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1.
Pharmacol Res ; 170: 105535, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34058326

RESUMO

Eukaryotic protein synthesis is the highly conserved, complex mechanism of translating genetic information into proteins. Although this process is essential for cellular homoeostasis, dysregulations are associated with cellular malfunctions and diseases including cancer and diabetes. In the challenging and ongoing search for adequate treatment possibilities, natural products represent excellent research tools and drug leads for new interactions with the translational machinery and for influencing mRNA translation. In this review, bacterial-, marine- and plant-derived natural compounds that interact with different steps of mRNA translation, comprising ribosomal assembly, translation initiation and elongation, are highlighted. Thereby, the exact binding and interacting partners are unveiled in order to accurately understand the mode of action of each natural product. The pharmacological relevance of these compounds is furthermore assessed by evaluating the observed biological activities in the light of translational inhibition and by enlightening potential obstacles and undesired side-effects, e.g. in clinical trials. As many of the natural products presented here possess the potential to serve as drug leads for synthetic derivatives, structural motifs, which are indispensable for both mode of action and biological activities, are discussed. Evaluating the natural products emphasises the strong diversity of their points of attack. Especially the fact that selected binding partners can be set in direct relation to different diseases emphasises the indispensability of natural products in the field of drug development. Discovery of new, unique and unusual interacting partners again renders them promising tools for future research in the field of eukaryotic mRNA translation.


Assuntos
Organismos Aquáticos , Bactérias , Produtos Biológicos/farmacologia , Extratos Vegetais/farmacologia , Biossíntese de Proteínas/efeitos dos fármacos , Inibidores da Síntese de Proteínas/farmacologia , RNA Mensageiro/metabolismo , Ribossomos/efeitos dos fármacos , Animais , Organismos Aquáticos/química , Bactérias/química , Produtos Biológicos/isolamento & purificação , Desenvolvimento de Medicamentos , Humanos , Myxococcales/química , Extratos Vegetais/isolamento & purificação , Inibidores da Síntese de Proteínas/isolamento & purificação , RNA Mensageiro/genética , Ribossomos/genética , Ribossomos/metabolismo
2.
Nat Commun ; 12(1): 833, 2021 02 05.
Artigo em Inglês | MEDLINE | ID: mdl-33547280

RESUMO

The structure of proline prevents it from adopting an optimal position for rapid protein synthesis. Poly-proline-tract (PPT) associated ribosomal stalling is resolved by highly conserved eIF5A, the only protein to contain the amino acid hypusine. We show that de novo heterozygous EIF5A variants cause a disorder characterized by variable combinations of developmental delay, microcephaly, micrognathia and dysmorphism. Yeast growth assays, polysome profiling, total/hypusinated eIF5A levels and PPT-reporters studies reveal that the variants impair eIF5A function, reduce eIF5A-ribosome interactions and impair the synthesis of PPT-containing proteins. Supplementation with 1 mM spermidine partially corrects the yeast growth defects, improves the polysome profiles and restores expression of PPT reporters. In zebrafish, knockdown eif5a partly recapitulates the human phenotype that can be rescued with 1 µM spermidine supplementation. In summary, we uncover the role of eIF5A in human development and disease, demonstrate the mechanistic complexity of EIF5A-related disorder and raise possibilities for its treatment.


Assuntos
Deficiências do Desenvolvimento/genética , Regulação da Expressão Gênica no Desenvolvimento , Microcefalia/genética , Micrognatismo/genética , Fatores de Iniciação de Peptídeos/genética , Proteínas de Ligação a RNA/genética , Adolescente , Sequência de Aminoácidos , Animais , Criança , Deficiências do Desenvolvimento/metabolismo , Deficiências do Desenvolvimento/patologia , Embrião não Mamífero , Feminino , Humanos , Lisina/análogos & derivados , Lisina/genética , Lisina/metabolismo , Masculino , Microcefalia/metabolismo , Microcefalia/patologia , Micrognatismo/metabolismo , Micrognatismo/patologia , Fatores de Iniciação de Peptídeos/deficiência , Peptídeos/genética , Peptídeos/metabolismo , Biossíntese de Proteínas , Conformação Proteica , Isoformas de Proteínas/deficiência , Isoformas de Proteínas/genética , Ribossomos/genética , Ribossomos/metabolismo , Saccharomyces cerevisiae/efeitos dos fármacos , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/crescimento & desenvolvimento , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Espermidina/farmacologia , Peixe-Zebra , Proteínas de Peixe-Zebra/genética , Proteínas de Peixe-Zebra/metabolismo , Fator de Iniciação de Tradução Eucariótico 5A
3.
Anal Sci ; 37(5): 707-712, 2021 May 10.
Artigo em Inglês | MEDLINE | ID: mdl-33487600

