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[PMID]:29202710
[Au] Autor:Parvathaneni RK; DeLeo VL; Spiekerman JJ; Chakraborty D; Devos KM
[Ad] Endereço:Institute of Plant Breeding, Genetics and Genomics, University of Georgia, 30602, Athens, Georgia, United States.
[Ti] Título:Parallel loss of introns in the ABCB1 gene in angiosperms.
[So] Source:BMC Evol Biol;17(1):238, 2017 Dec 04.
[Is] ISSN:1471-2148
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: The presence of non-coding introns is a characteristic feature of most eukaryotic genes. While the size of the introns, number of introns per gene and the number of intron-containing genes can vary greatly between sequenced eukaryotic genomes, the structure of a gene with reference to intron presence and positions is typically conserved in closely related species. Unexpectedly, the ABCB1 (ATP-Binding Cassette Subfamily B Member 1) gene which encodes a P-glycoprotein and underlies dwarfing traits in maize (br2), sorghum (dw3) and pearl millet (d2) displayed considerable variation in intron composition. RESULTS: An analysis of the ABCB1 gene structure in 80 angiosperms revealed that the number of introns ranged from one to nine. All introns in ABCB1 underwent either a one-time loss (single loss in one lineage/species) or multiple independent losses (parallel loss in two or more lineages/species) with the majority of losses occurring within the grass family. In contrast, the structure of the closest homolog to ABCB1, ABCB19, remained constant in the majority of angiosperms analyzed. Using known phylogenetic relationships within the grasses, we determined the ancestral branch-points where the losses occurred. Intron 7, the longest intron, was lost in only a single species, Mimulus guttatus, following duplication of ABCB1. Semiquantitative PCR showed that the M. guttatus ABCB1 gene copy without intron 7 had significantly lower transcript levels than the gene copy with intron 7. We further demonstrated that intron 7 carried two motifs that were highly conserved across the monocot-dicot divide. CONCLUSIONS: The ABCB1 gene structure is highly dynamic, while the structure of ABCB19 remained largely conserved through evolution. Precise removal of introns, preferential removal of smaller introns and presence of at least 2 bp of microhomology flanking most introns indicated that intron loss may have predominantly occurred through non-homologous end-joining (NHEJ) repair of double strand breaks. Lack of microhomology in the exon upstream of lost phase I introns was likely due to release of the selective constraint on the penultimate base (3rd base in codon) of the terminal codon by the splicing machinery. In addition to size, the presence of regulatory motifs will make introns recalcitrant to loss.
[Mh] Termos MeSH primário: Genes de Plantas
Íntrons/genética
Magnoliopsida/genética
Proteínas de Plantas/genética
[Mh] Termos MeSH secundário: Arabidopsis/genética
Sequência de Bases
Sequência Conservada/genética
DNA Complementar/genética
Evolução Molecular
Regulação da Expressão Gênica de Plantas
Mimulus/genética
Motivos de Nucleotídeos/genética
Oryza/genética
Filogenia
Reação em Cadeia da Polimerase
Polimorfismo Genético
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
Reprodutibilidade dos Testes
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Complementary); 0 (Plant Proteins); 0 (RNA, Messenger)
[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:171206
[St] Status:MEDLINE
[do] DOI:10.1186/s12862-017-1077-x


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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


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[PMID]:28461104
[Au] Autor:Prokop S; Perry NA; Vishnivetskiy SA; Toth AD; Inoue A; Milligan G; Iverson TM; Hunyady L; Gurevich VV
[Ad] Endereço:Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary.
[Ti] Título:Differential manipulation of arrestin-3 binding to basal and agonist-activated G protein-coupled receptors.
[So] Source:Cell Signal;36:98-107, 2017 Aug.
[Is] ISSN:1873-3913
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Non-visual arrestins interact with hundreds of different G protein-coupled receptors (GPCRs). Here we show that by introducing mutations into elements that directly bind receptors, the specificity of arrestin-3 can be altered. Several mutations in the two parts of the central "crest" of the arrestin molecule, middle-loop and C-loop, enhanced or reduced arrestin-3 interactions with several GPCRs in receptor subtype and functional state-specific manner. For example, the Lys139Ile substitution in the middle-loop dramatically enhanced the binding to inactive M muscarinic receptor, so that agonist activation of the M did not further increase arrestin-3 binding. Thus, the Lys139Ile mutation made arrestin-3 essentially an activation-independent binding partner of M , whereas its interactions with other receptors, including the ß -adrenergic receptor and the D and D dopamine receptors, retained normal activation dependence. In contrast, the Ala248Val mutation enhanced agonist-induced arrestin-3 binding to the ß -adrenergic and D dopamine receptors, while reducing its interaction with the D dopamine receptor. These mutations represent the first example of altering arrestin specificity via enhancement of the arrestin-receptor interactions rather than selective reduction of the binding to certain subtypes.
[Mh] Termos MeSH primário: Arrestinas/metabolismo
Receptores Acoplados a Proteínas-G/agonistas
Receptores Acoplados a Proteínas-G/metabolismo
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Animais
Arrestinas/química
Células COS
Bovinos
Cercopithecus aethiops
Sequência Conservada
Células HEK293
Seres Humanos
Lisina/metabolismo
Proteínas Mutantes/metabolismo
Mutação/genética
Ligação Proteica
Estrutura Secundária de Proteína
Rodopsina/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Arrestins); 0 (Mutant Proteins); 0 (Receptors, G-Protein-Coupled); 0 (arrestin3); 9009-81-8 (Rhodopsin); K3Z4F929H6 (Lysine)
[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:170503
[St] Status: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


