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1.
Med Hypotheses ; 143: 110197, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-33017906

RESUMO

Coronavirus disease 2019 (COVID-19) may have a metabolic origin given strong links with risk factors such as lipids and glucose and co-morbidities such as obesity and type 2 diabetes mellitus. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein mediates viral cellular entry via the ACE2 receptor. The cytoplasmic tail of this spike protein is heavily palmitoylated. Emerging studies suggest that SARS-CoV-2 alters lipid metabolism in the lung epithelial cells by modulating peroxisome proliferator-activated receptor alpha (PPARα), possibly contributing to lipotoxicity, inflammation and untoward respiratory effects. Disruption of this process may affect palmitoylation of SARS-CoV spike protein and thus infectivity and viral assembly. COVID-19 is also increasingly being recognized as a vascular disease, with several studies noting prominent systemic endothelial dysfunction. The pathogenesis of endothelial dysfunction may also be linked to COVID-19-mediated metabolic and inflammatory effects. Herein, exercise will be compared to fenofibrate as a possible therapeutic strategy to bolster resilience against (and help manage recovery from) COVID-19. This paper will explore the hypothesis that exercise may be a useful adjuvant in a setting of COVID-19 management/rehabilitation due to its effects on PPARα and vascular endothelial function.


Assuntos
Infecções por Coronavirus/terapia , Terapia por Exercício/métodos , PPAR alfa/metabolismo , Pneumonia Viral/terapia , Glicoproteína da Espícula de Coronavírus/metabolismo , Betacoronavirus , Comorbidade , Infecções por Coronavirus/tratamento farmacológico , Citoplasma/metabolismo , Diabetes Mellitus Tipo 2/complicações , Exercício Físico , Fenofibrato/química , Humanos , Inflamação , Metabolismo dos Lipídeos , Lipoilação , Pulmão/metabolismo , Obesidade/complicações , Pandemias
2.
BMC Bioinformatics ; 21(1): 399, 2020 Sep 09.
Artigo em Inglês | MEDLINE | ID: mdl-32907544

RESUMO

BACKGROUND: Cryo-electron tomography is an important and powerful technique to explore the structure, abundance, and location of ultrastructure in a near-native state. It contains detailed information of all macromolecular complexes in a sample cell. However, due to the compact and crowded status, the missing edge effect, and low signal to noise ratio (SNR), it is extremely challenging to recover such information with existing image processing methods. Cryo-electron tomogram simulation is an effective solution to test and optimize the performance of the above image processing methods. The simulated images could be regarded as the labeled data which covers a wide range of macromolecular complexes and ultrastructure. To approximate the crowded cellular environment, it is very important to pack these heterogeneous structures as tightly as possible. Besides, simulating non-deformable and deformable components under a unified framework also need to be achieved. RESULT: In this paper, we proposed a unified framework for simulating crowded cryo-electron tomogram images including non-deformable macromolecular complexes and deformable ultrastructures. A macromolecule was approximated using multiple balls with fixed relative positions to reduce the vacuum volume. A ultrastructure, such as membrane and filament, was approximated using multiple balls with flexible relative positions so that this structure could deform under force field. In the experiment, 400 macromolecules of 20 representative types were packed into simulated cytoplasm by our framework, and numerical verification proved that our method has a smaller volume and higher compression ratio than the baseline single-ball model. We also packed filaments, membranes and macromolecules together, to obtain a simulated cryo-electron tomogram image with deformable structures. The simulated results are closer to the real Cryo-ET, making the analysis more difficult. The DOG particle picking method and the image segmentation method are tested on our simulation data, and the experimental results show that these methods still have much room for improvement. CONCLUSION: The proposed multi-ball model can achieve more crowded packaging results and contains richer elements with different properties to obtain more realistic cryo-electron tomogram simulation. This enables users to simulate cryo-electron tomogram images with non-deformable macromolecular complexes and deformable ultrastructures under a unified framework. To illustrate the advantages of our framework in improving the compression ratio, we calculated the volume of simulated macromolecular under our multi-ball method and traditional single-ball method. We also performed the packing experiment of filaments and membranes to demonstrate the simulation ability of deformable structures. Our method can be used to do a benchmark by generating large labeled cryo-ET dataset and evaluating existing image processing methods. Since the content of the simulated cryo-ET is more complex and crowded compared with previous ones, it will pose a greater challenge to existing image processing methods.


