1051
|
Loch CM, Cuccherini CL, Leach CA, Strickler JE. Deubiquitylase, deSUMOylase, and deISGylase activity microarrays for assay of substrate preference and functional modifiers. Mol Cell Proteomics 2010; 10:M110.002402. [PMID: 20956615 DOI: 10.1074/mcp.m110.002402] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microarray-based proteomics expanded the information potential of DNA arrays to the level of protein translation and interaction, but so far, not much beyond. Although enzymatic activity from immobilized proteins has been reliably studied using surface plasmon resonance, a microarray of catalytically competent enzymes would facilitate high throughput, parallel study of their function. The ability to localize activity from soluble substrates has frustrated development of such an array. Here, we report the novel use of previously developed, highly specific suicide substrates for three families of enzymes: deubiquitylases, deSUMOylases, and deISGylases. We show specificity of each family to its cognate substrate, and demonstrate utility of the array in a secondary screen of small molecule inhibitors.
Collapse
Affiliation(s)
- Christian M Loch
- Division of Research & Development, LifeSensors, Inc., 271 Great Valley Parkway, Malvern, PA 19355, USA.
| | | | | | | |
Collapse
|
1052
|
Shi D, Grossman SR. Ubiquitin becomes ubiquitous in cancer: emerging roles of ubiquitin ligases and deubiquitinases in tumorigenesis and as therapeutic targets. Cancer Biol Ther 2010; 10:737-47. [PMID: 20930542 DOI: 10.4161/cbt.10.8.13417] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
By virtue of its ability to regulate both protein turnover and non-proteolytic signalling functions, ubiquitin protein conjugation has been implicated in the control of multiple cellular processes, including protein localization, cell cycle control, transcription regulation, DNA damage repair, and endocytosis. Ubiquitin metabolism enzymes have been identified as either oncogenes or tumor suppressors in a variety of cancers. Given that ubiquitin metabolism is governed by enzymes--E1, E2, E3, E4, deubiquitinases (DUBs), and the proteasome- the system as a whole is ripe for target and drug discovery in cancer. Of the ubiquitin/proteasome system components, the E3's and DUBs can recognize substrates with the most specificity, and are thus of key interest as drug targets in cancer. This review examines the molecular role in cancer, relevant substrates, and potential for pharmacologic development, of E3's and DUBs that have been associated thus far with human malignancies as oncogenes or tumor suppressors.
Collapse
Affiliation(s)
- Dingding Shi
- Departments of Cancer Biology, University of Massachusetts Medical School and UMass Memorial Cancer Center, Worcester, MA, USA
| | | |
Collapse
|
1053
|
Todi SV, Scaglione KM, Blount JR, Basrur V, Conlon KP, Pastore A, Elenitoba-Johnson K, Paulson HL. Activity and cellular functions of the deubiquitinating enzyme and polyglutamine disease protein ataxin-3 are regulated by ubiquitination at lysine 117. J Biol Chem 2010; 285:39303-13. [PMID: 20943656 DOI: 10.1074/jbc.m110.181610] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Deubiquitinating enzymes (DUbs) play important roles in many ubiquitin-dependent pathways, yet how DUbs themselves are regulated is not well understood. Here, we provide insight into the mechanism by which ubiquitination directly enhances the activity of ataxin-3, a DUb implicated in protein quality control and the disease protein in the polyglutamine neurodegenerative disorder, Spinocerebellar Ataxia Type 3. We identify Lys-117, which resides near the catalytic triad, as the primary site of ubiquitination in wild type and pathogenic ataxin-3. Further studies indicate that ubiquitin-dependent activation of ataxin-3 at Lys-117 is important for its ability to reduce high molecular weight ubiquitinated species in cells. Ubiquitination at Lys-117 also facilitates the ability of ataxin-3 to induce aggresome formation in cells. Finally, structure-function studies support a model of activation whereby ubiquitination at Lys-117 enhances ataxin-3 activity independent of the known ubiquitin-binding sites in ataxin-3, most likely through a direct conformational change in or near the catalytic domain.
Collapse
Affiliation(s)
- Sokol V Todi
- Department of Neurology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA.
| | | | | | | | | | | | | | | |
Collapse
|
1054
|
Drag M, Salvesen GS. Emerging principles in protease-based drug discovery. Nat Rev Drug Discov 2010; 9:690-701. [PMID: 20811381 DOI: 10.1038/nrd3053] [Citation(s) in RCA: 403] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteases have an important role in many signalling pathways, and represent potential drug targets for diseases ranging from cardiovascular disorders to cancer, as well as for combating many parasites and viruses. Although inhibitors of well-established protease targets such as angiotensin-converting enzyme and HIV protease have shown substantial therapeutic success, developing drugs for new protease targets has proved challenging in recent years. This in part could be due to issues such as the difficulty of achieving selectivity when targeting protease active sites. This Perspective discusses the general principles in protease-based drug discovery, highlighting the lessons learned and the emerging strategies, such as targeting allosteric sites, which could help harness the therapeutic potential of new protease targets.
Collapse
Affiliation(s)
- Marcin Drag
- Program in Apoptosis and Cell Death Research, Burnham Institute for Medical Research, La Jolla, California 92037, USA.
| | | |
Collapse
|
1055
|
Abstract
The NF-kappaB pathway is a ubiquitous stress response that activates the NF-kappaB family of transcription factors. Antigen receptors, receptors of the innate immune system, and certain intracellular stressors are potent activators of this pathway. The transcriptional program that is activated is both antiapoptotic and highly proinflammatory. Indeed, any compromise in engagement of the pathway results in immunodeficiency, whereas constitutive activation generates a sustained inflammatory response that may promote malignancy. As such, NF-kappaB activation is under tight regulation by a number of post-translational modifications, including phosphorylation and ubiquitination. This article attempts to synthesize our current knowledge regarding the regulation of NF-kappaB signaling by ubiquitination, specifically highlighting the biochemical basis for both positive and negative feedback loops that function in unison to generate coordinated signals that are essential for the viability of metazoan animals.
