1
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P T B, Sahu I. Decoding the ubiquitin landscape by cutting-edge ubiquitinomic approaches. Biochem Soc Trans 2024; 52:627-637. [PMID: 38572966 DOI: 10.1042/bst20230457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Functional consequences of protein ubiquitination have gone far beyond the degradation regulation as was initially imagined during its discovery 40 years back. The state-of-the-art has revealed the plethora of signaling pathways that are largely regulated by ubiquitination process in eukaryotes. To no surprise, ubiquitination is often dysregulated in many human diseases, including cancer, neurodegeneration and infection. Hence it has become a major focus with high-gain research value for many investigators to unravel new proteoforms, that are the targets of this ubiquitination modification. Despite many biochemical or proteomic approaches available for ubiquitination detection, mass-spectrometry stood out to be the most efficient and transformative technology to read this complex modification script. Here in this review, we have discussed how different ubiquitin codes can be decoded qualitatively and quantitatively following various sequential proteomic approaches to date reported and indicated the current limitations with scope for improvements.
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Affiliation(s)
- Brindhavanam P T
- Division of Medical Research, SRM-Medical College Hospital and Research Centre, Faculty of Medical and Health Sciences, SRMIST, Kattankulathur, Tamil Nadu, India
| | - Indrajit Sahu
- Division of Medical Research, SRM-Medical College Hospital and Research Centre, Faculty of Medical and Health Sciences, SRMIST, Kattankulathur, Tamil Nadu, India
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2
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Kim J, Chang N, Kim Y, Lee J, Oh D, Choi J, Kim O, Kim S, Choi M, Lee J, Lee J, Kim J, Cho M, Kim M, Lee K, Hwang D, Sa JK, Park S, Baek S, Im D. The Novel Tetra-Specific Drug C-192, Conjugated Using UniStac, Alleviates Non-Alcoholic Steatohepatitis in an MCD Diet-Induced Mouse Model. Pharmaceuticals (Basel) 2023; 16:1601. [PMID: 38004466 PMCID: PMC10674394 DOI: 10.3390/ph16111601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Non-alcoholic steatohepatitis (NASH) is a complex disease resulting from chronic liver injury associated with obesity, type 2 diabetes, and inflammation. Recently, the importance of developing multi-target drugs as a strategy to address complex diseases such as NASH has been growing; however, their manufacturing processes remain time- and cost-intensive and inefficient. To overcome these limitations, we developed UniStac, a novel enzyme-mediated conjugation platform for multi-specific drug development. UniStac demonstrated high conjugation yields, optimal thermal stabilities, and robust biological activities. We designed a tetra-specific compound, C-192, targeting glucagon-like peptide 1 (GLP-1), glucagon (GCG), fibroblast growth factor 21 (FGF21), and interleukin-1 receptor antagonist (IL-1RA) simultaneously for the treatment of NASH using UniStac. The biological activity and treatment efficacy of C-192 were confirmed both in vitro and in vivo using a methionine-choline-deficient (MCD) diet-induced mouse model. C-192 exhibited profound therapeutic efficacies compared to conventional drugs, including liraglutide and dulaglutide. C-192 significantly improved alanine transaminase levels, triglyceride accumulation, and the non-alcoholic fatty liver disease activity score. In this study, we demonstrated the feasibility of UniStac in creating multi-specific drugs and confirmed the therapeutic potential of C-192, a drug that integrates multiple mechanisms into a single molecule for the treatment of NASH.
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Affiliation(s)
- Jihye Kim
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Nakho Chang
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Yunki Kim
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Jaehyun Lee
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Daeseok Oh
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Jaeyoung Choi
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Onyou Kim
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Sujin Kim
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Myongho Choi
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Junyeob Lee
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Junghwa Lee
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Jungyul Kim
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Minji Cho
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Minsu Kim
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Kwanghwan Lee
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Dukhyun Hwang
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Jason K. Sa
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Sungjin Park
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Seungjae Baek
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Daeseong Im
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
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3
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Mangini V, Grasso G, Belviso BD, Sciacca MFM, Lanza V, Caliandro R, Milardi D. Stretching the chains: the destabilizing impact of Cu 2+ and Zn 2+ ions on K48-linked diubiquitin. Dalton Trans 2023; 52:11835-11849. [PMID: 37581921 DOI: 10.1039/d3dt01815f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Ubiquitin signalling and metal homeostasis play key roles in controlling several physiological cellular activities, including protein trafficking and degradation. While some relationships between these two biochemical pathways have started to surface, our knowledge of their interplay remains limited. Here, we employ a variety of techniques, such as circular dichroism, differential scanning calorimetry, pressure perturbation calorimetry, fluorescence emission, SDS-PAGE, and small-angle X-ray scattering (SAXS) to evaluate the impact of Cu2+ and Zn2+ ions on the structure and stability of K48 linked diubiquitin (K48-Ub2), a simple model for polyubiquitin chains. The SAXS analysis results show that the structure of the metal-free protein is similar to that observed when the protein is bound to the E2 conjugating enzyme, lending support to the idea that the structure of unanchored K48-linked ubiquitin chains is sufficient for identification by conjugating enzymes without the need for an induced fit mechanism. Our results indicate that K48-Ub2 can coordinate up to four metal ions with both copper and zinc ions inducing slight changes to the secondary structure of the protein. However, we noted significant distinctions in their impacts on protein stability and overall architecture. Specifically, Cu2+ ions resulted in a destabilization of the protein structure, which facilitated the formation of dimer aggregates. Next, we observed a shift in the conformational dynamics of K48-Ub2 toward less compact and more flexible states upon metal ion binding, with Zn2+ inducing a more significant effect than Cu2+ ions. Our structural modelling study demonstrates that both metal ions induced perturbations in the K48-Ub2 structure, leading to the separation of the two monomers thus inhibiting interactions with E2 enzymes. In conclusion, the findings from this study enhance our comprehension of the mechanisms underlying Ub chains recognition. Moreover, they strengthen the notion that drug discovery initiatives aimed at targeting metal-mediated disruptions in Ub signaling hold great potential for treating a wide range of diseases that stem from abnormal protein accumulation.
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Affiliation(s)
- Vincenzo Mangini
- Istituto di Cristallografia - CNR sede di Bari, Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Giulia Grasso
- Istituto di Cristallografia - CNR sede secondaria di Catania, Via P. Gaifami 18, 95126 Catania, Italy.
| | - Benny Danilo Belviso
- Istituto di Cristallografia - CNR sede di Bari, Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Michele F M Sciacca
- Istituto di Cristallografia - CNR sede secondaria di Catania, Via P. Gaifami 18, 95126 Catania, Italy.
| | - Valeria Lanza
- Istituto di Cristallografia - CNR sede secondaria di Catania, Via P. Gaifami 18, 95126 Catania, Italy.
| | - Rocco Caliandro
- Istituto di Cristallografia - CNR sede di Bari, Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Danilo Milardi
- Istituto di Cristallografia - CNR sede secondaria di Catania, Via P. Gaifami 18, 95126 Catania, Italy.
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4
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Harris LD, Le Pen J, Scholz N, Mieszczanek J, Vaughan N, Davis S, Berridge G, Kessler BM, Bienz M, Licchesi JDF. The deubiquitinase TRABID stabilizes the K29/K48-specific E3 ubiquitin ligase HECTD1. J Biol Chem 2021; 296:100246. [PMID: 33853758 PMCID: PMC7948964 DOI: 10.1074/jbc.ra120.015162] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/23/2020] [Accepted: 12/30/2020] [Indexed: 12/18/2022] Open
Abstract
Ubiquitin is a versatile posttranslational modification, which is covalently attached to protein targets either as a single moiety or as a ubiquitin chain. In contrast to K48 and K63-linked chains, which have been extensively studied, the regulation and function of most atypical ubiquitin chains are only starting to emerge. The deubiquitinase TRABID/ZRANB1 is tuned for the recognition and cleavage of K29 and K33-linked chains. Yet, substrates of TRABID and the cellular functions of these atypical ubiquitin signals remain unclear. We determined the interactome of two TRABID constructs rendered catalytic dead either through a point mutation in the catalytic cysteine residue or through removal of the OTU catalytic domain. We identified 50 proteins trapped by both constructs and which therefore represent candidate substrates of TRABID. The E3 ubiquitin ligase HECTD1 was then validated as a substrate of TRABID and used UbiCREST and Ub-AQUA proteomics to show that HECTD1 preferentially assembles K29- and K48-linked ubiquitin chains. Further in vitro autoubiquitination assays using ubiquitin mutants established that while HECTD1 can assemble short homotypic K29 and K48-linked chains, it requires branching at K29/K48 in order to achieve its full ubiquitin ligase activity. We next used transient knockdown and genetic knockout of TRABID in mammalian cells in order to determine the functional relationship between TRABID and HECTD1. This revealed that upon TRABID depletion, HECTD1 is readily degraded. Thus, this study identifies HECTD1 as a mammalian E3 ligase that assembles branched K29/K48 chains and also establishes TRABID-HECTD1 as a DUB/E3 pair regulating K29 linkages.
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Affiliation(s)
- Lee D Harris
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Janic Le Pen
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Nico Scholz
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Juliusz Mieszczanek
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Natalie Vaughan
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Simon Davis
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Georgina Berridge
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Mariann Bienz
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Julien D F Licchesi
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.
