151
|
Ouchida R, Yamasaki S, Hikida M, Masuda K, Kawamura K, Wada A, Mochizuki S, Tagawa M, Sakamoto A, Hatano M, Tokuhisa T, Koseki H, Saito T, Kurosaki T, Wang JY. A Lysosomal Protein Negatively Regulates Surface T Cell Antigen Receptor Expression by Promoting CD3ζ-Chain Degradation. Immunity 2008; 29:33-43. [PMID: 18619870 DOI: 10.1016/j.immuni.2008.04.024] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Revised: 02/22/2008] [Accepted: 04/14/2008] [Indexed: 11/29/2022]
Affiliation(s)
- Rika Ouchida
- Laboratory for Immune Diversity, Research Center for Allergy and Immunology, RIKEN Yokohama Institute, Yokohama 230-0045, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
152
|
Semangoen T, Sinchaikul S, Chen ST, Thongboonkerd V. Proteomic analysis of altered proteins in distal renal tubular cells in response to calcium oxalate monohydrate crystal adhesion: Implications for kidney stone disease. Proteomics Clin Appl 2008; 2:1099-109. [DOI: 10.1002/prca.200780136] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Indexed: 11/05/2022]
|
153
|
|
154
|
Antoniou AN, Powis SJ. Pathogen evasion strategies for the major histocompatibility complex class I assembly pathway. Immunology 2008; 124:1-12. [PMID: 18284468 DOI: 10.1111/j.1365-2567.2008.02804.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Major histocompatibility complex (MHC) class I molecules bind and present short antigenic peptides from endogenously or exogenously derived sources to CD8(+) cytotoxic T lymphocytes (CTL), with recognition of a foreign peptide normally targeting the cell for lysis. It is generally thought that the high level of MHC polymorphism, which is concentrated mostly within the peptide-binding groove, is driven by the 'evolutionary arms race' against pathogens. Many pathogens have developed novel and intriguing mechanisms for evading the continuous sampling of the intracellular and intercellular environments by MHC molecules, none more so than viruses. The characterization of immunoevasion mechanisms has improved our understanding of MHC biology. This review will highlight our current understanding of the MHC class I biosynthetic pathway and how it has been exploited by pathogens, especially viruses, to potentially evade CTL recognition.
Collapse
Affiliation(s)
- Antony N Antoniou
- Department of Immunology & Molecular Pathology, Division of Infection & Immunity, University College London, Windeyer Institute of Medical Science, London, UK.
| | | |
Collapse
|
155
|
Roth G, Freund S, Möhrle B, Wöllner K, Brünjes J, Gauglitz G, Wiesmüller KH, Jung G. Ubiquitin binds to a short peptide segment of hydrolase UCH-L3: a study by FCS, RIfS, ITC and NMR. Chembiochem 2008; 8:323-31. [PMID: 17211910 DOI: 10.1002/cbic.200600254] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Screening for small peptidic affinity tags for the detection of ubiquitin and ubiquitinated proteins yielded the dodecapeptide amide DPDELRFNAIAL-NH(2) as a specific ubiquitin-interacting ligand. A peptide collection--based on crystal structures with ubiquitin-interacting proteins--was designed and confirmed by sequence comparison of ubiquitin-interacting motifs. Four independent physical detection methods demonstrated that the peptide binds to monomeric ubiquitin with an affinity of about 10 muM and with fast on and off rates. Fluorescence correlation spectroscopy with fluorescent peptides showed specific interaction with ubiquitin. Reflectometric interference spectroscopy with surface-immobilized peptides and isothermal calorimetry measurements confirmed the specific binding of ubiquitin and fast rate constants. (1)H,(15)N heteronuclear NMR localised the interaction site across the beta sheet of ubiquitin. The peptide aligns well with the ubiquitin-interacting motif and represents a lead structure for the rational design of high-affinity tags for targeting ubiquitinated protein in vitro and in vivo.
Collapse
Affiliation(s)
- Günter Roth
- Institut für Organische Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | | | | | | | | | | | | | | |
Collapse
|
156
|
Santonico E, Panni S, Falconi M, Castagnoli L, Cesareni G. Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction. BMC BIOCHEMISTRY 2007; 8:29. [PMID: 18154663 PMCID: PMC2238750 DOI: 10.1186/1471-2091-8-29] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2007] [Accepted: 12/21/2007] [Indexed: 11/10/2022]
Abstract
Background Eps15 homology (EH) domains are protein interaction modules binding to peptides containing Asn-Pro-Phe (NPF) motifs and mediating critical events during endocytosis and signal transduction. The EH domain of POB1 associates with Eps15, a protein characterized by a striking string of DPF triplets, 15 in human and 13 in mouse Eps15, at the C-terminus and lacking the typical EH-binding NPF motif. Results By screening a multivalent nonapeptide phage display library we have demonstrated that the EH domain of POB1 has a different recognition specificity since it binds to both NPF and DPF motifs. The region of mouse Eps15 responsible for the interaction with the EH domain of POB1 maps within a 18 amino acid peptide (residues 623–640) that includes three DPF repeats. Finally, mutational analysis in the EH domain of POB1, revealed that several solvent exposed residues, while distal to the binding pocket, mediate specific recognition of binding partners through both hydrophobic and electrostatic contacts. Conclusion In the present study we have analysed the binding specificity of the POB1 EH domain. We show that it differs from other EH domains since it interacts with both NPF- and DPF-containing sequences. These unusual binding properties could be attributed to a different conformation of the binding pocket that allows to accommodate negative charges; moreover, we identified a cluster of solvent exposed Lys residues, which are only found in the EH domain of POB1, and influence binding to both NPF and DPF motifs. The characterization of structures of the DPF ligands described in this study and the POB1 EH domain will clearly determine the involvement of the positive patch and the rationalization of our findings.
Collapse
Affiliation(s)
- Elena Santonico
- Department of Biology, University of Rome Tor Vergata, Rome, Italy.
| | | | | | | | | |
Collapse
|
157
|
Elangovan M, Choi ES, Jang BG, Kim MS, Yoo YJ. The ubiquitin-interacting motif of 26S proteasome subunit S5a induces A549 lung cancer cell death. Biochem Biophys Res Commun 2007; 364:226-30. [PMID: 17949686 DOI: 10.1016/j.bbrc.2007.09.127] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Accepted: 09/25/2007] [Indexed: 10/22/2022]
Abstract
The subunit S5a is a key component for the recruitment of ubiquitinated substrates to the 26S proteasome. When the full-length S5a, the N-terminal half of S5a (S5aN) containing the von Willebrand A (vWA) domain, and the C-terminal half of S5a (S5aC) containing two ubiquitin(Ub)-interacting motifs (UIMs) were ectopically expressed in HEK293 cells, Ub-conjugates accumulated most prominently in S5aC-expressing cells. In addition, S5aC induced A549 lung cancer cell death but not non-cancer BEAS-2B cell death. Similar effects were observed using only S5a-UIMs. Our data therefore suggest that S5a-UIMs can be used as upstream inhibitors of the proteasome pathway.
Collapse
Affiliation(s)
- Muthukumar Elangovan
- Department of Life Science, Gwangju Institute of Science & Technology (GIST), 1 Oryong-dong Buk-ku, Gwangju, Republic of Korea
| | | | | | | | | |
Collapse
|
158
|
Yi H, Friedman JL, Ferreira PA. The cyclophilin-like domain of Ran-binding protein-2 modulates selectively the activity of the ubiquitin-proteasome system and protein biogenesis. J Biol Chem 2007; 282:34770-8. [PMID: 17911097 DOI: 10.1074/jbc.m706903200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) plays a critical role in protein degradation. The 19S regulatory particle (RP) of the 26S proteasome mediates the recognition, deubiquitylation, unfolding, and channeling of ubiquitylated substrates to the 20S proteasome. Several subunits of the 19S RP interact with a growing number of factors. The cyclophilin-like domain (CLD) of Ran-binding protein-2 (RanBP2/Nup358) associates specifically with at least one subunit, S1, of the base subcomplex of the 19S RP, but the functional implications of this interaction on the UPS activity are elusive. This study shows the CLD of RanBP2 promotes selectively the accumulation of a subset of reporter substrates of the UPS, such as the ubiquitin (Ub)-fusion yellow fluorescent protein (YFP) degradation substrate, Ub(G76V)-YFP, and the N-end rule substrate, Ub-R-YFP. Conversely, the degradation of endoplasmic reticulum and misfolded proteins, and of those linked to UPS-independent degradation, is not affected by CLD. The selective effect of CLD on the UPS in vivo is independent of, and synergistic with, proteasome inhibitors, and CLD does not affect the intrinsic proteolytic activity of the 20S proteasome. The inhibitory activity of CLD on the UPS resides in a purported SUMO binding motif. We also found two RanBP2 substrates, RanGTPase-activating protein and retinitis pigmentosa GTPase regulator interacting protein-1alpha1, whose steady-state levels are selectively modulated by CLD. Hence, the CLD of RanBP2 acts as a novel auxiliary modulator of the UPS activity; it may contribute to the molecular and subcellular compartmentation of the turnover of properly folded proteins and modulation of the expressivity of several neurological diseases.
