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Luo R, Yang K, Xiao W. Plant deubiquitinases: from structure and activity to biological functions. PLANT CELL REPORTS 2023; 42:469-486. [PMID: 36567335 DOI: 10.1007/s00299-022-02962-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
This article attempts to provide comprehensive review of plant deubiquitinases, paying special attention to recent advances in their biochemical activities and biological functions. Proteins in eukaryotes are subjected to post-translational modifications, in which ubiquitination is regarded as a reversible process. Cellular deubiquitinases (DUBs) are a key component of the ubiquitin (Ub)-proteasome system responsible for cellular protein homeostasis. DUBs recycle Ub by hydrolyzing poly-Ub chains on target proteins, and maintain a balance of the cellular Ub pool. In addition, some DUBs prefer to cleave poly-Ub chains not linked through the conventional K48 residue, which often alter the substrate activity instead of its stability. In plants, all seven known DUB subfamilies have been identified, namely Ub-binding protease/Ub-specific protease (UBP/USP), Ub C-terminal hydrolase (UCH), Machado-Joseph domain-containing protease (MJD), ovarian-tumor domain-containing protease (OTU), zinc finger with UFM1-specific peptidase domain protease (ZUFSP), motif interacting with Ub-containing novel DUB family (MINDY), and JAB1/MPN/MOV34 protease (JAMM). This review focuses on recent advances in the structure, activity, and biological functions of plant DUBs, particularly in the model plant Arabidopsis.
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Affiliation(s)
- Runbang Luo
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Kun Yang
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Wei Xiao
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China.
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.
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2
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Ma YS, Wang XF, Zhang YJ, Luo P, Long HD, Li L, Yang HQ, Xie RT, Jia CY, Lu GX, Chang ZY, Zhang JJ, Xue SB, Lv ZW, Yu F, Xia Q, Fu D. Inhibition of USP14 Deubiquitinating Activity as a Potential Therapy for Tumors with p53 Deficiency. MOLECULAR THERAPY-ONCOLYTICS 2020; 16:147-157. [PMID: 32055678 PMCID: PMC7005481 DOI: 10.1016/j.omto.2019.12.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/23/2019] [Indexed: 01/17/2023]
Abstract
Functional elimination of p53 is a common feature of a large percentage of human malignancies. Here, we report the development of a pharmacological strategy aimed at restoring p53 function and its use for targeted therapy in p53-deficient mice. Specific inhibition of deubiquitinases ubiquitin-specific peptidase 14 (USP14) resulted in durable tumor regressions of autochthonous lymphomas and sarcomas in p53-deficient mice without affecting normal tissues, and therapeutic response was correlated with an increase in the ubiquitination of constitutive photomorphogenesis 9 (COP9) signalosome subunit 5 (COPS5), a key negative regulatory effector for p53. Inhibition of USP14 resulted in durable tumor regression through COPS5 deubiquitilation and a p53-dependent and -independent regulation mechanism by USP14. This series highlights the utility of proteasome deubiquitinating activity inhibition as a novel treatment paradigm for p53-deficient cancers. In addition, it provides preliminary evidence that inhibition of USP14 resulted in durable tumor regression through COPS5 deubiquitilation and p53-dependent and -independent regulation mechanism by USP14. These findings suggest that the deubiquitinating activity of the 19S regulatory particle is a new anticancer drug target for patients with p53 deficiency.
