51
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Wang D, Kalume D, Pickart C, Pandey A, Cotter RJ. Identification of protein ubiquitylation by electrospray ionization tandem mass spectrometric analysis of sulfonated tryptic peptides. Anal Chem 2007; 78:3681-7. [PMID: 16737224 DOI: 10.1021/ac051904b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report here the application of electrospray ionization tandem mass spectrometry for the characterization of protein ubiquitylation, an important posttranslational modification of cellular proteins. Trypsin digestion of ubiquitin-conjugated proteins produces diglycine branched peptides containing the modification sites. Chemical derivatization by N-terminal sulfonation was carried out on several model peptides for the formation of a characteristic fragmentation pattern in their MS/MS analysis. The fragmentation of derivatized singly charged peptides results in a product ion distribution similar to that already observed by MALDI-TOF MS/MS. Signature fragments distinguished the diglycine branched peptides from other modified and unmodified peptides, while the sequencing product ions reveal the amino acid sequence and the location of the ubiquitylation site. Doubly charged peptide derivatives fragment in a somewhat different manner, but several fragments characteristic to diglycine branched peptides were observed under low collision energy conditions. These signature peaks can also be used to identify peptides containing ubiquitylation sites. In addition, a marker ion corresponding to a glycine-modified lysine residue produced by high-energy fragmentation provides useful information for identity verification. The method is demonstrated by the analysis of three ubiquitin-conjugated proteins using LC/MS/MS.
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Affiliation(s)
- Dongxia Wang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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52
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Azarkan M, Huet J, Baeyens-Volant D, Looze Y, Vandenbussche G. Affinity chromatography: A useful tool in proteomics studies. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:81-90. [PMID: 17113368 DOI: 10.1016/j.jchromb.2006.10.056] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Revised: 09/26/2006] [Accepted: 10/27/2006] [Indexed: 11/22/2022]
Abstract
Separation or fractionation of a biological sample in order to reduce its complexity is often a prerequisite to qualitative or quantitative proteomic approaches. Affinity chromatography is an efficient protein separation method based on the interaction between target proteins and specific immobilized ligands. The large range of available ligands allows to separate a complex biological extract in different protein classes or to isolate the low abundance species such as post-translationally modified proteins. This method plays an essential role in the isolation of protein complexes and in the identification of protein-protein interaction networks. Affinity chromatography is also required for quantification of protein expression by using isotope-coded affinity tags.
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Affiliation(s)
- Mohamed Azarkan
- Laboratoire de Chimie Générale (CP: 609), Faculté de Médecine, Université Libre de Bruxelles, Campus Erasme, 808, route de Lennik, B-1070 Bruxelles, Belgium
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53
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Ventadour S, Jarzaguet M, Wing SS, Chambon C, Combaret L, Béchet D, Attaix D, Taillandier D. A New Method of Purification of Proteasome Substrates Reveals Polyubiquitination of 20 S Proteasome Subunits. J Biol Chem 2007; 282:5302-9. [PMID: 17189251 DOI: 10.1074/jbc.m610005200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 26 S proteasome is implicated in the control of many major biological functions but a reliable method for the identification of its major substrates, i.e. polyubiquitin (Ub) conjugates, is still lacking. Based on the steps present in cells, i.e. recognition and deubiquitination, we developed an affinity matrix-based purification of polyUb conjugates suitable for any biological sample. Ub-conjugates were first purified from proteasome inhibitor-treated C2C12 cells using the Ub binding domains of the S5a proteasome subunit bound to an affinity matrix and then deubiquitinated by the catalytic domain of the USP2 enzyme. This two step purification of proteasome substrates involving both protein-protein interactions and enzyme-mediated release allowed highly specific isolation of polyUb 26 S proteasome substrates, which were then resolved on two-dimensional gels post-deubiquitination. To establish our method, we focused on a gel area where spots were best resolved. Surprisingly, spot analysis by mass spectrometry identified alpha2, alpha6, alpha7, beta2, beta3, beta4, and beta5 20 S proteasome subunits as potential substrates. Western blots using an anti-beta3 proteasome subunit antibody confirmed that high molecular weight forms of beta3 were present, particularly in proteasome inhibitor-treated cells. Sucrose gradients of cell lysates suggested that the proteasome was first disassembled before subunits were polyubiquitinated. Altogether, we provide a technique that enables large scale identification of 26 S proteasome substrates that should contribute to a better understanding of this proteolytic machinery in any living cell and/or organ/tissue. Furthermore, the data suggest that proteasome homeostasis involves an autoregulatory mechanism.
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Affiliation(s)
- Sophie Ventadour
- Human Nutrition Unit UMR 1019 and Proteomic Core Facility, Human Nutrition Research Center and Institut National de la Recherche Agronomique, 63122 Ceyrat, France
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54
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Wang Y, Dohlman HG. Regulation of G protein and mitogen-activated protein kinase signaling by ubiquitination: insights from model organisms. Circ Res 2007; 99:1305-14. [PMID: 17158346 DOI: 10.1161/01.res.0000251641.57410.81] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Guanine nucleotide binding proteins (G proteins) and mitogen-activated protein kinases are highly conserved signaling molecules engaged in a wide variety of cellular processes. The strength and duration of signaling mediated by G proteins and mitogen-activated protein kinases are well known to be regulated via phosphorylation of pathway components. Over the past few years, it has become evident that many of the same signaling proteins also undergo ubiquitination, a posttranslational modification that typically leads to protein degradation. Consequently the strength and duration of signaling can also be modulated by regulating the abundance of signaling proteins. This article describes G protein- and mitogen-activated protein kinase-mediated signaling pathways that are known to be regulated by ubiquitination. The focus is on studies performed in the budding yeast Saccharomyces cerevisiae, as many principles governing this new regulatory mechanism were initially discovered in this model organism. Similar mechanisms uncovered in other model systems are also briefly discussed to illustrate the importance and universality of signaling regulation by ubiquitination.
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Affiliation(s)
- Yuqi Wang
- Department of Biology, Saint Louis University, 128 Macelwane Hall, 3507 Laclede Ave, St Louis, MO 63103, USA.