Collapse
Affiliation(s)
- Haiqing Yi
- Department of Ophthalmology, Duke University, Medical Center, Durham, North Carolina 27710, USA
| | | | | |
Collapse
|
159
|
Hasskarl J, Mern DS, Münger K. Interference of the dominant negative helix-loop-helix protein ID1 with the proteasomal subunit S5A causes centrosomal abnormalities. Oncogene 2007; 27:1657-64. [PMID: 17891176 DOI: 10.1038/sj.onc.1210808] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The inhibitor of DNA-binding (ID) proteins are dominant-negative inhibitors of basic helix-loop-helix transcription factors that have multiple functions during development and cellular differentiation. High-level expression of some ID family members has been observed in human malignancies, and in some cases was correlated with poor clinical prognosis. Ectopic ID1 expression extends the life span of primary human epithelial cells, inhibits cellular differentiation and induces centrosome duplication errors, thus suggesting that ID1 may have oncogenic activities. ID1 can bind to the proteasomal subunit S5A/Rpn10, but the biological consequences of the interaction have not been studied in detail. Here, we show that ID1's ability to induce supernumerary centrosomes correlates with S5A binding. Similar to ID1, a fraction of the S5A protein localizes to centrosomal structures. Furthermore, partial depletion of S5A by RNA interference causes accumulation of cells with supernumerary centrosomes. These results are consistent with the model that ID1 dysregulates centrosome homeostasis at least in part by interfering with S5A activities at the centrosome.
Collapse
Affiliation(s)
- J Hasskarl
- Division of Hematology and Oncology, University of Freiburg Medical Center, Freiburg im Breisgau, Germany.
| | | | | |
Collapse
|
160
|
Tayama Y, Kawahara H, Minami R, Shimada M, Yokosawa H. Association of Rpn10 with high molecular weight complex is enhanced during retinoic acid-induced differentiation of neuroblastoma cells. Mol Cell Biochem 2007; 306:53-7. [PMID: 17668154 DOI: 10.1007/s11010-007-9553-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Accepted: 07/12/2007] [Indexed: 01/19/2023]
Abstract
The ubiquitin-binding Rpn10 protein serves as an ubiquitin receptor that delivers client proteins to the 26S proteasome, the protein degradation complex. It has been suggested that the ubiquitin-dependent protein degradation is critical for neuronal differentiation and for preventing neurodegenerative diseases. Our previous study indicated the importance of Rpn10 in control of cellular differentiation (Shimada et al., Mol Biol Cell 17:5356-5371, 2006), though the functional relevance of Rpn10 in neuronal cell differentiation remains a mystery to be uncovered. In the present study, we have examined the level of Rpn10 in a proteasome-containing high molecular weight (HMW) protein fraction prepared from the mouse neuroblastoma cell line Neuro2a. We here report that the protein level of Rpn10 in HMW fraction from un-differentiated Neuro2a cells was significantly lower than that of other cultured cell lines. We have found that retinoic acid-induced neural differentiation of Neuro2a cells significantly stimulates the incorporation of Rpn10 into HMW fractions, although the amounts of 26S proteasome subunits were not changed. Our findings provide the first evidence that the modulation of Rpn10 is linked to the control of retinoic acid-induced differentiation of neuroblastoma cells.
Collapse
Affiliation(s)
- Yoko Tayama
- Department of Biochemistry, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | | | | | | | | |
Collapse
|
161
|
Le TM, Wong HH, Tay FPL, Fang S, Keng CT, Tan YJ, Liu DX. Expression, post-translational modification and biochemical characterization of proteins encoded by subgenomic mRNA8 of the severe acute respiratory syndrome coronavirus. FEBS J 2007; 274:4211-22. [PMID: 17645546 PMCID: PMC7164070 DOI: 10.1111/j.1742-4658.2007.05947.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The most striking difference between the subgenomic mRNA8 of severe acute respiratory syndrome coronavirus isolated from human and some animal species is the deletion of 29 nucleotides, resulting in splitting of a single ORF (ORF8) into two ORFs (ORF8a and ORF8b). ORF8a and ORF8b are predicted to encode two small proteins, 8a and 8b, and ORF8 a single protein, 8ab (a fusion form of 8a and 8b). To understand the functions of these proteins, we cloned cDNA fragments covering these ORFs into expression plasmids, and expressed the constructs in both in vitro and in vivo systems. Expression of a construct containing ORF8a and ORF8b generated only a single protein, 8a; no 8b protein expression was obtained. Expression of a construct containing ORF8 generated the 8ab fusion protein. Site‐directed mutagenesis and enzymatic treatment revealed that protein 8ab is modified by N‐linked glycosylation on the N81 residue and by ubiquitination. In the absence of the 8a region, protein 8b undergoes rapid degradation by proteasomes, and addition of proteasome inhibitors inhibits the degradation of protein 8b as well as the protein 8b‐induced rapid degradation of the severe acute respiratory syndrome coronavirus E protein. Glycosylation could also stabilize protein 8ab. More interestingly, the two proteins could bind to monoubiquitin and polyubiquitin, suggesting the potential involvement of these proteins in the pathogenesis of severe acute respiratory syndrome coronavirus.
Collapse
Affiliation(s)
- Tra M Le
- Department of Biological Sciences, National University of Singapore, Singapore
| | | | | | | | | | | | | |
Collapse
|
162
|
Mayor T, Graumann J, Bryan J, MacCoss MJ, Deshaies RJ. Quantitative profiling of ubiquitylated proteins reveals proteasome substrates and the substrate repertoire influenced by the Rpn10 receptor pathway. Mol Cell Proteomics 2007; 6:1885-95. [PMID: 17644757 DOI: 10.1074/mcp.m700264-mcp200] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ubiquitin proteasome system (UPS) comprises hundreds of different conjugation/deconjugation enzymes and multiple receptors that recognize ubiquitylated proteins. A formidable challenge to deciphering the biology of ubiquitin is to map the networks of substrates and ligands for components of the UPS. Several different receptors guide ubiquitylated substrates to the proteasome, and neither the basis for specificity nor the relative contribution of each pathway is known. To address how broad of a role the ubiquitin receptor Rpn10 (S5a) plays in turnover of proteasome substrates, we implemented a method to perform quantitative analysis of ubiquitin conjugates affinity-purified from experimentally perturbed and reference cultures of Saccharomyces cerevisiae that were differentially labeled with 14N and 15N isotopes. Shotgun mass spectrometry coupled with relative quantification using metabolic labeling and statistical analysis based on q values revealed ubiquitylated proteins that increased or decreased in level in response to a particular treatment. We first identified over 225 candidate UPS substrates that accumulated as ubiquitin conjugates upon proteasome inhibition. To determine which of these proteins were influenced by Rpn10, we evaluated the ubiquitin conjugate proteomes in cells lacking either the entire Rpn10 (rpn10delta) (or only its UIM (ubiquitin-interacting motif) polyubiquitin-binding domain (uimdelta)). Twenty-seven percent of the UPS substrates accumulated as ubiquitylated species in rpn10delta cells, whereas only one-fifth as many accumulated in uimdelta cells. These findings underscore a broad role for Rpn10 in turnover of ubiquitylated substrates but a relatively modest role for its ubiquitin-binding UIM domain. This approach illustrates the feasibility of systems-level quantitative analysis to map enzyme-substrate networks in the UPS.
Collapse
Affiliation(s)
- Thibault Mayor
- Howard Hughes Medical Institute, Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.
| | | | | | | | | |
Collapse
|
163
|
Babushok DV, Ohshima K, Ostertag EM, Chen X, Wang Y, Mandal PK, Okada N, Abrams CS, Kazazian HH. A novel testis ubiquitin-binding protein gene arose by exon shuffling in hominoids. Genome Res 2007; 17:1129-38. [PMID: 17623810 PMCID: PMC1933510 DOI: 10.1101/gr.6252107] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Most new genes arise by duplication of existing gene structures, after which relaxed selection on the new copy frequently leads to mutational inactivation of the duplicate; only rarely will a new gene with modified function emerge. Here we describe a unique mechanism of gene creation, whereby new combinations of functional domains are assembled at the RNA level from distinct genes, and the resulting chimera is then reverse transcribed and integrated into the genome by the L1 retrotransposon. We characterized a novel gene, which we termed PIP5K1A and PSMD4-like (PIPSL), created by this mechanism from an intergenic transcript between the phosphatidylinositol-4-phosphate 5-kinase (PIP5K1A) and the 26S proteasome subunit (PSMD4) genes in a hominoid ancestor. PIPSL is transcribed specifically in the testis both in humans and chimpanzees, and is post-transcriptionally repressed by independent mechanisms in these primate lineages. The PIPSL gene encodes a chimeric protein combining the lipid kinase domain of PIP5K1A and the ubiquitin-binding motifs of PSMD4. Strong positive selection on PIPSL led to its rapid divergence from the parental genes PIP5K1A and PSMD4, forming a chimeric protein with a distinct cellular localization and minimal lipid kinase activity, but significant affinity for cellular ubiquitinated proteins. PIPSL is a tightly regulated, testis-specific novel ubiquitin-binding protein formed by an unusual exon-shuffling mechanism in hominoid primates and represents a key example of rapid evolution of a testis-specific gene.
