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Nuga O, Richardson K, Patel N, Wang X, Pagala V, Stephan A, Peng J, Demontis F, Todi SV. Linear ubiquitin chains remodel the proteome and influence the levels of hundreds of regulators in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593206. [PMID: 38766269 PMCID: PMC11100727 DOI: 10.1101/2024.05.09.593206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Ubiquitin controls many cellular processes via its post-translational conjugation onto substrates. Its use is highly variable due to its ability to form poly-ubiquitin with various topologies. Among them, linear chains have emerged as important regulators of immune responses and protein degradation. Previous studies in Drosophila melanogaster found that expression of linear poly-ubiquitin that cannot be dismantled into single moieties leads to their own ubiquitination and degradation or, alternatively, to their conjugation onto proteins. However, it remains largely unknown which proteins are sensitive to linear poly-ubiquitin. To address this question, here we expanded the toolkit to modulate linear chains and conducted ultra-deep coverage proteomics from flies that express non-cleavable, linear chains comprising 2, 4, or 6 moieties. We found that these chains regulate shared and distinct cellular processes in Drosophila by impacting hundreds of proteins. Our results provide key insight into the proteome subsets and cellular pathways that are influenced by linear poly-ubiquitin with distinct lengths and suggest that the ubiquitin system is exceedingly pliable.
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Ullah I, Uddin S, Zhao L, Wang X, Li H. Autophagy and UPS pathway contribute to nicotine-induced protection effect in Parkinson's disease. Exp Brain Res 2024:10.1007/s00221-023-06765-9. [PMID: 38430248 DOI: 10.1007/s00221-023-06765-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/11/2023] [Indexed: 03/03/2024]
Abstract
The gradual nature of age-related neurodegeneration causes Parkinson's disease (PD) and impairs movement, memory, intellectual ability, and social interaction. One of the most prevalent neurodegenerative conditions affecting the central nervous system (CNS) among the elderly is PD. PD affects both motor and cognitive functions. Degeneration of dopaminergic (DA) neurons and buildup of the protein α-synuclein (α-Syn) in the substantia nigra pars compacta (SNpc) are two major causes of this disorder. Both UPS and ALS systems serve to eliminate α-Syn. Autophagy and UPS deficits, shortened life duration, and lipofuscin buildup accelerate PD. This sickness has no cure. Innovative therapies are halting PD progression. Bioactive phytochemicals may provide older individuals with a natural substitute to help delay the onset of neurodegenerative illnesses. This study examines whether nicotine helps transgenic C. elegans PD models. According to numerous studies, nicotine enhances synaptic plasticity and dopaminergic neuronal survival. Upgrades UPS pathways, increases autophagy, and decreases oxidative stress and mitochondrial dysfunction. At 100, 150, and 200 µM nicotine levels, worms showed reduced α-Syn aggregation, repaired DA neurotoxicity after 6-OHDA intoxication, increased lifetime, and reduced lipofuscin accumulation. Furthermore, nicotine triggered autophagy and UPS. We revealed nicotine's potential as a UPS and autophagy activator to prevent PD and other neurodegenerative diseases.
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Affiliation(s)
- Inam Ullah
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shahab Uddin
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Longhe Zhao
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xin Wang
- School of Pharmacy, Lanzhou University, Lanzhou, China.
| | - Hongyu Li
- School of Life Sciences, Lanzhou University, Lanzhou, China.
- School of Pharmacy, Lanzhou University, Lanzhou, China.
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Diop A, Pietrangeli P, Pennacchietti V, Pagano L, Toto A, Di Felice M, Di Matteo S, Marcocci L, Malagrinò F, Gianni S. Addressing the Binding Mechanism of the Meprin and TRAF-C Homology Domain of the Speckle-Type POZ Protein Using Protein Engineering. Int J Mol Sci 2023; 24:17364. [PMID: 38139193 PMCID: PMC10743451 DOI: 10.3390/ijms242417364] [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: 10/31/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Protein-protein interactions play crucial roles in a wide range of biological processes, including metabolic pathways, cell cycle progression, signal transduction, and the proteasomal system. For PPIs to fulfill their biological functions, they require the specific recognition of a multitude of interacting partners. In many cases, however, protein-protein interaction domains are capable of binding different partners in the intracellular environment, but they require precise regulation of the binding events in order to exert their function properly and avoid misregulation of important molecular pathways. In this work, we focused on the MATH domain of the E3 Ligase adaptor protein SPOP in order to decipher the molecular features underlying its interaction with two different peptides that mimic its physiological partners: Puc and MacroH2A. By employing stopped-flow kinetic binding experiments, together with extensive site-directed mutagenesis, we addressed the roles of specific residues, some of which, although far from the binding site, govern these transient interactions. Our findings are compatible with a scenario in which the binding of the MATH domain with its substrate is characterized by a fine energetic network that regulates its interactions with different ligands. Results are briefly discussed in the context of previously existing work regarding the MATH domain.
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Affiliation(s)
- Awa Diop
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.); (P.P.); (S.D.M.); (L.M.)
| | - Paola Pietrangeli
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.); (P.P.); (S.D.M.); (L.M.)
| | - Valeria Pennacchietti
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.); (P.P.); (S.D.M.); (L.M.)
| | - Livia Pagano
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.); (P.P.); (S.D.M.); (L.M.)
| | - Angelo Toto
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.); (P.P.); (S.D.M.); (L.M.)
| | - Mariana Di Felice
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.); (P.P.); (S.D.M.); (L.M.)
| | - Sara Di Matteo
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.); (P.P.); (S.D.M.); (L.M.)
| | - Lucia Marcocci
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.); (P.P.); (S.D.M.); (L.M.)
| | - Francesca Malagrinò
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 Coppito, Italy
| | - Stefano Gianni
- Laboratory Affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.); (P.P.); (S.D.M.); (L.M.)
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Diop A, Pietrangeli P, Nardella C, Pennacchietti V, Pagano L, Toto A, Di Felice M, Di Matteo S, Marcocci L, Malagrinò F, Gianni S. Biophysical Characterization of the Binding Mechanism between the MATH Domain of SPOP and Its Physiological Partners. Int J Mol Sci 2023; 24:10138. [PMID: 37373284 DOI: 10.3390/ijms241210138] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
SPOP (Speckle-type POZ protein) is an E3 ubiquitin ligase adaptor protein that mediates the ubiquitination of several substrates. Furthermore, SPOP is responsible for the regulation of both degradable and nondegradable polyubiquitination of a number of substrates with diverse biological functions. The recognition of SPOP and its physiological partners is mediated by two protein-protein interaction domains. Among them, the MATH domain recognizes different substrates, and it is critical for orchestrating diverse cellular pathways, being mutated in several human diseases. Despite its importance, the mechanism by which the MATH domain recognizes its physiological partners has escaped a detailed experimental characterization. In this work, we present a characterization of the binding mechanism of the MATH domain of SPOP with three peptides mimicking the phosphatase Puc, the chromatin component MacroH2A, and the dual-specificity phosphatase PTEN. Furthermore, by taking advantage of site-directed mutagenesis, we address the role of some key residues of MATH in the binding process. Our findings are briefly discussed in the context of previously existing data on the MATH domain.
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Affiliation(s)
- Awa Diop
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Paola Pietrangeli
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Caterina Nardella
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Valeria Pennacchietti
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Livia Pagano
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Angelo Toto
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Mariana Di Felice
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Sara Di Matteo
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Lucia Marcocci
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Francesca Malagrinò
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Stefano Gianni
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
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