RESUMO

In vitro selection has been widely used to generate molecular-recognition elements in analytical sciences. Although reconstituted types of in vitro transcription and translation (IVTT) system, such as PURE system, are nowadays widely used for ribosome display and mRNA/cDNA display, use of E. coli extract is often avoided, presumably because it contains unfavorable contaminants, such as ribonuclease. Nevertheless, the initial speed of protein translation in E. coli extract is markedly faster than that of PURE system. We thus hypothesized that E. coli extract is more appropriate for instant translation in ribosome display than PURE system. Here, we first revisit the potency of E. coli extract for ribosome display by shortening the translation time, and then applied the optimized condition for selecting peptide aptamers for ovalbumin (OVA). The OVA-binding peptides selected using E. coli extract exhibited specific binding to OVA, even in the presence of 50% serum. We conclude that instant translation in ribosome display using E. coli extract has the potential to generate easy-to-use and economical molecular-recognition elements in analytical sciences.


Assuntos
Escherichia coli , Ribossomos , Escherichia coli/genética , Ovalbumina , Peptídeos , Extratos Vegetais , Ribossomos/genética
4.
Mol Cell Probes ; 48: 101441, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31470078

RESUMO

The potato cyst nematodes Globodera pallida and G. rostochiensis (PCN), and tobacco cyst nematode (TCN), G. tabacum, are the most important parasitic nematodes of potato and tobacco worldwide. Ribosomal DNA provides useful molecular data for diagnostics, the study of polymorphisms and for evolutionary research in eukaryotic organisms including nematodes. Here we present data on the structure and organization of a rarely studied part of the intergenic spacer (IGS) region of the PCN and TCN genome of cyst nematodes. This region has shown potential for diagnostic purposes and population studies in other organisms including nematodes. In nematodes, the ribosomal RNA gene cluster comprises three genes: 5.8S, 18S and 28S rRNA, which are separated by spacer regions: the intergenic spacer (IGS), non-transcribed spacer (NTS), externally transcribed spacer (EST) and the internally transcribed spacer (ITS). The intergenic spacer (IGS) region consists of an external transcribed spacer (ETS) and a non-transcribed spacer (NTS) which is located between the 28S of one repeat and the 18S gene of the next repeat within the rRNA genes cluster. In this study, the first flanking portion of the IGS was amplified, cloned and sequenced from PCN and TCN. Primers were then designed to amplify the whole IGS sequence. PCR amplification of IGS from G. tabacum, G. pallida, and G. rostochiensis yielded respectively: a single amplicon of 3 kb, three amplicons sized 2.5, 2.6 and 2.9 kb, and two amplicons sized 2.8 and 2.9 kb. Results showed that Globodera spp. has more than one variant copy of the IGS, with both long and short repetitive DNA elements. An approximately 400 bp long region without any internal repetitive elements, were identified in a position between the two repetitive regions suggesting that there is a 5S gene in the IGS of these species.


Assuntos
DNA Intergênico/genética , Nicotiana/parasitologia , Ribossomos/genética , Solanum tuberosum/parasitologia , Tylenchoidea/genética , Animais , Sequência de Bases , Primers do DNA/genética , DNA Ribossômico/genética , Variação Genética/genética , Filogenia , Sequências Repetitivas de Ácido Nucleico/genética , Alinhamento de Sequência
5.
Biochemistry ; 58(2): 75-84, 2019 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-30372045

RESUMO

The threat of bacteria resistant to multiple antibiotics poses a major public health problem requiring immediate and coordinated action worldwide. While infectious pathogens have become increasingly resistant to commercially available drugs, antibiotic discovery programs in major pharmaceutical companies have produced no new antibiotic scaffolds in 40 years. As a result, new strategies must be sought to obtain a steady supply of novel scaffolds capable of countering the spread of resistance. The bacterial ribosome is a major target for antimicrobials and is inhibited by more than half of the antibiotics used today. Recent studies showing that the ribosome is a target for several classes of ribosomally synthesized antimicrobial peptides point to ribosome-targeting peptides as a promising source of antibiotic scaffolds. In this Perspective, we revisit the current paradigm of antibiotic discovery by proposing that the bacterial ribosome can be used both as a target and as a tool for the production and selection of peptide-based antimicrobials. Turning the ribosome into a high-throughput platform for the directed evolution of peptide-based antibiotics could be achieved in different ways. One possibility would be to use a combination of state-of-the-art microfluidics and genetic reprogramming techniques, which we will review briefly. If it is successful, this strategy has the potential to produce new classes of antibiotics for treating multi-drug-resistant pathogens.