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5
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Crystal structure of HECT domain of UBE3C E3 ligase and its ubiquitination activity. Biochem J 2020; 477:905-923. [PMID: 32039437 DOI: 10.1042/bcj20200027] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/03/2020] [Accepted: 02/10/2020] [Indexed: 01/23/2023]
Abstract
The HECT family of E3 ubiquitin ligase is divided into three subfamilies: the NEDD4, the HERC, and the 'other'. Previous studies have mostly targeted members of the NEDD4 subfamily for structural and functional analysis. The UBE3C E3 ligase is a member of the 'other' subfamily HECT and influences several crucial cellular processes, including innate immunity, proteasome processivity, and cancer metastasis. Here, we report the crystal structure of the HECT domain of UBE3C (amino acids (aa) 744-1083) with an additional fifty N-terminal amino acids (aa 693-743) at 2.7 Å, along with multiple in vitro ubiquitination assays to understand its enzymatic activity. The UBE3C HECT domain forms an open, L-shaped, bilobed conformation, having a large N-lobe and a small C-lobe. We show that the N-terminal region (aa 693-743) preceding the UBE3C HECT domain as well as a loop region (aa 758-762) in the N-lobe of the HECT domain affect the stability and activity of UBE3C HECT domain. Moreover, we identified Lys903 in the UBE3C HECT domain as a major site of autoubiquitination. The deletion of the last three amino acids at the C-terminal completely abrogated UBE3C activity while mutations of Gln961 and Ser1049 residues in the HECT domain substantially decreased its autoubiquitination activity. We demonstrate that these region/residues are involved in the E2-E3 transthiolation process and affect the UBE3C mediated autoubiquitination. Collectively, our study identified key residues crucial for UBE3C enzymatic activity, and it may assist in the development of suitable inhibitors to regulate its activity in multiple cancers.
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6
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Ries LK, Sander B, Deol KK, Letzelter MA, Strieter ER, Lorenz S. Analysis of ubiquitin recognition by the HECT ligase E6AP provides insight into its linkage specificity. J Biol Chem 2019; 294:6113-6129. [PMID: 30737286 PMCID: PMC6463701 DOI: 10.1074/jbc.ra118.007014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/28/2019] [Indexed: 12/19/2022] Open
Abstract
Deregulation of the HECT-type ubiquitin ligase E6AP (UBE3A) is implicated in human papilloma virus-induced cervical tumorigenesis and several neurodevelopmental disorders. Yet the structural underpinnings of activity and specificity in this crucial ligase are incompletely understood. Here, we unravel the determinants of ubiquitin recognition by the catalytic domain of E6AP and assign them to particular steps in the catalytic cycle. We identify a functionally critical interface that is specifically required during the initial formation of a thioester-linked intermediate between the C terminus of ubiquitin and the ligase-active site. This interface resembles the one utilized by NEDD4-type enzymes, indicating that it is widely conserved across HECT ligases, independent of their linkage specificities. Moreover, we uncover surface regions in ubiquitin and E6AP, both in the N- and C-terminal portions of the catalytic domain, that are important for the subsequent reaction step of isopeptide bond formation between two ubiquitin molecules. We decipher key elements of linkage specificity, including the C-terminal tail of E6AP and a hydrophilic surface region of ubiquitin in proximity to the acceptor site Lys-48. Intriguingly, mutation of Glu-51, a single residue within this region, permits formation of alternative chain types, thus pointing to a key role of ubiquitin in conferring linkage specificity to E6AP. We speculate that substrate-assisted catalysis, as described previously for certain RING-associated ubiquitin-conjugating enzymes, constitutes a common principle during linkage-specific ubiquitin chain assembly by diverse classes of ubiquitination enzymes, including HECT ligases.
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Affiliation(s)
- Lena K Ries
- From the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany
| | - Bodo Sander
- From the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany
| | - Kirandeep K Deol
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003
| | - Marie-Annick Letzelter
- From the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany
| | - Eric Robert Strieter
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003; Departments of Biochemistry and Molecular Biology, University of Massachusetts at Amherst, Amherst, Massachusetts 01003
| | - Sonja Lorenz
- From the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany.
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7
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Buneeva OA, Medvedev AE. The role of atypical ubiquitination in cell regulation. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2017. [DOI: 10.1134/s1990750817010024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Buneeva OA, Medvedev AE. [Atypical ubiquitination of proteins]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2017; 62:496-509. [PMID: 27797324 DOI: 10.18097/pbmc20166205496] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ubiquitination is a type of posttranslational modification of intracellular proteins characterized by covalent attachment of one (monoubiquitination) or several (polyubiquitination) of ubiquitin molecules to target proteins. In the case of polyubiquitination, linear or branched polyubiquitin chains are formed. Their formation involves various lysine residues of monomeric ubiquitin. The best studied is Lys48-polyubiquitination, which targets proteins for proteasomal degradation. In this review we have considered examples of so-called atypical polyubiquitination, which mainly involves other lysine residues (Lys6, Lys11, Lys27, Lys29, Lys33, Lys63) and also N-terminal methionine. The considered examples convincingly demonstrate that polyubiquitination of proteins not necessarily targets proteins for their proteolytic degradation in proteasomes. Atypically polyubiquitinated proteins are involved in regulation of various processes and altered polyubiquitination of certain proteins is crucial for development of serious diseases.
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Affiliation(s)
- O A Buneeva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A E Medvedev
- Institute of Biomedical Chemistry, Moscow, Russia
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Smith G, Tomlinson D, Harrison M, Ponnambalam S. Chapter Eight - Ubiquitin-Mediated Regulation of Cellular Responses to Vascular Endothelial Growth Factors. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 141:313-38. [DOI: 10.1016/bs.pmbts.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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10
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Kim JH, Choi JS, Kim S, Kim K, Myung PK, Park SG, Seo YS, Park BC. Synergistic effect of two E2 ubiquitin conjugating enzymes in SCF(hFBH1) catalyzed polyubiquitination. BMB Rep 2015; 48:25-9. [PMID: 24667174 PMCID: PMC4345638 DOI: 10.5483/bmbrep.2015.48.1.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 03/24/2014] [Accepted: 03/24/2014] [Indexed: 11/20/2022] Open
Abstract
Ubiquitination is a post translational modification which mostly links with proteasome dependent protein degradation. This process has been known to play pivotal roles in the number of biological events including apoptosis, cell signaling, transcription and translation. Although the process of ubiquitination has been studied extensively, the mechanism of polyubiquitination by multi protein E3 ubiquitin ligase, SCF complex remains elusive. In the present study, we identified UbcH5a as a novel stimulating factor for poly-ubiquitination catalyzed by SCFhFBH1 using biochemical fractionations and MALDI-TOF. Moreover, we showed that recombinant UbcH5a and Cdc34 synergistically stimulate SCFhFBH1 catalyzed polyubiquitination in vitro. These data may provide an important cue to understand the mechanism how the SCF complex efficiently polyubiquitinates target substrates. [BMB Reports 2015; 48(1): 25-29]
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Affiliation(s)
- Jeong-Hoon Kim
- Targeted Gene Regulation Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 305-333; Department of Functional Genomics, University of Science and Technology (UST), Daejeon 305-350, Korea
| | - Jin Sun Choi
- Medical Proteomics Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 305-333; College of Pharmacy, Chungnam National University, Daejeon 305-764, Korea
| | - Sunhong Kim
- Targeted Medicine Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Chungbuk 363-883, Korea
| | - Kidae Kim
- Medical Proteomics Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 305-333, Korea
| | - Pyung Keun Myung
- College of Pharmacy, Chungnam National University, Daejeon 305-764, Korea
| | - Sung Goo Park
- Medical Proteomics Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 305-333, Korea
| | - Yeon-Soo Seo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Byoung Chul Park
- Medical Proteomics Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 305-333, Korea
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11
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Exploring the RING-catalyzed ubiquitin transfer mechanism by MD and QM/MM calculations. PLoS One 2014; 9:e101663. [PMID: 25003393 PMCID: PMC4086935 DOI: 10.1371/journal.pone.0101663] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 06/09/2014] [Indexed: 11/19/2022] Open
Abstract
Ubiquitylation is a universal mechanism for controlling cellular functions. A large family of ubiquitin E3 ligases (E3) mediates Ubiquitin (Ub) modification. To facilitate Ub transfer, RING E3 ligases bind both the substrate and ubiquitin E2 conjugating enzyme (E2) linked to Ub via a thioester bond to form a catalytic complex. The mechanism of Ub transfer catalyzed by RING E3 remains elusive. By employing a combined computational approach including molecular modeling, molecular dynamics (MD) simulations, and quantum mechanics/molecular mechanics (QM/MM) calculations, we characterized this catalytic mechanism in detail. The three-dimensional model of dimeric RING E3 ligase RNF4 RING, E2 ligase UbcH5A, Ub and the substrate SUMO2 shows close contact between the substrate and Ub transfer catalytic center. Deprotonation of the substrate lysine by D117 on UbcH5A occurs with almost no energy barrier as calculated by MD and QM/MM calculations. Then, the side chain of the activated lysine gets close to the thioester bond via a conformation change. The Ub transfer pathway begins with a nucleophilic addition that forms an oxyanion intermediate of a 4.23 kcal/mol energy barrier followed by nucleophilic elimination, resulting in a Ub modified substrate by a 5.65 kcal/mol energy barrier. These results provide insight into the mechanism of RING-catalyzed Ub transfer guiding the discovery of Ub system inhibitors.
