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Santelices J, Ou M, Maegawa GHB, Hercik K, Edelmann MJ. USP8 inhibition regulates autophagy flux and controls Salmonella infection. Front Cell Infect Microbiol 2023; 13:1070271. [PMID: 37026055 PMCID: PMC10072284 DOI: 10.3389/fcimb.2023.1070271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/13/2023] [Indexed: 04/08/2023] Open
Abstract
Introduction Ubiquitination is an important protein modification that regulates various essential cellular processes, including the functions of innate immune cells. Deubiquitinases are enzymes responsible for removing ubiquitin modification from substrates, and the regulation of deubiquitinases in macrophages during infection with Salmonella Typhimurium and Yersinia enterocolitica remains unknown. Methods To identify deubiquitinases regulated in human macrophages during bacterial infection, an activity-based proteomics screen was conducted. The effects of pharmacological inhibition of the identified deubiquitinase, USP8, were examined, including its impact on bacterial survival within macrophages and its role in autophagy regulation during Salmonella infection. Results Several deubiquiitnases were differentially regulated in infected macrophages. One of the deubiquitinases identified was USP8, which was downregulated upon Salmonella infection. Inhibition of USP8 was associated with a decrease in bacterial survival within macrophages, and it was found to play a distinct role in regulating autophagy during Salmonella infection. The inhibition of USP8 led to the downregulation of the p62 autophagy adaptor. Discussion The findings of this study suggest a novel role of USP8 in regulating autophagy flux, which restricts intracellular bacteria, particularly during Salmonella infection.
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Affiliation(s)
- John Santelices
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Mark Ou
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Gustavo H. B. Maegawa
- Department of Pediatrics and Genetics, Columbia University Irving Medical Center, Vagelos Physicians and Surgeons College of Medicine, New York, NY, United States
| | - Kamil Hercik
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czechia
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defense, Hradec Kralove, Czechia
| | - Mariola J. Edelmann
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
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Total Chemical Synthesis of LC3A and LC3B Activity-Based Probes. Biomedicines 2023; 11:biomedicines11030884. [PMID: 36979862 PMCID: PMC10045837 DOI: 10.3390/biomedicines11030884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023] Open
Abstract
Autophagy is a conserved cellular process involved in the degradation of intercellular materials. During this process, double-membrane vesicles called autophagosomes engulf cytoplasmic components ready for degradation. A key component in the formation of autophagosomes are the autophagy-related (Atg) proteins, including microtubule-associated protein light chain 3A (LC3A) and 3B (LC3B). After the C-terminus of LC3 is conjugated to a phospholipid, it promotes the elongation of the phagosome and provides a docking station for the delivery of proteins ready for degradation. Since dysregulation of the autophagy pathway has been associated with a variety of human diseases, components of this process have been considered as potential therapeutic targets. However, the mechanistic details of LC3-specific ligases and deconjugation enzymes are far from unraveled and chemical tools for activity profiling could aid in affording more insights into this process. Herein, we describe a native chemical ligation approach for the synthesis of two LC3 activity-based probes (ABPs). Initial studies show that the probes covalently interact with the cysteine protease ATG4B, showcasing the potential of these probes to unravel mechanistic and structural details.
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Nanduri B, Shack LA, Santelices J, Edelmann MJ. Using Activity-Based Proteomics for the Quantification of Deubiquitinases in Animal Tissue. Methods Mol Biol 2023; 2591:45-57. [PMID: 36350542 DOI: 10.1007/978-1-0716-2803-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ubiquitination is a post-translational modification, that regulates essential cellular functions, and the enzymes that control the removal of this modification, deubiquitinases (DUBs), have been well described for the model organisms. However, the information about DUBs is still largely lacking for the non-model organisms, such as agriculturally relevant animals. To understand the expression of these enzymes in animal tissues, we have used chemical proteomics which can be used to identify biologically active DUBs present in tissues based on their reactivity with the activity-based probes (ABPs). Here we describe a sample preparation protocol for ABP-based purification of DUBs from animal tissue using two approaches to homogenize and lyse the animal tissue compatible with ABP labeling of DUBs, including an ultrasonication-based tissue processing method and bead-beating method. Both of these methods retain the enzymatic activity of DUBs. In addition, we describe a protocol for ABP labeling of DUBs in tissue lysates and the immunoprecipitation of the probe-reactive DUBs that can be used along with mass spectrometric identification of proteins and the detection of these DUBs by Western blotting.