Assuntos
Antibacterianos/farmacologia , Bactérias/efeitos dos fármacos , Peptídeos/metabolismo , Peptídeos/farmacologia , Ribossomos/efeitos dos fármacos , Antibacterianos/química , Bactérias/genética , Bactérias/metabolismo , Evolução Molecular Direcionada/métodos , Descoberta de Drogas , Avaliação Pré-Clínica de Medicamentos/métodos , Estudos de Associação Genética , Ensaios de Triagem em Larga Escala/métodos , Biblioteca de Peptídeos , Peptídeos/química , Biossíntese de Proteínas/efeitos dos fármacos , Ribossomos/genética , Ribossomos/metabolismo
6.
Methods ; 156: 110-120, 2019 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-30391513

RESUMO

Among different RNA modifications, the helix 69 (H69) region of the bacterial ribosomal RNA (rRNA) contains three pseudouridines (Ψs). H69 is functionally important due to its location in the heart of the ribosome. Several structural and functional studies have shown the importance of Ψ modifications in influencing the H69 conformation as well as maintaining key interactions in the ribosome during protein synthesis. Therefore, a need exists to understand the influence of modified nucleosides on conformational dynamics of the ribosome under solution conditions that mimic the cellular environment. In this review on chemical probing, we provide detailed protocols for the use of dimethyl sulfate (DMS) to examine H69 conformational states and the influence of Ψ modifications under varying solution conditions in the context of both ribosomal subunits and full ribosomes. The use of DMS footprinting to study the binding of aminoglycosides to the H69 region of bacterial rRNA as a potential antibiotic target will also be discussed. As highlighted in this work, DMS probing and footprinting are versatile techniques that can be used to gain important insight into RNA local structure and RNA-ligand interactions, respectively.


Assuntos
Escherichia coli/genética , Impressão Molecular/métodos , Pseudouridina/química , RNA Ribossômico 16S/química , RNA Ribossômico 23S/química , Compostos de Anilina/química , Antibacterianos/farmacologia , Fracionamento Celular/métodos , DNA Complementar/biossíntese , DNA Complementar/química , DNA Complementar/genética , Escherichia coli/efeitos dos fármacos , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Gentamicinas/farmacologia , Hidroliases/genética , Hidroliases/metabolismo , Ligantes , Cloreto de Magnésio/farmacologia , Neomicina/farmacologia , Conformação de Ácido Nucleico , Fatores de Terminação de Peptídeos/genética , Fatores de Terminação de Peptídeos/metabolismo , Pseudouridina/genética , Pseudouridina/metabolismo , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/metabolismo , RNA Ribossômico 23S/genética , RNA Ribossômico 23S/metabolismo , Transcrição Reversa , Subunidades Ribossômicas Maiores de Bactérias/química , Subunidades Ribossômicas Maiores de Bactérias/efeitos dos fármacos , Subunidades Ribossômicas Maiores de Bactérias/genética , Subunidades Ribossômicas Maiores de Bactérias/metabolismo , Subunidades Ribossômicas Menores de Bactérias/química , Subunidades Ribossômicas Menores de Bactérias/efeitos dos fármacos , Subunidades Ribossômicas Menores de Bactérias/genética , Subunidades Ribossômicas Menores de Bactérias/metabolismo , Ribossomos/química , Ribossomos/efeitos dos fármacos , Ribossomos/genética , Ribossomos/metabolismo , Ésteres do Ácido Sulfúrico/química
7.
Plant Physiol ; 178(1): 258-282, 2018 09.
Artigo em Inglês | MEDLINE | ID: mdl-30007911

RESUMO

Reproduction success in angiosperm plants depends on robust pollen tube growth through the female pistil tissues to ensure successful fertilization. Accordingly, there is an apparent evolutionary trend to accumulate significant reserves during pollen maturation, including a population of stored mRNAs, that are utilized later for a massive translation of various proteins in growing pollen tubes. Here, we performed a thorough transcriptomic and proteomic analysis of stored and translated transcripts in three subcellular compartments of tobacco (Nicotiana tabacum), long-term storage EDTA/puromycin-resistant particles, translating polysomes, and free ribonuclear particles, throughout tobacco pollen development and in in vitro-growing pollen tubes. We demonstrated that the composition of the aforementioned complexes is not rigid and that numerous transcripts were redistributed among these complexes during pollen development, which may represent an important mechanism of translational regulation. Therefore, we defined the pollen sequestrome as a distinct and highly dynamic compartment for the storage of stable, translationally repressed transcripts and demonstrated its dynamics. We propose that EDTA/puromycin-resistant particle complexes represent aggregated nontranslating monosomes as the primary mediators of messenger RNA sequestration. Such organization is extremely useful in fast tip-growing pollen tubes, where rapid and orchestrated protein synthesis must take place in specific regions.


