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  1 / 93796 MEDLINE  
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[PMID]:29212533
[Au] Autor:Gutiérrez G; Millán-Zambrano G; Medina DA; Jordán-Pla A; Pérez-Ortín JE; Peñate X; Chávez S
[Ad] Endereço:Departamento de Genética, Universidad de Sevilla, Seville, Spain.
[Ti] Título:Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning.
[So] Source:Epigenetics Chromatin;10(1):58, 2017 12 07.
[Is] ISSN:1756-8935
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: TFIIS stimulates RNA cleavage by RNA polymerase II and promotes the resolution of backtracking events. TFIIS acts in the chromatin context, but its contribution to the chromatin landscape has not yet been investigated. Co-transcriptional chromatin alterations include subtle changes in nucleosome positioning, like those expected to be elicited by TFIIS, which are elusive to detect. The most popular method to map nucleosomes involves intensive chromatin digestion by micrococcal nuclease (MNase). Maps based on these exhaustively digested samples miss any MNase-sensitive nucleosomes caused by transcription. In contrast, partial digestion approaches preserve such nucleosomes, but introduce noise due to MNase sequence preferences. A systematic way of correcting this bias for massively parallel sequencing experiments is still missing. RESULTS: To investigate the contribution of TFIIS to the chromatin landscape, we developed a refined nucleosome-mapping method in Saccharomyces cerevisiae. Based on partial MNase digestion and a sequence-bias correction derived from naked DNA cleavage, the refined method efficiently mapped nucleosomes in promoter regions rich in MNase-sensitive structures. The naked DNA correction was also important for mapping gene body nucleosomes, particularly in those genes whose core promoters contain a canonical TATA element. With this improved method, we analyzed the global nucleosomal changes caused by lack of TFIIS. We detected a general increase in nucleosomal fuzziness and more restricted changes in nucleosome occupancy, which concentrated in some gene categories. The TATA-containing genes were preferentially associated with decreased occupancy in gene bodies, whereas the TATA-like genes did so with increased fuzziness. The detected chromatin alterations correlated with functional defects in nascent transcription, as revealed by genomic run-on experiments. CONCLUSIONS: The combination of partial MNase digestion and naked DNA correction of the sequence bias is a precise nucleosomal mapping method that does not exclude MNase-sensitive nucleosomes. This method is useful for detecting subtle alterations in nucleosome positioning produced by lack of TFIIS. Their analysis revealed that TFIIS generally contributed to nucleosome positioning in both gene promoters and bodies. The independent effect of lack of TFIIS on nucleosome occupancy and fuzziness supports the existence of alternative chromatin dynamics during transcription elongation.
[Mh] Termos MeSH primário: Nuclease do Micrococo/metabolismo
Nucleossomos/metabolismo
Fatores de Elongação da Transcrição/metabolismo
[Mh] Termos MeSH secundário: Sequenciamento de Nucleotídeos em Larga Escala
Reação em Cadeia da Polimerase em Tempo Real
Saccharomyces cerevisiae/metabolismo
Técnica de Subtração
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Nucleosomes); 0 (Transcriptional Elongation Factors); 0 (transcription factor S-II); EC 3.1.31.1 (Micrococcal Nuclease)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180310
[Lr] Data última revisão:
180310
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171208
[St] Status:MEDLINE
[do] DOI:10.1186/s13072-017-0165-x


  2 / 93796 MEDLINE  
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[PMID]:28743762
[Au] Autor:Hum YF; Jinks-Robertson S
[Ad] Endereço:Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27710.
[Ti] Título:Mitotic Gene Conversion Tracts Associated with Repair of a Defined Double-Strand Break in .
[So] Source:Genetics;207(1):115-128, 2017 09.