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55
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Mollah S, Wertz IE, Phung Q, Arnott D, Dixit VM, Lill JR. Targeted mass spectrometric strategy for global mapping of ubiquitination on proteins. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:3357-64. [PMID: 17883243 DOI: 10.1002/rcm.3227] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Post-translational modifications of proteins including phosphorylation, glycosylation, acetylation and ubiquitination facilitate the regulation of many cellular processes and intracellular signaling events. Ubiquitination plays a key role in the functional regulation and degradation of many classes of proteins, and the study of ubiquitination and poly-ubiquitination has emerged as one of the most active areas in proteomic research. A variety of mass spectrometric methods have been described for the identification of ubiquitination sites, the study of poly-ubiquitin topology and the identification of ubiquitin substrates. The most popular workflow for both ubiquitination site mapping and poly-ubiquitination chain topology characterization is to take advantage of the Gly-Gly signature on the substrate's lysine residue observed after tryptic digestion. Although a number of protocols have been described for the mapping of ubiquitination sites, one major challenge is that ubiquitination is typically heterogeneous, and several lysine residues may be ubiquitinated within a protein. When multiple ubiquitination sites are present, multiple analyses are often required to cover all of the potential modification sites which in turn can necessitate the usage of larger quantities of material. In addition, the level of ubiquitination on endogenous and recombinant proteins may be of low intensity, adding further analytical challenges in the identification of this modification. The use of the multiple reaction monitoring (MRM)-initiated detection and sequencing workflow (MIDAS) for the identification of phosphorylation sites has previously been described. Here, we explore the use of an MRM workflow for ubiquitination site mapping on the substrate protein, receptor interacting protein (RIP).
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56
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Xu P, Peng J. Dissecting the ubiquitin pathway by mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1940-7. [PMID: 17055348 PMCID: PMC1828906 DOI: 10.1016/j.bbapap.2006.09.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2006] [Revised: 08/30/2006] [Accepted: 09/06/2006] [Indexed: 11/27/2022]
Abstract
Protein modification by ubiquitin is a central regulatory mechanism in eukaryotic cells. Recent proteomics developments in mass spectrometry enable systematic analysis of cellular components in the ubiquitin pathway. Here, we review the advances in analyzing ubiquitinated substrates, determining modified lysine residues, quantifying polyubiquitin chain topologies, as well as profiling deubiquitinating enzymes based on the activity. Moreover, proteomic approaches have been developed for probing the interactome of proteasome and for identifying proteins with ubiquitin-binding domains. Similar strategies have been applied on the studies of the modification by ubiquitin-like proteins as well. These strategies are discussed with respect to their advantages, limitations and potential improvements. While the utilization of current methodologies has rapidly expanded the scope of protein modification by the ubiquitin family, a more active role is anticipated in the functional studies with the emergence of quantitative mass spectrometry.
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Affiliation(s)
- Ping Xu
- Department of Human Genetics, Center for Neurodegenerative Disease, Emory University, Atlanta, GA 30322
| | - Junmin Peng
- Department of Human Genetics, Center for Neurodegenerative Disease, Emory University, Atlanta, GA 30322
- Address correspondence to Junmin Peng, E-mail:
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57
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Xu P, Cheng D, Duong DM, Rush J, Roelofs J, Finley D, Peng J. A Proteomic Strategy for Quantifying Polyubiquitin Chain Topologies. Isr J Chem 2006. [DOI: 10.1560/1jvl-j4ee-fvw4-mxre] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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58
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Schulenborg T, Schmidt O, van Hall A, Meyer HE, Hamacher M, Marcus K. Proteomics in neurodegeneration – disease driven approaches. J Neural Transm (Vienna) 2006; 113:1055-73. [PMID: 16835692 DOI: 10.1007/s00702-006-0512-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2005] [Accepted: 04/05/2006] [Indexed: 10/24/2022]
Abstract
Proteins as a product from genetic information execute and determine how development, growth, aging and disease factors are orchestrated within the lifetime of an organism. Differential protein expression and/or modification are always context dependent i.e. they happen within a specific context of a tissue, organ, environmental situation and individual fate. Consequently, the function/dysfunction (in a certain disease) of a specific gene cannot be predicted comprehensively by its sequence only. Genetic information can only be understood when genes and proteins are analyzed in the context of the biological system and specific networks they are involved in. In regard to neurodegenerative diseases such as Alzheimer's (AD) and Parkinson's disease (PD) many proteins are known for long years to be the cause or the consequence of the pathomechanism of the respective disease. The treatment of these neurodegenerative diseases represents a major challenge for the pharmaceutical industry, whereas the understanding of their pathogenesis is still in its infancy. With the development of several powerful techniques for proteome analysis it is now possible to investigate the expression of thousands of proteins in single cells, tissues or whole organisms at the same time. These developments opened new doors in medical sciences, and identification of cellular alterations associated with e.g. neurodegeneration will result in the identification of novel diagnostic as well as therapeutic targets. In this review, general considerations and strategies of proteomics technologies, the advantages and challenges as well as the special needs for analyzing brain tissue in the context of AD and AD are described and summarized.
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Affiliation(s)
- T Schulenborg
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
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59
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Wang Y, Dohlman HG. Pheromone-regulated Sumoylation of Transcription Factors That Mediate the Invasive to Mating Developmental Switch in Yeast. J Biol Chem 2006; 281:1964-9. [PMID: 16306045 DOI: 10.1074/jbc.m508985200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A fundamental question in biology is how different signaling pathways use common signaling proteins to attain different developmental outcomes. The yeast transcription factor Ste12 is required in at least two distinct signaling processes, each regulated by many of the same protein kinases. Whereas Ste12-Ste12 homodimers promote transcription of genes required for mating, Ste12-Tec1 heterodimers activate genes required for invasive growth. We report that Ste12 and Tec1 undergo covalent modification by the ubiquitin-related modifier SUMO. Stimulation by mating pheromone promotes sumoylation of Ste12 and diminishes the sumoylation of Tec1. In the absence of sumoylation Tec1 is more rapidly degraded. We propose that pheromone-regulated sumoylation of Ste12 and Tec1 promotes a developmental switch from the invasive to the mating differentiation program.