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12
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Chu BW, Kovary KM, Guillaume J, Chen LC, Teruel MN, Wandless TJ. The E3 ubiquitin ligase UBE3C enhances proteasome processivity by ubiquitinating partially proteolyzed substrates. J Biol Chem 2013; 288:34575-87. [PMID: 24158444 DOI: 10.1074/jbc.m113.499350] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
To maintain protein homeostasis, cells must balance protein synthesis with protein degradation. Accumulation of misfolded or partially degraded proteins can lead to the formation of pathological protein aggregates. Here we report the use of destabilizing domains, proteins whose folding state can be reversibly tuned using a high affinity ligand, as model substrates to interrogate cellular protein quality control mechanisms in mammalian cells using a forward genetic screen. Upon knockdown of UBE3C, an E3 ubiquitin ligase, a reporter protein consisting of a destabilizing domain fused to GFP is degraded more slowly and incompletely by the proteasome. Partial proteolysis is also observed when UBE3C is present but cannot ubiquitinate substrates because its active site has been mutated, it is unable to bind to the proteasome, or the substrate lacks lysine residues. UBE3C knockdown also results in less substrate polyubiquitination. Finally, knockdown renders cells more susceptible to the Hsp90 inhibitor 17-AAG, suggesting that UBE3C protects against the harmful accumulation of protein fragments arising from incompletely degraded proteasome substrates.
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Affiliation(s)
- Bernard W Chu
- From the Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305
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13
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Du H, Huang Y, Zaghlula M, Walters E, Cox TC, Massiah MA. The MID1 E3 ligase catalyzes the polyubiquitination of Alpha4 (α4), a regulatory subunit of protein phosphatase 2A (PP2A): novel insights into MID1-mediated regulation of PP2A. J Biol Chem 2013; 288:21341-21350. [PMID: 23740247 DOI: 10.1074/jbc.m113.481093] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alpha4 (α4) is a key regulator of protein phosphatase 2A (PP2A) and mTOR in steps essential for cell-cycle progression. α4 forms a complex with PP2A and MID1, a microtubule-associated ubiquitin E3 ligase that facilitates MID1-dependent regulation of PP2A and the dephosphorylation of MID1 by PP2A. Ectopic overexpression of α4 is associated with hepatocellular carcinomas, breast cancer, and invasive adenocarcinomas. Here, we provide data suggesting that α4 is regulated by ubiquitin-dependent degradation mediated by MID1. In cells stably expressing a dominant-negative form of MID1, significantly elevated levels of α4 were observed. Treatment of cells with the specific proteasome inhibitor, lactacystin, resulted in a 3-fold increase in α4 in control cells and a similar level in mutant cells. Using in vitro assays, individual MID1 E3 domains facilitated monoubiquitination of α4, whereas full-length MID1 as well as RING-Bbox1 and RING-Bbox1-Bbox2 constructs catalyzed its polyubiquitination. In a novel non-biased functional screen, we identified a leucine to glutamine substitution at position 146 within Bbox1 that abolished MID1-α4 interaction and the subsequent polyubiquitination of α4, indicating that direct binding to Bbox1 was necessary for the polyubiquitination of α4. The mutant had little impact on the RING E3 ligase functionality of MID1. Mass spectrometry data confirmed Western blot analysis that ubiquitination of α4 occurs only within the last 105 amino acids. These novel findings identify a new role for MID1 and a mechanism of regulation of α4 that is likely to impact the stability and activity level of PP2Ac.
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Affiliation(s)
- Haijuan Du
- From the Department of Chemistry, George Washington University, Washington, D. C. 20052
| | - Yongzhao Huang
- the Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute and
| | - Manar Zaghlula
- From the Department of Chemistry, George Washington University, Washington, D. C. 20052
| | - Erica Walters
- From the Department of Chemistry, George Washington University, Washington, D. C. 20052
| | - Timothy C Cox
- the Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute and; Department of Pediatrics, University of Washington, Seattle, Washington 98101, and; the Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Michael A Massiah
- From the Department of Chemistry, George Washington University, Washington, D. C. 20052,.
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14
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Generation of free ubiquitin chains is up-regulated in stress and facilitated by the HECT domain ubiquitin ligases UFD4 and HUL5. Biochem J 2012; 444:611-7. [DOI: 10.1042/bj20111840] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Polyubiquitin chains serve a variety of physiological roles. Typically the chains are bound covalently to a protein substrate and in many cases target it for degradation by the 26S proteasome. However, several studies have demonstrated the existence of free polyubiquitin chains which are not linked to a specific substrate. Several physiological functions have been attributed to these chains, among them playing a role in signal transduction and serving as storage of ubiquitin for utilization under stress. In the present study, we have established a system for the detection of free ubiquitin chains and monitoring their level under changing conditions. Using this system, we show that UFD4 (ubiquitin fusion degradation 4), a HECT (homologous with E6-AP C-terminus) domain ubiquitin ligase, is involved in free chain generation. We also show that generation of these chains is stimulated in response to a variety of stresses, particularly those caused by DNA damage. However, it appears that the stress-induced synthesis of free chains is catalysed by a different ligase, HUL5 (HECT ubiquitin ligase 5), which is also a HECT domain E3.
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15
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Ziv I, Matiuhin Y, Kirkpatrick DS, Erpapazoglou Z, Leon S, Pantazopoulou M, Kim W, Gygi SP, Haguenauer-Tsapis R, Reis N, Glickman MH, Kleifeld O. A perturbed ubiquitin landscape distinguishes between ubiquitin in trafficking and in proteolysis. Mol Cell Proteomics 2011; 10:M111.009753. [PMID: 21427232 PMCID: PMC3098606 DOI: 10.1074/mcp.m111.009753] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Any of seven lysine residues on ubiquitin can serve as the base for chain-extension, resulting in a sizeable spectrum of ubiquitin modifications differing in chain length or linkage type. By optimizing a procedure for rapid lysis, we charted the profile of conjugated cellular ubiquitin directly from whole cell extract. Roughly half of conjugated ubiquitin (even at high molecular weights) was nonextended, consisting of monoubiquitin modifications and chain terminators (endcaps). Of extended ubiquitin, the primary linkages were via Lys48 and Lys63. All other linkages were detected, contributing a relatively small portion that increased at lower molecular weights. In vivo expression of lysineless ubiquitin (K0 Ub) perturbed the ubiquitin landscape leading to elevated levels of conjugated ubiquitin, with a higher mono-to-poly ratio. Affinity purification of these trapped conjugates identified a comprehensive list of close to 900 proteins including novel targets. Many of the proteins enriched by K0 ubiquitination were membrane-associated, or involved in cellular trafficking. Prime among them are components of the ESCRT machinery and adaptors of the Rsp5 E3 ubiquitin ligase. Ubiquitin chains associated with these substrates were enriched for Lys63 linkages over Lys48, indicating that K0 Ub is unevenly distributed throughout the ubiquitinome. Biological assays validated the interference of K0 Ub with protein trafficking and MVB sorting, minimally affecting Lys48-dependent turnover of proteasome substrates. We conclude that despite the shared use of the ubiquitin molecule, the two branches of the ubiquitin machinery—the ubiquitin-proteasome system and the ubiquitin trafficking system—were unevenly perturbed by expression of K0 ubiquitin.
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Affiliation(s)
- Inbal Ziv
- Department of Biology, Technion Israel institute of Technology, Haifa 32000, Israel
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16
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Grillari J, Grillari-Voglauer R, Jansen-Dürr P. Post-translational modification of cellular proteins by ubiquitin and ubiquitin-like molecules: role in cellular senescence and aging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 694:172-96. [PMID: 20886764 DOI: 10.1007/978-1-4419-7002-2_13] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ubiquitination ofendogenous proteins is one of the key regulatory steps that guides protein degradation through regulation of proteasome activity. During the last years evidence has accumulated that proteasome activity is decreased during the aging process in various model systems and that these changes might be causally related to aging and age-associated diseases. Since in most instances ubiquitination is the primary event in target selection, the system ofubiquitination and deubiquitination might be of similar importance. Furthermore, ubiquitination and proteasomal degradation are not completely congruent, since ubiquitination confers also functions different from targeting proteins for degradation. Depending on mono- and polyubiquitination and on how ubiquitin chains are linked together, post-translational modifications of cellular proteins by covalent attachment of ubiquitin and ubiquitin-like proteins are involved in transcriptional regulation, receptor internalization, DNA repair, stabilization of protein complexes and autophagy. Here, we summarize the current knowledge regarding the ubiquitinome and the underlying ubiquitin ligases and deubiquitinating enzymes in replicative senescence, tissue aging as well as in segmental progeroid syndromes and discuss potential causes and consequences for aging.
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Affiliation(s)
- Johannes Grillari
- Institute of Applied Microbiology, Department of Biotechnology, University for Natural Resources and Applied Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria.
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17
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Abstract
Okazaki fragment processing is an integral part of DNA replication. For a long time, we assumed that the maturation of these small RNA-primed DNA fragments did not necessarily have to occur during S phase, but could be postponed to late in S phase after the bulk of DNA synthesis had been completed. This view was primarily based on the arrest phenotype of temperature-sensitive DNA ligase I mutants in yeast, which accumulated with an almost fully duplicated set of chromosomes. However, many temperature-sensitive alleles can be leaky and the re-evaluation of DNA ligase I-deficient cells has offered new and unexpected insights into how cells keep track of lagging strand synthesis. It turns out that if Okazaki fragment joining goes awry, cells have their own alarm system in the form of ubiquitin that is conjugated to the replication clamp PCNA. Although this modification results in mono- and poly-ubiquitination of PCNA, it is genetically distinct from the known post-replicative repair mark at lysine 164. In this Extra View, we discuss the possibility that eukaryotic cells utilize different enzymatic pathways and ubiquitin attachment sites on PCNA to alert the replication machinery to the accumulation of single-stranded gaps or nicks behind the fork.