Assuntos
Citoplasma/ultraestrutura , Tomografia com Microscopia Eletrônica/métodos , Simulação de Dinâmica Molecular , Algoritmos , Análise por Conglomerados , Microscopia Crioeletrônica , Citoplasma/metabolismo , Processamento de Imagem Assistida por Computador , Substâncias Macromoleculares/química , Substâncias Macromoleculares/metabolismo , Razão Sinal-Ruído
3.
PLoS Pathog ; 16(8): e1008845, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32866210

RESUMO

Modified vaccinia virus Ankara (MVA) is an approved smallpox vaccine and a promising vaccine vector for other pathogens as well as for cancer therapeutics with more than 200 current or completed clinical trials. MVA was derived by passaging the parental Ankara vaccine virus hundreds of times in chick embryo fibroblasts during which it lost the ability to replicate in human and most other mammalian cells. Although this replication deficiency is an important safety feature, the genetic basis of the host restriction is not understood. Here, an unbiased human genome-wide RNAi screen in human A549 cells revealed that the zinc-finger antiviral protein (ZAP), previously shown to inhibit certain RNA viruses, is a host restriction factor for MVA, a DNA virus. Additional studies demonstrated enhanced MVA replication in several human cell lines following knockdown of ZAP. Furthermore, CRISPR-Cas9 knockout of ZAP in human A549 cells increased MVA replication and spread by more than one log but had no effect on a non-attenuated strain of vaccinia virus. The intact viral C16 protein, which had been disrupted in MVA, antagonized ZAP by binding and sequestering the protein in cytoplasmic punctate structures. Studies aimed at exploring the mechanism by which ZAP restricts MVA replication in the absence of C16 showed that knockout of ZAP had no discernible effect on viral DNA or individual mRNA or protein species as determined by droplet digital polymerase chain reaction, deep RNA sequencing and mass spectrometry, respectively. Instead, inactivation of ZAP reduced the number of aberrant, dense, spherical particles that typically form in MVA-infected human cells, suggesting that ZAP has a novel role in interfering with a late step in the assembly of infectious MVA virions in the absence of the C16 protein.


Assuntos
Proteínas de Ligação a RNA/metabolismo , Proteínas Repressoras/metabolismo , Vírus Vaccinia/fisiologia , Replicação Viral/fisiologia , Células A549 , Animais , Galinhas , Citoplasma/metabolismo , Citoplasma/virologia , DNA Viral/genética , DNA Viral/metabolismo , Técnicas de Silenciamento de Genes , Humanos , Camundongos , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA Viral/genética , RNA Viral/metabolismo , Proteínas de Ligação a RNA/genética , RNA-Seq , Proteínas Repressoras/genética
4.
Nat Commun ; 11(1): 4581, 2020 09 11.
Artigo em Inglês | MEDLINE | ID: mdl-32917893

RESUMO

Yes-associated protein 1 (YAP) is a transcriptional regulator with critical roles in mechanotransduction, organ size control, and regeneration. Here, using advanced tools for real-time visualization of native YAP and target gene transcription dynamics, we show that a cycle of fast exodus of nuclear YAP to the cytoplasm followed by fast reentry to the nucleus ("localization-resets") activates YAP target genes. These "resets" are induced by calcium signaling, modulation of actomyosin contractility, or mitosis. Using nascent-transcription reporter knock-ins of YAP target genes, we show a strict association between these resets and downstream transcription. Oncogenically-transformed cell lines lack localization-resets and instead show dramatically elevated rates of nucleocytoplasmic shuttling of YAP, suggesting an escape from compartmentalization-based control. The single-cell localization and transcription traces suggest that YAP activity is not a simple linear function of nuclear enrichment and point to a model of transcriptional activation based on nucleocytoplasmic exchange properties of YAP.


Assuntos
Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Fatores de Transcrição/metabolismo , Proteínas Adaptadoras de Transdução de Sinal/genética , Sistemas CRISPR-Cas , Cálcio/metabolismo , Linhagem Celular Tumoral , Núcleo Celular/metabolismo , Citoplasma/metabolismo , Regulação da Expressão Gênica , Técnicas de Introdução de Genes , Células HEK293 , Humanos , Mecanotransdução Celular/fisiologia , Oncogenes/genética , Fatores de Transcrição/genética
5.
Sheng Wu Gong Cheng Xue Bao ; 36(7): 1261-1268, 2020 Jul 25.
Artigo em Chinês | MEDLINE | ID: mdl-32748583

RESUMO

The phenomenon of phase separation of intracellular biological macromolecules is an emerging research field that has received great attention in recent years. As an aggregation and compartment mechanism of cell biochemical reactions, it widely exists in nature and participates in important physiological processes such as gene transcription and regulation, as well as influences organism's response to external stimuli. Disequilibrium of phase separation may lead to the occurrence of some major diseases. Researchers in cross-cutting fields are trying to examine dementia and other related diseases from a new perspective of phase separation, exploring its molecular mechanism and the potential possibility of intervention and treatment. This review intends to introduce the latest research progress in this field, summarize the major research directions, biochemical basis, its relationship with disease occurrence, and giving a future perspective of key problems to focus on.