[Is] ISSN:1943-2631
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Mitotic recombination between homologous chromosomes leads to the uncovering of recessive alleles through loss of heterozygosity. In the current study, a defined double-strand break was used to initiate reciprocal loss of heterozygosity between diverged homologs of chromosome IV in These events resulted from the repair of two broken chromatids, one of which was repaired as a crossover and the other as a noncrossover. Associated gene conversion tracts resulting from the donor-directed repair of mismatches formed during strand exchange (heteroduplex DNA) were mapped using microarrays. Gene conversion tracts associated with individual crossover and noncrossover events were similar in size and position, with half of the tracts being unidirectional and mapping to only one side of the initiating break. Among crossover events, this likely reflected gene conversion on only one side of the break, with restoration-type repair occurring on the other side. For noncrossover events, an ectopic system was used to directly compare gene conversion tracts produced in a wild-type strain to heteroduplex DNA tracts generated in the absence of the Mlh1 mismatch-repair protein. There was a strong bias for unidirectional tracts in the absence, but not in the presence, of Mlh1 This suggests that mismatch repair acts on heteroduplex DNA that is only transiently present in noncrossover intermediates of the synthesis dependent strand annealing pathway. Although the molecular features of events associated with loss of heterozygosity generally agreed with those predicted by current recombination models, there were unexpected complexities in associated gene conversion tracts.
[Mh] Termos MeSH primário: Quebras de DNA de Cadeia Dupla
Conversão Gênica
Mitose/genética
Reparo de DNA por Recombinação
Saccharomyces cerevisiae/genética
[Mh] Termos MeSH secundário: Troca Genética
Saccharomyces cerevisiae/citologia
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Em] Mês de entrada:1712
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170727
[St] Status:MEDLINE
[do] DOI:10.1534/genetics.117.300057


  3 / 93796 MEDLINE  
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[PMID]:29402931
[Au] Autor:Bianchi F; Syga L; Moiset G; Spakman D; Schavemaker PE; Punter CM; Seinen AB; van Oijen AM; Robinson A; Poolman B
[Ad] Endereço:Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700AB, Groningen, The Netherlands.
[Ti] Título:Steric exclusion and protein conformation determine the localization of plasma membrane transporters.
[So] Source:Nat Commun;9(1):501, 2018 02 05.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The plasma membrane (PM) of Saccharomyces cerevisiae contains membrane compartments, MCC/eisosomes and MCPs, named after the protein residents Can1 and Pma1, respectively. Using high-resolution fluorescence microscopy techniques we show that Can1 and the homologous transporter Lyp1 are able to diffuse into the MCC/eisosomes, where a limited number of proteins are conditionally trapped at the (outer) edge of the compartment. Upon addition of substrate, the immobilized proteins diffuse away from the MCC/eisosomes, presumably after taking a different conformation in the substrate-bound state. Our data indicate that the mobile fraction of all integral plasma membrane proteins tested shows extremely slow Brownian diffusion through most of the PM. We also show that proteins with large cytoplasmic domains, such as Pma1 and synthetic chimera of Can1 and Lyp1, are excluded from the MCC/eisosomes. We hypothesize that the distinct localization patterns found for these integral membrane proteins in S. cerevisiae arises from a combination of slow lateral diffusion, steric exclusion, and conditional trapping in membrane compartments.
[Mh] Termos MeSH primário: Sistemas de Transporte de Aminoácidos Básicos/química
Membrana Celular/metabolismo
ATPases Translocadoras de Prótons/química
Proteínas de Saccharomyces cerevisiae/química
Saccharomyces cerevisiae/metabolismo
[Mh] Termos MeSH secundário: Sistemas de Transporte de Aminoácidos Básicos/metabolismo
Membrana Celular/ultraestrutura
Difusão
Recuperação de Fluorescência Após Fotodegradação
Cinética
Microdomínios da Membrana
Conformação Proteica
Transporte Proteico
ATPases Translocadoras de Prótons/metabolismo
Saccharomyces cerevisiae/ultraestrutura
Proteínas de Saccharomyces cerevisiae/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Amino Acid Transport Systems, Basic); 0 (CAN1 protein, S cerevisiae); 0 (LYP1 protein, S cerevisiae); 0 (Saccharomyces cerevisiae Proteins); EC 3.6.1.- (PMA1 protein, S cerevisiae); EC 3.6.3.14 (Proton-Translocating ATPases)
[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:180207
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-018-02864-2


  4 / 93796 MEDLINE  
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[PMID]:29220449
[Au] Autor:Choi JA; Wyrick JJ
[Ad] Endereço:School of Molecular Biosciences.
