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  1 / 77512 MEDLINE  
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[PMID]:29339162
[Au] Autor:El-Lakkani A; Ibrahim EM
[Ad] Endereço:Biophysics Department, Faculty of Science, Cairo University, Giza, 12613, Egypt. Electronic address: lakkani@netscape.com.
[Ti] Título:A method to improve prediction of secondary structure for large single RNA sequences.
[So] Source:Biochem Biophys Res Commun;496(2):523-528, 2018 02 05.
[Is] ISSN:1090-2104
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The function of a particular RNA molecule within an organic system is principally determined by its structure. The current physical methods available for structure determination are time consuming and expensive. Hence, computational methods for structure prediction are often used. The prediction of the structure of a large single sequence of RNA needs a lot of research work. In the present work, a method is introduced to improve the prediction of large single sequence RNA secondary structure obtained by Mfold program using the concept of minimum free energy. The Mfold program contains a constraint option that allows forcing some helices in the predicted structure. In our method, some of the firstly formed hairpins that are expected, by a statistical study, to be present in the real structure are forced in the Mfold predicted structure. The results show improvement, toward the real structure, in the Mfold predicted structure and this gives evidence to the RNA kinetic folding.
[Mh] Termos MeSH primário: RNA/química
[Mh] Termos MeSH secundário: Cinética
Modelos Biológicos
Conformação de Ácido Nucleico
Software
Termodinâmica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
63231-63-0 (RNA)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180118
[St] Status:MEDLINE


  2 / 77512 MEDLINE  
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[PMID]:28468914
[Au] Autor:Engel C; Brügmann G; Lambing S; Mühlenbeck LH; Marx S; Hagen C; Horváth D; Goldeck M; Ludwig J; Herzner AM; Drijfhout JW; Wenzel D; Coch C; Tüting T; Schlee M; Hornung V; Hartmann G; Van den Boorn JG
[Ad] Endereço:Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany.
[Ti] Título:RIG-I Resists Hypoxia-Induced Immunosuppression and Dedifferentiation.
[So] Source:Cancer Immunol Res;5(6):455-467, 2017 Jun.
[Is] ISSN:2326-6074
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:A hypoxic tumor microenvironment is linked to poor prognosis. It promotes tumor cell dedifferentiation and metastasis and desensitizes tumor cells to type-I IFN, chemotherapy, and irradiation. The cytoplasmic immunoreceptor retinoic acid-inducible gene-I (RIG-I) is ubiquitously expressed in tumor cells and upon activation by 5'-triphosphate RNA (3pRNA) drives the induction of type I IFN and immunogenic cell death. Here, we analyzed the impact of hypoxia on the expression of RIG-I in various human and murine tumor and nonmalignant cell types and further investigated its function in hypoxic murine melanoma. 3pRNA-inducible RIG-I-expression was reduced in hypoxic melanoma cells compared with normoxic controls, a phenomenon that depended on the hypoxia-associated transcription factor HIF1α. Still, RIG-I functionality was conserved in hypoxic melanoma cells, whereas responsiveness to recombinant type-I IFN was abolished, due to hypoxia-induced loss of type I IFN receptor expression. Likewise, RIG-I activation in hypoxic melanoma cells, but not exposure to recombinant IFNα, provoked melanocyte antigen-specific CD8 T-cell and NK-cell attack. Scavenging of hypoxia-induced reactive oxygen species by vitamin C restored the inducible expression of RIG-I under hypoxia , boosted anti-melanoma NK- and CD8 T-cell attack, and augmented 3pRNA antitumor efficacy These results demonstrate that RIG-I remains operational under hypoxia and that RIG-I function is largely insensitive to lower cell surface expression of the IFNα receptor. RIG-I function could be fortified under hypoxia by the combined use of 3pRNA with antioxidants. .