Assuntos
Citoplasma , Substâncias Macromoleculares , Pesquisa , Animais , Técnicas de Química Analítica/tendências , Citoplasma/química , Citoplasma/metabolismo , Humanos , Substâncias Macromoleculares/isolamento & purificação , Pesquisa/tendências
6.
Nat Commun ; 11(1): 4305, 2020 08 27.
Artigo em Inglês | MEDLINE | ID: mdl-32855391

RESUMO

Oligomeric assemblies of tau and the RNA-binding proteins (RBPs) Musashi (MSI) are reported in Alzheimer's disease (AD). However, the role of MSI and tau interaction in their aggregation process and its effects are nor clearly known in neurodegenerative diseases. Here, we investigated the expression and cellular localization of MSI1 and MSI2 in the brains tissues of Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) as well as in the wild-type mice and tau knock-out and P301L tau mouse models. We observed that formation of pathologically relevant protein inclusions was driven by the aberrant interactions between MSI and tau in the nuclei associated with age-dependent extracellular depositions of tau/MSI complexes. Furthermore, tau and MSI interactions induced impairment of nuclear/cytoplasm transport, chromatin remodeling and nuclear lamina formation. Our findings provide mechanistic insight for pathological accumulation of MSI/tau aggregates providing a potential basis for therapeutic interventions in neurodegenerative proteinopathies.


Assuntos
Núcleo Celular/patologia , Proteínas do Tecido Nervoso/metabolismo , Doenças Neurodegenerativas/patologia , Proteínas de Ligação a RNA/metabolismo , Proteínas tau/metabolismo , Transporte Ativo do Núcleo Celular , Idoso , Idoso de 80 Anos ou mais , Animais , Núcleo Celular/metabolismo , Montagem e Desmontagem da Cromatina , Citoplasma/metabolismo , Modelos Animais de Doenças , Feminino , Lobo Frontal/citologia , Lobo Frontal/patologia , Células HEK293 , Humanos , Corpos de Inclusão/patologia , Masculino , Camundongos , Camundongos Transgênicos , Pessoa de Meia-Idade , Agregados Proteicos , Ligação Proteica , Proteínas tau/genética
7.
Tumour Biol ; 42(8): 1010428320951057, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32829673

RESUMO

The exchange of metabolites between mitochondria and cytosol occurs through pores formed by voltage-dependent anion channel proteins. Voltage-dependent anion channels appear to be master regulators of mitochondrial bioenergetics and the intracellular flow of energy. Deregulation of voltage-dependent anion channels expression is thought to be related to mitochondrial dysfunction in cancer. The aim of this study was to investigate the mRNA and protein expression levels of VDAC1, VDAC2, and VDAC3 in relation to clinicopathological characteristics of endometrial cancer as well as the prognostic significance of voltage-dependent anion channels expression for overall survival. VDAC1 and VDAC3 expressions were significantly higher in cancer compared to normal tissues. Kaplan-Meier analysis indicated that high expression of all VDAC genes or high VDAC2 protein level predicted poor overall survival. Multivariate analysis identified the VDAC1 and VDAC2 mRNA levels as well as VDAC2 protein level as independent prognostic factors. Our results suggest that increased expression of voltage-dependent anion channels correlates with tumor progression and may serve as a potential prognostic biomarker in endometrial cancer.


Assuntos
Neoplasias do Endométrio/patologia , Mitocôndrias/patologia , Proteínas de Transporte da Membrana Mitocondrial/genética , Canal de Ânion 1 Dependente de Voltagem/genética , Canal de Ânion 2 Dependente de Voltagem/genética , Canais de Ânion Dependentes de Voltagem/genética , Sequência de Aminoácidos , Biomarcadores Tumorais/genética , Citoplasma/metabolismo , Neoplasias do Endométrio/mortalidade , Feminino , Humanos , Pessoa de Meia-Idade , Mitocôndrias/metabolismo , Proteínas de Transporte da Membrana Mitocondrial/biossíntese , Prognóstico , RNA Mensageiro/genética , Canal de Ânion 1 Dependente de Voltagem/biossíntese , Canal de Ânion 2 Dependente de Voltagem/biossíntese , Canais de Ânion Dependentes de Voltagem/biossíntese
8.
Nat Commun ; 11(1): 3825, 2020 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-32732874

RESUMO

The malaria parasite interfaces with its host erythrocyte (RBC) using a unique organelle, the parasitophorous vacuole (PV). The mechanism(s) are obscure by which its limiting membrane, the parasitophorous vacuolar membrane (PVM), collaborates with the parasite plasma membrane (PPM) to support the transport of proteins, lipids, nutrients, and metabolites between the cytoplasm of the parasite and the cytoplasm of the RBC. Here, we demonstrate that the PV has structure characterized by micrometer-sized regions of especially close apposition between the PVM and the PPM. To determine if these contact sites are involved in any sort of transport, we localize the PVM nutrient-permeable and protein export channel EXP2, as well as the PPM lipid transporter PfNCR1. We find that EXP2 is excluded from, but PfNCR1 is included within these regions of close apposition. We conclude that the host-parasite interface is structured to segregate those transporters of hydrophilic and hydrophobic substrates.