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Affiliation(s)
- Yuqi Wang
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260, USA
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60
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Johansson BB, Minsaas L, Aragay AM. Proteasome involvement in the degradation of the G(q) family of Galpha subunits. FEBS J 2005; 272:5365-77. [PMID: 16218966 DOI: 10.1111/j.1742-4658.2005.04934.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metabolically unstable proteins are involved in a multitude of regulatory networks, including those that control cell signaling, the cell cycle and in many responses to physiological stress. In the present study, we have determined the stability and characterized the degradation process of some members of the G(q) class of heterotrimeric G proteins. Pulse-chase experiments in HEK293 cells indicated a rapid turnover of endogenously expressed Galpha(q) and overexpressed Galpha(q) and Galpha(16) subunits. Pretreatment with proteasome inhibitors attenuated the degradation of both G alpha subunits. In contrast, pretreatment of cells with inhibitors of lysosomal proteases and nonproteasomal cysteine proteases had very little effect on the stability of the proteins. Significantly, the turnover of these proteins is not affected by transient activation of their associated receptors. Fractionation studies showed that the rates of Galpha(q) and Galpha16 degradation are accelerated in the cytosol. In fact, we show that a mutant Galpha(q) which lacks its palmitoyl modification site, and which is localized almost entirely in the cytoplasm, has a marked increase in the rate of degradation. Taken together, these results suggest that the G(q) class proteins are degraded through the proteasome pathway and that cellular localization and/or other protein interactions determine their stability.
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Affiliation(s)
- Bente B Johansson
- Department of Biomedicine, Faculty of Medicine, University of Bergen, Norway
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61
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Chu F, Nusinow DA, Chalkley RJ, Plath K, Panning B, Burlingame AL. Mapping post-translational modifications of the histone variant MacroH2A1 using tandem mass spectrometry. Mol Cell Proteomics 2005; 5:194-203. [PMID: 16210244 DOI: 10.1074/mcp.m500285-mcp200] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Post-translational histone modifications modulate chromatin-templated processes and therefore affect cellular proliferation, growth, and development. Although post-translational modifications on the core histones have been under intense investigation for several years, the modifications on variant histones are poorly understood. We used tandem mass spectrometry to identify covalent modifications on a histone H2A variant, macroH2A1.2. MacroH2A1.2 can be monoubiquitinated; however, the site of monoubiquitination has not been documented. In this study we used green fluorescent protein-tagged macroH2A1.2 to determine that Lys(115) is a site of ubiquitination. In addition, we found that this variant H2A is methylated on the epsilon amino group of lysine residues Lys(17), Lys(122), and Lys(238) and phosphorylated on Thr(128). Three of these modifications were also found to be present in the endogenous protein by mass spectrometric analysis. These results provide the first direct evidence that multiple post-translational modifications are imposed on macroH2A1.2, suggesting that, like canonical H2A, this variant H2A is subject to regulation by combinatorial use of covalent modifications.
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Affiliation(s)
- Feixia Chu
- Mass Spectrometry Facility and Department of Pharmaceutical Chemistry, University of California, San Francisco, 94143, USA
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62
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Kirkpatrick DS, Denison C, Gygi SP. Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics. Nat Cell Biol 2005; 7:750-7. [PMID: 16056266 PMCID: PMC1224607 DOI: 10.1038/ncb0805-750] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mass-spectrometry-based proteomics has become an essential tool for the qualitative and quantitative analysis of cellular systems. The biochemical complexity and functional diversity of the ubiquitin system are well suited to proteomic studies. This review summarizes advances involving the identification of ubiquitinated proteins, the elucidation of ubiquitin-modification sites and the determination of polyubiquitin chain linkages, as well as offering a perspective on the application of emerging technologies for mechanistic and functional studies of protein ubiquitination.
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Affiliation(s)
| | | | - Steven P. Gygi
- Department of Cell Biology and
- Taplin Biological Mass Spectrometry Facility, Harvard Medical School, Boston, Massachusetts 02115, USA
- Correspondence: Steven P. Gygi, Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA, 617-432-3155,
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63
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Moulédous L, Neasta J, Uttenweiler-Joseph S, Stella A, Matondo M, Corbani M, Monsarrat B, Meunier JC. Long-Term Morphine Treatment Enhances Proteasome-Dependent Degradation of Gβ in Human Neuroblastoma SH-SY5Y Cells: Correlation with Onset of Adenylate Cyclase Sensitization. Mol Pharmacol 2005; 68:467-76. [PMID: 15901846 DOI: 10.1124/mol.105.013391] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
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.
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Affiliation(s)
- Lionel Moulédous
- IPBS-CNRS UMR5089, 205 route de Narbonne, 31077 Toulouse cédex 04, France
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64
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Kirkpatrick DS, Weldon SF, Tsaprailis G, Liebler DC, Gandolfi AJ. Proteomic identification of ubiquitinated proteins from human cells expressing His-tagged ubiquitin. Proteomics 2005; 5:2104-11. [PMID: 15852347 DOI: 10.1002/pmic.200401089] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A proteomics method has been developed to purify and identify the specific proteins modified by ubiquitin (Ub) from human cells. In purified samples, Ub and 21 other proteins were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) spectra using SEQUEST. These proteins included several of the expected carriers of Ub including Ub-conjugating enzymes and histone proteins. To perform these experiments, a cell line coexpressing epitope tagged His(6X)-Ub and green fluorescent protein (GFP) was generated by stably transfecting HEK293 cells. Ubiquitinated proteins were purified using nickel-affinity chromatography and digested in solution with trypsin. Complex mixtures of peptides were separated by reversed phase chromatography and analyzed by nano LC-MS/MS using the LCQ quadrupole ion-trap mass spectrometer. Proteins identified from His(6X)-Ub-GFP transfected cells were compared to a list of proteins from HEK293 cells, which associate with nickel-nitrilotriacetic acid (Ni-NTA)-agarose in the absence of His-tagged Ub. In a proof of principle experiment, His(6X)-Ub-GFP transfected cells were treated with As (III) (10 microM, 24 h) in an attempt to identify substrates increasingly modified by Ub. In this experiment, proliferating cell nuclear antigen, a DNA repair protein and known ubiquitin substrate, was confidently identified. This proteomics method, developed for the analysis of ubiquitinated proteins, is a step towards large-scale characterization of Ub-protein conjugates in numerous physiological and pathological states.