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Affiliation(s)
- Yu-Shui Ma
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.,Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Xiao-Feng Wang
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yun-Jie Zhang
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Pei Luo
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Hui-Deng Long
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Liu Li
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Hui-Qiong Yang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Ru-Ting Xie
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Cheng-You Jia
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Gai-Xia Lu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Zheng-Yan Chang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Jia-Jia Zhang
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Shao-Bo Xue
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Zhong-Wei Lv
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Fei Yu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Qing Xia
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Da Fu
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
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3
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Pereira RV, Vieira HGS, de Oliveira VF, Gomes MDS, Passos LKJ, Borges WDC, Guerra-Sá R. Conservation and developmental expression of ubiquitin isopeptidases in Schistosoma mansoni. Mem Inst Oswaldo Cruz 2014; 109:1-8. [PMID: 24271000 PMCID: PMC4005531 DOI: 10.1590/0074-0276130107] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 09/09/2013] [Indexed: 11/22/2022] Open
Abstract
Several genes related to the ubiquitin (Ub)-proteasome pathway, including those coding for proteasome subunits and conjugation enzymes, are differentially expressed during the Schistosoma mansoni life cycle. Although deubiquitinating enzymes have been reported to be negative regulators of protein ubiquitination and shown to play an important role in Ub-dependent processes, little is known about their role in S. mansoni . In this study, we analysed the Ub carboxyl-terminal hydrolase (UCHs) proteins found in the database of the parasite's genome. An in silico ana- lysis (GeneDB and MEROPS) identified three different UCH family members in the genome, Sm UCH-L3, Sm UCH-L5 and Sm BAP-1 and a phylogenetic analysis confirmed the evolutionary conservation of the proteins. We performed quantitative reverse transcription-polymerase chain reaction and observed a differential expression profile for all of the investigated transcripts between the cercariae and adult worm stages. These results were corroborated by low rates of Z-Arg-Leu-Arg-Gly-Gly-AMC hydrolysis in a crude extract obtained from cercariae in parallel with high Ub conjugate levels in the same extracts. We suggest that the accumulation of ubiquitinated proteins in the cercaria and early schistosomulum stages is related to a decrease in 26S proteasome activity. Taken together, our data suggest that UCH family members contribute to regulating the activity of the Ub-proteasome system during the life cycle of this parasite.
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Affiliation(s)
- Roberta Verciano Pereira
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de
Ouro Preto, Ouro Preto, MG, Brasil, Núcleo de Pesquisas em Ciências Biológicas,
Universidade Federal de Ouro Preto, Ouro Preto, MG, Brasil
| | - Helaine Graziele Santos Vieira
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de
Ouro Preto, Ouro Preto, MG, Brasil, Núcleo de Pesquisas em Ciências Biológicas,
Universidade Federal de Ouro Preto, Ouro Preto, MG, Brasil
| | - Victor Fernandes de Oliveira
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de
Ouro Preto, Ouro Preto, MG, Brasil, Núcleo de Pesquisas em Ciências Biológicas,
Universidade Federal de Ouro Preto, Ouro Preto, MG, Brasil
| | - Matheus de Souza Gomes
- Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia,
Patos de Minas, MG, Brasil, Instituto de Genética e Bioquímica, Universidade Federal de
Uberlândia, Campus Avançado Patos de Minas, MG, Brasil
| | | | - William de Castro Borges
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de
Ouro Preto, Ouro Preto, MG, Brasil, Núcleo de Pesquisas em Ciências Biológicas,
Universidade Federal de Ouro Preto, Ouro Preto, MG, Brasil
| | - Renata Guerra-Sá
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de
Ouro Preto, Ouro Preto, MG, Brasil, Núcleo de Pesquisas em Ciências Biológicas,
Universidade Federal de Ouro Preto, Ouro Preto, MG, Brasil
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4
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Chen YJ, Ma YS, Fang Y, Wang Y, Fu D, Shen XZ. Power and Promise of Ubiquitin Carboxyl-terminal Hydrolase 37 as a Target of Cancer Therapy. Asian Pac J Cancer Prev 2013; 14:2173-9. [DOI: 10.7314/apjcp.2013.14.4.2173] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Tian G, Lu Q, Kohalmi SE, Rothstein SJ, Cui Y. Evidence that the Arabidopsis Ubiquitin C-terminal Hydrolases 1 and 2 associate with the 26S proteasome and the TREX-2 complex. PLANT SIGNALING & BEHAVIOR 2012; 7:1415-9. [PMID: 22951400 PMCID: PMC3548861 DOI: 10.4161/psb.21899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The 26S proteasome interacts with a number of different proteins, while the TREX-2 complex is an important component of the mRNA export machinery. In animals and yeast, members of the Ubiquitin C-terminal Hydrolase 37 (UCH37) family are found to associate with the 26S proteasome, but this has not been demonstrated in plants. The Arabidopsis UCH1 and UCH2 are orthologous to UCH37. Here, we show that UCH1 and UCH2 interact with the 26S proteasome lid subunits. In addition, the two UCHs also interact with TREX-2 components. Our data suggest that Arabidopsis UCHs may serve as a link between the 26S proteasome lid complex and the TREX-2 complex.