Assuntos
Lipídeos , Malária Falciparum/metabolismo , Proteínas de Membrana Transportadoras/metabolismo , Plasmodium falciparum/metabolismo , Proteínas de Protozoários/metabolismo , Transporte Biológico , Membrana Celular/metabolismo , Citoplasma/metabolismo , Citoplasma/parasitologia , Eritrócitos/metabolismo , Eritrócitos/parasitologia , Interações Hospedeiro-Parasita , Humanos , Membranas Intracelulares/metabolismo , Membranas Intracelulares/parasitologia , Malária Falciparum/parasitologia , Plasmodium falciparum/fisiologia , Transporte Proteico , Vacúolos/metabolismo , Vacúolos/parasitologia
9.
Gene ; 760: 145017, 2020 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-32755655

RESUMO

Cytoplasmic vacuolization usually occurs in cells treated with different agents and substances. We found that LZ-106, an analog of enoxacin, is a potent lysosomotropic agent, contributing to the formation of cytoplasmic vacuoles in cells. Studies of LZ-106-induced vacuolization in H460 cells showed acid environment inside these vacuoles. Further study demonstrated that markers in the late endosomes and lysosomes, like LAMP1 and RAB7, on the surface of the vacuoles, implying that these vacuoles might derive from endosomes and/or lysosomes. By studying the fluorescence intensity of LZ-106, we discovered that LZ-106 tended to locate in acid organelles, and Bafilomycin A1, a V-ATPase inhibitor, was able to suppress its acid organelles localization. Also, we noticed that LZ-106 could induce lysosome stress, involving pH increment and lysosomal membrane damage. Moreover, the expression levels of some lysosome-related proteins, like LAMP1, EEA1, and Cathepsin B, were also altered upon LZ-106 treatment. At last, we confirmed LZ-106 can activate TFEB, a key regulator of lysosomes. Knockdown of TFEB could also reverse LZ-106's effect on vacuolization in H460 cells. Taken together, due to LZ-106's lysosomotropic properties, it is able to accumulate in the acid organelles and induce lysosomal dysfunction in H460 cells, leading to TFEB activation and the following cytoplasmic vacuolization.


Assuntos
Enoxacino/análogos & derivados , Enoxacino/farmacologia , Vacúolos/efeitos dos fármacos , Animais , Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos/metabolismo , Linhagem Celular Tumoral , Citoplasma/metabolismo , Endossomos/metabolismo , Humanos , Lisossomos/química , Macrolídeos/farmacologia
10.
Nat Commun ; 11(1): 4337, 2020 08 28.
Artigo em Inglês | MEDLINE | ID: mdl-32859897

RESUMO

Intracellular Na elevation in the heart is a hallmark of pathologies where both acute and chronic metabolic remodelling occurs. Here, we assess whether acute (75 µM ouabain 100 nM blebbistatin) or chronic myocardial Nai load (PLM3SA mouse) are causally linked to metabolic remodelling and whether the failing heart shares a common Na-mediated metabolic 'fingerprint'. Control (PLMWT), transgenic (PLM3SA), ouabain-treated and hypertrophied Langendorff-perfused mouse hearts are studied by 23Na, 31P, 13C NMR followed by 1H-NMR metabolomic profiling. Elevated Nai leads to common adaptive metabolic alterations preceding energetic impairment: a switch from fatty acid to carbohydrate metabolism and changes in steady-state metabolite concentrations (glycolytic, anaplerotic, Krebs cycle intermediates). Inhibition of mitochondrial Na/Ca exchanger by CGP37157 ameliorates the metabolic changes. In silico modelling indicates altered metabolic fluxes (Krebs cycle, fatty acid, carbohydrate, amino acid metabolism). Prevention of Nai overload or inhibition of Na/Camito may be a new approach to ameliorate metabolic dysregulation in heart failure.


Assuntos
Reprogramação Celular/fisiologia , Citoplasma/metabolismo , Insuficiência Cardíaca/metabolismo , Miocárdio/metabolismo , Sódio/metabolismo , Animais , Modelos Animais de Doenças , Metabolismo Energético , Técnicas de Introdução de Genes , Coração , Hipertrofia , Preparação de Coração Isolado , Masculino , Doenças Metabólicas/metabolismo , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , Mitocôndrias/efeitos dos fármacos , Mitocôndrias/metabolismo , Ratos , Ratos Wistar , Sódio/sangue , Trocador de Sódio e Cálcio/efeitos dos fármacos , Tiazepinas/farmacologia
11.
PLoS Pathog ; 16(8): e1008794, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32813725

