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1.
EMBO J ; 42(15): e113079, 2023 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-37303231

RESUMO

Acetate, a major by-product of glycolytic metabolism in Escherichia coli and many other microorganisms, has long been considered a toxic waste compound that inhibits microbial growth. This counterproductive auto-inhibition represents a major problem in biotechnology and has puzzled the scientific community for decades. Recent studies have however revealed that acetate is also a co-substrate of glycolytic nutrients and a global regulator of E. coli metabolism and physiology. Here, we used a systems biology strategy to investigate the mutual regulation of glycolytic and acetate metabolism in E. coli. Computational and experimental analyses demonstrate that decreasing the glycolytic flux enhances co-utilization of acetate with glucose. Acetate metabolism thus compensates for the reduction in glycolytic flux and eventually buffers carbon uptake so that acetate, rather than being toxic, actually enhances E. coli growth under these conditions. We validated this mechanism using three orthogonal strategies: chemical inhibition of glucose uptake, glycolytic mutant strains, and alternative substrates with a natively low glycolytic flux. In summary, acetate makes E. coli more robust to glycolytic perturbations and is a valuable nutrient, with a beneficial effect on microbial growth.


Assuntos
Escherichia coli , Glicólise , Escherichia coli/metabolismo , Acetatos/metabolismo , Carbono/metabolismo , Biotecnologia , Glucose/metabolismo
2.
Elife ; 102021 03 15.
Artigo em Inglês | MEDLINE | ID: mdl-33720011

RESUMO

Overflow metabolism refers to the production of seemingly wasteful by-products by cells during growth on glucose even when oxygen is abundant. Two theories have been proposed to explain acetate overflow in Escherichia coli - global control of the central metabolism and local control of the acetate pathway - but neither accounts for all observations. Here, we develop a kinetic model of E. coli metabolism that quantitatively accounts for observed behaviours and successfully predicts the response of E. coli to new perturbations. We reconcile these theories and clarify the origin, control, and regulation of the acetate flux. We also find that, in turns, acetate regulates glucose metabolism by coordinating the expression of glycolytic and TCA genes. Acetate should not be considered a wasteful end-product since it is also a co-substrate and a global regulator of glucose metabolism in E. coli. This has broad implications for our understanding of overflow metabolism.


Assuntos
Acetatos/metabolismo , Escherichia coli/metabolismo , Glucose/metabolismo , Cinética , Modelos Biológicos
3.
Circ Res ; 122(6): e34-e48, 2018 03 16.
Artigo em Inglês | MEDLINE | ID: mdl-29374072

RESUMO

RATIONALE: Heart development involves differentiation of cardiac progenitors and assembly of the contractile sarcomere apparatus of cardiomyocytes. However, little is known about the mechanisms that regulate actin cytoskeleton remodeling during cardiac cell differentiation. OBJECTIVE: The Asb2α (Ankyrin repeat-containing protein with a suppressor of cytokine signaling box 2) CRL5 (cullin 5 RING E3 ubiquitin ligase) triggers polyubiquitylation and subsequent degradation by the proteasome of FLNs (filamins). Here, we investigate the role of Asb2α in heart development and its mechanisms of action. METHODS AND RESULTS: Using Asb2 knockout embryos, we show that Asb2 is an essential gene, critical to heart morphogenesis and function, although its loss does not interfere with the overall patterning of the embryonic heart tube. We show that the Asb2α E3 ubiquitin ligase controls Flna stability in immature cardiomyocytes. Importantly, Asb2α-mediated degradation of the actin-binding protein Flna marks a previously unrecognized intermediate step in cardiac cell differentiation characterized by cell shape changes and actin cytoskeleton remodeling. We further establish that in the absence of Asb2α, myofibrils are disorganized and that heartbeats are inefficient, leading to embryonic lethality in mice. CONCLUSIONS: These findings identify Asb2α as an unsuspected key regulator of cardiac cell differentiation and shed light on the molecular and cellular mechanisms determining the onset of myocardial cell architecture and its link with early cardiac function. Although Flna is known to play roles in cytoskeleton organization and to be required for heart function, this study now reveals that its degradation mediated by Asb2α ensures essential functions in differentiating cardiac progenitors.