Assuntos
Perfilação da Expressão Gênica/métodos , Pólen/genética , Pólen/metabolismo , Proteômica/métodos , Regulação da Expressão Gênica no Desenvolvimento , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Pólen/crescimento & desenvolvimento , Tubo Polínico/genética , Tubo Polínico/crescimento & desenvolvimento , Tubo Polínico/metabolismo , Polirribossomos/genética , Polirribossomos/metabolismo , Proteoma/genética , Proteoma/metabolismo , Ribonucleoproteínas/genética , Ribonucleoproteínas/metabolismo , Ribossomos/genética , Ribossomos/metabolismo , Nicotiana/genética , Nicotiana/crescimento & desenvolvimento , Nicotiana/metabolismo
8.
Sci Rep ; 7(1): 11908, 2017 09 19.
Artigo em Inglês | MEDLINE | ID: mdl-28928456

RESUMO

Amyloid aggregation of the eukaryotic translation terminator eRF3/Sup35p, the [PSI +] prion, empowers yeast ribosomes to read-through UGA stop codons. No similar functional prion, skipping a stop codon, has been found in Escherichia coli, a fact possibly due to the efficient back-up systems found in bacteria to rescue non-stop complexes. Here we report that engineering hydrophobic amyloidogenic repeats from a synthetic bacterial prion-like protein (RepA-WH1) into the E. coli releasing factor RF1 promotes its aggregation and enables ribosomes to continue with translation through a premature UAG stop codon located in a ß-galactosidase reporter. To our knowledge, intended aggregation of a termination factor is a way to overcome the bacterial translation quality checkpoint that had not been reported so far. We also show the feasibility of using the amyloidogenic RF1 chimeras as a reliable, rapid and cost-effective system to screen for molecules inhibiting intracellular protein amyloidogenesis in vivo, by testing the effect on the chimeras of natural polyphenols with known anti-amyloidogenic properties. Resveratrol exhibits a clear amyloid-solubilizing effect in this assay, showing no toxicity to bacteria or interference with the enzymatic activity of ß-galactosidase.


Assuntos
Amiloide/genética , Códon de Terminação/genética , Proteínas de Escherichia coli/genética , Escherichia coli/genética , Fatores de Terminação de Peptídeos/genética , Avaliação Pré-Clínica de Medicamentos , Regulação Bacteriana da Expressão Gênica , Polifenóis/farmacologia , Agregados Proteicos/efeitos dos fármacos , Biossíntese de Proteínas , Engenharia de Proteínas , Proteínas Recombinantes de Fusão/genética , Ribossomos/genética
9.
FEBS Lett ; 591(9): 1266-1277, 2017 05.
Artigo em Inglês | MEDLINE | ID: mdl-28369795

RESUMO

Arabidopsis bZIP11 is a transcription factor that modulates amino acid metabolism under high-sucrose conditions. Expression of bZIP11 is downregulated in a sucrose-dependent manner during translation. Previous in vivo studies have identified the second upstream open reading frame (uORF2) as an essential regulatory element for the sucrose-dependent translational repression of bZIP11. However, it remains unclear how uORF2 represses bZIP11 expression under high-sucrose conditions. Through biochemical experiments using cell-free translation systems, we report on sucrose-mediated ribosome stalling at the stop codon of uORF2. The C-terminal 10 amino acids (29-SFSVxFLxxLYYV-41) of uORF2 are important for ribosome stalling. Our results demonstrate that uORF2 encodes a regulatory nascent peptide that functions to sense intracellular sucrose abundance. This is the first biochemical identification of the intracellular sucrose sensor.


Assuntos
Proteínas de Arabidopsis/genética , Fatores de Transcrição de Zíper de Leucina Básica/genética , Códon de Terminação/genética , Fases de Leitura Aberta/genética , Peptídeos/genética , Ribossomos/genética , Sacarose/metabolismo , Sequência de Aminoácidos , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/metabolismo , Fatores de Transcrição de Zíper de Leucina Básica/metabolismo , Sistema Livre de Células/metabolismo , Regulação da Expressão Gênica de Plantas , Immunoblotting , Mutação , Peptídeos/metabolismo , Biossíntese de Proteínas/genética , Ribossomos/metabolismo , Homologia de Sequência de Aminoácidos
10.
Plant Physiol ; 171(1): 359-68, 2016 05.
Artigo em Inglês | MEDLINE | ID: mdl-26966170