RESUMO

Wolbachia are the world's most common, maternally-inherited, arthropod endosymbionts. Their worldwide distribution is due, in part, to a selfish drive system termed cytoplasmic incompatibility (CI) that confers a relative fitness advantage to females that transmit Wolbachia to their offspring. CI results in embryonic death when infected males mate with uninfected females but not infected females. Under the Two-by-One genetic model of CI, males expressing the two phage WO proteins CifA and CifB cause CI, and females expressing CifA rescue CI. While each protein is predicted to harbor three functional domains, there is no knowledge on how sites across these Cif domains, rather than in any one particular domain, contribute to CI and rescue. Here, we use evolution-guided, substitution mutagenesis of conserved amino acids across the Cif proteins, coupled with transgenic expression in uninfected Drosophila melanogaster, to determine the functional impacts of conserved residues evolving mostly under purifying selection. We report that amino acids in CifA's N-terminal unannotated region and annotated catalase-related domain are important for both complete CI and rescue, whereas C-terminal residues in CifA's putative domain of unknown function are solely important for CI. Moreover, conserved CifB amino acids in the predicted nucleases, peptidase, and unannotated regions are essential for CI. Taken together, these findings indicate that (i) all CifA amino acids determined to be crucial in rescue are correspondingly crucial in CI, (ii) an additional set of CifA amino acids are uniquely important in CI, and (iii) CifB amino acids across the protein, rather than in one particular domain, are all crucial for CI. We discuss how these findings advance an expanded view of Cif protein evolution and function, inform the mechanistic and biochemical bases of Cif-induced CI/rescue, and continue to substantiate the Two-by-One genetic model of CI.


Assuntos
Proteínas de Bactérias/metabolismo , Evolução Biológica , Citoplasma/metabolismo , Drosophila melanogaster/microbiologia , Infecções por Bactérias Gram-Negativas/metabolismo , Mutação , Wolbachia/fisiologia , Animais , Animais Geneticamente Modificados/microbiologia , Animais Geneticamente Modificados/fisiologia , Proteínas de Bactérias/genética , Citoplasma/microbiologia , Drosophila melanogaster/fisiologia , Feminino , Infecções por Bactérias Gram-Negativas/microbiologia , Infecções por Bactérias Gram-Negativas/patologia , Masculino
12.
PLoS One ; 15(8): e0237448, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32790800

RESUMO

We established that Endosidin2 (ES2) affected the trafficking routes of both newly synthesized and endocytic pools of PIN-FORMED2 (PIN2) in Arabidopsis root epidermal cells. PIN2 populations accumulated in separated patches, which gradually merged into large and compact ES2 aggregates (ES2As). FM4-64 endocytic tracer labeled ES2As as well. Both PIN2 pools also appeared in vacuoles. Accelerated endocytosis of PIN2, its aggregation in the cytoplasm, and redirection of PIN2 flows to vacuoles led to a substantial reduction of the abundance of this protein in the plasma membrane. Whereas PIN-FORMED3 and PIN-FORMED4 also aggregated in the cytoplasm, SYT1 was not sensitive to ES2 treatment and did not appear either in the cytoplasmic aggregates or vacuoles. Ultrastructural analysis revealed that ES2 affects the Golgi apparatus so that stacks acquired cup-shape and even circular shape surrounded by several vesicles. Abnormally shaped Golgi stacks, stack remnants, multi-lamellar structures, separated Golgi cisterna rings, tubular structures, and vesicles formed discrete clusters.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Endocitose/efeitos dos fármacos , Limoninas/farmacologia , Proteínas de Membrana Transportadoras/metabolismo , Parede Celular/metabolismo , Citoplasma/metabolismo , Complexo de Golgi/metabolismo , Raízes de Plantas/citologia , Raízes de Plantas/metabolismo , Plantas Geneticamente Modificadas/metabolismo , Transporte Proteico/efeitos dos fármacos , Sinaptotagmina I/metabolismo
13.
Phys Rev Lett ; 125(5): 058101, 2020 Jul 31.
Artigo em Inglês | MEDLINE | ID: mdl-32794890

RESUMO

Diffusion of tracer particles in the cytoplasm of mammalian cells is often anomalous with a marked heterogeneity even within individual particle trajectories. Despite considerable efforts, the mechanisms behind these observations have remained largely elusive. To tackle this problem, we performed extensive single-particle tracking experiments on quantum dots in the cytoplasm of living mammalian cells at varying conditions. Analyses of the trajectories reveal a strong, microtubule-dependent subdiffusion with antipersistent increments and a substantial heterogeneity. Furthermore, particles stochastically switch between different mobility states, most likely due to transient associations with the cytoskeleton-shaken endoplasmic reticulum network. Comparison to simulations highlight that all experimental observations can be fully described by an intermittent fractional Brownian motion, alternating between two states of different mobility.