Assuntos
Citoesqueleto de Actina/metabolismo , Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Filaminas/metabolismo , Coração/crescimento & desenvolvimento , Miócitos Cardíacos/metabolismo , Ubiquitinação , Proteínas Adaptadoras de Transdução de Sinal/genética , Animais , Diferenciação Celular , Células Cultivadas , Filaminas/genética , Camundongos , Camundongos Endogâmicos C57BL , Miócitos Cardíacos/citologia , Proteólise , Proteínas Supressoras da Sinalização de Citocina
4.
Biochimie ; 122: 339-47, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-26253693

RESUMO

Ubiquitylation is a reversible post-translational modification of proteins that controls a myriad of functions and cellular processes. It occurs through the sequential action of three distinct enzymes. E3 ubiquitin ligases (E3s) play the role of conductors of the ubiquitylation pathway making them attractive therapeutic targets. This review is dedicated to the largest family of multimeric E3s, the Cullin-RING E3 (CRL) family and more specifically to cullin 5 based CRLs that remains poorly characterized.


Assuntos
Proteínas Culina/metabolismo , Complexo de Endopeptidases do Proteassoma/metabolismo , Ubiquitina-Proteína Ligases/metabolismo , Ubiquitinação , Antineoplásicos/uso terapêutico , Humanos , Modelos Biológicos , Neoplasias/tratamento farmacológico , Neoplasias/metabolismo , Transdução de Sinais/efeitos dos fármacos , Ubiquitina/metabolismo
5.
Sci Rep ; 5: 16269, 2015 Nov 05.
Artigo em Inglês | MEDLINE | ID: mdl-26537633

RESUMO

Conventional dendritic cells (cDCs) comprise distinct populations with specialized immune functions that are mediators of innate and adaptive immune responses. Transcriptomic and proteomic approaches have been used so far to identify transcripts and proteins that are differentially expressed in these subsets to understand the respective functions of cDCs subsets. Here, we showed that the Cullin 5-RING E3 ubiquitin ligase (E3) ASB2α, by driving degradation of filamin A (FLNa) and filamin B (FLNb), is responsible for the difference in FLNa and FLNb abundance in the different spleen cDC subsets. Importantly, the ability of these cDC subsets to migrate correlates with the level of FLNa. Furthermore, our results strongly point to CD4 positive and double negative cDCs as distinct populations. Finally, we develop quantitative global proteomic approaches to identify ASB2α substrates in DCs using ASB2 conditional knockout mice. As component of the ubiquitin-proteasome system (UPS) are amenable to pharmacological manipulation, these approaches aimed to the identification of E3 substrates in physiological relevant settings could potentially lead to novel targets for therapeutic strategies.


Assuntos
Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Células Dendríticas/metabolismo , Ubiquitina-Proteína Ligases/metabolismo , Animais , Linhagem Celular Tumoral , Filaminas/metabolismo , Células HeLa , Humanos , Camundongos , Camundongos Knockout , Complexo de Endopeptidases do Proteassoma/metabolismo , Proteômica/métodos , Proteínas Supressoras da Sinalização de Citocina , Ubiquitina/metabolismo
6.
Cell Signal ; 25(12): 2823-30, 2013 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-24044920

RESUMO

ASB proteins are the specificity subunits of cullin5-RING E3 ubiquitin ligases (CRL5) that play roles in ubiquitin-mediated protein degradation. However, how their activity is regulated remains poorly understood. Here, we unravel a novel mechanism of regulation of a CRL5 through phosphorylation of its specificity subunit ASB2α. Indeed, using mass spectrometry, we showed for the first time that ASB2α is phosphorylated and that phosphorylation of serine-323 (Ser-323) of ASB2α is crucial for the targeting of the actin-binding protein filamin A (FLNa) to degradation. Mutation of ASB2α Ser-323 to Ala had no effect on intrinsic E3 ubiquitin ligase activity of ASB2α but abolished the ability of ASB2α to induce degradation of FLNa. In contrast, the ASB2α Ser-323 to Asp phosphomimetic mutant induced acute degradation of FLNa. Moreover, inhibition of the extracellular signal-regulated kinases 1 and 2 (Erk1/2) activity reduced ASB2α-mediated FLNa degradation. We further showed that the subcellular localization of ASB2α to actin-rich structures is dependent on ASB2α Ser-323 phosphorylation and propose that the interaction with FLNa depends on the electrostatic potential redistribution induced by the Ser-323 phosphate group. Taken together, these data unravel an important mechanism by which ASB2α-mediated FLNa degradation can be regulated.


