region also prevented formation of subnuclear foci, structures potentially important for epigenetic repression.
[Mh] Termos MeSH primário: Proteínas de Arabidopsis/genética
Arabidopsis/genética
Proteínas Cromossômicas não Histona/metabolismo
Repressão Epigenética/genética
[Mh] Termos MeSH secundário: Proteínas Cromossômicas não Histona/genética
Regulação da Expressão Gênica de Plantas/genética
Histonas/metabolismo
Mutação/genética
Proteínas do Grupo Polycomb/genética
Proteínas do Grupo Polycomb/metabolismo
Motivos de Ligação ao RNA/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Arabidopsis Proteins); 0 (Chromosomal Proteins, Non-Histone); 0 (Histones); 0 (Polycomb-Group Proteins); 0 (like heterochromatin protein 1)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:180130
[Lr] Data última revisão:
180130
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171208
[St] Status:MEDLINE
[do] DOI:10.1101/gad.305227.117


  2 / 17 MEDLINE  
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[PMID]:29095441
[Au] Autor:Castello A; Frese CK; Fischer B; Järvelin AI; Horos R; Alleaume AM; Foehr S; Curk T; Krijgsveld J; Hentze MW
[Ad] Endereço:European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
[Ti] Título:Identification of RNA-binding domains of RNA-binding proteins in cultured cells on a system-wide scale with RBDmap.
[So] Source:Nat Protoc;12(12):2447-2464, 2017 Dec.
[Is] ISSN:1750-2799
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:This protocol is an extension to: Nat. Protoc. 8, 491-500 (2013); doi:10.1038/nprot.2013.020; published online 14 February 2013RBDmap is a method for identifying, in a proteome-wide manner, the regions of RNA-binding proteins (RBPs) engaged in native interactions with RNA. In brief, cells are irradiated with UV light to induce protein-RNA cross-links. Following stringent denaturing washes, the resulting covalently linked protein-RNA complexes are purified with oligo(dT) magnetic beads. After elution, RBPs are subjected to partial proteolysis, in which the protein regions still bound to the RNA and those released to the supernatant are separated by a second oligo(dT) selection. After sample preparation and mass-spectrometric analysis, peptide intensity ratios between the RNA-bound and released fractions are used to determine the RNA-binding regions. As a Protocol Extension, this article describes an adaptation of an existing Protocol and offers additional applications. The earlier protocol (for the RNA interactome capture method) describes how to identify the active RBPs in cultured cells, whereas this Protocol Extension also enables the identification of the RNA-binding domains of RBPs. The experimental workflow takes 1 week plus 2 additional weeks for proteomics and data analysis. Notably, RBDmap presents numerous advantages over classic methods for determining RNA-binding domains: it produces proteome-wide, high-resolution maps of the protein regions contacting the RNA in a physiological context and can be adapted to different biological systems and conditions. Because RBDmap relies on the isolation of polyadenylated RNA via oligo(dT), it will not provide RNA-binding information on proteins interacting exclusively with nonpolyadenylated transcripts. Applied to HeLa cells, RBDmap uncovered 1,174 RNA-binding sites in 529 proteins, many of which were previously unknown.
[Mh] Termos MeSH primário: Algoritmos
Proteômica/métodos
RNA Mensageiro/metabolismo
Motivos de Ligação ao RNA
Proteínas de Ligação a RNA/química
[Mh] Termos MeSH secundário: Sítios de Ligação
Expressão Gênica
Células HeLa
Seres Humanos
Espectrometria de Massas
Oligodesoxirribonucleotídeos/química
Ligação Proteica
Proteólise
Proteômica/instrumentação
RNA Mensageiro/genética
Proteínas de Ligação a RNA/genética
Proteínas de Ligação a RNA/isolamento & purificação
Raios Ultravioleta
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Oligodeoxyribonucleotides); 0 (RNA, Messenger); 0 (RNA-Binding Proteins); 0 (oligo (dT))
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171114
[Lr] Data última revisão:
171114
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171103
[St] Status:MEDLINE
[do] DOI:10.1038/nprot.2017.106


  3 / 17 MEDLINE  
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[PMID]:29050934
[Au] Autor:Wang L; Yan F
[Ad] Endereço:Division of Nephrology, Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, United States.