[Ti] Título:RegulatorDB: a resource for the analysis of yeast transcriptional regulation.
[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://wyrickbioinfo2.smb.wsu.edu/RegulatorDB.
[Mh] Termos MeSH primário: DNA Fúngico
Proteínas de Ligação a DNA
Bases de Dados Genéticas
Proteínas Fúngicas
Regulação Fúngica da Expressão Gênica/genética
Saccharomyces cerevisiae
[Mh] Termos MeSH secundário: Sítios de Ligação
DNA Fúngico/genética
DNA Fúngico/metabolismo
Proteínas de Ligação a DNA/genética
Proteínas de Ligação a DNA/metabolismo
Proteínas Fúngicas/genética
Proteínas Fúngicas/metabolismo
Saccharomyces cerevisiae/genética
Saccharomyces cerevisiae/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Fungal); 0 (DNA-Binding Proteins); 0 (Fungal Proteins)
[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/bax058


  5 / 93796 MEDLINE  
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[PMID]:29178831
[Au] Autor:Myschyshyn M; Farren-Dai M; Chuang TJ; Vocadlo D
[Ad] Endereço:Department of Molecular Biology and Biochemistry, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada. mmyschyshyn@gmail.com.
[Ti] Título:Software for rapid time dependent ChIP-sequencing analysis (TDCA).
[So] Source:BMC Bioinformatics;18(1):521, 2017 Nov 25.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) and associated methods are widely used to define the genome wide distribution of chromatin associated proteins, post-translational epigenetic marks, and modifications found on DNA bases. An area of emerging interest is to study time dependent changes in the distribution of such proteins and marks by using serial ChIP-seq experiments performed in a time resolved manner. Despite such time resolved studies becoming increasingly common, software to facilitate analysis of such data in a robust automated manner is limited. RESULTS: We have designed software called Time-Dependent ChIP-Sequencing Analyser (TDCA), which is the first program to automate analysis of time-dependent ChIP-seq data by fitting to sigmoidal curves. We provide users with guidance for experimental design of TDCA for modeling of time course (TC) ChIP-seq data using two simulated data sets. Furthermore, we demonstrate that this fitting strategy is widely applicable by showing that automated analysis of three previously published TC data sets accurately recapitulates key findings reported in these studies. Using each of these data sets, we highlight how biologically relevant findings can be readily obtained by exploiting TDCA to yield intuitive parameters that describe behavior at either a single locus or sets of loci. TDCA enables customizable analysis of user input aligned DNA sequencing data, coupled with graphical outputs in the form of publication-ready figures that describe behavior at either individual loci or sets of loci sharing common traits defined by the user. TDCA accepts sequencing data as standard binary alignment map (BAM) files and loci of interest in browser extensible data (BED) file format. CONCLUSIONS: TDCA accurately models the number of sequencing reads, or coverage, at loci from TC ChIP-seq studies or conceptually related TC sequencing experiments. TC experiments are reduced to intuitive parametric values that facilitate biologically relevant data analysis, and the uncovering of variations in the time-dependent behavior of chromatin. TDCA automates the analysis of TC ChIP-seq experiments, permitting researchers to easily obtain raw and modeled data for specific loci or groups of loci with similar behavior while also enhancing consistency of data analysis of TC data within the genomics field.
