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Wang D, Wang W, Song M, Xie Y, Kuang W, Yang P. Regulation of protein phosphorylation by PTPN2 and its small-molecule inhibitors/degraders as a potential disease treatment strategy. Eur J Med Chem 2024; 277:116774. [PMID: 39178726 DOI: 10.1016/j.ejmech.2024.116774] [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] [Received: 07/04/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 08/26/2024]
Abstract
Protein tyrosine phosphatase nonreceptor type 2 (PTPN2) is an enzyme that dephosphorylates proteins with tyrosine residues, thereby modulating relevant signaling pathways in vivo. PTPN2 acts as tumor suppressor or tumor promoter depending on the context. In some cancers, such as colorectal, and lung cancer, PTPN2 defects could impair the protein tyrosine kinase pathway, which is often over-activated in cancer cells, and inhibit tumor development and progression. However, PTPN2 can also suppress tumor immunity by regulating immune cells and cytokines. The structure, functions, and substrates of PTPN2 in various tumor cells were reviewed in this paper. And we summarized the research status of small molecule inhibitors and degraders of PTPN2. It also highlights the potential opportunities and challenges for developing PTPN2 inhibitors as anticancer drugs.
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Affiliation(s)
- Dawei Wang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Wenmu Wang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Mingge Song
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yishi Xie
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Wenbin Kuang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China; Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China.
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2
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Van der Hoeven G, Lemaire S, Cao X, Claes Z, Karamanou S, Bollen M. Spontaneous and chaperone-assisted metal loading in the active site of protein phosphatase-1. FEBS Lett 2024. [PMID: 39245796 DOI: 10.1002/1873-3468.15012] [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: 06/03/2024] [Revised: 08/22/2024] [Accepted: 08/22/2024] [Indexed: 09/10/2024]
Abstract
Protein phosphatase PP1 has two active-site metals (Zn2+/Fe2+) that are essential for catalysis. However, when expressed in bacteria, PP1 has two Mn2+-ions in its active site, indicating that the incorporation of Zn2+/Fe2+ depends on additional eukaryotic component(s). Here, we used purified, metal-deficient PP1 to study metal incorporation. Fe2+ was incorporated spontaneously, but Zn2+ was not. Mn2+-incorporation at physiological pH depended on the co-expression of PP1 with PPP1R2 (Inhibitor-2) or PPP1R11 (Inhibitor-3), or a pre-incubation of PP1 at pH 4. We also demonstrate that PPP1R2 and PPP1R11 are Zn2+-binding proteins but are, by themselves, not able to load PP1 with Zn2+. Our data suggest that PPP1R2 and PPP1R11 function as metal chaperones for PP1 but depend on co-chaperone(s) and/or specific modification(s) for the transfer of associated Zn2+ to PP1.
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Affiliation(s)
- Gerd Van der Hoeven
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, Belgium
| | - Sarah Lemaire
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, Belgium
| | - Xinyu Cao
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, Belgium
| | - Zander Claes
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, Belgium
| | - Spyridoula Karamanou
- Laboratory of Molecular Bacteriology, KU Leuven Department of Microbiology and Immunology, University of Leuven, Belgium
| | - Mathieu Bollen
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, Belgium
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3
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Zhao JF, Shpiro N, Sathe G, Brewer A, Macartney TJ, Wood NT, Negoita F, Sakamoto K, Sapkota GP. Targeted dephosphorylation of TFEB promotes its nuclear translocation. iScience 2024; 27:110432. [PMID: 39081292 PMCID: PMC11284556 DOI: 10.1016/j.isci.2024.110432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/07/2024] [Accepted: 06/28/2024] [Indexed: 08/02/2024] Open
Abstract
Reversible phosphorylation of the transcription factor EB (TFEB) coordinates cellular responses to metabolic and other stresses. During nutrient replete and stressor-free conditions, phosphorylated TFEB is primarily localized to the cytoplasm. Stressor-mediated reduction of TFEB phosphorylation promotes its nuclear translocation and context-dependent transcriptional activity. In this study, we explored targeted dephosphorylation of TFEB as an approach to activate TFEB in the absence of nutrient deprivation or other cellular stress. Through an induction of proximity between TFEB and several phosphatases using the AdPhosphatase system, we demonstrate targeted dephosphorylation of TFEB in cells. Furthermore, by developing a heterobifunctional molecule BDPIC (bromoTAG-dTAG proximity-inducing chimera), we demonstrate targeted dephosphorylation of TFEB-dTAG through induced proximity to bromoTAG-PPP2CA. Targeted dephosphorylation of TFEB-dTAG by bromoTAG-PPP2CA with BDPIC at the endogenous levels is sufficient to induce nuclear translocation and some transcriptional activity of TFEB.
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Affiliation(s)
- Jin-Feng Zhao
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Natalia Shpiro
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Gajanan Sathe
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Abigail Brewer
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Thomas J. Macartney
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Nicola T. Wood
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Florentina Negoita
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kei Sakamoto
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Gopal P. Sapkota
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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4
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Lauritano C, Bazzani E, Montuori E, Bolinesi F, Mangoni O, Riccio G, Buondonno A, Saggiomo M. Salinity Stress Acclimation Strategies in Chlamydomonas sp. Revealed by Physiological, Morphological and Transcriptomic Approaches. Mar Drugs 2024; 22:351. [PMID: 39195467 DOI: 10.3390/md22080351] [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] [Received: 06/16/2024] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 08/29/2024] Open
Abstract
Climate changes may include variations in salinity concentrations at sea by changing ocean dynamics. These variations may be especially challenging for marine photosynthetic organisms, affecting their growth and distribution. Chlamydomonas spp. are ubiquitous and are often found in extreme salinity conditions. For this reason, they are considered good model species to study salinity adaptation strategies. In the current study, we used an integrated approach to study the Chlamydomonas sp. CCMP225 response to salinities of 20‱ and 70‱, by combining physiological, morphological, and transcriptomic analyses, and comparing differentially expressed genes in the exponential and stationary growth phases under the two salinity conditions. The results showed that the strain is able to grow under all tested salinity conditions and maintains a surprisingly high photosynthetic efficiency even under high salinities. However, at the highest salinity condition, the cells lose their flagella. The transcriptomic analysis highlighted the up- or down-regulation of specific gene categories, helping to identify key genes responding to salinity stress. Overall, the findings may be of interest to the marine biology, ecology, and biotechnology communities, to better understand species adaptation mechanisms under possible global change scenarios and the potential activation of enzymes involved in the synthesis of bioactive molecules.