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65
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Lee JS, Hong US, Lee TH, Yoon SK, Yoon JB. Mass spectrometric analysis of tumor necrosis factor receptor-associated factor 1 ubiquitination mediated by cellular inhibitor of apoptosis 2. Proteomics 2005; 4:3376-82. [PMID: 15468071 DOI: 10.1002/pmic.200401000] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Signaling complexes formed on tumor necrosis factor receptor 2 (TNF-R2) contain adaptor proteins TNF-R-associated factors (TRAFs) 1 and 2, and cellular inhibitors of apoptosis (cIAPs) 1 and 2 which function as regulators of programmed cell death. TRAF2, cIAP1 and cIAP2 all have RING finger domains known to possess E3 ubiquitin ligase activity, implying that ubiquitination may play an important role in the TNF signaling pathway. In this report, we have shown that cIAP2 specifically mediated ubiquitination and proteasome-dependent degradation of TRAF1. To identify the sites for cIAP2-mediated ubiquitination of TRAF1, we used high pressure liquid chromatography coupled with tandem mass spectrometry. Lys185 and Lys193 of TRAF1 were found to be modified with ubiquitin chains. Mutation of Lys185 and Lys193 to Arg almost completely blocked cIAP2-mediated ubiquitination of TRAF1, indicating that they are the major, if not the only, sites of TRAF1 ubiquitination. Our data suggest that cIAP2 may regulate the turnover of TRAF1 by adding polyubiquitin chains on Lys185 or Lys193 following its recruitment to TNF-R signaling complexes.
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Affiliation(s)
- Jong-Sik Lee
- Department of Biochemistry and Protein Network Research Center, Yonsei University, Seoul, Korea
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66
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Naviglio S, Pagano M, Romano M, Sorrentino A, Fusco A, Illiano F, Chiosi E, Spina A, Illiano G. Adenylate cyclase regulation via proteasome-mediated modulation of Galphas levels. Cell Signal 2005; 16:1229-37. [PMID: 15337522 DOI: 10.1016/j.cellsig.2004.03.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2004] [Accepted: 03/16/2004] [Indexed: 11/23/2022]
Abstract
The adenylate cyclase (AC)/cyclic AMP (cAMP)/cAMP-dependent protein kinase pathway controls many biological phenomena. The ubiquitin/proteasome system, controlling the levels of many proteins, modulates important cellular processes such as cell cycle and cell growth. Here we describe a novel mechanism for AC regulation by proteasome pathway. Pharmacological inhibition of proteasome function in human osteosarcoma U2OS cells results in up-regulation of AC activity, increase of levels of alpha subunit of heterotrimeric stimulatory GTP-binding proteins (alphas) and, remarkably, also in preventing of beta-adrenergic receptor-mediated down-regulation of alphas protein levels. Accumulation of alphas protein is also accompanied by the appearance of polyubiquitinated alphas species. Our results: (1) identify alphas protein as a novel proteasome substrate in mammalian cells; (2) indicate that proteasome might play a physiological role in controlling AC/cAMP mediated pathways by modulating the levels of Galphas protein; (3) suggest a role for the proteasome also in controlling alphas-mediated signaling pathways other than those affecting AC complex.
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Affiliation(s)
- Silvio Naviglio
- Department of Biochemistry and Biophysics, Second University of Naples, Via L. De Crecchio 7, 80138 Napoli, Italy
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67
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Denison C, Kirkpatrick DS, Gygi SP. Proteomic insights into ubiquitin and ubiquitin-like proteins. Curr Opin Chem Biol 2005; 9:69-75. [PMID: 15701456 DOI: 10.1016/j.cbpa.2004.10.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The dynamic and specific modification of cellular proteins by members of the ubiquitin protein family is a vital regulatory mechanism that lies at the heart of almost all biological processes. Because of both their pervasive and complex nature, these regulatory pathways have been the target of many recent proteomic studies. Such works have provided numerous insights. Through the use of various mass spectrometry techniques, affinity purification methods, and/or chemical probes, large lists have begun to be compiled for the multitude of substrates, interacting partners, and enzymatic components of these regulatory circuits. Furthermore, similar tools have provided many insights into functional aspects such as their mechanisms of substrate specificity and enzymatic activity. This review provides a summary of these recent proteomic works, along with comments on future directions of the field.
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Affiliation(s)
- Carilee Denison
- Department of Cell Biology, 240 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115, USA
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68
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Gundersen RE, You J, Rauch S, Farnham K, McCarty C, Willis N, Prince A. Loss-of-function mutations identified in the Helical domain of the G protein alpha-subunit, G alpha2, of Dictyostelium discoideum. Biochim Biophys Acta Gen Subj 2005; 1722:262-70. [PMID: 15715993 DOI: 10.1016/j.bbagen.2004.12.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2004] [Revised: 12/15/2004] [Accepted: 12/20/2004] [Indexed: 10/25/2022]
Abstract
The guanine nucleotide binding regulatory proteins (G proteins) play essential roles in a wide variety of physiological processes, such as vision, hormone responses, olfaction, immune response, and development. The heterotrimeric G proteins consist of alpha-, beta-, and gamma-subunits and act as molecular switches to relay information from transmembrane receptors to intracellular effectors. The switch mechanism is a function of the inherent GTPase activity of the alpha-subunit. The alpha-subunit is comprised of two domains, the GTPase domain and the Helical domain. The GTPase domain performs all of the known alpha-subunit functions while little is know about the role of the Helical domain. To gain a better understanding of alpha-subunit function, we performed a screen for loss-of-function mutations, using the G alpha2-subunit of Dictyostelium. G alpha2 is essential for the developmental life cycle of Dictyostelium. It is known that the loss of G alpha2 function results in a failure of cells to enter the developmental phase, producing a visibly abnormal phenotype. This allows the easy identification of amino acids essential to G alpha2 function. A library of random point mutations in the g alpha2 cDNA was constructed using low fidelity polymerase chain reaction (PCR). The library was then expressed in a g alpha2 null cell line and screened for loss-of-function mutations. Mutations were identified in isolated clones by sequencing the g alpha2 insert. To date, sixteen single amino acids changes have been identified in G alpha2 which result in loss-of-function. Of particular interest are seven mutations found in the Helical domain of the alpha-subunit. These loss-of-function mutations in the alpha-subunit Helical domain may provide important insight into its function.