[Mh] Termos MeSH primário: Imunoprecipitação da Cromatina/métodos
Sequenciamento de Nucleotídeos em Larga Escala/métodos
Software
[Mh] Termos MeSH secundário: Algoritmos
Animais
Linhagem Celular
Cromossomos/química
Cromossomos/metabolismo
DNA/química
DNA/isolamento & purificação
DNA/metabolismo
Proteínas de Ligação a DNA/química
Proteínas de Ligação a DNA/genética
Proteínas de Ligação a DNA/metabolismo
Histonas/química
Histonas/genética
Histonas/metabolismo
Seres Humanos
Saccharomyces cerevisiae/metabolismo
Proteínas de Saccharomyces cerevisiae/química
Proteínas de Saccharomyces cerevisiae/genética
Proteínas de Saccharomyces cerevisiae/metabolismo
Análise de Sequência de DNA
Fatores de Transcrição/química
Fatores de Transcrição/genética
Fatores de Transcrição/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (ABF1 protein, S cerevisiae); 0 (DNA-Binding Proteins); 0 (Histones); 0 (Saccharomyces cerevisiae Proteins); 0 (Transcription Factors); 9007-49-2 (DNA)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180306
[Lr] Data última revisão:
180306
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171128
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1936-x


  6 / 93796 MEDLINE  
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[PMID]:29362354
[Au] Autor:Garcia-Alai MM; Heidemann J; Skruzny M; Gieras A; Mertens HDT; Svergun DI; Kaksonen M; Uetrecht C; Meijers R
[Ad] Endereço:European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany.
[Ti] Título:Epsin and Sla2 form assemblies through phospholipid interfaces.
[So] Source:Nat Commun;9(1):328, 2018 01 23.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:In clathrin-mediated endocytosis, adapter proteins assemble together with clathrin through interactions with specific lipids on the plasma membrane. However, the precise mechanism of adapter protein assembly at the cell membrane is still unknown. Here, we show that the membrane-proximal domains ENTH of epsin and ANTH of Sla2 form complexes through phosphatidylinositol 4,5-bisphosphate (PIP2) lipid interfaces. Native mass spectrometry reveals how ENTH and ANTH domains form assemblies by sharing PIP2 molecules. Furthermore, crystal structures of epsin Ent2 ENTH domain from S. cerevisiae in complex with PIP2 and Sla2 ANTH domain from C. thermophilum illustrate how allosteric phospholipid binding occurs. A comparison with human ENTH and ANTH domains reveal only the human ENTH domain can form a stable hexameric core in presence of PIP2, which could explain functional differences between fungal and human epsins. We propose a general phospholipid-driven multifaceted assembly mechanism tolerating different adapter protein compositions to induce endocytosis.
[Mh] Termos MeSH primário: Proteínas Adaptadoras de Transporte Vesicular/química
Proteínas Fúngicas/química
Fosfatidilinositol 4,5-Difosfato/química
Domínios Proteicos
[Mh] Termos MeSH secundário: Proteínas Adaptadoras de Transporte Vesicular/genética
Proteínas Adaptadoras de Transporte Vesicular/metabolismo
Sequência de Aminoácidos
Sítios de Ligação/genética
Membrana Celular/metabolismo
Chaetomium/genética
Chaetomium/metabolismo
Cristalografia por Raios X
Endocitose
Proteínas Fúngicas/genética
Proteínas Fúngicas/metabolismo
Seres Humanos
Modelos Moleculares
Fosfatidilinositol 4,5-Difosfato/metabolismo
Ligação Proteica
Multimerização Proteica
Saccharomyces cerevisiae/genética
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 (Adaptor Proteins, Vesicular Transport); 0 (Fungal Proteins); 0 (Phosphatidylinositol 4,5-Diphosphate); 0 (epsin)
[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:180125
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-017-02443-x


  7 / 93796 MEDLINE  
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[PMID]:29351565
[Au] Autor:Peek J; Harvey C; Gray D; Rosenberg D; Kolla L; Levy-Myers R; Yin R; McMurry JL; Kerscher O
[Ad] Endereço:Biology Department, The College of William & Mary, Williamsburg, Virginia, United States of America.
[Ti] Título:SUMO targeting of a stress-tolerant Ulp1 SUMO protease.