Collapse
Affiliation(s)
- Daria V. Babushok
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kazuhiko Ohshima
- Nagahama Institute of Bio-Science and Technology, Nagahama 526-0829, Japan
| | - Eric M. Ostertag
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Xinsheng Chen
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yanfeng Wang
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Prabhat K. Mandal
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | | | - Charles S. Abrams
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Haig H. Kazazian
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Corresponding author.E-mail ; fax (215) 573-7760
| |
Collapse
|
164
|
Galasso A, Pane LS, Russo M, Grimaldi MR, Verrotti AC, Gigliotti S, Graziani F. dSTAM expression pattern during wild type and mutant egg chamber development in D. melanogaster. Gene Expr Patterns 2007; 7:730-7. [PMID: 17664083 DOI: 10.1016/j.modgep.2007.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Revised: 06/06/2007] [Accepted: 06/17/2007] [Indexed: 11/25/2022]
Abstract
STAM (signal-transducing adaptor molecule) is a protein highly conserved from yeast to mammals. In Drosophila melanogaster the basic molecular architecture of the protein is comprised of a N-terminal VHS domain, an ubiquitin-interacting motif and a central Src homology-3 domain. In this paper we examine the expression pattern of the stam gene and the localisation of the STAM protein during D. melanogaster oogenesis. Its transcript is present throughout egg chamber development in all germ-line cells, including the oocyte. dSTAM is firstly detected in germarial region 2, where the protein is present in the newly formed germ-line cysts and is mainly accumulated into the oocyte. As oogenesis proceeds, dSTAM is enriched in the perinuclear region of the nurse cells and is also found in the somatic polar follicular cells. In the oocyte, the protein is more abundant posteriorly and becomes restricted to the posterior pole just before disappearing at stage 10b. We show that dSTAM localisation is unaffected in the oocyte of grk mutant egg chambers, indicating that it is not dependent on the polarity of the microtubule network. In contrast, dSTAM distribution is remarkably altered in cup mutant oocytes where the protein accumulates in a round central spot and never reaches the posterior pole.
Collapse
|
165
|
French M, Swanson K, Shih SC, Radhakrishnan I, Hicke L. Identification and characterization of modular domains that bind ubiquitin. Methods Enzymol 2007; 399:135-57. [PMID: 16338353 DOI: 10.1016/s0076-6879(05)99009-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
To receive and transmit the information carried by ubiquitin signals, cells have evolved an array of modular ubiquitin-binding domains. These domains bind directly and noncovalently to monoubiquitin and polyubiquitin chains and are found within proteins that function in diverse biological processes. Ubiquitin-binding domains characterized thus far are generally small and structurally diverse, yet they all interact with the same hydrophobic patch on the surface of ubiquitin. The rapid identification and characterization of ubiquitin-binding domains has been accomplished through the extensive use of bioinformatics, biochemistry, molecular biology, and biophysics. Here, we discuss the strategies and tools that have been most successful in the identification and characterization of ubiquitin-binding domains.
Collapse
Affiliation(s)
- Michael French
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois, USA
| | | | | | | | | |
Collapse
|
166
|
Iyer LM, Burroughs AM, Aravind L. The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. Genome Biol 2007; 7:R60. [PMID: 16859499 PMCID: PMC1779556 DOI: 10.1186/gb-2006-7-7-r60] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Revised: 06/12/2006] [Accepted: 07/06/2006] [Indexed: 11/14/2022] Open
Abstract
A systematic analysis of prokaryotic ubiquitin-related beta-grasp fold proteins provides new insights into the Ubiquitin family functional history. Background Ubiquitin (Ub)-mediated signaling is one of the hallmarks of all eukaryotes. Prokaryotic homologs of Ub (ThiS and MoaD) and E1 ligases have been studied in relation to sulfur incorporation reactions in thiamine and molybdenum/tungsten cofactor biosynthesis. However, there is no evidence for entire protein modification systems with Ub-like proteins and deconjugation by deubiquitinating enzymes in prokaryotes. Hence, the evolutionary assembly of the eukaryotic Ub-signaling apparatus remains unclear. Results We systematically analyzed prokaryotic Ub-related β-grasp fold proteins using sensitive sequence profile searches and structural analysis. Consequently, we identified novel Ub-related proteins beyond the characterized ThiS, MoaD, TGS, and YukD domains. To understand their functional associations, we sought and recovered several conserved gene neighborhoods and domain architectures. These included novel associations involving diverse sulfur metabolism proteins, siderophore biosynthesis and the gene encoding the transfer mRNA binding protein SmpB, as well as domain fusions between Ub-like domains and PIN-domain related RNAses. Most strikingly, we found conserved gene neighborhoods in phylogenetically diverse bacteria combining genes for JAB domains (the primary de-ubiquitinating isopeptidases of the proteasomal complex), along with E1-like adenylating enzymes and different Ub-related proteins. Further sequence analysis of other conserved genes in these neighborhoods revealed several Ub-conjugating enzyme/E2-ligase related proteins. Genes for an Ub-like protein and a JAB domain peptidase were also found in the tail assembly gene cluster of certain caudate bacteriophages. Conclusion These observations imply that members of the Ub family had already formed strong functional associations with E1-like proteins, UBC/E2-related proteins, and JAB peptidases in the bacteria. Several of these Ub-like proteins and the associated protein families are likely to function together in signaling systems just as in eukaryotes.
Collapse
Affiliation(s)
- Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
- Bioinformatics Program, Boston University, Cummington Street, Boston, Massachusetts 02215, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| |
Collapse
|
167
|
Traub LM, Lukacs GL. Decoding ubiquitin sorting signals for clathrin-dependent endocytosis by CLASPs. J Cell Sci 2007; 120:543-53. [PMID: 17287393 DOI: 10.1242/jcs.03385] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Cargo selectivity is a hallmark of clathrin-mediated endocytosis. A wide range of structurally unrelated internalization signals specify the preferential clustering of transmembrane cargo into clathrin coats forming on the plasma membrane. Intriguingly, the classical endocytic adaptor AP-2 appears to recognize only a subset of these endocytic sorting signals. New data now reveal the molecular basis for recognition of other internalization signals, including post-translationally appended ubiquitin, by clathrin-coat-associated sorting proteins (CLASPs). Curiously, structurally related ubiquitin-recognition modules are shared by select CLASPs and the 26S proteasome, and recent work indicates that both display similar requirements for ubiquitin binding. During endocytosis, these modules engage oligoubiquitylated cargo in the form of polyubiquitin chains and/or multiple single ubiquitin molecules appended to different acceptor lysines. Functional separation between clathrin-mediated endocytosis and proteasome-dependent proteolysis is probably ensured by temporally regulated, local assembly of ubiquitin-tagged membrane cargo at sorting stations on the cell surface, shielding ubiquitin sorting signals from the proteasome. Thus, an expanded repertoire of CLASPs couples the process of clathrin-coat assembly with high-fidelity incorporation of assorted, cargo-specific sorting signals.
Collapse
Affiliation(s)
- Linton M Traub
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, PA 15261, USA, and Program in Cell and Lung Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.
| | | |
Collapse
|
168
|
Tomlinson E, Palaniyappan N, Tooth D, Layfield R. Methods for the purification of ubiquitinated Proteins. Proteomics 2007; 7:1016-22. [PMID: 17351889 DOI: 10.1002/pmic.200601008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Post-translational protein modification by the covalent conjugation of ubiquitin, originally implicated as a signal for proteolytic degradation by 26S proteasome, has now been realised to play important roles in the regulation of almost all biological processes in eukaryotes. In order to understand these processes in greater detail there is a requirement for techniques that can purify mixtures of ubiquitin-conjugated proteins, as a prerequisite to their identification and characterisation. Here we review the methods that have been applied to the bulk purification of ubiquitinated proteins and discuss their applications in proteomic analyses of the 'ubiquitome'.
Collapse
Affiliation(s)
- Emma Tomlinson
- School of Biomedical Sciences, University of Nottingham Medical School, Nottingham, UK
| | | | | | | |
Collapse
|
169
|
Woelk T, Sigismund S, Penengo L, Polo S. The ubiquitination code: a signalling problem. Cell Div 2007; 2:11. [PMID: 17355622 PMCID: PMC1832185 DOI: 10.1186/1747-1028-2-11] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Accepted: 03/13/2007] [Indexed: 11/10/2022] Open
Abstract
Ubiquitin is a highly versatile post-translational modification that controls virtually all types of cellular events. Over the past ten years we have learned that diverse forms of ubiquitin modifications and of ubiquitin binding modules co-exist in the cell, giving rise to complex networks of protein:protein interactions. A central problem that continues to puzzle ubiquitinologists is how cells translate this myriad of stimuli into highly specific responses. This is a classical signalling problem. Here, we draw parallels with the phosphorylation signalling pathway and we discuss the expanding repertoire of ubiquitin signals, signal tranducers and signalling-regulated E3 enzymes. We examine recent advances in the field, including a new mechanism of regulation of E3 ligases that relies on ubiquitination.
Collapse
Affiliation(s)
- Tanja Woelk
- IFOM, Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy
| | - Sara Sigismund
- IFOM, Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy
| | - Lorenza Penengo
- IFOM, Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy
| | - Simona Polo
- IFOM, Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy
| |
Collapse
|
170
|
Yan J, Kim YS, Yang XP, Albers M, Koegl M, Jetten AM. Ubiquitin-interaction motifs of RAP80 are critical in its regulation of estrogen receptor alpha. Nucleic Acids Res 2007; 35:1673-86. [PMID: 17311814 PMCID: PMC1865050 DOI: 10.1093/nar/gkl1112] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In this study, we demonstrate that receptor-associated protein 80 (RAP80) interacts with estrogen receptor alpha (ERα) in an agonist-dependent manner. The interaction is specific for ERα as ERβ and several other nuclear receptors tested did not interact with RAP80. Interaction between RAP80 and ERα was supported by mammalian two-hybrid, GST pull-down, and co-immunoprecipitation analyses. The hinge/ligand-binding domain of ERα is sufficient for interaction with RAP80. RAP80 overexpression reduces ERα polyubiquitination, increases the level of ERα protein, and enhances ERα-mediated transactivation. Knockdown of endogenous RAP80 expression by small-interfering RNA (siRNA) reduced ERα protein level and the E2-dependent induction of pS2. In this study, we also demonstrate that RAP80 contains two functional ubiquitin-interaction motifs (UIMs) that are able to bind ubiquitin and to direct monoubiquitination of RAP80. Deletion of these UIMs does not affect the ability of RAP80 to interact with ERα, but eliminates the effects of RAP80 on ERα polyubiquitination, the level of ERα protein, and ERα-mediated transcription. These data indicate that the UIMs in RAP80 are critical for the function of RAP80. Our study identifies ERα as a new RAP80-interacting protein and suggests that RAP80 may be an important modulator of ERα activity.