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Affiliation(s)
- Sapna Das-Bradoo
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics, Minneapolis, MN, USA
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18
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Day IN, Thompson RJ. UCHL1 (PGP 9.5): Neuronal biomarker and ubiquitin system protein. Prog Neurobiol 2010; 90:327-62. [DOI: 10.1016/j.pneurobio.2009.10.020] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Revised: 10/18/2009] [Accepted: 10/21/2009] [Indexed: 12/16/2022]
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19
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Huzil JT, Pannu R, Ptak C, Garen G, Ellison MJ. Direct Catalysis of Lysine 48-linked Polyubiquitin Chains by the Ubiquitin-activating Enzyme. J Biol Chem 2007; 282:37454-60. [DOI: 10.1074/jbc.m705242200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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20
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Grillari J, Katinger H, Voglauer R. Aging and the ubiquitinome: traditional and non-traditional functions of ubiquitin in aging cells and tissues. Exp Gerontol 2006; 41:1067-79. [PMID: 17052881 DOI: 10.1016/j.exger.2006.07.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 07/13/2006] [Accepted: 07/18/2006] [Indexed: 01/01/2023]
Abstract
Ubiquitination of endogenous proteins is one of the key regulatory steps of protein degradation followed by regulation of proteasome activity. During the last years evidence has increased that proteasome activity is decreased during the aging process in various model systems and that these changes might be causally related to aging and aging associated diseases. Since in most instances ubiquitination is the primary event in target selection, the system of ubiquitination and deubiquitination might be of similar importance. Furthermore, ubiquitination and proteasomal degradation are not completely congruent, since ubiquitination also confers functions different from giving "the kiss of death" to proteins. Depending on mono- and polyubiquitination and on how ubiquitin chains are linked together, ubiquitination is involved in transcriptional regulation, receptor internalization, DNA repair, and stabilization of protein complexes. This review is therefore the first to summarize the current knowledge regarding the ubiquitinome and the underlying ubiquitin ligases and deubiquitinating enzymes in replicative senescence, tissue aging as well as in segmental progeroid syndromes and to discuss potential causes and consequences for aging.
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Affiliation(s)
- Johannes Grillari
- Department of Biotechnology, Institute of Applied Microbiology, University of Natural Resources and Applied Life Sciences, Vienna Muthgasse 18, A-1190 Vienna, Austria.
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21
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Kirkpatrick DS, Hathaway NA, Hanna J, Elsasser S, Rush J, Finley D, King RW, Gygi SP. Quantitative analysis of in vitro ubiquitinated cyclin B1 reveals complex chain topology. Nat Cell Biol 2006; 8:700-10. [PMID: 16799550 DOI: 10.1038/ncb1436] [Citation(s) in RCA: 348] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2006] [Accepted: 05/15/2006] [Indexed: 11/08/2022]
Abstract
Protein ubiquitination regulates many cellular processes, including protein degradation, signal transduction, DNA repair and cell division. In the classical model, a uniform polyubiquitin chain that is linked through Lys 48 is required for recognition and degradation by the 26S proteasome. Here, we used a reconstituted system and quantitative mass spectrometry to demonstrate that cyclin B1 is modified by ubiquitin chains of complex topology, rather than by homogeneous Lys 48-linked chains. The anaphase-promoting complex was found to attach monoubiquitin to multiple lysine residues on cyclin B1, followed by poly-ubiquitin chain extensions linked through multiple lysine residues of ubiquitin (Lys 63, Lys 11 and Lys 48). These heterogeneous ubiquitin chains were sufficient for binding to ubiquitin receptors, as well as for degradation by the 26S proteasome, even when they were synthesized with mutant ubiquitin that lacked Lys 48. Together, our observations expand the context of what can be considered to be a sufficient degradation signal and provide unique insights into the mechanisms of substrate ubiquitination.
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Affiliation(s)
- Donald S Kirkpatrick
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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22
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Haas A. Cecile Pickart 1954–2006. Nat Struct Mol Biol 2006. [DOI: 10.1038/nsmb0606-468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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Wang M, Cheng D, Peng J, Pickart CM. Molecular determinants of polyubiquitin linkage selection by an HECT ubiquitin ligase. EMBO J 2006; 25:1710-9. [PMID: 16601690 PMCID: PMC1440828 DOI: 10.1038/sj.emboj.7601061] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2005] [Accepted: 03/03/2006] [Indexed: 01/19/2023] Open
Abstract
Ubiquitin (Ub)-protein ligases (E3s) frequently modify their substrates with multiple Ub molecules in the form of a polyubiquitin (poly-Ub) chain. Although structurally distinct poly-Ub chains (linked through different Ub lysine (Lys) residues) can confer different fates on target proteins, little is known about how E3s select the Lys residue to be used in chain synthesis. Here, we used a combination of mutagenesis, biochemistry, and mass spectrometry to map determinants of linkage choice in chain assembly catalyzed by KIAA10, an HECT (Homologous to E6AP C-Terminus) domain E3 that synthesizes K29- and K48-linked chains. Focusing on the Ub molecule that contributes the Lys residue for chain formation, we found that specific surface residues adjacent to K48 and K29 are critical for the usage of the respective Lys residues in chain synthesis. This direct mechanism of linkage choice bears similarities to the mechanism of substrate site selection in sumoylation catalyzed by Ubc9, but is distinct from the mechanism of chain linkage selection used by the Mms2/Ubc13 (Ub E2 variant (UEV)/E2) complex.
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Affiliation(s)
- Min Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Dongmei Cheng
- Department of Human Genetics, Center for Neurodegenerative Disease, Emory University, Atlanta, GA, USA
| | - Junmin Peng
- Department of Human Genetics, Center for Neurodegenerative Disease, Emory University, Atlanta, GA, USA
| | - Cecile M Pickart
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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24
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Plans V, Scheper J, Soler M, Loukili N, Okano Y, Thomson TM. The RING finger protein RNF8 recruits UBC13 for lysine 63-based self polyubiquitylation. J Cell Biochem 2006; 97:572-82. [PMID: 16215985 DOI: 10.1002/jcb.20587] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The heterodimeric ubiquitin conjugating enzyme (E2) UBC13-UEV mediates polyubiquitylation through lysine 63 of ubiquitin (K63), rather than lysine 48 (K48). This modification does not target proteins for proteasome-dependent degradation. Searching for potential regulators of this variant polyubiquitylation we have identified four proteins, namely RNF8, KIA00675, KF1, and ZNRF2, that interact with UBC13 through their RING finger domains. These domains can recruit, in addition to UBC13, other E2s that mediate canonical (K48) polyubiquitylation. None of these RING finger proteins were known previously to recruit UBC13. For one of these proteins, RNF8, we show its activity as a ubiquitin ligase that elongates chains through either K48 or K63 of ubiquitin, and its nuclear co-localization with UBC13. Thus, our screening reveals new potential regulators of non-canonical polyubiquitylation.
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Affiliation(s)
- Vanessa Plans
- Institut de Biologia Molecular de Barcelona, CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
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25
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Wang M, Pickart CM. Different HECT domain ubiquitin ligases employ distinct mechanisms of polyubiquitin chain synthesis. EMBO J 2005; 24:4324-33. [PMID: 16341092 PMCID: PMC1356336 DOI: 10.1038/sj.emboj.7600895] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2005] [Accepted: 11/09/2005] [Indexed: 11/09/2022] Open
Abstract
Individual ubiquitin (Ub)-protein ligases (E3s) cooperate with specific Ub-conjugating enzymes (E2s) to modify cognate substrates with polyubiquitin chains. E3s belonging to the Really Interesting New Gene (RING) and Homologous to E6-Associated Protein (E6AP) C-Terminus (HECT) domain families utilize distinct molecular mechanisms. In particular, HECT E3s, but not RING E3s, form a thiol ester with Ub before transferring Ub to the substrate lysine. Here we report that different HECT domain E3s can employ distinct mechanisms of polyubiquitin chain synthesis. We show that E6AP builds up a K48-linked chain on its HECT cysteine residue, while KIAA10 builds up K48- and K29-linked chains as free entities. A small region near the N-terminus of the conserved HECT domain helps to bring about this functional distinction. Thus, a given HECT domain can specify both the linkage of a polyubiquitin chain and the mechanism of its assembly.
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Affiliation(s)
- Min Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Cecile M Pickart
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD 21205, USA. Tel.: +1 410 614 4554; Fax: +1 410 955 2926; E-mail:
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26
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Kirkpatrick DS, Denison C, Gygi SP. Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics. Nat Cell Biol 2005; 7:750-7. [PMID: 16056266 PMCID: PMC1224607 DOI: 10.1038/ncb0805-750] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mass-spectrometry-based proteomics has become an essential tool for the qualitative and quantitative analysis of cellular systems. The biochemical complexity and functional diversity of the ubiquitin system are well suited to proteomic studies. This review summarizes advances involving the identification of ubiquitinated proteins, the elucidation of ubiquitin-modification sites and the determination of polyubiquitin chain linkages, as well as offering a perspective on the application of emerging technologies for mechanistic and functional studies of protein ubiquitination.