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Affiliation(s)
- Robert E Gundersen
- Department of Biochemistry, Microbiology and Molecular Biology, 5735 Hitchner Hall, University of Maine, Orono, ME 04469-5735, USA.
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69
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Warren MRE, Parker CE, Mocanu V, Klapper D, Borchers CH. Electrospray ionization tandem mass spectrometry of model peptides reveals diagnostic fragment ions for protein ubiquitination. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:429-437. [PMID: 15655800 DOI: 10.1002/rcm.1798] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In this work, synthetic peptides were used to determine the fragmentation behavior of ubiquitinated peptides and to find ions diagnostic for peptide ubiquitination. The ubiquitin-calmodulin peptide1 was chosen as the model peptide for naturally occurring ubiquitinated proteins cleaved with endoproteinase gluC. In addition, the fragmentation behavior of model ubiquitinated peptides produced by tryptic digestion was also of great interest since the standard protocols for proteomics-based protein identification use trypsin as the protease. Attachment of ubiquitin to a target protein results in a branched structure, but only ions from the ubiquitin side chain (and the lysine to which it is attached) can be used as diagnostic ions, since fragment ions that contain other amino acids from the parent protein will vary in mass. Characteristic b-type fragment ions from the gluC cleavage of the ubiquitin side chain (designated as b ions) were found which involve only the ubiquitin tail (b2, b3, b4, b5 and b6 ions at m/z 189.06, 302.12, 439.18, 552.30 and 651.30, respectively). Maximum production of these ions occurred at a collision energy of 45 eV in a Q-TOF instrument. Although a non-ubiquitinated peptide may produce isobaric fragment ions, it is unlikely that it can produce these ions in combination. With liquid chromatography/tandem mass spectrometry (LC/MS/MS) experiments, ubiquitinated peptides can readily be determined by surveying the reconstructed or extracted ion chromatograms of the diagnostic fragment ions for common peaks. Characteristic ions resulting from tryptic cleavage of the side chain were found in cleavage products with a missed cleavage, resulting in a LRGG- tag instead of a GG- tag. For the LRGG-tagged peptide, diagnostic MS/MS fragment ions (at m/z 270.17 and 384.21) from the ubiquitin tail (b2 and b4, respectively) were found, along with an internal fragment ion (LRGGK-28) at m/z 484.30. These ions should prove useful in precursor-ion scanning experiments for identifying peptides modified by attachment of ubiquitin, and for locating the site of ubiquitin attachment.
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Affiliation(s)
- Maria R Esteban Warren
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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70
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Yang K, Zhu J, Sun S, Tang Y, Zhang B, Diao L, Wang C. The coiled-coil domain of TRAF6 is essential for its auto-ubiquitination. Biochem Biophys Res Commun 2004; 324:432-9. [PMID: 15465037 DOI: 10.1016/j.bbrc.2004.09.070] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2004] [Indexed: 12/22/2022]
Abstract
Tumor necrosis factor receptor-associated factor 6 (TRAF6) is a crucial signaling transducer that regulates a diverse array of physiological processes, including adaptive immunity, innate immunity, and bone metabolism. Importantly, it is essential for activating NF-kappaB signaling pathway in response to interleukin-1 and Toll-like receptor ligands. Previously, we characterized TRAF6 to be a ubiquitin ligase. In combination with the ubiquitin conjugating enzyme complex Ubc13/Uev1A, TRAF6 could catalyze the formation on itself of unique Lys-63 linked polyubiquitin chain that positively regulated NF-kappaB signaling pathway. However, it remains unknown how this auto-ubiquitination process is regulated. In this study, we found that the coiled-coil domain of TRAF6 was essential for its auto-ubiquitination and activating NF-kappaB signaling pathway. This domain served not as the specific target where the polyubiquitin chain was linked, but as a specific bridge to recruit Ubc13/Uev1A.
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Affiliation(s)
- Kai Yang
- Laboratory of Molecular Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, PR China
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71
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Urano Y, Sakurai T, Ueda H, Ogasawara J, Sakurai T, Takei M, Izawa T. Desensitization of the inhibitory effect of norepinephrine on insulin secretion from pancreatic islets of exercise-trained rats. Metabolism 2004; 53:1424-32. [PMID: 15536596 DOI: 10.1016/j.metabol.2004.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The effect of exercise training (9 weeks of running) on norepinephrine-induced inhibition of insulin secretion was examined in rat islets. Insulin secretions from islets in the presence of glucose (> or =5.5 mmol/L) were significantly lower in trained (TR) than in control rats (CR). Norepinephrine inhibited 5.5 mmol/L glucose-stimulated insulin secretions and cyclic adenosine monophosphate (cAMP) contents in a dose-dependent manner in CR. Norepinephrine (10 micromol/L)-induced inhibition of insulin secretion was reversed by the blockade of the alpha(2)-adrenergic receptor in CR, but not in TR. Exercise training substantially shifted the dose-dependent curve for clonidine-induced inhibition of insulin secretions and that of cAMP contents to the right. Exercise training did not alter the density of the alpha(2)-adrenergic receptor either per islet or per protein of islet crude membrane. However, exercise training significantly reduced the protein expression of G alpha i-2 without change in G alpha i-2 mRNA. In CR but not in TR, norepinephrine significantly inhibited insulin secretions elicited by a combination of high glucose, a protein kinase C activator, and an adenylate cyclase activator under Ca(2+)-free conditions. Thus, exercise training appears to provoke a decreased expression of G alpha i-2 protein. This, at least in part, results in loss of the inhibitory effect of norepinephrine either on cAMP content or on insulin secretion at the post-calcium events in stimulus-secretion coupling, which, in turn, leads to the blunted inhibitory effects of norepinephrine on insulin secretion.