Assuntos
Filaminas/metabolismo , Proteólise , Serina/metabolismo , Proteínas Supressoras da Sinalização de Citocina/metabolismo , Sequência de Aminoácidos , Animais , MAP Quinases Reguladas por Sinal Extracelular/metabolismo , Células HeLa , Humanos , Modelos Moleculares , Dados de Sequência Molecular , Fosforilação , Serina/análise , Proteínas Supressoras da Sinalização de Citocina/química , Ubiquitina-Proteína Ligases/metabolismo
7.
Int J Biochem Cell Biol ; 45(10): 2136-46, 2013 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-23764619

RESUMO

Ubiquitination is a posttranslational modification of proteins that involves the covalent attachment of ubiquitin, either as a single moiety or as polymers. This process controls almost every cellular metabolic pathway through a variety of combinations of linkages. Mass spectrometry now allows high throughput approaches for the identification of the thousands of ubiquitinated proteins and of their ubiquitination sites. Despite major technological improvements in mass spectrometry in terms of sensitivity, resolution and acquisition speed, the use of efficient purification methods of ubiquitinated proteins prior to mass spectrometry analysis is critical to achieve an efficient characterization of the ubiquitome. This critical step is achieved using different approaches that possess advantages and pitfalls. Here, we discuss the limits that can be encountered when deciphering the ubiquitome. This article is part of a Directed Issue entitled: Molecular basis of muscle wasting.


Assuntos
Espectrometria de Massas/métodos , Proteoma/química , Proteoma/metabolismo , Ubiquitina/química , Ubiquitina/metabolismo , Humanos , Processamento de Proteína Pós-Traducional , Ubiquitinação
8.
Proteomics ; 13(1): 37-47, 2013 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-23135970

RESUMO

The ubiquitin-proteasome system allows the targeted degradation of proteins and plays a critical role in the regulation of many cellular processes. Proteasome inhibition is a recent antitumor therapeutic strategy and bortezomib was the first proteasome inhibitor approved for clinical use. In this study, we used the NB4 cell line to investigate the effects of bortezomib toward acute promyelocytic leukemia cells before and after retinoic acid-induced differentiation. We showed that apoptosis level after bortezomib treatment is higher in NB4 cells than in differentiated NB4 cells. To compare early protein variations upon bortezomib treatment in both NB4 cell populations, we performed a quantitative proteomic analysis based on iTRAQ peptide labeling followed by data analysis with in-house developed scripts. This strategy revealed the regulation of 14 proteins principally involved in protein stress response and apoptosis in NB4 cells after proteasome inhibition. Altogether, our results suggest that the differential level of apoptosis induced by bortezomib treatment in both NB4 cell populations could result from distinct protein toxicity level.


Assuntos
Ácidos Borônicos/administração & dosagem , Leucemia Promielocítica Aguda/metabolismo , Proteínas , Pirazinas/administração & dosagem , Tretinoína/administração & dosagem , Antineoplásicos/administração & dosagem , Apoptose , Bortezomib , Diferenciação Celular/efeitos dos fármacos , Linhagem Celular Tumoral , Estudos de Avaliação como Assunto , Humanos , Peptídeos/genética , Peptídeos/metabolismo , Complexo de Endopeptidases do Proteassoma/efeitos dos fármacos , Inibidores de Proteassoma/administração & dosagem , Proteínas/metabolismo , Proteínas/toxicidade , Receptores do Ácido Retinoico/genética , Receptores do Ácido Retinoico/metabolismo , Estresse Fisiológico/efeitos dos fármacos , Ubiquitina
9.
FASEB J ; 25(11): 3790-802, 2011 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-21764995

RESUMO

Muscle atrophy prevails in numerous diseases (cancer cachexia, renal failure, infections, etc.), mainly results from elevated proteolysis, and is accelerated by bed rest. This largely contributes to increased health costs. Devising new strategies to prevent muscle wasting is a major clinical challenge. The ubiquitin proteasome system (UPS) degrades myofibrillar proteins, but the precise mechanisms responsible for actin breakdown are surprisingly poorly characterized. We report that chimeric flag-actin was destabilized and polyubiquitinylated in stably transfected C2C12 myotubes treated with the catabolic agent dexamethasone (1 µM) and that only proteasome inhibitors blocked its breakdown. Actin polyubiquitinylation was also detected in wild-type C2C12 myotubes and human muscle biopsies from control participants and patients with cancer. The muscle-specific E3 ubiquitin ligase MuRF1 is up-regulated in catabolic conditions and polyubiquitinylates components of the thick filament. We also demonstrate that recombinant GST-MuRF1 physically interacted and polyubiquitinylated actin in vitro and that MuRF1 is a critical component for actin breakdown, since MuRF1 siRNA stabilized flag-actin. These data identify unambiguously the abundant contractile protein actin as a target of the UPS in skeletal muscle both in vitro and in vivo, further supporting the need for new strategies blocking specifically the activation of this pathway in muscle wasting conditions.