Collapse
Affiliation(s)
- Jun Yan
- Cell Biology Section, Division of Intramural Research, National Institute of Enironmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA, Phenex Pharmaceuticals AG, D-67056 Ludwigshafen, Germany and RZPD German Resource Center for Genome Research, D-69120 Heidelberg, Germany
| | - Yong-Sik Kim
- Cell Biology Section, Division of Intramural Research, National Institute of Enironmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA, Phenex Pharmaceuticals AG, D-67056 Ludwigshafen, Germany and RZPD German Resource Center for Genome Research, D-69120 Heidelberg, Germany
| | - Xiao-Ping Yang
- Cell Biology Section, Division of Intramural Research, National Institute of Enironmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA, Phenex Pharmaceuticals AG, D-67056 Ludwigshafen, Germany and RZPD German Resource Center for Genome Research, D-69120 Heidelberg, Germany
| | - Michael Albers
- Cell Biology Section, Division of Intramural Research, National Institute of Enironmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA, Phenex Pharmaceuticals AG, D-67056 Ludwigshafen, Germany and RZPD German Resource Center for Genome Research, D-69120 Heidelberg, Germany
| | - Manfred Koegl
- Cell Biology Section, Division of Intramural Research, National Institute of Enironmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA, Phenex Pharmaceuticals AG, D-67056 Ludwigshafen, Germany and RZPD German Resource Center for Genome Research, D-69120 Heidelberg, Germany
| | - Anton M. Jetten
- Cell Biology Section, Division of Intramural Research, National Institute of Enironmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA, Phenex Pharmaceuticals AG, D-67056 Ludwigshafen, Germany and RZPD German Resource Center for Genome Research, D-69120 Heidelberg, Germany
- *To whom correspondence should be addressed. 919-541-2768919-541-4133
| |
Collapse
|
171
|
Bomar MG, Pai MT, Tzeng SR, Li SSC, Zhou P. Structure of the ubiquitin-binding zinc finger domain of human DNA Y-polymerase eta. EMBO Rep 2007; 8:247-51. [PMID: 17304240 PMCID: PMC1808033 DOI: 10.1038/sj.embor.7400901] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Revised: 12/04/2006] [Accepted: 12/07/2006] [Indexed: 11/08/2022] Open
Abstract
The ubiquitin-binding zinc finger (UBZ) domain of human DNA Y-family polymerase (pol) eta is important in the recruitment of the polymerase to the stalled replication machinery in translesion synthesis. Here, we report the solution structure of the pol eta UBZ domain and its interaction with ubiquitin. We show that the UBZ domain adopts a classical C(2)H(2) zinc-finger structure characterized by a betabetaalpha fold. Nuclear magnetic resonance titration maps the binding interfaces between UBZ and ubiquitin to the alpha-helix of the UBZ domain and the canonical hydrophobic surface of ubiquitin defined by residues L8, I44 and V70. Although the UBZ domain binds ubiquitin through a single alpha-helix, in a manner similar to the inverted ubiquitin-interacting motif, its structure is distinct from previously characterized ubiquitin-binding domains. The pol eta UBZ domain represents a novel member of the C(2)H(2) zinc finger family that interacts with ubiquitin to regulate translesion synthesis.
Collapse
Affiliation(s)
- Martha G Bomar
- Department of Biochemistry, Duke University Medical Center, Research Drive, 242 Nanaline Duke Building, Durham, North Carolina 27710, USA
| | - Ming-Tao Pai
- Department of Biochemistry, Duke University Medical Center, Research Drive, 242 Nanaline Duke Building, Durham, North Carolina 27710, USA
| | - Shiou-Ru Tzeng
- Department of Biochemistry and the Siebens–Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario N6G 2V4, Canada
| | - Shawn Shun-Cheng Li
- Department of Biochemistry and the Siebens–Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario N6G 2V4, Canada
| | - Pei Zhou
- Department of Biochemistry, Duke University Medical Center, Research Drive, 242 Nanaline Duke Building, Durham, North Carolina 27710, USA
- Tel: +1 919 668 6409; Fax: +1 919 684 8885; E-mail:
| |
Collapse
|
172
|
Miller SLH, Scappini EL, O'Bryan J. Ubiquitin-interacting motifs inhibit aggregation of polyQ-expanded huntingtin. J Biol Chem 2007; 282:10096-10103. [PMID: 17276991 DOI: 10.1074/jbc.m611151200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Expansion of polyglutamine (polyQ) tracts within proteins underlies a number of neurodegenerative diseases, such as Huntington disease, Kennedy disease, and spinocerebellar ataxias. The resulting mutant proteins are unstable, forming insoluble aggregates that are associated with components of the ubiquitin system, including ubiquitin, ubiquitin-like proteins, and proteins that bind to ubiquitin. Given the presence of these ubiquitin-binding proteins in the insoluble aggregates, we examined whether heterologous expression of short motifs that bind ubiquitin, termed ubiquitin-interacting motifs (UIMs), altered the aggregation of polyQ-expanded huntingtin (Htt), the protein product of the Huntington disease gene. We found that a subset of UIMs associated with mutant Htt. The ability to interact with ubiquitin was necessary, but not sufficient, for interaction with mutant Htt. Furthermore, we found that expression of single, isolated UIMs inhibited aggregation of mutant Htt. These data suggest that isolated UIMs might serve as potential inhibitors of polyQ-aggregation in vivo.
Collapse
Affiliation(s)
- Stephanie L H Miller
- Laboratory of Signal Transduction, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709
| | - Erica L Scappini
- Laboratory of Signal Transduction, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709
| | - John O'Bryan
- Laboratory of Signal Transduction, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709; Department of Pharmacology, University of Illinois College of Medicine, Chicago, Illinois 60612.
| |
Collapse
|
173
|
Pak Y, Glowacka WK, Bruce MC, Pham N, Rotin D. Transport of LAPTM5 to lysosomes requires association with the ubiquitin ligase Nedd4, but not LAPTM5 ubiquitination. ACTA ACUST UNITED AC 2007; 175:631-45. [PMID: 17116753 PMCID: PMC2064599 DOI: 10.1083/jcb.200603001] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
LAPTM5 is a lysosomal transmembrane protein expressed in immune cells. We show that LAPTM5 binds the ubiquitin-ligase Nedd4 and GGA3 to promote LAPTM5 sorting from the Golgi to the lysosome, an event that is independent of LAPTM5 ubiquitination. LAPTM5 contains three PY motifs (L/PPxY), which bind Nedd4-WW domains, and a ubiquitin-interacting motif (UIM) motif. The Nedd4-LAPTM5 complex recruits ubiquitinated GGA3, which binds the LAPTM5-UIM; this interaction does not require the GGA3-GAT domain. LAPTM5 mutated in its Nedd4-binding sites (PY motifs) or its UIM is retained in the Golgi, as is LAPTM5 expressed in cells in which Nedd4 or GGA3 is knocked-down with RNAi. However, ubiquitination-impaired LAPTM5 can still traffic to the lysosome, suggesting that Nedd4 binding to LAPTM5, not LAPTM5 ubiquitination, is required for targeting. Interestingly, Nedd4 is also able to ubiquitinate GGA3. These results demonstrate a novel mechanism by which the ubiquitin-ligase Nedd4, via interactions with GGA3 and cargo (LAPTM5), regulates cargo trafficking to the lysosome without requiring cargo ubiquitination.
Collapse
Affiliation(s)
- Youngshil Pak
- Program in Cell Biology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada, M5G 1X8
| | | | | | | | | |
Collapse
|
174
|
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.
Collapse
Affiliation(s)
- Yuqi Wang
- Department of Biology, Saint Louis University, 128 Macelwane Hall, 3507 Laclede Ave, St Louis, MO 63103, USA.
| | | |
Collapse
|
175
|
Kerscher O, Felberbaum R, Hochstrasser M. Modification of proteins by ubiquitin and ubiquitin-like proteins. Annu Rev Cell Dev Biol 2006; 22:159-80. [PMID: 16753028 DOI: 10.1146/annurev.cellbio.22.010605.093503] [Citation(s) in RCA: 1173] [Impact Index Per Article: 65.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Following the discovery of protein modification by the small, highly conserved ubiquitin polypeptide, a number of distinct ubiquitin-like proteins (Ubls) have been found to function as protein modifiers as well. These Ubls, which include SUMO, ISG15, Nedd8, and Atg8, function as critical regulators of many cellular processes, including transcription, DNA repair, signal transduction, autophagy, and cell-cycle control. A growing body of data also implicates the dysregulation of Ubl-substrate modification and mutations in the Ubl-conjugation machinery in the etiology and progression of a number of human diseases. The primary aim of this review is to summarize the latest developments in our understanding of the different Ubl-protein modification systems, including the shared and unique features of these related pathways.