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Affiliation(s)
| | | | - Steven P. Gygi
- Department of Cell Biology and
- Taplin Biological Mass Spectrometry Facility, Harvard Medical School, Boston, Massachusetts 02115, USA
- Correspondence: Steven P. Gygi, Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA, 617-432-3155,
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27
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Tsui C, Raguraj A, Pickart CM. Ubiquitin binding site of the ubiquitin E2 variant (UEV) protein Mms2 is required for DNA damage tolerance in the yeast RAD6 pathway. J Biol Chem 2005; 280:19829-35. [PMID: 15772086 DOI: 10.1074/jbc.m414060200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Different ubiquitin modifications to proliferating cell nuclear antigen (PCNA) signal distinct modes of lesion bypass in the RAD6 pathway of DNA damage tolerance. The modification of PCNA with monoubiquitin signals an error-prone bypass, whereas the extension of this modification into a Lys-63-linked polyubiquitin chain promotes error-free bypass. Chain formation is catalyzed by the Mms2/Ubc13 conjugating enzyme variant/conjugating enzyme (UEV.E2) complex together with the Rad5 ubiquitin ligase. In vitro studies of this UEV.E2 complex have identified a ubiquitin binding site that is mainly localized on Mms2. However, the role of this site in DNA damage tolerance and the molecular features of the ubiquitin/Mms2 interaction are poorly understood. Here we identify two molecular determinants, the side chains of Mms2-Ile-57 and ubiquitin-Ile-44, that are required for chain assembly in vitro and error-free lesion bypass in vivo. Mutating either of these side chains to alanine elicits a severe 10-20-fold inhibition of chain synthesis that is caused by compromised binding of the acceptor ubiquitin to Mms2. These results suggest that the ubiquitin binding site of Mms2 is necessary for error-free lesion bypass in the RAD6 pathway and provide new insights into ubiquitin recognition by UEV proteins.
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Affiliation(s)
- Colleen Tsui
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
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28
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Arnason TG, Pisclevich MG, Dash MD, Davies GF, Harkness TAA. Novel interaction between Apc5p and Rsp5p in an intracellular signaling pathway in Saccharomyces cerevisiae. EUKARYOTIC CELL 2005; 4:134-46. [PMID: 15643069 PMCID: PMC544157 DOI: 10.1128/ec.4.1.134-146.2005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2004] [Accepted: 11/02/2004] [Indexed: 11/20/2022]
Abstract
The ubiquitin-targeting pathway is evolutionarily conserved and critical for many cellular functions. Recently, we discovered a role for two ubiquitin-protein ligases (E3s), Rsp5p and the Apc5p subunit of the anaphase-promoting complex (APC), in mitotic chromatin assembly in Saccharomyces cerevisiae. In the present study, we investigated whether Rsp5p and Apc5p interact in an intracellular pathway regulating chromatin remodeling. Our genetic studies strongly suggest that Rsp5p and Apc5p do interact and that Rsp5p acts upstream of Apc5p. Since E3 enzymes typically require the action of a ubiquitin-conjugating enzyme (E2), we screened E2 mutants for chromatin assembly defects, which resulted in the identification of Cdc34p and Ubc7p. Cdc34p is the E2 component of the SCF (Skp1p/Cdc53p/F-box protein). Therefore, we analyzed additional SCF mutants for chromatin assembly defects. Defective chromatin assembly extracts generated from strains harboring a mutation in the Cdc53p SCF subunit or a nondegradable SCF target, Sic1(Deltaphos), confirmed that the SCF was involved in mitotic chromatin assembly. Furthermore, we demonstrated that Ubc7p physically and genetically interacts with Rsp5p, suggesting that Ubc7p acts as an E2 for Rsp5p. However, rsp5CA and Deltaubc7 mutations had opposite genetic effects on apc5CA and cdc34-2 phenotypes. Therefore, the antagonistic interplay between Deltaubc7 and rsp5CA, with respect to cdc34-2 and apc5CA, indicates that the outcome of Rsp5p's interaction with Cdc34p and Apc5p may depend on the E2 interacting with Rsp5p.
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Affiliation(s)
- Terra G Arnason
- Department of Medicine, Royal University Hospital, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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29
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Volk S, Wang M, Pickart CM. Chemical and genetic strategies for manipulating polyubiquitin chain structure. Methods Enzymol 2005; 399:3-20. [PMID: 16338345 DOI: 10.1016/s0076-6879(05)99001-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Ubiquitin can be conjugated to lysine residues of other ubiquitin molecules to form polymers called polyubiquitin chains. Ubiquitin has seven lysine residues, creating the potential for seven distinct types of chains, at least five of which have been observed in vitro or in vivo. A subset of these chains mediates substrate targeting to proteasomes, whereas other types of chains have been implicated in nonproteolytic signaling pathways. In this chapter, we outline chemical and genetic strategies that can be used to deduce (or control) the structures of polyubiquitin chains in vitro and in living cells.
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Affiliation(s)
- Sara Volk
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Baltimore, Maryland, USA
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30
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Passmore LA, Barford D. Getting into position: the catalytic mechanisms of protein ubiquitylation. Biochem J 2004; 379:513-25. [PMID: 14998368 PMCID: PMC1224133 DOI: 10.1042/bj20040198] [Citation(s) in RCA: 213] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2004] [Accepted: 02/25/2004] [Indexed: 12/25/2022]
Abstract
The role of protein ubiquitylation in the control of diverse cellular pathways has recently gained widespread attention. Ubiquitylation not only directs the targeted destruction of tagged proteins by the 26 S proteasome, but it also modulates protein activities, protein-protein interactions and subcellular localization. An understanding of the components involved in protein ubiquitylation (E1s, E2s and E3s) is essential to understand how specificity and regulation are conferred upon these pathways. Much of what we know about the catalytic mechanisms of protein ubiquitylation comes from structural studies of the proteins involved in this process. Indeed, structures of ubiquitin-activating enzymes (E1s) and ubiquitin-conjugating enzymes (E2s) have provided insight into their mechanistic details. E3s (ubiquitin ligases) contain most of the substrate specificity and regulatory elements required for protein ubiquitylation. Although several E3 structures are available, the specific mechanistic role of E3s is still unclear. This review will discuss the different types of ubiquitin signals and how they are generated. Recent advances in the field of protein ubiquitylation will be examined, including the mechanisms of E1, E2 and E3. In particular, we discuss the complexity of molecular recognition required to impose selectivity on substrate selection and topology of poly-ubiquitin chains.
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Affiliation(s)
- Lori A Passmore
- Section of Structural Biology, The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK.
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31
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Hegde AN. Ubiquitin-proteasome-mediated local protein degradation and synaptic plasticity. Prog Neurobiol 2004; 73:311-57. [PMID: 15312912 DOI: 10.1016/j.pneurobio.2004.05.005] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2003] [Accepted: 05/28/2004] [Indexed: 02/07/2023]
Abstract
A proteolytic pathway in which attachment of a small protein, ubiquitin, marks the substrates for degradation by a multi-subunit complex called the proteasome has been shown to function in synaptic plasticity and in several other physiological processes of the nervous system. Attachment of ubiquitin to protein substrates occurs through a series of highly specific and regulated steps. Degradation by the proteasome is subject to multiple levels of regulation as well. How does the ubiquitin-proteasome pathway contribute to synaptic plasticity? Long-lasting, protein synthesis-dependent, changes in the synaptic strength occur through activation of molecular cascades in the nucleus in coordination with signaling events in specific synapses. Available evidence indicates that ubiquitin-proteasome-mediated degradation has a role in the molecular mechanisms underlying synaptic plasticity that operate in the nucleus as well as at the synapse. Since the ubiquitin-proteasome pathway has been shown to be versatile in having roles in addition to proteolysis in several other cellular processes relevant to synaptic plasticity, such as endocytosis and transcription, this pathway is highly suited for a localized role in the neuron. Because of its numerous roles, malfunctioning of this pathway leads to several diseases and disorders of the nervous system. In this review, I examine the ubiquitin-proteasome pathway in detail and describe the role of regulated proteolysis in long-term synaptic plasticity. Also, using synaptic tagging theory of synapse-specific plasticity, I provide a model on the possible roles and regulation of local protein degradation by the ubiquitin-proteasome pathway.
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Affiliation(s)
- Ashok N Hegde
- Department of Neurobiology and Anatomy, Medical Center Boulevard, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA.
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32
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Mueller TD, Kamionka M, Feigon J. Specificity of the Interaction between Ubiquitin-associated Domains and Ubiquitin. J Biol Chem 2004; 279:11926-36. [PMID: 14707125 DOI: 10.1074/jbc.m312865200] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ubiquitin-associated (UBA) domains are found in a large number of proteins with diverse functions involved in ubiquitination, DNA repair, and signaling pathways. Recent studies have shown that several UBA domain proteins interact with ubiquitin (Ub), specifically p62, the phosphotyrosine-independent ligand of the SH2 domain of p56(lck); HHR23A, a human nucleotide excision repair protein; and DDI1, another damage-inducible protein. NMR chemical shift mapping reveals that Ub binds specifically but weakly to a conserved hydrophobic epitope on HHR23A UBA(1) and UBA(2) and that the UBA domains bind on the hydrophobic patch on the surface of the five-stranded beta-sheet of Ub. Models of the UBA(1)-Ub and UBA(2)-Ub complexes obtained from de novo docking reveal different orientations of the UBA domains on the Ub surface compared with those obtained by homology modeling with the related CUE domains, which also bind Ub. Our results suggest that UBA domains may interact with Ub as well as other proteins in more than one way while utilizing the same binding surface.