Collapse
Affiliation(s)
- Ingrid E Wertz
- Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080, USA.
| | | |
Collapse
|
1056
|
Tauriello DVF, Maurice MM. The various roles of ubiquitin in Wnt pathway regulation. Cell Cycle 2010; 9:3700-9. [PMID: 20930545 DOI: 10.4161/cc.9.18.13204] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Wnt signaling mediates key developmental and homeostatic processes including stem cell maintenance, growth and cell fate specification, cell polarity and migration. Inappropriate activation of Wnt signaling is linked to a range of human disorders, most notably cancer and neurodegenerative diseases. In the Wnt/β-catenin cascade, signaling events converge on the regulation of ubiquitin-mediated degradation of the crucial transcriptional regulator β-catenin. The emerging mechanisms by which ubiquitin modification of proteins controls cellular pathways comprise both proteolytic and nonproteolytic functions. In nonproteolytic functions, ubiquitin acts as a signaling device in the control of protein activity, subcellular localization and complex formation. Here, we review and discuss recent developments that implicate ubiquitin-mediated mechanisms at multiple steps of Wnt pathway activation.
Collapse
Affiliation(s)
- Daniele V F Tauriello
- Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | |
Collapse
|
1057
|
Kouranti I, McLean JR, Feoktistova A, Liang P, Johnson AE, Roberts-Galbraith RH, Gould KL. A global census of fission yeast deubiquitinating enzyme localization and interaction networks reveals distinct compartmentalization profiles and overlapping functions in endocytosis and polarity. PLoS Biol 2010; 8. [PMID: 20838651 PMCID: PMC2935449 DOI: 10.1371/journal.pbio.1000471] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Accepted: 07/20/2010] [Indexed: 11/20/2022] Open
Abstract
Proteomic, localization, and enzymatic activity screens in fission yeast reveal how deubiquitinating enzyme localization and function are tuned. Ubiquitination and deubiquitination are reciprocal processes that tune protein stability, function, and/or localization. The removal of ubiquitin and remodeling of ubiquitin chains is catalyzed by deubiquitinating enzymes (DUBs), which are cysteine proteases or metalloproteases. Although ubiquitination has been extensively studied for decades, the complexity of cellular roles for deubiquitinating enzymes has only recently been explored, and there are still several gaps in our understanding of when, where, and how these enzymes function to modulate the fate of polypeptides. To address these questions we performed a systematic analysis of the 20 Schizosaccharomyces pombe DUBs using confocal microscopy, proteomics, and enzymatic activity assays. Our results reveal that S. pombe DUBs are present in almost all cell compartments, and the majority are part of stable protein complexes essential for their function. Interestingly, DUB partners identified by our study include the homolog of a putative tumor suppressor gene not previously linked to the ubiquitin pathway, and two conserved tryptophan-aspartate (WD) repeat proteins that regulate Ubp9, a DUB that we show participates in endocytosis, actin dynamics, and cell polarity. In order to understand how DUB activity affects these processes we constructed multiple DUB mutants and find that a quintuple deletion of ubp4 ubp5 ubp9 ubp15 sst2/amsh displays severe growth, polarity, and endocytosis defects. This mutant allowed the identification of two common substrates for five cytoplasmic DUBs. Through these studies, a common regulatory theme emerged in which DUB localization and/or activity is modulated by interacting partners. Despite apparently distinct cytoplasmic localization patterns, several DUBs cooperate in regulating endocytosis and cell polarity. These studies provide a framework for dissecting DUB signaling pathways in S. pombe and may shed light on DUB functions in metazoans. The post-translational modification of proteins by conjugation of monomers or chains of ubiquitin is a regulatory mechanism for tuning protein stability, localization and function. Given these vital functions, ubiquitination has to be highly regulated so that protein degradation and cell signaling are controlled in space and time. Although the ubiquitin-conjugation machinery has been thoroughly studied, there are still several gaps in our understanding of when, where and how ubiquitin is removed by deubiquitinating enzymes (DUBs). To address these questions we performed a systematic analysis of the 20 DUBs in the fission yeast Schizosaccharomyces pombe using confocal microscopy, proteomics and enzymatic activity assays. We first showed that S. pombe DUBs are present in almost all cell compartments and that the majority are part of stable protein complexes essential for their function. Then, we constructed strains mutant for a number of the DUBs involved in the newly identified protein complexes and showed that five cytoplasmic DUBs have redundant roles in controlling endocytosis and cell polarity. We postulate that regulatory networks identified in our study might be conserved and hence shed light on DUB function in metazoans.
Collapse
Affiliation(s)
- Ilektra Kouranti
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Howard Hughes Medical Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Janel R. McLean
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Howard Hughes Medical Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Anna Feoktistova
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Howard Hughes Medical Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Ping Liang
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Howard Hughes Medical Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Alyssa E. Johnson
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Howard Hughes Medical Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Rachel H. Roberts-Galbraith
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Howard Hughes Medical Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Howard Hughes Medical Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- * E-mail:
| |
Collapse
|
1058
|
Lee MJ, Lee BH, Hanna J, King RW, Finley D. Trimming of ubiquitin chains by proteasome-associated deubiquitinating enzymes. Mol Cell Proteomics 2010; 10:R110.003871. [PMID: 20823120 DOI: 10.1074/mcp.r110.003871] [Citation(s) in RCA: 185] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The proteasome generally recognizes substrate via its multiubiquitin chain followed by ATP-dependent unfolding and translocation of the substrate from the regulatory particle into the proteolytic core particle to be degraded. Substrate-bound ubiquitin groups are for the most part not delivered to the core particle and broken down together with substrate but instead recovered as intact free ubiquitin and ubiquitin chains. Substrate deubiquitination on the proteasome is mediated by three distinct deubiquitinating enzymes associated with the regulatory particle: RPN11, UCH37, and USP14. RPN11 cleaves at the base of the ubiquitin chain where it is linked to the substrate, whereas UCH37 and apparently USP14 mediate a stepwise removal of ubiquitin from the substrate by disassembling the chain from its distal tip. In contrast to UCH37 and USP14, RPN11 shows degradation-coupled activity; RPN11-mediated deubiquitination is apparently delayed until the proteasome is committed to degrade the substrate. Accordingly, RPN11-mediated deubiquitination promotes substrate degradation. In contrast, removal of ubiquitin prior to commitment could antagonize substrate degradation by promoting substrate dissociation from the proteasome. Emerging evidence suggests that USP14 and UCH37 can both suppress substrate degradation in this way. One line of study has shown that small molecule USP14 inhibitors can enhance proteasome function in cells, which is consistent with this model. Enhancing protein degradation could potentially have therapeutic applications for diseases involving toxic proteins that are proteasome substrates. However, the responsiveness of substrates to inhibition of proteasomal deubiquitinating enzymes may vary substantially. This substrate specificity and its mechanistic basis should be addressed in future studies.