Assuntos
Actinas/metabolismo , Proteínas Musculares/metabolismo , Miofibrilas/metabolismo , Poliubiquitina/metabolismo , Ubiquitina-Proteína Ligases/metabolismo , Animais , Linhagem Celular , Dexametasona/farmacologia , Humanos , Leupeptinas/farmacologia , Camundongos , Músculos/metabolismo , Oligopeptídeos , Peptídeos/química , Peptídeos/metabolismo , Inibidores de Proteassoma , RNA Interferente Pequeno/farmacologia , Ratos , Proteínas com Motivo Tripartido
10.
Exp Dermatol ; 19(12): 1054-9, 2010 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-20707810

RESUMO

Plasmatic proteasome (p-proteasome) also called circulating proteasome has recently been described as a tumor marker. We investigated the diagnostic and prognostic accuracies of p-proteasome levels in a melanoma population classified according to the American Joint Committee on Cancer staging system. Using an ELISA test, we measured p-proteasome levels in 90 patients and 40 controls between March 2003 and March 2008. The subunit composition of p-proteasomes was determined in metastatic melanoma by proteomic analysis. The mean p-proteasome levels were correlated with stages (P < 0.0001; r(S) = 0.664). They were significantly higher in patients with stage IV and stage III with lymph node metastasis (9187 ± 1294 and 5091 ± 454 ng/ml, respectively) compared to controls (2535 ± 187 ng/ml; P < 0.001), to stage I/II (2864 ± 166 ng/ml; P < 0.001) and to stage III after curative lymphadenectomy (2859 ± 271 ng/ml; P < 0.001). The diagnostic accuracy of p-proteasome was evaluated by receiver operating characteristic analysis. With a cut-off of 4300 ng/ml, diagnostic specificity and sensitivity of p-proteasome for regional or visceral metastases were respectively 96.3% and 72.2%. In univariate analysis, high p-proteasome levels (>4300 ng/ml) were significantly correlated with an increased risk of progression [hazard ratio (HR) = 7.34; 95% CI 3.54-15.21, P < 0.0001] and a risk of death (HR = 5.92; 95% CI 2.84-12.33, P < 0.0001). In multivariate analysis, high p-proteasome levels were correlated with a poorer clinical outcome in the subgroup analysis limited to patients with disease stages I, II and III. Proteomic analysis confirmed the presence of all proteasome and immunoproteasome subunits. Taken together, these results indicate that p-proteasomes are a new marker for metastatic dissemination in patients with melanoma.


Assuntos
Melanoma/sangue , Melanoma/diagnóstico , Complexo de Endopeptidases do Proteassoma/sangue , Adulto , Idoso , Idoso de 80 Anos ou mais , Biomarcadores/sangue , Intervalo Livre de Doença , Feminino , Humanos , L-Lactato Desidrogenase/sangue , Masculino , Melanoma/patologia , Pessoa de Meia-Idade , Metástase Neoplásica/diagnóstico , Estadiamento de Neoplasias , Valor Preditivo dos Testes , Prognóstico , Subunidades Proteicas/sangue , Curva ROC , Recidiva , Análise de Sobrevida , Adulto Jovem
11.
Leuk Res ; 34(4): 498-506, 2010 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-19811823

RESUMO

The proteasome plays a critical role in the regulation of many cellular processes, including the cell cycle and tumor growth. The proteasome inhibitor bortezomib has recently been approved for the treatment of relapsed and refractory multiple myeloma. In this study, we investigated the induction of apoptosis by proteasome inhibitors in several human acute myeloid leukemia (AML) cell lines and in primary cells from patients. We demonstrate that these drugs induce a high level of apoptosis in the KG1a cell line, in which the therapeutic drug daunorubicin is poorly active, compared to other AML cell lines. In parallel, we found that significantly different levels of apoptosis were induced in primary cells from patients depending on the FAB-based differentiation status of these cells. Moreover, the level of 20S proteasome in KG1a cells was also high compared to other AML cell lines, suggesting a relationship between the high sensitivity to proteasome inhibitors and an elevated amount of 20S proteasome. In good accordance, we identified two groups of patient cells expressing high and low levels of 20S proteasome, with respective high and low sensitivity to proteasome inhibitors. Further comparison of the proteasome status in KG1a and U937 cells also suggests that a high proportion of the 19S regulatory complex in U937 cells compared to the 20S core complex may explain an increased proteasome activity. Altogether, our results suggest that various AML subtypes may present different responses to proteasome inhibitors, that these molecules can be potentially considered as interesting therapeutic alternatives for these pathologies, and that the amount of 20S proteasome in AML cells may be predictive of the cellular response to these inhibitors.