[Mh] Termos MeSH primário: Hipóxia/metabolismo
Tolerância Imunológica
Melanoma/metabolismo
Receptores do Ácido Retinoico/metabolismo
[Mh] Termos MeSH secundário: Animais
Antioxidantes/farmacologia
Ácido Ascórbico/farmacologia
Linhagem Celular
Linhagem Celular Tumoral
Feminino
Técnicas de Inativação de Genes
Seres Humanos
Camundongos Endogâmicos C57BL
RNA/farmacologia
Espécies Reativas de Oxigênio/metabolismo
Receptores do Ácido Retinoico/genética
Baço/citologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Antioxidants); 0 (RARRES3 protein, human); 0 (Reactive Oxygen Species); 0 (Receptors, Retinoic Acid); 63231-63-0 (RNA); PQ6CK8PD0R (Ascorbic Acid)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170505
[St] Status:MEDLINE
[do] DOI:10.1158/2326-6066.CIR-16-0129-T


  3 / 77512 MEDLINE  
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[PMID]:29422501
[Au] Autor:Collopy LC; Ware TL; Goncalves T; Í Kongsstovu S; Yang Q; Amelina H; Pinder C; Alenazi A; Moiseeva V; Pearson SR; Armstrong CA; Tomita K
[Ad] Endereço:Chromosome Maintenance Group, UCL Cancer Institute, University College London, London, WC1E 6DD, UK.
[Ti] Título:LARP7 family proteins have conserved function in telomerase assembly.
[So] Source:Nat Commun;9(1):557, 2018 02 08.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Understanding the intricacies of telomerase regulation is crucial due to the potential health benefits of modifying its activity. Telomerase is composed of an RNA component and reverse transcriptase. However, additional factors required during biogenesis vary between species. Here we have identified fission yeast Lar7 as a member of the conserved LARP7 family, which includes the Tetrahymena telomerase-binding protein p65 and human LARP7. We show that Lar7 has conserved RNA-recognition motifs, which bind telomerase RNA to protect it from exosomal degradation. In addition, Lar7 is required to stabilise the association of telomerase RNA with the protective complex LSm2-8, and telomerase reverse transcriptase. Lar7 remains a component of the mature telomerase complex and is required for telomerase localisation to the telomere. Collectively, we demonstrate that Lar7 is a crucial player in fission yeast telomerase biogenesis, similarly to p65 in Tetrahymena, and highlight the LARP7 family as a conserved factor in telomere maintenance.
[Mh] Termos MeSH primário: Proteínas Nucleares/genética
Fosfoproteínas/genética
Proteínas de Protozoários/genética
RNA Fúngico/genética
DNA Polimerase Dirigida por RNA/genética
RNA/genética
Ribonucleoproteínas/genética
Schizosaccharomyces/genética
Telomerase/genética
[Mh] Termos MeSH secundário: Motivos de Aminoácidos
Sequência Conservada
Expressão Gênica
Seres Humanos
Isoenzimas/genética
Isoenzimas/metabolismo
Proteínas Nucleares/metabolismo
Fosfoproteínas/metabolismo
Ligação Proteica
Proteínas de Protozoários/metabolismo
RNA/metabolismo
Estabilidade de RNA
RNA Fúngico/metabolismo
DNA Polimerase Dirigida por RNA/metabolismo
Ribonucleoproteínas/metabolismo
Schizosaccharomyces/metabolismo
Telomerase/metabolismo
Telômero/química
Telômero/ultraestrutura
Tetrahymena thermophila/genética
Tetrahymena thermophila/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Isoenzymes); 0 (Larp7 protein, human); 0 (Nuclear Proteins); 0 (Pdd1 protein, Tetrahymena); 0 (Phosphoproteins); 0 (Protozoan Proteins); 0 (RNA, Fungal); 0 (Ribonucleoproteins); 0 (Ter1 telomerase subunit, S pombe); 63231-63-0 (RNA); EC 2.7.7.49 (RNA-Directed DNA Polymerase); EC 2.7.7.49 (Telomerase)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180307
[Lr] Data última revisão:
180307
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180210
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-017-02296-4


  4 / 77512 MEDLINE  
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[PMID]:29244013
[Au] Autor:Zhao C; Sahni S
[Ad] Endereço:Department of Computer and Information Science and Engineering, University of Florida, Gainesville, 32611, FL, USA. czhao@cise.ufl.edu.
[Ti] Título:Cache and energy efficient algorithms for Nussinov's RNA Folding.