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Affiliation(s)
- Chiara Lauritano
- Ecosustainable Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Via Acton, 80133 Naples, Italy
| | - Emma Bazzani
- Research Infrastructure for Marine Biological Resources Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin 2, D02 VF25 Dublin, Ireland
| | - Eleonora Montuori
- Ecosustainable Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Via Acton, 80133 Naples, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Francesco Bolinesi
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Naples, Italy
- CoNISMa, Piazzale Flaminio, 9, 00196 Roma, Italy
| | - Olga Mangoni
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Naples, Italy
- CoNISMa, Piazzale Flaminio, 9, 00196 Roma, Italy
| | - Gennaro Riccio
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Angela Buondonno
- Research Infrastructure for Marine Biological Resources Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Maria Saggiomo
- Research Infrastructure for Marine Biological Resources Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
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5
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Bartol TM, Ordyan M, Sejnowski TJ, Rangamani P, Kennedy MB. A spatial model of autophosphorylation of Ca 2+ /calmodulin-dependent protein kinase II in a glutamatergic spine reveals dynamics of kinase activation in the first several seconds after a complex synaptic stimulus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578696. [PMID: 38352446 PMCID: PMC10862815 DOI: 10.1101/2024.02.02.578696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Long-term potentiation (LTP) is a biochemical process in excitatory glutamatergic synapses in the Central Nervous System (CNS). It is initiated by a bout of synaptic activation that is strong enough to contribute to production of an action potential in the axon of the postsynaptic neuron, and it results in an increase in the size of postsynaptic depolarization during subsequent activity. The first step leading to LTP is activation and autophosphorylation of an abundant postsynaptic enzyme, Ca 2+ /calmodulin-dependent protein kinase II (CaMKII). We use simulation of activation of CaMKII holoenzymes in a realistic spatial model of a spine synapse, created in MCell4, to test three hypotheses about how the autophosphorylation response of CaMKII is shaped during a repeated high-frequency stimulus. First, the simulation results indicate that autophosphorylation of CaMKII does not constitute a bistable switch under biologically realistic conditions. Instead, prolonged autophosphorylation of CaMKII may contribute to a biochemical "kinetic proof-reading" mechanism that controls induction of synaptic plasticity. Second, concentration of CaMKII near the postsynaptic membrane increases the local concentration of kinase activity. However, neither localization nor "Ca 2+ -calmodulin-trapping (CaM-trapping)" increase the proportion of autophosphorylated subunits in holoenzymes after a complex stimulus, as previously hypothesized. Finally, we show that, as hypothesized, the amplitude of autophosphorylation in the first 30 seconds after a stimulus is extremely sensitive to the level and location of PP1 activity when PP1 is present in biologically accurate amounts. We further show that prolonged steric hindrance of dephosphorylation of CaMKII, caused by CaM-trapping, can increase the amplitude of autophosphorylation after a complex stimulus. These simulation results sharpen our quantitative understanding of the early events leading to LTP at excitatory synapses. Author Summary Neurons in the brain are interconnected in an organized fashion by synapses that transmit neuronal activity from one neuron to another. Most of the billions of neurons in the brain have about 10,000 synapses spread over the neuronal membrane. Information is stored in the brain when the ability of specific synapses to pass along neuronal activity is strengthened resulting in formation of new networks. The increase in strength of a synapse is tightly controlled by the frequency and amplitude of its activity, and by neurohormonal signals, which, in combination, can cause long-lasting biochemical changes at the synapse that underlie learning and memory. Defects in these biochemical pathways cause mental and neurological diseases. To develop treatments, we need to understand the precise choreography of these critical biochemical changes. However, the tiny size of the synaptic compartment makes precise measurements of the biochemical reactions impossible. We have used computer simulation techniques and information gathered from experiments on purified synaptic proteins to simulate, within a single synapse, the choreography of the first biochemical step in synaptic strengthening: activation of the enzyme Ca 2+ / calmodulin-dependent protein kinase II. Our results provide insights that can be used in future studies to develop treatments for neuronal diseases.
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6
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Cao X, Lake M, Van der Hoeven G, Claes Z, Del Pino García J, Lemaire S, Greiner EC, Karamanou S, Van Eynde A, Kettenbach AN, Natera de Benito D, Carrera García L, Hernando Davalillo C, Ortez C, Nascimento A, Urreizti R, Bollen M. SDS22 coordinates the assembly of holoenzymes from nascent protein phosphatase-1. Nat Commun 2024; 15:5359. [PMID: 38918402 PMCID: PMC11199634 DOI: 10.1038/s41467-024-49746-4] [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: 11/24/2023] [Accepted: 06/18/2024] [Indexed: 06/27/2024] Open
Abstract
SDS22 forms an inactive complex with nascent protein phosphatase PP1 and Inhibitor-3. SDS22:PP1:Inhibitor-3 is a substrate for the ATPase p97/VCP, which liberates PP1 for binding to canonical regulatory subunits. The exact role of SDS22 in PP1-holoenzyme assembly remains elusive. Here, we show that SDS22 stabilizes nascent PP1. In the absence of SDS22, PP1 is gradually lost, resulting in substrate hyperphosphorylation and a proliferation arrest. Similarly, we identify a female individual with a severe neurodevelopmental disorder bearing an unstable SDS22 mutant, associated with decreased PP1 levels. We furthermore find that SDS22 directly binds to Inhibitor-3 and that this is essential for the stable assembly of SDS22:PP1: Inhibitor-3, the recruitment of p97/VCP, and the extraction of SDS22 during holoenzyme assembly. SDS22 with a disabled Inhibitor-3 binding site co-transfers with PP1 to canonical regulatory subunits, thereby forming non-functional holoenzymes. Our data show that SDS22, through simultaneous interaction with PP1 and Inhibitor-3, integrates the major steps of PP1 holoenzyme assembly.
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Affiliation(s)
- Xinyu Cao
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000, Leuven, Belgium
| | - Madryn Lake
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000, Leuven, Belgium
| | - Gerd Van der Hoeven
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000, Leuven, Belgium
| | - Zander Claes
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000, Leuven, Belgium
| | - Javier Del Pino García
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000, Leuven, Belgium
| | - Sarah Lemaire
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000, Leuven, Belgium
| | - Elora C Greiner
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Dartmouth Cancer Center, Lebanon, NH, USA
| | - Spyridoula Karamanou
- Laboratory of Molecular Bacteriology, KU Leuven Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Aleyde Van Eynde
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000, Leuven, Belgium
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Dartmouth Cancer Center, Lebanon, NH, USA
| | | | - Laura Carrera García
- Neuromuscular Unit, Department of Neurology, Hospital Sant Joan de Deu, Barcelona, Spain
| | | | - Carlos Ortez
- Neuromuscular Unit, Department of Neurology, Hospital Sant Joan de Deu, Barcelona, Spain
| | - Andrés Nascimento
- Neuromuscular Unit, Department of Neurology, Hospital Sant Joan de Deu, Barcelona, Spain
| | - Roser Urreizti
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Mathieu Bollen
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000, Leuven, Belgium.
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7
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Bradley D, Garand C, Belda H, Gagnon-Arsenault I, Treeck M, Elowe S, Landry CR. The substrate quality of CK2 target sites has a determinant role on their function and evolution. Cell Syst 2024; 15:544-562.e8. [PMID: 38861992 DOI: 10.1016/j.cels.2024.05.005] [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] [Received: 07/03/2023] [Revised: 02/29/2024] [Accepted: 05/20/2024] [Indexed: 06/13/2024]
Abstract
Most biological processes are regulated by signaling modules that bind to short linear motifs. For protein kinases, substrates may have full or only partial matches to the kinase recognition motif, a property known as "substrate quality." However, it is not clear whether differences in substrate quality represent neutral variation or if they have functional consequences. We examine this question for the kinase CK2, which has many fundamental functions. We show that optimal CK2 sites are phosphorylated at maximal stoichiometries and found in many conditions, whereas minimal substrates are more weakly phosphorylated and have regulatory functions. Optimal CK2 sites tend to be more conserved, and substrate quality is often tuned by selection. For intermediate sites, increases or decreases in substrate quality may be deleterious, as we demonstrate for a CK2 substrate at the kinetochore. The results together suggest a strong role for substrate quality in phosphosite function and evolution. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- David Bradley
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec City, QC G1V 0A6, Canada; Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada.
| | - Chantal Garand
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Axe de Reproduction, Santé de la mère et de l'enfant, CHU de Québec, Université Laval, Québec City, QC, Canada
| | - Hugo Belda
- Signalling in Host-Pathogen Interaction Laboratory, The Francis Crick Institute, London NW11AT, UK
| | - Isabelle Gagnon-Arsenault
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec City, QC G1V 0A6, Canada; Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Moritz Treeck
- Signalling in Host-Pathogen Interaction Laboratory, The Francis Crick Institute, London NW11AT, UK; Cell Biology of Host-Pathogen Interaction Laboratory, The Gulbenkian Institute of Science, Oeiras 2780-156, Portugal
| | - Sabine Elowe
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Axe de Reproduction, Santé de la mère et de l'enfant, CHU de Québec, Université Laval, Québec City, QC, Canada; Department of Pediatrics, Faculty of Medicine, Université Laval, Québec City, QC, Canada; Centre de Recherche sur le Cancer, CHU de Québec, Université Laval, Québec City, QC, Canada
| | - Christian R Landry
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec City, QC G1V 0A6, Canada; Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec City, QC G1V 0A6, Canada; Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada.