Assuntos
Apoptose/efeitos dos fármacos , Leucemia Mieloide Aguda/patologia , Inibidores de Proteases/farmacologia , Complexo de Endopeptidases do Proteassoma/metabolismo , Inibidores de Proteassoma , Adulto , Idoso , Idoso de 80 Anos ou mais , Antineoplásicos/farmacologia , Ácidos Borônicos/farmacologia , Bortezomib , Daunorrubicina/farmacologia , Resistencia a Medicamentos Antineoplásicos/efeitos dos fármacos , Resistencia a Medicamentos Antineoplásicos/fisiologia , Feminino , Células HL-60 , Humanos , Leucemia Mieloide Aguda/diagnóstico , Leucemia Mieloide Aguda/metabolismo , Leupeptinas/farmacologia , Masculino , Pessoa de Meia-Idade , Prognóstico , Complexo de Endopeptidases do Proteassoma/análise , Pirazinas/farmacologia , Células Tumorais Cultivadas , Células U937
12.
Mol Cell Proteomics ; 8(7): 1719-27, 2009 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-19376791

RESUMO

The ubiquitin-proteasome system is a central mechanism for controlled proteolysis that regulates numerous cellular processes in eukaryotes. As such, defects in this system can contribute to disease pathogenesis. In this pathway, E3 ubiquitin ligases provide platforms for binding specific substrates, thereby coordinating their ubiquitylation and subsequent degradation by the proteasome. Despite the identification of many E3 ubiquitin ligases, the identities of their specific substrates are still largely unresolved. The ankyrin repeat-containing protein with a suppressor of cytokine signaling box 2 (ASB2) gene that we initially identified as a retinoic acid-response gene in acute promyelocytic leukemia cells encodes the specificity subunit of an E3 ubiquitin ligase complex that is involved in hematopoietic cell differentiation. We have recently identified filamin A and filamin B as the first ASB2 targets and shown that ASB2 triggers ubiquitylation and proteasome-mediated degradation of these proteins. Here a global quantitative proteomics strategy is provided to identify substrates of E3 ubiquitin ligases targeted to proteasomal degradation. Indeed we used label-free methods for quantifying proteins identified by shotgun proteomics in extracts of cells expressing wild-type ASB2 or an E3 ubiquitin ligase-defective mutant of ASB2 under the control of an inducible promoter. Measurements of spectral count and mass spectrometric signal intensity demonstrated a drastic decrease of filamin A and filamin B in myeloid leukemia cells expressing wild-type ASB2 compared with cells expressing an E3 ubiquitin ligase-defective mutant of ASB2. Altogether we provide an original strategy that enables identification of E3 ubiquitin ligase substrates that have to be degraded.


Assuntos
Complexo de Endopeptidases do Proteassoma/metabolismo , Proteômica/métodos , Ubiquitina-Proteína Ligases/metabolismo , Sequência de Aminoácidos , Linhagem Celular Tumoral , Proteínas Contráteis/genética , Proteínas Contráteis/metabolismo , Filaminas , Humanos , Leucemia Mieloide/metabolismo , Proteínas dos Microfilamentos/genética , Proteínas dos Microfilamentos/metabolismo , Dados de Sequência Molecular , Proteínas Supressoras da Sinalização de Citocina/genética , Proteínas Supressoras da Sinalização de Citocina/metabolismo , Talina/genética , Talina/metabolismo , Ubiquitina/metabolismo , Ubiquitina-Proteína Ligases/genética
13.
Mol Cell Proteomics ; 8(5): 1150-64, 2009 May.
Artigo em Inglês | MEDLINE | ID: mdl-19193609

RESUMO

An affinity purification strategy was developed to characterize human proteasome complexes diversity as well as endogenous proteasome-interacting proteins (PIPs). This single step procedure, initially used for 20 S proteasome purification, was adapted to purify all existing physiological proteasome complexes associated to their various regulatory complexes and to their interacting partners. The method was applied to the purification of proteasome complexes and their PIPs from human erythrocytes but can be used to purify proteasomes from any human sample as starting material. The benefit of in vivo formaldehyde cross-linking as a stabilizer of protein-protein interactions was studied by comparing the status of purified proteasomes and the identified proteins in both protocols (with or without formaldehyde cross-linking). Subsequent proteomics analyses identified all proteasomal subunits, known regulators, and recently assigned partners. Moreover other proteins implicated at different levels of the ubiquitin-proteasome system were also identified for the first time as PIPs. One of them, the ubiquitin-specific protease USP7, also known as HAUSP, is an important player in the p53-HDM2 pathway. The specificity of the interaction was further confirmed using a complementary approach that consisted of the reverse immunoprecipitation with HAUSP as a bait. Altogether we provide a valuable tool that should contribute, through the identification of partners likely to affect proteasomal function, to a better understanding of this complex proteolytic machinery in any living human cell and/or organ/tissue and in different cell physiological states.