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Affiliation(s)
- Gang Tian
- Agriculture and Agri-Food Canada; Southern Crop Protection and Food Research Centre; London, ON Canada
- Department of Biology; Western University; London, ON Canada
| | - Qing Lu
- Agriculture and Agri-Food Canada; Southern Crop Protection and Food Research Centre; London, ON Canada
- Department of Molecular and Cellular Biology; University of Guelph; Guelph, ON Canada
| | | | - Steven J. Rothstein
- Department of Molecular and Cellular Biology; University of Guelph; Guelph, ON Canada
| | - Yuhai Cui
- Agriculture and Agri-Food Canada; Southern Crop Protection and Food Research Centre; London, ON Canada
- Department of Biology; Western University; London, ON Canada
- Correspondence to: Yuhai Cui,
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6
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Förster F, Lasker K, Nickell S, Sali A, Baumeister W. Toward an integrated structural model of the 26S proteasome. Mol Cell Proteomics 2010; 9:1666-77. [PMID: 20467039 PMCID: PMC2938054 DOI: 10.1074/mcp.r000002-mcp201] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 03/26/2010] [Indexed: 11/06/2022] Open
Abstract
The 26S proteasome is the end point of the ubiquitin-proteasome pathway and degrades ubiquitylated substrates. It is composed of the 20S core particle (CP), where degradation occurs, and the 19S regulatory particle (RP), which ensures substrate specificity of degradation. Whereas the CP is resolved to atomic resolution, the architecture of the RP is largely unknown. We provide a comprehensive analysis of the current structural knowledge on the RP, including structures of the RP subunits, physical protein-protein interactions, and cryoelectron microscopy data. These data allowed us to compute an atomic model for the CP-AAA-ATPase subcomplex. In addition to this atomic model, further subunits can be mapped approximately, which lets us hypothesize on the substrate path during its degradation.
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Affiliation(s)
- Friedrich Förster
- From the ‡Department of Structural Biology, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Keren Lasker
- ¶Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, California 94158, and
- ‖Blavatnik School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Stephan Nickell
- From the ‡Department of Structural Biology, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Andrej Sali
- ¶Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, California 94158, and
| | - Wolfgang Baumeister
- From the ‡Department of Structural Biology, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany
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7
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Yi YJ, Manandhar G, Sutovsky M, Jonáková V, Park CS, Sutovsky P. Inhibition of 19S proteasomal regulatory complex subunit PSMD8 increases polyspermy during porcine fertilization in vitro. J Reprod Immunol 2010; 84:154-63. [DOI: 10.1016/j.jri.2009.11.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 08/20/2009] [Accepted: 11/05/2009] [Indexed: 01/24/2023]
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8
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Abstract
Protein modification by ubiquitin and ubiquitin-like molecules is a critical regulatory process. Like most regulated protein modifications, ubiquitination is reversible. Deubiquitination, the reversal of ubiquitination, is quickly being recognized as an important regulatory strategy. Nearly one hundred human DUBs (deubiquitinating enzymes) in five different gene families oppose the action of several hundred ubiquitin ligases, suggesting that both ubiquitination and its reversal are highly regulated and specific processes. It has long been recognized that ubiquitin ligases are modular enzyme systems that often depend on scaffolds and adaptors to deliver substrates to the catalytically active macromolecular complex. Although many DUBs bind ubiquitin with reasonable affinities (in the nM to microM range), a larger number have little affinity but exhibit robust catalytic capability. Thus it is apparent that these DUBs must acquire their substrates by binding the target protein in a conjugate or by associating with other macromolecular complexes. We would then expect that a study of protein partners of DUBs would reveal a variety of substrates, scaffolds, adaptors and ubiquitin receptors. In the present review we suggest that, like ligases, much of the regulation and specificity of deubiquitination arises from the association of DUBs with these protein partners.