Collapse
Affiliation(s)
- Oliver Kerscher
- Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.
| | | | | |
Collapse
|
176
|
Shimada M, Kanematsu K, Tanaka K, Yokosawa H, Kawahara H. Proteasomal ubiquitin receptor RPN-10 controls sex determination in Caenorhabditis elegans. Mol Biol Cell 2006; 17:5356-71. [PMID: 17050737 PMCID: PMC1687211 DOI: 10.1091/mbc.e06-05-0437] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2006] [Revised: 09/06/2006] [Accepted: 10/06/2006] [Indexed: 11/11/2022] Open
Abstract
The ubiquitin-binding RPN-10 protein serves as a ubiquitin receptor that delivers client proteins to the 26S proteasome. Although ubiquitin recognition is an essential step for proteasomal destruction, deletion of the rpn-10 gene in yeast does not influence viability, indicating redundancy of the substrate delivery pathway. However, their specificity and biological relevance in higher eukaryotes is still enigmatic. We report herein that knockdown of the rpn-10 gene, but not any other proteasome subunit genes, sexually transforms hermaphrodites to females by eliminating hermaphrodite spermatogenesis in Caenorhabditis elegans. The feminization phenotype induced by deletion of the rpn-10 gene was rescued by knockdown of tra-2, one of sexual fate decision genes promoting female development, and its downstream target tra-1, indicating that the TRA-2-mediated sex determination pathway is crucial for the Delta rpn-10-induced sterile phenotype. Intriguingly, we found that co-knockdown of rpn-10 and functionally related ubiquitin ligase ufd-2 overcomes the germline-musculinizing effect of fem-3(gf). Furthermore, TRA-2 proteins accumulated in rpn-10-defective worms. Our results show that the RPN-10-mediated ubiquitin pathway is indispensable for control of the TRA-2-mediated sex-determining pathway.
Collapse
Affiliation(s)
- Masumi Shimada
- *Department of Biochemistry, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan; and
| | - Kenji Kanematsu
- *Department of Biochemistry, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan; and
| | - Keiji Tanaka
- Department of Molecular Oncology, The Tokyo Metropolitan Institute of Medical Sciences, Tokyo 113-8613, Japan
| | - Hideyoshi Yokosawa
- *Department of Biochemistry, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan; and
| | - Hiroyuki Kawahara
- *Department of Biochemistry, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan; and
| |
Collapse
|
177
|
Abstract
The covalent modification of proteins by ubiquitination is a major regulatory mechanism of protein degradation and quality control, endocytosis, vesicular trafficking, cell-cycle control, stress response, DNA repair, growth-factor signalling, transcription, gene silencing and other areas of biology. A class of specific ubiquitin-binding domains mediates most of the effects of protein ubiquitination. The known membership of this group has expanded rapidly and now includes at least sixteen domains: UBA, UIM, MIU, DUIM, CUE, GAT, NZF, A20 ZnF, UBP ZnF, UBZ, Ubc, UEV, UBM, GLUE, Jab1/MPN and PFU. The structures of many of the complexes with mono-ubiquitin have been determined, revealing interactions with multiple surfaces on ubiquitin. Inroads into understanding polyubiquitin specificity have been made for two UBA domains, whose structures have been characterized in complex with Lys48-linked di-ubiquitin. Several ubiquitin-binding domains, including the UIM, CUE and A20 ZnF (zinc finger) domains, promote auto-ubiquitination, which regulates the activity of proteins that contain them. At least one of these domains, the A20 ZnF, acts as a ubiquitin ligase by recruiting a ubiquitin-ubiquitin-conjugating enzyme thiolester adduct in a process that depends on the ubiquitin-binding activity of the A20 ZnF. The affinities of the mono-ubiquitin-binding interactions of these domains span a wide range, but are most commonly weak, with Kd>100 microM. The weak interactions between individual domains and mono-ubiquitin are leveraged into physiologically relevant high-affinity interactions via several mechanisms: ubiquitin polymerization, modification multiplicity, oligomerization of ubiquitinated proteins and binding domain proteins, tandem-binding domains, binding domains with multiple ubiquitin-binding sites and co-operativity between ubiquitin binding and binding through other domains to phospholipids and small G-proteins.
Collapse
Affiliation(s)
- James H Hurley
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20892, USA.
| | | | | |
Collapse
|
178
|
Heir R, Ablasou C, Dumontier E, Elliott M, Fagotto-Kaufmann C, Bedford FK. The UBL domain of PLIC-1 regulates aggresome formation. EMBO Rep 2006; 7:1252-8. [PMID: 17082820 PMCID: PMC1794689 DOI: 10.1038/sj.embor.7400823] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Revised: 09/04/2006] [Accepted: 09/04/2006] [Indexed: 12/25/2022] Open
Abstract
Defects in protein folding and the proteasomal pathway have been linked with many neurodegenerative diseases. PLIC-1 (protein linking IAP to the cytoskeleton) is a ubiquitin-like protein that binds to the ubiquitin-interacting motif (UIM) of the proteasomal subunit S5a. Here, we show that PLIC-1 also binds to the UIM proteins ataxin 3--a deubiquitinating enzyme--HSJ1a--a co-chaperone--and EPS15 (epidermal growth factor substrate 15)--an endocytic protein. Using a polyglutamine (polyQ) disease model, we found that both endogenous PLIC-1 and EPS15 localize to perinuclear aggresomes, and that polyQ enhances their in vivo interaction. We show that knockdown of PLIC-1 and EPS15 by RNA interference reduces aggresome formation. In addition, PLIC-1(DeltaUBL) functions as a dominant-negative mutant, blocking both polyQ transport to aggresomes and the association of EPS15 with dispersed aggregates. We also show that PLIC-1 is upregulated by arsenite-induced protein misfolding. These results indicate a role for PLIC-1 in the protein aggregation-stress pathway, and we propose a novel function for the ubiquitin-like (UBL) domain--by means of UBL-UIM interactions--in transport to aggresomes.
Collapse
Affiliation(s)
- Renu Heir
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec H3A2B2, Canada
| | - Celine Ablasou
- Laboratoire d'Immunologie Equipe d'Accueil 2686, Faculte de Medecine, Pole Recherche, 1 Place de Verdun, 59045 Lille, France
| | - Emilie Dumontier
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec H3A2B2, Canada
| | - Meghan Elliott
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec H3A2B2, Canada
| | - Christine Fagotto-Kaufmann
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec H3A2B2, Canada
| | - Fiona K Bedford
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec H3A2B2, Canada
- Tel: +1 514 398 1426; Fax: +1 514 398 5047; E-mail:
| |
Collapse
|
179
|
Mauri PL, Riva M, Ambu D, De Palma A, Secundo F, Benazzi L, Valtorta M, Tortora P, Fusi P. Ataxin-3 is subject to autolytic cleavage. FEBS J 2006; 273:4277-86. [PMID: 16939621 DOI: 10.1111/j.1742-4658.2006.05419.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The protein ataxin-3 is responsible for spinocerebellar ataxia type 3, a neurodegenerative disease triggered when the length of a stretch of consecutive glutamines exceeds a critical threshold. Different physiologic roles have been suggested for this protein. More specifically, recent papers have shown that the highly conserved N-terminal Josephin domain of ataxin-3 binds ubiquitin and has ubiquitin hydrolase activity, thanks to a catalytic device specific to cysteine proteases. This article shows that the protein also has autoproteolytic activity, sustained by the same residues responsible for the ubiquitin hydrolase activity. The autolytic activity was abolished when these residues, i.e. Cys14 and His119, were replaced by noncatalytic ones. Furthermore, we found that pretreatment of the protein with tosyl l-phenylalanine chloromethyl ketone also abolished this activity, and that this site-specific reagent covalently bound His119, findings supported by MS experiments. MS also allowed us to establish that the attack was aspecific, as cleavage sites were observed at the carboxyl side of apolar, acidic and polar uncharged residues, clustered in the C-terminal, unstructured domain of the protein. In contrast, the Josephin domain was preserved from attack. We propose that the autolytic activity reported here may play a role in pathogenesis, as fragments carrying expanded polyglutamines are thought to be significantly more toxic than the whole protein.
Collapse
|
180
|
Scheel H, Hofmann K. The GI-UEV Domain, a Catalytically Inactive Ubiquitin-Conjugating Enzyme Variant With a Role in Translational Regulation. Isr J Chem 2006. [DOI: 10.1560/5bra-fgyk-tu1q-0xa8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
181
|
Raiborg C, Slagsvold T, Stenmark H. A new side to ubiquitin. Trends Biochem Sci 2006; 31:541-4. [PMID: 16901703 DOI: 10.1016/j.tibs.2006.07.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2006] [Revised: 07/10/2006] [Accepted: 07/31/2006] [Indexed: 11/26/2022]
Abstract
Mono-ubiquitination is a common mechanism of protein regulation, and more than ten ubiquitin-interacting domains that recognize the hydrophobic region centered on Ile44 of ubiquitin have been characterized. Two recent reports describe the crystal structure of the Rab5 guanine-nucleotide-exchange factor Rabex-5 and show that it contains two novel ubiquitin-binding domains. One of these is an A20 zinc finger that binds to a polar interaction interface of ubiquitin centered on Asp58. The discovery of an alternative interaction face of ubiquitin opens new avenues for understanding how this small protein regulates protein function.