Assuntos
Cromatografia de Afinidade/métodos , Complexo de Endopeptidases do Proteassoma/isolamento & purificação , Animais , Anticorpos/farmacologia , Reagentes de Ligações Cruzadas/farmacologia , Eletroforese em Gel de Poliacrilamida , Eritrócitos/efeitos dos fármacos , Eritrócitos/enzimologia , Formaldeído/farmacologia , Humanos , Imunoprecipitação , Camundongos , Ligação Proteica/efeitos dos fármacos , Subunidades Proteicas/metabolismo , Proteômica , Ratos , Reprodutibilidade dos Testes , Ubiquitina Tiolesterase/metabolismo , Peptidase 7 Específica de Ubiquitina
14.
Methods Mol Biol ; 484: 111-30, 2008.
Artigo em Inglês | MEDLINE | ID: mdl-18592176

RESUMO

The 20S proteasome is a multicatalytic protein complex, present in all eukaryotic cells, that plays a major role in intracellular protein degradation. In mammalian cells, this symmetrical cylindrical complex is composed of two copies each of seven different alpha and beta subunits arranged into four stacked rings (alpha(7)beta(7)beta(7)alpha(7)). Separation by two-dimensional (2D) gel electrophoresis of the human erythrocytes 20S proteasome subunits and mass spectrometry (MS) identification of all the observed spots reveal the presence of multiple isoforms for most of the subunits. These isoforms could correspond to protein variants and/or posttranslational modifications that may influence the 20S proteasome proteolytic activity. Their characterization is therefore important to establish the rules governing structure/activity relationships of the human 20S proteasome. This chapter describes the use of a combination of proteomic approaches to characterize the human 20S proteasome subunit isoforms separated by 2D gel electrophoresis. A "top-down" strategy was developed to determine by electrospray MS the molecular mass of the intact protein after its passive elution from the gel. Comparison of the experimental molecular mass to the theoretical one can reveal the presence of possible modifications. "Bottom-up" proteomic approaches are then performed and, after protein digestion, tandem MS analyses of the modified peptides allow the characterization and location of the modification. These methods are discussed for the study of the human erythrocytes 20S proteasome subunit isoforms.


Assuntos
Complexo de Endopeptidases do Proteassoma/química , Isoformas de Proteínas/análise , Subunidades Proteicas/análise , Proteômica/métodos , Sequência de Aminoácidos , Eletroforese em Gel Bidimensional/métodos , Eritrócitos/química , Humanos , Espectrometria de Massas/métodos , Dados de Sequência Molecular , Isoformas de Proteínas/genética , Subunidades Proteicas/genética , Reprodutibilidade dos Testes
15.
J Proteome Res ; 7(7): 2852-9, 2008 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-18510353

RESUMO

The proteasome is a proteolytic complex that constitutes the main pathway for degradation of intracellular proteins in eukaryotic cells. It regulates many physiological processes and its dysfunction can lead to several pathologies like cancer. To study the 20S proteasome structure/activity relationship in cells that derive from human biopsy samples, we optimized an immuno-purification protocol for the analysis of samples containing a small number of cells using magnetic beads. This scaled-down protocol was used to purify the cytoplasmic 20S proteasome of adjacent normal and tumor colorectal cells arising from tissue samples of several patients. Proteomic analyses based on two-dimensional gel electrophoresis (2DE) and mass spectrometry showed that the subunit composition of 20S proteasomes from these normal and tumor cells were not significantly different. The proteasome activity was also assessed in the cytoplasmic extracts and was similar or higher in tumor colorectal than in the corresponding normal cells. The scaled-down 20S proteasome purification protocol developed here can be applied to any human clinical tissue samples and is compatible with further proteomic analyses.


Assuntos
Neoplasias Colorretais/química , Complexo de Endopeptidases do Proteassoma/isolamento & purificação , Idoso , Idoso de 80 Anos ou mais , Linhagem Celular Tumoral , Neoplasias Colorretais/patologia , Feminino , Humanos , Imunoprecipitação , Magnetismo , Masculino , Pessoa de Meia-Idade , Complexo de Endopeptidases do Proteassoma/química , Subunidades Proteicas/química , Subunidades Proteicas/isolamento & purificação , Proteômica , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Espectrometria de Massas em Tandem
16.
Methods Mol Biol ; 432: 301-20, 2008.
Artigo em Inglês | MEDLINE | ID: mdl-18370027

