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Here, we present a large-scale FLAG immunoprecipitation protocol to isolate large protein complexes driving DNA replication at replicating chromatin assembled in Xenopus laevis egg extract. We describe how to prepare demembranated sperm nuclei (DNA) and low-speed supernatant egg extract (LSS) and present detailed procedures for sample preparation and application onto grids for negative stain electron microscopy (NS-EM) and cryoelectron microscopy (cryo-EM). For complete details on the use and execution of this protocol, please refer to Cvetkovic et al.1.
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Background and Objectives: Early diagnosis of the exudative form of age-related macular degeneration (AMD) is very important for a timely first treatment, which is directly related to the preservation of functional visual acuity over a long period. The goal of this paper was to examine the correlation between the double-layer sign (DLS) and the presence of non-exudative macular neovascularization (MNV). Materials and Methods: Our research included 60 patients with AMD, exudative in one eye and non-exudative in the other eye. We analyzed only the non-exudative form using optical coherence tomography (OCT) and optical coherence tomography angiography (OCT-A). The patients were classified into three groups, depending on the duration of the disease (<2 years, 2 to 5 years, >5 years). The onset of the disease was deemed the moment of establishing a diagnosis of exudative AMD in one eye. We defined the presence or absence of a DLS using OCT and the presence of non-exudative MNV using OCT-A, both on 3 × 3 mm and 6 × 6 mm sections. DLS was used as a projection biomarker for non-exudative MNV, with the aim of establishing a rapid diagnosis and achieving early treatment of the disease. Results: We found that there was a statistically significant correlation between the DLS diagnosed using OCT and non-exudative MNV diagnosed by OCT-A for both 3 × 3 mm (p < 0.001) and 6 × 6 mm (p < 0.001) imaging. There was a statistically significant difference between the frequencies of both DLS and MNV in Groups I and III on both 3 × 3 and 6 × 6 mm imaging. A statistically significant difference was also noted in the frequencies of DLS and MNV on 6 × 6 mm imaging, but not on 3 × 3 mm imaging, between Groups I and II. No differences were found between the frequencies of DLS and MNV between Groups II and III. Conclusions: The DLS on OCT can be used as a projection biomarker to assess the presence of a non-exudative MNV.
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Degeneración Macular , Tomografía de Coherencia Óptica , Humanos , Tomografía de Coherencia Óptica/métodos , Angiografía con Fluoresceína/métodos , Estudios Prospectivos , Degeneración Macular/diagnóstico por imagen , Neovascularización Patológica , Biomarcadores , Estudios RetrospectivosRESUMEN
The MCM motor of the replicative helicase is loaded onto origin DNA as an inactive double hexamer before replication initiation. Recruitment of activators GINS and Cdc45 upon S-phase transition promotes the assembly of two active CMG helicases. Although work with yeast established the mechanism for origin activation, how CMG is formed in higher eukaryotes is poorly understood. Metazoan Downstream neighbor of Son (DONSON) has recently been shown to deliver GINS to MCM during CMG assembly. What impact this has on the MCM double hexamer is unknown. Here, we used cryoelectron microscopy (cryo-EM) on proteins isolated from replicating Xenopus egg extracts to identify a double CMG complex bridged by a DONSON dimer. We find that tethering elements mediating complex formation are essential for replication. DONSON reconfigures the MCM motors in the double CMG, and primordial dwarfism patients' mutations disrupting DONSON dimerization affect GINS and MCM engagement in human cells and DNA synthesis in Xenopus egg extracts.
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Proteínas de Ciclo Celular , ADN Helicasas , Proteínas Nucleares , Animales , Humanos , Proteínas de Ciclo Celular/química , Proteínas de Ciclo Celular/metabolismo , Microscopía por Crioelectrón , ADN/genética , ADN/metabolismo , ADN Helicasas/metabolismo , Replicación del ADN , Proteínas de Mantenimiento de Minicromosoma/genética , Proteínas de Mantenimiento de Minicromosoma/metabolismo , Proteínas Nucleares/química , Proteínas Nucleares/metabolismo , Saccharomyces cerevisiae/genética , Activación EnzimáticaRESUMEN
Pol epsilon is a tetrameric assembly that plays distinct roles during eukaryotic chromosome replication. It catalyses leading strand DNA synthesis; yet this function is dispensable for viability. Its non-catalytic domains instead play an essential role in the assembly of the active replicative helicase and origin activation, while non-essential histone-fold subunits serve a critical function in parental histone redeposition onto newly synthesised DNA. Furthermore, Pol epsilon plays a structural role in linking the RFC-Ctf18 clamp loader to the replisome, supporting processive DNA synthesis, DNA damage response signalling as well as sister chromatid cohesion. In this minireview, we discuss recent biochemical and structural work that begins to explain various aspects of eukaryotic chromosome replication, with a focus on the multiple roles of Pol epsilon in this process.