Collapse
Affiliation(s)
- Min Jae Lee
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | | | | | |
Collapse
|
1059
|
The ubiquitin carboxyl hydrolase BAP1 forms a ternary complex with YY1 and HCF-1 and is a critical regulator of gene expression. Mol Cell Biol 2010; 30:5071-85. [PMID: 20805357 DOI: 10.1128/mcb.00396-10] [Citation(s) in RCA: 198] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The candidate tumor suppressor BAP1 is a deubiquitinating enzyme (DUB) involved in the regulation of cell proliferation, although the molecular mechanisms governing its function remain poorly defined. BAP1 was recently shown to interact with and deubiquitinate the transcriptional regulator host cell factor 1 (HCF-1). Here we show that BAP1 assembles multiprotein complexes containing numerous transcription factors and cofactors, including HCF-1 and the transcription factor Yin Yang 1 (YY1). Through its coiled-coil motif, BAP1 directly interacts with the zinc fingers of YY1. Moreover, HCF-1 interacts with the middle region of YY1 encompassing the glycine-lysine-rich domain and is essential for the formation of a ternary complex with YY1 and BAP1 in vivo. BAP1 activates transcription in an enzymatic-activity-dependent manner and regulates the expression of a variety of genes involved in numerous cellular processes. We further show that BAP1 and HCF-1 are recruited by YY1 to the promoter of the cox7c gene, which encodes a mitochondrial protein used here as a model of BAP1-activated gene expression. Our findings (i) establish a direct link between BAP1 and the transcriptional control of genes regulating cell growth and proliferation and (ii) shed light on a novel mechanism of transcription regulation involving ubiquitin signaling.
Collapse
|
1060
|
Imkamp F, Striebel F, Sutter M, Ozcelik D, Zimmermann N, Sander P, Weber-Ban E. Dop functions as a depupylase in the prokaryotic ubiquitin-like modification pathway. EMBO Rep 2010; 11:791-7. [PMID: 20798673 DOI: 10.1038/embor.2010.119] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 07/25/2010] [Accepted: 07/26/2010] [Indexed: 12/21/2022] Open
Abstract
Post-translational modification of proteins with prokaryotic ubiquitin-like protein (Pup) is the bacterial equivalent of ubiquitination in eukaryotes. Mycobacterial pupylation is a two-step process in which the carboxy-terminal glutamine of Pup is first deamidated by Dop (deamidase of Pup) before ligation of the generated γ-carboxylate to substrate lysines by the Pup ligase PafA. In this study, we identify a new feature of the pupylation system by demonstrating that Dop also acts as a depupylase in the Pup proteasome system in vivo and in vitro. Dop removes Pup from substrates by specific cleavage of the isopeptide bond. Depupylation can be enhanced by the unfolding activity of the mycobacterial proteasomal ATPase Mpa.
Collapse
Affiliation(s)
- Frank Imkamp
- Department of Biology, Eidgenössische Technische Hochschule Zurich, Institute of Molecular Biology and Biophysics, Schafmattstrasse 20, Zurich CH-8093, Switzerland
| | | | | | | | | | | | | |
Collapse
|
1061
|
Burns KE, Cerda-Maira FA, Wang T, Li H, Bishai WR, Darwin KH. "Depupylation" of prokaryotic ubiquitin-like protein from mycobacterial proteasome substrates. Mol Cell 2010; 39:821-7. [PMID: 20705495 DOI: 10.1016/j.molcel.2010.07.019] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 04/07/2010] [Accepted: 06/29/2010] [Indexed: 01/31/2023]
Abstract
Ubiquitin (Ub) provides the recognition and specificity required to deliver proteins to the eukaryotic proteasome for destruction. Prokaryotic ubiquitin-like protein (Pup) is functionally analogous to Ub in Mycobacterium tuberculosis (Mtb), as it dooms proteins to the Mtb proteasome. Studies suggest that Pup and Ub do not share similar mechanisms of activation and conjugation to target proteins. Dop (deamidase of Pup; Mtb Rv2112c/MT2172) deamidates the C-terminal glutamine of Pup to glutamate, preparing it for ligation to target proteins by proteasome accessory factor A (PafA). While studies have shed light on the conjugation of Pup to proteins, it was not known if Pup could be removed from substrates in a manner analogous to the deconjugation of Ub from eukaryotic proteins. Here, we show that Mycobacteria have a "depupylase" activity provided by Dop. The discovery of a depupylase strengthens the parallels between the Pup- and Ub-tagging systems of prokaryotes and eukaryotes, respectively.
Collapse
Affiliation(s)
- Kristin E Burns
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | | | | | | | | | | |
Collapse
|
1062
|
Gorbea C, Pratt G, Ustrell V, Bell R, Sahasrabudhe S, Hughes RE, Rechsteiner M. A protein interaction network for Ecm29 links the 26 S proteasome to molecular motors and endosomal components. J Biol Chem 2010; 285:31616-33. [PMID: 20682791 DOI: 10.1074/jbc.m110.154120] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Ecm29 is a 200-kDa HEAT repeat protein that binds the 26 S proteasome. Genome-wide two-hybrid screens and mass spectrometry have identified molecular motors, endosomal components, and ubiquitin-proteasome factors as Ecm29-interacting proteins. The C-terminal half of human Ecm29 binds myosins and kinesins; its N-terminal region binds the endocytic proteins, Vps11, Rab11-FIP4, and rabaptin. Whereas full-length FLAG-Ecm29, its C-terminal half, and a small central fragment of Ecm29 remain bound to glycerol-gradient-separated 26 S proteasomes, the N-terminal half of Ecm29 does not. Confocal microscopy showed that Ecm-26 S proteasomes are present on flotillin-positive endosomes, but they are virtually absent from caveolin- and clathrin-decorated endosomes. Expression of the small central fragment of Ecm29 markedly reduces proteasome association with flotillin-positive endosomes. Identification of regions within Ecm29 capable of binding molecular motors, endosomal proteins, and the 26 S proteasome supports the hypothesis that Ecm29 serves as an adaptor for coupling 26 S proteasomes to specific cellular compartments.
Collapse
Affiliation(s)
- Carlos Gorbea
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | | | | | | | | | | | | |
Collapse
|
1063
|
Graciet E, Wellmer F. The plant N-end rule pathway: structure and functions. TRENDS IN PLANT SCIENCE 2010; 15:447-453. [PMID: 20627801 DOI: 10.1016/j.tplants.2010.04.011] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2010] [Revised: 04/25/2010] [Accepted: 04/29/2010] [Indexed: 05/29/2023]
Abstract
The N-end rule pathway is a protein degradation pathway that relates the stability of a protein to the nature of its N-terminal amino acid residue. This pathway is part of the ubiquitin-proteasome system in eukaryotes and has been shown to be involved in a multitude of cellular and developmental processes in animals and fungi. However, in plants, its structure and functions have long been enigmatic. In this review, we discuss recent advances in the identification of the enzymatic components that mediate protein degradation through the N-end rule pathway in plants. We further describe the known functions of this pathway in the control of plant growth and development and outline open questions that will likely be the focus of future research.
