301
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Elu N, Osinalde N, Beaskoetxea J, Ramirez J, Lectez B, Aloria K, Rodriguez JA, Arizmendi JM, Mayor U. Detailed Dissection of UBE3A-Mediated DDI1 Ubiquitination. Front Physiol 2019; 10:534. [PMID: 31130875 PMCID: PMC6509411 DOI: 10.3389/fphys.2019.00534] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 04/15/2019] [Indexed: 12/22/2022] Open
Abstract
The ubiquitin E3 ligase UBE3A has been widely reported to interact with the proteasome, but it is still unclear how this enzyme regulates by ubiquitination the different proteasomal subunits. The proteasome receptor DDI1 has been identified both in Drosophila photoreceptor neurons and in human neuroblastoma cells in culture as a direct substrate of UBE3A. Here, we further characterize this regulation, by identifying the UBE3A-dependent ubiquitination sites and ubiquitin chains formed on DDI1. Additionally, we found one deubiquitinating enzyme that is capable of reversing the action of UBE3A on DDI1. The complete characterization of the ubiquitination pathway of an UBE3A substrate is important due to the role of this E3 ligase in rare neurological disorders as Angelman syndrome.
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Affiliation(s)
- Nagore Elu
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Nerea Osinalde
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Javier Beaskoetxea
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Juanma Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Benoit Lectez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Kerman Aloria
- Proteomics Core Facility-SGIKER, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Jose Antonio Rodriguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Jesus M Arizmendi
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain.,Ikerbasque - Basque Foundation for Science, Bilbao, Spain
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302
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Sayago C, Martinez-Val A, Munoz J. Proteotyping pluripotency with mass spectrometry. Expert Rev Proteomics 2019; 16:391-400. [PMID: 30947573 DOI: 10.1080/14789450.2019.1604229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Pluripotency emerges transiently during embryogenesis in two main forms with different developmental potential, termed naïve and primed states. Importantly, these pluripotent states can be recapitulated in vitro under specific culture conditions, representing a unique model to study the regulatory principles of development and cellular plasticity. Areas covered: A complex network of signaling pathways that senses intrinsic and extrinsic cues controls the fine balance between self-renewal and differentiation. Much of our knowledge on this tight regulation originates from epigenetic and transcriptomic approaches. However, the presence of post-transcriptional and post-translational mechanisms demands a direct assessment of the proteome in its multiple facets. Mass spectrometry-based proteomics is now a mature technique and has started to deliver new insights in the stem cell field. Expert opinion: Here, we review our current understanding on the mechanisms that dictate the spectrum of pluripotency levels. We put special emphasis on the emerging proteomic studies that focused on the molecular properties behind the naïve and primed states. In addition, we hypothesize on the impact that future developments in proteomic technologies can have to improve our view of pluripotency.
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Affiliation(s)
- Cristina Sayago
- a Proteomics Unit , Spanish National Cancer Research Centre (CNIO) , Madrid , Spain.,b ISCIII-ProteoRed , Spain
| | - Ana Martinez-Val
- a Proteomics Unit , Spanish National Cancer Research Centre (CNIO) , Madrid , Spain.,b ISCIII-ProteoRed , Spain
| | - Javier Munoz
- a Proteomics Unit , Spanish National Cancer Research Centre (CNIO) , Madrid , Spain.,b ISCIII-ProteoRed , Spain
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303
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Chua NK, Hart-Smith G, Brown AJ. Non-canonical ubiquitination of the cholesterol-regulated degron of squalene monooxygenase. J Biol Chem 2019; 294:8134-8147. [PMID: 30940729 DOI: 10.1074/jbc.ra119.007798] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/11/2019] [Indexed: 12/21/2022] Open
Abstract
Squalene monooxygenase (SM) is a rate-limiting enzyme in cholesterol synthesis. The region comprising the first 100 amino acids, termed SM N100, represents the shortest cholesterol-responsive degron and enables SM to sense excess cholesterol in the endoplasmic reticulum (ER) membrane. Cholesterol accelerates the ubiquitination of SM by membrane-associated ring-CH type finger 6 (MARCH6), a key E3 ubiquitin ligase involved in ER-associated degradation. However, the ubiquitination site required for cholesterol regulation of SM N100 is unknown. Here, we used SM N100 fused to GFP as a model degron to recapitulate cholesterol-mediated SM degradation and show that neither SM lysine residues nor the N terminus impart instability. Instead, we discovered four serines (Ser-59, Ser-61, Ser-83, and Ser-87) that are critical for cholesterol-accelerated degradation, with MS analysis confirming Ser-83 as a ubiquitination site. Notably, these two clusters of closely spaced serine residues are located in disordered domains flanking a 12-amino acid-long amphipathic helix (residues Gln-62-Leu-73) that together confer cholesterol responsiveness. In summary, our findings reveal the degron architecture of SM N100, introducing the role of non-canonical ubiquitination sites and deepening our molecular understanding of how SM is degraded in response to cholesterol.