[Ti] Título:Molecular insights into the specific recognition between the RNA binding domain qRRM2 of hnRNP F and G-tract RNA: A molecular dynamics study.
[So] Source:Biochem Biophys Res Commun;494(1-2):95-100, 2017 Dec 09.
[Is] ISSN:1090-2104
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Heterogeneous nuclear ribonucleoprotein F (hnRNP F) controls the expression of various genes through regulating the alternative splicing of pre-mRNAs in the nucleus. It uses three quasi-RNA recognition motifs (qRRMs) to recognize G-tract RNA which contains at least three consecutive guanines. The structures containing qRRMs of hnRNP F in complex with G-tract RNA have been determined by nuclear magnetic resonance (NMR) spectroscopy, shedding light on the recognition mechanism of qRRMs with G-tract RNA. However, knowledge of the recognition details is still lacking. To investigate how qRRMs specifically bind with G-tract RNA and how the mutations of any guanine to an adenine in the G-tract affect the binding, molecular dynamics simulations with binding free energy analysis were performed based on the NMR structure of qRRM2 in complex with G-tract RNA. Simulation results demonstrate that qRRM2 binds strongly with G-tract RNA, but any mutation of the G-tract leads to a drastic reduction of the binding free energy. Further comparisons of the energetic components reveal that van der Waals and non-polar interactions play essential roles in the binding between qRRM2 and G-tract RNA, but the interactions are weakened by the effect of RNA mutations. Structural and dynamical analyses indicate that when qRRM2 binds with G-tract RNA, both qRRM2 and G-tract maintain stabilized structures and dynamics; however, the stability is disrupted by the mutations of the G-tract. These results provide novel insights into the recognition mechanism of qRRM2 with G-tract RNA that are not elucidated by the NMR technique.
[Mh] Termos MeSH primário: Ribonucleoproteínas Nucleares Heterogêneas Grupo F-H/química
Ribonucleoproteínas Nucleares Heterogêneas Grupo F-H/metabolismo
RNA/química
RNA/metabolismo
[Mh] Termos MeSH secundário: Sequência de Bases
Sítios de Ligação
Seres Humanos
Simulação de Dinâmica Molecular
Mutação
Ressonância Magnética Nuclear Biomolecular
Conformação de Ácido Nucleico
Ligação Proteica
Conformação Proteica
Estabilidade Proteica
RNA/genética
Motivo de Reconhecimento de RNA
Motivos de Ligação ao RNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Heterogeneous-Nuclear Ribonucleoprotein Group F-H); 63231-63-0 (RNA)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171113
[Lr] Data última revisão:
171113
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171021
[St] Status:MEDLINE


  4 / 17 MEDLINE  
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[PMID]:28911098
[Au] Autor:Märtens B; Sharma K; Urlaub H; 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 SmAP2 RNA binding motif in the 3'UTR affects mRNA stability in the crenarchaeum Sulfolobus solfataricus.
[So] Source:Nucleic Acids Res;45(15):8957-8967, 2017 Sep 06.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Sm and Sm-like proteins represent an evolutionarily conserved family with key roles in RNA metabolism in Pro- and Eukaryotes. In this study, a collection of 53 mRNAs that co-purified with Sulfolobus solfataricus (Sso) SmAP2 were surveyed for a specific RNA binding motif (RBM). SmAP2 was shown to bind with high affinity to the deduced consensus RNA binding motif (SmAP2-cRBM) in vitro. Residues in SmAP2 interacting with the SmAP2-cRBM were mapped by UV-induced crosslinking in combination with mass-spectrometry, and verified by mutational analyses. The RNA-binding site on SmAP2 includes a modified uracil binding pocket containing a unique threonine (T40) located on the L3 face and a second residue, K25, located in the pore. To study the function of the SmAP2-RBM in vivo, three authentic RBMs were inserted in the 3'UTR of a lacS reporter gene. The presence of the SmAP2-RBM in the reporter-constructs resulted in decreased LacS activity and reduced steady state levels of lacS mRNA. Moreover, the presence of the SmAP2-cRBM in and the replacement of the lacS 3'UTR with that of Sso2194 encompassing a SmAP2-RBM apparently impacted on the stability of the chimeric transcripts. These results are discussed in light of the function(s) of eukaryotic Lsm proteins in RNA turnover.