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Proteínas de Saccharomyces cerevisiae , Cromosomas/metabolismo , ADN/genética , ADN Polimerasa II/metabolismo , Replicación del ADN , Histonas/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismoRESUMEN
The γ-tubulin ring complex (γTuRC) is the major microtubule nucleator in cells. The mechanism of its regulation is not understood. We purified human γTuRC and measured its nucleation properties in a total internal reflection fluorescence (TIRF) microscopy-based real-time nucleation assay. We find that γTuRC stably caps the minus ends of microtubules that it nucleates stochastically. Nucleation is inefficient compared with microtubule elongation. The 4 Šresolution cryoelectron microscopy (cryo-EM) structure of γTuRC, combined with crosslinking mass spectrometry analysis, reveals an asymmetric conformation with only part of the complex in a "closed" conformation matching the microtubule geometry. Actin in the core of the complex, and MZT2 at the outer perimeter of the closed part of γTuRC appear to stabilize the closed conformation. The opposite side of γTuRC is in an "open," nucleation-incompetent conformation, leading to a structural asymmetry explaining the low nucleation efficiency of purified human γTuRC. Our data suggest possible regulatory mechanisms for microtubule nucleation by γTuRC closure.
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Proteínas Asociadas a Microtúbulos/metabolismo , Microtúbulos/ultraestructura , Tubulina (Proteína)/química , Actinas/química , Actinas/metabolismo , Microscopía por Crioelectrón , Células HeLa , Humanos , Proteínas Asociadas a Microtúbulos/química , Microtúbulos/química , Microtúbulos/metabolismo , Simulación de Dinámica Molecular , Conformación Proteica , Imagen Individual de Molécula , Tubulina (Proteína)/metabolismoRESUMEN
The exosome is a large molecular machine involved in RNA degradation and processing. Here we address how the trimeric Rrp4 cap enhances the activity of the archaeal enzyme complex. Using methyl-TROSY NMR methods we identified a 50-Å long RNA binding path on each Rrp4 protomer. We show that the Rrp4 cap can thus simultaneously recruit three substrates, one of which is degraded in the core while the others are positioned for subsequent degradation rounds. The local interaction energy between the substrate and the Rrp4-exosome increases from the periphery of the complex toward the active sites. Notably, the intrinsic interaction strength between the cap and the substrate is weakened as soon as substrates enter the catalytic barrel, which provides a means to reduce friction during substrate movements toward the active sites. Our data thus reveal a sophisticated exosome-substrate interaction mechanism that enables efficient RNA degradation.
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Proteínas Arqueales/metabolismo , Exosomas/metabolismo , ARN de Archaea/metabolismo , Sulfolobus solfataricus/metabolismo , Proteínas Arqueales/química , Exosomas/química , Resonancia Magnética Nuclear Biomolecular , ARN de Archaea/química , Sulfolobus solfataricus/químicaRESUMEN
The exosome plays an important role in RNA degradation and processing. In archaea, three Rrp41:Rrp42 heterodimers assemble into a barrel like structure that contains a narrow RNA entrance pore and a lumen that contains three active sites. Here, we demonstrate that this quaternary structure of the exosome is important for efficient RNA degradation. We find that the entrance pore of the barrel is required for nM substrate affinity. This strong interaction is crucial for processive substrate degradation and prevents premature release of the RNA from the enzyme. Using methyl TROSY NMR techniques, we establish that the 3' end of the substrate remains highly flexible inside the lumen. As a result, the RNA jumps between the three active sites that all equally participate in substrate degradation. The RNA jumping rate is, however, much faster than the cleavage rate, indicating that not all active site:substrate encounters result in catalysis. Enzymatic turnover therefore benefits from the confinement of the active sites and substrate in the lumen, which ensures that the RNA is at all times bound to one of the active sites. The evolution of the exosome into a hexameric complex and the optimization of its catalytic efficiency were thus likely co-occurring events.