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[PMID]:29351555
[Au] Autor:Xue Y; Chen B; Win AN; Fu C; Lian J; Liu X; Wang R; Zhang X; Chai Y
[Ad] Endereço:College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
[Ti] Título:Omega-3 fatty acid desaturase gene family from two ω-3 sources, Salvia hispanica and Perilla frutescens: Cloning, characterization and expression.
[So] Source:PLoS One;13(1):e0191432, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Omega-3 fatty acid desaturase (ω-3 FAD, D15D) is a key enzyme for α-linolenic acid (ALA) biosynthesis. Both chia (Salvia hispanica) and perilla (Perilla frutescens) contain high levels of ALA in seeds. In this study, the ω-3 FAD gene family was systematically and comparatively cloned from chia and perilla. Perilla FAD3, FAD7, FAD8 and chia FAD7 are encoded by single-copy (but heterozygous) genes, while chia FAD3 is encoded by 2 distinct genes. Only 1 chia FAD8 sequence was isolated. In these genes, there are 1 to 6 transcription start sites, 1 to 8 poly(A) tailing sites, and 7 introns. The 5'UTRs of PfFAD8a/b contain 1 to 2 purine-stretches and 2 pyrimidine-stretches. An alternative splice variant of ShFAD7a/b comprises a 5'UTR intron. Their encoded proteins harbor an FA_desaturase conserved domain together with 4 trans-membrane helices and 3 histidine boxes. Phylogenetic analysis validated their identity of dicot microsomal or plastidial ω-3 FAD proteins, and revealed some important evolutionary features of plant ω-3 FAD genes such as convergent evolution across different phylums, single-copy status in algae, and duplication events in certain taxa. The qRT-PCR assay showed that the ω-3 FAD genes of two species were expressed at different levels in various organs, and they also responded to multiple stress treatments. The functionality of the ShFAD3 and PfFAD3 enzymes was confirmed by yeast expression. The systemic molecular and functional features of the ω-3 FAD gene family from chia and perilla revealed in this study will facilitate their use in future studies on genetic improvement of ALA traits in oilseed crops.
[Mh] Termos MeSH primário: Ácidos Graxos Dessaturases/genética
Genes de Plantas
Perilla frutescens/enzimologia
Perilla frutescens/genética
Proteínas de Plantas/genética
Salvia/enzimologia
Salvia/genética
[Mh] Termos MeSH secundário: Regiões 5' não Traduzidas
Processamento Alternativo
Sequência de Aminoácidos
Clonagem Molecular
Sequência Conservada
Evolução Molecular
Ácidos Graxos Dessaturases/química
Ácidos Graxos Dessaturases/metabolismo
Regulação Enzimológica da Expressão Gênica
Regulação da Expressão Gênica de Plantas
Família Multigênica
Especificidade de Órgãos
Filogenia
Proteínas de Plantas/química
Proteínas de Plantas/metabolismo
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
RNA de Plantas/genética
RNA de Plantas/metabolismo
Proteínas Recombinantes/química
Proteínas Recombinantes/genética
Proteínas Recombinantes/metabolismo
Homologia de Sequência de Aminoácidos
Estresse Fisiológico
Transcriptoma
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (5' Untranslated Regions); 0 (Plant Proteins); 0 (RNA, Messenger); 0 (RNA, Plant); 0 (Recombinant Proteins); EC 1.14.19.- (Fatty Acid Desaturases); EC 1.14.99.- (omega-3 fatty acid desaturase)
[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.0191432


