151
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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.
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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
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152
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Kalesnikoff J, Rios EJ, Chen CC, Alejandro Barbieri M, Tsai M, Tam SY, Galli SJ. Roles of RabGEF1/Rabex-5 domains in regulating Fc epsilon RI surface expression and Fc epsilon RI-dependent responses in mast cells. Blood 2007; 109:5308-17. [PMID: 17341663 PMCID: PMC1890836 DOI: 10.1182/blood-2007-01-067363] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
RabGEF1/Rabex-5, a guanine nucleotide exchange factor (GEF) for the endocytic pathway regulator, Rab5, contains a Vps9 domain, an A20-like zinc finger (ZnF) domain, and a coiled coil domain. To investigate the importance of these domains in regulating receptor internalization and cell activation, we lentivirally delivered RabGEF1 mutants into RabGEF1-deficient (-/-) mast cells and examined Fc epsilon RI-dependent responses. Wild-type RabGEF1 expression corrected phenotypic abnormalities in -/- mast cells, including decreased basal Fc epsilon RI expression, slowed Fc epsilon RI internalization, elevated IgE + Ag-induced degranulation and IL-6 production, and the decreased ability of -/- cytosol to support endosome fusion. We showed that RabGEF1's ZnF domain has ubiquitin ligase activity. Moreover, the coiled coil domain of RabGEF1 is required for Rabaptin-5 binding and for maintaining basal levels of Rabaptin-5 and surface Fc epsilon RI. However, mutants lacking either of these domains normalized phenotypic abnormalities in IgE + antigen-activated -/- mast cells. By contrast, correction of these -/- phenotypes required a functional Vps9 domain. Thus, Fc epsilon RI-mediated mast cell functional activation is dependent on RabGEF1's GEF activity.
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Affiliation(s)
- Janet Kalesnikoff
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305-5324, USA
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153
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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.
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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:
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154
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Kirkin V, Dikic I. Role of ubiquitin- and Ubl-binding proteins in cell signaling. Curr Opin Cell Biol 2007; 19:199-205. [PMID: 17303403 DOI: 10.1016/j.ceb.2007.02.002] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Accepted: 02/05/2007] [Indexed: 12/15/2022]
Abstract
Besides tagging proteins for degradation, ubiquitin is now recognized as a signaling module for diverse cellular processes, including progression through the cell cycle, DNA repair, gene transcription, receptor trafficking and endocytosis. Recent advances have indicated the existence of a wide variety of ubiquitin-binding proteins that, upon recognition of conjugated ubiquitin moieties, can control assembly of complex signaling networks. Small ubiquitin-like proteins, like SUMO, emerge to play biological roles distinct from ubiquitin, and require specific recognition by a dedicated set of proteins. Identification and characterization of recognition motifs and domains for ubiquitin-like proteins have just begun, promising new insights into the diversity of functions ubiquitin family proteins have in physiological and pathological settings.
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Affiliation(s)
- Vladimir Kirkin
- Institute of Biochemistry II, Goethe University Hospital, Theodor-Stern-Kai 7, D-60590 Frankfurt (Main), Germany
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155
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Ottmann C, Yasmin L, Weyand M, Veesenmeyer JL, Diaz MH, Palmer RH, Francis MS, Hauser AR, Wittinghofer A, Hallberg B. Phosphorylation-independent interaction between 14-3-3 and exoenzyme S: from structure to pathogenesis. EMBO J 2007; 26:902-13. [PMID: 17235285 PMCID: PMC1794388 DOI: 10.1038/sj.emboj.7601530] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2006] [Accepted: 12/04/2006] [Indexed: 01/04/2023] Open
Abstract
14-3-3 proteins are phosphoserine/phosphothreonine-recognizing adapter proteins that regulate the activity of a vast array of targets. There are also examples of 14-3-3 proteins binding their targets via unphosphorylated motifs. Here we present a structural and biological investigation of the phosphorylation-independent interaction between 14-3-3 and exoenzyme S (ExoS), an ADP-ribosyltransferase toxin of Pseudomonas aeruginosa. ExoS binds to 14-3-3 in a novel binding mode mostly relying on hydrophobic contacts. The 1.5 A crystal structure is supported by cytotoxicity analysis, which reveals that substitution of the corresponding hydrophobic residues significantly weakens the ability of ExoS to modify the endogenous targets RAS/RAP1 and to induce cell death. Furthermore, mutation of key residues within the ExoS binding site for 14-3-3 impairs virulence in a mouse pneumonia model. In conclusion, we show that ExoS binds 14-3-3 in a novel reversed orientation that is primarily dependent on hydrophobic residues. This interaction is phosphorylation independent and is required for the function of ExoS.