RESUMO

trans-Acting small interfering RNAs (tasiRNAs) participate in the regulation of organ morphogenesis and determination of developmental timing in plants by down-regulating target genes through mRNA cleavage. The production of tasiRNAs is triggered by microRNA173 (miR173) and other specific microRNA-mediated cleavage of 5'-capped and 3'-polyadenylated primary TAS transcripts (pri-TASs). Although pri-TASs are not thought to encode functional proteins, they contain multiple short open reading frames (ORFs). For example, the primary TAS2 transcript (pri-TAS2) contains 11 short ORFs, and the third ORF from the 5' terminus (ORF3) encompasses the miR173 target site. Here, we show that nonsense mutations in ORF3 of pri-TAS2 upstream of the miR173 recognition site suppress tasiRNA accumulation and that ORF3 is translated in vitro. Glycerol gradient centrifugation analysis of Arabidopsis (Arabidopsis thaliana) plant extracts revealed that pri-TAS2 and its miR173-cleaved 5' and 3' fragments are fractionated together in the polysome fractions. These and previous results suggest that the 3' fragment of pri-TAS2, which is a source of tasiRNAs, forms a huge complex containing SGS3, miR173-programmed AGO1 RNA-induced silencing complex, the 5' fragment, and ribosomes. This complex overaccumulated, moderately accumulated, and did not accumulate in rdr6, sde5, and sgs3 mutants, respectively. The sgs3 sde5 and rdr6 sde5 double mutants showed phenotypes similar to those of sgs3 and sde5 single mutants, respectively, with regard to the TAS2-related RNA accumulation, suggesting that the complex is formed in an SGS3-dependent manner, somehow modified and stabilized by SDE5, and becomes competent for RDR6 action. Ribosomes in this complex likely play an important role in this process.


Assuntos
Arabidopsis/genética , MicroRNAs/genética , Fases de Leitura Aberta , RNA Interferente Pequeno/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Regulação da Expressão Gênica de Plantas , Plantas Geneticamente Modificadas , Biossíntese de Proteínas , RNA de Plantas , RNA Interferente Pequeno/genética , RNA Polimerase Dependente de RNA/genética , RNA Polimerase Dependente de RNA/metabolismo , Ribossomos/genética , Nicotiana/genética
11.
Neural Plast ; 2016: 3289187, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-26839715

RESUMO

Chronic social defeat stress leads to the development of anxiety- and depression-like states in male mice and is accompanied by numerous molecular changes in brain. The influence of 21-day period of social stress on ribosomal gene expression in five brain regions was studied using the RNA-Seq database. Most Rps, Rpl, Mprs, and Mprl genes were upregulated in the hypothalamus and downregulated in the hippocampus, which may indicate ribosomal dysfunction following chronic social defeat stress. There were no differentially expressed ribosomal genes in the ventral tegmental area, midbrain raphe nuclei, or striatum. This approach may be used to identify a pharmacological treatment of ribosome biogenesis abnormalities in the brain of patients with "ribosomopathies."


Assuntos
Dominação-Subordinação , Expressão Gênica , Hipocampo/metabolismo , Hipotálamo/metabolismo , Ribossomos/genética , Estresse Psicológico/genética , Animais , Comportamento Animal/fisiologia , Hipotálamo/fisiopatologia , Masculino , Camundongos , Ribossomos/metabolismo , Estresse Psicológico/metabolismo , Estresse Psicológico/fisiopatologia , Regulação para Cima
12.
PLoS One ; 10(9): e0137270, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26382047

RESUMO

Understanding which organisms are capable of reducing uranium at historically contaminated sites provides crucial information needed to evaluate treatment options and outcomes. One approach is determination of the bacteria which directly respond to uranium addition. In this study, uranium amendments were made to groundwater samples from a site of ongoing biostimulation with acetate. The active microbes in the planktonic phase were deduced by monitoring ribosomes production via RT-PCR. The results indicated several microorganisms were synthesizing ribosomes in proportion with uranium amendment up to 2 µM. Concentrations of U (VI) >2 µM were generally found to inhibit ribosome synthesis. Two active bacteria responding to uranium addition in the field were close relatives of Desulfobacter postgateii and Geobacter bemidjiensis. Since RNA content often increases with growth rate, our findings suggest it is possible to rapidly elucidate active bacteria responding to the addition of uranium in field samples and provides a more targeted approach to stimulate specific populations to enhance radionuclide reduction in contaminated sites.


Assuntos
Deltaproteobacteria/metabolismo , Geobacter/metabolismo , Água Subterrânea/microbiologia , RNA Bacteriano/metabolismo , RNA Ribossômico/metabolismo , Urânio/metabolismo , Poluentes Radioativos da Água/metabolismo , Biodegradação Ambiental , Colorado , Deltaproteobacteria/genética , Geobacter/genética , Água Subterrânea/análise , Filogenia , RNA Bacteriano/genética , RNA Ribossômico/genética , Ribossomos/genética , Ribossomos/metabolismo , Urânio/análise , Poluentes Radioativos da Água/análise
13.
J Neurosci ; 35(31): 10911-26, 2015 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-26245956