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8
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Provost JJ, Cornely KA, Mertz PS, Peterson CN, Riley SG, Tarbox HJ, Narasimhan SR, Pulido AJ, Springer AL. Phosphorylation of mammalian cytosolic and mitochondrial malate dehydrogenase: insights into regulation. Essays Biochem 2024:EBC20230079. [PMID: 38864157 DOI: 10.1042/ebc20230079] [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: 03/12/2024] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/13/2024]
Abstract
Malate dehydrogenase (MDH) is a key enzyme in mammalian metabolic pathways in cytosolic and mitochondrial compartments. Regulation of MDH through phosphorylation remains an underexplored area. In this review we consolidate evidence supporting the potential role of phosphorylation in modulating the function of mammalian MDH. Parallels are drawn with the phosphorylation of lactate dehydrogenase, a homologous enzyme, to reveal its regulatory significance and to suggest a similar regulatory strategy for MDH. Comprehensive mining of phosphorylation databases, provides substantial experimental (primarily mass spectrometry) evidence of MDH phosphorylation in mammalian cells. Experimentally identified phosphorylation sites are overlaid with MDH's functional domains, offering perspective on how these modifications could influence enzyme activity. Preliminary results are presented from phosphomimetic mutations (serine/threonine residues changed to aspartate) generated in recombinant MDH proteins serving as a proof of concept for the regulatory impact of phosphorylation. We also examine and highlight several approaches to probe the structural and cellular impact of phosphorylation. This review highlights the need to explore the dynamic nature of MDH phosphorylation and calls for identifying the responsible kinases and the physiological conditions underpinning this modification. The synthesis of current evidence and experimental data aims to provide insights for future research on understanding MDH regulation, offering new avenues for therapeutic interventions in metabolic disorders and cancer.
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Affiliation(s)
- Joseph J Provost
- Department of Chemistry and Biochemistry, University of San Diego, San Diego CA, U.S.A
| | - Kathleen A Cornely
- Department of Chemistry and Biochemistry, Providence College, Providence RI, U.S.A
| | - Pamela S Mertz
- Department of Chemistry and Biochemistry, St. Mary's College of Maryland, St. Mary's City, MD, U.S.A
| | | | - Sophie G Riley
- Department of Chemistry and Biochemistry, University of San Diego, San Diego CA, U.S.A
| | - Harrison J Tarbox
- Department of Chemistry and Biochemistry, University of San Diego, San Diego CA, U.S.A
| | - Shree R Narasimhan
- Department of Chemistry and Biochemistry, University of San Diego, San Diego CA, U.S.A
| | - Andrew J Pulido
- Department of Chemistry and Biochemistry, University of San Diego, San Diego CA, U.S.A
| | - Amy L Springer
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, U.S.A
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9
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Wu D, Van der Hoeven G, Claes Z, Van Eynde A, Bollen M. DNA damage-induced allosteric activation of protein phosphatase PP1:NIPP1 through Src kinase-induced circularization of NIPP1. FEBS J 2024; 291:2615-2635. [PMID: 38303113 DOI: 10.1111/febs.17064] [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: 07/03/2023] [Revised: 12/06/2023] [Accepted: 12/28/2023] [Indexed: 02/03/2024]
Abstract
Protein phosphatase-1 (PP1) complexed to nuclear inhibitor of PP1 (NIPP1) limits DNA repair through dephosphorylation of NIPP1-recruited substrates. However, the PP1:NIPP1 holoenzyme is completely inactive under basal conditions, hinting at a DNA damage-regulated activation mechanism. Here, we report that DNA damage caused the activation of PP1:NIPP1 after a time delay of several hours through phosphorylation of NIPP1 at the C-terminal tyrosine 335 (Y335) by a Src-family kinase. PP1:NIPP1 activation partially resulted from the dissociation of the C terminus of NIPP1 from the active site of PP1. In addition, the released Y335-phosphorylated C terminus interacted with the N terminus of NIPP1 to enhance substrate recruitment by the flanking forkhead-associated (FHA) domain. Constitutive activation of PP1:NIPP1 by knock-in of a phospho-mimicking (Y335E) NIPP1 mutant led to the hypo-phosphorylation of FHA ligands and an accumulation of DNA double-strand breaks. Our data indicate that PP1:NIPP1 activation through circularization of NIPP1 is a late response to DNA damage that contributes to the timely recovery from damage repair.
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Affiliation(s)
- Dan Wu
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, Belgium
| | - Gerd Van der Hoeven
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, Belgium
| | - Zander Claes
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, Belgium
| | - Aleyde Van Eynde
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, Belgium
| | - Mathieu Bollen
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, Belgium
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10
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Banerjee A, Mathew S, Naqvi MM, Yilmaz SZ, Zacharopoulou M, Doruker P, Kumita JR, Yang SH, Gur M, Itzhaki LS, Gordon R, Bahar I. Influence of point mutations on PR65 conformational adaptability: Insights from molecular simulations and nanoaperture optical tweezers. SCIENCE ADVANCES 2024; 10:eadn2208. [PMID: 38820156 PMCID: PMC11141623 DOI: 10.1126/sciadv.adn2208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/29/2024] [Indexed: 06/02/2024]
Abstract
PR65 is the HEAT repeat scaffold subunit of the heterotrimeric protein phosphatase 2A (PP2A) and an archetypal tandem repeat protein. Its conformational mechanics plays a crucial role in PP2A function by opening/closing substrate binding/catalysis interface. Using in silico saturation mutagenesis, we identified PR65 "hinge" residues whose substitutions could alter its conformational adaptability and thereby PP2A function, and selected six mutations that were verified to be expressed and soluble. Molecular simulations and nanoaperture optical tweezers revealed consistent results on the specific effects of the mutations on the structure and dynamics of PR65. Two mutants observed in simulations to stabilize extended/open conformations exhibited higher corner frequencies and lower translational scattering in experiments, indicating a shift toward extended conformations, whereas another displayed the opposite features, confirmed by both simulations and experiments. The study highlights the power of single-molecule nanoaperture-based tweezers integrated with in silico approaches for exploring the effect of mutations on protein structure and dynamics.
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Affiliation(s)
- Anupam Banerjee
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Samuel Mathew
- Department of Electrical and Computer Engineering, University of Victoria, Victoria V8P 5C2, Canada
| | - Mohsin M. Naqvi
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Sema Z. Yilmaz
- Department of Mechanical Engineering, Istanbul Technical University, 34437 Istanbul, Turkey
| | - Maria Zacharopoulou
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Pemra Doruker
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Janet R. Kumita
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Shang-Hua Yang
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Mert Gur
- Department of Mechanical Engineering, Istanbul Technical University, 34437 Istanbul, Turkey
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Laura S. Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Reuven Gordon
- Department of Electrical and Computer Engineering, University of Victoria, Victoria V8P 5C2, Canada
| | - Ivet Bahar
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
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11
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Xu W, Hua Z, Wang Y, Tang W, Ou W, Liu F, Yang Y, Ding W, Wang Z, Cui L, Ge W, Gu Y, Wang X, Chen Y, Liu CY, Du P. AMBRA1 promotes intestinal inflammation by antagonizing PP4R1/PP4c mediated IKK dephosphorylation in an autophagy-independent manner. Cell Death Differ 2024; 31:618-634. [PMID: 38424148 PMCID: PMC11094188 DOI: 10.1038/s41418-024-01275-9] [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: 12/11/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/02/2024] Open
Abstract
IκB kinase (IKK) complex is central regulators of the NF-κB pathway, and dysregulation of IKK phosphorylation leads to hyperactivation of proinflammatory response in various chronic inflammatory diseases, including inflammatory bowel disease (IBD). However, the dynamic modulation of IKK phosphorylation and dephosphorylation in intestinal inflammation remains uncharacterized. Here, we found that autophagy/beclin-1 regulator 1 (AMBRA1) was highly expressed in inflamed colons in a colitis mouse model and in clinical IBD samples. Importantly, AMBRA1 deletion significantly decreased proinflammatory cytokine expression and enhanced the therapeutic effect of infliximab on intestinal inflammation. Mechanistically, the N-term F1 domain of AMBRA1 was required for AMBRA1 to competitively interact with protein phosphatase 4 regulatory subunit 1 (PP4R1) and catalytic protein phosphatase 4 (PP4c) to suppress their interactions with IKK, promote the dissociation of the PP4R1/PP4c complex, and antagonize the dephosphorylation activity of this complex towards the IKK complex. In response to TNF-α stimulation, IKKα phosphorylates AMBRA1 at S1043 to stabilize AMBRA1 expression by impairing its binding to Cullin4A (CUL4A) to decrease its CUL4A-mediated K48-linked ubiquitination. Overall, our study identifies an autophagy-independent function of AMBRA1 as a positive modulator of IKK phosphorylation to promote intestinal inflammation, thus providing a new targeted therapeutic strategy for patients with refractory IBD.