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MESH Headings
- Adrenergic alpha-Agonists/pharmacology
- Adrenergic alpha-Antagonists/pharmacology
- Animals
- Blood Glucose/metabolism
- Blotting, Western
- Clonidine/pharmacology
- Cyclic AMP/metabolism
- Dose-Response Relationship, Drug
- Down-Regulation
- GTP-Binding Protein alpha Subunit, Gi2
- GTP-Binding Protein alpha Subunits, Gi-Go/genetics
- GTP-Binding Protein alpha Subunits, Gi-Go/metabolism
- In Vitro Techniques
- Insulin/metabolism
- Insulin Secretion
- Islets of Langerhans/metabolism
- Male
- Norepinephrine/pharmacology
- Norepinephrine/physiology
- Physical Conditioning, Animal
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- RNA/analysis
- Rats
- Rats, Wistar
- Receptors, Adrenergic, alpha-2/drug effects
- Receptors, Adrenergic, alpha-2/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Yohimbine/pharmacology
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Affiliation(s)
- Yuriko Urano
- Department of Kinesiology, Graduate School of Sciene, Tokyo Metropolitan University, Tokyo 192-0397, Japan
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72
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Wang Y, Marotti LA, Lee MJ, Dohlman HG. Differential regulation of G protein alpha subunit trafficking by mono- and polyubiquitination. J Biol Chem 2004; 280:284-91. [PMID: 15519996 DOI: 10.1074/jbc.m411624200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Previously we used mass spectrometry to show that the yeast G protein alpha subunit Gpa1 is ubiquitinated at Lys-165, located within a subdomain not present in other G alpha proteins (Marotti, L. A., Jr., Newitt, R., Wang, Y., Aebersold, R., and Dohlman, H. G. (2002) Biochemistry 41, 5067-5074). Here we describe the functional role of Gpa1 ubiquitination. We find that Gpa1 expression is elevated in mutants deficient in either proteasomal or vacuolar protease function. Vacuolar protease pep4 mutants accumulate monoubiquitinated Gpa1, and much of the protein is localized within the vacuolar compartment. In contrast, proteasome-defective rpt6/cim3 mutants accumulate polyubiquitinated Gpa1, and in this case the protein exhibits cytoplasmic localization. Cells that lack Ubp12 ubiquitin-processing protease activity accumulate both mono- and polyubiquitinated forms of Gpa1. In this case, Gpa1 accumulates in both the cytoplasm and vacuole. Finally, a Gpa1 mutant that lacks the ubiquitinated subdomain remains unmodified and is predominantly localized at the plasma membrane. These data reveal a strong relationship between the extent of ubiquitination and trafficking of the G protein alpha subunit to its site of degradation.
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Affiliation(s)
- Yuqi Wang
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599-7260, USA
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73
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Ogasawara J, Sakurai T, Rahman N, Kizaki T, Hitomi Y, Ohno H, Izawa T. Acute exercise alters Gαi2 protein expressions through the ubiquitin–proteasome proteolysis pathway in rat adipocytes. Biochem Biophys Res Commun 2004; 323:1109-15. [PMID: 15381114 DOI: 10.1016/j.bbrc.2004.08.202] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2004] [Indexed: 11/24/2022]
Abstract
The effects of acute exercise on the protein expressions of heterotrimeric G protein alpha subunits were examined in rat adipocytes. Galphai2 protein expression was significantly reduced 0 and 3h after exercise but increased 24h after exercise, without alterations in Galphai2 mRNA expressions. The protein expressions of other alpha subunits, Galphas, Galphai1, and Galphai3, were not influenced. Both the 26S proteasome activity and polyubiquitination of Galphai2 protein were significantly increased 0 and 3h after exercise. Whereas, proteasome activity was decreased, and the polyubiquitination of Galphai2 protein was returned to the control level 24h after exercise. The reductions in Galphai2 protein expressions 0 and 3h after exercise were completely prevented by the injection either of a proteasome inhibitor or of a beta-adrenergic receptor blocker prior to exercise. Thus, acute exercise altered the expression of Galphai2 protein via mechanisms which involve the coupling of beta-adrenergic receptors to an agonist with subsequent ubiquitin-proteasome-dependent proteolysis.
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Affiliation(s)
- Junetsu Ogasawara
- Department of Kinesiology, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
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74
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Zhang H, Yan W, Aebersold R. Chemical probes and tandem mass spectrometry: a strategy for the quantitative analysis of proteomes and subproteomes. Curr Opin Chem Biol 2004; 8:66-75. [PMID: 15036159 DOI: 10.1016/j.cbpa.2003.12.001] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Quantitative proteome profiling using mass spectrometry and stable isotope dilution is being widely applied for the functional analysis of biological systems and for the detection of clinical, diagnostic or prognostic marker proteins. Because of the enormous complexity of proteomes, their comprehensive analysis is unlikely to be routinely achieved in the near future. However, in recent years, significant progress has been achieved focusing quantitative proteomic analyses on specific protein classes or subproteomes that are rich in biologically or clinically important information. Such projects typically combine the use of chemical probes that are specific for a targeted group of proteins and may contain stable isotope signatures for accurate quantification with automated tandem mass spectrometry and bioinformatics tools for data analysis. In this review, we summarize technical and conceptual advances in quantitative subproteome profiling based on tandem mass spectrometry and chemical probes.
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Affiliation(s)
- Hui Zhang
- Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103-8904, USA
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75
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Wojcikiewicz RJH. Regulated ubiquitination of proteins in GPCR-initiated signaling pathways. Trends Pharmacol Sci 2004; 25:35-41. [PMID: 14723977 DOI: 10.1016/j.tips.2003.11.008] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The transmission of information through G-protein-coupled receptor (GPCR)-initiated signaling pathways is modulated in several ways. Although phosphorylation of some of the proteins that populate these pathways is a well-known modulatory process, recent studies have shown that signaling proteins can also undergo regulated ubiquitination in response to GPCR activation, with diverse consequences. To date, three GPCRs, some of their associated proteins and certain downstream mediators, notably inositol (1,4,5)-trisphosphate [Ins(1,4,5)P(3)] receptors, have been shown to be ubiquitinated following GPCR activation. Regulated ubiquitination causes proteasomal degradation of Ins(1,4,5)P(3) receptors and appears to control GPCR endocytosis and trafficking. Defining the roles of ubiquitination in GPCR-mediated signaling is an important task because novel drugs that perturb the ubiquitin-proteasome pathway are now being approved as therapeutic agents.