Collapse
Affiliation(s)
- Camilla Raiborg
- Department of Biochemistry, the Norwegian Radium Hospital and the University of Oslo, Montebello, N-0310 Oslo, Norway
| | | | | |
Collapse
|
182
|
Abstract
The ESCRT complexes and associated proteins comprise a major pathway for the lysosomal degradation of transmembrane proteins and are critical for receptor downregulation, budding of the HIV virus, and other normal and pathological cell processes. The ESCRT system is conserved from yeast to humans. The ESCRT complexes form a network that recruits monoubiquitinated proteins and drives their internalization into lumenal vesicles within a type of endosome known as a multivesicular body. The structures and interactions of many of the components have been determined over the past three years, revealing mechanisms for membrane and cargo recruitment and for complex assembly.
Collapse
Affiliation(s)
- James H. Hurley
- Laboratory of Molecular Biology, National Institute of Diabetes
and Digestive and Kidney Diseases, National Institutes of Health, U. S.
Department of Health and Human Services, Bethesda, MD 20892-0580.
| | - Scott D. Emr
- Department of Cellular and Molecular Medicine and Howard Hughes
Medical Institute, University of California at San Diego, 9500 Gilman Dr., La
Jolla, CA 92093-0668.
| |
Collapse
|
183
|
Rost M, Mann S, Lambert C, Döring T, Thomé N, Prange R. Gamma-adaptin, a novel ubiquitin-interacting adaptor, and Nedd4 ubiquitin ligase control hepatitis B virus maturation. J Biol Chem 2006; 281:29297-308. [PMID: 16867982 DOI: 10.1074/jbc.m603517200] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hepatitis B virus (HBV) budding from infected cells is a tightly regulated process that requires both core and envelope structures. Here we report that HBV uses cellular gamma2-adaptin and Nedd4, possibly in conjunction with ubiquitin, to coordinate its assembly and release. In search of interaction partners of the viral L envelope protein, we previously discovered gamma2-adaptin, a putative endosomal sorting and trafficking adaptor of the adaptor protein complex family. We now demonstrate that the viral core interacts with the same gamma2-adaptor and that disruption of the HBV/gamma2-adaptin interactions inhibits virus production. Mutational analyses revealed a hitherto unknown ubiquitin-binding activity of gamma2-adaptin, specified by a ubiquitin-interacting motif, which contributes to its interaction with core. For core, the lysine residue at position 96, a potential target for ubiquitination, was identified to be essential for both gamma2-adaptin-recognition and virus production. The participation of the cellular ubiquitin system in HBV assembly was further suggested by our finding that core interacts with the endosomal ubiquitin ligase Nedd4, partly via its late domain-like PPAY sequence. Overexpression of a catalytically inactive Nedd4 mutant diminished HBV egress, indicating that protein ubiquitination is functionally involved in virus production. Additional evidence for a link of HBV assembly to the endosomal machinery was provided by immunolabeling studies that demonstrated colocalization of core and L with gamma2-adaptin in compartments positive for the late endosomal marker CD63. Together, these data indicate that an enveloped DNA virus exploits a new ubiquitin receptor together with endosomal pathway functions for egress from hepatocytes.
Collapse
Affiliation(s)
- Martina Rost
- Department of Medical Microbiology and Hygiene, Johannes Gutenberg-Universität Mainz, Augustusplatz, D-55101 Mainz, Germany
| | | | | | | | | | | |
Collapse
|
184
|
Pullan L, Mullapudi S, Huang Z, Baldwin PR, Chin C, Sun W, Tsujimoto S, Kolodziej SJ, Stoops JK, Lee JC, Waxham MN, Bean AJ, Penczek PA. The endosome-associated protein Hrs is hexameric and controls cargo sorting as a "master molecule". Structure 2006; 14:661-71. [PMID: 16615908 DOI: 10.1016/j.str.2006.01.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2005] [Revised: 12/22/2005] [Accepted: 01/19/2006] [Indexed: 11/20/2022]
Abstract
The structure of the endosomal-associated protein, Hrs, has been determined with cryo-electron microscopy. Hrs interacts with a number of proteins, including SNAP-25 and STAM1, forming a complex that binds ubiquitin moieties. Analytical ultracentrifugation studies revealed that Hrs exists as a hexamer. The symmetry and the structure of the hexameric form of Hrs were determined with the single-particle reconstruction method. Hrs comprises three antiparallel dimers with a central core and distinct caps on either end. Crystal structures of VHS and FYVE domains fit into the Hrs end caps in the EM density map. Thus, the location of domains that interact with the endosomal membrane, the VHS, FYVE, and C-terminal domains, facilitates the anchorage of Hrs to the membrane, initiating the functional processes of Hrs on the endosome. Based on our model, the Hrs hexamer interacts with the membrane and acts as a "master molecule" that presents multiple sites for protein binding.
Collapse
Affiliation(s)
- Lee Pullan
- Department of Biochemistry and Molecular Biology, The University of Texas-Houston Medical School, 6431 Fannin, Houston, Texas 77030, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
185
|
Myromslien FD, Grøvdal LM, Raiborg C, Stenmark H, Madshus IH, Stang E. Both clathrin-positive and -negative coats are involved in endosomal sorting of the EGF receptor. Exp Cell Res 2006; 312:3036-48. [PMID: 16859684 DOI: 10.1016/j.yexcr.2006.06.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Revised: 06/02/2006] [Accepted: 06/02/2006] [Indexed: 01/09/2023]
Abstract
Sorting of endocytosed EGF receptor (EGFR) to internal vesicles of multivesicular bodies (MVBs) depends on sustained activation and ubiquitination of the EGFR. Ubiquitination of EGFR is mediated by the ubiquitin ligase Cbl, being recruited to the EGFR both directly and indirectly through association with Grb2. Endosomal sorting of ubiquitinated proteins further depends on interaction with ubiquitin binding adaptors like Hrs. Hrs localizes to flat, clathrin-coated domains on the limiting membrane of endosomes. In the present study, we have investigated the localization of EGFR, Cbl and Grb2 with respect to coated and non-coated domains of the endosomal membrane and to vesicles within MVBs. Both EGFR, Grb2, and Cbl were concentrated in coated domains of the limiting membrane before translocation to inner vesicles of MVBs. While almost all Hrs was in clathrin-positive coats, EGFR and Grb2 in coated domains only partially colocalized with Hrs and clathrin. The extent of colocalization of EGFR and Grb2 with Hrs and clathrin varied with time of incubation with EGF. These results demonstrate that both clathrin-positive and clathrin-negative electron dense coats exist on endosomes and are involved in endosomal sorting of the EGFR.
Collapse
Affiliation(s)
- Frøydis D Myromslien
- Institute of Pathology, University of Oslo, Rikshospitalet-Radiumhospitalet HF, 0027 Oslo, Norway
| | | | | | | | | | | |
Collapse
|
186
|
Bao WJ, Gao YG, Chang YG, Zhang TY, Lin XJ, Yan XZ, Hu HY. Highly efficient expression and purification system of small-size protein domains in Escherichia coli for biochemical characterization. Protein Expr Purif 2006; 47:599-606. [PMID: 16427307 DOI: 10.1016/j.pep.2005.11.021] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Revised: 11/23/2005] [Accepted: 11/25/2005] [Indexed: 11/29/2022]
Abstract
It is often essential to focus the study on the small-size domains of large proteins in eukaryotic cells in the post-genomic era, but the low expression level, insolubility, and instability of the domains have been continuing to hinder the massive purification of domain peptides for structural and biological investigation. In this work, a highly efficient expression and purification system based on a small-size fusion partner GB1 and histidine tag was utilized to solve these problems. Two vectors, namely pGBTNH and pGBH, were constructed to improve expression and facilitate purification. The linker and thrombin cleavage site have been optimized for minimal degradation during purification process. This system has been tested for eight domain peptides varying in size, linker, hydrophobicity, and predicted secondary structure. The results indicate that this system is achievable to produce these domain peptides with high solubility and stability for further biochemical characterization. Moreover, the fusion protein without the linker and thrombin cleavage site is also suitable for spectroscopic studies especially for NMR structural elucidation, if the target peptide is prone to precipitation or easily degraded during purification. This system will be beneficial to the research field of structure and function of small domain and peptide fragment.
Collapse
Affiliation(s)
- Wen-Jing Bao
- Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China
| | | | | | | | | | | | | |
Collapse
|
187
|
Hawryluk MJ, Keyel PA, Mishra SK, Watkins SC, Heuser JE, Traub LM. Epsin 1 is a polyubiquitin-selective clathrin-associated sorting protein. Traffic 2006; 7:262-81. [PMID: 16497222 DOI: 10.1111/j.1600-0854.2006.00383.x] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Epsin 1 engages several core components of the endocytic clathrin coat, yet the precise mode of operation of the protein remains controversial. The occurrence of tandem ubiquitin-interacting motifs (UIMs) suggests that epsin could recognize a ubiquitin internalization tag, but the association of epsin with clathrin-coat components or monoubiquitin is reported to be mutually exclusive. Here, we show that endogenous epsin 1 is clearly an integral component of clathrin coats forming at the cell surface and is essentially absent from caveolin-1-containing structures under normal conditions. The UIM region of epsin 1 associates directly with polyubiquitin chains but has extremely poor affinity for monoubiquitin. Polyubiquitin binding is retained when epsin synchronously associates with phosphoinositides, the AP-2 adaptor complex and clathrin. The enrichment of epsin within clathrin-coated vesicles purified from different tissue sources varies and correlates with sorting of multiubiquitinated cargo, and in cultured cells, polyubiquitin, rather than non-conjugable monoubiquitin, promotes rapid internalization. As epsin interacts with eps15, which also contains a UIM region that binds to polyubiquitin, epsin and eps15 appear to be central components of the vertebrate poly/multiubiquitin-sorting endocytic clathrin machinery.
