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  1 / 989 MEDLINE  
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[PMID]:28935369
[Au] Autor:Gao X; Oshima K; Ueda T; Nakashima T; Kimura M
[Ad] Endereço:Laboratory of Structural Biology, Graduate School of Systems Life Sciences, Hakozaki 6-10-1, Fukuoka, 812-8581, Japan.
[Ti] Título:A three-dimensional model of RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
[So] Source:Biochem Biophys Res Commun;493(2):1063-1068, 2017 Nov 18.
[Is] ISSN:1090-2104
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Ribonuclease P (RNase P) is an endoribonuclease involved in maturation of the 5'-end of tRNA. We found previously that RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of a catalytic RNase P RNA (PhopRNA) and five protein cofactors designated PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, and PhoRpp38. The crystal structures of the five proteins have been determined, a three-dimensional (3-D) model of PhopRNA has been constructed, and biochemical data, including protein-RNA interaction sites, have become available. Here, this information was combined to orient the crystallographic structures of the proteins relative to their RNA binding sites in the PhopRNA model. Some alterations were made to the PhopRNA model to improve the fit. In the resulting structure, a heterotetramer composed of PhoPop5 and PhoRpp30 bridges helices P3 and P16 in the PhopRNA C-domain, thereby probably stabilizing a double-stranded RNA structure (helix P4) containing catalytic Mg ions, while a heterodimer of PhoRpp21 and PhoRpp29 locates on a single-stranded loop connecting helices P11 and P12 in the specificity domain (S-domain) in PhopRNA, probably forming an appropriate conformation of the precursor tRNA (pre-tRNA) binding site. The fifth protein PhoRpp38 binds each kink-turn (K-turn) motif in helices P12.1, P12.2, and P16 in PhopRNA. Comparison of the structure of the resulting 3-D model with that of bacterial RNase P suggests transition from RNA-RNA interactions in bacterial RNase P to protein-RNA interactions in archaeal RNase P. The proposed 3-D model of P. horikoshii RNase P will serve as a framework for further structural and functional studies on archaeal, as well as eukaryotic, RNase Ps.
[Mh] Termos MeSH primário: Proteínas Arqueais/química
Pyrococcus horikoshii/química
RNA Arqueal/química
Ribonuclease P/química
[Mh] Termos MeSH secundário: Sítios de Ligação
Cristalografia por Raios X
Modelos Moleculares
Conformação de Ácido Nucleico
Conformação Proteica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Archaeal Proteins); 0 (RNA, Archaeal); EC 3.1.26.5 (Ribonuclease P)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171023
[Lr] Data última revisão:
171023
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170923
[St] Status:MEDLINE


  2 / 989 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


  3 / 989 MEDLINE  
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[PMID]:28715256
[Au] Autor:Kimura M
[Ad] Endereço:a Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School , Kyushu University , Fukuoka , Japan.
[Ti] Título:Structural basis for activation of an archaeal ribonuclease P RNA by protein cofactors.
[So] Source:Biosci Biotechnol Biochem;81(9):1670-1680, 2017 Sep.
[Is] ISSN:1347-6947
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Ribonuclease P (RNase P) is an endoribonuclease that catalyzes the processing of the 5'-leader sequence of precursor tRNA (pre-tRNA) in all phylogenetic domains. We have found that RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of RNase P RNA (PhopRNA) and five protein cofactors designated PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, and PhoRpp38. Biochemical characterizations over the past 10 years have revealed that PhoPop5 and PhoRpp30 fold into a heterotetramer and cooperate to activate a catalytic domain (C-domain) in PhopRNA, whereas PhoRpp21 and PhoRpp29 form a heterodimer and function together to activate a specificity domain (S-domain) in PhopRNA. PhoRpp38 plays a role in elevation of the optimum temperature of RNase P activity, binding to kink-turn (K-turn) motifs in two stem-loops in PhopRNA. This review describes the structural and functional information on P. horikoshii RNase P, focusing on the structural basis for the PhopRNA activation by the five RNase P proteins.
[Mh] Termos MeSH primário: Proteínas Arqueais/metabolismo
Pyrococcus horikoshii/genética
Pyrococcus horikoshii/metabolismo
RNA Arqueal/metabolismo
RNA de Transferência/metabolismo
Ribonuclease P/genética
[Mh] Termos MeSH secundário: Sequência de Bases
Seres Humanos
RNA Arqueal/genética
Ribonuclease P/química
Ribonuclease P/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (Archaeal Proteins); 0 (RNA, Archaeal); 9014-25-9 (RNA, Transfer); EC 3.1.26.5 (Ribonuclease P)
[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:170718
[St] Status:MEDLINE
[do] DOI:10.1080/09168451.2017.1353404