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Affiliation(s)
- Christian Ottmann
- Department of Structural Biology, Max-Planck-Institute for Molecular Physiology, Dortmund, Germany
- Chemical Genomics Centre, Dortmund, Germany
| | - Lubna Yasmin
- Department of Medical Biosciences/Pathology, Umeå University, Umeå, Sweden
| | - Michael Weyand
- Department of Structural Biology, Max-Planck-Institute for Molecular Physiology, Dortmund, Germany
| | - Jeffrey L Veesenmeyer
- Departments of Microbiology/Immunology and Medicine, Northwestern University, Chicago, IL, USA
| | - Maureen H Diaz
- Departments of Microbiology/Immunology and Medicine, Northwestern University, Chicago, IL, USA
| | - Ruth H Palmer
- Umeå Center for Molecular Pathogenesis, Umeå University, Umeå, Sweden
| | | | - Alan R Hauser
- Departments of Microbiology/Immunology and Medicine, Northwestern University, Chicago, IL, USA
| | - Alfred Wittinghofer
- Department of Structural Biology, Max-Planck-Institute for Molecular Physiology, Dortmund, Germany
| | - Bengt Hallberg
- Department of Medical Biosciences/Pathology, Umeå University, Umeå, Sweden
- Department of Medical Biosciences/Pathology, Buil. 6M, Umeå University, Umeå 90187, Sweden. Tel.: +46 907 852 523; Fax: +46 907 852 829; E-mail:
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156
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Rich RL, Myszka DG. Survey of the year 2006 commercial optical biosensor literature. J Mol Recognit 2007; 20:300-66. [DOI: 10.1002/jmr.862] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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157
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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.
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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.
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158
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Vij S, Tyagi AK. Genome-wide analysis of the stress associated protein (SAP) gene family containing A20/AN1 zinc-finger(s) in rice and their phylogenetic relationship with Arabidopsis. Mol Genet Genomics 2006; 276:565-75. [PMID: 17033811 DOI: 10.1007/s00438-006-0165-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 08/31/2006] [Indexed: 10/24/2022]
Abstract
Proteins with the A20/AN1 zinc-finger domain are present in all eukaryotes and are well characterized in animals, but little is known about their function in plants. Earlier, we have identified an A20/AN1 zinc-finger containing stress associated protein 1 gene (SAP1) in rice and validated its function in abiotic stress tolerance. In this study, genome-wide survey of genes encoding proteins possessing A20/AN1 zinc-finger, named SAP gene family, has been carried out in rice and Arabidopsis. The genomic distribution and gene architecture as well as domain structure and phylogenetic relationship of encoded proteins numbering 18 and 14 in rice and Arabidopsis, respectively, have been studied. Expression analysis of the rice SAP family was done to investigate their response under abiotic stress conditions. All the genes were inducible by one or the other abiotic stresses indicating that the OsSAP gene family is an important component of stress response in rice. Manipulation of their expression and identification of their superior alleles should help confer stress tolerance in target crops.
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Affiliation(s)
- Shubha Vij
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
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159
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Seet BT, Dikic I, Zhou MM, Pawson T. Reading protein modifications with interaction domains. Nat Rev Mol Cell Biol 2006; 7:473-83. [PMID: 16829979 DOI: 10.1038/nrm1960] [Citation(s) in RCA: 503] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Proteins are controlled by a vast and dynamic array of post-translational modifications, many of which create binding sites for specific protein-interaction domains. We propose that these domains, working together, read the state of the proteome and therefore couple post-translational modifications to cellular organization. We also identify common strategies through which modification-dependent interactions synergize to regulate cell behaviour.
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Affiliation(s)
- Bruce T Seet
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
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160
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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.