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Affiliation(s)
- Weimin Xu
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Zhebin Hua
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Yaosheng Wang
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Wenbo Tang
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Weijun Ou
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Fangyuan Liu
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Yiqing Yang
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Wenjun Ding
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Zhongchuan Wang
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Long Cui
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Wensong Ge
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200092, China
| | - Yubei Gu
- Department of Gastroenterology, Rui Jin Hospital, affiliate to Shanghai Jiao Tong University, school of Medicine, 197 Rui Jin Er Road, Shanghai, 200025, China
| | - Xiaolei Wang
- Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University, Shanghai, 200072, China
| | - YingWei Chen
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200092, China.
| | - Chen-Ying Liu
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200092, China.
- Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China.
| | - Peng Du
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200092, China.
- Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China.
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12
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Ando S, Tanaka K, Matsumoto M, Oyama Y, Tomabechi Y, Yamagata A, Shirouzu M, Nakagawa R, Okimoto N, Taiji M, Sato K, Ohama T. The luciferase-based in vivo protein-protein interaction assay revealed that CHK1 promotes PP2A and PME-1 interaction. J Biol Chem 2024; 300:107277. [PMID: 38588804 PMCID: PMC11098961 DOI: 10.1016/j.jbc.2024.107277] [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] [Received: 12/21/2023] [Revised: 03/12/2024] [Accepted: 04/02/2024] [Indexed: 04/10/2024] Open
Abstract
Protein phosphatase 2A (PP2A) is an essential serine/threonine protein phosphatase, and its dysfunction is involved in the onset of cancer and neurodegenerative disorders. PP2A functions as a trimeric holoenzyme whose composition is regulated by the methyl-esterification (methylation) of the PP2A catalytic subunit (PP2Ac). Protein phosphatase methylesterase-1 (PME-1) is the sole PP2Ac methylesterase, and the higher PME-1 expression is observed in various cancer and neurodegenerative diseases. Apart from serving as a methylesterase, PME-1 acts as a PP2A inhibitory protein, binding directly to PP2Ac and suppressing its activity. The intricate function of PME-1 hinders drug development by targeting the PME-1/PP2Ac axis. This study applied the NanoBiT system, a bioluminescence-based protein interaction assay, to elucidate the molecular mechanism that modulates unknown PME-1/PP2Ac protein-protein interaction (PPI). Compound screening identified that the CHK1 inhibitors inhibited PME-1/PP2Ac association without affecting PP2Ac methylation levels. CHK1 directly phosphorylates PP2Ac to promote PME-1 association. Phospho-mass spectrometry identified multiple phospho-sites on PP2Ac, including the Thr219, that affect PME-1 interaction. An anti-phospho-Thr219 PP2Ac antibody was generated and showed that CHK1 regulates the phosphorylation levels of this site in cells. On the contrary, in vitro phosphatase assay showed that CHK1 is the substrate of PP2A, and PME-1 hindered PP2A-mediated dephosphorylation of CHK1. Our data provides novel insights into the molecular mechanisms governing the PME-1/PP2Ac PPI and the triad relationship between PP2A, PME-1, and CHK1.
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Affiliation(s)
- Sana Ando
- Laboratory of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Keiko Tanaka
- Laboratory of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Maharu Matsumoto
- Laboratory of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Yuki Oyama
- Laboratory of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Yuri Tomabechi
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Atsushi Yamagata
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Reiko Nakagawa
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Noriaki Okimoto
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka, Japan; Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka, Japan
| | - Makoto Taiji
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka, Japan; Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka, Japan
| | - Koichi Sato
- Laboratory of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan; Research Institute for Cell Design Medical Science, Yamaguchi University, Yamaguchi, Japan
| | - Takashi Ohama
- Laboratory of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan; Research Institute for Cell Design Medical Science, Yamaguchi University, Yamaguchi, Japan.
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13
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Bao J, Tang Y, Chen Y, Jin J, Wang X, An G, Cao L, Zhang H, Cheng G, Pan G, Zhou Z. E. hellem Ser/Thr protein phosphatase PP1 targets the DC MAPK pathway and impairs immune functions. Life Sci Alliance 2024; 7:e202302375. [PMID: 38199846 PMCID: PMC10781585 DOI: 10.26508/lsa.202302375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 01/12/2024] Open
Abstract
Microsporidia are difficult to be completely eliminated once infected, and the persistence disrupts host cell functions. Here in this study, we aimed to elucidate the impairing effects and consequences of microsporidia on host DCs. Enterocytozoon hellem, one of the most commonly diagnosed zoonotic microsporidia species, was applied. In vivo models demonstrated that E. hellem-infected mice were more susceptible to further pathogenic challenges, and DCs were identified as the most affected groups of cells. In vitro assays revealed that E. hellem infection impaired DCs' immune functions, reflected by down-regulated cytokine expressions, lower extent of maturation, phagocytosis ability, and antigen presentations. E. hellem infection also detained DCs' potencies to prime and stimulate T cells; therefore, host immunities were disrupted. We found that E. hellem Ser/Thr protein phosphatase PP1 directly interacts with host p38α (MAPK14) to manipulate the p38α(MAPK14)/NFAT5 axis of the MAPK pathway. Our study is the first to elucidate the molecular mechanisms of the impairing effects of microsporidia on host DCs' immune functions. The emergence of microsporidiosis may be of great threat to public health.
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Affiliation(s)
- Jialing Bao
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Yunlin Tang
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Yebo Chen
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Jiangyan Jin
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Xue Wang
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Guozhen An
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Lu Cao
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Huarui Zhang
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Gong Cheng
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Guoqing Pan
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Zeyang Zhou
- https://ror.org/01kj4z117 The State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- https://ror.org/01kj4z117 Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
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14
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Qiu M, Sun Y, Tu S, Li H, Yang X, Zhao H, Yin M, Li Y, Ye W, Wang M, Wang Y. Mining oomycete proteomes for phosphatome leads to the identification of specific expanded phosphatases in oomycetes. MOLECULAR PLANT PATHOLOGY 2024; 25:e13425. [PMID: 38462784 PMCID: PMC10925823 DOI: 10.1111/mpp.13425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 12/23/2023] [Accepted: 01/11/2024] [Indexed: 03/12/2024]
Abstract
Phosphatases are important regulators of protein phosphorylation and various cellular processes, and they serve as counterparts to kinases. In this study, our comprehensive analysis of oomycete complete proteomes unveiled the presence of approximately 3833 phosphatases, with most species estimated to have between 100 and 300 putative phosphatases. Further investigation of these phosphatases revealed a significant increase in protein serine/threonine phosphatases (PSP) within oomycetes. In particular, we extensively studied the metallo-dependent protein phosphatase (PPM) within the PSP family in the model oomycete Phytophthora sojae. Our results showed notable differences in the expression patterns of PPMs throughout 10 life stages of P. sojae, indicating their vital roles in various stages of oomycete pathogens. Moreover, we identified 29 PPMs in P. sojae, and eight of them possessed accessory domains in addition to phosphate domains. We investigated the biological function of one PPM protein with an extra PH domain (PPM1); this protein exhibited high expression levels in both asexual developmental and infectious stages. Our analysis confirmed that PPM1 is indeed an active protein phosphatase, and its accessory domain does not affect its phosphatase activity. To delve further into its function, we generated knockout mutants of PPM1 and validated its essential roles in mycelial growth, sporangia and oospore production, as well as infectious stages. To the best of our knowledge, this study provides the first comprehensive inventory of phosphatases in oomycetes and identifies an important phosphatase within the expanded serine/threonine phosphatase group in oomycetes.