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Affiliation(s)
- Ngee Kiat Chua
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, New South Wales 2052, Australia
| | - Gene Hart-Smith
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, New South Wales 2052, Australia
| | - Andrew J Brown
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, New South Wales 2052, Australia.
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304
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Aksnes H, Ree R, Arnesen T. Co-translational, Post-translational, and Non-catalytic Roles of N-Terminal Acetyltransferases. Mol Cell 2019; 73:1097-1114. [PMID: 30878283 DOI: 10.1016/j.molcel.2019.02.007] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/23/2019] [Accepted: 02/04/2019] [Indexed: 02/07/2023]
Abstract
Recent studies of N-terminal acetylation have identified new N-terminal acetyltransferases (NATs) and expanded the known functions of these enzymes beyond their roles as ribosome-associated co-translational modifiers. For instance, the identification of Golgi- and chloroplast-associated NATs shows that acetylation of N termini also happens post-translationally. In addition, we now appreciate that some NATs are highly specific; for example, a dedicated NAT responsible for post-translational N-terminal acetylation of actin was recently revealed. Other studies have extended NAT function beyond Nt acetylation, including functions as lysine acetyltransferases (KATs) and non-catalytic roles. Finally, emerging studies emphasize the physiological relevance of N-terminal acetylation, including roles in calorie-restriction-induced longevity and pathological α-synuclein aggregation in Parkinson's disease. Combined, the NATs rise as multifunctional proteins, and N-terminal acetylation is gaining recognition as a major cellular regulator.
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Affiliation(s)
- Henriette Aksnes
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.
| | - Rasmus Ree
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway; Department of Biological Sciences, University of Bergen, 5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, 5021 Bergen, Norway.
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305
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Wei CY, Zhu MX, Yang YW, Zhang PF, Yang X, Peng R, Gao C, Lu JC, Wang L, Deng XY, Lu NH, Qi FZ, Gu JY. Downregulation of RNF128 activates Wnt/β-catenin signaling to induce cellular EMT and stemness via CD44 and CTTN ubiquitination in melanoma. J Hematol Oncol 2019; 12:21. [PMID: 30832692 PMCID: PMC6399928 DOI: 10.1186/s13045-019-0711-z] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 02/21/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Ring finger proteins (RNFs) were involved in carcinogenesis. Here, we aimed to explore the detailed mechanism of RNF128 in the progression of melanoma. METHODS We reanalyzed several gene expression profiles from the Gene Expression Omnibus (GEO) database and obtained the overlapped differential expressed RNF genes. Among them, RNF128 was selected to further explore its expression, the biological significance, and the underlying molecular mechanism, as well as the clinical relevance in melanoma patients. RESULTS RNF128 was found to be significantly downregulated in the selected datasets, which was further verified in our melanoma tissues. Moreover, RNF128 downregulation was shown to correlate with the malignant phenotype of melanoma, and further functional assays demonstrated that low levels of RNF128 promoted melanoma progression via inducing cell epithelial-mesenchymal transition (EMT) and the acquisition of stemness. Mechanistically, RNF128 interference activated the Wnt pathway via simultaneously ubiquitinating CD44/cortactin (CTTN), resulting in CD44 and c-Myc transcription, thus revealed that RNF128 participated in a positive feedback of the Wnt pathway-CD44 loop. Clinically, we found that patients expressing low RNF128 and high CD44/CTTN levels had a poor prognosis. CONCLUSION Downregulated RNF128 activates Wnt signaling to induce cellular EMT and stemness by ubiquitinating and degrading CD44/CTTN, and RNF128 is a reliable diagnostic and prognostic biomarker, and a deeper understanding of RNF128 may contribute to the treatment of melanoma.