[So] Source:BMC Bioinformatics;18(Suppl 15):518, 2017 Dec 06.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: An RNA folding/RNA secondary structure prediction algorithm determines the non-nested/pseudoknot-free structure by maximizing the number of complementary base pairs and minimizing the energy. Several implementations of Nussinov's classical RNA folding algorithm have been proposed. Our focus is to obtain run time and energy efficiency by reducing the number of cache misses. RESULTS: Three cache-efficient algorithms, ByRow, ByRowSegment and ByBox, for Nussinov's RNA folding are developed. Using a simple LRU cache model, we show that the Classical algorithm of Nussinov has the highest number of cache misses followed by the algorithms Transpose (Li et al.), ByRow, ByRowSegment, and ByBox (in this order). Extensive experiments conducted on four computational platforms-Xeon E5, AMD Athlon 64 X2, Intel I7 and PowerPC A2-using two programming languages-C and Java-show that our cache efficient algorithms are also efficient in terms of run time and energy. CONCLUSION: Our benchmarking shows that, depending on the computational platform and programming language, either ByRow or ByBox give best run time and energy performance. The C version of these algorithms reduce run time by as much as 97.2% and energy consumption by as much as 88.8% relative to Classical and by as much as 56.3% and 57.8% relative to Transpose. The Java versions reduce run time by as much as 98.3% relative to Classical and by as much as 75.2% relative to Transpose. Transpose achieves run time and energy efficiency at the expense of memory as it takes twice the memory required by Classical. The memory required by ByRow, ByRowSegment, and ByBox is the same as that of Classical. As a result, using the same amount of memory, the algorithms proposed by us can solve problems up to 40% larger than those solvable by Transpose.
[Mh] Termos MeSH primário: Algoritmos
Biologia Computacional/métodos
Dobramento de RNA
RNA
[Mh] Termos MeSH secundário: Conformação de Ácido Nucleico
RNA/química
RNA/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
63231-63-0 (RNA)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180307
[Lr] Data última revisão:
180307
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171216
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1917-0


  5 / 77512 MEDLINE  
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[PMID]:29220443
[Au] Autor:Rosikiewicz W; Kabza M; Kosinski JG; Ciomborowska-Basheer J; Kubiak MR; Makalowska I
[Ad] Endereço:Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland.
[Ti] Título:RetrogeneDB-a database of plant and animal retrocopies.
[So] Source:Database (Oxford);2017, 2017 Jan 01.
[Is] ISSN:1758-0463
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Database URL: http://yeti.amu.edu.pl/retrogenedb. Secondary database URL: http://rhesus.amu.edu.pl/retrogenedb.
[Mh] Termos MeSH primário: Bases de Dados Genéticas
Eucariotos/genética
Genoma/genética
Plantas/genética
RNA/genética
Análise de Sequência de RNA
[Mh] Termos MeSH secundário: Animais
Etiquetas de Sequências Expressas
Filogenia
Interface Usuário-Computador
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
63231-63-0 (RNA)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171209
[St] Status:MEDLINE
[do] DOI:10.1093/database/bax038


  6 / 77512 MEDLINE  
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[PMID]:28903484
[Au] Autor:Yang Y; Gao X; Zhang M; Yan S; Sun C; Xiao F; Huang N; Yang X; Zhao K; Zhou H; Huang S; Xie B; Zhang N
[Ad] Endereço:Department of Neurosurgery, The 1st Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, PR China; Guangdong Provincial Key Laboratory of Pituitary Tumor, Guangzhou, Guangdong Province, PR China; Department of Scientific Research Section, The 1st Affiliated Hospital of Sun Y
[Ti] Título:Novel Role of FBXW7 Circular RNA in Repressing Glioma Tumorigenesis.
[So] Source:J Natl Cancer Inst;110(3), 2018 Mar 01.