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Affiliation(s)
- Bindu Nanduri
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Leslie A Shack
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - John Santelices
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Mariola J Edelmann
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA.
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Nanduri B, Gresham CR, Jones G, Bailey RH, Edelmann MJ. Identification of active deubiquitinases in the chicken tissues. Proteomics 2021; 22:e2100122. [PMID: 34643985 DOI: 10.1002/pmic.202100122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 11/06/2022]
Abstract
The existing protein annotation in chicken is mostly limited to computational predictions based on orthology to other proteins, which often leads to a significant underestimation of the function of these proteins. Genome-scale experimental annotation can provide insight into the actual enzymatic activities of chicken proteins. Amongst post-translational modifications, ubiquitination is of interest as anomalies in ubiquitination are implicated in such diseases as inflammatory disorders, infectious diseases, or malignancies. Ubiquitination is controlled by deubiquitinases (DUBs), which remove ubiquitin from protein substrates. However, the DUBs have not been systematically annotated and quantified in chicken tissues. Here we used a chemoproteomics approach, which is based on active-site probes specific to DUBs, and identified 26 active DUBs in the chicken spleen, cecum, and liver.
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Affiliation(s)
- Bindu Nanduri
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA.,Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, Mississippi, USA
| | - Cathy R Gresham
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, Mississippi, USA
| | - Gary Jones
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, USA
| | - Richard H Bailey
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
| | - Mariola J Edelmann
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, USA
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An atlas of the catalytically active liver and spleen kinases in chicken identified by chemoproteomics. J Proteomics 2020; 225:103850. [PMID: 32502695 DOI: 10.1016/j.jprot.2020.103850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 05/08/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022]
Abstract
Phosphorylation is a post-translational protein modification regulating most known cellular processes. While protein kinases constitute a large family of highly conserved enzymes, identification of active kinases is challenging due to a low abundance of some of these signaling molecules. Although chicken is the first agricultural animal to have a sequenced genome, annotation of the kinome, i.e., a complement of all protein kinases in the genome is limited. We used chemical probes consisting of ATP and ADP derivatives binding to specific lysine (Lys) residues within the ATP-binding pocket of kinases, combined with proteomics, to identify 267 peptides labeled with the ATP and ADP acyl derivatives and 188 corresponding chicken kinases in chicken spleen and liver. Our description of active chicken kinases and ATP binding sites will support future studies focused on identifying the role of this important class of enzymes in chicken health and disease. SIGNIFICANCE: Advances made in understanding chicken enzymes are critical for the improved knowledge of the regulatory pathways controlling physiological processes in chicken. Since protein phosphorylation controls multiple aspects of cell fate, it is often linked to pathological conditions, and understanding of the kinase expression in chicken is essential for future therapeutic approaches. We coupled proteomics and labeling with active-site probes binding to Lys residues within the ATP-binding pocket of kinases to identify 188 kinases and corresponding 267 peptides labeled with the ATP and ADP acyl derivatives in chicken spleen and liver. Results of the present study describing catalytically active kinases is a starting point for chemoproteomic-based interrogation of kinases in chicken exposed to different conditions. Kinases identified in this study are available through the Chickspress genome browser that has previously published mRNA, miRNA, and shotgun proteomics data.