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Affiliation(s)
- Richard J H Wojcikiewicz
- Department of Pharmacology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210-2339, USA.
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76
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Hao N, Yildirim N, Wang Y, Elston TC, Dohlman HG. Regulators of G protein signaling and transient activation of signaling: experimental and computational analysis reveals negative and positive feedback controls on G protein activity. J Biol Chem 2003; 278:46506-15. [PMID: 12968019 DOI: 10.1074/jbc.m308432200] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellular responses to hormones and neurotransmitters are necessarily transient. The mating pheromone signal in yeast is typical. Signal initiation requires cell surface receptors, a G protein heterotrimer, and down-stream effectors. Signal inactivation requires Sst2, a regulator of G protein signaling (RGS) protein that accelerates GTPase activity. We conducted a quantitative analysis of RGS and G protein expression and devised computational models that describe their activity in vivo. These results indicated that pheromone-dependent transcriptional induction of the RGS protein constitutes a negative feedback loop that leads to desensitization. Modeling also suggested the presence of a positive feedback loop leading to resensitization of the pathway. In confirmation of the model, we found that the RGS protein is ubiquitinated and degraded in response to pheromone stimulation. We identified and quantitated these positive and negative feedback loops, which account for the transient response to external signals observed in vivo.
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Affiliation(s)
- Nan Hao
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-0812, USA
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77
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Chen L, Smith L, Wang Z, Smith JB. Preservation of caspase-3 subunits from degradation contributes to apoptosis evoked by lactacystin: any single lysine or lysine pair of the small subunit is sufficient for ubiquitination. Mol Pharmacol 2003; 64:334-45. [PMID: 12869638 DOI: 10.1124/mol.64.2.334] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Procaspase-3 (p32) is processed by upstream caspases to p12 and p20 subunits, which heterodimerize. Concomitant with formation of the active heterotetramer, p20 is autoprocessed to p17. Treatment of HL-60 cells with lactacystin, a selective inhibitor of the proteasome, exponentially increased caspase-3-like hydrolytic activity and induced apoptosis but had little or no effect on the activity of upstream caspase-8, caspase-9, or granzyme B. Lactacystin treatment decreased the p32 zymogen and evoked the accumulation of the p17 and p12 subunits. Treatment of transfected human retinoblast 911 cells with a proteasome inhibitor evoked the accumulation of epitope-tagged p12, p17, and p20 but had no effect on p32 zymogen. This result suggests that caspase-3 subunits, in contrast to the zymogen, are unstable because of degradation by the ubiquitin-proteasome system. Ubiquitin conjugates of p12 and p17 accumulated in cells that were cotransfected with p12 and a caspase inactive mutant of p17. Substitution of arginine for all eight lysines of p12 almost abolished its ubiquitination. Any single lysine or lysine pair was sufficient for p12 ubiquitination. Lactacystin treatment of HL-60 cells induced proteolytic processing of the X-linked inhibitor of apoptosis (XIAP) and decreased full-length XIAP, which is known to have ubiquitin-protein ligase activity for active caspase-3. These findings indicate that caspase-3 subunits can be degraded by the ubiquitin-proteasome system and suggest that lactacystin induces apoptosis in part by disabling the ubiquitin-protein ligase function of XIAP and by stabilizing active caspase-3 subunits.
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Affiliation(s)
- Lei Chen
- Department of Pharmacology and Toxicology, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, AL 35294-0019, USA
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78
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Fischer T, De Vries L, Meerloo T, Farquhar MG. Promotion of G alpha i3 subunit down-regulation by GIPN, a putative E3 ubiquitin ligase that interacts with RGS-GAIP. Proc Natl Acad Sci U S A 2003; 100:8270-5. [PMID: 12826607 PMCID: PMC166218 DOI: 10.1073/pnas.1432965100] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have isolated an RGS-GAIP interacting protein that links RGS proteins to protein degradation. GIPN (GAIP interacting protein N terminus) is a 38-kDa protein with an N-terminal leucine-rich region, a central RING finger-like domain, and a putative C-terminal transmembrane domain. GIPN binds exclusively to RGS proteins of subfamily A, RGS-GAIP, RGSZ1, and RGSZ2. The N-terminal leucine-rich region of GIPN interacts with the cysteine-rich motif of RGS-GAIP. GIPN mRNA is ubiquitously expressed, and GIPN is found on the plasma membrane of transfected HEK293 cells. Endogenous GIPN is concentrated along the basolateral plasma membrane of proximal and distal tubules in rat kidney, where many G protein-coupled receptors and some G proteins are also located. Two immunoreactive species are found in rat kidney, a 38-kDa cytosolic form and an approximately 94-kDa membrane form. GIPN shows Zn2+- and E1/E2-dependent autoubiquitination in vitro, suggesting that it has E3 ubiquitin ligase activity. Overexpression of GIPN stimulates proteasome-dependent reduction of endogenous G alpha i3 in HEK293 cells and reduces the half-life of overexpressed G alpha i3-YFP. Thus, our findings suggest that GIPN is involved in the degradation of G alpha i3 subunits via the proteasome pathway. RGS-GAIP functions as a bifunctional adaptor that binds to G alpha subunits through its RGS domain and to GIPN through its cysteine string motif.