[Is] ISSN:1460-2105
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Background: Circular RNAs (circRNAs) are RNA transcripts that are widespread in the eukaryotic genome. Recent evidence indicates that circRNAs play important roles in tissue development, gene regulation, and carcinogenesis. However, whether circRNAs encode functional proteins remains elusive, although translation of several circRNAs was recently reported. Methods: CircRNA deep sequencing was performed by using 10 pathologically diagnosed glioblastoma samples and their paired adjacent normal brain tissues. Northern blotting, Sanger sequencing, antibody, and liquid chromatograph Tandem Mass Spectrometer were used to confirm the existence of circ-FBXW7 and its encoded protein in in two cell lines. Lentivirus-transfected stable U251 and U373 cells were used to assess the biological functions of the novel protein invitro and invivo (five mice per group). Clinical implications of circ-FBXW7 were assessed in 38 pathologically diagnosed glioblastoma samples and their paired periphery normal brain tissues by using quantitative polymerase chain reaction (two-sided log-rank test). Results: Circ-FBXW7 is abundantly expressed in the normal human brain (reads per kilobase per million mapped reads [RPKM] = 9.31). The spanning junction open reading frame in circ-FBXW7 driven by internal ribosome entry site encodes a novel 21-kDa protein, which we termed FBXW7-185aa. Upregulation of FBXW7-185aa in cancer cells inhibited proliferation and cell cycle acceleration, while knockdown of FBXW7-185aa promoted malignant phenotypes invitro and invivo. FBXW7-185aa reduced the half-life of c-Myc by antagonizing USP28-induced c-Myc stabilization. Moreover, circ-FBXW7 and FBXW7-185aa levels were reduced in glioblastoma clinical samples compared with their paired tumor-adjacent tissues (P < .001). Circ-FBXW7 expression positively associated with glioblastoma patient overall survival (P = .03). Conclusions: Endogenous circRNA encodes a functional protein in human cells, and circ-FBXW7 and FBXW7-185aa have potential prognostic implications in brain cancer.
[Mh] Termos MeSH primário: Neoplasias Encefálicas/genética
Proteínas de Ciclo Celular/genética
Transformação Celular Neoplásica/genética
Proteínas F-Box/genética
Glioblastoma/genética
RNA/análise
Ubiquitina-Proteína Ligases/genética
[Mh] Termos MeSH secundário: Animais
Encéfalo/metabolismo
Neoplasias Encefálicas/química
Ciclo Celular/genética
Proteínas de Ciclo Celular/análise
Linhagem Celular Tumoral
Proliferação Celular/genética
Proteínas F-Box/análise
Proteína 7 com Repetições F-Box-WD
Feminino
Glioblastoma/química
Meia-Vida
Seres Humanos
Camundongos
Camundongos Endogâmicos BALB C
Camundongos Nus
Transplante de Neoplasias
Fases de Leitura Aberta
Proteínas Proto-Oncogênicas c-myc/metabolismo
Análise de Sequência de RNA
Taxa de Sobrevida
Ubiquitina Tiolesterase/metabolismo
Ubiquitina-Proteína Ligases/análise
Regulação para Cima
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Cell Cycle Proteins); 0 (F-Box Proteins); 0 (F-Box-WD Repeat-Containing Protein 7); 0 (FBXW7 protein, human); 0 (Proto-Oncogene Proteins c-myc); 0 (RNA, circular); 63231-63-0 (RNA); EC 2.3.2.27 (Ubiquitin-Protein Ligases); EC 3.1.2.15 (USP28 protein, human); EC 3.4.19.12 (Ubiquitin Thiolesterase)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170915
[St] Status:MEDLINE
[do] DOI:10.1093/jnci/djx166


  7 / 77512 MEDLINE  
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[PMID]:28453672
[Au] Autor:Tian S; Das R
[Ad] Endereço:Department of Biochemistry.
[Ti] Título:Primerize-2D: automated primer design for RNA multidimensional chemical mapping.
[So] Source:Bioinformatics;33(9):1405-1406, 2017 May 01.
[Is] ISSN:1367-4811
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Summary: Rapid RNA synthesis of comprehensive single mutant libraries and targeted multiple mutant libraries is enabling new multidimensional chemical approaches to solve RNA structures. PCR assembly of DNA templates and in vitro transcription allow synthesis and purification of hundreds of RNA mutants in a cost-effective manner, with sharing of primers across constructs allowing significant reductions in expense. However, these protocols require organization of primer locations across numerous 96 well plates and guidance for pipetting, non-trivial tasks for which informatics and visualization tools can prevent costly errors. We report here an online tool to accelerate synthesis of large libraries of desired mutants through design and efficient organization of primers. The underlying program and graphical interface have been experimentally tested in our laboratory for RNA domains with lengths up to 300 nucleotides and libraries encompassing up to 960 variants. In addition to the freely available Primerize-2D server, the primer design code is available as a stand-alone Python package for broader applications. Availability and Implementation: http://primerize2d.stanford.edu. Contact: rhiju@stanford.edu. Supplementary information: Supplementary data are available at Bioinformatics online.