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[PMID]:29261646
[Au] Autor:Hamm DC; Larson ED; Nevil M; Marshall KE; Bondra ER; Harrison MM
[Ad] Endereço:Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America.
[Ti] Título:A conserved maternal-specific repressive domain in Zelda revealed by Cas9-mediated mutagenesis in Drosophila melanogaster.
[So] Source:PLoS Genet;13(12):e1007120, 2017 12.
[Is] ISSN:1553-7404
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:In nearly all metazoans, the earliest stages of development are controlled by maternally deposited mRNAs and proteins. The zygotic genome becomes transcriptionally active hours after fertilization. Transcriptional activation during this maternal-to-zygotic transition (MZT) is tightly coordinated with the degradation of maternally provided mRNAs. In Drosophila melanogaster, the transcription factor Zelda plays an essential role in widespread activation of the zygotic genome. While Zelda expression is required both maternally and zygotically, the mechanisms by which it functions to remodel the embryonic genome and prepare the embryo for development remain unclear. Using Cas9-mediated genome editing to generate targeted mutations in the endogenous zelda locus, we determined the functional relevance of protein domains conserved amongst Zelda orthologs. We showed that neither a conserved N-terminal zinc finger nor an acidic patch were required for activity. Similarly, a previously identified splice isoform of zelda is dispensable for viability. By contrast, we identified a highly conserved zinc-finger domain that is essential for the maternal, but not zygotic functions of Zelda. Animals homozygous for mutations in this domain survived to adulthood, but embryos inheriting these loss-of-function alleles from their mothers died late in embryogenesis. These mutations did not interfere with the capacity of Zelda to activate transcription in cell culture. Unexpectedly, these mutations generated a hyperactive form of the protein and enhanced Zelda-dependent gene expression. These data have defined a protein domain critical for controlling Zelda activity during the MZT, but dispensable for its roles later in development, for the first time separating the maternal and zygotic requirements for Zelda. This demonstrates that highly regulated levels of Zelda activity are required for establishing the developmental program during the MZT. We propose that tightly regulated gene expression is essential to navigate the MZT and that failure to precisely execute this developmental program leads to embryonic lethality.
[Mh] Termos MeSH primário: Proteínas de Drosophila/genética
Proteínas de Drosophila/metabolismo
Herança Materna/genética
Fatores de Transcrição/genética
Fatores de Transcrição/metabolismo
[Mh] Termos MeSH secundário: Animais
Sistemas CRISPR-Cas
Sequência Conservada
Drosophila melanogaster
Edição de Genes
Regulação da Expressão Gênica no Desenvolvimento
Mutação
Regiões Promotoras Genéticas
Domínios Proteicos
Estabilidade de RNA/genética
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
Dedos de Zinco/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Nm] Nome de substância:
0 (Drosophila Proteins); 0 (RNA, Messenger); 0 (Transcription Factors); 0 (Zelda protein, Drosophila)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180227
[Lr] Data última revisão:
180227
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171221
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pgen.1007120


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[PMID]:29338040
[Au] Autor:Yang X; Li H; Yang Y; Wang Y; Mo Y; Zhang R; Zhang Y; Ma J; Wei C; Zhang X
[Ad] Endereço:State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China.
[Ti] Título:Identification and expression analyses of WRKY genes reveal their involvement in growth and abiotic stress response in watermelon (Citrullus lanatus).
[So] Source:PLoS One;13(1):e0191308, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Despite identification of WRKY family genes in numerous plant species, a little is known about WRKY genes in watermelon, one of the most economically important fruit crops around the world. Here, we identified a total of 63 putative WRKY genes in watermelon and classified them into three major groups (I-III) and five subgroups (IIa-IIe) in group II. The structure analysis indicated that ClWRKYs with different WRKY domains or motifs may play different roles by regulating respective target genes. The expressions of ClWRKYs in different tissues indicate that they are involved in various tissue growth and development. Furthermore, the diverse responses of ClWRKYs to drought, salt, or cold stress suggest that they positively or negatively affect plant tolerance to various abiotic stresses. In addition, the altered expression patterns of ClWRKYs in response to phytohormones such as, ABA, SA, MeJA, and ETH, imply the occurrence of complex cross-talks between ClWRKYs and plant hormone signals in regulating plant physiological and biological processes. Taken together, our findings provide valuable clues to further explore the function and regulatory mechanisms of ClWRKY genes in watermelon growth, development, and adaption to environmental stresses.
[Mh] Termos MeSH primário: Citrullus/genética
Citrullus/fisiologia
Regulação da Expressão Gênica de Plantas
Proteínas de Plantas/genética
Estresse Fisiológico/genética
Fatores de Transcrição/genética
[Mh] Termos MeSH secundário: Motivos de Aminoácidos
Sequência de Aminoácidos
Citrullus/efeitos dos fármacos
Sequência Conservada
Evolução Molecular
Duplicação Gênica
Regulação da Expressão Gênica de Plantas/efeitos dos fármacos
Filogenia
Reguladores de Crescimento de Planta/farmacologia
Proteínas de Plantas/química
Alinhamento de Sequência
Estresse Fisiológico/efeitos dos fármacos
Sintenia
Fatores de Transcrição/química
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Plant Growth Regulators); 0 (Plant Proteins); 0 (Transcription Factors)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180226
[Lr] Data última revisão:
180226
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180117
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191308