[So] Source:PLoS One;13(1):e0191391, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:SUMO proteases of the SENP/Ulp family are master regulators of both sumoylation and desumoylation and regulate SUMO homeostasis in eukaryotic cells. SUMO conjugates rapidly increase in response to cellular stress, including nutrient starvation, hypoxia, osmotic stress, DNA damage, heat shock, and other proteotoxic stressors. Nevertheless, little is known about the regulation and targeting of SUMO proteases during stress. To this end we have undertaken a detailed comparison of the SUMO-binding activity of the budding yeast protein Ulp1 (ScUlp1) and its ortholog in the thermotolerant yeast Kluyveromyces marxianus, KmUlp1. We find that the catalytic UD domains of both ScUlp1 and KmUlp1 show a high degree of sequence conservation, complement a ulp1Δ mutant in vivo, and process a SUMO precursor in vitro. Next, to compare the SUMO-trapping features of both SUMO proteases we produced catalytically inactive recombinant fragments of the UD domains of ScUlp1 and KmUlp1, termed ScUTAG and KmUTAG respectively. Both ScUTAG and KmUTAG were able to efficiently bind a variety of purified SUMO isoforms and bound immobilized SUMO1 with nanomolar affinity. However, KmUTAG showed a greatly enhanced ability to bind SUMO and SUMO-modified proteins in the presence of oxidative, temperature and other stressors that induce protein misfolding. We also investigated whether a SUMO-interacting motif (SIM) in the UD domain of KmULP1 that is not conserved in ScUlp1 may contribute to the SUMO-binding properties of KmUTAG. In summary, our data reveal important details about how SUMO proteases target and bind their sumoylated substrates, especially under stress conditions. We also show that the robust pan-SUMO binding features of KmUTAG can be exploited to detect and study SUMO-modified proteins in cell culture systems.
[Mh] Termos MeSH primário: Cisteína Endopeptidases/metabolismo
Proteínas Fúngicas/metabolismo
Proteínas de Saccharomyces cerevisiae/metabolismo
Proteínas Modificadoras Pequenas Relacionadas à Ubiquitina/metabolismo
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Domínio Catalítico/genética
Sequência Conservada
Cisteína Endopeptidases/química
Cisteína Endopeptidases/genética
Proteínas Fúngicas/química
Proteínas Fúngicas/genética
Teste de Complementação Genética
Kluyveromyces/genética
Kluyveromyces/metabolismo
Modelos Moleculares
Proteínas Mutantes/química
Proteínas Mutantes/genética
Proteínas Mutantes/metabolismo
Ligação Proteica
Processamento de Proteína Pós-Traducional
Saccharomyces cerevisiae/genética
Saccharomyces cerevisiae/metabolismo
Proteínas de Saccharomyces cerevisiae/química
Proteínas de Saccharomyces cerevisiae/genética
Homologia de Sequência de Aminoácidos
Estresse Fisiológico
Sumoilação
Temperatura Ambiente
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Fungal Proteins); 0 (Mutant Proteins); 0 (Saccharomyces cerevisiae Proteins); 0 (Small Ubiquitin-Related Modifier Proteins); EC 3.4.22.- (Cysteine Endopeptidases); EC 3.4.22.- (Ulp1 protease)
[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:180120
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191391


  8 / 93796 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


  9 / 93796 MEDLINE  
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[PMID]:29311542
[Au] Autor:Cao J; Perez-Pinera P; Lowenhaupt K; Wu MR; Purcell O; de la Fuente-Nunez C; Lu TK
[Ad] Endereço:Synthetic Biology Group, Department of Biological Engineering and Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
[Ti] Título:Versatile and on-demand biologics co-production in yeast.
[So] Source:Nat Commun;9(1):77, 2018 01 08.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Current limitations to on-demand drug manufacturing can be addressed by technologies that streamline manufacturing processes. Combining the production of two or more drugs into a single batch could not only be useful for research, clinical studies, and urgent therapies but also effective when combination therapies are needed or where resources are scarce. Here we propose strategies to concurrently produce multiple biologics from yeast in single batches by multiplexing strain development, cell culture, separation, and purification. We demonstrate proof-of-concept for three biologics co-production strategies: (i) inducible expression of multiple biologics and control over the ratio between biologic drugs produced together; (ii) consolidated bioprocessing; and (iii) co-expression and co-purification of a mixture of two monoclonal antibodies. We then use these basic strategies to produce drug mixtures as well as to separate drugs. These strategies offer a diverse array of options for on-demand, flexible, low-cost, and decentralized biomanufacturing applications without the need for specialized equipment.