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9
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Koulich E, Li X, DeMartino GN. Relative structural and functional roles of multiple deubiquitylating proteins associated with mammalian 26S proteasome. Mol Biol Cell 2007; 19:1072-82. [PMID: 18162577 DOI: 10.1091/mbc.e07-10-1040] [Citation(s) in RCA: 173] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
We determined composition and relative roles of deubiquitylating proteins associated with the 26S proteasome in mammalian cells. Three deubiquitylating activities were associated with the 26S proteasome: two from constituent subunits, Rpn11/S13 and Uch37, and one from a reversibly associated protein, Usp14. RNA interference (RNAi) of Rpn11/S13 inhibited cell growth, decreased cellular proteasome activity via disrupted 26S proteasome assembly, and inhibited cellular protein degradation. In contrast, RNAi of Uch37 or Usp14 had no detectable effect on cell growth, proteasome structure or proteolytic capacity, but accelerated cellular protein degradation. RNAi of both Uch37 and Usp14 also had no effect on proteasome structure or proteolytic capacity, but inhibited cellular protein degradation. Thus, proper proteasomal processing of ubiquitylated substrates requires Rpn11 plus either Uch37 or Usp14. Although the latter proteins feature redundant deubiquitylation functions, they also appear to exert noncatalyic effects on proteasome activity that are similar to but independent of one another. These results reveal unexpected functional relationships among multiple deubiquitylating proteins and suggest a model for mammalian 26S proteasome function whereby their concerted action governs proteasome function by linking deubiquitylation to substrate hydrolysis.
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Affiliation(s)
- Elena Koulich
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
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10
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Yang P, Smalle J, Lee S, Yan N, Emborg TJ, Vierstra RD. Ubiquitin C-terminal hydrolases 1 and 2 affect shoot architecture in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 51:441-57. [PMID: 17559514 DOI: 10.1111/j.1365-313x.2007.03154.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Ubiquitin C-terminal hydrolases (UCHs) are a subset of de-ubiquitinating proteases that release covalently linked ubiquitin (Ub), and as such play essential roles in recycling Ub and reversing the action of Ub conjugation. We show here that two related Arabidopsis UCHs, UCH1, and UCH2, are important for shoot development. The UCH1 and 2 genes are ubiquitously expressed, with the corresponding proteins present in both the cytoplasm and nucleus. Unlike their animal and fungal counterparts, we found no evidence that the Arabidopsis UCH1 and 2 proteins stably associate with the 26S proteasome. Altering the levels of UCH1 and 2 has substantial effects on Arabidopsis shoot development, especially with respect to inflorescence architecture, with over-expression and double mutants enhancing and suppressing the outgrowth of cauline branches, respectively. Neither UCH1-over-expressing nor uch1-1 uch2-1 plants have detectably altered sensitivity to cytokinins or auxins individually, but exhibit an altered sensitivity to the ratio of the two hormones. UCH1-over-expressing plants show dramatically enhanced phenotypes when combined with auxin-insensitive mutants axr1-3 and axr2-1, suggesting that one or more aspects of auxin signaling are affected by this enzyme pair. Previous studies revealed that the ubiquitination and degradation of the AUX/IAA family of repressors is a key step in auxin signaling. Here, we show that turnover of a reporter fused to a representative AUX/IAA protein AXR3 is faster in the uch1-1 uch2-1 double mutant but slower in the UCH1 over-expression backgrounds. Taken together, our results indicate that de-ubiquitination helps to modify plant shoot architecture, possibly via its ability to directly or indirectly protect upstream target proteins involved in auxin/cytokinin signaling from Ub-mediated degradation.
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Affiliation(s)
- Peizhen Yang
- Department of Genetics, University of Wisconsin-Madison, Madison, WI 53706-1574, USA
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11
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Hamazaki J, Iemura SI, Natsume T, Yashiroda H, Tanaka K, Murata S. A novel proteasome interacting protein recruits the deubiquitinating enzyme UCH37 to 26S proteasomes. EMBO J 2006; 25:4524-36. [PMID: 16990800 PMCID: PMC1589993 DOI: 10.1038/sj.emboj.7601338] [Citation(s) in RCA: 196] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Accepted: 08/15/2006] [Indexed: 11/10/2022] Open
Abstract
The 26S proteasome is a multisubunit protease responsible for regulated proteolysis in eukaryotic cells. It is composed of one catalytic 20S proteasome and two 19S regulatory particles attached on both ends of 20S proteasomes. Here, we describe the identification of Adrm1 as a novel proteasome interacting protein in mammalian cells. Although the overall sequence of Adrm1 has weak homology with the yeast Rpn13, the amino- and carboxyl-terminal regions exhibit significant homology. Therefore, we designated it as hRpn13. hRpn13 interacts with a base subunit Rpn2 via its amino-terminus. The majority of 26S proteasomes contain hRpn13, but a portion of them does not, indicating that hRpn13 is not an integral subunit. Intriguingly, we found that hRpn13 recruits UCH37, a deubiquitinating enzyme known to associate with 26 proteasomes. The carboxyl-terminal regions containing KEKE motifs of both hRpn13 and UCH37 are involved in their physical interaction. Knockdown of hRpn13 caused no obvious proteolytic defect but loss of UCH37 proteins and decrease in deubiquitinating activity of 26S proteasomes. Our results indicate that hRpn13 is essential for the activity of UCH37.
