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Suskiewicz MJ. The logic of protein post-translational modifications (PTMs): Chemistry, mechanisms and evolution of protein regulation through covalent attachments. Bioessays 2024; 46:e2300178. [PMID: 38247183 DOI: 10.1002/bies.202300178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
Protein post-translational modifications (PTMs) play a crucial role in all cellular functions by regulating protein activity, interactions and half-life. Despite the enormous diversity of modifications, various PTM systems show parallels in their chemical and catalytic underpinnings. Here, focussing on modifications that involve the addition of new elements to amino-acid sidechains, I describe historical milestones and fundamental concepts that support the current understanding of PTMs. The historical survey covers selected key research programmes, including the study of protein phosphorylation as a regulatory switch, protein ubiquitylation as a degradation signal and histone modifications as a functional code. The contribution of crucial techniques for studying PTMs is also discussed. The central part of the essay explores shared chemical principles and catalytic strategies observed across diverse PTM systems, together with mechanisms of substrate selection, the reversibility of PTMs by erasers and the recognition of PTMs by reader domains. Similarities in the basic chemical mechanism are highlighted and their implications are discussed. The final part is dedicated to the evolutionary trajectories of PTM systems, beginning with their possible emergence in the context of rivalry in the prokaryotic world. Together, the essay provides a unified perspective on the diverse world of major protein modifications.
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Affiliation(s)
- Marcin J Suskiewicz
- Centre de Biophysique Moléculaire, CNRS - Orléans, UPR 4301, affiliated with Université d'Orléans, Orléans, France
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Li C, Liu S, Dong B, Li C, Jian L, He J, Zeng J, Zhou Q, Jia D, Luo Y, Sun Q. Discovery and Mechanistic Study of Mycobacterium tuberculosis PafA Inhibitors. J Med Chem 2022; 65:11058-11065. [PMID: 35926511 DOI: 10.1021/acs.jmedchem.2c00289] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Tuberculosis is caused by the bacterium Mycobacterium tuberculosis (Mtb) and is ranked as the second killer infectious disease after COVID-19. Proteasome accessory factor A (PafA) is considered an attractive target because of its low sequence conservation in humans and its role in virulence. In this study, we designed a mutant of Mtb PafA that enabled large-scale purification of active PafA. Using a devised high-throughput screening assay, two PafA inhibitors were discovered. ST1926 inhibited Mtb PafA by binding in the Pup binding groove, but it was less active against Corynebacterium glutamicum PafA because the ST1926-binding residues are not conserved. Bithionol bound to the conserved ATP-binding pocket, thereby, inhibits PafA in an ATP-competitive manner. Both ST1926 and bithionol inhibited the growth of an attenuated Mtb strain (H37Ra) at micromolar concentrations. Our work thus provides new tools for tuberculosis research and a foundation for future PafA-targeted drug development for treating tuberculosis.
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Affiliation(s)
- Cong Li
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu 610041, P. R. China
| | - Song Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Baoyu Dong
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, Sichuan, P. R. China
| | - Chungen Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Lunan Jian
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu 610041, P. R. China
| | - Juan He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, Sichuan, P. R. China
| | - Qiao Zhou
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu 610041, P. R. China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, Division of Neurology, West China Second University Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Qingxiang Sun
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu 610041, P. R. China
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Janssen GV, Zhang S, Merkx R, Schiesswohl C, Chatterjee C, Darwin KH, Geurink PP, van der Heden van Noort GJ, Ovaa H. Development of Tyrphostin Analogues to Study Inhibition of the Mycobacterium tuberculosis Pup Proteasome System*. Chembiochem 2021; 22:3082-3089. [PMID: 34387015 PMCID: PMC8596589 DOI: 10.1002/cbic.202100333] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/12/2021] [Indexed: 11/29/2022]
Abstract
Tuberculosis is a global health problem caused by infection with the Mycobacterium tuberculosis (Mtb) bacteria. Although antibiotic treatment has dramatically reduced the impact of tuberculosis on the population, the existence and spreading of drug resistant strains urgently demands the development of new drugs that target Mtb in a different manner than currently used antibiotics. The prokaryotic ubiquitin-like protein (Pup) proteasome system is an attractive target for new drug development as it is unique to Mtb and related bacterial genera. Using a Pup-based fluorogenic substrate, we screened for inhibitors of Dop, the Mtb depupylating protease, and identified I-OMe-Tyrphostin AG538 (1) and Tyrphostin AG538 (2). The hits were validated and determined to be fast-reversible, non-ATP competitive inhibitors. We synthesized >25 analogs of 1 and 2 and show that several of the synthesized compounds also inhibit the depupylation actions of Dop on native substrate, FabD-Pup. Importantly, the pupylation activity of PafA, the sole Pup ligase in Mtb, was also inhibited by some of these compounds.