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Affiliation(s)
- Min Qiu
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
- The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingJiangsuChina
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Yaru Sun
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
| | - Siqun Tu
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
| | - Huaibo Li
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
| | - Xin Yang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
| | - Haiyang Zhao
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
| | - Maozhu Yin
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
| | - Yaning Li
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
| | - Wenwu Ye
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
- The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingJiangsuChina
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Ming Wang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
- The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingJiangsuChina
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Yuanchao Wang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
- The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingJiangsuChina
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs)Nanjing Agricultural UniversityNanjingJiangsuChina
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15
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Lacroix B, Vigneron S, Labbé JC, Pintard L, Lionne C, Labesse G, Castro A, Lorca T. Increases in cyclin A/Cdk activity and in PP2A-B55 inhibition by FAM122A are key mitosis-inducing events. EMBO J 2024; 43:993-1014. [PMID: 38378890 PMCID: PMC10943098 DOI: 10.1038/s44318-024-00054-z] [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: 06/19/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
Entry into mitosis has been classically attributed to the activation of a cyclin B/Cdk1 amplification loop via a partial pool of this kinase becoming active at the end of G2 phase. However, how this initial pool is activated is still unknown. Here we discovered a new role of the recently identified PP2A-B55 inhibitor FAM122A in triggering mitotic entry. Accordingly, depletion of the orthologue of FAM122A in C. elegans prevents entry into mitosis in germline stem cells. Moreover, data from Xenopus egg extracts strongly suggest that FAM122A-dependent inhibition of PP2A-B55 could be the initial event promoting mitotic entry. Inhibition of this phosphatase allows subsequent phosphorylation of early mitotic substrates by cyclin A/Cdk, resulting in full cyclin B/Cdk1 and Greatwall (Gwl) kinase activation. Subsequent to Greatwall activation, Arpp19/ENSA become phosphorylated and now compete with FAM122A, promoting its dissociation from PP2A-B55 and taking over its phosphatase inhibition role until the end of mitosis.
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Affiliation(s)
- Benjamin Lacroix
- Université de Montpellier, Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), CNRS UMR 5237, 1919 Route de Mende, 34293, Montpellier cedex 5, France
- Programme équipes Labellisées Ligue Contre le Cancer, Paris, France
| | - Suzanne Vigneron
- Université de Montpellier, Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), CNRS UMR 5237, 1919 Route de Mende, 34293, Montpellier cedex 5, France
- Programme équipes Labellisées Ligue Contre le Cancer, Paris, France
| | - Jean Claude Labbé
- Université de Montpellier, Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), CNRS UMR 5237, 1919 Route de Mende, 34293, Montpellier cedex 5, France
- Programme équipes Labellisées Ligue Contre le Cancer, Paris, France
| | - Lionel Pintard
- Programme équipes Labellisées Ligue Contre le Cancer, Paris, France
- Université Paris Cité, Institut Jacques Monod, F-75013, Paris, France
| | - Corinne Lionne
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Montpellier University, Montpellier, France
| | - Gilles Labesse
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Montpellier University, Montpellier, France
| | - Anna Castro
- Université de Montpellier, Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), CNRS UMR 5237, 1919 Route de Mende, 34293, Montpellier cedex 5, France.
- Programme équipes Labellisées Ligue Contre le Cancer, Paris, France.
| | - Thierry Lorca
- Université de Montpellier, Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), CNRS UMR 5237, 1919 Route de Mende, 34293, Montpellier cedex 5, France.
- Programme équipes Labellisées Ligue Contre le Cancer, Paris, France.
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16
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Lu J, Feng Y, Yu D, Li H, Li W, Chen H, Chen L. A review of nuclear Dbf2-related kinase 1 (NDR1) protein interaction as promising new target for cancer therapy. Int J Biol Macromol 2024; 259:129188. [PMID: 38184050 DOI: 10.1016/j.ijbiomac.2023.129188] [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] [Received: 10/26/2023] [Revised: 12/19/2023] [Accepted: 12/31/2023] [Indexed: 01/08/2024]
Abstract
Nuclear Dbf2-related kinase 1 (NDR1) is a nuclear Dbf2-related (NDR) protein kinase family member, which regulates cell functions and participates in cell proliferation and differentiation through kinase activity. NDR1 regulates physiological functions by interacting with different proteins. Protein-protein interactions (PPIs) are crucial for regulating biological processes and controlling cell fate, and as a result, it is beneficial to study the actions of PPIs to elucidate the pathological mechanism of diseases. The previous studies also show that the expression of NDR1 is deregulated in numerous human cancer samples and it needs the context-specific targeting strategies for NDR1. Thus, a comprehensive understanding of the direct interaction between NDR1 and varieties of proteins may provide new insights into cancer therapies. In this review, we summarize recent studies of NDR1 in solid tumors, such as prostate cancer and breast cancer, and explore the mechanism of action of PPIs of NDR1 in tumors.
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Affiliation(s)
- Jiani Lu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yanjun Feng
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Danmei Yu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hongtao Li
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Hongzhuan Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lili Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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17
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Egbert JR, Silbern I, Uliasz TF, Lowther KM, Yee SP, Urlaub H, Jaffe LA. Phosphatases modified by LH signaling in ovarian follicles: testing their role in regulating the NPR2 guanylyl cyclase†. Biol Reprod 2024; 110:102-115. [PMID: 37774352 PMCID: PMC10790345 DOI: 10.1093/biolre/ioad130] [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] [Indexed: 10/01/2023] Open
Abstract
In response to luteinizing hormone (LH), multiple proteins in rat and mouse granulosa cells are rapidly dephosphorylated, but the responsible phosphatases remain to be identified. Because the phosphorylation state of phosphatases can regulate their interaction with substrates, we searched for phosphatases that might function in LH signaling by using quantitative mass spectrometry. We identified all proteins in rat ovarian follicles whose phosphorylation state changed detectably in response to a 30-min exposure to LH, and within this list, identified protein phosphatases or phosphatase regulatory subunits that showed changes in phosphorylation. Phosphatases in the phosphoprotein phosphatase (PPP) family were of particular interest because of their requirement for dephosphorylating the natriuretic peptide receptor 2 (NPR2) guanylyl cyclase in the granulosa cells, which triggers oocyte meiotic resumption. Among the PPP family regulatory subunits, PPP1R12A and PPP2R5D showed the largest increases in phosphorylation, with 4-10 fold increases in signal intensity on several sites. Although follicles from mice in which these phosphorylations were prevented by serine-to-alanine mutations in either Ppp1r12a or Ppp2r5d showed normal LH-induced NPR2 dephosphorylation, these regulatory subunits and others could act redundantly to dephosphorylate NPR2. Our identification of phosphatases and other proteins whose phosphorylation state is rapidly modified by LH provides clues about multiple signaling pathways in ovarian follicles.
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Affiliation(s)
- Jeremy R Egbert
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Ivan Silbern
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
- Institute of Clinical Chemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Tracy F Uliasz
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Katie M Lowther
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
- Center for Mouse Genome Modification, University of Connecticut Health Center, Farmington CT, USA
| | - Siu-Pok Yee
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
- Center for Mouse Genome Modification, University of Connecticut Health Center, Farmington CT, USA
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
- Institute of Clinical Chemistry, University Medical Center Goettingen, Goettingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Göttingen, Germany
| | - Laurinda A Jaffe
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
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18
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Padi SKR, Vos MR, Godek RJ, Fuller JR, Kruse T, Hein JB, Nilsson J, Kelker MS, Page R, Peti W. Cryo-EM structures of PP2A:B55-FAM122A and PP2A:B55-ARPP19. Nature 2024; 625:195-203. [PMID: 38123684 PMCID: PMC10765524 DOI: 10.1038/s41586-023-06870-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023]
Abstract
Progression through the cell cycle is controlled by regulated and abrupt changes in phosphorylation1. Mitotic entry is initiated by increased phosphorylation of mitotic proteins, a process driven by kinases2, whereas mitotic exit is achieved by counteracting dephosphorylation, a process driven by phosphatases, especially PP2A:B553. Although the role of kinases in mitotic entry is well established, recent data have shown that mitosis is only successfully initiated when the counterbalancing phosphatases are also inhibited4. Inhibition of PP2A:B55 is achieved by the intrinsically disordered proteins ARPP195,6 and FAM122A7. Despite their critical roles in mitosis, the mechanisms by which they achieve PP2A:B55 inhibition is unknown. Here, we report the single-particle cryo-electron microscopy structures of PP2A:B55 bound to phosphorylated ARPP19 and FAM122A. Consistent with our complementary NMR spectroscopy studies, both intrinsically disordered proteins bind PP2A:B55, but do so in highly distinct manners, leveraging multiple distinct binding sites on B55. Our extensive structural, biophysical and biochemical data explain how substrates and inhibitors are recruited to PP2A:B55 and provide a molecular roadmap for the development of therapeutic interventions for PP2A:B55-related diseases.