[Mh] Termos MeSH primário: Primers do DNA
Mutação
RNA/química
Análise de Sequência de RNA/métodos
Software
[Mh] Termos MeSH secundário: Conformação de Ácido Nucleico
Reação em Cadeia da Polimerase/métodos
RNA/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA Primers); 63231-63-0 (RNA)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1093/bioinformatics/btw814


  8 / 77512 MEDLINE  
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[PMID]:29480850
[Au] Autor:Cho HY; Cho Y; Shin YJ; Park J; Shim S; Jung Y; Shim S; Cha D
[Ad] Endereço:Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam.
[Ti] Título:Functional analysis of cell-free RNA using mid-trimester amniotic fluid supernatant in pregnancy with the fetal growth restriction.
[So] Source:Medicine (Baltimore);97(2):e9572, 2018 Jan.
[Is] ISSN:1536-5964
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The prediction and monitoring of fetal growth restriction (FGR) fetuses has become with the use of ultrasound. However, these tools lack the fundamental evidence for the growth of fetus with FGR excluding pathogenic factors.Amniotic fluid samples were obtained from pregnant women for fetal karyotyping and genetic diagnosis at 16 to 19 weeks of gestation. For this study, 15 FGR and 9 control samples were selected, and cell-free fetal RNA was isolated from each supernatant of the amniotic fluid for microarray analysis.In this study, 411 genes were differentially expressed between the FGR and control group. Of these genes, 316 genes were up-regulated, while 95 genes were down-regulated. In terms of gene ontology, the up-regulated genes were highly related to metabolic process as well as protein synthesis, while the down-regulated genes were related to receptor activity and biological adhesion. In terms of tissue-specific expression, the up-regulated genes were involved in various organs while down-regulated genes were involved only in the brain. In terms of organ-specific expression, many genes were enriched for B-cell lymphoma, pancreas, eye, placenta, epithelium, skin, and muscle. In the functional significance of gene, low-density lipoprotein receptor-related protein 10 (LRP10) was significantly increased (6-fold) and insulin-like growth factor (IGF-2) was dramatically increased (17-fold) in the FGR cases.The results show that the important brain-related genes are predominantly down-regulated in the intrauterine growth restriction fetuses during the second trimester of pregnancy. This study also suggested possible genes related to fetal development such as B-cell lymphoma, LRP10, and IGF-2. To monitor the fetal development, further study may be needed to elucidate the role of the genes identified.
[Mh] Termos MeSH primário: Líquido Amniótico/química
Retardo do Crescimento Fetal/diagnóstico
RNA/análise
[Mh] Termos MeSH secundário: Adulto
Líquido Amniótico/metabolismo
Feminino
Retardo do Crescimento Fetal/metabolismo
Seres Humanos
Masculino
Análise em Microsséries
Gravidez
Segundo Trimestre da Gravidez
Cuidado Pré-Natal
Estudos Prospectivos
RNA/metabolismo
Reação em Cadeia da Polimerase em Tempo Real
Transcriptoma
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
63231-63-0 (RNA)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180305
[Lr] Data última revisão:
180305
[Sb] Subgrupo de revista:AIM; IM
[Da] Data de entrada para processamento:180227
[St] Status:MEDLINE
[do] DOI:10.1097/MD.0000000000009572


  9 / 77512 MEDLINE  
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[PMID]:29323115
[Au] Autor:Becker S; Schneider C; Okamura H; Crisp A; Amatov T; Dejmek M; Carell T
[Ad] Endereço:Center for Integrated Protein Science Munich CiPSM at the Department of Chemistry, Ludwig-Maximilians-Universität München, 81377, Munich, Germany.
[Ti] Título:Wet-dry cycles enable the parallel origin of canonical and non-canonical nucleosides by continuous synthesis.
[So] Source:Nat Commun;9(1):163, 2018 01 11.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The molecules of life were created by a continuous physicochemical process on an early Earth. In this hadean environment, chemical transformations were driven by fluctuations of the naturally given physical parameters established for example by wet-dry cycles. These conditions might have allowed for the formation of (self)-replicating RNA as the fundamental biopolymer during chemical evolution. The question of how a complex multistep chemical synthesis of RNA building blocks was possible in such an environment remains unanswered. Here we report that geothermal fields could provide the right setup for establishing wet-dry cycles that allow for the synthesis of RNA nucleosides by continuous synthesis. Our model provides both the canonical and many ubiquitous non-canonical purine nucleosides in parallel by simple changes of physical parameters such as temperature, pH and concentration. The data show that modified nucleosides were potentially formed as competitor molecules. They could in this sense be considered as molecular fossils.