Collapse
Affiliation(s)
- Emmanuelle Graciet
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
| | | |
Collapse
|
1064
|
Feng L, Wang J, Chen J. The Lys63-specific deubiquitinating enzyme BRCC36 is regulated by two scaffold proteins localizing in different subcellular compartments. J Biol Chem 2010; 285:30982-8. [PMID: 20656690 DOI: 10.1074/jbc.m110.135392] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
BRCC36 is a member of the JAMM/MPN(+) family of zinc metalloproteases that specifically cleaves Lys 63-linked polyubiquitin chains in vitro. We and others showed previously that BRCC36 is a component of the BRCA1-A complex, which consists of RAP80, CCDC98/ABRAXAS, BRCC45/BRE, MERIT40/NBA1, BRCC36, and BRCA1. This complex participates in the regulation of BRCA1 localization in response to DNA damage. Here we provide evidence indicating that BRCC36 regulates the abundance of Lys(63)-linked ubiquitin chains at chromatin and that one of its substrates is diubiquitinated histone H2A. Moreover, besides interacting with CCDC98 within the BRCA1-A complex, BRCC36 also associates with another protein KIAA0157, which shares significant sequence homology with CCDC98. Interestingly, although CCDC98 functions as an adaptor of BRCC36 and regulates BRCC36 activity in the nucleus, KIAA0157 mainly localizes in cytosol and activates BRCC36 in the cytoplasm. Moreover, these two complexes appear to exist in fine balance in vivo because reduction of KIAA0157 expression led to an increase of the BRCA1-A complex in the nucleus. Together, these results suggest that scaffold proteins not only participate in the regulation of BRCC36 activity but also determine its subcellular localization and cellular functions.
Collapse
Affiliation(s)
- Lin Feng
- Department of Experimental Radiation Oncology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA
| | | | | |
Collapse
|
1065
|
Matsumoto ML, Wickliffe KE, Dong KC, Yu C, Bosanac I, Bustos D, Phu L, Kirkpatrick DS, Hymowitz SG, Rape M, Kelley RF, Dixit VM. K11-linked polyubiquitination in cell cycle control revealed by a K11 linkage-specific antibody. Mol Cell 2010; 39:477-84. [PMID: 20655260 DOI: 10.1016/j.molcel.2010.07.001] [Citation(s) in RCA: 306] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Revised: 06/02/2010] [Accepted: 06/29/2010] [Indexed: 01/12/2023]
Abstract
Polyubiquitination is a posttranslational modification where ubiquitin chains containing isopeptide bonds linking one of seven ubiquitin lysines with the C terminus of an adjoining ubiquitin are covalently attached to proteins. While functions of K48- and K63-linked polyubiquitin are understood, the role(s) of noncanonical K11-linked chains is less clear. A crystal structure of K11-linked diubiquitin demonstrates a distinct conformation from K48- or K63-linked diubiquitin. We engineered a K11 linkage-specific antibody and use it to demonstrate that K11 chains are highly upregulated in mitotic human cells precisely when substrates of the ubiquitin ligase anaphase-promoting complex (APC/C) are degraded. These chains increased with proteasomal inhibition, suggesting they act as degradation signals in vivo. Inhibition of the APC/C strongly impeded the formation of K11-linked chains, suggesting that a single ubiquitin ligase is the major source of mitotic K11-linked chains. Our results underscore the importance of K11-linked ubiquitin chains as critical regulators of mitotic protein degradation.
Collapse
Affiliation(s)
- Marissa L Matsumoto
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA 94080, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
1066
|
Song EJ, Werner SL, Neubauer J, Stegmeier F, Aspden J, Rio D, Harper JW, Elledge SJ, Kirschner MW, Rape M. The Prp19 complex and the Usp4Sart3 deubiquitinating enzyme control reversible ubiquitination at the spliceosome. Genes Dev 2010; 24:1434-47. [PMID: 20595234 DOI: 10.1101/gad.1925010] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The spliceosome, a dynamic assembly of proteins and RNAs, catalyzes the excision of intron sequences from nascent mRNAs. Recent work has suggested that the activity and composition of the spliceosome are regulated by ubiquitination, but the underlying mechanisms have not been elucidated. Here, we report that the spliceosomal Prp19 complex modifies Prp3, a component of the U4 snRNP, with nonproteolytic K63-linked ubiquitin chains. The K63-linked chains increase the affinity of Prp3 for the U5 snRNP component Prp8, thereby allowing for the stabilization of the U4/U6.U5 snRNP. Prp3 is deubiquitinated by Usp4 and its substrate targeting factor, the U4/U6 recycling protein Sart3, which likely facilitates ejection of U4 proteins from the spliceosome during maturation of its active site. Loss of Usp4 in cells interferes with the accumulation of correctly spliced mRNAs, including those for alpha-tubulin and Bub1, and impairs cell cycle progression. We propose that the reversible ubiquitination of spliceosomal proteins, such as Prp3, guides rearrangements in the composition of the spliceosome at distinct steps of the splicing reaction.
Collapse
Affiliation(s)
- Eun Joo Song
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
1067
|
Isono E, Katsiarimpa A, Müller IK, Anzenberger F, Stierhof YD, Geldner N, Chory J, Schwechheimer C. The deubiquitinating enzyme AMSH3 is required for intracellular trafficking and vacuole biogenesis in Arabidopsis thaliana. THE PLANT CELL 2010; 22:1826-37. [PMID: 20543027 PMCID: PMC2910964 DOI: 10.1105/tpc.110.075952] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Revised: 05/21/2010] [Accepted: 05/26/2010] [Indexed: 05/18/2023]
Abstract
Ubiquitination, deubiquitination, and the formation of specific ubiquitin chain topologies have been implicated in various cellular processes. Little is known, however, about the role of ubiquitin in the development of cellular organelles. Here, we identify and characterize the deubiquitinating enzyme AMSH3 from Arabidopsis thaliana. AMSH3 hydrolyzes K48- and K63-linked ubiquitin chains in vitro and accumulates both ubiquitin chain types in vivo. amsh3 mutants fail to form a central lytic vacuole, accumulate autophagosomes, and mis-sort vacuolar protein cargo to the intercellular space. Furthermore, AMSH3 is required for efficient endocytosis of the styryl dye FM4-64 and the auxin efflux facilitator PIN2. We thus present evidence for a role of deubiquitination in intracellular trafficking and vacuole biogenesis.