Collapse
Affiliation(s)
- Matthew J Hawryluk
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | | | | | | | | | | |
Collapse
|
188
|
|
189
|
Flick K, Raasi S, Zhang H, Yen JL, Kaiser P. A ubiquitin-interacting motif protects polyubiquitinated Met4 from degradation by the 26S proteasome. Nat Cell Biol 2006; 8:509-15. [PMID: 16604062 DOI: 10.1038/ncb1402] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Accepted: 03/07/2006] [Indexed: 01/11/2023]
Abstract
Covalent attachment of ubiquitin to proteins regulates a host of cellular events by proteolysis dependent and independent mechanisms. A variety of protein domains that bind non-covalently to ubiquitin have been described and functionally linked to diverse cellular processes. Overall, however, the understanding and knowledge of the mechanisms by which ubiquitin-binding domains (UBDs) regulate these processes is limited. Here, we describe identification of a UBD in the yeast transcription factor Met4. Met4 activity, but not its stability, is regulated by polyubiquitination. We found that the UBD restricts the length of the polyubiquitin chain that is assembled on Met4, and prevents proteasomal recognition and degradation of polyubiquitinated Met4. Inactivation of the UBD allowed synthesis of longer ubiquitin chains on Met4 and transformed the normally stable polyubiquitinated Met4 into a short-lived protein. Our results demonstrate a function for UBDs in ubiquitin-chain synthesis and regulation of protein degradation.
Collapse
Affiliation(s)
- Karin Flick
- University of California Irvine, Department of Biological Chemistry, School of Medicine, 240D Med Sci I, Irvine, CA 92697-1700, USA
| | | | | | | | | |
Collapse
|
190
|
Duncan LM, Piper S, Dodd RB, Saville MK, Sanderson CM, Luzio JP, Lehner PJ. Lysine-63-linked ubiquitination is required for endolysosomal degradation of class I molecules. EMBO J 2006; 25:1635-45. [PMID: 16601694 PMCID: PMC1440841 DOI: 10.1038/sj.emboj.7601056] [Citation(s) in RCA: 215] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Accepted: 02/27/2006] [Indexed: 12/25/2022] Open
Abstract
MHC class I molecules display peptides from endogenous and viral proteins for immunosurveillance by cytotoxic T lymphocytes (CTL). The importance of the class I pathway is emphasised by the remarkable strategies employed by different viruses to downregulate surface class I and avoid CTL recognition. The K3 gene product from Kaposi's sarcoma-associated herpesvirus (KSHV) is a viral ubiquitin E3 ligase which ubiquitinates and degrades cell surface MHC class I molecules. We now show that modification of K3-associated class I by lysine-63-linked polyubiquitin chains is necessary for their efficient endocytosis and endolysosomal degradation and present three lines of evidence that monoubiquitination of class I molecules provides an inefficient internalisation signal. This lysine-63-linked polyubiquitination requires both UbcH5b/c and Ubc13-conjugating enzymes for initiating mono- and subsequent polyubiquitination of class I, and the clathrin-dependent internalisation is mediated by the epsin endocytic adaptor. Our results explain how lysine-63-linked polyubiquitination leads to degradation by an endolysosomal pathway and demonstrate a novel mechanism for endocytosis and endolysosomal degradation of class I, which may be applicable to other receptors.
Collapse
Affiliation(s)
- Lidia M Duncan
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, UK
| | - Siân Piper
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Roger B Dodd
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, UK
| | - Mark K Saville
- Cancer Research UK, Cell Transformation Research Group, Department of Surgery and Molecular Oncology, University of Dundee, Scotland, UK
| | - Chris M Sanderson
- Physiological Laboratory, School of Biomedical Sciences, University of Liverpool, Liverpool, UK
| | - J Paul Luzio
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Paul J Lehner
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, UK
- Department of Medicine, Cambridge Institute for Medical Research, Lab 5.19, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge CB2 2XY, UK. Tel.: +44 1223 762113; Fax: +44 1223 762640; E-mail:
| |
Collapse
|
191
|
Abstract
Ubiquitylation of membrane proteins has gained considerable interest in recent years. It has been recognized as a signal that negatively regulates the cell surface expression of many plasma membrane proteins both in yeast and in mammalian cells. Moreover, it is also involved in endoplasmic reticulum-associated degradation of membrane proteins, and it acts as a sorting signal both in the secretory pathway and in endosomes, where it targets proteins into multivesicular bodies in the lumen of vacuoles/lysosomes. In this review we discuss the progress in understanding these processes, achieved during the past several years.
Collapse
Affiliation(s)
- Olivier Staub
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, Switzerland.
| | | |
Collapse
|
192
|
Ivantsiv Y, Kaplun L, Tzirkin-Goldin R, Shabek N, Raveh D. Unique role for the UbL-UbA protein Ddi1 in turnover of SCFUfo1 complexes. Mol Cell Biol 2006; 26:1579-88. [PMID: 16478980 PMCID: PMC1430233 DOI: 10.1128/mcb.26.5.1579-1588.2006] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2005] [Revised: 07/10/2005] [Accepted: 11/18/2005] [Indexed: 01/21/2023] Open
Abstract
SCF complexes are E3 ubiquitin-protein ligases that mediate degradation of regulatory and signaling proteins and control G1/S cell cycle progression by degradation of G1 cyclins and the cyclin-dependent kinase inhibitor, Sic1. Interchangeable F-box proteins bind the core SCF components; each recruits a specific subset of substrates for ubiquitylation. The F-box proteins themselves are rapidly turned over by autoubiquitylation, allowing rapid recycling of SCF complexes. Here we report a role for the UbL-UbA protein Ddi1 in the turnover of the F-box protein, Ufo1. Ufo1 is unique among F-box proteins in having a domain comprising multiple ubiquitin-interacting motifs (UIMs) that mediate its turnover. Deleting the UIMs leads to stabilization of Ufo1 and to cell cycle arrest at G1/S of cells with long buds resembling skp1 mutants. Cells accumulate substrates of other F-box proteins, indicating that the SCF pathway of substrate ubiquitylation is inhibited. Ufo1 interacts with Ddi1 via its UIMs, and Deltaddi1 cells arrest when full-length UFO1 is overexpressed. These results imply a role for the UIMs in turnover of SCF(Ufo1) complexes that is dependent on Ddi1, a novel activity for an UbL-UbA protein.
Collapse
Affiliation(s)
- Yelena Ivantsiv
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheba 84105, Israel
| | | | | | | | | |
Collapse
|
193
|
Mattera R, Tsai YC, Weissman AM, Bonifacino JS. The Rab5 Guanine Nucleotide Exchange Factor Rabex-5 Binds Ubiquitin (Ub) and Functions as a Ub Ligase through an Atypical Ub-interacting Motif and a Zinc Finger Domain. J Biol Chem 2006; 281:6874-83. [PMID: 16407276 DOI: 10.1074/jbc.m509939200] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rabex-5, the mammalian orthologue of yeast Vps9p, is a guanine nucleotide exchange factor for Rab5. Rabex-5 forms a tight complex with Rabaptin-5, a multivalent adaptor protein that also binds to Rab4, Rab5, and to domains present in gamma-adaptins and the Golgi-localized, gamma-ear-containing, ARF-binding proteins (GGAs). Rabaptin-5 augments the Rabex-5 exchange activity, thus generating GTP-bound, membrane-associated Rab5 that, in turn, binds Rabaptin-5 and stabilizes the Rabex-5.Rabaptin-5 complex on endosomes. Although the Rabex-5.Rabaptin-5 complex is critical to the regulation of endosomal fusion, the structural determinants of this interaction are unknown. Likewise, the possible binding and covalent attachment of ubiquitin to Rabex-5, two modifications that are critical to the function of yeast Vps9p in endosomal transport, have not been studied. In this study, we identify the 401-462 and 551-661 coiled-coils as the regions in Rabex-5 and Rabaptin-5, respectively, that interact with one another. We also demonstrate that Rabex-5 undergoes ubiquitination and binds ubiquitin, though not via its proposed C-terminal CUE-like domain. Instead, the N-terminal region of Rabex-5 (residues 1-76), comprising an A20-like Cys2/Cys2 zinc finger and an adjacent alpha-helix, is important for ubiquitin binding and ubiquitination. Importantly, we demonstrate that the Rabex-5 zinc finger displays ubiquitin ligase (E3) activity. These observations extend our understanding of the regulation of Rabex-5 by Rabaptin-5. Moreover, the demonstration that Rabex-5 is a ubiquitin ligase that binds ubiquitin and undergoes ubiquitination indicates that its role in endosome fusion may be subject to additional regulation by ubiquitin-dependent modifications.