[Mh] Termos MeSH primário: Regiões 3´ não Traduzidas
Proteínas Arqueais/química
RNA Arqueal/genética
Motivos de Ligação ao RNA
Proteínas de Ligação a RNA/química
Sulfolobus solfataricus/genética
[Mh] Termos MeSH secundário: Proteínas Arqueais/genética
Proteínas Arqueais/metabolismo
Sequência de Bases
Sítios de Ligação
Clonagem Molecular
Escherichia coli/genética
Escherichia coli/metabolismo
Expressão Gênica
Genes Reporter
Cinética
Proteínas de Membrana Transportadoras/genética
Proteínas de Membrana Transportadoras/metabolismo
Modelos Moleculares
Ligação Proteica
Conformação Proteica em alfa-Hélice
Conformação Proteica em Folha beta
Domínios e Motivos de Interação entre Proteínas
Estabilidade de RNA
RNA Arqueal/metabolismo
Proteínas de Ligação a RNA/genética
Proteínas de Ligação a RNA/metabolismo
Proteínas Recombinantes/química
Proteínas Recombinantes/genética
Proteínas Recombinantes/metabolismo
Especificidade por Substrato
Sulfolobus solfataricus/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (3' Untranslated Regions); 0 (Archaeal Proteins); 0 (Membrane Transport Proteins); 0 (RNA, Archaeal); 0 (RNA-Binding Proteins); 0 (Recombinant Proteins); 9068-45-5 (lactose permease)
[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:170916
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx581


  5 / 17 MEDLINE  
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[PMID]:28328139
[Au] Autor:Soma N; Higashimoto K; Imamura M; Saitoh A; Soejima H; Nagasaki K
[Ad] Endereço:Department of Homeostatic Regulation and Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.
[Ti] Título:Long term survival of a patient with Perlman syndrome due to novel compound heterozygous missense mutations in RNB domain of DIS3L2.
[So] Source:Am J Med Genet A;173(4):1077-1081, 2017 Apr.
[Is] ISSN:1552-4833
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Perlman syndrome is a rare overgrowth syndrome characterized by polyhydramnios, macrosomia, distinctive facial appearance, renal dysplasia, and a predisposition to Wilms' tumor. The syndrome is often associated with a high neonatal mortality rate and there are few reports of long-term survivors. We studied a 6-year-old Japanese female patient, who was diagnosed with Perlman syndrome, with novel compound heterozygous mutations in DIS3L2 (c.[367-2A > G];[1328T > A]), who has survived long term. Most reported DIS3L2 mutations have been the homozygous deletion of exon 6 or exon 9, and these mutations would certainly have caused the loss of both RNA binding and degradation activity. We have identified new compound heterozygous mutations in the DIS3L2 of this long-term survivor of Perlman syndrome. The reason our patient has survived long-term would be a missense mutation (c.1328 T > A, p.Met443Lys) having retained RNA binding in both the cold-shock domains and the S1 domain, and through partial RNA degradation. If partial exonuclease functions remain in at least one allele, long-term survival may be possible. Further studies of Perlman syndrome patients with proven DIS3L2 mutations are needed to clarify genotype-phenotype correlation.