  4 / 989 MEDLINE  
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[PMID]:28576826
[Au] Autor:Tomkuviene M; Licyte J; Olendraite I; Liutkeviciute Z; Clouet-d'Orval B; Klimasauskas S
[Ad] Endereço:Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania.
[Ti] Título:Archaeal fibrillarin-Nop5 heterodimer 2'- -methylates RNA independently of the C/D guide RNP particle.
[So] Source:RNA;23(9):1329-1337, 2017 Sep.
[Is] ISSN:1469-9001
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Archaeal fibrillarin (aFib) is a well-characterized -adenosyl methionine (SAM)-dependent RNA 2'- -methyltransferase that is known to act in a large C/D ribonucleoprotein (RNP) complex together with Nop5 and L7Ae proteins and a box C/D guide RNA. In the reaction, the guide RNA serves to direct the methylation reaction to a specific site in tRNA or rRNA by sequence complementarity. Here we show that a aFib-Nop5 heterodimer can alone perform SAM-dependent 2'- -methylation of 16S and 23S ribosomal RNAs in vitro independently of L7Ae and C/D guide RNAs. Using tritium-labeling, mass spectrometry, and reverse transcription analysis, we identified three in vitro 2'- -methylated positions in the 16S rRNA of , positions lying outside of previously reported pyrococcal C/D RNP methylation sites. This newly discovered stand-alone activity of aFib-Nop5 may provide an example of an ancestral activity retained in enzymes that were recruited to larger complexes during evolution.
[Mh] Termos MeSH primário: Archaea/genética
Archaea/metabolismo
Proteínas Cromossômicas não Histona/metabolismo
RNA Arqueal/genética
RNA Arqueal/metabolismo
Ribonucleoproteínas Nucleolares Pequenas/metabolismo
Ribonucleoproteínas/metabolismo
[Mh] Termos MeSH secundário: Proteínas Cromossômicas não Histona/química
Metilação
Conformação de Ácido Nucleico
Ligação Proteica
Multimerização Proteica
RNA Ribossômico 16S/química
RNA Ribossômico 16S/genética
RNA Ribossômico 16S/metabolismo
RNA Ribossômico 23S/química
RNA Ribossômico 23S/genética
RNA Ribossômico 23S/metabolismo
Ribonucleoproteínas/química
Ribonucleoproteínas Nucleolares Pequenas/química
Especificidade por Substrato
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Chromosomal Proteins, Non-Histone); 0 (RNA, Archaeal); 0 (RNA, Ribosomal, 16S); 0 (RNA, Ribosomal, 23S); 0 (Ribonucleoproteins); 0 (Ribonucleoproteins, Small Nucleolar); 0 (fibrillarin)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171009
[Lr] Data última revisão:
171009
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170604
[St] Status:MEDLINE
[do] DOI:10.1261/rna.059832.116