Assuntos
Citoplasma/metabolismo , Modelos Biológicos , Citoesqueleto de Actina/metabolismo , Compostos Bicíclicos Heterocíclicos com Pontes/farmacologia , Simulação por Computador , Citocalasina D/farmacologia , Citoplasma/efeitos dos fármacos , Citoesqueleto/efeitos dos fármacos , Citoesqueleto/metabolismo , Difusão , Retículo Endoplasmático/efeitos dos fármacos , Retículo Endoplasmático/metabolismo , Células HeLa , Humanos , Microtúbulos/efeitos dos fármacos , Microtúbulos/metabolismo , Nocodazol/farmacologia , Pontos Quânticos , Processos Estocásticos , Tiazolidinas/farmacologia
14.
PLoS Comput Biol ; 16(7): e1007972, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32658891

RESUMO

Although quantitative insights into the killing behaviour of Cytotoxic T Lymphocytes (CTLs) are necessary for the rational design of immune-based therapies, CTL killing function remains insufficiently characterised. One established model of CTL killing treats CTL cytotoxicity as a Poisson process, based on the assumption that CTLs serially kill antigen-presenting target cells via delivery of lethal hits, each lethal hit corresponding to a single injection of cytotoxic proteins into the target cell cytoplasm. Contradicting this model, a recent in vitro study of individual CTLs killing targets over a 12-hour period found significantly greater heterogeneity in CTL killing performance than predicted by Poisson-based killing. The observed killing process was dynamic and varied between CTLs, with the best performing CTLs exhibiting a marked increase in killing during the final hours of the experiments, along with a "burst killing" kinetic. Despite a search for potential differences between CTLs, no mechanistic explanation for the heterogeneous killing kinetics was found. Here we have used stochastic simulations to assess whether target cells might require multiple hits from CTLs before undergoing apoptosis, in order to verify whether multiple-hitting could explain the late onset, burst killing dynamics observed in vitro. We found that multiple-hitting from CTLs was entirely consistent with the observed killing kinetics. Moreover, the number of available targets and the spatiotemporal kinetics of CTL:target interactions influenced the realised CTL killing rate. We subsequently used realistic, spatial simulations to assess methods for estimating the hitting rate and the number of hits required for target death, to be applied to microscopy data of individual CTLs killing targets. We found that measuring the cumulative duration of individual contacts that targets have with CTLs would substantially improve accuracy when estimating the killing kinetics of CTLs.


Assuntos
Citoplasma/metabolismo , Processos Estocásticos , Linfócitos T Citotóxicos/citologia , Linfócitos T Citotóxicos/imunologia , Actinas/química , Algoritmos , Células Apresentadoras de Antígenos , Apoptose , Movimento Celular , Simulação por Computador , Citotoxicidade Imunológica , Humanos , Cinética , Funções Verossimilhança , Método de Monte Carlo , Distribuição de Poisson
15.
Nat Commun ; 11(1): 3393, 2020 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-32636388

RESUMO

Meiotic divisions in oocytes are extremely asymmetric and require pre- and post-anaphase-onset phases of spindle migration. The latter induces membrane protrusion that is moulded around the spindle thereby reducing cytoplasmic loss. Here, we find that depleting the NAD biosynthetic enzyme, nicotinamide phosphoribosyl-transferase (Nampt), in mouse oocytes results in markedly longer spindles and compromises asymmetry. By analysing spindle speed in live oocytes, we identify a striking and transient acceleration after anaphase-onset that is severely blunted following Nampt-depletion. Slow-moving midzones of elongated spindles induce cortical furrowing deep within the oocyte before protrusions can form, altogether resulting in larger oocyte fragments being cleaved off. Additionally, we find that Nampt-depletion lowers NAD and ATP levels and that reducing NAD using small molecule Nampt inhibitors also compromises asymmetry. These data show that rapid midzone displacement is critical for extreme asymmetry by delaying furrowing to enable protrusions to form and link metabolic status to asymmetric division.


Assuntos
Anáfase , Citocinas/metabolismo , Nicotinamida Fosforribosiltransferase/metabolismo , Oócitos/citologia , Fuso Acromático , Actinas/metabolismo , Trifosfato de Adenosina/metabolismo , Animais , Ciclo Celular , Segregação de Cromossomos , Citoplasma/metabolismo , Citosol/metabolismo , Feminino , Meiose , Camundongos , Microscopia Confocal , NAD/química
16.
Proc Natl Acad Sci U S A ; 117(28): 16346-16355, 2020 07 14.
Artigo em Inglês | MEDLINE | ID: mdl-32601232

RESUMO

Agonists to the µ-opioid G protein-coupled receptor (µOR) can alleviate pain through activation of G protein signaling, but they can also induce ß-arrestin activation, leading to such side effects as respiratory depression. Biased ligands to µOR that induce G protein signaling without inducing ß-arrestin signaling can alleviate pain while reducing side effects. However, the mechanism for stimulating ß-arrestin signaling is not known, making it difficult to design optimum biased ligands. We use extensive molecular dynamics simulations to determine three-dimensional (3D) structures of activated ß-arrestin2 stabilized by phosphorylated µOR bound to the morphine and D-Ala2, N-MePhe4, Gly-ol]-enkephalin (DAMGO) nonbiased agonists and to the TRV130 biased agonist. For nonbiased agonists, we find that the ß-arrestin2 couples to the phosphorylated µOR by forming strong polar interactions with intracellular loop 2 (ICL2) and either the ICL3 or cytoplasmic region of transmembrane (TM6). Strikingly, Gi protein makes identical strong bonds with these same ICLs. Thus, the Gi protein and ß-arrestin2 compete for the same binding site even though their recruitment leads to much different outcomes. On the other hand, we find that TRV130 has a greater tendency to bind the extracellular portion of TM2 and TM3, which repositions TM6 in the cytoplasmic region of µOR, hindering ß-arrestin2 from making polar anchors to the ICL3 or to the cytosolic end of TM6. This dramatically reduces the affinity between µOR and ß-arrestin2.