RESUMO

Neocortical development requires tightly controlled spatiotemporal gene expression. However, the mechanisms regulating ribosomal complexes and the timed specificity of neocortical mRNA translation are poorly understood. We show that active mRNA translation complexes (polysomes) contain ribosomal protein subsets that undergo dynamic spatiotemporal rearrangements during mouse neocortical development. Ribosomal protein specificity within polysome complexes is regulated by the arrival of in-growing thalamic axons, which secrete the morphogen Wingless-related MMTV (mouse mammary tumor virus) integration site 3 (WNT3). Thalamic WNT3 release during midneurogenesis promotes a change in the levels of Ribosomal protein L7 in polysomes, thereby regulating neocortical translation machinery specificity. Furthermore, we present an RNA sequencing dataset analyzing mRNAs that dynamically associate with polysome complexes as neocortical development progresses, and thus may be regulated spatiotemporally at the level of translation. Thalamic WNT3 regulates neocortical translation of two such mRNAs, Foxp2 and Apc, to promote FOXP2 expression while inhibiting APC expression, thereby driving neocortical neuronal differentiation and suppressing oligodendrocyte maturation, respectively. This mechanism may enable targeted and rapid spatiotemporal control of ribosome composition and selective mRNA translation in complex developing systems like the neocortex. SIGNIFICANCE STATEMENT: The neocortex is a highly complex circuit generating the most evolutionarily advanced complex cognitive and sensorimotor functions. An intricate progression of molecular and cellular steps during neocortical development determines its structure and function. Our goal is to study the steps regulating spatiotemporal specificity of mRNA translation that govern neocortical development. In this work, we show that the timed secretion of Wingless-related MMTV (mouse mammary tumor virus) integration site 3 (WNT3) by ingrowing axons from the thalamus regulates the combinatorial composition of ribosomal proteins in developing neocortex, which we term the "neocortical ribosome signature." Thalamic WNT3 further regulates the specificity of mRNA translation and development of neurons and oligodendrocytes in the neocortex. This study advances our overall understanding of WNT signaling and the spatiotemporal regulation of mRNA translation in highly complex developing systems.


Assuntos
Regulação da Expressão Gênica no Desenvolvimento , Neocórtex/citologia , Neurogênese/fisiologia , Biossíntese de Proteínas , Ribossomos/metabolismo , Tálamo/metabolismo , Proteína Wnt3/metabolismo , Animais , Axônios/metabolismo , Camundongos , Neocórtex/metabolismo , Neurônios/citologia , Neurônios/metabolismo , Oligodendroglia/citologia , Oligodendroglia/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Ribossomos/genética
14.
Chem Biol Drug Des ; 86(6): 1331-8, 2015 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26147927

RESUMO

Novel antimicrobials that effectively inhibit bacterial growth are essential to fight the growing threat of antibiotic resistance. A promising target is the bacterial ribosome, a 2.5 MDa organelle susceptible to several biorthogonal modes of action used by different classes of antibiotics. To promote the discovery of unique inhibitors, we have miniaturized a coupled transcription/translation assay using E. coli and applied it to screen a natural product library of ~30 000 extracts. We significantly reduced the scale of the assay to 2 µL in a 1536-well plate format and decreased the effective concentration of costly reagents. The improved assay returned 1327 hits (4.6% hit rate) with %CV and Z' values of 8.5% and 0.74, respectively. This assay represents a significant advance in molecular screening, both in miniaturization and its application to a natural product extract library, and we intend to apply it to a broad array of pathogenic microbes in the search for novel anti-infective agents.


Assuntos
Produtos Biológicos/farmacologia , Avaliação Pré-Clínica de Medicamentos/métodos , Ensaios de Triagem em Larga Escala/métodos , Anti-Infecciosos/farmacologia , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Luciferases/genética , Miniaturização/métodos , Biossíntese de Proteínas/efeitos dos fármacos , Ribossomos/efeitos dos fármacos , Ribossomos/genética , Bibliotecas de Moléculas Pequenas , Transcrição Gênica/efeitos dos fármacos
15.
Microb Drug Resist ; 21(4): 416-23, 2015 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-25826283

RESUMO

Staphylococcus aureus is one of the most frequent pathogens infecting the respiratory tract of patients with cystic fibrosis (CF). This study was the first to examine S. aureus isolates from CF patients in the Czech Republic. Among 100 S. aureus isolates from 92 of 107 observed patients, we found a high prevalence of resistance to macrolide-lincosamide-streptogramin B (MLS(B)) antibiotics (56%). More than half of the resistant strains (29 of 56) carried a mutation in the MLS(B) target site. The emergence of MLS(B) resistance and mutations conferring resistance to MLS(B) antibiotics was associated with azithromycin treatment (p=0.000000184 and p=0.000681, respectively). Methicillin resistance was only detected in 3% of isolates and the rate of resistance to other antibiotics did not exceed 12%. The prevalence of small-colony variant (SCV) strains was relatively low (9%) and eight of nine isolates with the SCV phenotype were thymidine dependent. The study population of S. aureus was heterogeneous in structure and both the most prevalent community-associated and hospital-acquired clonal lineages were represented. Of the virulence genes, enterotoxin genes seg (n=52), sei (n=49), and sec (n=16) were the most frequently detected among the isolates. The PVL genes (lukS-PV and lukF-PV) have not been revealed in any of the isolates.