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Affiliation(s)
- Sathish K R Padi
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Margaret R Vos
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Rachel J Godek
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | | | - Thomas Kruse
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jamin B Hein
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Nilsson
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Rebecca Page
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA.
| | - Wolfgang Peti
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA.
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19
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Choy MS, Srivastava G, Robinson LC, Tatchell K, Page R, Peti W. The SDS22:PP1:I3 complex: SDS22 binding to PP1 loosens the active site metal to prime metal exchange. J Biol Chem 2024; 300:105515. [PMID: 38042495 PMCID: PMC10776994 DOI: 10.1016/j.jbc.2023.105515] [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: 10/13/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/04/2023] Open
Abstract
SDS22 and Inhibitor-3 (I3) are two ancient regulators of protein phosphatase 1 (PP1) that regulate multiple essential biological processes. Both SDS22 and I3 form stable dimeric complexes with PP1; however, and atypically for PP1 regulators, they also form a triple complex, where both proteins bind to PP1 simultaneously (SPI complex). Here we report the crystal structure of the SPI complex. While both regulators bind PP1 in conformations identical to those observed in their individual PP1 complexes, PP1 adopts the SDS22-bound conformation, which lacks its M1 metal. Unexpectedly, surface plasmon resonance (SPR) revealed that the affinity of I3 for the SDS22:PP1 complex is ∼10-fold lower than PP1 alone. We show that this change in binding affinity is solely due to the interaction of I3 with the PP1 active site, specifically PP1's M2 metal, demonstrating that SDS22 likely allows for PP1 M2 metal exchange and thus PP1 biogenesis.
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Affiliation(s)
- Meng S Choy
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Gautam Srivastava
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Lucy C Robinson
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, USA
| | - Kelly Tatchell
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, USA
| | - Rebecca Page
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut, USA.
| | - Wolfgang Peti
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA.
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20
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Li YM, He HW, Zhang N. Targeting Protein Phosphatases for the Treatment of Chronic Liver Disease. Curr Drug Targets 2024; 25:171-189. [PMID: 38213163 DOI: 10.2174/0113894501278886231221092522] [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: 10/12/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024]
Abstract
There exists a huge number of patients suffering from chronic liver disease worldwide. As a disease with high incidence and mortality worldwide, strengthening the research on the pathogenesis of chronic liver disease and the development of novel drugs is an important issue related to the health of all human beings. Phosphorylation modification of proteins plays a crucial role in cellular signal transduction, and phosphatases are involved in the development of liver diseases. Therefore, this article summarized the important role of protein phosphatases in chronic liver disease with the aim of facilitating the development of drugs targeting protein phosphatases for the treatment of chronic liver disease.
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Affiliation(s)
- Yi-Ming Li
- NHC Key Laboratory of Biotechnology for Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Hong-Wei He
- NHC Key Laboratory of Biotechnology for Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Na Zhang
- NHC Key Laboratory of Biotechnology for Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
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21
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High-resolution structures of two phosphatase-inhibitor complexes. Nature 2023:10.1038/d41586-023-03833-6. [PMID: 38123854 DOI: 10.1038/d41586-023-03833-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
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22
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Iannotta L, Emanuele M, Favetta G, Tombesi G, Vandewynckel L, Lara Ordóñez AJ, Saliou JM, Drouyer M, Sibran W, Civiero L, Nichols RJ, Athanasopoulos PS, Kortholt A, Chartier-Harlin MC, Greggio E, Taymans JM. PAK6-mediated phosphorylation of PPP2R2C regulates LRRK2-PP2A complex formation. Front Mol Neurosci 2023; 16:1269387. [PMID: 38169846 PMCID: PMC10759229 DOI: 10.3389/fnmol.2023.1269387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are a common cause of inherited and sporadic Parkinson's disease (PD) and previous work suggests that dephosphorylation of LRRK2 at a cluster of heterologous phosphosites is associated to disease. We have previously reported subunits of the PP1 and PP2A classes of phosphatases as well as the PAK6 kinase as regulators of LRRK2 dephosphorylation. We therefore hypothesized that PAK6 may have a functional link with LRRK2's phosphatases. To investigate this, we used PhosTag gel electrophoresis with purified proteins and found that PAK6 phosphorylates the PP2A regulatory subunit PPP2R2C at position S381. While S381 phosphorylation did not affect PP2A holoenzyme formation, a S381A phosphodead PPP2R2C showed impaired binding to LRRK2. Also, PAK6 kinase activity changed PPP2R2C subcellular localization in a S381 phosphorylation-dependent manner. Finally, PAK6-mediated dephosphorylation of LRRK2 was unaffected by phosphorylation of PPP2R2C at S381, suggesting that the previously reported mechanism whereby PAK6-mediated phosphorylation of 14-3-3 proteins promotes 14-3-3-LRRK2 complex dissociation and consequent exposure of LRRK2 phosphosites for dephosphorylation is dominant. Taken together, we conclude that PAK6-mediated phosphorylation of PPP2R2C influences the recruitment of PPP2R2C to the LRRK2 complex and PPP2R2C subcellular localization, pointing to an additional mechanism in the fine-tuning of LRRK2 phosphorylation.
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Affiliation(s)
- Lucia Iannotta
- Department of Biology, University of Padova, Padua, Italy
- National Research Council, c/o Humanitas Research Hospital, Institute of Neuroscience, Rozzano, Italy
| | - Marco Emanuele
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Giulia Favetta
- Department of Biology, University of Padova, Padua, Italy
| | - Giulia Tombesi
- Department of Biology, University of Padova, Padua, Italy
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Laurine Vandewynckel
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | | | - Jean-Michel Saliou
- University of Lille, CNRS, Inserm, CHU Lille, Institute Pasteur de Lille, US 41 – UAR 2014 – PLBS, Lille, France
| | - Matthieu Drouyer
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - William Sibran
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Laura Civiero
- Department of Biology, University of Padova, Padua, Italy
- IRCSS, San Camillo Hospital, Venice, Italy
| | - R. Jeremy Nichols
- Department of Pathology, Stanford University, Stanford, CA, United States
| | | | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, Groningen, Netherlands
- YETEM-Innovative Technologies Application and Research Centre, Suleyman Demirel University West Campus, Isparta, Turkey
| | | | - Elisa Greggio
- Department of Biology, University of Padova, Padua, Italy
- Centro Studi per la Neurodegenerazione (CESNE), University of Padova, Padua, Italy
| | - Jean-Marc Taymans
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
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23
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Hicks D, Giresh K, Wrischnik LA, Weiser DC. The PPP1R15 Family of eIF2-alpha Phosphatase Targeting Subunits (GADD34 and CReP). Int J Mol Sci 2023; 24:17321. [PMID: 38139150 PMCID: PMC10743859 DOI: 10.3390/ijms242417321] [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: 10/28/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The vertebrate PPP1R15 family consists of the proteins GADD34 (growth arrest and DNA damage-inducible protein 34, the product of the PPP1R15A gene) and CReP (constitutive repressor of eIF2α phosphorylation, the product of the PPP1R15B gene), both of which function as targeting/regulatory subunits for protein phosphatase 1 (PP1) by regulating subcellular localization, modulating substrate specificity and assembling complexes with target proteins. The primary cellular function of these proteins is to facilitate the dephosphorylation of eukaryotic initiation factor 2-alpha (eIF2α) by PP1 during cell stress. In this review, we will provide a comprehensive overview of the cellular function, biochemistry and pharmacology of GADD34 and CReP, starting with a brief introduction of eIF2α phosphorylation via the integrated protein response (ISR). We discuss the roles GADD34 and CReP play as feedback inhibitors of the unfolded protein response (UPR) and highlight the critical function they serve as inhibitors of the PERK-dependent branch, which is particularly important since it can mediate cell survival or cell death, depending on how long the stressful stimuli lasts, and GADD34 and CReP play key roles in fine-tuning this cellular decision. We briefly discuss the roles of GADD34 and CReP homologs in model systems and then focus on what we have learned about their function from knockout mice and human patients, followed by a brief review of several diseases in which GADD34 and CReP have been implicated, including cancer, diabetes and especially neurodegenerative disease. Because of the potential importance of GADD34 and CReP in aspects of human health and disease, we will discuss several pharmacological inhibitors of GADD34 and/or CReP that show promise as treatments and the controversies as to their mechanism of action. This review will finish with a discussion of the biochemical properties of GADD34 and CReP, their regulation and the additional interacting partners that may provide insight into the roles these proteins may play in other cellular pathways. We will conclude with a brief outline of critical areas for future study.