Collapse
Affiliation(s)
- Rafael Mattera
- Cell Biology and Metabolism Branch, NICHD, National Institutes of Health, Bethesda, Maryland 20892
| | | | | | | |
Collapse
|
194
|
Penengo L, Mapelli M, Murachelli AG, Confalonieri S, Magri L, Musacchio A, Di Fiore PP, Polo S, Schneider TR. Crystal structure of the ubiquitin binding domains of rabex-5 reveals two modes of interaction with ubiquitin. Cell 2006; 124:1183-95. [PMID: 16499958 DOI: 10.1016/j.cell.2006.02.020] [Citation(s) in RCA: 227] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 02/06/2006] [Accepted: 02/14/2006] [Indexed: 01/25/2023]
Abstract
The interaction between ubiquitinated proteins and intracellular proteins harboring ubiquitin binding domains (UBDs) is critical to a multitude of cellular processes. Here, we report that Rabex-5, a guanine nucleotide exchange factor for Rab5, binds to Ub through two independent UBDs. These UBDs determine a number of properties of Rabex-5, including its coupled monoubiquitination and interaction in vivo with ubiquitinated EGFRs. Structural and biochemical characterization of the UBDs of Rabex-5 revealed that one of them (MIU, motif interacting with ubiquitin) binds to Ub with modes superimposable to those of the UIM (ubiquitin-interacting motif):Ub interaction, although in the opposite orientation. The other UBD, RUZ (Rabex-5 ubiquitin binding zinc finger) binds to a surface of Ub centered on Asp58(Ub) and distinct from the "canonical" Ile44(Ub)-based surface. The two binding surfaces allow Ub to interact simultaneously with different UBDs, thus opening new perspectives in Ub-mediated signaling.
Collapse
Affiliation(s)
- Lorenza Penengo
- IFOM, the FIRC Institute for Molecular Oncology Foundation, Via Adamello 16, 20139 Milan, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
195
|
Hirano S, Kawasaki M, Ura H, Kato R, Raiborg C, Stenmark H, Wakatsuki S. Double-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting. Nat Struct Mol Biol 2006; 13:272-7. [PMID: 16462748 DOI: 10.1038/nsmb1051] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2005] [Accepted: 12/12/2005] [Indexed: 11/08/2022]
Abstract
Hrs has an essential role in sorting of monoubiquitinated receptors to multivesicular bodies for lysosomal degradation, through recognition of ubiquitinated receptors by its ubiquitin-interacting motif (UIM). Here, we present the structure of a complex of Hrs-UIM and ubiquitin at 1.7-A resolution. Hrs-UIM forms a single alpha-helix, which binds two ubiquitin molecules, one on either side. These two ubiquitin molecules are related by pseudo two-fold screw symmetry along the helical axis of the UIM, corresponding to a shift by two residues on the UIM helix. Both ubiquitin molecules interact with the UIM in the same manner, using the Ile44 surface, with equal binding affinities. Mutational experiments show that both binding sites of Hrs-UIM are required for efficient degradative protein sorting. Hrs-UIM belongs to a new subclass of double-sided UIMs, in contrast to its yeast homolog Vps27p, which has two tandem single-sided UIMs.
Collapse
Affiliation(s)
- Satoshi Hirano
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0801, Japan
| | | | | | | | | | | | | |
Collapse
|
196
|
Lee S, Tsai YC, Mattera R, Smith WJ, Kostelansky MS, Weissman AM, Bonifacino JS, Hurley JH. Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5. Nat Struct Mol Biol 2006; 13:264-71. [PMID: 16462746 PMCID: PMC1578505 DOI: 10.1038/nsmb1064] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Accepted: 01/17/2006] [Indexed: 11/09/2022]
Abstract
Rabex-5 is an exchange factor for Rab5, a master regulator of endosomal trafficking. Rabex-5 binds monoubiquitin, undergoes covalent ubiquitination and contains an intrinsic ubiquitin ligase activity, all of which require an N-terminal A20 zinc finger followed immediately by a helix. The structure of the N-terminal portion of Rabex-5 bound to ubiquitin at 2.5-A resolution shows that Rabex-5-ubiquitin interactions occur at two sites. The first site is a new type of ubiquitin-binding domain, an inverted ubiquitin-interacting motif, which binds with approximately 29-microM affinity to the canonical Ile44 hydrophobic patch on ubiquitin. The second is a diaromatic patch on the A20 zinc finger, which binds with approximately 22-microM affinity to a polar region centered on Asp58 of ubiquitin. The A20 zinc-finger diaromatic patch mediates ubiquitin-ligase activity by directly recruiting a ubiquitin-loaded ubiquitin-conjugating enzyme.
Collapse
Affiliation(s)
- Sangho Lee
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Yien Che Tsai
- Laboratory of Protein Dynamics and Signaling, National Cancer Institute-Frederick, National Institutes of Health, U. S. Department of Health and Human Services, Frederick, MD 21702
| | - Rafael Mattera
- Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892, USA
| | - William J. Smith
- Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Michael S. Kostelansky
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Allan M. Weissman
- Laboratory of Protein Dynamics and Signaling, National Cancer Institute-Frederick, National Institutes of Health, U. S. Department of Health and Human Services, Frederick, MD 21702
| | - Juan S. Bonifacino
- Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892, USA
| | - James H. Hurley
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892, USA
- correspondence should be addressed to James H. Hurley at
| |
Collapse
|
197
|
Kikukawa Y, Minami R, Shimada M, Kobayashi M, Tanaka K, Yokosawa H, Kawahara H. Unique proteasome subunit Xrpn10c is a specific receptor for the antiapoptotic ubiquitin-like protein Scythe. FEBS J 2006; 272:6373-86. [PMID: 16336274 DOI: 10.1111/j.1742-4658.2005.05032.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The Rpn10 subunit of the 26S proteasome can bind to polyubiquitinoylated and/or ubiquitin-like proteins via ubiquitin-interacting motifs (UIMs). Vertebrate Rpn10 consists of five distinct spliced isoforms, but the specific functions of these variants remain largely unknown. We report here that one of the alternative products of Xenopus Rpn10, named Xrpn10c, functions as a specific receptor for Scythe/BAG-6, which has been reported to regulate Reaper-induced apoptosis. Deletional analyses revealed that Scythe has at least two distinct domains responsible for its binding to Xrpn10c. Conversely, an Xrpn10c has a UIM-independent Scythe-binding site. The forced expression of a Scythe mutant protein lacking Xrpn10c-binding domains in Xenopus embryos induces inappropriate embryonic death, whereas the wild-type Scythe did not show any abnormality. The results indicate that Xrpn10c-binding sites of Scythe act as an essential segment linking the ubiquitin/proteasome machinery to the control of proper embryonic development.
Collapse
Affiliation(s)
- Yuhsuke Kikukawa
- Department of Biochemistry, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | | | | | | | | | | | | |
Collapse
|
198
|
Bienko M, Green CM, Crosetto N, Rudolf F, Zapart G, Coull B, Kannouche P, Wider G, Peter M, Lehmann AR, Hofmann K, Dikic I. Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis. Science 2006; 310:1821-4. [PMID: 16357261 DOI: 10.1126/science.1120615] [Citation(s) in RCA: 560] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Translesion synthesis (TLS) is the major pathway by which mammalian cells replicate across DNA lesions. Upon DNA damage, ubiquitination of proliferating cell nuclear antigen (PCNA) induces bypass of the lesion by directing the replication machinery into the TLS pathway. Yet, how this modification is recognized and interpreted in the cell remains unclear. Here we describe the identification of two ubiquitin (Ub)-binding domains (UBM and UBZ), which are evolutionarily conserved in all Y-family TLS polymerases (pols). These domains are required for binding of poleta and poliota to ubiquitin, their accumulation in replication factories, and their interaction with monoubiquitinated PCNA. Moreover, the UBZ domain of poleta is essential to efficiently restore a normal response to ultraviolet irradiation in xeroderma pigmentosum variant (XP-V) fibroblasts. Our results indicate that Ub-binding domains of Y-family polymerases play crucial regulatory roles in TLS.
Collapse
Affiliation(s)
- Marzena Bienko
- Institute for Biochemistry II, Goethe University Medical School, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
199
|
|
200
|
Katiyar S, Lennarz WJ. Studies on the intracellular localization of hHR23B. Biochem Biophys Res Commun 2005; 337:1296-300. [PMID: 16253613 DOI: 10.1016/j.bbrc.2005.09.192] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2005] [Accepted: 09/29/2005] [Indexed: 11/15/2022]
Abstract
Yeast Rad23, originally identified as a DNA repair protein, has been proposed to participate in other cellular functions, i.e., the proteasome-degradation pathway, the process of spindle pole body duplication and as a component of the anaphase checkpoint. Two human homologs of yeast Rad23, hHR23A and hHR23B, exhibit high sequence homology with yRad23 and also have been shown to be involved in DNA repair and proteasome-dependent degradation. Previous studies on the intracellular localization of hHR23A and hHR23B revealed their predominant localization in the nucleus during interphase and in the cytoplasm during mitosis. We have analyzed the localization of hHR23B during all the phases of the cell cycle using immunofluorescence. Unlike previous studies, our results suggest localization of hHR23B in the nucleus as well as in the cytoplasm during G1 phase. The nuclear levels of hHR23B decrease during S-phase of the cell cycle. When the cell enters mitosis, hHR23B relocalizes in the cytoplasm without association with chromatin. These results indicate that the intracellular distribution hHR23B is cell cycle dependent.
Collapse
Affiliation(s)
- Samiksha Katiyar
- Department of Biochemistry and Cell Biology, The Institute for Cell and Developmental Biology, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | | |
Collapse
|