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Affiliation(s)
- Thomas D Mueller
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, USA
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Chernova TA, Allen KD, Wesoloski LM, Shanks JR, Chernoff YO, Wilkinson KD. Pleiotropic effects of Ubp6 loss on drug sensitivities and yeast prion are due to depletion of the free ubiquitin pool. J Biol Chem 2003; 278:52102-15. [PMID: 14559899 DOI: 10.1074/jbc.m310283200] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mutation of the mouse Usp14 gene, encoding the homolog of yeast deubiquitinating enzyme Ubp6, causes ataxia. Here we show that deletion of the UBP6 gene in Saccharomyces cerevisiae causes sensitivity to a broad range of toxic compounds and antagonizes phenotypic expression and de novo induction of the yeast prion [PSI+], a functionally defective self-perpetuating isoform of the translation termination factor Sup35. Conversely, overexpression of ubiquitin (Ub) increases phenotypic expression and induction of [PSI+] in the wild type cells and suppresses all tested ubp6Delta defects, indicating that they are primarily due to depletion of cellular Ub levels. Several lines of evidence suggest that Ubp6 functions on the proteasome. First, Ub levels in the ubp6Delta cells can be partly restored by proteasome inhibitors, suggesting that deletion of Ubp6 decreases Ub levels by increasing proteasome-dependent degradation of Ub. Second, fluorescence microscopy analysis shows that Ubp6-GFP fusion protein is localized to the nucleus of yeast cell, as are most proteasomes. Third, the N-terminal Ub-like domain, although it is not required for nuclear localization of Ubp6, targets Ubp6 to the proteasome and cannot be functionally replaced by Ub. The human ortholog of Ubp6, USP14, probably plays a similar role in higher eukaryotes, since it fully compensates for ubp6Delta defects and binds to the yeast proteasome. These data link the Ub system to prion expression and propagation and have broad implications for other neuronal inclusion body diseases.
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Affiliation(s)
- Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Sundd M, Robertson AD. Rearrangement of charge-charge interactions in variant ubiquitins as detected by double-mutant cycles and NMR. J Mol Biol 2003; 332:927-36. [PMID: 12972262 DOI: 10.1016/s0022-2836(03)00995-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Previous studies of ubiquitin disclosed numerous charge-charge interactions on the protein's surface. To investigate how neighboring residues influence the strength of these interactions, double-mutant cycles are combined with pK(a) determinations by 2D NMR. More specifically, the environment around the Asp21-Lys29 ion pair has been altered through mutations at position 25, which is an asparagine in mammalian ubiquitin and a positively-charged residue in many other ubiquitin-like proteins. The pK(a) value of Asp21 decreases by 0.4 to 0.7 pH unit when Asn25 is substituted with a positively charged residue, suggesting a new and favorable ion pair interaction between positions 21 and 25. However, analysis of double mutants reveals that the favorable interaction between Asp21 and Lys29 is weakened when position 25 is a positively charged residue. Interestingly, while the pK(a) value of His25 in the N25H variant agrees with model compound values, additional mutants reveal that this agreement is fortuitous, resulting from a balance of favorable and unfavorable interactions; similar results were observed previously for Glu34 in ubiquitin and His8 in staphylococcal nuclease. Ionizable groups may thus have pK(a) values similar to model compound values and yet still be involved in significant interactions with other protein groups. One surprising result of introducing positively charged residues at position 25 is a new interaction between Lys29 and Glu18, an interaction not present in wild-type ubiquitin. This unanticipated result illustrates a key advantage of using NMR to determine pK(a) values for many residues simultaneously in the variant proteins. Overall, the strength of an interaction between two residues at the surface of ubiquitin is sensitive to the identity of neighboring residues. The results also demonstrate that relatively conservative and common point mutations such as substitutions of polar with charged residues and vice versa can have effects on interactions beyond the site of mutation per se.
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Affiliation(s)
- Monica Sundd
- Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
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35
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Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D, Marsischky G, Roelofs J, Finley D, Gygi SP. A proteomics approach to understanding protein ubiquitination. Nat Biotechnol 2003; 21:921-6. [PMID: 12872131 DOI: 10.1038/nbt849] [Citation(s) in RCA: 1239] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2003] [Accepted: 05/28/2003] [Indexed: 11/09/2022]
Abstract
There is a growing need for techniques that can identify and characterize protein modifications on a large or global scale. We report here a proteomics approach to enrich, recover, and identify ubiquitin conjugates from Saccharomyces cerevisiae lysate. Ubiquitin conjugates from a strain expressing 6xHis-tagged ubiquitin were isolated, proteolyzed with trypsin and analyzed by multidimensional liquid chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for amino acid sequence determination. We identified 1,075 proteins from the sample. In addition, we detected 110 precise ubiquitination sites present in 72 ubiquitin-protein conjugates. Finally, ubiquitin itself was found to be modified at seven lysine residues providing evidence for unexpected diversity in polyubiquitin chain topology in vivo. The methodology described here provides a general tool for the large-scale analysis and characterization of protein ubiquitination.
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Affiliation(s)
- Junmin Peng
- Department of Cell Biology, 240 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115, USA
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36
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You J, Wang M, Aoki T, Tamura TA, Pickart CM. Proteolytic targeting of transcriptional regulator TIP120B by a HECT domain E3 ligase. J Biol Chem 2003; 278:23369-75. [PMID: 12692129 DOI: 10.1074/jbc.m212887200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ubiquitin-protein ligases (E3s) of the HECT family share a conserved catalytic region that is homologous to the E6-AP C terminus. The HECT domain defines a large E3 family, but only a handful of these enzymes have been defined with respect to substrate specificity or biological function. We showed previously that the C-terminal domain of one family member, KIAA10, catalyzes the assembly of polyubiquitin chains, whereas the N-terminal domain binds to proteasomes in vitro (You, J., and Pickart, C. M. (2001) J. Biol. Chem. 276, 19871-19878). We show here that KIAA10 also associates with proteasomes within cells but that this association probably involves additional contacts with proteasome subunits other than the one (S2/Rpn1) identified in our previous work. We report that the N-domain of KIAA10 also mediates an association with TIP120B (TATA-binding protein-interacting protein 120B), a putative transcriptional regulator. Biochemical and co-transfection studies revealed that TIP120B, but not the closely related protein TIP120A, is a specific substrate of KIAA10 in vitro and within C2C12 myoblasts but not in Cos-1 cells. KIAA10 and TIP120B are both highly expressed in human skeletal muscle, suggesting that KIAA10 may regulate TIP120B homeostasis specifically in this tissue.
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Affiliation(s)
- Jianxin You
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
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37
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Kreft SG, Nassal M. hRUL138, a novel human RNA-binding RING-H2 ubiquitin-protein ligase. J Cell Sci 2003; 116:605-16. [PMID: 12538761 DOI: 10.1242/jcs.00261] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Cellular as well as viral RNAs are usually found complexed with proteins. In an attempt to identify proteins that interact with transcripts of hepatitis B virus (HBV), a DNA virus that replicates through reverse transcription, a partial cDNA was isolated from a human cDNA expression library whose gene product bound to an HBV-derived RNA. Using an overlapping clone from a molecular hybridization screen a full-length cDNA was assembled. It contained a large open reading frame for a 1208 amino-acid protein of 138 kDa identical to the hypothetical product of the KIAA0675 clone. Closely related sequences are present in mouse cDNA libraries but not in the genomes of lower organisms. The protein sequence contained no known RNA-binding domain and, apart from a probable coiled-coil domain, the only significant homology involved a complete RING-H2 motif. This suggested that the protein might be a novel RNA-binding RING-dependent ubiquitin-protein ligase or E3 enzyme. A motif critical for RNA binding was experimentally mapped to a central Lys-rich region. Binding specificity is either broad or the protein has as yet unknown physiological targets; hence, at present, a potential importance for HBV biology remains open. The RING-H2 domain was functional in and essential for self- and trans-ubiquitylation in vitro and for proteasome-mediated turnover of the protein in vivo. We therefore termed it hRUL138 for human RNA-binding ubiquitin ligase of 138 kDa. hRUL138 mRNAs are expressed at low levels in most tissues. GFP-tagged hRUL138 derivatives were found associated with cytoplasmic structures, possibly the ER, but excluded from the nucleus. The combined presence of RNA binding and E3 activity in hRUL138 raises the possibility that both are mechanistically linked.
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Affiliation(s)
- Stefan G Kreft
- University Hospital Freiburg, Department of Internal Medicine II, Molecular Biology, Hugstetter Str 55, D-79106 Freiburg, Germany
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38
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Badciong JC, Haas AL. MdmX is a RING finger ubiquitin ligase capable of synergistically enhancing Mdm2 ubiquitination. J Biol Chem 2002; 277:49668-75. [PMID: 12393902 DOI: 10.1074/jbc.m208593200] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
It has been well documented that Mdm2 and its homologue MdmX not only are critical negative regulators of the tumor suppressor p53 but that both Mdm2 and MdmX interact to affect the function of the other. The mechanisms through which these effects are manifested, however, remain unclear. Although Mdm2 has been established as a RING finger ubiquitin ligase, MdmX has not been shown to possess this activity despite the extensive sequence homology between their respective RING finger domains. Here we demonstrate that MdmX acts as a ubiquitin ligase in vitro, being capable of autoubiquitination, as well as mediating the ubiquitination of p53. The addition of Mdm2 to in vitro ubiquitination assays containing MdmX results in a synergistic increase of ubiquitin conjugation. Analysis of the resulting ubiquitin conjugates reveals that this observed synergy reflects an increase in Mdm2 ubiquitination. This study also suggests that ubiquitination of Mdm2 and MdmX may not serve as a signal for degradation, as we show that each are capable of synthesizing non-lysine 48 polyubiquitin chains and, in fact, utilize multiple lysine linkages. Taken together, these findings suggest a more active role for MdmX in the Mdm2-MdmX-p53 regulatory network than has been proposed previously.
