1
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Tyagi A, Haq S, Ramakrishna S. Redox regulation of DUBs and its therapeutic implications in cancer. Redox Biol 2021; 48:102194. [PMID: 34814083 PMCID: PMC8608616 DOI: 10.1016/j.redox.2021.102194] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/19/2021] [Indexed: 02/06/2023] Open
Abstract
Reactive oxygen species (ROS) act as a double-edged sword in cancer, where low levels of ROS are beneficial but excessive accumulation leads to cancer progression. Elevated levels of ROS in cancer are counteracted by the antioxidant defense system. An imbalance between ROS generation and the antioxidant system alters gene expression and cellular signaling, leading to cancer progression or death. Post-translational modifications, such as ubiquitination, phosphorylation, and SUMOylation, play a critical role in the maintenance of ROS homeostasis by controlling ROS production and clearance. Recent evidence suggests that deubiquitinating enzymes (DUBs)-mediated ubiquitin removal from substrates is regulated by ROS. ROS-mediated oxidation of the catalytic cysteine (Cys) of DUBs, leading to their reversible inactivation, has emerged as a key mechanism regulating DUB-controlled cellular events. A better understanding of the mechanism by which DUBs are susceptible to ROS and exploring the ways to utilize ROS to pharmacologically modulate DUB-mediated signaling pathways might provide new insight for anticancer therapeutics. This review assesses the recent findings regarding ROS-mediated signaling in cancers, emphasizes DUB regulation by oxidation, highlights the relevant recent findings, and proposes directions of future research based on the ROS-induced modifications of DUB activity.
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Affiliation(s)
- Apoorvi Tyagi
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Saba Haq
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea; College of Medicine, Hanyang University, Seoul, 04763, South Korea.
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2
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Deol KK, Strieter ER. The ubiquitin proteoform problem. Curr Opin Chem Biol 2021; 63:95-104. [PMID: 33813043 PMCID: PMC8384647 DOI: 10.1016/j.cbpa.2021.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 12/23/2022]
Abstract
The diversity of ubiquitin modifications is immense. A protein can be monoubiquitylated, multi-monoubiquitylated, and polyubiquitylated with chains varying in size and shape. Ubiquitin itself can be adorned with other ubiquitin-like proteins and smaller functional groups. Considering different combinations of post-translational modifications can give rise to distinct biological outcomes, characterizing ubiquitylated proteoforms of a given protein is paramount. In this Opinion, we review recent advances in detecting and quantifying various ubiquitin proteoforms using mass spectrometry.
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Affiliation(s)
- Kirandeep K Deol
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA; Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA
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3
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Gopinath P, Ohayon S, Nawatha M, Brik A. Chemical and semisynthetic approaches to study and target deubiquitinases. Chem Soc Rev 2018; 45:4171-98. [PMID: 27049734 DOI: 10.1039/c6cs00083e] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ubiquitination is a key posttranslational modification, which affects numerous biological processes and is reversed by a class of enzymes known as deubiquitinases (DUBs). This family of enzymes cleaves mono-ubiquitin or poly-ubiquitin chains from a target protein through different mechanisms and mode of interactions with their substrates. Studying the role of DUBs in health and diseases has been a major goal for many laboratories both in academia and in industry. However, the field has been challenged by the difficulties in obtaining native substrates and novel reagents using traditional enzymatic and molecular biology approaches. Recent advancements in the synthesis and semisynthesis of proteins made it possible to prepare several unique ubiquitin conjugates to study various aspects of DUBs such as their specificities and structures. Moreover, these approaches enable the preparation of novel activity based probes and assays to monitor DUB activities in vitro and in cellular contexts. Efforts made to bring new chemical entities for the selective inhibition of DUBs based on these tools are also highlighted with selected examples.
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Affiliation(s)
- Pushparathinam Gopinath
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Shimrit Ohayon
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Mickal Nawatha
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
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4
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Hameed DS, Sapmaz A, Ovaa H. How Chemical Synthesis of Ubiquitin Conjugates Helps To Understand Ubiquitin Signal Transduction. Bioconjug Chem 2016; 28:805-815. [PMID: 27077728 DOI: 10.1021/acs.bioconjchem.6b00140] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ubiquitin (Ub) is a small post-translational modifier protein involved in a myriad of biochemical processes including DNA damage repair, proteasomal proteolysis, and cell cycle control. Ubiquitin signaling pathways have not been completely deciphered due to the complex nature of the enzymes involved in ubiquitin conjugation and deconjugation. Hence, probes and assay reagents are important to get a better understanding of this pathway. Recently, improvements have been made in synthesis procedures of Ub derivatives. In this perspective, we explain various research reagents available and how chemical synthesis has made an important contribution to Ub research.
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Affiliation(s)
- Dharjath S Hameed
- Division of Cell Biology II, The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Aysegul Sapmaz
- Division of Cell Biology II, The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Huib Ovaa
- Division of Cell Biology II, The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,Department of Chemical Immunology, Leiden University Medical Center , Einthovenweg 20, 2333 ZC Leiden, The Netherlands
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5
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Huang YC, Fang GM, Liu L. Chemical synthesis of proteins using hydrazide intermediates. Natl Sci Rev 2015. [DOI: 10.1093/nsr/nwv072] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Protein chemical synthesis offers useful and otherwise-difficulty-to-obtain biomacromolecules for biological and pharmaceutical studies. Recently, the hydrazide chemistry has drawn attentions in this field as peptide or protein hydrazides can be used as key intermediates for different synthesis and modification purposes. Besides being a traditional bioorthogonal chemical handle, a hydrazide group can serve as a readily accessible precursor of a thioester. This strategy significantly improves the efficiency and scope of native chemical ligation for protein chemical synthesis. Here we review the chemical transformations of peptide or protein hydrazides and total/semi/enzymatic protein synthesis methods involving peptide or protein hydrazides. Several examples of protein chemical synthesis using peptide hydrazides as key intermediates are described.
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Catching a DUB in the act: novel ubiquitin-based active site directed probes. Curr Opin Chem Biol 2015; 23:63-70. [PMID: 25461387 PMCID: PMC7185813 DOI: 10.1016/j.cbpa.2014.10.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/30/2014] [Accepted: 10/08/2014] [Indexed: 01/21/2023]
Abstract
Activity-based probes used to probe DUB inhibitor specificity. Developments in DUB activity-based probe use. Determination of linkage preference of DUBs using activity-based probes. Outlook for development in DUB probe design and current challenges.
Protein ubiquitylation is an important regulator of protein function, localization and half-life. It plays a key role in most cellular processes including immune signaling. Deregulation of this process is a major causative factor for many diseases. A major advancement in the identification and characterization of the enzymes that remove ubiquitin, deubiquitylases (DUBs) was made by the development of activity-based probes (ABPs). Recent advances in chemical protein synthesis and ligation methodology has yielded novel reagents for use in ubiquitylation research. We describe recent advances and discuss future directions in reagent development for studying DUBs.