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Affiliation(s)
- Danielle Hicks
- Department of Science, Mathematics and Engineering, Modesto Junior College, Modesto, CA 95350, USA
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, USA
| | - Krithika Giresh
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, USA
| | - Lisa A. Wrischnik
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, USA
| | - Douglas C. Weiser
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, USA
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24
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Bahar I, Banerjee A, Mathew S, Naqvi M, Yilmaz S, Zachoropoulou M, Doruker P, Kumita J, Yang SH, Gur M, Itzhaki L, Gordon R. Influence of Point Mutations on PR65 Conformational Adaptability: Insights from Nanoaperture Optical Tweezer Experiments and Molecular Simulations. RESEARCH SQUARE 2023:rs.3.rs-3599809. [PMID: 38014259 PMCID: PMC10680943 DOI: 10.21203/rs.3.rs-3599809/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
PR65 is the HEAT-repeat scaffold subunit of the heterotrimeric protein phosphatase 2A (PP2A) and an archetypal tandem-repeat protein, forming a spring-like architecture. PR65 conformational mechanics play a crucial role in PP2A function by opening/closing the substrate-binding/catalysis interface. Using in-silico saturation mutagenesis we identified "hinge" residues of PR65, whose substitutions are predicted to restrict its conformational adaptability and thereby disrupt PP2A function. Molecular simulations revealed that a subset of hinge mutations stabilized the extended/open conformation, whereas another had the opposite effect. By trapping in nanoaperture optical tweezer, we characterized PR65 motion and showed that the former mutants exhibited higher corner frequencies and lower translational scattering, indicating a shift towards extended conformations, whereas the latter showed the opposite behavior. Thus, experiments confirm the conformations predicted computationally. The study highlights the utility of nanoaperture-based tweezers for exploring structure and dynamics, and the power of integrating this single-molecule method with in silico approaches.
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25
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Geng Q, Kong Y, Li W, Zhang J, Ma H, Zhang Y, Da L, Zhao Y, Du H. Dynamic Phosphorylation of G9a Regulates its Repressive Activity on Chromatin Accessibility and Mitotic Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303224. [PMID: 37661576 PMCID: PMC10602519 DOI: 10.1002/advs.202303224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/18/2023] [Indexed: 09/05/2023]
Abstract
Phosphorylation of Ser10 of histone H3 (H3S10p), together with the adjacent methylation of Lys9 (H3K9me), has been proposed to function as a 'phospho-methyl switch' to regulate mitotic chromatin architecture. Despite of immense understanding of the roles of H3S10 phosphorylation, how H3K9me2 are dynamically regulated during mitosis is poorly understood. Here, it is identified that Plk1 kinase phosphorylates the H3K9me1/2 methyltransferase G9a/EHMT2 at Thr1045 (pT1045) during early mitosis, which attenuates its catalytic activity toward H3K9me2. Cells bearing Thr1045 phosphomimic mutant of G9a (T1045E) show decreased H3K9me2 levels, increased chromatin accessibility, and delayed mitotic progression. By contrast, dephosphorylation of pT1045 during late mitosis by the protein phosphatase PPP2CB reactivates G9a activity and upregulates H3K9me2 levels, correlated with decreased levels of H3S10p. Therefore, the results provide a mechanistic explanation of the essential of a 'phospho-methyl switch' and highlight the importance of Plk1 and PPP2CB-mediated dynamic regulation of G9a activity in chromatin organization and mitotic progression.
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Affiliation(s)
- Qizhi Geng
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesHubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan Hospital of Wuhan UniversityFrontier Science Center for Immunology and MetabolismRNA InstituteWuhan UniversityWuhan430072China
| | - Yue‐Yu Kong
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesHubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan Hospital of Wuhan UniversityFrontier Science Center for Immunology and MetabolismRNA InstituteWuhan UniversityWuhan430072China
| | - Weizhe Li
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesHubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan Hospital of Wuhan UniversityFrontier Science Center for Immunology and MetabolismRNA InstituteWuhan UniversityWuhan430072China
| | - Jianhao Zhang
- School of Life Sciences and BiotechnologyShanghai JiaoTong UniversityShanghai200240China
| | - Haoli Ma
- Hubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan Hospital of Wuhan UniversityWuhan UniversityWuhan430071China
| | - Yuhang Zhang
- School of Life Sciences and BiotechnologyShanghai JiaoTong UniversityShanghai200240China
| | - Lin‐Tai Da
- Shanghai Center for Systems BiomedicineShanghai JiaoTong UniversityShanghai200240China
| | - Yan Zhao
- Hubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan Hospital of Wuhan UniversityWuhan UniversityWuhan430071China
| | - Hai‐Ning Du
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesHubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan Hospital of Wuhan UniversityFrontier Science Center for Immunology and MetabolismRNA InstituteWuhan UniversityWuhan430072China
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Egbert JR, Silbern I, Uliasz TF, Lowther KM, Yee SP, Urlaub H, Jaffe LA. Phosphatases modified by LH signaling in ovarian follicles: testing their role in regulating the NPR2 guanylyl cyclase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544636. [PMID: 37333193 PMCID: PMC10274890 DOI: 10.1101/2023.06.12.544636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
In response to luteinizing hormone, multiple proteins in rat and mouse granulosa cells are rapidly dephosphorylated, but the responsible phosphatases remain to be identified. Because the phosphorylation state of phosphatases can regulate their interaction with substrates, we searched for phosphatases that might function in LH signaling by using quantitative mass spectrometry. We identified all proteins in rat ovarian follicles whose phosphorylation state changed detectably in response to a 30-minute exposure to LH, and within this list, identified protein phosphatases or phosphatase regulatory subunits that showed changes in phosphorylation. Phosphatases in the PPP family were of particular interest because of their requirement for dephosphorylating the natriuretic peptide receptor 2 (NPR2) guanylyl cyclase in the granulosa cells, which triggers oocyte meiotic resumption. Among the PPP family regulatory subunits, PPP1R12A and PPP2R5D showed the largest increases in phosphorylation, with 4-10 fold increases in signal intensity on several sites. Although follicles from mice in which these phosphorylations were prevented by serine-to-alanine mutations in either Ppp1r12a or Ppp2r5d showed normal LH-induced NPR2 dephosphorylation, these regulatory subunits and others could act redundantly to dephosphorylate NPR2. Our identification of phosphatases and other proteins whose phosphorylation state is rapidly modified by LH provides clues about multiple signaling pathways in ovarian follicles. Summary sentence Quantitative mass spectrometric analysis of phosphatases whose phosphorylation state is rapidly modified by luteinizing hormone provides clues about how LH signaling dephosphorylates NPR2 as well as a resource for future studies.