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Affiliation(s)
- James C Badciong
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
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Kim AL, Gautier J, Bickers DR, Athar M. Reduced cyclin D1 ubiquitination in UVB-induced murine squamous cell carcinomas. Biochem Biophys Res Commun 2002; 298:377-82. [PMID: 12413951 DOI: 10.1016/s0006-291x(02)02435-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Ubiquitination of cyclin D1 signals for its proteosomal degradation. To assess the possibility that reduced cyclin D1 proteolysis is a putative mechanism for its accumulation during UVB-induced skin tumorigenesis, ubiquitination activity of cyclin D1 was assessed in UVB-induced murine SCCs. Cyclin D1 was rapidly ubiquitinated by control skin extract, whereas ubiquitination of cyclin D1 was significantly reduced in SCCs. Mutant cyclin D1, in which residues important for GSK3beta-mediated degradation of cyclin D1 are altered to non-phosphorylatable alanine, was not ubiquitinated. We also observed phosphorylation-dependent inactivation of GSK3beta in SCCs. Our results indicate reduced ubiquitination of cyclin D1 in UVB-induced murine SCCs and suggest that inactivation of GSK3beta-dependent cyclin D1 degradation pathway contributes to the accumulation of cyclin D1 in UVB-induced murine SCCs.
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Affiliation(s)
- Arianna L Kim
- Department of Dermatology, Columbia University College of Physicians and Surgeons, 630 West 168th Street, New York, NY 10032, USA
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40
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Liu Y, Fallon L, Lashuel HA, Liu Z, Lansbury PT. The UCH-L1 gene encodes two opposing enzymatic activities that affect alpha-synuclein degradation and Parkinson's disease susceptibility. Cell 2002; 111:209-18. [PMID: 12408865 DOI: 10.1016/s0092-8674(02)01012-7] [Citation(s) in RCA: 595] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The assumption that each enzyme expresses a single enzymatic activity in vivo is challenged by the linkage of the neuronal enzyme ubiquitin C-terminal hydrolase-L1 (UCH-L1) to Parkinson's disease (PD). UCH-L1, especially those variants linked to higher susceptibility to PD, causes the accumulation of alpha-synuclein in cultured cells, an effect that cannot be explained by its recognized hydrolase activity. UCH-L1 is shown here to exhibit a second, dimerization-dependent, ubiquityl ligase activity. A polymorphic variant of UCH-L1 that is associated with decreased PD risk (S18Y) has reduced ligase activity but comparable hydrolase activity as the wild-type enzyme. Thus, the ligase activity as well as the hydrolase activity of UCH-L1 may play a role in proteasomal protein degradation, a critical process for neuronal health.
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Affiliation(s)
- Yichin Liu
- Center for Neurologic Diseases, Brigham and Women's Hospital, Department of Neurology, Harvard Medical School, Cambridge, MA 02139, USA
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41
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Ulrich HD. Natural substrates of the proteasome and their recognition by the ubiquitin system. Curr Top Microbiol Immunol 2002; 268:137-74. [PMID: 12083004 DOI: 10.1007/978-3-642-59414-4_6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The multitude of natural substrates of the 26S proteasome demonstrates convincingly the diversity and flexibility of the ubiquitin/proteasome system: at the same time, the number of pathways in which ubiquitin-dependent degradation is involved highlights the importance of regulated proteolysis for cellular metabolism. This review has addressed recent advances in our understanding of the principles that govern the recognition and targeting of potential substrates. While the mechanism of ubiquitin activation and conjugation is largely understood, the determination of substrate specificity by ubiquitin protein ligases remains a field of active research. Several conserved degradation signals within substrate proteins have been identified, and it is becoming increasingly clear that these serve as docking sites for specific sets of E3s, which in turn adhere to a number of well-defined strategies for the recognition of these motifs. In particular, RING finger proteins are now emerging as a new and apparently widespread class of ubiquitin ligases. The discovery of more and more E3s will undoubtedly reveal even better the common principles in architecture and mechanisms of this class of enzymes. In contrast to substrate recognition by the ubiquitin conjugation system, the way in which a ubiquitylated protein is delivered to the 26S proteasome is poorly understood. There is no doubt that multiubiquitin chains serve as the principal determinant for recognition by the proteasome, and a number of receptors and candidate targeting factors are known, some of which are associated with the proteasome itself; however, unresolved issues are the significance of the different geometries that alternatively linked multiubiquitin chains can adopt, the role of transport between subcellular compartments, as well as the participation of chaperones in the delivery step. Finally, the analysis of ubiquitin-independent, substrate-specific targeting mechanisms, such as the AZ-dependent degradation of ODC, may provide unexpected answers to questions about protein recognition by the 26S proteasome.
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Affiliation(s)
- H D Ulrich
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Karl-von-Frisch-Strasse, 35043 Marburg/Lahn, Germany
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42
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Chen A, Kleiman FE, Manley JL, Ouchi T, Pan ZQ. Autoubiquitination of the BRCA1*BARD1 RING ubiquitin ligase. J Biol Chem 2002; 277:22085-92. [PMID: 11927591 DOI: 10.1074/jbc.m201252200] [Citation(s) in RCA: 161] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RING finger of BRCA1 confers ubiquitin ligase activity that is markedly enhanced when complexed with another RING-containing protein, BARD1, and is required for the function of this tumor suppressor protein in protecting genomic integrity. Here, we report that co-expression of BRCA1-(1-639) and BARD1 in bacteria can assemble a potent ubiquitin ligase activity. Purified BRCA1-(1-639)*BARD1 stimulated the Ubc5c-mediated monoubiquitination of histone H2A/H2AX in vitro, suggesting a possible role for BRCA1*BARD1 in modifying chromatin structure. Moreover, the truncated BRCA1*BARD1 complex exhibited efficient autoubiquitination activity in vitro capable of assembling non-lysine 48-linked polyubiquitin chains on both BRCA1-(1-639) and BARD1. When co-expressed in cells by transient transfection, the recombinant BRCA1-(1-300).BARD1 complex was found to be associated with polyubiquitin chains, suggesting that BRCA1-(1-300)*BARD1 was ubiquitinated in vivo as well. These results raise the possibility that BRCA1*BARD1 acts to assemble non-lysine 48-linked polyubiquitin chains that may serve as part of a signaling platform required for coordinating DNA repair-related events.
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Affiliation(s)
- Angus Chen
- Derald H. Ruttenberg Cancer Center, The Mount Sinai School of Medicine, New York, New York 10029-6574, USA
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43
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Ungureanu D, Saharinen P, Junttila I, Hilton DJ, Silvennoinen O. Regulation of Jak2 through the ubiquitin-proteasome pathway involves phosphorylation of Jak2 on Y1007 and interaction with SOCS-1. Mol Cell Biol 2002; 22:3316-26. [PMID: 11971965 PMCID: PMC133778 DOI: 10.1128/mcb.22.10.3316-3326.2002] [Citation(s) in RCA: 208] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2001] [Revised: 07/26/2001] [Accepted: 02/19/2002] [Indexed: 01/17/2023] Open
Abstract
The family of cytoplasmic Janus (Jak) tyrosine kinases plays an essential role in cytokine signal transduction, regulating cell survival and gene expression. Ligand-induced receptor dimerization results in phosphorylation of Jak2 on activation loop tyrosine Y1007 and stimulation of its catalytic activity, which, in turn, results in activation of several downstream signaling cascades. Recently, the catalytic activity of Jak2 has been found to be subject to negative regulation through various mechanisms including association with SOCS proteins. Here we show that the ubiquitin-dependent proteolysis pathway is involved in the regulation of the turnover of activated Jak2. In unstimulated cells Jak2 was monoubiquitinated, and interleukin-3 or gamma interferon stimulation induced polyubiquitination of Jak2. The polyubiquitinated Jak2 was rapidly degraded through proteasomes. By using different Jak2 mutants we show that tyrosine-phosphorylated Jak2 is preferentially polyubiquitinated and degraded. Furthermore, phosphorylation of Y1007 on Jak2 was required for proteasomal degradation and for SOCS-1-mediated downregulation of Jak2. The proteasome inhibitor treatment stabilized the Jak2-SOCS-1 protein complex and inhibited the proteolysis of Jak2. In summary, these results indicate that the ubiquitin-proteasome pathway negatively regulates tyrosine-phosphorylated Jak2 in cytokine receptor signaling, which provides an additional mechanism to control activation of Jak2 and maintain cellular homeostasis.