Assuntos
Receptores Opioides mu/metabolismo , beta-Arrestina 2/metabolismo , Analgésicos Opioides/metabolismo , Animais , Sítios de Ligação , Membrana Celular/metabolismo , Citoplasma/metabolismo , Ala(2)-MePhe(4)-Gly(5)-Encefalina/metabolismo , Proteínas de Ligação ao GTP/metabolismo , Humanos , Camundongos , Simulação de Dinâmica Molecular , Morfina/metabolismo , Fosforilação , Ligação Proteica , Domínios Proteicos , Receptores Opioides mu/agonistas , Receptores Opioides mu/química , Transdução de Sinais , Compostos de Espiro/metabolismo , Tiofenos/metabolismo , beta-Arrestina 2/química
17.
PLoS One ; 15(7): e0236185, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32730344

RESUMO

Fluorescent markers are a powerful tool and have been widely applied in biology for different purposes. The genome sequence of Xanthomonas citri subsp. citri (X. citri) revealed that approximately 30% of the genes encoded hypothetical proteins, some of which could play an important role in the success of plant-pathogen interaction and disease triggering. Therefore, revealing their functions is an important strategy to understand the bacterium pathways and mechanisms involved in plant-host interaction. The elucidation of protein function is not a trivial task, but the identification of the subcellular localization of a protein is key to understanding its function. We have constructed an integrative vector, pMAJIIc, under the control of the arabinose promoter, which allows the inducible expression of red fluorescent protein (mCherry) fusions in X. citri, suitable for subcellular localization of target proteins. Fluorescence microscopy was used to track the localization of VrpA protein, which was visualized surrounding the bacterial outer membrane, and the GyrB protein, which showed a diffused cytoplasmic localization, sometimes with dots accumulated near the cellular poles. The integration of the vector into the amy locus of X. citri did not affect bacterial virulence. The vector could be stably maintained in X. citri, and the disruption of the α-amylase gene provided an ease screening method for the selection of the transformant colonies. The results demonstrate that the mCherry-containing vector here described is a powerful tool for bacterial protein localization in cytoplasmic and periplasmic environments.


Assuntos
Proteínas de Bactérias/metabolismo , Citoplasma/metabolismo , Periplasma/metabolismo , Proteínas Recombinantes de Fusão/metabolismo , Xanthomonas/metabolismo , Arabinose/farmacologia , Cromossomos Bacterianos/genética , Vetores Genéticos/metabolismo , Viabilidade Microbiana/efeitos dos fármacos , Transporte Proteico/efeitos dos fármacos , Amido/metabolismo , Frações Subcelulares/efeitos dos fármacos , Xanthomonas/patogenicidade
18.
PLoS One ; 15(7): e0236829, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32730367

RESUMO

Cytoplasmic male sterility (CMS) is a widely used trait in angiosperms caused by perturbations in nucleus-mitochondrion interactions that suppress the production of functional pollen. MicroRNAs (miRNAs) are small non-coding RNAs that act as regulatory molecules of transcriptional or post-transcriptional gene silencing in plants. The discovery of miRNAs and their possible implications in CMS induction provides clues for the intricacies and complexity of this phenomenon. Previously, we characterized an Ogura-CMS line of turnip (Brassica rapa ssp. rapifera) that displays distinct impaired anther development with defective microspore production and premature tapetum degeneration. In the present study, high-throughput sequencing was employed for a genome-wide investigation of miRNAs. Six small RNA libraries of inflorescences collected from the Ogura-CMS line and its maintainer fertile (MF) line of turnip were constructed. A total of 120 pre-miRNAs corresponding to 89 mature miRNAs were identified, including 87 conversed miRNAs and 33 novel miRNAs. Among these miRNAs, the expression of 10 differentially expressed mature miRNAs originating from 12 pre-miRNAs was shown to have changed by more than two-fold between inflorescences of the Ogura-CMS line and inflorescences of the MF line, including 8 down- and 2 up-regulated miRNAs. The expression profiles of the differentially expressed miRNAs were confirmed by stem-loop quantitative real-time PCR. In addition, to identify the targets of the identified miRNAs, a degradome analysis was performed. A total of 22 targets of 25 miRNAs and 17 targets of 28 miRNAs were identified as being involved in the reproductive development for Ogura-CMS and MF lines of turnip, respectively. Negative correlations of expression patterns between partial miRNAs and their targets were detected. Some of these identified targets, such as squamosa promoter-binding-like transcription factor family proteins, auxin response factors and pentatricopeptide repeat-containing proteins, were previously reported to be involved in reproductive development in plants. Taken together, our results can help improve the understanding of miRNA-mediated regulatory pathways that might be involved in CMS occurrence in turnip.