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Affiliation(s)
- Chuan-Yuan Wei
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China.,Department of Liver Surgery and Transplantation, Liver Cancer Institute and Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, People's Republic of China
| | - Meng-Xuan Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Yan-Wen Yang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China
| | - Peng-Fei Zhang
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200032, People's Republic of China
| | - Xuan Yang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, People's Republic of China
| | - Rui Peng
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, People's Republic of China
| | - Chao Gao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Jia-Cheng Lu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, People's Republic of China
| | - Lu Wang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China
| | - Xin-Yi Deng
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China
| | - Nan-Hang Lu
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China
| | - Fa-Zhi Qi
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China
| | - Jian-Ying Gu
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China.
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306
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Mattern M, Sutherland J, Kadimisetty K, Barrio R, Rodriguez MS. Using Ubiquitin Binders to Decipher the Ubiquitin Code. Trends Biochem Sci 2019; 44:599-615. [PMID: 30819414 DOI: 10.1016/j.tibs.2019.01.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/13/2022]
Abstract
Post-translational modifications (PTMs) by ubiquitin (Ub) are versatile, highly dynamic, and involved in nearly all aspects of eukaryote biological function. The reversibility and heterogeneity of Ub chains attached to protein substrates have complicated their isolation, quantification, and characterization. Strategies have emerged to isolate endogenous ubiquitylated targets, including technologies based on the use of Ub-binding peptides, such as tandem-repeated Ub-binding entities (TUBEs). TUBEs allow the identification and characterization of Ub chains, and novel substrates for deubiquitylases (DUBs) and Ub ligases (E3s). Here we review their impact on purification, analysis of pan or chain-selective polyubiquitylated proteins and underline the biological relevance of this information. Together with peptide aptamers and other Ub affinity-based approaches, TUBEs will contribute to unraveling the secrets of the Ub code.
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Affiliation(s)
- Michael Mattern
- Progenra Inc., 277 Great Valley Parkway, Malvern 19355, Pennsylvania, USA; These authors contributed equally
| | - James Sutherland
- CIC bioGUNE, Technology Park of Bizkaia, Bldg. 801A, 48160 Derio, Spain; These authors contributed equally
| | - Karteek Kadimisetty
- LifeSensors Inc., 271 Great Valley Parkway, Malvern 19355, Pennsylvania, USA
| | - Rosa Barrio
- CIC bioGUNE, Technology Park of Bizkaia, Bldg. 801A, 48160 Derio, Spain
| | - Manuel S Rodriguez
- ITAV-IPBS-UPS CNRS USR3505, 1 place Pierre Potier, Oncopole entrée B, 31106 Toulouse, France.
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307
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Luciano AK, Guertin DA. Oncogenic AKTivation by methylation. Nat Cell Biol 2019; 21:114-115. [PMID: 30692624 DOI: 10.1038/s41556-019-0275-8] [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]
Affiliation(s)
- Amelia K Luciano
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - David A Guertin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA. .,Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.
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308
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Pascovici D, Wu JX, McKay MJ, Joseph C, Noor Z, Kamath K, Wu Y, Ranganathan S, Gupta V, Mirzaei M. Clinically Relevant Post-Translational Modification Analyses-Maturing Workflows and Bioinformatics Tools. Int J Mol Sci 2018; 20:E16. [PMID: 30577541 PMCID: PMC6337699 DOI: 10.3390/ijms20010016] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/09/2018] [Accepted: 12/17/2018] [Indexed: 01/04/2023] Open
Abstract
Post-translational modifications (PTMs) can occur soon after translation or at any stage in the lifecycle of a given protein, and they may help regulate protein folding, stability, cellular localisation, activity, or the interactions proteins have with other proteins or biomolecular species. PTMs are crucial to our functional understanding of biology, and new quantitative mass spectrometry (MS) and bioinformatics workflows are maturing both in labelled multiplexed and label-free techniques, offering increasing coverage and new opportunities to study human health and disease. Techniques such as Data Independent Acquisition (DIA) are emerging as promising approaches due to their re-mining capability. Many bioinformatics tools have been developed to support the analysis of PTMs by mass spectrometry, from prediction and identifying PTM site assignment, open searches enabling better mining of unassigned mass spectra-many of which likely harbour PTMs-through to understanding PTM associations and interactions. The remaining challenge lies in extracting functional information from clinically relevant PTM studies. This review focuses on canvassing the options and progress of PTM analysis for large quantitative studies, from choosing the platform, through to data analysis, with an emphasis on clinically relevant samples such as plasma and other body fluids, and well-established tools and options for data interpretation.