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Affiliation(s)
- Jun Hamazaki
- Laboratory of Frontier Science, Core Technology and Research Center, Tokyo Metropolitan Institute of Medical Science, Bunkyko-ku, Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachiohji, Tokyo, Japan
| | - Shun-ichiro Iemura
- National Institutes of Advanced Industrial Science and Technology, Biological Information Research Center, Kohtoh-ku, Tokyo, Japan
| | - Tohru Natsume
- National Institutes of Advanced Industrial Science and Technology, Biological Information Research Center, Kohtoh-ku, Tokyo, Japan
| | - Hideki Yashiroda
- Laboratory of Frontier Science, Core Technology and Research Center, Tokyo Metropolitan Institute of Medical Science, Bunkyko-ku, Tokyo, Japan
| | - Keiji Tanaka
- Laboratory of Frontier Science, Core Technology and Research Center, Tokyo Metropolitan Institute of Medical Science, Bunkyko-ku, Tokyo, Japan
| | - Shigeo Murata
- Laboratory of Frontier Science, Core Technology and Research Center, Tokyo Metropolitan Institute of Medical Science, Bunkyko-ku, Tokyo, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Laboratory of Frontier Science, Core Technology and Research Center, Tokyo Metropolitan Institute of Medical Science, 3-18-22 Honkomagome, Bunkyko-ku, Tokyo 113-9613, Japan. Tel./Fax: +81 3 3823 2237; E-mail:
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12
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Yao T, Song L, Xu W, DeMartino GN, Florens L, Swanson SK, Washburn MP, Conaway RC, Conaway JW, Cohen RE. Proteasome recruitment and activation of the Uch37 deubiquitinating enzyme by Adrm1. Nat Cell Biol 2006; 8:994-1002. [PMID: 16906146 DOI: 10.1038/ncb1460] [Citation(s) in RCA: 258] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Accepted: 07/12/2006] [Indexed: 11/09/2022]
Abstract
Uch37 is one of the three principal deubiquitinating enzymes (DUBs), and the only ubiquitin carboxy-terminal hydrolase (UCH)-family protease, that is associated with mammalian proteasomes. We show that Uch37 is responsible for the ubiquitin isopeptidase activity in the PA700 (19S) proteasome regulatory complex. PA700 isopeptidase disassembles Lys 48-linked polyubiquitin specifically from the distal end of the chain, a property that may be used to clear poorly ubiquitinated or unproductively bound substrates from the proteasome. To better understand Uch37 function and the mechanism responsible for its specificity, we investigated how Uch37 is recruited to proteasomes. Uch37 binds through Adrm1, a previously unrecognized orthologue of Saccharomyces cerevisiae Rpn13p, which in turn is bound to the S1 (also known as Rpn2) subunit of the 19S complex. Adrm1 (human Rpn13, hRpn13) binds the carboxy-terminal tail of Uch37, a region that is distinct from the UCH catalytic domain, which we show inhibits Uch37 activity. Following binding, Adrm1 relieves Uch37 autoinhibition, accelerating the hydrolysis of ubiquitin-7-amido-4-methylcoumarin (ubiquitin-AMC). However, neither Uch37 alone nor the Uch37-Adrm1 or Uch37-Adrm1-S1 complexes can hydrolyse di-ubiquitin efficiently; rather, incorporation into the 19S complex is required to enable processing of polyubiquitin chains.