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Affiliation(s)
| | | | | | - Marilyn Gist Farquhar
- Department of Cellular and Molecular Medicine, University of California
at San Diego, La Jolla, CA 92093
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79
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Wang Y, Ge Q, Houston D, Thorner J, Errede B, Dohlman HG. Regulation of Ste7 ubiquitination by Ste11 phosphorylation and the Skp1-Cullin-F-box complex. J Biol Chem 2003; 278:22284-9. [PMID: 12668671 DOI: 10.1074/jbc.m301272200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ste7 is a mitogen-activated protein kinase kinase that mediates pheromone signaling in Saccharomyces cerevisiae. We showed previously that Ste7 is ubiquitinated upon prolonged stimulation by pheromone and that accumulation of ubiquitinated Ste7 results in enhanced transcription and cell division arrest responses (Wang, Y., and Dohlman, H. G. (2002) J. Biol. Chem. 277, 15766-15772). We now report that ubiquitination of Ste7 requires Ste11 kinase and Skp1/Cullin/F-box (SCF) ubiquitin-conjugating activities. Ste7 is not ubiquitinated in Ste11-deficient cells or when the Ste11 phosphorylation sites have been mutated. Ste7 ubiquitination and degradation (but not phosphorylation) is specifically blocked in mutants defective for the E2 ubiquitin-conjugating enzyme Cdc34 or the cullin homologue Cdc53. Both are components of the SCF complex that ubiquitinates proteins during the G1-S transition of the cell cycle. Our findings suggest that SCF promotes the ubiquitination and degradation of Ste7, thereby favoring the resumption of cell division cycling after pheromone-induced growth arrest.
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Affiliation(s)
- Yuqi Wang
- Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-2852, USA
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80
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Hamilton MH, Cook LA, McRackan TR, Schey KL, Hildebrandt JD. Gamma 2 subunit of G protein heterotrimer is an N-end rule ubiquitylation substrate. Proc Natl Acad Sci U S A 2003; 100:5081-6. [PMID: 12700354 PMCID: PMC154301 DOI: 10.1073/pnas.0831228100] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heterotrimeric G proteins transduce signals from activated transmembrane G protein-coupled receptors to appropriate downstream effectors within cells. Signaling specificity is achieved in part by the specific alpha, beta, and gamma subunits that compose a given heterotrimer. Additional structural and functional diversity in these subunits is generated at the level of posttranslational modification, offering alternate regulatory mechanisms for G protein signaling. Presented here is the identification of a variant of the gamma(2) subunit of G protein heterotrimer purified from bovine brain and the demonstration that this RDTASIA gamma(2) variant, containing unique amino acid sequence at its N terminus, is a substrate for ubiquitylation and degradation via the N-end rule pathway. Although N-end-dependent degradation has been shown to have important functions in peptide import, chromosome segregation, angiogenesis, and cardiovascular development, the identification of cellular substrates in mammalian systems has remained elusive. The isolation of RDTASIA gamma(2) from a native tissue represents identification of a mammalian N-end rule substrate from a physiological source, and elucidates a mechanism for the targeting of G protein gamma subunits for ubiquitylation and degradation.
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Affiliation(s)
- Maria H Hamilton
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA
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81
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Gold SJ, Han MH, Herman AE, Ni YG, Pudiak CM, Aghajanian GK, Liu RJ, Potts BW, Mumby SM, Nestler EJ. Regulation of RGS proteins by chronic morphine in rat locus coeruleus. Eur J Neurosci 2003; 17:971-80. [PMID: 12653973 DOI: 10.1046/j.1460-9568.2003.02529.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The present study explored a possible role for RGS (regulators of G protein signalling) proteins in the long term actions of morphine in the locus coeruleus (LC), a brainstem region implicated in opiate physical dependence and withdrawal. Morphine influences LC neurons through activation of micro -opioid receptors, which, being Gi/o-linked, would be expected to be modulated by RGS proteins. We focused on several RGS subtypes that are known to be expressed in this brain region. Levels of mRNAs encoding RGS2, -3, -4, -5, -7, -8 and -11 are unchanged following chronic morphine, but RGS2 and -4 mRNA levels are increased 2-3-fold 6 h following precipitation of opiate withdrawal. The increases in RGS2 and -4 mRNA peak after 6 h of withdrawal and return to control levels by 24 h. Immunoblot analysis of RGS4 revealed a striking divergence between mRNA and protein responses in LC: protein levels are elevated twofold following chronic morphine and decrease to control values by 6 h of withdrawal. In contrast, levels of RGS7 and -11 proteins, the only other subtypes for which antibodies are available, were not altered by these treatments. Intracellular application of wild-type RGS4, but not a GTPase accelerating-deficient mutant of RGS4, into LC neurons diminished electrophysiological responses to morphine. The observed subtype- and time-specific regulation of RGS4 protein and mRNA, and the diminished morphine-induced currents in the presence of elevated RGS4 protein levels, indicate that morphine induction of RGS4 could contribute to aspects of opiate tolerance and dependence displayed by LC neurons.
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Affiliation(s)
- Stephen J Gold
- Department of Psychiatry, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas TX 75390, USA.
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82
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Esch RK, Errede B. Pheromone induction promotes Ste11 degradation through a MAPK feedback and ubiquitin-dependent mechanism. Proc Natl Acad Sci U S A 2002; 99:9160-5. [PMID: 12077316 PMCID: PMC123111 DOI: 10.1073/pnas.142034399] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2002] [Indexed: 11/18/2022] Open
Abstract
Ste11 is the mitogen-activated protein kinase (MAPK) kinase kinase in the MAPK cascades that mediate mating, high osmolarity glycerol, and filamentous growth responses in Saccharomyces cerevisiae. We show stimulation of the mating pathway by pheromone promotes an accelerated turnover of Ste11 through a MAPK feedback and ubiquitin-dependent mechanism. This degradation is pathway specific, because Ste11 is stable during activation of the high osmolarity glycerol pathway. Because the steady-state amount of Ste11 does not change significantly during pheromone induction, we infer that maintenance of MAPK activation involves repeated cycles in which naive Ste11 is activated and then targeted for degradation. This model predicts that elimination of active Ste11 would rapidly curtail MAPK activation upon attenuation of the upstream signal. This prediction is confirmed by the finding that blocking ubiquitin-dependent Ste11 degradation during pheromone induction abolishes the characteristic attenuation profile for MAPK activation.
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Affiliation(s)
- R K Esch
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
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