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Hameed DS, Sapmaz A, Burggraaff L, Amore A, Slingerland CJ, Westen GJP, Ovaa H. Development of Ubiquitin‐Based Probe for Metalloprotease Deubiquitinases. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Dharjath S. Hameed
- Department of Cell Biology II The Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Department of Cell and Chemical Biology, Oncode Institute Leiden University Medical Center Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Aysegul Sapmaz
- Department of Cell Biology II The Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Department of Cell and Chemical Biology, Oncode Institute Leiden University Medical Center Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Lindsey Burggraaff
- Drug Discovery and Safety Leiden Academic Center for Drug Research Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Alessia Amore
- Department of Cell Biology II The Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam The Netherlands
| | - Cornelis J. Slingerland
- Department of Cell and Chemical Biology, Oncode Institute Leiden University Medical Center Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Gerard J. P. Westen
- Drug Discovery and Safety Leiden Academic Center for Drug Research Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Huib Ovaa
- Department of Cell Biology II The Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Department of Cell and Chemical Biology, Oncode Institute Leiden University Medical Center Einthovenweg 20 2333 ZC Leiden The Netherlands
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Hameed DS, Sapmaz A, Burggraaff L, Amore A, Slingerland CJ, Westen GJP, Ovaa H. Development of Ubiquitin‐Based Probe for Metalloprotease Deubiquitinases. Angew Chem Int Ed Engl 2019; 58:14477-14482. [DOI: 10.1002/anie.201906790] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/01/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Dharjath S. Hameed
- Department of Cell Biology II The Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Department of Cell and Chemical Biology, Oncode Institute Leiden University Medical Center Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Aysegul Sapmaz
- Department of Cell Biology II The Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Department of Cell and Chemical Biology, Oncode Institute Leiden University Medical Center Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Lindsey Burggraaff
- Drug Discovery and Safety Leiden Academic Center for Drug Research Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Alessia Amore
- Department of Cell Biology II The Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam The Netherlands
| | - Cornelis J. Slingerland
- Department of Cell and Chemical Biology, Oncode Institute Leiden University Medical Center Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Gerard J. P. Westen
- Drug Discovery and Safety Leiden Academic Center for Drug Research Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Huib Ovaa
- Department of Cell Biology II The Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Department of Cell and Chemical Biology, Oncode Institute Leiden University Medical Center Einthovenweg 20 2333 ZC Leiden The Netherlands
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Hameed DS, Sapmaz A, Gjonaj L, Merkx R, Ovaa H. Enhanced Delivery of Synthetic Labelled Ubiquitin into Live Cells by Using Next-Generation Ub-TAT Conjugates. Chembiochem 2018; 19:2553-2557. [PMID: 30351505 DOI: 10.1002/cbic.201800649] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Indexed: 12/12/2022]
Abstract
Proteins and other macromolecules can be delivered into live cells by noninvasive techniques using cell-penetrating peptides. These peptides are easily synthesised by solid-phase peptide synthesis and can be conjugated onto cargo molecules to mediate cellular delivery. We designed a TAT-based cell-penetrating ubiquitin (Ub) reagent by conjugating a dimeric disulfide-linked TAT peptide to the C terminus of a rhodamine-labelled Ub (RhoUb) protein. This reagent efficiently enters the cell by endocytosis and escapes from endosomes into the cytoplasm. Once the conjugate is inside the cytoplasm, the delivery vehicle is proteolytically removed by endogenous deubiquitinases (DUBs), at which point the intrinsic ubiquitination machinery is able to incorporate the RhoUb into ubiquitin conjugates. Our approach enables the controlled delivery of labelled or mutant Ub derivatives into cells, increasing our options for studying the ubiquitin system.
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Affiliation(s)
- Dharjath S Hameed
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Aysegul Sapmaz
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Lorina Gjonaj
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Remco Merkx
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Present address: Medicines Evaluation Board, Graadt van Roggenweg 500, 3531 AH, Utrecht, The Netherlands
| | - Huib Ovaa
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
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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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Wang K, Yang T, Wu Q, Zhao X, Nice EC, Huang C. Chemistry-based functional proteomics for drug target deconvolution. Expert Rev Proteomics 2013; 9:293-310. [PMID: 22809208 DOI: 10.1586/epr.12.19] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Drug target deconvolution, a process that identifies targets to small molecules in complex biological samples, which underlie the biological responses that are observed when a drug is administered, plays an important role in current drug discovery. Despite the fact that genomics and proteomics have provided a flood of information that contributes to the progress of drug target identification and validation, the current approach to drug target deconvolution still poses dilemmas. Chemistry-based functional proteomics, a multidisciplinary strategy, has become the preferred method of choice to deconvolute drug target pools, based on direct interactions between small molecules and their protein targets. This approach has already identified a broad panel of previously undefined enzymes with potential as drug targets and defined targets that can rationalize side effects and toxicity for new drug candidates and existing therapeutics. Herein, the authors discuss both activity-based protein profiling and compound-centric chemical proteomics approaches used in chemistry-based functional proteomics and their applications for the identification and characterization of small molecular targets.