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Affiliation(s)
- Daniela Ungureanu
- Institute of Medical Technology, University of Tampere, FIN-33014 Tampere, Finland
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44
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Regulation of Jak2 through the ubiquitin-proteasome pathway involves phosphorylation of Jak2 on Y1007 and interaction with SOCS-1. Mol Cell Biol 2002. [PMID: 11971965 DOI: 10.1128/mcb.22.10.3316‐3326.2002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The family of cytoplasmic Janus (Jak) tyrosine kinases plays an essential role in cytokine signal transduction, regulating cell survival and gene expression. Ligand-induced receptor dimerization results in phosphorylation of Jak2 on activation loop tyrosine Y1007 and stimulation of its catalytic activity, which, in turn, results in activation of several downstream signaling cascades. Recently, the catalytic activity of Jak2 has been found to be subject to negative regulation through various mechanisms including association with SOCS proteins. Here we show that the ubiquitin-dependent proteolysis pathway is involved in the regulation of the turnover of activated Jak2. In unstimulated cells Jak2 was monoubiquitinated, and interleukin-3 or gamma interferon stimulation induced polyubiquitination of Jak2. The polyubiquitinated Jak2 was rapidly degraded through proteasomes. By using different Jak2 mutants we show that tyrosine-phosphorylated Jak2 is preferentially polyubiquitinated and degraded. Furthermore, phosphorylation of Y1007 on Jak2 was required for proteasomal degradation and for SOCS-1-mediated downregulation of Jak2. The proteasome inhibitor treatment stabilized the Jak2-SOCS-1 protein complex and inhibited the proteolysis of Jak2. In summary, these results indicate that the ubiquitin-proteasome pathway negatively regulates tyrosine-phosphorylated Jak2 in cytokine receptor signaling, which provides an additional mechanism to control activation of Jak2 and maintain cellular homeostasis.
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45
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Glickman MH, Ciechanover A. The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction. Physiol Rev 2002; 82:373-428. [PMID: 11917093 DOI: 10.1152/physrev.00027.2001] [Citation(s) in RCA: 3050] [Impact Index Per Article: 138.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Between the 1960s and 1980s, most life scientists focused their attention on studies of nucleic acids and the translation of the coded information. Protein degradation was a neglected area, considered to be a nonspecific, dead-end process. Although it was known that proteins do turn over, the large extent and high specificity of the process, whereby distinct proteins have half-lives that range from a few minutes to several days, was not appreciated. The discovery of the lysosome by Christian de Duve did not significantly change this view, because it became clear that this organelle is involved mostly in the degradation of extracellular proteins, and their proteases cannot be substrate specific. The discovery of the complex cascade of the ubiquitin pathway revolutionized the field. It is clear now that degradation of cellular proteins is a highly complex, temporally controlled, and tightly regulated process that plays major roles in a variety of basic pathways during cell life and death as well as in health and disease. With the multitude of substrates targeted and the myriad processes involved, it is not surprising that aberrations in the pathway are implicated in the pathogenesis of many diseases, certain malignancies, and neurodegeneration among them. Degradation of a protein via the ubiquitin/proteasome pathway involves two successive steps: 1) conjugation of multiple ubiquitin moieties to the substrate and 2) degradation of the tagged protein by the downstream 26S proteasome complex. Despite intensive research, the unknown still exceeds what we currently know on intracellular protein degradation, and major key questions have remained unsolved. Among these are the modes of specific and timed recognition for the degradation of the many substrates and the mechanisms that underlie aberrations in the system that lead to pathogenesis of diseases.
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Affiliation(s)
- Michael H Glickman
- Faculty of Biology and the Institute for Catalysis Science and Technology, Haifa, Israel.
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46
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Abstract
The conjugation of ubiquitin to other cellular proteins regulates a broad range of eukaryotic cell functions. The high efficiency and exquisite selectivity of ubiquitination reactions reflect the properties of enzymes known as ubiquitin-protein ligases or E3s. An E3 recognizes its substrates based on the presence of a specific ubiquitination signal, and catalyzes the formation of an isopeptide bond between a substrate (or ubiquitin) lysine residue and the C terminus of ubiquitin. Although a great deal is known about the molecular basis of E3 specificity, much less is known about molecular mechanisms of catalysis by E3s. Recent findings reveal that all known E3s utilize one of just two catalytic domains--a HECT domain or a RING finger--and crystal structures have provided the first detailed views of an active site of each type. The new findings shed light on many aspects of E3 structure, function, and mechanism, but also emphasize that key features of E3 catalysis remain to be elucidated.
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Affiliation(s)
- C M Pickart
- School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, Maryland 21205, USA.
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47
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Funakoshi M, Sasaki T, Nishimoto T, Kobayashi H. Budding yeast Dsk2p is a polyubiquitin-binding protein that can interact with the proteasome. Proc Natl Acad Sci U S A 2002; 99:745-50. [PMID: 11805328 PMCID: PMC117376 DOI: 10.1073/pnas.012585199] [Citation(s) in RCA: 195] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dsk2p from Saccharomyces cerevisiae belongs to the class of proteins that contain a ubiquitin-like (UbL) domain at the N terminus together with a ubiquitin-associated (UBA) domain at the C terminus. We show here that the C-terminal UBA domain of Dsk2p binds to K48-linked polyubiquitin chains, and the N-terminal UbL domain of Dsk2p interacts with the proteasome. Overexpression of Dsk2p caused the accumulation of large amounts of polyubiquitin, and extragenic suppressors of the Dsk2p-mediated lethality proved to be temperature-sensitive mutations in two proteasome subunits, rpn1 and pre2. K48-linked ubiquitin-dependent degradation was impaired by disruption of the DSK2 gene. These results indicate that Dsk2p is K48-linked polyubiquitin-binding protein and also interacts with the proteasome. We discuss a possible role of adaptor function of Dsk2p via its UbL and UBA domains in the ubiquitin-proteasome pathway.
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Affiliation(s)
- Minoru Funakoshi
- Department of Molecular Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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48
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Wu K, Chen A, Tan P, Pan ZQ. The Nedd8-conjugated ROC1-CUL1 core ubiquitin ligase utilizes Nedd8 charged surface residues for efficient polyubiquitin chain assembly catalyzed by Cdc34. J Biol Chem 2002; 277:516-27. [PMID: 11675391 DOI: 10.1074/jbc.m108008200] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Lysine 48-linked polyubiquitin chains are the principle signal for targeting proteins for degradation by the 26 S proteasome. Here we report that the conjugation of Nedd8 to ROC1-CUL1, a subcomplex of the SCF-ROC1 E3 ubiquitin ligase, selectively stimulates Cdc34-catalyzed lysine 48-linked multiubiquitin chain assembly. We have further demonstrated that separate regions within the human Cdc34 C-terminal tail are responsible for multiubiquitin chain assembly and for physical interactions with the Nedd8-conjugated ROC1-CUL1 to assemble extensive ubiquitin polymers. Structural comparisons between Nedd8 and ubiquitin reveal that six charged residues (Lys4, Glu12, Glu14, Arg25, Glu28, and Glu31) are uniquely present on the surface of Nedd8. Replacement of each of the six residues with the corresponding amino acid in ubiquitin decreases the ability of Nedd8 to activate the ubiquitin ligase activity of ROC1-CUL1. Moreover, maintenance of the proper charges at amino acid positions 14 and 25 are necessary for retaining wild type levels of activity, whereas introduction of the opposite charges at these positions abolishes the Nedd8 activation function. These results suggest that Nedd8 charged surface residues mediate the activation of ROC1-CUL1 to specifically support Cdc34-catalyzed ubiquitin polymerization.
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Affiliation(s)
- Kenneth Wu
- Derald H. Ruttenberg Cancer Center, The Mount Sinai School of Medicine, New York, New York 10029-6574, USA
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49
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De Vrij FM, Sluijs JA, Gregori L, Fischer DF, Hermens WT, Goldgaber D, Verhaagen J, Van Leeuwen FW, Hol EM. Mutant ubiquitin expressed in Alzheimer's disease causes neuronal death. FASEB J 2001; 15:2680-8. [PMID: 11726544 DOI: 10.1096/fj.01-0438com] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Ubiquitin-B+1 (UBB+1) is a mutant ubiquitin that accumulates in the neurones of patients with Alzheimer's disease (AD). Here we report on the biochemical and functional differences between ubiquitin and UBB+1 and the effect of the mutant protein on neuronal cells. UBB+1 lacks the capacity to ubiquitinate, and although it is ubiquitinated itself, UBB+1 is not degraded by the ubiquitin-proteasomal system and is quite stable in neuronal cells. Overexpression of UBB+1 in neuroblastoma cells significantly induces nuclear fragmentation and cell death. Our results demonstrate that accumulation of UBB+1 in neurones is detrimental and may contribute to neuronal dysfunction in AD patients.
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Affiliation(s)
- F M De Vrij
- Graduate School for Neurosciences Amsterdam, Netherlands Institute for Brain Research, Research Group Molecular Misreading, Amsterdam, The Netherlands
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50
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Abstract
Polyubiquitin chains assembled through lysine 48 (Lys-48) of ubiquitin act as a signal for substrate proteolysis by 26 S proteasomes, whereas chains assembled through Lys-63 play a mechanistically undefined role in post-replicative DNA repair. We showed previously that the products of the UBC13 and MMS2 genes function in error-free post-replicative DNA repair in the yeast Saccharomyces cerevisiae and form a complex that assembles Lys-63-linked polyubiquitin chains in vitro. Here we confirm that the Mms2.Ubc13 complex functions as a high affinity heterodimer in the chain assembly reaction in vitro and report the results of a kinetic characterization of the polyubiquitin chain assembly reaction. To test whether a Lys-63-linked polyubiquitin chain can signal degradation, we conjugated Lys-63-linked tetra-ubiquitin to a model substrate of 26 S proteasomes. Although the noncanonical chain effectively signaled substrate degradation, the results of new genetic epistasis studies agree with previous genetic data in suggesting that the proteolytic activity of proteasomes is not required for error-free post-replicative repair.
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Affiliation(s)
- R M Hofmann
- Department of Biochemistry and Molecular Biology, School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
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