Collapse
Affiliation(s)
- Erika Isono
- Department of Plant Systems Biology, Technische Universität München, 85354 Freising, Germany
- Department of Developmental Genetics, Center for Plant Molecular Biology, Tübingen University, 72076 Tuebingen, Germany
| | - Anthi Katsiarimpa
- Department of Plant Systems Biology, Technische Universität München, 85354 Freising, Germany
- Department of Developmental Genetics, Center for Plant Molecular Biology, Tübingen University, 72076 Tuebingen, Germany
| | - Isabel Karin Müller
- Department of Plant Systems Biology, Technische Universität München, 85354 Freising, Germany
- Department of Developmental Genetics, Center for Plant Molecular Biology, Tübingen University, 72076 Tuebingen, Germany
| | - Franziska Anzenberger
- Department of Plant Systems Biology, Technische Universität München, 85354 Freising, Germany
| | - York-Dieter Stierhof
- Microscopy Unit, Center for Plant Molecular Biology, Tübingen University, 72076 Tuebingen, Germany
| | - Niko Geldner
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute, La Jolla, California 92037
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Joanne Chory
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute, La Jolla, California 92037
| | - Claus Schwechheimer
- Department of Plant Systems Biology, Technische Universität München, 85354 Freising, Germany
- Department of Developmental Genetics, Center for Plant Molecular Biology, Tübingen University, 72076 Tuebingen, Germany
- Address correspondence to
| |
Collapse
|
1068
|
Köhler A, Zimmerman E, Schneider M, Hurt E, Zheng N. Structural basis for assembly and activation of the heterotetrameric SAGA histone H2B deubiquitinase module. Cell 2010; 141:606-17. [PMID: 20434206 PMCID: PMC2901531 DOI: 10.1016/j.cell.2010.04.026] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Revised: 03/22/2010] [Accepted: 04/16/2010] [Indexed: 01/07/2023]
Abstract
Deubiquitinating enzymes (DUBs) regulate diverse cellular functions by cleaving ubiquitin from specific protein substrates. How their activities are modulated in various cellular contexts remains poorly understood. The yeast deubiquitinase Ubp8 protein is recruited and activated by the SAGA complex and, together with Sgf11, Sus1, and Sgf73, forms a DUB module responsible for deubiquitinating histone H2B during gene expression. Here, we report the crystal structure of the complete SAGA DUB module, which features two functional lobes structurally coupled by Sgf73. In the "assembly lobe," a long Sgf11 N-terminal helix is clamped onto the Ubp8 ZnF-UBP domain by Sus1. In the "catalytic lobe," an Sgf11 C-terminal zinc-finger domain binds to the Ubp8 catalytic domain next to its active site. Our structural and functional analyses reveal a central role of Sgf11 and Sgf73 in activating Ubp8 for deubiquitinating histone H2B and demonstrate how a DUB can be allosterically regulated by its nonsubstrate partners.
Collapse
Affiliation(s)
- Alwin Köhler
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany,Correspondence: ;
| | - Erik Zimmerman
- Howard Hughes Medical Institute & Department of Pharmacology, Box 357280, University of Washington, Seattle, WA 98195
| | - Maren Schneider
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Ed Hurt
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Ning Zheng
- Howard Hughes Medical Institute & Department of Pharmacology, Box 357280, University of Washington, Seattle, WA 98195,Correspondence: ;
| |
Collapse
|
1069
|
Sgorbissa A, Potu H, Brancolini C. Isopeptidases in anticancer therapy: looking for inhibitors. Am J Transl Res 2010; 2:235-247. [PMID: 20589164 PMCID: PMC2892408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 05/06/2010] [Indexed: 05/29/2023]
Abstract
Addition of polypeptides belonging to the ubiquitin family to selected lysines residues is a widespread post-translation modification (PTM) that controls many fundamental aspects of cell's life. Specific alterations in the normal turnover of this PTM are frequently observed in tumors. The conjugation/deconjugation cycle of ubiquitin (Ub) or ubiquitin-like (Ubl) proteins influences the activities of oncogenes and tumor suppressor genes. Two families of enzymes work in antagonizing manner to add or remove Ub and Ubl-proteins on target proteins: the E3 ligases and the isopeptidases. These enzymes are the subjects of fervent research with the ambition to comprehend their regulation, their mechanisms of action, their involvement in human diseases, and to develop specific inhibitors for therapeutic intervention. Here we will discuss of isopeptidases, the deconjugating enzymes, with particular emphasis on the proapoptotic activities of the relative inhibitors identified so far.
Collapse
Affiliation(s)
- Andrea Sgorbissa
- Department of Biomedical Sciences and Technologies (DSTB), University of Udine P.le Kolbe 4 3100 Udine, Italy
| | | | | |
Collapse
|
1070
|
Abstract
Clinicians have suspected for hundreds of years that chronic activation of the immune system contributes to the development of cancer. However, the molecular mechanisms that mediate this precarious interplay are only now being elucidated. Recent reports have identified A20 as a crucial tumour suppressor in various lymphomas. A20 is a ubiquitin-editing enzyme that attenuates the activity of proximal signalling complexes at pro-inflammatory receptors. In this Review we summarize the evidence linking chronic inflammation with tumorigenesis and consider how A20 modulates inflammatory signalling cascades, thereby providing a mechanism to explain how deregulation of ubiquitylation can promote tumorigenesis.
Collapse
Affiliation(s)
- Sarah G Hymowitz
- Department of Structural Biology, Genentech, Inc.1 DNA Way, M/S 40, South San Francisco, CA 94080, USA
| | | |
Collapse
|
1071
|
Abstract
Protein degradation is the cell's mechanism of eliminating misfolded or unwanted proteins. The pathway by which proteins are degraded occurs through the ubiquitin-proteasome system. Ubiquitin is a small 9-kD (kDa) protein that is attached to proteins. A minimum of four ubiquitins are required for proteins to be recognized by the degradation machinery, known as the 26S proteasome. Defects in ubiquitination have been identified in a number of diseases, including cancer, neurodegenerative diseases, and metabolic disorders. We sought to exploit the delicate balance between protein synthesis and degradation to treat cancer by designing a chimeric molecule, known as Protac (Proteolysis Targeting Chimeric molecule). Protacs are heterobifunctional nanomolecules that are approximately 10 nm in size and can recruit proteins that cause cancer to the ubiquitin-proteasome machinery for degradation. In this review, we discuss the development of this novel technology for the treatment of cancer.