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Affiliation(s)
- Guido V. Janssen
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CenterEinthovenweg 202333 ZCLeidenThe Netherlands
- Division of Cell BiologyNetherlands Cancer InstitutePlesmanlaan 1211066 CXAmsterdamThe Netherlands
| | - Susan Zhang
- Department of MicrobiologyNew York University School of Medicine430 E. 29th StreetNew YorkNew York 10016USA
| | - Remco Merkx
- Division of Cell BiologyNetherlands Cancer InstitutePlesmanlaan 1211066 CXAmsterdamThe Netherlands
| | | | - Champak Chatterjee
- Department of ChemistryUniversity of WashingtonSeattleWashington 98195USA
| | - K. Heran Darwin
- Department of MicrobiologyNew York University School of Medicine430 E. 29th StreetNew YorkNew York 10016USA
| | - Paul P. Geurink
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CenterEinthovenweg 202333 ZCLeidenThe Netherlands
- Division of Cell BiologyNetherlands Cancer InstitutePlesmanlaan 1211066 CXAmsterdamThe Netherlands
| | - Gerbrand J. van der Heden van Noort
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CenterEinthovenweg 202333 ZCLeidenThe Netherlands
- Division of Cell BiologyNetherlands Cancer InstitutePlesmanlaan 1211066 CXAmsterdamThe Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CenterEinthovenweg 202333 ZCLeidenThe Netherlands
- Division of Cell BiologyNetherlands Cancer InstitutePlesmanlaan 1211066 CXAmsterdamThe Netherlands
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Zerbib E, Schlussel S, Hecht N, Bagdadi N, Eichler J, Gur E. The prokaryotic ubiquitin-like protein presents poor cleavage sites for proteasomal degradation. Cell Rep 2021; 36:109428. [PMID: 34320347 DOI: 10.1016/j.celrep.2021.109428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 05/09/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022] Open
Abstract
In an event reminiscent of eukaryotic ubiquitination, the bacterial prokaryotic ubiquitin-like protein (Pup)-proteasome system (PPS) marks target proteins for proteasomal degradation by covalently attaching Pup, the bacterial tagging molecule. Yet, ubiquitin is released from its conjugated target following proteasome binding, whereas Pup enters the proteasome and remains conjugated to the target. Here, we report that although Pup can be degraded by the bacterial proteasome, it lacks favorable 20S core particle (CP) cleavage sites and is thus a very poor 20S CP substrate. Reconstituting the PPS in vitro, we demonstrate that during pupylated protein degradation, Pup can escape unharmed and remain conjugated to a target-derived degradation fragment. Removal of this degradation fragment by Dop, a depupylase, facilitates Pup recycling and re-conjugation to a new target. This study thus offers a mechanistic model for Pup recycling and demonstrates how a lack of protein susceptibility to proteasome-mediated cleavage can play a mechanistic role in a biological system.
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Affiliation(s)
- Erez Zerbib
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Shai Schlussel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nir Hecht
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Noy Bagdadi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Eyal Gur
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
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Hecht N, Monteil CL, Perrière G, Vishkautzan M, Gur E. Exploring Protein Space: From Hydrolase to Ligase by Substitution. Mol Biol Evol 2021; 38:761-776. [PMID: 32870983 PMCID: PMC7947786 DOI: 10.1093/molbev/msaa215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The understanding of how proteins evolve to perform novel functions has long been sought by biologists. In this regard, two homologous bacterial enzymes, PafA and Dop, pose an insightful case study, as both rely on similar mechanistic properties, yet catalyze different reactions. PafA conjugates a small protein tag to target proteins, whereas Dop removes the tag by hydrolysis. Given that both enzymes present a similar fold and high sequence similarity, we sought to identify the differences in the amino acid sequence and folding responsible for each distinct activity. We tackled this question using analysis of sequence–function relationships, and identified a set of uniquely conserved residues in each enzyme. Reciprocal mutagenesis of the hydrolase, Dop, completely abolished the native activity, at the same time yielding a catalytically active ligase. Based on the available Dop and PafA crystal structures, this change of activity required a conformational change of a critical loop at the vicinity of the active site. We identified the conserved positions essential for stabilization of the alternative loop conformation, and tracked alternative mutational pathways that lead to a change in activity. Remarkably, all these pathways were combined in the evolution of PafA and Dop, despite their redundant effect on activity. Overall, we identified the residues and structural elements in PafA and Dop responsible for their activity differences. This analysis delineated, in molecular terms, the changes required for the emergence of a new catalytic function from a preexisting one.