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Affiliation(s)
- Dana Pascovici
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Jemma X Wu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Matthew J McKay
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Chitra Joseph
- Department of Clinical Medicine, Macquarie University, Sydney, NSW 2109, Australia.
| | - Zainab Noor
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Karthik Kamath
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Yunqi Wu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Vivek Gupta
- Department of Clinical Medicine, Macquarie University, Sydney, NSW 2109, Australia.
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
- Department of Clinical Medicine, Macquarie University, Sydney, NSW 2109, Australia.
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309
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Li Y, Evers J, Luo A, Erber L, Postler Z, Chen Y. A Quantitative Chemical Proteomics Approach for Site-specific Stoichiometry Analysis of Ubiquitination. Angew Chem Int Ed Engl 2018; 58:537-541. [DOI: 10.1002/anie.201810569] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/07/2018] [Indexed: 02/02/2023]
Affiliation(s)
- Yunan Li
- Department of Biochemistry, Molecular Biology and Biophysics; University of Minnesota at Twin Cities; Minneapolis MN 55455 USA
| | - Jonathan Evers
- Department of Biochemistry, Molecular Biology and Biophysics; University of Minnesota at Twin Cities; Minneapolis MN 55455 USA
| | - Ang Luo
- Department of Biochemistry, Molecular Biology and Biophysics; University of Minnesota at Twin Cities; Minneapolis MN 55455 USA
| | - Luke Erber
- Department of Biochemistry, Molecular Biology and Biophysics; University of Minnesota at Twin Cities; Minneapolis MN 55455 USA
| | - Zachary Postler
- Department of Biochemistry, Molecular Biology and Biophysics; University of Minnesota at Twin Cities; Minneapolis MN 55455 USA
| | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics; University of Minnesota at Twin Cities; Minneapolis MN 55455 USA
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310
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Li Y, Evers J, Luo A, Erber L, Postler Z, Chen Y. A Quantitative Chemical Proteomics Approach for Site-specific Stoichiometry Analysis of Ubiquitination. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810569] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yunan Li
- Department of Biochemistry, Molecular Biology and Biophysics; University of Minnesota at Twin Cities; Minneapolis MN 55455 USA
| | - Jonathan Evers
- Department of Biochemistry, Molecular Biology and Biophysics; University of Minnesota at Twin Cities; Minneapolis MN 55455 USA
| | - Ang Luo
- Department of Biochemistry, Molecular Biology and Biophysics; University of Minnesota at Twin Cities; Minneapolis MN 55455 USA
| | - Luke Erber
- Department of Biochemistry, Molecular Biology and Biophysics; University of Minnesota at Twin Cities; Minneapolis MN 55455 USA
| | - Zachary Postler
- Department of Biochemistry, Molecular Biology and Biophysics; University of Minnesota at Twin Cities; Minneapolis MN 55455 USA
| | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics; University of Minnesota at Twin Cities; Minneapolis MN 55455 USA
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311
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Abstract
Access to well-defined ubiquitin conjugates has been key to elucidating the biochemical functions of proteins in the ubiquitin signaling network. Yet, we have a poor understanding of how deubiquitinases and ubiquitin-binding proteins respond to ubiquitin modifications when anchored to a protein other than ubiquitin or a ubiquitin-like protein. This is due to the difficulty of synthesizing ubiquitinated proteins comprised of native isopeptide bonds. Here we report on the evolution of a deubiquitinase capable of site-specifically modifying itself with defined ubiquitin chains. Following mutagenesis and yeast display screening, we identify a variant of the yeast ubiquitin C-terminal hydrolase Yuh1 that has a 28-fold improvement in the transamidation to hydrolysis ratio relative to the wild type enzyme. The switch in activity enables robust autoubiquitination of a lysine in the crossover loop to form an isopeptide bond. We demonstrate the utility of autoubiquitinating the evolved Yuh1 variant by investigating the consequences of ubiquitin chain anchoring on the activities of other deubiquitinases. Much to our surprise, we find that certain deubiquitinases are exquisitely sensitive to chain anchoring. These results highlight the importance of investigating the biochemical activities of deubiquitinases with both substrate-anchored and unanchored ubiquitin chains.
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