Collapse
Affiliation(s)
- Kathleen M Sakamoto
- Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA.
| |
Collapse
|
1072
|
Kimura Y, Tanaka K. Regulatory mechanisms involved in the control of ubiquitin homeostasis. J Biochem 2010; 147:793-8. [PMID: 20418328 DOI: 10.1093/jb/mvq044] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Ubiquitin (Ub) modification plays an essential role in the regulation of various cellular processes. Ub performs a remarkable array of cellular tasks through the production of a large number of ubiquitinated proteins; such tasks require many Ubs. Ubs are expressed abundantly from several Ub encoding genes, though not in excess. Rather, Ub expression is tightly regulated through various control mechanisms. Recent studies have shown that the cellular Ub level is regulated by balanced activities of deubiquitinating enzymes and their regulators. Here, we review the current understandings of the regulatory mechanisms that control Ub expression and its metabolism and maintain Ub homeostasis.
Collapse
Affiliation(s)
- Yoko Kimura
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.
| | | |
Collapse
|
1073
|
Setsuie R, Suzuki M, Tsuchiya Y, Wada K. Skeletal muscles of Uchl3 knockout mice show polyubiquitinated protein accumulation and stress responses. Neurochem Int 2010; 56:911-8. [PMID: 20380862 DOI: 10.1016/j.neuint.2010.03.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 03/27/2010] [Accepted: 03/31/2010] [Indexed: 10/19/2022]
Abstract
Ubiquitin C-terminal hydrolase (UCH)-L3 is an enzyme with a strongly suggested de-ubiquitinating function by in vitro studies, but has poorly been investigated in vivo. In this study, we show that skeletal muscles of Uchl3(-/-) mice exhibit the up-regulation of cleaved ATF6, Grp78, and PDI as well as HSP27, HSP70, HSP90 and HSP110, which indicate the induction of stress responses. The prominent accumulation of polyubiquitinated proteins, one of the factors reported to induce stress responses, was observed in the skeletal muscle of Uchl3(-/-) mice. Mouse embryonic fibroblasts (MEFs) from Uchl3(-/-) mice also showed an accumulation of polyubiquitinated proteins. Moreover, the polyubiquitinated protein accumulation in Uchl3(-/-) MEFs was attenuated by the exogenous expression of wild-type, but not hydrolase activity deficient, UCH-L3. In addition, wild-type, but not its hydrolase activity or ubiquitin binding activity deficient UCH-L3 showed the ability to cleave ubiquitin from polyubiquitinated lysozyme in vitro. These results suggest that UCH-L3 functions as a de-ubiquitinating enzyme in vivo where lack of its hydrolase activity may result in the prominent accumulation of ubiquitinated proteins and subsequent induction of stress responses in skeletal muscle.
Collapse
Affiliation(s)
- Rieko Setsuie
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo 187-8502, Japan
| | | | | | | |
Collapse
|
1074
|
Willis MS, Townley-Tilson WHD, Kang EY, Homeister JW, Patterson C. Sent to destroy: the ubiquitin proteasome system regulates cell signaling and protein quality control in cardiovascular development and disease. Circ Res 2010; 106:463-78. [PMID: 20167943 DOI: 10.1161/circresaha.109.208801] [Citation(s) in RCA: 161] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The ubiquitin proteasome system (UPS) plays a crucial role in biological processes integral to the development of the cardiovascular system and cardiovascular diseases. The UPS prototypically recognizes specific protein substrates and places polyubiquitin chains on them for subsequent destruction by the proteasome. This system is in place to degrade not only misfolded and damaged proteins, but is essential also in regulating a host of cell signaling pathways involved in proliferation, adaptation to stress, regulation of cell size, and cell death. During the development of the cardiovascular system, the UPS regulates cell signaling by modifying transcription factors, receptors, and structural proteins. Later, in the event of cardiovascular diseases as diverse as atherosclerosis, cardiac hypertrophy, and ischemia/reperfusion injury, ubiquitin ligases and the proteasome are implicated in protecting and exacerbating clinical outcomes. However, when misfolded and damaged proteins are ubiquitinated by the UPS, their destruction by the proteasome is not always possible because of their aggregated confirmations. Recent studies have discovered how these ubiquitinated misfolded proteins can be destroyed by alternative "specific" mechanisms. The cytosolic receptors p62, NBR, and histone deacetylase 6 recognize aggregated ubiquitinated proteins and target them for autophagy in the process of "selective autophagy." Even the ubiquitination of multiple proteins within whole organelles that drive the more general macro-autophagy may be due, in part, to similar ubiquitin-driven mechanisms. In summary, the crosstalk between the UPS and autophagy highlight the pivotal and diverse roles the UPS plays in maintaining protein quality control and regulating cardiovascular development and disease.
Collapse
Affiliation(s)
- Monte S Willis
- Division of Cardiology, McAllister Heart Institute, University of North Carolina at Chapel Hill, 8200 Medical Biomolecular Research Building, Chapel Hill, NC 27599-7126, USA
| | | | | | | | | |
Collapse
|
1075
|
Nakayama K. Growth and progression of melanoma and non-melanoma skin cancers regulated by ubiquitination. Pigment Cell Melanoma Res 2010; 23:338-51. [DOI: 10.1111/j.1755-148x.2010.00692.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
1076
|
A deneddylase encoded by Epstein-Barr virus promotes viral DNA replication by regulating the activity of cullin-RING ligases. Nat Cell Biol 2010; 12:351-61. [PMID: 20190741 DOI: 10.1038/ncb2035] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Accepted: 02/03/2010] [Indexed: 12/30/2022]
Abstract
The large tegument proteins of herpesviruses encode conserved cysteine proteases of unknown function. Here we show that BPLF1, the Epstein-Barr-virus-encoded member of this protease family, is a deneddylase that regulates virus production by modulating the activity of cullin-RING ligases (CRLs). BPLF1 hydrolyses NEDD8 conjugates in vitro, acts as a deneddylase in vivo, binds to cullins and stabilizes CRL substrates. Expression of BPLF1 alone or in the context of the productive virus cycle induces accumulation of the licensing factor CDT1 and deregulates S-phase DNA synthesis. Inhibition of BPLF1 during the productive virus cycle prevents cellular DNA re-replication and inhibits virus replication. Viral DNA synthesis is restored by overexpression of CDT1. Homologues encoded by other herpesviruses share the deneddylase activity. Thus, these enzymes are likely to have a key function in the virus life cycle by inducing a replication-permissive S-phase-like cellular environment.