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7
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Kuang Z, Yao Y, Shi Y, Gu Z, Sun Z, Tso J. Winter hibernation and UCHL1-p34cdc2 association in toad oocyte maturation competence. PLoS One 2013; 8:e78785. [PMID: 24194953 PMCID: PMC3806854 DOI: 10.1371/journal.pone.0078785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 09/21/2013] [Indexed: 11/18/2022] Open
Abstract
Currently, it is believed that toad oocyte maturation is dependent on the physiological conditions of winter hibernation. Previous antibody-blocking experiments have demonstrated that toad ubiquitin carboxyl-terminal hydrolase L1 (tUCHL1) is necessary for germinal vesicle breakdown during toad oocyte maturation. In this paper, we first supply evidence that tUCHL1 is highly evolutionarily conserved. Then, we exclude protein availability and ubiquitin carboxyl-terminal hydrolase enzyme activity as factors in the response of oocytes to winter hibernation. In the context of MPF (maturation promoting factor) controlling oocyte maturation and to further understand the role of UCHL1 in oocyte maturation, we performed adsorption and co-immunoprecipitation experiments using toad oocyte protein extracts and determined that tUCHL1 is associated with MPF in toad oocytes. Recombinant tUCHL1 absorbed p34(cdc2), a component of MPF, in obviously larger quantities from mature oocytes than from immature oocytes, and p13(suc1) was isolated from tUCHL1 with a dependence on the ATP regeneration system, suggesting that still other functions may be involved in their association that require phosphorylation. In oocytes from hibernation-interrupted toads, the p34(cdc2) protein level was significantly lower than in oocytes from toads in artificial hibernation, providing an explanation for the different quantities isolated by recombinant tUCHL1 pull-down and, more importantly, identifying a mechanism involved in the toad oocyte's dependence on a low environmental temperature during winter hibernation. Therefore, in toads, tUCHL1 binds p34(cdc2) and plays a role in oocyte maturation. However, neither tUCHL1 nor cyclin B1 respond to low temperatures to facilitate oocyte maturation competence during winter hibernation.
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Affiliation(s)
- Zhichao Kuang
- Institute of Reproduction & Development, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuwei Yao
- Institute of Reproduction & Development, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yan Shi
- Key Laboratory of Contraceptive Drugs and Devices of National Population and Family Planning Commission of China, Shanghai Institute of Planned Parenthood Research, Shanghai, China
| | - Zheng Gu
- Key Laboratory of Contraceptive Drugs and Devices of National Population and Family Planning Commission of China, Shanghai Institute of Planned Parenthood Research, Shanghai, China
| | - Zhaogui Sun
- Institute of Reproduction & Development, Shanghai Medical College, Fudan University, Shanghai, China
- Key Laboratory of Contraceptive Drugs and Devices of National Population and Family Planning Commission of China, Shanghai Institute of Planned Parenthood Research, Shanghai, China
- * E-mail:
| | - Jiake Tso
- Key Laboratory of Contraceptive Drugs and Devices of National Population and Family Planning Commission of China, Shanghai Institute of Planned Parenthood Research, Shanghai, China
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8
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Reversible inactivation of deubiquitinases by reactive oxygen species in vitro and in cells. Nat Commun 2013; 4:1568. [PMID: 23463011 PMCID: PMC3615374 DOI: 10.1038/ncomms2532] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 01/21/2013] [Indexed: 12/12/2022] Open
Abstract
In eukaryotes, deubiquitinases (DUBs) remove ubiquitin conjugates from diverse substrates, altering their stabilities, localizations or activities. Here we show that many DUBs of the USP and UCH subfamilies can be reversibly inactivated upon oxidation by reactive oxygen species in vitro and in cells. Oxidation occurs preferentially on the catalytic cysteine, abrogating the isopeptide-cleaving activity without affecting these enzymes’ affinity to ubiquitin. Sensitivity to oxidative inhibition is associated with DUB activation wherein the active site cysteine is converted to a deprotonated state prone to oxidation. We demonstrate that this redox regulation is essential for mono-ubiquitination of proliferating-cell nuclear antigen in response to oxidative DNA damage, which initiates a DNA damage-tolerance programme. These findings establish a novel mechanism of DUB regulation that may be integrated with other redox-dependent signalling circuits to govern cellular adaptation to oxidative stress, a process intimately linked to aging and cancer. Deubiquitinases regulate protein stability, localization and activity, and yet the mechanisms controlling their activity remain poorly understood. Lee et al. show that these enzymes are reversibly inhibited by reactive oxygen species through oxidation of catalytic cysteine residues.
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9
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Trang VH, Valkevich EM, Minami S, Chen YC, Ge Y, Strieter ER. Nonenzymatic polymerization of ubiquitin: single-step synthesis and isolation of discrete ubiquitin oligomers. Angew Chem Int Ed Engl 2012; 51:13085-8. [PMID: 23161800 PMCID: PMC4083817 DOI: 10.1002/anie.201207171] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/26/2012] [Indexed: 11/05/2022]
Abstract
Linked: a method based on thiol-ene chemistry enables the synthesis and purification of ubiquitin oligomers with ≥4 units. This approach, which employs free-radical polymerization, can be applied towards the synthesis of homogeneous Lys6-linked ubiquitin oligomers currently inaccessible by enzymatic methods. By using these chains, one can study their roles in the ubiquitin proteasome system and the DNA damage response pathway.
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Affiliation(s)
- Vivian H. Trang
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Wi 53706
| | - Ellen M. Valkevich
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Wi 53706
| | - Shoko Minami
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Wi 53706
| | - Yi-Chen Chen
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, 1300 University Ave. Madison, WI 53706
| | - Ying Ge
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, 1300 University Ave. Madison, WI 53706
| | - Eric R. Strieter
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Wi 53706
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10
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Trang VH, Valkevich EM, Minami S, Chen YC, Ge Y, Strieter ER. Nonenzymatic Polymerization of Ubiquitin: Single-Step Synthesis and Isolation of Discrete Ubiquitin Oligomers. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207171] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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12
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Spasser L, Brik A. Chemistry and Biology of the Ubiquitin Signal. Angew Chem Int Ed Engl 2012; 51:6840-62. [DOI: 10.1002/anie.201200020] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Indexed: 01/07/2023]
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13
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Abstract
Protein ubiquitination, the covalent attachment of ubiquitin to target proteins, has emerged as one of the most prevalent posttranslational modifications (PTMs), regulating nearly every cellular pathway. The diversity of signaling associated with this particular PTM stems from the myriad ways in which a target protein can be modified by ubiquitin, e.g., monoubiquitin, multi-monoubiquitin, and polyubiquitin linkages. In this Review, we focus on developments in both enzymatic and chemical methods that engender ubiquitin with new chemical and physical properties. Moreover, we highlight how these methods have enabled studies directed toward (i) characterizing enzymes responsible for reversing the ubiquitin modification, (ii) understanding the influence of ubiquitin on protein function and crosstalk with other PTMs, and (iii) uncovering the impact of polyubiquitin chain linkage and length on downstream signaling events.