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Proteínas Arqueales/química , Complejo Multienzimático de Ribonucleasas del Exosoma/química , Exosomas/química , ARN de Archaea/química , Proteínas de Unión al ARN/química , Sulfolobus solfataricus/enzimología , Secuencia de Aminoácidos , Proteínas Arqueales/genética , Proteínas Arqueales/metabolismo , Sitios de Unión , Biocatálisis , Dominio Catalítico , Clonación Molecular , Escherichia coli/genética , Escherichia coli/metabolismo , Complejo Multienzimático de Ribonucleasas del Exosoma/genética , Complejo Multienzimático de Ribonucleasas del Exosoma/metabolismo , Exosomas/enzimología , Expresión Génica , Cinética , Modelos Moleculares , Datos de Secuencia Molecular , Unión Proteica , Multimerización de Proteína , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Estabilidad del ARN , ARN de Archaea/genética , ARN de Archaea/metabolismo , Proteínas de Unión al ARN/genética , Proteínas de Unión al ARN/metabolismo , Alineación de Secuencia , Sulfolobus solfataricus/química , Sulfolobus solfataricus/genéticaRESUMEN
BACKGROUND/AIM: Diabetes mellitus is associated with an increased risk for neonatal morbidity and mortality. One of the most important goals in treating pregnancies complicated with diabetes is keeping glucose level within the normal range, especially in the first trimester. A portable insulin pump for continuous subcutaneous insulin infusion (CSII) represents the best form of therapy for patients with type 1 diabetes mellitus during pregnancy. The aim of our study was to evaluate the effects of therapy with a portable insulin pump for continuous subcutaneous insulin infusion during the first trimester of pregnancy on the quality of glycoregulation and pregnancy outcome in women with type 1 diabetes mellitus. METHODS: A total of 17 newly diagnosed pregnant women with type 1 diabetes mellitus were treated with CSII therapy for three months. The parameters of glycoregulation (hemoglobin A, glycosylated--HbAlc, mean blood glucose value in daily profiles--MBG, daily requirement for insulin--IJ/kg BM), lipid levels, blood preassure and renal function were estimated before and after the therapy. These parameters were correlated with parameters of pregnancy outcome: fetal weight, APGAR score, duration of pregnancy. RESULTS: There was a significant improvement in HbA1c (8.94 +/- 1.62 vs. 6.90 +/- 1.22 %,p < 0.05), MBG (9.23 +/- 2.22 vs. 6.41 +/- 1.72 mmol/l, p < 0.01), and daily requirement for insulin (0.66 +/- 0.22 vs. 0.55 +/- 0.13 IJ/kg BM, p < 0.05) during the CSII therapy. There were significant correlations between fetal weight and HbAlc (r = -0.60, p < 0.05), triglyceride levels (r = -0.63, p < 0.01), and the number of pregnancies (r = -0.62, p < 0.01), as well as between APGAR score and MBG (r = -0.52, p < 0.05) and cholesterol levels (r = -0.65, p < 0,01) before a portable insulin pump was applicated. CONCLUSIONS: There was a significant improvement in the quality of glycoregulation during CSII therapy in the pregnant women with type 1 diabetes mellitus. The quality of glycoregulation in the moment of conception was the important factor for pregnancy outcome.
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Diabetes Mellitus Tipo 1/tratamiento farmacológico , Sistemas de Infusión de Insulina , Embarazo en Diabéticas/tratamiento farmacológico , Glucemia/análisis , Diabetes Mellitus Tipo 1/sangre , Femenino , Humanos , EmbarazoRESUMEN
Here we show that maternal smoking downregulated, in a dose-dependent manner, cytotrophoblast expression of l-selectin and its TRA-1-81-reactive carbohydrate ligands. Cell islands -- cell columns that fail to make uterine attachments, often more numerous in the placentas of smokers -- exhibited an even greater downregulation of the l-selectin adhesion system. These effects were attributable to nicotine, since exposure of explanted villi to this drug in vitro reproduced the effects observed in situ. Videomicroscopy showed that the downstream consequences included inhibition of all stages of cytotrophoblast outgrowth from columns, including rolling adhesion within columns and generation of invasive cells at the distal ends. These results suggest that nicotine, acting through the l-selectin adhesion system, impairs the development of cell columns that connect the fetal portion of the placenta to the uterus, one possible reason why women who smoke have a much harder time achieving and sustaining pregnancy than their nonsmoking counterparts.