Collapse
|
1077
|
Kee Y, Yang K, Cohn MA, Haas W, Gygi SP, D'Andrea AD. WDR20 regulates activity of the USP12 x UAF1 deubiquitinating enzyme complex. J Biol Chem 2010; 285:11252-7. [PMID: 20147737 DOI: 10.1074/jbc.m109.095141] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The UAF1 (Usp1-associated factor 1) protein binds and stimulates three deubiquitinating enzymes: USP1, USP12, and USP46. Although the USP1 x UAF1 complex is required for regulation of the Fanconi anemia (FA) DNA repair pathway, less is known about the USP12 x UAF1 and the USP46 x UAF1 complexes. To understand further the nature of the USP12 and USP46 complexes, we attempted to identify proteins that interact with the USP12 and USP46 deubiquitinating enzyme complexes. We identified WDR20, a WD40-repeat containing protein, as a common binding partner of UAF1, USP12, and USP46. Further analysis showed that WDR20 associates exclusively with USP12 and USP46, not with USP1. Furthermore, we demonstrate the purification of a ternary USP12 x UAF1 x WDR20 complex. Interestingly, and consistent with the binding assays, WDR20 stimulated the enzymatic activity of USP12 x UAF1, but not of USP1 x UAF1. Consistent with our previous report that USP12 and USP46 do not regulate the FA pathway, small interference RNA-mediated depletion of WDR20 protein did not affect the FA pathway or DNA damage responses. We provide a model in which WDR20 serves as a stimulatory subunit for preserving and regulating the activity of the subset of the UAF1 x USP complexes.
Collapse
Affiliation(s)
- Younghoon Kee
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | | | | | | | | | | |
Collapse
|
1078
|
Sacco JJ, Coulson JM, Clague MJ, Urbé S. Emerging roles of deubiquitinases in cancer-associated pathways. IUBMB Life 2010; 62:140-57. [PMID: 20073038 PMCID: PMC7165618 DOI: 10.1002/iub.300] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 12/05/2009] [Indexed: 01/11/2023]
Abstract
Deubiquitinases (DUBs) are emerging as important regulators of many pathways germane to cancer. They may regulate the stability of key oncogenes, exemplified by USP28 stabilisation of c-Myc. Alternatively they can negatively regulate ubiquitin-dependent signalling cascades such as the NF-kappaB activation pathway. We review the current literature that associates DUBs with cancer and discuss their suitability as drug targets of the future.
Collapse
Affiliation(s)
- Joseph J. Sacco
- Physiological Laboratory, School of Biomedical Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Judy M. Coulson
- Physiological Laboratory, School of Biomedical Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Michael J. Clague
- Physiological Laboratory, School of Biomedical Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Sylvie Urbé
- Physiological Laboratory, School of Biomedical Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| |
Collapse
|
1079
|
Abstract
The intimate relationship between DNA double-strand break (DSB) repair and cancer susceptibility has sparked profound interest in how transactions on DNA and chromatin surrounding DNA damage influence genome integrity. Recent evidence implicates a substantial commitment of the cellular DNA damage response machinery to the synthesis, recognition, and hydrolysis of ubiquitin chains at DNA damage sites. In this review, we propose that, in order to accommodate parallel processes involved in DSB repair and checkpoint signaling, DSB-associated ubiquitin structures must be nonuniform, using different linkages for distinct functional outputs. We highlight recent advances in the study of nondegradative ubiquitin signaling at DSBs, and discuss how recognition of different ubiquitin structures may influence DNA damage responses.
Collapse
Affiliation(s)
- Troy E Messick
- Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | | |
Collapse
|
1080
|
Burns KE, Darwin KH. Pupylation versus ubiquitylation: tagging for proteasome-dependent degradation. Cell Microbiol 2010; 12:424-31. [PMID: 20109157 DOI: 10.1111/j.1462-5822.2010.01447.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Prokaryotic ubiquitin-like protein (Pup) is the first identified prokaryotic protein that is functionally analogous to ubiquitin. Despite using the proteasome as the end-point for proteolysis, Pup differs from ubiquitin both biochemically and structurally. We will discuss these differences that have been highlighted by several recent studies. Finally, we will speculate on the possible interactions between the two analogous pathways in pathogen and host.
Collapse
Affiliation(s)
- Kristin E Burns
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA.
| | | |
Collapse
|
1081
|
Abstract
Ubiquitin chains are assembled, when a ubiquitin is connected to one of the seven Lys residues or the amino-terminus of a ubiquitin molecule already attached to a substrate. K48-linked ubiquitin chains target proteins for degradation by the 26S proteasome, while those chains connected through K63 regulate intracellular signaling cascades independently of protein degradation. Although all other linkages are detected in cells, their function is not well understood. Here, we review recent progress in delineating substrates, enzymes and functions of K11-linked ubiquitin chains. In particular, we discuss the mechanism of assembly for K11-linked chains by the human anaphase-promoting complex and its physiological E2s UbcH10 and Ube2S and we speculate on the particularities of these noncanonical chains in cells.
Collapse
Affiliation(s)
- Michael Rape
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, 94720, USA,
| |
Collapse
|
1082
|
Abstract
Removal of ubiquitin from modified proteins is an important process to regulate the ubiquitin system. Roughly 100 dedicated enzymes for this purpose, the deubiquitinases, exist in human cells and are intricately involved in a wide variety of cellular processes, although many enzymes remain unstudied to date. The deubiquitinases consist of five enzyme families that contain USP, OTU, UCH, Josephin, or JAMM/MPN+ domains providing catalytic activity. We now understand the catalytic mechanisms of all deubiquitinase families from structural work and more importantly, have obtained insight into an unanticipated variety of ways to exercise specificity. It emerges that deubiquitinases exploit the entire complexity of the ubiquitin system by recognizing their substrates, particular ubiquitin chain linkages and even the position within a ubiquitin chain. This chapter describes the mechanisms of deubiquitination and the different layers of deubiquitinase specificity. The individual deubiquitinase families are discussed with a focus on structure, regulation and specificity features for selected enzymes.