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Affiliation(s)
- Eric R. Strieter
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706,
United States
| | - David A. Korasick
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706,
United States
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14
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Bavikar SN, Spasser L, Haj-Yahya M, Karthikeyan SV, Moyal T, Ajish Kumar KS, Brik A. Chemical Synthesis of Ubiquitinated Peptides with Varying Lengths and Types of Ubiquitin Chains to Explore the Activity of Deubiquitinases. Angew Chem Int Ed Engl 2011; 51:758-63. [DOI: 10.1002/anie.201106430] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Revised: 10/12/2011] [Indexed: 01/27/2023]
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15
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Bavikar SN, Spasser L, Haj-Yahya M, Karthikeyan SV, Moyal T, Ajish Kumar KS, Brik A. Chemical Synthesis of Ubiquitinated Peptides with Varying Lengths and Types of Ubiquitin Chains to Explore the Activity of Deubiquitinases. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106430] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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Labean TH, Butt TR, Kauffman SA, Schultes EA. Protein folding absent selection. Genes (Basel) 2011; 2:608-26. [PMID: 24710212 PMCID: PMC3927614 DOI: 10.3390/genes2030608] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2011] [Revised: 08/05/2011] [Accepted: 08/11/2011] [Indexed: 11/16/2022] Open
Abstract
Biological proteins are known to fold into specific 3D conformations. However, the fundamental question has remained: Do they fold because they are biological, and evolution has selected sequences which fold? Or is folding a common trait, widespread throughout sequence space? To address this question arbitrary, unevolved, random-sequence proteins were examined for structural features found in folded, biological proteins. Libraries of long (71 residue), random-sequence polypeptides, with ensemble amino acid composition near the mean for natural globular proteins, were expressed as cleavable fusions with ubiquitin. The structural properties of both the purified pools and individual isolates were then probed using circular dichroism, fluorescence emission, and fluorescence quenching techniques. Despite this necessarily sparse "sampling" of sequence space, structural properties that define globular biological proteins, namely collapsed conformations, secondary structure, and cooperative unfolding, were found to be prevalent among unevolved sequences. Thus, for polypeptides the size of small proteins, natural selection is not necessary to account for the compact and cooperative folded states observed in nature.
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Affiliation(s)
- Thomas H Labean
- Sequenomics LLC, 1428 Chanterelle Lane, Hillsborough, NC 27278, USA.
| | - Tauseef R Butt
- LifeSensors Inc., 271 Great Valley Parkway, Suite 100, Malvern, PA 19355, USA.
| | - Stuart A Kauffman
- Complex Systems Center University of Vermont, 200C Farrell Hall, 210 Colchester Ave., Burlington, VT 05405, USA.
| | - Erik A Schultes
- Sequenomics LLC, 1428 Chanterelle Lane, Hillsborough, NC 27278, USA.
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Yao YW, Shi Y, Jia ZF, Jiang YH, Gu Z, Wang J, Aljofan M, Sun ZG. PTOV1 is associated with UCH-L1 and in response to estrogen stimuli during the mouse oocyte development. Histochem Cell Biol 2011; 136:205-15. [PMID: 21678139 DOI: 10.1007/s00418-011-0825-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2011] [Indexed: 01/24/2023]
Abstract
To investigate the biological significance of ubiquitin carboxyl-terminal hydrolase L1 (UCH-L1) involvement in oocyte maturation, we screened for proteins that bound to UCH-L1 in mouse ovaries, and we found that the prostate tumor overexpressed-1 (PTOV1) protein was able to bind to UCH-L1. PTOV1 is highly expressed in prostate cancers and considered as a potential marker for carcinogenesis and the progress of prostate cancer. It was reported that PTOV1 plays an important role in cell cycle regulation, but its role in mammalian oocyte development and meiosis is still unclear. In this paper, it was found that the expression levels of PTOV1 in mouse ovaries progressively increased from prepubescence to adulthood. And we found by immunohistochemistry that PTOV1 spreaded in both the cytoplasm and nuclei of oocytes during prepuberty, but in normal adult mouse oocytes, it concentrated not only in nuclei but also on the plasma membrane, though in some oocytes with abnormal shapes, PTOV1 did not display the typical distribution patterns. In granulosa cells, however, it was found to locate in the cytoplasm at all the selected ages. In postnatal mouse ovaries (28 days), estradiol treatment induced the adult-specific distribution pattern of PTOV1 in oocytes. In addition, UCH-L1 was shown to be associated with CDK1, which participated in the regulation of cell cycle and oocyte maturation. Therefore, we propose that the distribution changes of PTOV1 are age-dependent, and significant for mouse oocyte development and maturation. Moreover, the discovery that PTOV1 is associated with UCH-L1 in mouse oocytes supports the explanations for that UCH-L1 is involved in oocyte development and maturation, especially under the regulation of estrogen.
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Affiliation(s)
- Yu-Wei Yao
- Shanghai Medical College, Fudan University, Shanghai, China
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Affiliation(s)
- Tomasz Fekner
- Department of Chemistry, The Ohio State University, 484 W 12th Avenue, Columbus, OH 43210, USA
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Kumar KSA, Spasser L, Ohayon S, Erlich LA, Brik A. Expeditious chemical synthesis of ubiquitinated peptides employing orthogonal protection and native chemical ligation. Bioconjug Chem 2011; 22:137-43. [PMID: 21235224 DOI: 10.1021/bc1004735] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ubiquitination-the attachment of ubiquitin to a protein target-is involved in a wide range of cellular processes in eukaryotes. This dynamic posttranslational modification utilizes three enzymes to link, through an isopeptide bond, the C-terminal Gly of ubiquitin to the lysine side chain from a protein target. Progress in the field aiming at deciphering the role of ubiquitination in biological processes has been very dependent on the discovery of the enzymatic machinery, which is known to be very specific to each protein target. Chemical approaches offer a complementary route to the biochemical methods to construct these conjugates in vitro in order to assist in unraveling the role of ubiquitination on protein function. Herein is presented a novel method for the rapid synthesis of ubiquitinated peptides employing solid-phase peptide to generate the critical isopeptide linkage. Using these tools, several ubiquitinated peptides derived from known ubiquitinated proteins were prepared. Among them is the ubiquitinated C-terminal fragment of H2B, which can be used in the synthesis of monoubiquitinated H2B. For the first time, we systematically assessed the effect of the length of the ubiquitinated peptides on the UCH-L3 activity and found that peptides of up to ∼20 residues are preferred substrates.
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Affiliation(s)
- K S Ajish Kumar
- Department of Chemistry, Ben Gurion University, Beer Sheva, Israel 84105
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20
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Sixt SU, Jennissen HP, Winterhalter M, Laub M. Detection of ubiquityl-calmodulin conjugates with a novel high-molecular weight ubiquitylprotein-isopeptidase in rabbit tissues. Eur J Med Res 2010; 15:428-47. [PMID: 21156402 PMCID: PMC3352187 DOI: 10.1186/2047-783x-15-10-428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The selective degradation of many proteins in eukaryotic cells is carried out by the ubiquitin system. In this pathway, proteins are targeted for degradation by covalent ligation to ubiquitin, a highly conserved protein [1]. Ubiquitylated proteins were degraded by the 26S proteasome in an ATP-depended manner. The degradation of ubiquitylated proteins were controlled by isopeptidase cleavage. A well characterised system of ubiquitylation and deubiquitylation is the calmodulin system in vitro [2]. Detection of ubiquityl-calmodulin conjugtates in vivo have not been shown so far. In this article we discuss the detection of ubiquitin calmodulin conjugates in vivo by incubation with a novel high-molecular weight ubiquitylprotein-isopeptidase in rabbit tissues. Proteins with a molecular weight of ubiquityl-calmodulin conjugates could be detected in all organs tested. Incubation with ubiquitylprotein-isopeptidase showed clearly a decrease of ubiquitin calmodulin conjugates in vivo with an origination of unbounded ubiquitin. These results suggest that only few ubiquitin calmodulin conjugates exist in rabbit tissues.
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Affiliation(s)
- S U Sixt
- Klinik für Anästhesiologie, Universitätsklinikum Düsseldorf, Germany.