[Mh] Termos MeSH primário: Exorribonucleases/genética
Macrossomia Fetal/genética
Mutação de Sentido Incorreto
Sobreviventes
Tumor de Wilms/genética
[Mh] Termos MeSH secundário: Sequência de Bases
Criança
Exorribonucleases/metabolismo
Feminino
Macrossomia Fetal/diagnóstico
Macrossomia Fetal/patologia
Macrossomia Fetal/cirurgia
Expressão Gênica
Estudos de Associação Genética
Heterozigoto
Seres Humanos
Linhagem
Motivos de Ligação ao RNA
Tumor de Wilms/diagnóstico
Tumor de Wilms/patologia
Tumor de Wilms/cirurgia
[Pt] Tipo de publicação:CASE REPORTS; JOURNAL ARTICLE
[Nm] Nome de substância:
EC 3.1.- (DIS3L2 protein, human); EC 3.1.- (Exoribonucleases)
[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:170323
[St] Status:MEDLINE
[do] DOI:10.1002/ajmg.a.38111


  6 / 17 MEDLINE  
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[PMID]:28179533
[Au] Autor:Matsumoto Y; Ohta K; Kolakofsky D; Nishio M
[Ad] Endereço:Department of Microbiology, School of Medicine, Wakayama Medical University, Wakayama, Japan ymatsu@wakayama-med.ac.jp.
[Ti] Título:A Point Mutation in the RNA-Binding Domain of Human Parainfluenza Virus Type 2 Nucleoprotein Elicits Abnormally Enhanced Polymerase Activity.
[So] Source:J Virol;91(9), 2017 May 01.
[Is] ISSN:1098-5514
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The genome RNA of human parainfluenza virus type 2 (hPIV2) that acts as the template for the polymerase complex is entirely encapsidated by the nucleoprotein (NP). Recently, the crystal structure of NP of PIV5, a virus closely related to hPIV2, was resolved in association with RNA. Ten amino acids that contact the bound RNA were identified and are strictly conserved between PIV5 and hPIV2 NP. Mutation of hPIV2 NP Q202 (which contacts a base rather than the RNA backbone) to various amino acids resulted in an over 30-fold increase of polymerase activity as evidenced by a minireplicon assay, even though the RNA-binding affinity was unaltered. Using various modified minireplicons, we found that the enhanced reporter gene expression could be accounted for by increased minigenome replication, whereas mRNA synthesis itself was not affected by Q202 mutation. Moreover, the enhanced activities were still observed in minigenomes partially lacking the leader sequence and which were not of hexamer genome length. Unexpectedly, recombinant hPIV2 possessing the NP Q202A mutation could not be recovered from cDNA. We examined the importance of amino acids in the putative RNA-binding domain of hPIV2 NP for polymerase activity using minireplicons. Abnormally enhanced genome replication was observed upon substitution mutation of the NP Q202 position to various amino acids. Surprisingly, this mutation enabled polymerase to use minigenomes that were partially lacking the leader sequence and not of hexamer genome length. This mutation does not affect fundamental properties of NP, e.g., recognition of gene junctional and editing signals. However, the strongly enhanced polymerase activity may not be viable for the infectious life cycle. This report highlights the potential of the polymerase complex with point mutations in NP and helps our detailed understanding of the molecular basis of gene expression.
[Mh] Termos MeSH primário: Nucleocapsídeo/metabolismo
Nucleoproteínas/genética
Vírus da Parainfluenza 2 Humana/genética
RNA Replicase/metabolismo
Motivos de Ligação ao RNA/genética
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Sítios de Ligação/genética
Linhagem Celular
Genoma Viral/genética
Seres Humanos
Mutação Puntual/genética
RNA Replicase/genética
RNA Viral/biossíntese
RNA Viral/genética
Transcrição Genética
Proteínas Virais/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Nucleoproteins); 0 (RNA, Viral); 0 (Viral Proteins); EC 2.7.7.48 (RNA Replicase)
[Em] Mês de entrada:1705
[Cu] Atualização por classe:171013
[Lr] Data última revisão:
171013
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170210
[St] Status:MEDLINE


  7 / 17 MEDLINE  
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[PMID]:27630136
[Au] Autor:Methawasin M; Strom JG; Slater RE; Fernandez V; Saripalli C; Granzier H
[Ad] Endereço:From Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson.