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[PMID]:27773523
[Au] Autor:Omer S; Harlow TJ; Gogarten JP
[Ad] Endereço:Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125, USA.
[Ti] Título:Does Sequence Conservation Provide Evidence for Biological Function?
[So] Source:Trends Microbiol;25(1):11-18, 2017 Jan.
[Is] ISSN:1878-4380
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Finding a signature of purifying selection in a gene is usually interpreted as evidence for the gene providing a function that is targeted by natural selection. This opinion offers a very different hypothesis: purifying selection may be due to removing harmful mutations from the population, that is, the gene and its encoded protein become harmful after a mutation occurred, possibly because the mutated protein interferes with the translation machinery, or because of toxicity of the misfolded protein. Finding a signature of purifying selection should not automatically be considered proof of the gene's selectable function.
[Mh] Termos MeSH primário: Sequência Conservada/genética
Escherichia coli/genética
Evolução Molecular
Variação Genética/genética
Modelos Genéticos
Salmonella enterica/genética
[Mh] Termos MeSH secundário: Sequência de Bases
Mutação/genética
Filogenia
Seleção Genética/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Em] Mês de entrada:1711
[Cu] Atualização por classe:180227
[Lr] Data última revisão:
180227
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161025
[St] Status:MEDLINE


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[PMID]:29351342
[Au] Autor:van der Ven AT; Kobbe B; Kohl S; Shril S; Pogoda HM; Imhof T; Ityel H; Vivante A; Chen J; Hwang DY; Connaughton DM; Mann N; Widmeier E; Taglienti M; Schmidt JM; Nakayama M; Senguttuvan P; Kumar S; Tasic V; Kehinde EO; Mane SM; Lifton RP; Soliman N; Lu W; Bauer SB; Hammerschmidt M; Wagener R; Hildebrandt F
[Ad] Endereço:Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America.
[Ti] Título:A homozygous missense variant in VWA2, encoding an interactor of the Fraser-complex, in a patient with vesicoureteral reflux.
[So] Source:PLoS One;13(1):e0191224, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Congenital anomalies of the kidney and urinary tract (CAKUT) are the most common cause (40-50%) of chronic kidney disease (CKD) in children. About 40 monogenic causes of CAKUT have so far been discovered. To date less than 20% of CAKUT cases can be explained by mutations in these 40 genes. To identify additional monogenic causes of CAKUT, we performed whole exome sequencing (WES) and homozygosity mapping (HM) in a patient with CAKUT from Indian origin and consanguineous descent. We identified a homozygous missense mutation (c.1336C>T, p.Arg446Cys) in the gene Von Willebrand factor A domain containing 2 (VWA2). With immunohistochemistry studies on kidneys of newborn (P1) mice, we show that Vwa2 and Fraser extracellular matrix complex subunit 1 (Fras1) co-localize in the nephrogenic zone of the renal cortex. We identified a pronounced expression of Vwa2 in the basement membrane of the ureteric bud (UB) and derivatives of the metanephric mesenchyme (MM). By applying in vitro assays, we demonstrate that the Arg446Cys mutation decreases translocation of monomeric VWA2 protein and increases translocation of aggregated VWA2 protein into the extracellular space. This is potentially due to the additional, unpaired cysteine residue in the mutated protein that is used for intermolecular disulfide bond formation. VWA2 is a known, direct interactor of FRAS1 of the Fraser-Complex (FC). FC-encoding genes and interacting proteins have previously been implicated in the pathogenesis of syndromic and/or isolated CAKUT phenotypes in humans. VWA2 therefore constitutes a very strong candidate in the search for novel CAKUT-causing genes. Our results from in vitro experiments indicate a dose-dependent neomorphic effect of the Arg446Cys homozygous mutation in VWA2.
[Mh] Termos MeSH primário: Biomarcadores Tumorais/genética
Síndrome de Fraser/genética
Mutação de Sentido Incorreto
Anormalidades Urogenitais/genética
Refluxo Vesicoureteral/genética
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Substituição de Aminoácidos
Animais
Animais Recém-Nascidos
Biomarcadores Tumorais/química
Criança
Consanguinidade
Sequência Conservada
Éxons
Proteínas da Matriz Extracelular/genética
Proteínas da Matriz Extracelular/metabolismo
Regulação da Expressão Gênica no Desenvolvimento
Homozigoto
Seres Humanos
Masculino
Camundongos
Modelos Animais
Modelos Moleculares
Linhagem
Homologia de Sequência de Aminoácidos
Sistema Urogenital/crescimento & desenvolvimento
Sistema Urogenital/metabolismo
[Pt] Tipo de publicação:CASE REPORTS; JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Biomarkers, Tumor); 0 (Extracellular Matrix Proteins); 0 (Fras1 protein, mouse); 0 (VWA2 protein, human); 0 (Vwa2 protein, mouse)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180221
[Lr] Data última revisão:
180221
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180120
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191224