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21
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Shanmugham A, Fish A, Luna-Vargas MPA, Faesen AC, El Oualid F, Sixma TK, Ovaa H. Nonhydrolyzable ubiquitin-isopeptide isosteres as deubiquitinating enzyme probes. J Am Chem Soc 2010; 132:8834-5. [PMID: 20540574 DOI: 10.1021/ja101803s] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate that oxime ligation is an efficient, straightforward, and generally applicable strategy for generating nonhydrolyzable ubiquitin (Ub)-isopeptide isosteres. We synthesized nonhydrolyzable K48- and K63-linked Ub-isopeptide isosteres to investigate the selectivity of deubiquitinating enzymes for specific linkages employing surface plasmon resonance spectroscopy. The results indicate that deubiquitinating enzymes specifically recognize the local peptide sequence flanking Ub-branched lysine residues in target proteins. The described strategy allows the systematic investigation of sequence requirements for substrate selectivity of deubiquitinating enzymes.
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Affiliation(s)
- Anitha Shanmugham
- Division of Cell Biology and The Netherlands Proteomics Centre, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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22
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Abstract
The addition of ubiquitin (Ub) and ubiquitin-like (Ubl) modifiers to proteins serves to modulate function and is a key step in protein degradation, epigenetic modification and intracellular localization. Deubiquitinating enzymes and Ubl-specific proteases, the proteins responsible for the removal of Ub and Ubls, act as an additional level of control over the ubiquitin-proteasome system. Their conservation and widespread occurrence in eukaryotes, prokaryotes and viruses shows that these proteases constitute an essential class of enzymes. Here, we discuss how chemical tools, including activity-based probes and suicide inhibitors, have enabled (i) discovery of deubiquitinating enzymes, (ii) their functional profiling, crystallographic characterization and mechanistic classification and (iii) development of molecules for therapeutic purposes.
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Abstract
Irreversible covalent inhibitors equipped with reporter groups, also termed activity-based probes, allow the study of target enzymes based on catalytic activity instead of expression level, which does not necessarily indicate protein function and subsequent cellular consequences. Activity-based probes offer advantages over traditional techniques: they can be applied to the cell or tissue of choice and molecular imaging and pharmacology applications are possible. Here the design and use of probes directed at enzymatic activities in the ubiquitin proteasome system are discussed. This system holds promise for the development of new, targeted anticancer therapies and the probes discussed here might aid in fulfilling this promise.
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Affiliation(s)
- Huib Ovaa
- Division of Cellular Biochemistry, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
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Burchak ON, Jaquinod M, Cottin C, Mugherli L, Iwai K, Chatelain F, Balakirev MY. Chemoenzymatic ubiquitination of artificial substrates. Chembiochem 2007; 7:1667-9. [PMID: 17009276 DOI: 10.1002/cbic.200600283] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Olga N Burchak
- Département Réponse et Dynamique Cellulaires, Commissariat à l'Energie Atomique, 17 rue des Martyrs, 38054 Grenoble, France
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25
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Otsuki T, Yata K, Takata-Tomokuni A, Hyodoh F, Miura Y, Sakaguchi H, Hatayama T, Hatada S, Tsujioka T, Sato Y, Murakami H, Sadahira Y, Sugihara T. Expression of protein gene product 9.5 (PGP9.5)/ubiquitin-C-terminal hydrolase 1 (UCHL-1) in human myeloma cells. Br J Haematol 2004; 127:292-8. [PMID: 15491288 DOI: 10.1111/j.1365-2141.2004.05205.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The neuron cytoplasmic protein gene product 9.5 (PGP9.5)/ubiquitin-C-terminal hydrolase 1 (UCHL-1) protein is a thiol protease that recognizes and hydrolyzes a peptide bond at the C-terminal of ubiquitin, and is involved in the processing of ubiquitin precursors and ubiquinated proteins. Although this molecule is known as a specific tissue marker for the neuroendocrine system, many reports have indicated that PGP9.5 is a marker for certain tumour types, such as cancer of the lung, colon, and pancreas. The expression of PGP9.5 in myeloma cells was examined. PGP9.5 seemed to be expressed specifically in myeloma cells as compared with other haematological malignant cells. In addition, in myeloma cells subjected to growth-factor starvation, the upregulation of PGP9.5 was observed in association with that of p27(Kip1), a cyclin-dependent-kinase inhibitor, although the upregulation caused by irradiation was milder. In contrast, the hypoxic culture of myeloma cells induced down-regulation of PGP9.5. These results suggested that PGP9.5 may be a good marker for myeloma among haematological malignancies. In addition, it may indicate certain cellular features of myeloma cells, such as sensitivity to proteasome inhibitors.
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Affiliation(s)
- T Otsuki
- Department of Hygiene, Kawasaki Medical School, 577 Matsushima, Kurashiki, Japan.
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26
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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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27
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Gan-Erdene T, Nagamalleswari K, Yin L, Wu K, Pan ZQ, Wilkinson KD. Identification and characterization of DEN1, a deneddylase of the ULP family. J Biol Chem 2003; 278:28892-900. [PMID: 12759362 DOI: 10.1074/jbc.m302890200] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To identify deneddylases, proteases with specificity for hydrolysis of Nedd8 derivatives, a facile method was developed for the synthesis of Nedd8 amidomethylcoumarin (a substrate) and Nedd8 vinyl sulfone (an inhibitor). Deneddylase activity is necessary to reverse the conjugation of Nedd8 to cullin, a modification that regulates at least some ubiquitin ligases. The reaction of Nedd8 vinyl sulfone with L-M(TK-) mouse fibroblast lysates identified two deneddylases. The deubiquitinating enzyme UCH-L3 is labeled by both ubiquitin vinyl sulfone and Nedd8 vinyl sulfone. In contrast, a second and more selective enzyme is labeled only by Nedd8 vinyl sulfone. This protein, DEN1, is a 221-amino acid thiol protease that is encoded by an open reading frame previously annotated as SENP8. Recombinant human DEN1 shows significant specificity for Nedd8 and catalyzes the hydrolysis of Nedd8 amidomethylcoumarin with a Km of 51 nm and a kcat of7s-1. The catalytic efficiency of DEN1 acting upon ubiquitin amidomethylcoumarin is 6 x 10-4 that of Nedd8 amidomethylcoumarin and its activity on SUMO-1 amidomethylcoumarin is undetectable. This selectivity was unexpected as DEN1 is most closely related to enzymes that catalyze desumoylation. This observation expands to four the number of DUB families with members that can process the C terminus of Nedd8.
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Affiliation(s)
- Tudeviin Gan-Erdene
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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28
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Deubiquitinating enzymes--the importance of driving in reverse along the ubiquitin-proteasome pathway. Int J Biochem Cell Biol 2003; 35:590-605. [PMID: 12672452 DOI: 10.1016/s1357-2725(02)00392-8] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ubiquitination of proteins is now recognized to target proteins for degradation by the proteasome and for internalization into the lysosomal system, as well as to modify functions of some target proteins. Although much progress has been made in characterizing enzymes that link ubiquitin to proteins, our understanding of deubiquitinating enzymes is less developed. These enzymes are involved in processing the products of ubiquitin genes which all encode fusion proteins, in negatively regulating the functions of ubiquitination (editing), in regenerating free ubiquitin after proteins have been targeted to the proteasome or lysosome (recycling) and in salvaging ubiquitin from possible adducts formed with small molecule nucleophiles in the cell. A large number of genes encode deubiquitinating enzymes suggesting that many have highly specific and regulated functions. Indeed, recent findings provide strong support for the concept that ubiquitination is regulated by both specific pathways of ubiquitination and deubiquitination. Interestingly, many of these enzymes are localized to subcellular structures or to molecular complexes. These localizations play important roles in determining specificity of function and can have major influences on their catalytic activities. Future studies, particularly aimed at characterizing the interacting partners and potential substrates in these complexes as well as at determining the effects of loss of function of specific deubiquitinating enzymes will rapidly advance our understanding of the important roles of these enzymes as biological regulators.