[Ti] Título:Experimentally Increasing the Compliance of Titin Through RNA Binding Motif-20 (RBM20) Inhibition Improves Diastolic Function In a Mouse Model of Heart Failure With Preserved Ejection Fraction.
[So] Source:Circulation;134(15):1085-1099, 2016 Oct 11.
[Is] ISSN:1524-4539
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Left ventricular (LV) stiffening contributes to heart failure with preserved ejection fraction (HFpEF), a syndrome with no effective treatment options. Increasing the compliance of titin in the heart has become possible recently through inhibition of the splicing factor RNA binding motif-20. Here, we investigated the effects of increasing the compliance of titin in mice with diastolic dysfunction. METHODS: Mice in which the RNA recognition motif (RRM) of one of the RNA binding motif-20 alleles was floxed and that expressed the MerCreMer transgene under control of the αMHC promoter (referred to as cRbm20 mice) were used. Mice underwent transverse aortic constriction (TAC) surgery and deoxycorticosterone acetate (DOCA) pellet implantation. RRM deletion in adult mice was triggered by injecting raloxifene (cRbm20 -raloxifene), with dimethyl sulfoxide (DMSO)-injected mice (cRbm20 -DMSO) as the control. Diastolic function was investigated with echocardiography and pressure-volume analysis; passive stiffness was studied in LV muscle strips and isolated cardiac myocytes before and after elimination of titin-based stiffness. Treadmill exercise performance was also studied. Titin isoform expression was evaluated with agarose gels. RESULTS: cRbm20 -raloxifene mice expressed large titins in the hearts, called supercompliant titin (N2BAsc), which, within 3 weeks after raloxifene injection, made up ≈45% of total titin. TAC/DOCA cRbm20 -DMSO mice developed LV hypertrophy and a marked increase in LV chamber stiffness as shown by both pressure-volume analysis and echocardiography. LV chamber stiffness was normalized in TAC/DOCA cRbm20 -raloxifene mice that expressed N2BAsc. Passive stiffness measurements on muscle strips isolated from the LV free wall revealed that extracellular matrix stiffness was equally increased in both groups of TAC/DOCA mice (cRbm20 -DMSO and cRbm20 -raloxifene). However, titin-based muscle stiffness was reduced in the mice that expressed N2BAsc (TAC/DOCAcRbm20 -raloxifene). Exercise testing demonstrated significant improvement in exercise tolerance in TAC/DOCA mice that expressed N2BAsc. CONCLUSIONS: Inhibition of the RNA binding motif-20-based titin splicing system upregulates compliant titins, which improves diastolic function and exercise tolerance in the TAC/DOCA model. Titin holds promise as a therapeutic target for heart failure with preserved ejection fraction.
[Mh] Termos MeSH primário: Diástole/genética
Tolerância ao Exercício/genética
Insuficiência Cardíaca/genética
Proteínas de Ligação a RNA/genética
Função Ventricular Esquerda/genética
[Mh] Termos MeSH secundário: Animais
Complacência (Medida de Distensibilidade)
Conectina/fisiologia
Diástole/fisiologia
Modelos Animais de Doenças
Insuficiência Cardíaca/metabolismo
Insuficiência Cardíaca/fisiopatologia
Hipertrofia Ventricular Esquerda/metabolismo
Camundongos
Camundongos Transgênicos
Motivos de Ligação ao RNA/genética
Volume Sistólico/fisiologia
Função Ventricular Esquerda/fisiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Connectin); 0 (RBM20 protein, mouse); 0 (RNA-Binding Proteins)
[Em] Mês de entrada:1704
[Cu] Atualização por classe:171011
[Lr] Data última revisão:
171011
[Sb] Subgrupo de revista:AIM; IM
[Da] Data de entrada para processamento:160916
[St] Status:MEDLINE


  8 / 17 MEDLINE  
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[PMID]:27453046
[Au] Autor:Castello A; Fischer B; Frese CK; Horos R; Alleaume AM; Foehr S; Curk T; Krijgsveld J; Hentze MW
[Ad] Endereço:European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
[Ti] Título:Comprehensive Identification of RNA-Binding Domains in Human Cells.