Assuntos
Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Azitromicina/uso terapêutico , Fibrose Cística/microbiologia , Farmacorresistência Bacteriana/genética , Ribossomos/genética , Staphylococcus aureus/efeitos dos fármacos , Staphylococcus aureus/genética , Infecção Hospitalar/microbiologia , República Tcheca , Humanos , Assistência de Longa Duração , Staphylococcus aureus Resistente à Meticilina/efeitos dos fármacos , Testes de Sensibilidade Microbiana , Mutação/genética , Infecções Estafilocócicas/tratamento farmacológico , Infecções Estafilocócicas/microbiologia , Timidina/genética
16.
Proc Natl Acad Sci U S A ; 111(45): 16166-71, 2014 Nov 11.
Artigo em Inglês | MEDLINE | ID: mdl-25344531

RESUMO

Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48A(NPL4) complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Proteínas de Ciclo Celular/metabolismo , Centrômero/metabolismo , Cromossomos de Plantas/metabolismo , Heterocromatina/metabolismo , Chaperonas Moleculares/metabolismo , RNA de Plantas/biossíntese , RNA Ribossômico/biossíntese , Sumoilação/fisiologia , ATPases Associadas a Diversas Atividades Celulares , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Proteínas de Ciclo Celular/genética , Nucléolo Celular/genética , Nucléolo Celular/metabolismo , Centrômero/genética , Cromossomos de Plantas/genética , DNA de Plantas/genética , DNA de Plantas/metabolismo , DNA Ribossômico/genética , DNA Ribossômico/metabolismo , Loci Gênicos/fisiologia , Heterocromatina/genética , Humanos , Chaperonas Moleculares/genética , Pólen/genética , Pólen/metabolismo , RNA de Plantas/genética , RNA Ribossômico/genética , Ribossomos/genética , Ribossomos/metabolismo
17.
J Agric Food Chem ; 62(2): 443-53, 2014 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-24354337

RESUMO

The consumption of wine and spirits, traditionally aged in oak barrels, exposes humans to roburin ingestion. These molecules belong to a class of ellagitannins (ETs), and their only known source is oak wood. Very little is currently known about roburin bioavailability and biological activity. We reported for the first time human absorption of roburins from a French oak wood (Quercus robur) water extract (Robuvit) by measuring the increase of total phenols (from 0.63 ± 0.06 to 1.26 ± 0.18 µg GAE equiv/mL plasma) and the appearance of roburin metabolites (three different glucoronidate urolithins and ellagic acid), in plasma, after 5 days of supplementation. Robuvit supplementation induced also the increase of plasma antioxidant capacity from 1.8 ± 0.05 to 1.9 ± 0.01 nmol Trolox equiv/mL plasma. Moreover, utilizing a combined ex vivo cell culture approach, we assessed the effect of Q. robur metabolites (present in human serum after supplementation) on gene expression modulation, utilizing an Affymetrix array matrix, in endothelial, neuronal, and keratinocyte cell lines. The functional analysis reveals that Robuvit metabolites affect ribosome, cell cycle, and spliceosome pathways.


Assuntos
Taninos Hidrolisáveis/farmacocinética , Extratos Vegetais/farmacocinética , Quercus/química , Antioxidantes/análise , Ciclo Celular/efeitos dos fármacos , Ciclo Celular/genética , Cumarínicos/sangue , Suplementos Nutricionais , Ácido Elágico/sangue , França , Regulação da Expressão Gênica/efeitos dos fármacos , Glucuronídeos/sangue , Humanos , Taninos Hidrolisáveis/metabolismo , Taninos Hidrolisáveis/farmacologia , Fenóis/sangue , Projetos Piloto , Extratos Vegetais/química , Extratos Vegetais/metabolismo , Extratos Vegetais/farmacologia , Ribossomos/efeitos dos fármacos , Ribossomos/genética , Spliceossomos/efeitos dos fármacos , Spliceossomos/genética , Transcriptoma
18.
Anal Chem ; 85(20): 9692-8, 2013 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-23987474

RESUMO

Dimethyl sulfoxide (DMSO) is widely used as a cosolvent to solubilize hydrophobic compounds in RNA-ligand binding assays. Although it is known that high concentrations of DMSO (>75%) can significantly affect RNA structure and folding energetics, a thorough analysis of how lower concentrations (<10%) of DMSO typically used in binding assays affects RNA structure and ligand binding has not been undertaken. Here, we use NMR and 2-aminopurine fluorescence spectroscopy to examine how DMSO affects the structure, dynamics, and ligand binding properties of two flexible hairpin RNAs: the transactivation response element from HIV-1 and bacterial ribosomal A-site. In both cases, 5-10% DMSO decreased stacking interactions and increased local disorder in noncanonical residues within bulges and loops and resulted in 0.3-4-fold reduction in the measured binding affinities for different small molecules, with the greatest reduction observed for an intercalating compound that binds RNA nonspecifically. Our results suggest that, by competing for hydrophobic interactions, DMSO can have a small but significant effect on RNA structure and ligand binding. These effects should be considered when developing ligand binding assays and high throughput screens.