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29
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Sun ZG, Kong WH, Zhang YJ, Yan S, Lu JN, Gu Z, Lin F, Tso JK. A novel ubiquitin carboxyl terminal hydrolase is involved in toad oocyte maturation. Cell Res 2003; 12:199-206. [PMID: 12296378 DOI: 10.1038/sj.cr.7290125] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
p28, a 28kD protein from toad (Bufo bufo gargarizans) oocytes, was identified by using p13(suc1)-agarose affinity chromatography. Sequence homology analysis of the full-length cDNA of p28 (Gene Bank accession number: AF 314091) indicated that it encodes a protein containing 224 amino-acids with about 55% identities and more than 70% positives to human, rat or mouse UCH-L1, and contains homological functional domains of UCH family. Anti-p28 monoclonal antibody, on injecting into the oocytes, could inhibit the progesterone-induced resumption of meiotic division in a dose-dependent manner. The recombinant protein p28 showed similar SDS/PAGE behaviors to the native one, and promoted ubiquitin ethyl ester hydrolysis, a classical catalytic reaction for ubiquitin carboxyl terminal hydrolases (UCHs). The results in this paper reveal that a novel protein, p28, exists in the toad oocytes, is a UCH L1 homolog, was engaged in the process of progesterone-induced oocyte maturation possibly through an involvement in protein turnover and degradation.
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Affiliation(s)
- Zhao Gui Sun
- National Laboratory of Contraceptives and Devices Research, Shanghai Institute of Planned Parenthood Research, China
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30
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Rajapurohitam V, Bedard N, Wing SS. Control of ubiquitination of proteins in rat tissues by ubiquitin conjugating enzymes and isopeptidases. Am J Physiol Endocrinol Metab 2002; 282:E739-45. [PMID: 11882492 DOI: 10.1152/ajpendo.00511.2001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The activity of the ubiquitin-dependent proteolytic system in differentiated tissues under basal conditions remains poorly explored. We measured rates of ubiquitination in rat tissue extracts. Accumulation of ubiquitinated proteins increased in the presence of ubiquitin aldehyde, indicating that deubiquitinating enzymes can regulate ubiquitination. Rates of ubiquitination varied fourfold, with the highest rate in the testis. We tested whether ubiquitin-activating enzyme (E1) or ubiquitin-conjugating enzymes (E2s) could be limiting for conjugation. Immunodepletion of the E2s UBC2 or UBC4 lowered rates of conjugation similarly. Supplementation of extracts with excess UBC2 or UBC4, but not E1, stimulated conjugation. However, UBC2-stimulated rates of ubiquitination still differed among tissues, indicating that tissue differences in E3s or substrate availability may also be rate controlling. UBC2 and UBC4 stimulated conjugation half-maximally at concentrations of 10-50 and 28-44 nM, respectively. Endogenous tissue levels of UBC2, but not UBC4, appeared saturating for conjugation, suggesting that in vivo modulation of UBC4 levels can likely control ubiquitin conjugation. Thus the pool of ubiquitin conjugates and therefore the rate of degradation of proteins by this system may be controlled by E2s, E3s, and isopeptidases. The regulation of the ubiquitin pathway appears complex, but precise.
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31
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Strayhorn WD, Wadzinski BE. A novel in vitro assay for deubiquitination of I kappa B alpha. Arch Biochem Biophys 2002; 400:76-84. [PMID: 11913973 DOI: 10.1006/abbi.2002.2760] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The ubiquitin-proteasome pathway (UPP) controls a wide range of signal transduction cascades by targeting key regulatory proteins for 26S proteasome-mediated degradation. Several observations suggest that protein deubiquitination may modulate this process; however, few experiments have been performed to test this idea. An excellent model system for studying the regulatory role of the UPP is signal transduction via the nuclear factor-kappa B (NF-kappa B) family of transcription factors. The principal inhibitor of NF-kappa B, I kappa B alpha, is polyubiquitinated and degraded in response to diverse stimuli. In this study, we sought to determine whether I kappa B alpha deubiquitination also occurs. We established an in vitro deubiquitination assay using polyubiquitinated I kappa B alpha as the substrate. Our data provide evidence of an I kappa B alpha-directed deubiquitinating activity present in lysates of several cell lines. This activity was inhibited by ubiquitin aldehyde, a specific inhibitor of deubiquitinating enzymes, as well as by alkylating reagents or heat, but was unaffected by the inhibition of several other classes of proteases. Cell lysates and the deubiquitinating enzyme, UCH-L3, hydrolyzed ubiquitin 7-amido-4-methylcoumarin, a model substrate for assaying deubiquitinating activities. However, UCH-L3 had no detectable activity toward ubiquitinated I kappa B alpha, thus suggesting a degree of enzymatic specificity in the deubiquitination of I kappa B alpha. This assay will be useful for the study of I kappa B alpha deubiquitination. Moreover, this assay can be adapted to monitor the deubiquitination of other proteins modified by ubiquitin conjugation.
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Affiliation(s)
- W David Strayhorn
- Department of Cell Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.
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32
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Borodovsky A, Kessler BM, Casagrande R, Overkleeft HS, Wilkinson KD, Ploegh HL. A novel active site-directed probe specific for deubiquitylating enzymes reveals proteasome association of USP14. EMBO J 2001; 20:5187-96. [PMID: 11566882 PMCID: PMC125629 DOI: 10.1093/emboj/20.18.5187] [Citation(s) in RCA: 391] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A C-terminally modified ubiquitin (Ub) derivative, ubiquitin vinyl sulfone (UbVS), was synthesized as an active site-directed probe that irreversibly modifies a subset of Ub C-terminal hydrolases (UCHs) and Ub-specific processing proteases (UBPs). Specificity of UbVS for deubiquitylating enzymes (DUBs) is demonstrated not only by inhibition of [(125)I]UbVS labeling with N-ethylmaleimide and Ub aldehyde, but also by genetic analysis. [(125)I]UbVS modifies six of the 17 known and putative yeast deubiquitylating enzymes (Yuh1p, Ubp1p, Ubp2p, Ubp6p, Ubp12p and Ubp15p), as revealed by analysis of corresponding mutant strains. In mammalian cells, greater numbers of polypeptides are labeled, most of which are likely to be DUBs. Using [(125)I]UbVS as a probe, we report the association of an additional DUB with the mammalian 26S proteasome. In addition to the 37 kDa enzyme reported to be part of the 19S cap, we identified USP14, a mammalian homolog of yeast Ubp6p, as being bound to the proteasome. Remarkably, labeling of 26S-associated USP14 with [(125)I]UbVS is increased when proteasome function is impaired, suggesting functional coupling between the activities of USP14 and the proteasome.