  5 / 989 MEDLINE  
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[PMID]:28525600
[Au] Autor:Lai LB; Tanimoto A; Lai SM; Chen WY; Marathe IA; Westhof E; Wysocki VH; Gopalan V
[Ad] Endereço:Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
[Ti] Título:A novel double kink-turn module in euryarchaeal RNase P RNAs.
[So] Source:Nucleic Acids Res;45(12):7432-7440, 2017 Jul 07.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:RNase P is primarily responsible for the 5΄ maturation of transfer RNAs (tRNAs) in all domains of life. Archaeal RNase P is a ribonucleoprotein made up of one catalytic RNA and five protein cofactors including L7Ae, which is known to bind the kink-turn (K-turn), an RNA structural element that causes axial bending. However, the number and location of K-turns in archaeal RNase P RNAs (RPRs) are unclear. As part of an integrated approach, we used native mass spectrometry to assess the number of L7Ae copies that bound the RPR and site-specific hydroxyl radical-mediated footprinting to localize the K-turns. Mutagenesis of each of the putative K-turns singly or in combination decreased the number of bound L7Ae copies, and either eliminated or changed the L7Ae footprint on the mutant RPRs. In addition, our results support an unprecedented 'double K-turn' module in type A and type M archaeal RPR variants.
[Mh] Termos MeSH primário: Proteínas Arqueais/química
Regulação da Expressão Gênica em Archaea
Methanocaldococcus/enzimologia
Pyrococcus furiosus/enzimologia
RNA Arqueal/química
RNA de Transferência/química
Ribonuclease P/química
[Mh] Termos MeSH secundário: Proteínas Arqueais/genética
Proteínas Arqueais/metabolismo
Sequência de Bases
Radical Hidroxila/química
Radical Hidroxila/metabolismo
Isoenzimas/química
Isoenzimas/genética
Isoenzimas/metabolismo
Methanocaldococcus/genética
Mathanococcus/enzimologia
Mathanococcus/genética
Mutação
Conformação de Ácido Nucleico
Ligação Proteica
Pyrococcus furiosus/genética
Precursores de RNA
RNA Arqueal/genética
RNA Arqueal/metabolismo
RNA de Transferência/genética
RNA de Transferência/metabolismo
Ribonuclease P/genética
Ribonuclease P/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Archaeal Proteins); 0 (Isoenzymes); 0 (RNA Precursors); 0 (RNA, Archaeal); 3352-57-6 (Hydroxyl Radical); 9014-25-9 (RNA, Transfer); 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:170520
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx388


  6 / 989 MEDLINE  
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[PMID]:28520934
[Au] Autor:Märtens B; Hou L; Amman F; Wolfinger MT; Evguenieva-Hackenberg E; Bläsi U
[Ad] Endereço:Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria.
[Ti] Título:The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts.
[So] Source:Nucleic Acids Res;45(13):7938-7949, 2017 Jul 27.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The conserved Sm and Sm-like proteins are involved in different aspects of RNA metabolism. Here, we explored the interactome of SmAP1 and SmAP2 of the crenarchaeon Sulfolobus solfataricus (Sso) to shed light on their physiological function(s). Both, SmAP1 and SmAP2 co-purified with several proteins involved in RNA-processing/modification, translation and protein turnover as well as with components of the exosome involved in 3΄ to 5΄ degradation of RNA. In follow-up studies a direct interaction with the poly(A) binding and accessory exosomal subunit DnaG was demonstrated. Moreover, elevated levels of both SmAPs resulted in increased abundance of the soluble exosome fraction, suggesting that they affect the subcellular localization of the exosome in the cell. The increased solubility of the exosome was accompanied by augmented levels of RNAs with A-rich tails that were further characterized using RNASeq. Hence, the observation that the Sso SmAPs impact on the activity of the exosome revealed a hitherto unrecognized function of SmAPs in archaea.
[Mh] Termos MeSH primário: Proteínas Arqueais/metabolismo
RNA Arqueal/metabolismo
Sulfolobus solfataricus/metabolismo
[Mh] Termos MeSH secundário: Sequência Rica em At
Proteínas Arqueais/genética
DNA Primase/genética
DNA Primase/metabolismo
Exossomos/genética
Exossomos/metabolismo
Estabilidade de RNA
RNA Arqueal/química
RNA Arqueal/genética
Solubilidade
Sulfolobus solfataricus/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Archaeal Proteins); 0 (RNA, Archaeal); 0 (SmAP protein, Pyrobaculum aerophilum); EC 2.7.7.- (DNA Primase)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171010
[Lr] Data última revisão:
171010
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170519
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx437