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Affiliation(s)
- Kui Wang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, PR China
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Kramer HB, Nicholson B, Kessler BM, Altun M. Detection of ubiquitin-proteasome enzymatic activities in cells: application of activity-based probes to inhibitor development. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1823:2029-37. [PMID: 22613766 PMCID: PMC7125640 DOI: 10.1016/j.bbamcr.2012.05.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 05/04/2012] [Accepted: 05/11/2012] [Indexed: 01/10/2023]
Abstract
BACKGROUND Synthetic probes that mimic natural substrates can enable the detection of enzymatic activities in a cellular environment. One area where such activity-based probes have been applied is the ubiquitin-proteasome pathway, which is emerging as an important therapeutic target. A family of reagents has been developed that specifically label deubiquitylating enzymes (DUBs) and facilitate characterization of their inhibitors. SCOPE OF REVIEW Here we focus on the application of probes for intracellular DUBs, a group of specific proteases involved in the ubiquitin proteasome system. In particular, the functional characterization of the active subunits of this family of proteases that specifically recognize ubiquitin and ubiquitin-like proteins will be discussed. In addition we present the potential and design of activity-based probes targeting kinases and phosphatases to study phosphorylation. MAJOR CONCLUSIONS Synthetic molecular probes have increased our understanding of the functional role of DUBs in living cells. In addition to the detection of enzymatic activities of known members, activity-based probes have contributed to a number of functional assignments of previously uncharacterized enzymes. This method enables cellular validation of the specificity of small molecule DUB inhibitors. GENERAL SIGNIFICANCE Molecular probes combined with mass spectrometry-based proteomics and cellular assays represent a powerful approach for discovery and functional validation, a concept that can be expanded to other enzyme classes. This addresses a need for more informative cell-based assays that are required to accelerate the drug development process. This article is part of a Special Issue entitled: Ubiquitin Drug Discovery and Diagnostics.
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Key Words
- abp, activity-based probe
- adp, adenosine diphosphate
- atp, adenosine triphosphate
- dub, deubiquitylating enzyme
- e1, ubiquitin activating enzyme
- e2, ubiquitin conjugating enzyme
- e3, ubiquitin-protein ligase
- haubbr2, ha-tagged ubiquitin ethyl bromide
- haubvme, ha-tagged ubiquitin vinyl methyl ester
- haubvs, ha-tagged ubiquitin vinyl sulfone
- ip, immunoprecipitation
- ms, mass spectrometry
- ptm, post-translational modification
- ptp, protein tyrosine phosphatase
- sds-page, sodium dodecylsulfate polyacrylamide gel electrophoresis
- spps, solid phase peptide synthesis
- ub, ubiquitin
- ubl, ubiquitin-like protein
- uch-l1, ubiquitin carboxyl terminal hydrolase isozyme l1
- uch-l3, ubiquitin carboxyl terminal hydrolase isozyme l3
- uch-l5, ubiquitin carboxyl terminal hydrolase isozyme l5
- usp7, ubiquitin specific processing protease 7
- ubiquitin
- small molecular inhibitor
- deubiquitinating enzyme
- ubiquitin specific protease
- proteomics
- active site-directed molecular probe
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Affiliation(s)
- Holger B Kramer
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford OX1 3QX, UK
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Ubiquitin and ubiquitin-like specific proteases targeted by infectious pathogens: Emerging patterns and molecular principles. Biochim Biophys Acta Mol Basis Dis 2008; 1782:809-16. [PMID: 18817868 PMCID: PMC7126189 DOI: 10.1016/j.bbadis.2008.08.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Revised: 08/26/2008] [Accepted: 08/27/2008] [Indexed: 01/08/2023]
Abstract
Attachment of ubiquitin (Ub) or ubiquitin-like (Ubl) modifiers is a reversible post-translational modification that regulates the fate and function of proteins. In particular, proteolytic enzymes with Ub/Ubl processing activity appear to be more widespread than originally anticipated. It is therefore not surprising that bacterial and viral pathogens have exploited many ways to interfere with Ub/Ubl conjugation, but also de-conjugation. On one hand, pathogens were shown to manipulate host encoded enzymes. On the other hand, pathogen derived sequences of proteases specific for Ub/Ubls are emerging as a common feature shared by many viruses, bacteria and protozoa, and we are at an early stage of understanding how these proteases contribute to the pathogenesis of infection. Whereas some of these proteases share a common origin with mammalian cell encoded hydrolases with specific properties towards Ub/Ubls, most of them have ancient intrinsic functions, such as processing pathogen protein components, and may have acquired the specificity for Ub/Ubls by interacting with mammalian hosts and their immune system throughout evolution. Since many of these proteases are clearly distinct from their mammalian counterparts, they represent attractive targets for drug design against infectious diseases.
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Uttamchandani M, Li J, Sun H, Yao SQ. Activity-Based Protein Profiling: New Developments and Directions in Functional Proteomics. Chembiochem 2008; 9:667-75. [DOI: 10.1002/cbic.200700755] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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