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Affiliation(s)
| | | | | | | | - Keith D. Wilkinson
- Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115 and
Department of Biochemistry, 4017 Rollins Research Building, Emory University Medical School, 1510 Clifton Road, Atlanta, GA 30322, USA Corresponding author e-mail:
| | - Hidde L. Ploegh
- Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115 and
Department of Biochemistry, 4017 Rollins Research Building, Emory University Medical School, 1510 Clifton Road, Atlanta, GA 30322, USA Corresponding author e-mail:
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33
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Lin H, Yin L, Reid J, Wilkinson KD, Wing SS. Divergent N-terminal sequences of a deubiquitinating enzyme modulate substrate specificity. J Biol Chem 2001; 276:20357-63. [PMID: 11278432 DOI: 10.1074/jbc.m008761200] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ubiquitin-specific processing proteases (UBPs) are characterized by a conserved core domain with surrounding divergent sequences, particularly at the N-terminal end. We previously cloned two isoforms of a testis UBP, UBP-t1 and UBP-t2, which contain identical core regions but distinct N termini that target the two isoforms to different subcellular locations (Lin, H., Keriel, A., Morales, C. R., Bedard, N., Zhao, Q., Hingamp, P., Lefrancois, S., Combaret, L., and Wing, S. S. (2000) Mol. Cell. Biol. 20, 6568-6578). To determine whether the N termini also influence the biochemical functions of the UBP, we expressed UBP-t1, UBP-t2, and the common core domain, UBP core, in Escherichia coli. The three isoforms cleaved branched triubiquitin at >20-fold faster rates than linear diubiquitin, suggesting that UBP-testis functions as an isopeptidase. Both N-terminal extensions inhibited the ability of UBP-core to generate free ubiquitin when linked in a peptide bond with itself, another peptide, or to small adducts. The N-terminal extension of UBP-t2 increased the ability of UBP-core to cleave branched triubiquitin. UBP-core removed ubiquitin from testis ubiquitinated proteins more rapidly than UBP-t2 and UBP-t1. Thus, UBP enzymes appear to contain a catalytic core domain, the activities and specificities of which can be modulated by N-terminal extensions. These divergent N termini can alter localization and confer multiple functions to the various members of the large UBP family.
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Affiliation(s)
- H Lin
- Polypeptide Laboratory, Department of Medicine and Department of Biochemistry, McGill University, Montreal, Quebec, H3A 2B2, Canada
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34
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Layfield R, Franklin K, Landon M, Walker G, Wang P, Ramage R, Brown A, Love S, Urquhart K, Muir T, Baker R, Mayer RJ. Chemically synthesized ubiquitin extension proteins detect distinct catalytic capacities of deubiquitinating enzymes. Anal Biochem 1999; 274:40-9. [PMID: 10527495 DOI: 10.1006/abio.1999.4234] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have used solid-phase chemistry to synthesize proteins equivalent to a human ubiquitin precursor (ubiquitin-52-amino-acid ribosomal protein fusion; UBICEP52) and representative of isopeptide-linked ubiquitin-protein conjugates [ubiquitin-(epsilonN)-lysine]; these proteins were precisely cleaved by a purified recombinant Drosophila deubiquitinating enzyme (DUB), UCH-D. Along with the previously synthesized ubiquitin-(alphaN)-valine, these synthetic proteins were used as substrates to assess the catalytic capacities of a number of diverse DUBs expressed in Escherichia coli: human HAUSP; mouse Unp; and yeast Ubps 1p, 2p, 3p, 6p, 11p, and 15p and Yuh1p. Distinct specificities of these enzymes were detected; notably, in addition to UCH-D, isopeptidase activity [ubiquitin-(epsilonN)-lysine cleavage] was only associated with Yuh1p, Unp, Ubp1p, and Ubp2p. Additionally, human placental 26S proteasomes were only able to cleave UBICEP52 and ubiquitin-(epsilonN)-lysine, suggesting that 26S proteasome-associated DUBs are class II-like. This work demonstrates that the synthetic approach offers an alternative to recombinant methods for the production of small proteins in vitro.
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Affiliation(s)
- R Layfield
- Laboratory of Intracellular Proteolysis, School of Biomedical Sciences, University of Nottingham Medical School, Queen's Medical Centre, Nottingham, NG7 2UH, United Kingdom.
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35
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Franklin K, Layfield R, Landon M, Ramage R, Brown A, Love S, Muir T, Urquhart K, Bownes M, Mayer RJ. Capillary electrophoresis assay for ubiquitin carboxyl-terminal hydrolases with chemically synthesized ubiquitin-valine as substrate. Anal Biochem 1997; 247:305-9. [PMID: 9177692 DOI: 10.1006/abio.1997.2099] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Ubiquitin is expressed in eukaryotic cells as precursors, fused via its carboxyl terminus either to other ubiquitin sequences in linear polyubiquitin arrays or to specific ribosomal proteins. In some of the polyubiquitin fusions a single amino acid (e.g., valine in humans) is attached to the carboxyl terminus. These gene products are rapidly (probably cotranslationally) cleaved by ubiquitin carboxyl-terminal hydrolase (UCH) enzymes; therefore, although ubiquitin precursors are suitable substrates for assays of UCH activity, they are difficult to isolate from nucleated cells. While the recombinant approach allows the production of ubiquitin precursors in prokaryotic cells (which do not contain the ubiquitin system), proteins produced in this manner require purification and may also be susceptible to modification by bacterial enzymes, e.g., adventitious proteolysis. As an alternative we have chemically synthesized human ubiquitin-valine. In the assay described here the cleavage of ubiquitin-valine to ubiquitin (77 and 76 residue proteins, respectively) by a purified recombinant Drosophila UCH was monitored by capillary electrophoresis. Mass spectrometry verified the precise cleavage of ubiquitin-valine, confirming that this synthetic protein is a UCH substrate. Synthetic ubiquitin-valine may serve as a generic substrate for UCHs allowing the purification and identification of new members of this enzyme family.
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Affiliation(s)
- K Franklin
- Department of Biochemistry, University of Nottingham Medical School, Queen's Medical Centre, United Kingdom
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36
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Piccinini M, Merighi A, Bruno R, Cascio P, Curto M, Mioletti S, Ceruti C, Rinaudo MT. Affinity purification and characterization of protein gene product 9.5 (PGP9.5) from retina. Biochem J 1996; 318 ( Pt 2):711-6. [PMID: 8809066 PMCID: PMC1217676 DOI: 10.1042/bj3180711] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Protein gene product 9.5 (PGP9.5) is a cytosolic protein that is highly expressed in vertebrate neurons, which is now included in the ubiquitin C-terminal hydrolase subclass (UCH) on the basis of primary-structure homology and hydrolytic activity on the synthetic substrate ubiquitin ethyl ester (UbOEt). Some UCHs show affinity for immobilized ubiquitin, a property exploited to purify them. In this study we show that this property can also be applied to PGP9.5, since a protein has been purified to homogeneity from bovine retina by affinity chromatography on a ubiquitin-Sepharose column that can be identified with: (a) PGP9.5 with respect to molecular mass, primary structure and immunological reactivity; (b) the known UCHs with respect to some catalytic properties, such as hydrolytic activity on UbOEt, (which also characterizes PGP9.5), Km value and reactivity with cysteine and histidine-specific reagents. However, it differs with respect to other properties, e.g. inhibition by UbOEt and a wider pH range of activity.