Collapse
Affiliation(s)
- David Komander
- Protein and Nucleic Acid Chemistry Division, Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK,
| |
Collapse
|
1083
|
Wong EWP, Cheng CY. Polarity proteins and cell-cell interactions in the testis. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2009; 278:309-53. [PMID: 19815182 DOI: 10.1016/s1937-6448(09)78007-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In mammalian testes, extensive junction restructuring takes place in the seminiferous epithelium at the Sertoli-Sertoli and Sertoli-germ cell interface to facilitate the different cellular events of spermatogenesis, such as mitosis, meiosis, spermiogenesis, and spermiation. Recent studies in the field have shown that Rho GTPases and polarity proteins play significant roles in the events of cell-cell interactions. Furthermore, Rho GTPases, such as Cdc42, are working in concert with polarity proteins in regulating cell polarization and cell adhesion at both the blood-testis barrier (BTB) and apical ectoplasmic specialization (apical ES) in the testis of adult rats. In this chapter, we briefly summarize recent findings on the latest status of research and development regarding Cdc42 and polarity proteins and how they affect cell-cell interactions in the testis and other epithelia. More importantly, we provide a new model in which how Cdc42 and components of the polarity protein complexes work in concert with laminin fragments, cytokines, and testosterone to regulate the events of cell-cell interactions in the seminiferous epithelium via a local autocrine-based regulatory loop known as the apical ES-BTB-basement membrane axis. This new functional axis coordinates various cellular events during different stages of the seminiferous epithelium cycle of spermatogenesis.
Collapse
Affiliation(s)
- Elissa W P Wong
- Mary M. Wohlford Laboratory for Male Contraceptive Research, Center for Biomedical Research, Population Council, New York, New York 10065, USA
| | | |
Collapse
|
1084
|
Sundaram P, Pang Z, Miao M, Yu L, Wing SS. USP19-deubiquitinating enzyme regulates levels of major myofibrillar proteins in L6 muscle cells. Am J Physiol Endocrinol Metab 2009; 297:E1283-90. [PMID: 19773579 DOI: 10.1152/ajpendo.00409.2009] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The ubiquitin-proteasome system plays an important role in the degradation of myofibrillar proteins that occurs in muscle wasting. Many studies have demonstrated the importance of enzymes mediating conjugation of ubiquitin. However, little is known about the role of deubiquitinating enzymes. We previously showed that the USP19-deubiquitinating enzyme is induced in atrophying skeletal muscle (Combaret L, Adegoke OA, Bedard N, Baracos V, Attaix D, Wing SS. Am J Physiol Endocrinol Metab 288: E693-E700, 2005). To further explore the role of USP19, we used small interfering RNA (siRNA) in L6 muscle cells. Lowering USP19 by 70-90% in myotubes resulted in a 20% decrease in the rate of proteolysis and an 18% decrease in the rate of protein synthesis, with no net change in protein content. Despite the decrease in overall synthesis, there were approximately 1.5-fold increases in protein levels of myosin heavy chain (MHC), actin, and troponin T and a approximately 2.5-fold increase in tropomyosin. USP19 depletion also increased MHC and tropomyosin mRNA levels, suggesting that this effect is due to increased transcription. Consistent with this, USP19 depletion increased myogenin protein and mRNA levels approximately twofold. Lowering myogenin using siRNA prevented the increase in MHC and tropomyosin upon USP19 depletion, indicating that myogenin mediated the increase in myofibrillar proteins. Dexamethasone treatment lowered MHC and increased USP19. Depletion of USP19 reversed the dexamethasone suppression of MHC. These studies demonstrate that USP19 modulates transcription of major myofibrillar proteins and indicate that the ubiquitin system not only mediates the increased protein breakdown but is also involved in the decreased protein synthesis in atrophying skeletal muscle.
Collapse
Affiliation(s)
- Priyanka Sundaram
- Department of Medicine, Polypeptide Laboratory, McGill University and the McGill University Health Centre Research Institute, Montreal, Canada
| | | | | | | | | |
Collapse
|
1085
|
Nishio K, Kim SW, Kawai K, Mizushima T, Yamane T, Hamazaki J, Murata S, Tanaka K, Morimoto Y. Crystal structure of the de-ubiquitinating enzyme UCH37 (human UCH-L5) catalytic domain. Biochem Biophys Res Commun 2009; 390:855-60. [DOI: 10.1016/j.bbrc.2009.10.062] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Accepted: 10/13/2009] [Indexed: 11/17/2022]
|
1086
|
Abstract
Protein ubiquitination and protein phosphorylation are two fundamental regulatory post-translational modifications controlling intracellular signalling events. However, the ubiquitin system is vastly more complex compared with phosphorylation. This is due to the ability of ubiquitin to form polymers, i.e. ubiquitin chains, of at least eight different linkages. The linkage type of the ubiquitin chain determines whether a modified protein is degraded by the proteasome or serves to attract proteins to initiate signalling cascades or be internalized. The present review focuses on the emerging complexity of the ubiquitin system. I review what is known about individual chain types, and highlight recent advances that explain how the ubiquitin system achieves its intrinsic specificity. There is much to be learnt from the better-studied phosphorylation system, and many key regulatory mechanisms underlying control by protein phosphorylation may be similarly employed within the ubiquitin system. For example, ubiquitination may have important allosteric roles in protein regulation that are currently not appreciated.
Collapse
|
1087
|
Abstract
Although the critical role of T-cell receptor (TCR) microclusters in T-cell activation is now widely accepted, the mechanisms of regulation of these TCR-rich structures, which also contain enzymes, adapters, and effectors, remain poorly defined. Soon after microcluster formation, several signaling proteins rapidly dissociate from the TCR. Recent studies from our laboratory demonstrated that the movement of the adapters linker for activation of T cells (LAT) and Src homology 2 domain-containing leukocyte protein of 76 kDa (SLP-76) away from initial microcluster formation sites represents endocytic events. Ubiquitylation, Cbl proteins, and multiple endocytic pathways are involved in the internalization events that disassemble signaling microclusters. Several recent studies have indicated that microcluster movement and centralization plays an important role in signal termination. We suggest that microcluster movement is directly linked to endocytic events, thus implicating endocytosis of microclusters as a means to regulate signaling output of the T cell.
Collapse
Affiliation(s)
- Lakshmi Balagopalan
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Valarie A. Barr
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lawrence E. Samelson
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
1088
|
Xu M, Takanashi M, Oikawa K, Tanaka M, Nishi H, Isaka K, Kudo M, Kuroda M. USP15 plays an essential role for caspase-3 activation during Paclitaxel-induced apoptosis. Biochem Biophys Res Commun 2009; 388:366-71. [DOI: 10.1016/j.bbrc.2009.08.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 08/02/2009] [Indexed: 10/20/2022]
|
1089
|
|
1090
|
Abstract
Deubiquitinating enzymes (DUBs) act on ubiquitinated substrates to regulate their modification and stability. In this issue, Sowa et al. (2009) present a comprehensive proteomic analysis of DUB interacting proteins in humans and a new quantitative scoring system for hits (CompPASS), providing a resource that links DUBs to biological pathways.
Collapse
|