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Affiliation(s)
- Tingting Yao
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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13
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Hahn Y, Lee B. Human-specific nonsense mutations identified by genome sequence comparisons. Hum Genet 2006; 119:169-78. [PMID: 16395595 DOI: 10.1007/s00439-005-0125-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2005] [Accepted: 12/10/2005] [Indexed: 11/29/2022]
Abstract
The comparative study of the human and chimpanzee genomes may shed light on the genetic ingredients for the evolution of the unique traits of humans. Here, we present a simple procedure to identify human-specific nonsense mutations that might have arisen since the human-chimpanzee divergence. The procedure involves collecting orthologous sequences in which a stop codon of the human sequence is aligned to a non-stop codon in the chimpanzee sequence and verifying that the latter is ancestral by finding homologs in other species without a stop codon. Using this procedure, we identify nine genes (CML2, FLJ14640, MT1L, NPPA, PDE3B, SERPINA13, TAP2, UIP1, and ZNF277) that would produce human-specific truncated proteins resulting in a loss or modification of the function. The premature terminations of CML2, MT1L, and SERPINA13 genes appear to abolish the original function of the encoded protein because the mutation removes a major part of the known active site in each case. The other six mutated genes are either known or presumed to produce functionally modified proteins. The mutations of five genes (CML2, FLJ14640, MT1L, NPPA, TAP2) are known or predicted to be polymorphic in humans. In these cases, the stop codon alleles are more prevalent than the ancestral allele, suggesting that the mutant alleles are approaching fixation since their emergence during the human evolution. The findings support the notion that functional modification or inactivation of genes by nonsense mutation is a part of the process of adaptive evolution and acquisition of species-specific features.
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Affiliation(s)
- Yoonsoo Hahn
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37, MSC 4264, 37 Convent Drive Room 5120A, Bethesda, MD 20892-4264, USA
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14
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Stone M, Hartmann-Petersen R, Seeger M, Bech-Otschir D, Wallace M, Gordon C. Uch2/Uch37 is the major deubiquitinating enzyme associated with the 26S proteasome in fission yeast. J Mol Biol 2005; 344:697-706. [PMID: 15533439 DOI: 10.1016/j.jmb.2004.09.057] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2004] [Revised: 09/01/2004] [Accepted: 09/09/2004] [Indexed: 12/29/2022]
Abstract
Conjugation of proteins to ubiquitin plays a central role for a number of cellular processes including endocytosis, DNA repair and degradation by the 26S proteasome. However, ubiquitination is reversible as a number of deubiquitinating enzymes mediate the disassembly of ubiquitin-protein conjugates. Some deubiquitinating enzymes are associated with the 26S proteasome contributing to and regulating the particle's activity. Here, we characterise fission yeast Uch2 and Ubp6, two proteasome associated deubiquitinating enzymes. The human orthologues of these enzymes are known as Uch37 and Usp14, respectively. We report that the subunit Uch2/Uch37 is the major deubiquitinating enzyme associated with the fission yeast 26S proteasome. In contrast, the activity of Ubp6 appears to play a more regulatory and/or structural role involving the proteasome subunits Mts1/Rpn9, Mts2/Rpt2 and Mts3/Rpn12, as Ubp6 becomes essential when activity of these subunits is compromised by conditional mutations. Finally, when the genes encoding Uch2/Uch37 and Ubp6 are disrupted, the cells are viable without showing obvious signs of impaired ubiquitin-dependent proteolysis, indicating that other deubiquitinating enzymes may remedy for the redundancy of these enzymes.
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Affiliation(s)
- Miranda Stone
- MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland, UK
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15
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Ovaa H, Kessler BM, Rolén U, Galardy PJ, Ploegh HL, Masucci MG. Activity-based ubiquitin-specific protease (USP) profiling of virus-infected and malignant human cells. Proc Natl Acad Sci U S A 2004; 101:2253-8. [PMID: 14982996 PMCID: PMC356937 DOI: 10.1073/pnas.0308411100] [Citation(s) in RCA: 157] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The family of ubiquitin (Ub)-specific proteases (USP) removes Ub from Ub conjugates and regulates a variety of cellular processes. The human genome contains many putative USP-encoding genes, but little is known about USP tissue distribution, pattern of expression, activity, and substrate specificity. We have used a chemistry-based functional proteomics approach to identify active USPs in normal, virus-infected, and tumor-derived human cells. Depending on tissue origin and stage of activation/differentiation, different USP activity profiles were revealed. The activity of specific USPs, including USP5, -7, -9, -13, -15, and -22, was up-regulated by mitogen activation or virus infection in normal T and B lymphocytes. UCH-L1 was highly expressed in tumor cell lines of epithelial and hematopoietic cell origin but was not detected in freshly isolated and mitogen-activated cells. Up-regulation of this USP was a late event in the establishment of Epstein-Barr virus-immortalized lymphoblastoid cell lines and correlated with enhanced proliferation, suggesting a possible role in growth transformation.