  7 / 989 MEDLINE  
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[PMID]:28288106
[Au] Autor:Cvetkovic MA; Wurm JP; Audin MJ; Schütz S; Sprangers R
[Ad] Endereço:Max Planck Institute for Developmental Biology, Tübingen, Germany.
[Ti] Título:The Rrp4-exosome complex recruits and channels substrate RNA by a unique mechanism.
[So] Source:Nat Chem Biol;13(5):522-528, 2017 May.
[Is] ISSN:1552-4469
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The exosome is a large molecular machine involved in RNA degradation and processing. Here we address how the trimeric Rrp4 cap enhances the activity of the archaeal enzyme complex. Using methyl-TROSY NMR methods we identified a 50-Å long RNA binding path on each Rrp4 protomer. We show that the Rrp4 cap can thus simultaneously recruit three substrates, one of which is degraded in the core while the others are positioned for subsequent degradation rounds. The local interaction energy between the substrate and the Rrp4-exosome increases from the periphery of the complex toward the active sites. Notably, the intrinsic interaction strength between the cap and the substrate is weakened as soon as substrates enter the catalytic barrel, which provides a means to reduce friction during substrate movements toward the active sites. Our data thus reveal a sophisticated exosome-substrate interaction mechanism that enables efficient RNA degradation.
[Mh] Termos MeSH primário: Proteínas Arqueais/metabolismo
Exossomos/metabolismo
RNA Arqueal/metabolismo
Sulfolobus solfataricus/metabolismo
[Mh] Termos MeSH secundário: Proteínas Arqueais/química
Exossomos/química
Ressonância Magnética Nuclear Biomolecular
RNA Arqueal/química
Sulfolobus solfataricus/química
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Archaeal Proteins); 0 (RNA, Archaeal)
[Em] Mês de entrada:1704
[Cu] Atualização por classe:170922
[Lr] Data última revisão:
170922
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170314
[St] Status:MEDLINE
[do] DOI:10.1038/nchembio.2328


  8 / 989 MEDLINE  
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[PMID]:28235095
[Au] Autor:Nitahara S; Kato S; Usui A; Urabe T; Suzuki K; Yamagishi A
[Ad] Endereço:Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo, Japan.
[Ti] Título:Archaeal and bacterial communities in deep-sea hydrogenetic ferromanganese crusts on old seamounts of the northwestern Pacific.
[So] Source:PLoS One;12(2):e0173071, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Deep-sea ferromanganese crusts are found ubiquitously on the surface of seamounts of the world's oceans. Considering the wide distribution of the crusts, archaeal and bacterial communities on these crusts potentially play a significant role in biogeochemical cycling between oceans and seamounts; however little is known about phylogenetic diversity, abundance and function of the crust communities. To this end, we collected the crusts from the northwest Pacific basin and the Philippine Sea. We performed comprehensive analysis of the archaeal and bacterial communities of the collected crust samples by culture-independent molecular techniques. The distance between the sampling points was up to approximately 2,000 km. Surrounding sediments and bottom seawater were also collected as references near the sampling points of the crusts, and analyzed together. 16S rRNA gene analyses showed that the community structure of the crusts was significantly different from that of the seawater. Several members related to ammonia-oxidizers of Thaumarchaeota and Betaproteobacteria were detected in the crusts at most of all regions and depths by analyses of 16S rRNA and amoA genes, suggesting that the ammonia-oxidizing members are commonly present in the crusts. Although members related to the ammonia-oxidizers were also detected in the seawater, they differed from those in the crusts phylogenetically. In addition, members of uncultured groups of Alpha-, Delta- and Gammaproteobacteria were commonly detected in the crusts but not in the seawater. Comparison with previous studies of ferromanganese crusts and nodules suggests that the common members determined in the present study are widely distributed in the crusts and nodules on the vast seafloor. They may be key microbes for sustaining microbial ecosystems there.
[Mh] Termos MeSH primário: Archaea/genética
Bactérias/genética
Consórcios Microbianos/genética
[Mh] Termos MeSH secundário: Sedimentos Geológicos
Tipagem Molecular
Oceano Pacífico
Filogenia
RNA Arqueal/genética
RNA Bacteriano/genética
RNA Ribossômico 16S/genética
Microbiologia da Água
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Archaeal); 0 (RNA, Bacterial); 0 (RNA, Ribosomal, 16S)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170821
[Lr] Data última revisão:
170821
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170225
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0173071