[Mh] Termos MeSH primário: Produtos Biológicos/metabolismo
Preparações Farmacêuticas/metabolismo
Saccharomyces cerevisiae/metabolismo
Tecnologia Farmacêutica/métodos
[Mh] Termos MeSH secundário: Anticorpos Monoclonais/biossíntese
Anticorpos Monoclonais/isolamento & purificação
Produtos Biológicos/isolamento & purificação
Análise Custo-Benefício
Seres Humanos
Preparações Farmacêuticas/isolamento & purificação
Saccharomyces cerevisiae/crescimento & desenvolvimento
Tecnologia Farmacêutica/economia
Tecnologia Farmacêutica/instrumentação
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (Antibodies, Monoclonal); 0 (Biological Products); 0 (Pharmaceutical Preparations)
[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/s41467-017-02587-w


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[PMID]:28748404
[Au] Autor:Scariot FJ; Jahn L; Delamare APL; Echeverrigaray S
[Ad] Endereço:Institute of Biotechnology, University of Caxias do Sul, Caxias do Sul, Rio Grande Do Sul, Brazil.
[Ti] Título:Necrotic and apoptotic cell death induced by Captan on Saccharomyces cerevisiae.
[So] Source:World J Microbiol Biotechnol;33(8):159, 2017 Aug.
[Is] ISSN:1573-0972
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:Captan is one of the most widely used broad-spectrum fungicide applied to control several early and late diseases of grapes, apples, and other fruits and vegetables, and as other phthalimide fungicides is defined as a multisite compound with thiol-reactivity. Captan can affect non-target organisms as yeasts, modifying microbial populations and fermentation processes. In this study, we asked whether Captan thiol-reactivity and other mechanisms are involved in acute Captan-induced cell death on aerobic growing Saccharomyces cerevisiae. Thus for, we analyze cellular protein and non-protein thiols, cell membrane integrity, reactive oxygen species accumulation, phosphatidylserine externalization, and apoptotic mutants behavior. The results showed that when submitted to acute Captan treatment most cells lost their membrane integrity and died by necrosis due to Captan reaction with thiols. However, part of the cells, even maintaining their membrane integrity, lost their culture ability. These cells showed an apoptotic behavior that may be the result of non-protein thiol depletion and consequent increase of reactive oxygen species (ROS). ROS accumulation triggers a metacaspase-dependent apoptotic cascade, as shown by the higher viability of the yca1-deleted mutant. Together, necrosis and apoptosis are responsible for the high mortality detected after acute Captan treatment of aerobically growing cells of S. cerevisiae.
[Mh] Termos MeSH primário: Apoptose/efeitos dos fármacos
Captana/farmacologia
Morte Celular/efeitos dos fármacos
Saccharomyces cerevisiae/efeitos dos fármacos
[Mh] Termos MeSH secundário: Membrana Celular/efeitos dos fármacos
Fermentação
Fungicidas Industriais/farmacologia
Viabilidade Microbiana/efeitos dos fármacos
Mutação
Necrose
Espécies Reativas de Oxigênio/metabolismo
Saccharomyces cerevisiae/genética
Saccharomyces cerevisiae/crescimento & desenvolvimento
Proteínas de Saccharomyces cerevisiae/genética
Proteínas de Saccharomyces cerevisiae/metabolismo
Compostos de Sulfidrila/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Fungicides, Industrial); 0 (Reactive Oxygen Species); 0 (Saccharomyces cerevisiae Proteins); 0 (Sulfhydryl Compounds); EOL5G26Q9F (Captan)
[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:170728
[St] Status:MEDLINE
[do] DOI:10.1007/s11274-017-2325-3



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