Assuntos
Dimetil Sulfóxido/farmacologia , RNA/química , RNA/metabolismo , Sequência de Bases , Avaliação Pré-Clínica de Medicamentos , HIV-1/genética , Sequências Repetidas Invertidas , Ligantes , RNA/genética , RNA Viral/química , RNA Viral/genética , RNA Viral/metabolismo , Elementos de Resposta , Ribossomos/genética
19.
J Med Chem ; 55(3): 1161-70, 2012 Feb 09.
Artigo em Inglês | MEDLINE | ID: mdl-22185196

RESUMO

Recently a novel method termed compound set enrichment (CSE) has been described that uses the activity distribution of a structural class of compounds to identify hit series from primary screening data. This report describes how this method can be used to identify such hit series, even when no hits according to conventional hit-calling methods for a given structural class are present in the data set. Such series, which were called latent hit series, were identified prospectively in a cell-based screening campaign and also in a series of retrospective analyses of publicly available data sets from PubChem. The assay used for the prospective case study was developed to identify compounds modulating protein translation directed from the internal ribosome entry site (IRES) of the encephalomyocarditis virus (EMCV) genomic RNA. The assay was designed with the ability to detect two assay readouts. The first assay readout monitors compound effects on IRES-directed translation, and the second readout monitors the cell viability and general effect on protein expression. By applying CSE separately to both of them, six validated latent hit series with apparently no effects on cell viability were identified. For each of these series, further testing of new compounds enabled identification of additional hits, also apparently with no effect on cell viability. These validated latent hit series would have been missed by a conventional cutoff-based hit-calling approach. This prospective study further supports CSE as a method for the analysis of high-throughput screening experiments.


Assuntos
Bases de Dados Factuais , Desenho de Fármacos , Avaliação Pré-Clínica de Medicamentos/métodos , Ensaios de Triagem em Larga Escala , Relação Quantitativa Estrutura-Atividade , Linhagem Celular Tumoral , Sobrevivência Celular/efeitos dos fármacos , Vírus da Encefalomiocardite/genética , Genes Reporter , Humanos , Luciferases de Vaga-Lume/biossíntese , Luciferases de Vaga-Lume/genética , Biossíntese de Proteínas/efeitos dos fármacos , RNA Viral/genética , Ribossomos/genética , Internalização do Vírus
20.
Phytomedicine ; 19(3-4): 364-8, 2012 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-22112725

RESUMO

An endophytic fungus, strain L18, isolated from the medicinal plant Curcuma wenyujin Y.H. Chen et C. Ling was identified as Chaetomium globosum Kunze based on morphological characteristics and sequence data for the internal transcribed spacer (ITS-5.8S-ITS2) of the nuclear ribosomal DNA. A new metabolite named chaetoglobosin X (1), together with three known compounds erogosterol (2), ergosterol 5α,8-peroside (3) and 2-methyl-3-hydroxy indole (4), were isolated from C. globosum L18. Their structures were elucidated by spectroscopic methods including NMR, UV, IR and MS data and comparison with published data. Chaetoglobosin X (1) is hitherto unknown, whereas 2-methyl-3-hydroxy indole (4) is reported for the first time as a fungal metabolite, and erogosterol (2) and ergosterol 5α,8-peroside (3) are known fungal metabolites previously identified in other genera. Chaetoglobosin X (1) exhibited a broader antifungal spectrum and showed the strongest cytotoxic activity against H22 and MFC cancer cell lines.


Assuntos
Chaetomium/química , Curcuma/microbiologia , Endófitos/química , Alcaloides Indólicos/farmacologia , Animais , Antifúngicos/química , Antifúngicos/isolamento & purificação , Antifúngicos/farmacologia , Antineoplásicos/química , Antineoplásicos/farmacologia , Linhagem Celular Tumoral , Chaetomium/genética , Chaetomium/crescimento & desenvolvimento , Chaetomium/isolamento & purificação , DNA Fúngico/genética , DNA Espaçador Ribossômico/genética , Ergosterol/química , Alcaloides Indólicos/química , Espectroscopia de Ressonância Magnética , Camundongos , Testes de Sensibilidade Microbiana , Folhas de Planta/microbiologia , Ribossomos/genética
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