  9 / 989 MEDLINE  
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[PMID]:28143889
[Au] Autor:Monestier A; Aleksandrov A; Coureux PD; Panvert M; Mechulam Y; Schmitt E
[Ad] Endereço:Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France.
[Ti] Título:The structure of an tRNA A -U variant shows an unusual conformation of the A -U base pair.
[So] Source:RNA;23(5):673-682, 2017 May.
[Is] ISSN:1469-9001
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Translation initiation in eukaryotes and archaea involves a methionylated initiator tRNA delivered to the ribosome in a ternary complex with e/aIF2 and GTP. Eukaryotic and archaeal initiator tRNAs contain a highly conserved A -U base pair at the top of the acceptor stem. The importance of this base pair to discriminate initiator tRNAs from elongator tRNAs has been established previously using genetics and biochemistry. However, no structural data illustrating how the A -U base pair participates in the accurate selection of the initiator tRNAs by the translation initiation systems are available. Here, we describe the crystal structure of a mutant initiator tRNA A -U , aminoacylated with methionine, in which the C :A mismatch at the end of the tRNA acceptor stem has been changed to an A -U base pair. Sequence alignments show that the mutant tRNA is a good mimic of archaeal initiator tRNAs. The crystal structure, determined at 2.8 Å resolution, shows that the A -U pair adopts an unusual arrangement. A is in a conformation and forms a single H-bond interaction with U This interaction requires protonation of the N1 atom of A Moreover, the 5' phosphoryl group folds back into the major groove of the acceptor stem and interacts with the N7 atom of G A possible role of this unusual geometry of the A -U pair in the recognition of the initiator tRNA by its partners during eukaryotic and archaeal translation initiation is discussed.
[Mh] Termos MeSH primário: Escherichia coli/genética
RNA de Transferência de Metionina/química
[Mh] Termos MeSH secundário: Anticódon
Pareamento de Bases
Escherichia coli/metabolismo
Modelos Moleculares
Simulação de Dinâmica Molecular
RNA Arqueal/química
RNA Bacteriano/química
RNA Bacteriano/metabolismo
RNA de Transferência de Metionina/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Anticodon); 0 (RNA, Archaeal); 0 (RNA, Bacterial); 0 (RNA, Transfer, Met)
[Em] Mês de entrada:1706
[Cu] Atualização por classe:170609
[Lr] Data última revisão:
170609
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170202
[St] Status:MEDLINE
[do] DOI:10.1261/rna.057877.116


  10 / 989 MEDLINE  
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[PMID]:28074284
[Au] Autor:Morten MJ; Gamsjaeger R; Cubeddu L; Kariawasam R; Peregrina J; Penedo JC; White MF
[Ad] Endereço:Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK.
[Ti] Título:High-affinity RNA binding by a hyperthermophilic single-stranded DNA-binding protein.
[So] Source:Extremophiles;21(2):369-379, 2017 Mar.
[Is] ISSN:1433-4909
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:Single-stranded DNA-binding proteins (SSBs), including replication protein A (RPA) in eukaryotes, play a central role in DNA replication, recombination, and repair. SSBs utilise an oligonucleotide/oligosaccharide-binding (OB) fold domain to bind DNA, and typically oligomerise in solution to bring multiple OB fold domains together in the functional SSB. SSBs from hyperthermophilic crenarchaea, such as Sulfolobus solfataricus, have an unusual structure with a single OB fold coupled to a flexible C-terminal tail. The OB fold resembles those in RPA, whilst the tail is reminiscent of bacterial SSBs and mediates interaction with other proteins. One paradigm in the field is that SSBs bind specifically to ssDNA and much less strongly to RNA, ensuring that their functions are restricted to DNA metabolism. Here, we use a combination of biochemical and biophysical approaches to demonstrate that the binding properties of S. solfataricus SSB are essentially identical for ssDNA and ssRNA. These features may represent an adaptation to a hyperthermophilic lifestyle, where DNA and RNA damage is a more frequent event.
[Mh] Termos MeSH primário: Proteínas Arqueais/química
Proteínas de Ligação a DNA/química
RNA Arqueal/química
Proteínas de Ligação a RNA/química
Sulfolobus solfataricus/química
[Mh] Termos MeSH secundário: Proteínas Arqueais/metabolismo
Proteínas de Ligação a DNA/metabolismo
RNA Arqueal/metabolismo
Proteínas de Ligação a RNA/metabolismo
Sulfolobus solfataricus/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Archaeal Proteins); 0 (DNA-Binding Proteins); 0 (RNA, Archaeal); 0 (RNA-Binding Proteins)
[Em] Mês de entrada:1703
[Cu] Atualização por classe:170323
[Lr] Data última revisão:
170323
[Sb] Subgrupo de revista:IM; S
[Da] Data de entrada para processamento:170112
[St] Status:MEDLINE
[do] DOI:10.1007/s00792-016-0910-2



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