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[PMID]:29338035
[Au] Autor:Bradai M; Mahjoubi H; Chini A; Chabouté ME; Hanin M; Ebel C
[Ad] Endereço:Laboratory of Biotechnology and Plant Improvement, Center of Biotechnology of Sfax, Sfax, Tunisia.
[Ti] Título:Genome wide identification of wheat and Brachypodium type one protein phosphatases and functional characterization of durum wheat TdPP1a.
[So] Source:PLoS One;13(1):e0191272, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Reversible phosphorylation is an essential mechanism regulating signal transduction during development and environmental stress responses. An important number of dephosphorylation events in the cell are catalyzed by type one protein phosphatases (PP1), which catalytic activity is driven by the binding of regulatory proteins that control their substrate specificity or subcellular localization. Plants harbor several PP1 isoforms accounting for large functional redundancies. While animal PP1s were reported to play relevant roles in controlling multiple cellular processes, plant orthologs remain poorly studied. To decipher the role of plant PP1s, we compared PP1 genes from three monocot species, Brachypodium, common wheat and rice at the genomic and transcriptomic levels. To gain more insight into the wheat PP1 proteins, we identified and characterized TdPP1a, the first wheat type one protein phosphatase from a Tunisian durum wheat variety Oum Rabiaa3. TdPP1a is highly conserved in sequence and structure when compared to mammalian, yeast and other plant PP1s. We demonstrate that TdPP1a is an active, metallo-dependent phosphatase in vitro and is able to interact with AtI2, a typical regulator of PP1 functions. Also, TdPP1a is capable to complement the heat stress sensitivity of the yeast mutant indicating that TdPP1a is functional also in vivo. Moreover, transient expression of TdPP1a::GFP in tobacco leaves revealed that it is ubiquitously distributed within the cell, with a strong accumulation in the nucleus. Finally, transcriptional analyses showed similar expression levels in roots and leaves of durum wheat seedlings. Interestingly, the expression in leaves is significantly induced following salinity stress, suggesting a potential role of TdPP1a in wheat salt stress response.
[Mh] Termos MeSH primário: Brachypodium/enzimologia
Brachypodium/genética
Fosfoproteínas Fosfatases/genética
Proteínas de Plantas/genética
Triticum/enzimologia
Triticum/genética
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Sequência Conservada
Evolução Molecular
Regulação Enzimológica da Expressão Gênica
Regulação da Expressão Gênica de Plantas
Isoenzimas/genética
Isoenzimas/metabolismo
Oryza/enzimologia
Oryza/genética
Fosfoproteínas Fosfatases/metabolismo
Filogenia
Proteínas de Plantas/metabolismo
Proteína Fosfatase 1/genética
Proteína Fosfatase 1/metabolismo
Homologia de Sequência de Aminoácidos
Especificidade da Espécie
Estresse Fisiológico
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Isoenzymes); 0 (Plant Proteins); EC 3.1.3.16 (Phosphoprotein Phosphatases); EC 3.1.3.16 (Protein Phosphatase 1)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180220
[Lr] Data última revisão:
180220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180117
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191272



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