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Affiliation(s)
- M Piccinini
- Dipartimento di Morfofisiologia Veterinaria, Universit di Torino, Italy
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37
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Larsen CN, Price JS, Wilkinson KD. Substrate binding and catalysis by ubiquitin C-terminal hydrolases: identification of two active site residues. Biochemistry 1996; 35:6735-44. [PMID: 8639624 DOI: 10.1021/bi960099f] [Citation(s) in RCA: 163] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Ubiquitin C-terminal hydrolases (UCH's) are a newly-defined class of thiol proteases implicated in the proteolytic processing of polymeric ubiquitin. They are important for the generation of monomeric ubiquitin, the active component of the eukaryotic ubiquitin-dependent proteolytic system. There are at least three mammalian isozymes which are tissue specific and developmentally regulated. To study the structure and functional roles of these highly homologous enzymes, we have subcloned and overexpressed two of these isozymes, UCH-L1 and UCH-L3. Here, we report their purification, physical characteristics, and the mutagenesis of UCH-L1. Site-directed mutagenesis of UCH-L1 reveals that C90 and H161 are involved in catalytic rate enhancement. Data from circular dichroic and Raman spectroscopy, as well as secondary structure prediction algorithms, indicate that both isozymes have a significant amount of alpha-helix (> 35%), and contain no disulfide bonds. Both enzymes are reasonably stable, undergoing a reversible thermal denaturation at 52 degrees C. These transitions are characterized by thermodynamic parameters typical of single domain globular proteins. Substrate binding affinity to UCH-L3 was directly measured by equilibrium gel filtration (Kd = 0.5 microM), and the results are similar to the kinetically determined Km for ubiquitin ethyl ester (o.6 microM). The binding is primarily electrostatic in nature and indicates the existence of a specific and extensive binding site for ubiquitin on the surface of the enzyme.
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Affiliation(s)
- C N Larsen
- Department of Biochemistry, Emory University, Atlanta, Georgia 30322, USA
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38
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Beal R, Deveraux Q, Xia G, Rechsteiner M, Pickart C. Surface hydrophobic residues of multiubiquitin chains essential for proteolytic targeting. Proc Natl Acad Sci U S A 1996; 93:861-6. [PMID: 8570649 PMCID: PMC40148 DOI: 10.1073/pnas.93.2.861] [Citation(s) in RCA: 214] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Ubiquitin conjugation is a signal for degradation of eukaryotic proteins by the 26S protease. Conjugation of a homopolymeric multiubiquitin chain to a substrate lysine residue results in 10-fold faster degradation than does conjugation of monoubiquitin, but the molecular basis of enhanced targeting by chains is unknown. We show that ubiquitin residues L8, I44, and V70 are critical for targeting. Mutation of pairs of these residues to alanine had little effect on attachment of ubiquitin to substrates but severely inhibited degradation of the resulting conjugates. The same mutations blocked the binding of chains to a specific subunit (S5a) of the regulatory complex of the 26S protease. The side chains implicated in this binding--L8, I44, and V70--form repeating patches on the chain surface. Thus, hydrophobic interactions between these patches and S5a apparently contribute to enhanced proteolytic targeting by multiubiquitin chains.
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Affiliation(s)
- R Beal
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York, Buffalo 14214, USA
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39
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Abstract
Contrary to widespread belief, the regulation and mechanism of degradation for the mass of intracellular proteins (i.e. differential, selective protein turnover) in vertebrate tissues is still a major biological enigma. There is no evidence for the conclusion that ubiquitin plays any role in these processes. The primary function of the ubiquitin-dependent protein degradation pathway appears to lie in the removal of abnormal, misfolded, denatured or foreign proteins in some eukaryotic cells. ATP/ubiquitin-dependent proteolysis probably also plays a role in the degradation of some so-called 'short-lived' proteins. Evidence obtained from the covalent modification of such natural substrates as calmodulin, histones (H2A, H2B) and some cell membrane receptors with ubiquitin indicates that the reversible interconversion of proteins with ubiquitin followed by concomitant functional changes may be of prime importance.
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Affiliation(s)
- H P Jennissen
- Institut für Physiologische Chemie, Universität-GHS-Essen, Germany
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40
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LaBean TH, Kauffman SA, Butt TR. Libraries of random-sequence polypeptides produced with high yield as carboxy-terminal fusions with ubiquitin. Mol Divers 1995; 1:29-38. [PMID: 9237192 DOI: 10.1007/bf01715807] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Libraries of random-sequence polypeptides have been shown to be valuable sources of novel molecules possessing a variety of useful biologic-like activities, some of which may hold promise as potential vaccines and therapeutics. Previous random peptide expression systems were limited to low levels of peptide production and often to short sequences. Here we describe a series of libraries designed for increased polypeptide length. Cloned as carboxy-terminal extensions of ubiquitin, the fusions were produced in E. coli at high levels, and were purified to homogeneity. The majority of the extension proteins examined could be cleaved from ubiquitin by treatment with a ubiquitin-fusion hydrolase. The libraries described here are appropriate sources of novel polypeptides with desired binding or catalytic function, as well as tools with which to examine inherent properties of proteins as a whole. Toward the latter goal, we have examined structural properties of random-sequence proteins purified from these libraries. Quite surprisingly, fluorescence emission spectra of intrinsic tryptophan residues in several purified fusion proteins, under native-like and denaturing conditions, often resemble those expected for folded and unfolded states, respectively. The results presented here detail an important expansion in the range of potential uses for random-sequence polypeptide libraries.
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Affiliation(s)
- T H LaBean
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia 19104, USA
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Celis JE, Olsen E. A qualitative and quantitative protein database approach identifies individual and groups of functionally related proteins that are differentially regulated in simian virus 40 (SV40) transformed human keratinocytes: an overview of the functional changes associated with the transformed phenotype. Electrophoresis 1994; 15:309-44. [PMID: 8055864 DOI: 10.1002/elps.1150150153] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A qualitative and quantitative two-dimensional (2-D) gel database approach has been used to identify individual and groups of proteins that are differentially regulated in simian virus 40 (SV40) transformed human keratinocytes (K14). Five hundred and sixty [35S]methionine-labeled proteins (462 isoelectric focusing, IEF; 98 nonequilibrium pH gradient electrophoresis, NEPHGE), out of the 3038 recorded in the master keratinocyte database, were excised from dry, silver-stained gels of normal proliferating primary keratinocytes and K14 cells and the radioactivity was determined by liquid scintillation counting. Two hundred and thirty five proteins were found to be either up- (177) or down-regulated (58) in the transformed cells by 50% or more, and of these, 115 corresponded to known proteins in the keratinocyte database (J.E. Celis et al., Electrophoresis 1993, 14, 1091-1198). The lowest abundance acidic protein quantitated was present in about 60,000 molecules per cell, assuming a value of 10(8) molecules per cell for total actin. The results identified individual, and groups of functionally related proteins that are differentially regulated in K14 keratinocytes and that play a role in a variety of cellular activities that include general metabolism, the cytoskeleton, DNA replication and cell proliferation, transcription and translation, protein folding, assembly, repair and turnover, membrane traffic, signal transduction, and differentiation. In addition, the results revealed several transformation sensitive proteins of unknown identity in the database as well as known proteins of yet undefined functions. Within the latter group, members of the S100 protein family--whose genes are clustered on human chromosome 1q21--were among the highest down-regulated proteins in K14 keratinocytes. Visual inspection of films exposed for different periods of time revealed only one new protein in the transformed K14 keratinocytes and this corresponded to keratin 18, a cytokeratin expressed mainly by simple epithelia. Besides providing with the first global overview of the functional changes associated with the transformed phenotype of human keratinocytes, the data strengthened previous evidence indicating that transformation results in the abnormal expression of normal genes rather than in the expression of new ones.