[So] Source:Mol Cell;63(4):696-710, 2016 Aug 18.
[Is] ISSN:1097-4164
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Mammalian cells harbor more than a thousand RNA-binding proteins (RBPs), with half of these employing unknown modes of RNA binding. We developed RBDmap to determine the RNA-binding sites of native RBPs on a proteome-wide scale. We identified 1,174 binding sites within 529 HeLa cell RBPs, discovering numerous RNA-binding domains (RBDs). Catalytic centers or protein-protein interaction domains are in close relationship with RNA-binding sites, invoking possible effector roles of RNA in the control of protein function. Nearly half of the RNA-binding sites map to intrinsically disordered regions, uncovering unstructured domains as prevalent partners in protein-RNA interactions. RNA-binding sites represent hot spots for defined posttranslational modifications such as lysine acetylation and tyrosine phosphorylation, suggesting metabolic and signal-dependent regulation of RBP function. RBDs display a high degree of evolutionary conservation and incidence of Mendelian mutations, suggestive of important functional roles. RBDmap thus yields profound insights into native protein-RNA interactions in living cells.
[Mh] Termos MeSH primário: Proteômica/métodos
Motivos de Ligação ao RNA
Proteínas de Ligação a RNA/metabolismo
RNA/metabolismo
[Mh] Termos MeSH secundário: Acetilação
Biologia Computacional
Bases de Dados de Proteínas
Evolução Molecular
Células HeLa
Seres Humanos
Metilação
Modelos Moleculares
Mutação
Conformação de Ácido Nucleico
Fosforilação
Ligação Proteica
Domínios e Motivos de Interação entre Proteínas
Processamento de Proteína Pós-Traducional
RNA/química
RNA/genética
Proteínas de Ligação a RNA/química
Proteínas de Ligação a RNA/genética
Relação Estrutura-Atividade
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA-Binding Proteins); 63231-63-0 (RNA)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170922
[Lr] Data última revisão:
170922
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160726
[St] Status:MEDLINE


  9 / 17 MEDLINE  
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[PMID]:27393659
[Au] Autor:Fish I; Boissinot S
[Ad] Endereço:Biology Department, Queens College, The City University of New York, 65-30 Kissena Boulevard, Flushing, NY 11367, USA; Graduate Center, Sub-program in Molecular, Cellular and Developmental Biology, The City University of New York, 365(th) avenue, New York, NY 10016, USA. Electronic address: bloodcell@gmail.com.
[Ti] Título:Functional evolution of the OAS1 viral sensor: Insights from old world primates.
[So] Source:Infect Genet Evol;44:341-50, 2016 Oct.
[Is] ISSN:1567-7257
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Infections with viral pathogens impose considerable selective pressure on host defensive genes. Those genes at the forefront, responsible for identifying and binding exogenous molecular viral components, will carry the hallmarks of this struggle. Oligoadenylate synthetase (OAS) enzymes play a major role in the innate defense against a large number of viruses by acting as sensors of viral infections. Following their up-regulation by the interferon pathway, OASs bind viral dsRNA and then signal ribonuclease L (RNase L) to degrade RNA, shutting down viral and host protein synthesis. We have investigated the evolution of OAS1 in twenty-two Old World monkey species. We identified a total of 35 codons with the earmarks of positive selection and we performed a comprehensive analysis of their functional significance using in silico modeling of the OAS1 protein. Subdividing OAS1 into functional domains revealed intense purifying selection in the active domain but significant positive directional selection in the RNA-binding domain (RBD), the region where OAS1 binds viral dsRNA. The modeling analysis revealed a concentration of rapidly evolving residues in one region of the RBD suggestive of the sub-functionalization of different regions of the RBD. This analysis also identified several positively selected residues circumscribing the entry to the active site suggesting adaptive evasion of viral antagonism and/or selection for production of oligoadenylate of different length.