Assuntos
Brassica rapa/genética , Brassica rapa/metabolismo , Citoplasma/metabolismo , Inflorescência/genética , MicroRNAs/genética , Infertilidade das Plantas , Proteínas de Plantas/metabolismo , Brassica rapa/crescimento & desenvolvimento , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Sequenciamento de Nucleotídeos em Larga Escala , Proteínas de Plantas/genética , Interferência de RNA
19.
Mol Cell Biol ; 40(18)2020 08 28.
Artigo em Inglês | MEDLINE | ID: mdl-32631902

RESUMO

hRpn13/ADRM1 links substrate recruitment with deubiquitination at the proteasome through its proteasome- and ubiquitin-binding Pru domain and DEUBAD domain, which binds and activates deubiquitinating enzyme (DUB) UCHL5/Uch37. Here, we edit the HCT116 colorectal cancer cell line to delete part of the hRpn13 Pru, producing cells that express truncated hRpn13 (trRpn13), which is competent for UCHL5 binding but defective for proteasome interaction. trRpn13 cells demonstrate reduced levels of proteasome-bound ubiquitinated proteins, indicating that the loss of hRpn13 function at proteasomes cannot be fully compensated for by the two other dedicated substrate receptors (hRpn1 and hRpn10). Previous studies indicated that the loss of full-length hRpn13 causes a corresponding reduction of UCHL5. We find UCHL5 levels unaltered in trRpn13 cells, but hRpn11 is elevated in ΔhRpn13 and trRpn13 cells, perhaps from cell stress. Despite the ∼90 DUBs in human cells, including two others in addition to UCHL5 at the proteasome, we found deletion of UCHL5 from HCT116 cells to cause increased levels of ubiquitinated proteins in whole-cell extract and at proteasomes, suggesting that UCHL5 activity cannot be fully assumed by other DUBs. We also report anticancer molecule RA190, which binds covalently to hRpn13 and UCHL5, to require hRpn13 Pru and not UCHL5 for cytotoxicity.


Assuntos
Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Chaperonas Moleculares/metabolismo , Ubiquitina Tiolesterase/metabolismo , Sequência de Aminoácidos , Sítios de Ligação , Citoplasma/metabolismo , Células HCT116 , Humanos , Peptídeos e Proteínas de Sinalização Intracelular/genética , Glicoproteínas de Membrana/metabolismo , Chaperonas Moleculares/genética , Complexo de Endopeptidases do Proteassoma/metabolismo , Ligação Proteica , Ubiquitina/metabolismo , Ubiquitina Tiolesterase/genética , Proteínas Ubiquitinadas/metabolismo
20.
Anticancer Res ; 40(6): 3485-3489, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32487648

RESUMO

BACKGROUND/AIM: Despite early detection by widespread use of abdominal imaging more than 40% of patients with conventional renal cell carcinoma (RCC) will die due to metastatic disease. Small kinase inhibitors for AXL receptor tyrosine kinase may delay the progression of metastatic cRCC. PATIENTS AND METHODS: We analysed AXL expression by immunohistochemistry on tissue multi arrays of 691 conventional RCC without metastasis at the time of nephrectomy. RESULTS: The Kaplan-Meier survival analysis indicated a poor disease-specific survival rates for patients with tumour showing cytoplasmic AXL staining, whereas expression on the cell membrane is associated with excellent disease outcome. Multivariate Cox regression analysis identified cytoplasmic AXL expression as an independent prognostic factor indicating a five-times higher risk of postoperative tumour progression (RR=5.048; 95% CI=2.391-10.657; p<0.001). CONCLUSION: Detecting cytoplasmic expression of AXL can be used to define a subset of conventional RCC with high risk of progression, thus identifying patients for more aggressive surveillance and adjuvant AXL inhibitor treatment as early as possible.


Assuntos
Biomarcadores Tumorais , Carcinoma de Células Renais/metabolismo , Carcinoma de Células Renais/patologia , Neoplasias Renais/metabolismo , Neoplasias Renais/patologia , Proteínas Proto-Oncogênicas/metabolismo , Receptores Proteína Tirosina Quinases/metabolismo , Adulto , Idoso , Idoso de 80 Anos ou mais , Carcinoma de Células Renais/mortalidade , Carcinoma de Células Renais/cirurgia , Citoplasma/metabolismo , Progressão da Doença , Feminino , Seguimentos , Humanos , Estimativa de Kaplan-Meier , Neoplasias Renais/mortalidade , Neoplasias Renais/cirurgia , Masculino , Pessoa de Meia-Idade , Gradação de Tumores , Proteínas Proto-Oncogênicas/genética , Receptores Proteína Tirosina Quinases/genética , Recidiva , Resultado do Tratamento , Adulto Jovem
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