RESUMO

The 20S proteasome is a multicatalytic protein complex present in all eukaryotic cells. Associated to regulatory complexes, it plays a major role in cellular protein degradation and in the generation of Major Histocompatibility Complex (MHC) class I antigenic peptides. In mammalian cells, this symmetrical cylindrical complex is composed of two copies of 14 distinct subunits, three of which possess a proteolytic activity. The catalytic standard subunits can be replaced by immunosubunits to form the immunoproteasome, which possesses different proteolytic efficiencies. Both types of 20S proteasomes can be present in cells in varying distributions. The heterogeneity of 20S proteasome complexes in cells leads to different protein degradation patterns. The characterization of the subunit composition of 20S proteasomes in cells thus represents an important step in the understanding of the effect of the heterogeneity of proteasome complexes on their activity. This chapter describes the use of proteomic approaches to study the subunit composition of 20S proteasome complexes purified from human cells. An immunoaffinity purification method is presented. The separation of all 20S proteasome subunits by 2D gel electrophoresis and the subunit identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis and database search are then described. These methods are discussed with the study of 20S proteasomes purified from two human cancer cell lines.


Assuntos
Peptídeos/isolamento & purificação , Complexo de Endopeptidases do Proteassoma/química , Complexo de Endopeptidases do Proteassoma/isolamento & purificação , Linhagem Celular , Cromatografia de Afinidade/métodos , Eletroforese em Gel Bidimensional/métodos , Antígenos de Histocompatibilidade Classe I/análise , Humanos , Peptídeos/química , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos
17.
Proteome Sci ; 4: 23, 2006 Dec 21.
Artigo em Inglês | MEDLINE | ID: mdl-17184524

RESUMO

BACKGROUND: Opiate addiction reflects plastic changes that endurably alter synaptic transmission within relevant neuronal circuits. The biochemical mechanisms of these adaptations remain largely unknown and proteomics-based approaches could lead to a broad characterization of the molecular events underlying adaptations to chronic drug exposure. RESULTS: Thus, we have started proteomic analyses of the effects of chronic morphine exposure in a recombinant human neuroblastoma SH-SY5Y clone that stably overexpresses the mu-opioid receptor. Cells were treated with morphine for 6, 24 and 72 hours, the proteins were separated by 2-D gel electrophoresis and stained with Coomassie blue, and the protein map was compared with that obtained from untreated cells. Spots showing a statistically significant variation were selected for identification using mass spectrometric analyses. CONCLUSION: A total of 45 proteins were identified, including proteins involved in cellular metabolism, cytoskeleton organization, vesicular trafficking, transcriptional and translational regulation, and cell signaling.

18.
J Biol Chem ; 281(7): 4434-45, 2006 Feb 17.
Artigo em Inglês | MEDLINE | ID: mdl-16356931

RESUMO

Mycolic acids are major and specific components of the cell envelope of Mycobacteria that include Mycobacterium tuberculosis, the causative agent of tuberculosis. Their metabolism is the target of the most efficient antitubercular drug currently used in therapy, and the enzymes that are involved in the production of mycolic acids represent important targets for the development of new drugs effective against multidrug-resistant strains. Among these are the S-adenosylmethionine-dependent methyltransferases (SAM-MTs) that catalyze the introduction of key chemical modifications in defined positions of mycolic acids. Some of these subtle structural variations are known to be crucial for both the virulence of the tubercle bacillus and the permeability of the mycobacterial cell envelope. We report here the structural characterization of the enzyme Hma (MmaA4), a SAM-MT that is unique in catalyzing the introduction of a methyl branch together with an adjacent hydroxyl group essential for the formation of both keto- and methoxymycolates in M. tuberculosis. Despite the high propensity of Hma to proteolytic degradation, the enzyme was produced and crystallized, and its three-dimensional structure in the apoform and in complex with S-adenosylmethionine was solved to about 2 A. Thestructuresshowtheimportantroleplayedbythemodificationsfound within mycolic acid SAM-MTs, especially thealpha2-alpha3 motif and the chemical environment of the active site. Essential information with respect to cofactor and substrate binding, selectivity and specificity, and about the mechanism of catalytic reaction were derived.