[Mh] Termos MeSH primário: 2´,5´-Oligoadenilato Sintetase/genética
2´,5´-Oligoadenilato Sintetase/metabolismo
Evolução Biológica
Interações Hospedeiro-Patógeno
Viroses/genética
Viroses/metabolismo
[Mh] Termos MeSH secundário: 2',5'-Oligoadenilato Sintetase/química
Sequência de Aminoácidos
Animais
Sítios de Ligação
Domínio Catalítico
Cercopithecidae
Resistência à Doença/genética
Evolução Molecular
Variação Genética
Interações Hospedeiro-Patógeno/genética
Interações Hospedeiro-Patógeno/imunologia
Imunidade Inata
Modelos Moleculares
Filogenia
Conformação Proteica
RNA de Cadeia Dupla/metabolismo
Motivos de Ligação ao RNA
Seleção Genética
Análise de Sequência de DNA
Viroses/virologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Double-Stranded); EC 2.7.7.84 (2',5'-Oligoadenylate Synthetase)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:171001
[Lr] Data última revisão:
171001
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160710
[St] Status:MEDLINE


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[PMID]:27325738
[Au] Autor:Hirata A; Nishiyama S; Tamura T; Yamauchi A; Hori H
[Ad] Endereço:Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan ahirata@ehime-u.ac.jp.
[Ti] Título:Structural and functional analyses of the archaeal tRNA m2G/m22G10 methyltransferase aTrm11 provide mechanistic insights into site specificity of a tRNA methyltransferase that contains common RNA-binding modules.
[So] Source:Nucleic Acids Res;44(13):6377-90, 2016 Jul 27.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:N(2)-methylguanosine is one of the most universal modified nucleosides required for proper function in transfer RNA (tRNA) molecules. In archaeal tRNA species, a specific S-adenosyl-L-methionine (SAM)-dependent tRNA methyltransferase (MTase), aTrm11, catalyzes formation of N(2)-methylguanosine and N(2),N(2)-dimethylguanosine at position 10. Here, we report the first X-ray crystal structures of aTrm11 from Thermococcus kodakarensis (Tko), of the apo-form, and of its complex with SAM. The structures show that TkoTrm11 consists of three domains: an N-terminal ferredoxinlike domain (NFLD), THUMP domain and Rossmann-fold MTase (RFM) domain. A linker region connects the THUMP-NFLD and RFM domains. One SAM molecule is bound in the pocket of the RFM domain, suggesting that TkoTrm11 uses a catalytic mechanism similar to that of other tRNA MTases containing an RFM domain. Furthermore, the conformation of NFLD and THUMP domains in TkoTrm11 resembles that of other tRNA-modifying enzymes specifically recognizing the tRNA acceptor stem. Our docking model of TkoTrm11-SAM in complex with tRNA, combined with biochemical analyses and pre-existing evidence, provides insights into the substrate tRNA recognition mechanism: The THUMP domain recognizes a 3'-ACCA end, and the linker region and RFM domain recognize the T-stem, acceptor stem and V-loop of tRNA, thereby causing TkoTrm11 to specifically identify its methylation site.
[Mh] Termos MeSH primário: Metilação de DNA/genética
RNA de Transferência/genética
Thermococcus/química
tRNA Metiltransferases/química
[Mh] Termos MeSH secundário: Sequência de Aminoácidos/genética
Sítios de Ligação
Cristalografia por Raios X
Guanosina/análogos & derivados
Guanosina/química
Guanosina/metabolismo
Simulação de Acoplamento Molecular
RNA de Transferência/química
Motivos de Ligação ao RNA/genética
S-Adenosilmetionina/química
Alinhamento de Sequência
Thermococcus/enzimologia
tRNA Metiltransferases/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
12133JR80S (Guanosine); 2140-77-4 (7-methylguanosine); 7LP2MPO46S (S-Adenosylmethionine); 9014-25-9 (RNA, Transfer); EC 2.1.1.- (tRNA Methyltransferases)
[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:160622
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkw561



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