[Mh] Termos MeSH primário: Biopolímeros/química
Nucleosídeos/química
RNA/química
Água/química
[Mh] Termos MeSH secundário: Terra (Planeta)
Evolução Química
Modelos Químicos
Estrutura Molecular
Origem da Vida
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Biopolymers); 0 (Nucleosides); 059QF0KO0R (Water); 63231-63-0 (RNA)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180305
[Lr] Data última revisão:
180305
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180112
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-017-02639-1


  10 / 77512 MEDLINE  
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[PMID]:29311576
[Au] Autor:Razew M; Warkocki Z; Taube M; Kolondra A; Czarnocki-Cieciura M; Nowak E; Labedzka-Dmoch K; Kawinska A; Piatkowski J; Golik P; Kozak M; Dziembowski A; Nowotny M
[Ad] Endereço:Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland.
[Ti] Título:Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components.
[So] Source:Nat Commun;9(1):97, 2018 01 08.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Nuclease and helicase activities play pivotal roles in various aspects of RNA processing and degradation. These two activities are often present in multi-subunit complexes from nucleic acid metabolism. In the mitochondrial exoribonuclease complex (mtEXO) both enzymatic activities are tightly coupled making it an excellent minimal system to study helicase-exoribonuclease coordination. mtEXO is composed of Dss1 3'-to-5' exoribonuclease and Suv3 helicase. It is the master regulator of mitochondrial gene expression in yeast. Here, we present the structure of mtEXO and a description of its mechanism of action. The crystal structure of Dss1 reveals domains that are responsible for interactions with Suv3. Importantly, these interactions are compatible with the conformational changes of Suv3 domains during the helicase cycle. We demonstrate that mtEXO is an intimate complex which forms an RNA-binding channel spanning its entire structure, with Suv3 helicase feeding the 3' end of the RNA toward the active site of Dss1.
[Mh] Termos MeSH primário: Endorribonucleases/metabolismo
Exorribonucleases/metabolismo
Proteínas Mitocondriais/metabolismo
Complexos Multienzimáticos/metabolismo
Polirribonucleotídeo Nucleotidiltransferase/metabolismo
RNA Helicases/metabolismo
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Sequência de Bases
Candida glabrata/enzimologia
Candida glabrata/genética
Candida glabrata/metabolismo
Cristalografia por Raios X
RNA Helicases DEAD-box/química
RNA Helicases DEAD-box/genética
RNA Helicases DEAD-box/metabolismo
Endorribonucleases/química
Endorribonucleases/genética
Exorribonucleases/química
Exorribonucleases/genética
Proteínas Mitocondriais/química
Proteínas Mitocondriais/genética
Complexos Multienzimáticos/química
Complexos Multienzimáticos/genética
Conformação de Ácido Nucleico
Polirribonucleotídeo Nucleotidiltransferase/química
Polirribonucleotídeo Nucleotidiltransferase/genética
Ligação Proteica
Conformação Proteica
RNA/química
RNA/genética
RNA/metabolismo
RNA Helicases/química
RNA Helicases/genética
Saccharomyces cerevisiae/enzimologia
Saccharomyces cerevisiae/genética
Saccharomyces cerevisiae/metabolismo
Proteínas de Saccharomyces cerevisiae/química
Proteínas de Saccharomyces cerevisiae/genética
Proteínas de Saccharomyces cerevisiae/metabolismo
Homologia de Sequência de Aminoácidos
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Mitochondrial Proteins); 0 (Multienzyme Complexes); 0 (RNA, mitochondrial); 0 (Saccharomyces cerevisiae Proteins); 0 (degradosome); 63231-63-0 (RNA); EC 2.7.7.8 (Polyribonucleotide Nucleotidyltransferase); EC 3.1.- (Endoribonucleases); EC 3.1.- (Exoribonucleases); EC 3.1.13.1 (DSS1 protein, S cerevisiae); EC 3.6.1.- (SUV3 protein, S cerevisiae); EC 3.6.4.13 (DEAD-box RNA Helicases); EC 3.6.4.13 (RNA Helicases)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180305
[Lr] Data última revisão:
180305
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180110
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-017-02570-5



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