Assuntos
Proteínas de Bactérias/química , Metiltransferases/química , Oxigenases de Função Mista/química , Mycobacterium tuberculosis/enzimologia , Ácidos Micólicos/metabolismo , S-Adenosilmetionina/metabolismo , Sequência de Aminoácidos , Sítios de Ligação , Cristalização , Dados de Sequência Molecular , Estrutura Terciária de Proteína
19.
J Cell Biol ; 170(4): 607-18, 2005 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-16103228

RESUMO

Generation and turnover of phosphoinositides (PIs) must be coordinated in a spatial- and temporal-restricted manner. The small GTPase Rab5 interacts with two PI 3-kinases, Vps34 and PI3Kbeta, suggesting that it regulates the production of 3-PIs at various stages of the early endocytic pathway. Here, we discovered that Rab5 also interacts directly with PI 5- and PI 4-phosphatases and stimulates their activity. Rab5 regulates the production of phosphatidylinositol 3-phosphate (PtdIns[3]P) through a dual mechanism, by directly phosphorylating phosphatidylinositol via Vps34 and by a hierarchical enzymatic cascade of phosphoinositide-3-kinasebeta (PI3Kbeta), PI 5-, and PI 4-phosphatases. The functional importance of such an enzymatic pathway is demonstrated by the inhibition of transferrin uptake upon silencing of PI 4-phosphatase and studies in weeble mutant mice, where deficiency of PI 4-phosphatase causes an increase of PtdIns(3,4)P2 and a reduction in PtdIns(3)P. Activation of PI 3-kinase at the plasma membrane is accompanied by the recruitment of Rab5, PI 4-, and PI 5-phosphatases to the cell cortex. Our data provide the first evidence for a dual role of a Rab GTPase in regulating both generation and turnover of PIs via PI kinases and phosphatases to coordinate signaling functions with organelle homeostasis.


Assuntos
Endocitose , Fosfatidilinositóis/metabolismo , Proteínas rab5 de Ligação ao GTP/metabolismo , Animais , Astrócitos/citologia , Astrócitos/metabolismo , Encéfalo/metabolismo , Catálise , Compartimento Celular , Cromatografia de Afinidade , Regulação para Baixo/genética , Ativação Enzimática , Células HeLa , Humanos , Camundongos , Células NIH 3T3 , Fosfatidilinositol 3-Quinases/metabolismo , Fosfatos de Fosfatidilinositol/metabolismo , Fosfoproteínas Fosfatases/genética , Fosfoproteínas Fosfatases/metabolismo , Ligação Proteica , Transporte Proteico , Soro , Transferrina/metabolismo , Proteínas rab5 de Ligação ao GTP/isolamento & purificação
20.
Mol Pharmacol ; 68(2): 467-76, 2005 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-15901846

RESUMO

The initial aim of this study was to identify protein changes associated with long-term morphine treatment in a recombinant human neuroblastoma SH-SY5Y clone (sc2) stably overexpressing the human mu-opioid (MOP) receptor. In MOP receptor-overexpressing sc2 cells, short-term morphine exposure was found to be much more potent and efficacious in inhibiting forskolin-elicited production of cAMP, and long-term morphine exposure was shown to induce a substantially higher degree of opiate dependence, as reflected by adenylate cyclase sensitization, than it did in wild-type neuroblastoma cells. Differential proteomic analysis of detergent-resistant membrane rafts isolated from untreated and chronically morphine-treated sc2 cells revealed long-term morphine exposure to have reliably induced a 30 to 40% decrease in the abundance of five proteins, subsequently identified by mass spectrometry as G protein subunits alphai(2), alphai(3), beta(1), and beta(2), and prohibitin. Quantitative Western blot analyses of whole-cell extracts showed that long-term morphine treatment-induced down-regulation of Gbeta but not of the other proteins is highly correlated (r(2) = 0.96) with sensitization of adenylate cyclase. Down-regulation of Gbeta and adenylate cyclase sensitization elicited by long-term morphine treatment were suppressed in the presence of carbobenzoxy-l-leucyl-l-leucyl-l-norvalinal (MG-115) or lactacystin. Thus, sustained activation of the MOP receptor by morphine in sc2 cells seems to promote proteasomal degradation of Gbeta to sensitize adenylate cyclase. Together, our data suggest that the long-term administration of opiates may elicit dependence by altering the neuronal balance of heterotrimeric G proteins and adenylate cyclases, with the ubiquitin-proteasome pathway playing a pivotal role.


Assuntos
Adenilil Ciclases/metabolismo , Subunidades beta da Proteína de Ligação ao GTP/metabolismo , Morfina/administração & dosagem , Neuroblastoma/metabolismo , Complexo de Endopeptidases do Proteassoma/metabolismo , Adenilil Ciclases/genética , Linhagem Celular Tumoral , Relação Dose-Resposta a Droga , Regulação para Baixo/efeitos dos fármacos , Regulação para Baixo/fisiologia , Subunidades beta da Proteína de Ligação ao GTP/genética , Humanos , Neuroblastoma/genética , Complexo de Endopeptidases do Proteassoma/genética , Fatores de Tempo
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