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Affiliation(s)
- Nir Hecht
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Caroline L Monteil
- Laboratoire de Biométrie et Biologie Evolutive, Université Claude Bernard - Lyon 1, Villeurbanne, France
| | - Guy Perrière
- Laboratoire de Biométrie et Biologie Evolutive, Université Claude Bernard - Lyon 1, Villeurbanne, France
| | - Marina Vishkautzan
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Eyal Gur
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Hecht N, Becher M, Korman M, Vishkautzan M, Gur E. Inter- and intramolecular regulation of protein depupylation in Mycobacterium smegmatis. FEBS J 2020; 287:4389-4400. [PMID: 32037686 DOI: 10.1111/febs.15245] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/30/2019] [Accepted: 01/28/2020] [Indexed: 12/24/2022]
Abstract
Whereas intracellular proteolysis is essential for proper cellular function, it is a destructive process, which must be tightly regulated. In some bacteria, a Pup-proteasome system tags target proteins for degradation by a bacterial proteasome. Pup, a small modifier protein, is attached to target proteins by PafA, the sole Pup ligase, in a process termed pupylation. In mycobacteria, including Mycobacterium smegmatis and Mycobacterium tuberculosis, Pup undergoes a deamidation step by the enzyme Dop prior to its PafA-mediated attachment to a target. The catalytic mechanism of Pup deamidation is also used by Dop to perform depupylation, namely the removal of Pup from already tagged proteins. Hence, Dop appears to play contradictory roles: On the one hand, deamidation of Pup promotes pupylation, while on the other hand, depupylation reduces tagged protein levels. To avoid futile pupylation-depupylation cycles, Dop activity must be regulated. An intramolecular regulatory mechanism directs Dop to catalyze deamidation more effectively than depupylation. A complementary intermolecular mechanism results in Dop depletion under conditions where protein pupylation and degradation are favorable. In this work, we studied these regulatory mechanisms and identified a flexible loop in Dop, previously termed the Dop-loop, that acts as an intramolecular regulatory element that allosterically controls substrate preference. To investigate regulation at the intermolecular level, we used the CRISPR interference system to knock down the expression of M. smegmatis ATP-dependent intracellular proteases and found that the ClpCP protease is responsible for Dop depletion under starvation conditions. These findings clarify previous observations and introduce a new level for the regulation of Dop activity. DATABASE: Structural data are available in the PDB database under the accession numbers 4BJR and 4B0S.
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Affiliation(s)
- Nir Hecht
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Mika Becher
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Maayan Korman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Marina Vishkautzan
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Eyal Gur
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Chen J, Xu Y, Han Q, Yao Y, Xing H, Teng X. Immunosuppression, oxidative stress, and glycometabolism disorder caused by cadmium in common carp (Cyprinus carpio L.): Application of transcriptome analysis in risk assessment of environmental contaminant cadmium. JOURNAL OF HAZARDOUS MATERIALS 2019; 366:386-394. [PMID: 30551084 DOI: 10.1016/j.jhazmat.2018.12.014] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/02/2018] [Accepted: 12/03/2018] [Indexed: 06/09/2023]
Abstract
Cadmium (Cd), a hazardous environmental contaminant with irreversible toxicity to fish, has been detected in aquatic environment of many countries. The common carp is one of the most widely distributed fish in the world, so we used common carp to assess environmental contaminant risk. In present study, we investigated effects of Cd on immune function, oxidative defense, and glycometabolism in the spleens of common carp by transcriptome analysis. Obtained 3794 differentially expressed genes (including 1848 up-regulated and 1946 down-regulated genes) were enriched using databases of Kyoto Encyclopedia of Genes and Genomes, and Gene Ontology in David bioinformatics software (version 6.8). The pathways and gene functions of immune, oxidative defense, and glycometabolism were obtained and identified. Some relative genes were validated using qRT-PCR and gene expression of IL-1β, INF-γ, IL-6, Cxcl18b, HO-1a, CAT, GPx1, GCK, and FBA decreased; and gene expression of B4GALT1, GPAT3, and CYP26B1 increased. Our results indicated that Cd exposure led to immunosuppression, oxidative stress, and glycometabolism disorder in the common carp spleens. The present study gives a novel insight and method on environmental risk assessment.
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Affiliation(s)
- Jianqing Chen
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Yanmin Xu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Qi Han
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Yuchang Yao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Houjuan Xing
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China.
| | - Xiaohua Teng
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China.
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