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Affiliation(s)
- J E Celis
- Institute of Medical Biochemistry, Aarhus University, Denmark
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Abstract
This chapter presents families of cysteine peptidases. The activity of all cysteine peptidases depends on a catalytic dyad of cysteine and histidine. The order of the cysteine and histidine residues (Cys/His or His/Cys) in the linear sequence differs between families and this is among the lines of evidence suggesting that cysteine peptidases have had many separate evolutionary origins. The families C1, C2, and C10 can be described as “papainlike,” and form clan CA. The papain family contains peptidases with a wide variety of activities, including endopeptidases with broad specificity, endopeptidases with narrow specificity, aminopeptidases, and peptidases with both endopeptidase and exopeptidase activities. Papain homologs are generally either lysosomal or secreted proteins. The calpain family includes the calcium-dependent cytosolic endopeptidase calpain, which is known from birds and mammals, and the product of the sol gene in Drosophila. Calpain is a complex of two peptide chains. Picornains are a family of polyprotein-processing endopeptidases from single-stranded RNA viruses. Each picornavirus has two picornains (2A and 3C).
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Affiliation(s)
- N D Rawlings
- Strangeways Research Laboratory, Cambridge, United Kingdom
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Chun PW, Jou WS. Molecular conformation of ubiquitinated structures and the implications for regulatory function. JOURNAL OF MOLECULAR GRAPHICS 1992; 10:7-11, 18-20. [PMID: 1323999 DOI: 10.1016/0263-7855(92)80002-u] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The molecular conformation of ubiquitinated structures and the validity of the N-end rule were examined by simulating the molecular mechanics to ascertain the global energy-minimized structure. We examined the chemical linkage involved in attaching the ubiquitin carboxyl terminus to the N-terminus of three different x-hexapeptides, where x is the amino group of the acceptor peptide--either valine, arginine or glutamic acid--(x-K linkage) and to the epsilon-amino group of lysine of the acceptor hexapeptide x-glu1-his2-lys3-gly4-lys5-val6 (K-K linkage) through the formation of an isopeptide bond. Changes in conformation and molecular stability of the multi-ubiquitinated structures were determined by energy-minimization procedures using the SYBYL program developed by Tripos Associates. In the x-K linkage, the ubiquitin molecule is stretched in the beta-pleated sheets and beta-turns while the alpha-helices expand, as the molecule continues to unfold linearly. In the K-K linkage, the ubiquitin molecules have turned into a u-shaped, semi-circular alignment, contracting into a compact, folded structure.
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Affiliation(s)
- P W Chun
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville 32610
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Bamezai S, Breslow E. Demonstration of a factor in fraction I of reticulocyte lysates necessary for the steady state accumulation of ubiquitin conjugates of des-75-76-ubiquitin. Arch Biochem Biophys 1991; 289:343-9. [PMID: 1654857 DOI: 10.1016/0003-9861(91)90421-e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Addition of des-75-76-ubiquitin (ubiquitin lacking its two C-terminal glycine residues) to reticulocyte lysates leads to the inhibition of proteolysis and the formation of conjugates between it and native ubiquitin, as demonstrated by the incorporation of both 125I-labeled des-75-76-ubiquitin and 125I-labeled ubiquitin into these conjugates. Conjugate formation is blocked by methylation of the amino groups of des-75-76-ubiquitin, consistent with the concept that the conjugates represent attachment of the ubiquitin alpha-carboxyl group to amino groups of des-75-76-ubiquitin. The lack of significant direct competition for conjugate formation by typical ubiquitinatable proteolysis substrates or by des-73-76-ubiquitin, together with differences in conjugate formation between des-73-76-ubiquitin and des-75-76-ubiquitin demonstrated earlier, indicates that the enzyme involved recognizes the ubiquitin sequence as a substrate for ubiquitination. Increasing concentrations of native ubiquitin first increase and then reduce the steady state level of conjugates of the des-75-76-protein, the inhibitory effects of high concentrations consistent with competition by native ubiquitin for conjugate formation. Upon fractionation of reticulocyte lysates, a factor essential to the net synthesis of conjugates of des-75-76-ubiquitin was demonstrated to be present in Fraction I and to behave as a protein of molecular weight 38,000. The role in this system of a factor from Fraction I other than ubiquitin indicates that a novel pathway is involved.
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Affiliation(s)
- S Bamezai
- Department of Biochemistry, Cornell University Medical College, New York, New York 10021
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Wilkinson KD, Lee KM, Deshpande S, Duerksen-Hughes P, Boss JM, Pohl J. The neuron-specific protein PGP 9.5 is a ubiquitin carboxyl-terminal hydrolase. Science 1989; 246:670-3. [PMID: 2530630 DOI: 10.1126/science.2530630] [Citation(s) in RCA: 667] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A complementary DNA (cDNA) for ubiquitin carboxyl-terminal hydrolase isozyme L3 was cloned from human B cells. The cDNA encodes a protein of 230 amino acids with a molecular mass of 26.182 daltons. The human protein is very similar to the bovine homolog, with only three amino acids differing in over 100 residues compared. The amino acid sequence deduced from the cDNA was 54% identical to that of the neuron-specific protein PGP 9.5. Purification of bovine PGP 9.5 confirmed that it is also a ubiquitin carboxyl-terminal hydrolase. These results suggest that a family of such related proteins exists and that their expression is tissue-specific.
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Affiliation(s)
- K D Wilkinson
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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Duerksen-Hughes PJ, Williamson MM, Wilkinson KD. Affinity chromatography using protein immobilized via arginine residues: purification of ubiquitin carboxyl-terminal hydrolases. Biochemistry 1989; 28:8530-6. [PMID: 2532544 DOI: 10.1021/bi00447a039] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
4-(Oxoacetyl)phenoxyacetic acid (OAPA) forms a stable, covalent bond between its glyoxal group and the guanidino group of arginine and arginine derivatives [Duerksen, P. J., & Wilkinson, K. D. (1987) Anal. Biochem. 160, 444-454]. Studies were carried out to determine the chemical nature of this linkage, and the structure of the stable adduct between OAPA and methylguanidine was elucidated. The stable product results from an internal oxidation-reduction of the Schiff base adduct to form a cyclic alpha-aminoamide, 4-[4-(carboxymethoxy)phenyl]-2-(methylimino)-5-oxoimidazolidine. OAPA coupled to polyacrylamide beads was used to immobilize ubiquitin via its arginine residues, and the resulting affinity support was shown to specifically and reversibly bind a previously described enzyme, ubiquitin carboxyl-terminal hydrolase [Pickart, C. M., & Rose, I. A. (1985) J. Biol. Chem. 260, 7903-7910]. The resin was then used to isolate three newly identified ubiquitin carboxyl-terminal hydrolytic activities, which did not bind to ubiquitin immobilized via lysine residues. Significant purification was achieved in each case, and one isozyme was further purified to homogeneity.
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