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Affiliation(s)
- Camilla Raiborg
- Department of Biochemistry, the Norwegian Radium Hospital and the University of Oslo, Montebello, N-0310 Oslo, Norway
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161
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Tashiro K, Konishi H, Sano E, Nabeshi H, Yamauchi E, Taniguchi H. Suppression of the Ligand-mediated Down-regulation of Epidermal Growth Factor Receptor by Ymer, a Novel Tyrosine-phosphorylated and Ubiquitinated Protein. J Biol Chem 2006; 281:24612-22. [PMID: 16803894 DOI: 10.1074/jbc.m604184200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The ligand-mediated down-regulation of the growth factor receptors is preceded by the involvement of various other factors. In particular, a ubiquitin ligase, Cbl, plays a central role in this event. Several candidates that have potential effects on the negative control of the epidermal growth factor (EGF) receptor have now been identified by our recent studies in phospho-proteomics. Among these molecules, we focus on characterizing a novel protein, Ymer, which is a tyrosine-phosphorylated and ubiquitinated protein. Ymer is found to be phosphorylated at tyrosine 145 and 146 upon EGF stimulation, and lysine 129 of Ymer has been identified as a ubiquitination site. Ymer has two motifs interacting with the ubiquitin (MIU) domains that might function as a binding site for the ubiquitinated EGF receptor. Although Ymer and EGF receptors are associated in an EGF-dependent manner, their interaction is required not only for MIU domains but also for the tyrosine phosphorylation of Ymer. Phosphorylated Ymer is mainly located at the plasma membrane with EGF receptor and functions in its endocytosis and degradation. Furthermore, EGF-mediated secondary modifications of an activated-EGF receptor are inhibited by overexpressing Ymer in COS7 cells. Therefore, Ymer may have competitive effects on the activation of the EGF receptor. Our findings suggest that Ymer functions as a novel inhibitor for the down-regulation of the EGF receptor and plays a crucial role for regulating the amount of the EGF receptor on the cell surface membrane.
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Affiliation(s)
- Kyoko Tashiro
- Institute for Enzyme Research, University of Tokushima, Tokushima 770-8503, Japan and Harima Institute at Spring-8, RIKEN, Hyogo 679-5148, Japan
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162
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Reyes-Turcu FE, Horton JR, Mullally JE, Heroux A, Cheng X, Wilkinson KD. The ubiquitin binding domain ZnF UBP recognizes the C-terminal diglycine motif of unanchored ubiquitin. Cell 2006; 124:1197-208. [PMID: 16564012 DOI: 10.1016/j.cell.2006.02.038] [Citation(s) in RCA: 256] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Revised: 01/14/2006] [Accepted: 02/28/2006] [Indexed: 11/28/2022]
Abstract
Ubiquitin binding proteins regulate the stability, function, and/or localization of ubiquitinated proteins. Here we report the crystal structures of the zinc-finger ubiquitin binding domain (ZnF UBP) from the deubiquitinating enzyme isopeptidase T (IsoT, or USP5) alone and in complex with ubiquitin. Unlike other ubiquitin binding domains, this domain contains a deep binding pocket where the C-terminal diglycine motif of ubiquitin is inserted, thus explaining the specificity of IsoT for an unmodified C terminus on the proximal subunit of polyubiquitin. Mutations in the domain demonstrate that it is required for optimal catalytic activation of IsoT. This domain is present in several other protein families, and the ZnF UBP domain from an E3 ligase also requires the C terminus of ubiquitin for binding. These data suggest that binding the ubiquitin C terminus may be necessary for the function of other proteins.
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163
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Abstract
Ubiquitinated proteins are sorted into distinct pathways via association with several classes of ubiquitin binding domain-containing proteins. A virtual explosion in the field of ubiquitin binding proteins has revealed several new classes and interactions with distinct surfaces on ubiquitin, providing a clearer understanding of how sorting of ubiquitinated proteins is achieved.
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Affiliation(s)
- J Wade Harper
- Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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164
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165
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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.
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Affiliation(s)
- Lorenza Penengo
- IFOM, the FIRC Institute for Molecular Oncology Foundation, Via Adamello 16, 20139 Milan, Italy
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