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Affiliation(s)
- Huib Ovaa
- Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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16
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Yang P, Fu H, Walker J, Papa CM, Smalle J, Ju YM, Vierstra RD. Purification of the Arabidopsis 26 S Proteasome. J Biol Chem 2004; 279:6401-13. [PMID: 14623884 DOI: 10.1074/jbc.m311977200] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 26 S proteasome is a multisubunit protease complex responsible for degrading a wide range of intracellular proteins in eukaryotes, especially those modified with polyubiquitin chains. It is composed of a self-compartmentalized core protease (CP) that houses the peptidase active sites appended on either or both ends by a regulatory particle (RP) that identifies appropriate substrates and translocates them into the lumen of the CP for breakdown. Here, we describe the molecular and biochemical properties of the 26 S proteasome from the plant Arabidopsis thaliana. Like the CP and the ATPase ring of the RP, the RP non-ATPase subunits are often encoded by two transcriptionally active genes with some pairs displaying sufficient sequence divergence to suggest functional differences. Most RPN subunits could functionally replace their yeast counterparts, implying that they have retained their positions and activities within the complex. A method was developed to purify the 26 S proteasome intact from whole Arabidopsis seedlings. These preparations are biochemically indistinguishable from those from yeast and mammals, including the need for ATP to maintain integrity and a strong sensitivity to the inhibitors MG115, MG132, lactacystin, and epoxomicin. Mass spectrometric analysis of the complex detected the presence of almost all CP and RP subunits. In many cases, both products of paralogous genes were detected, demonstrating that each isoform assembles into the mature particle. As with the yeast and animal 26 S proteasomes, attenuation of individual RP genes induces a coordinated up-regulation of many of the other 26 S proteasome genes, suggesting that plants contain a negative feedback mechanism to regulate the 26 S proteasome levels. The incorporation of paralogous subunits into the Arabidopsis holoprotease raises the intriguing possibility that plants synthesize multiple 26 S proteasome types with unique properties and/or target specificities.
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Affiliation(s)
- Peizhen Yang
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706-1574, USA
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17
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Soares L, Seroogy C, Skrenta H, Anandasabapathy N, Lovelace P, Chung CD, Engleman E, Fathman CG. Two isoforms of otubain 1 regulate T cell anergy via GRAIL. Nat Immunol 2003; 5:45-54. [PMID: 14661020 DOI: 10.1038/ni1017] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2003] [Accepted: 10/28/2003] [Indexed: 11/08/2022]
Abstract
The active ubiquitin E3 ligase GRAIL is crucial in the induction of CD4 T cell anergy. Here we show that GRAIL is associated with and regulated by two isoforms of the ubiquitin-specific protease otubain 1. In lethally irradiated mice reconstituted with bone marrow cells from T cell receptor-transgenic mice retrovirally transduced to express the genes encoding these proteases, otubain 1-expressing cells contained negligible amounts of endogenous GRAIL, proliferated well and produced large amounts of interleukin 2 after antigenic stimulation. In contrast, cells expressing the alternatively spliced isoform, otubain 1 alternative reading frame 1, contained large amounts of endogenous GRAIL and were functionally anergic, and they proliferated poorly and produced undetectable interleukin 2 when stimulated in a similar way. Thus, these two proteins have opposing epistatic functions in controlling the stability of GRAIL expression and the resultant anergy phenotype in T cells.
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Affiliation(s)
- Luis Soares
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California 94305, USA
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18
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Zwickl P, Seemüller E, Kapelari B, Baumeister W. The proteasome: a supramolecular assembly designed for controlled proteolysis. ADVANCES IN PROTEIN CHEMISTRY 2002; 59:187-222. [PMID: 11868272 DOI: 10.1016/s0065-3233(01)59006-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- P Zwickl
- Department of Molecular Structural Biology, Max-Planck Institute for Biochemistry, Am Klopferspitz 18a, 82152 Martinsried, Germany
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