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Affiliation(s)
- Jeremy R. Egbert
- Department of Cell Biology, University of Connecticut Health Center, Farmington CT 06030 USA
| | - Ivan Silbern
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Goettingen, Germany
- Institute of Clinical Chemistry, University Medical Center Goettingen, 37075 Goettingen, Germany
| | - Tracy F. Uliasz
- Department of Cell Biology, University of Connecticut Health Center, Farmington CT 06030 USA
| | - Katie M. Lowther
- Department of Cell Biology, University of Connecticut Health Center, Farmington CT 06030 USA
- Center for Mouse Genome Modification, University of Connecticut Health Center, Farmington CT 06030 USA
| | - Siu-Pok Yee
- Department of Cell Biology, University of Connecticut Health Center, Farmington CT 06030 USA
- Center for Mouse Genome Modification, University of Connecticut Health Center, Farmington CT 06030 USA
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Goettingen, Germany
- Institute of Clinical Chemistry, University Medical Center Goettingen, 37075 Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Laurinda A. Jaffe
- Department of Cell Biology, University of Connecticut Health Center, Farmington CT 06030 USA
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27
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Peris I, Romero-Murillo S, Vicente C, Narla G, Odero MD. Regulation and role of the PP2A-B56 holoenzyme family in cancer. Biochim Biophys Acta Rev Cancer 2023; 1878:188953. [PMID: 37437699 DOI: 10.1016/j.bbcan.2023.188953] [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: 05/14/2023] [Revised: 07/07/2023] [Accepted: 07/08/2023] [Indexed: 07/14/2023]
Abstract
Protein phosphatase 2A (PP2A) inactivation is common in cancer, leading to sustained activation of pro-survival and growth-promoting pathways. PP2A consists of a scaffolding A-subunit, a catalytic C-subunit, and a regulatory B-subunit. The functional complexity of PP2A holoenzymes arises mainly through the vast repertoire of regulatory B-subunits, which determine both their substrate specificity and their subcellular localization. Therefore, a major challenge for developing more effective therapeutic strategies for cancer is to identify the specific PP2A complexes to be targeted. Of note, the development of small molecules specifically directed at PP2A-B56α has opened new therapeutic avenues in both solid and hematological tumors. Here, we focus on the B56/PR61 family of PP2A regulatory subunits, which have a central role in directing PP2A tumor suppressor activity. We provide an overview of the mechanisms controlling the formation and regulation of these complexes, the pathways they control, and the mechanisms underlying their deregulation in cancer.
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Affiliation(s)
- Irene Peris
- Department of Biochemistry and Genetics, University of Navarra, Pamplona, Spain; Centro de Investigación Médica Aplicada (CIMA), University of Navarra, Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain.
| | - Silvia Romero-Murillo
- Department of Biochemistry and Genetics, University of Navarra, Pamplona, Spain; Centro de Investigación Médica Aplicada (CIMA), University of Navarra, Pamplona, Spain
| | - Carmen Vicente
- Centro de Investigación Médica Aplicada (CIMA), University of Navarra, Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Goutham Narla
- Division of Genetic Medicine, Department of Internal Medicine, The University of Michigan Medical School, Ann Arbor, MI, USA
| | - Maria D Odero
- Department of Biochemistry and Genetics, University of Navarra, Pamplona, Spain; Centro de Investigación Médica Aplicada (CIMA), University of Navarra, Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid, Spain.
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28
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Smolen KA, Papke CM, Swingle MR, Musiyenko A, Li C, Salter EA, Camp AD, Honkanen RE, Kettenbach AN. Quantitative proteomics and phosphoproteomics of PP2A-PPP2R5D variants reveal deregulation of RPS6 phosphorylation via converging signaling cascades. J Biol Chem 2023; 299:105154. [PMID: 37572851 PMCID: PMC10485637 DOI: 10.1016/j.jbc.2023.105154] [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: 01/11/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/14/2023] Open
Abstract
Genetic germline variants of PPP2R5D (encoding: phosphoprotein phosphatase 2 regulatory protein 5D) result in PPP2R5D-related disorder (Jordan's Syndrome), which is characterized by intellectual disability, hypotonia, seizures, macrocephaly, autism spectrum disorder, and delayed motor skill development. The disorder originates from de novo single nucleotide mutations, generating missense variants that act in a dominant manner. Pathogenic mutations altering 13 different amino acids have been identified, with the E198K variant accounting for ∼40% of reported cases. However, the generation of a heterozygous E198K variant cell line to study the molecular effects of the pathogenic mutation has been challenging. Here, we use CRISPR-PRIME genomic editing to introduce a transition (c.592G>A) in a single PPP2R5D allele in HEK293 cells, generating E198K-heterozygous lines to complement existing E420K variant lines. We generate global protein and phosphorylation profiles of WT, E198K, and E420K cell lines and find unique and shared changes between variants and WT cells in kinase- and phosphatase-controlled signaling cascades. We observed ribosomal protein S6 (RPS6) hyperphosphorylation as a shared signaling alteration, indicative of increased ribosomal protein S6-kinase activity. Treatment with rapamycin or an RPS6-kinase inhibitor (LY2584702) suppressed RPS6 phosphorylation in both, suggesting upstream activation of mTORC1/p70S6K. Intriguingly, our data suggests ERK-dependent activation of mTORC1 in both E198K and E420K variant cells, with additional AKT-mediated mTORC1 activation in the E420K variant. Thus, although upstream activation of mTORC1 differs between PPP2R5D-related disorder genotypes, inhibition of mTORC1 or RPS6 kinases warrants further investigation as potential therapeutic strategies for patients.
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Affiliation(s)
- Kali A Smolen
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Cinta M Papke
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Mark R Swingle
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Alla Musiyenko
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Chenchen Li
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - E Alan Salter
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Ashley D Camp
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Richard E Honkanen
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA.
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA.
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29
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Padi SK, Vos MR, Godek RJ, Fuller JR, Kruse T, Hein JB, Nilsson J, Kelker MS, Page R, Peti W. Cryo-EM structures of PP2A:B55-FAM122A and PP2A:B55-ARPP19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555365. [PMID: 37693408 PMCID: PMC10491220 DOI: 10.1101/2023.08.31.555365] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Progression through the cell cycle is controlled by regulated and abrupt changes in phosphorylation.1 Mitotic entry is initiated by increased phosphorylation of mitotic proteins, a process driven by kinases,2 while mitotic exit is achieved by counteracting dephosphorylation, a process driven by phosphatases, especially PP2A:B55.3 While the role of kinases in mitotic entry is well-established, recent data have shown that mitosis is only successfully initiated when the counterbalancing phosphatases are also inhibited.4 For PP2A:B55, inhibition is achieved by the two intrinsically disordered proteins (IDPs), ARPP19 (phosphorylation-dependent)6,7 and FAM122A5 (inhibition is phosphorylation-independent). Despite their critical roles in mitosis, the mechanisms by which they achieve PP2A:B55 inhibition is unknown. Here, we report the cryo-electron microscopy structures of PP2A:B55 bound to phosphorylated ARPP19 and FAM122A. Consistent with our complementary NMR spectroscopy studies both IDPs bind PP2A:B55, but do so in highly distinct manners, unexpectedly leveraging multiple distinct binding sites on B55. Our extensive structural, biophysical and biochemical data explain how substrates and inhibitors are recruited to PP2A:B55 and provides a molecular roadmap for the development of therapeutic interventions for PP2A:B55 related diseases.
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Affiliation(s)
- Sathish K.R. Padi
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, USA
| | - Margaret R. Vos
- Department of Cell Biology, University of Connecticut Health Center, Farmington, USA
| | - Rachel J. Godek
- Department of Cell Biology, University of Connecticut Health Center, Farmington, USA
| | | | - Thomas Kruse
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jamin B. Hein
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Nilsson
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Rebecca Page
- Department of Cell Biology, University of Connecticut Health Center, Farmington, USA
| | - Wolfgang Peti
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, USA
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30
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Rasool RU, O'Connor CM, Das CK, Alhusayan M, Verma BK, Islam S, Frohner IE, Deng Q, Mitchell-Velasquez E, Sangodkar J, Ahmed A, Linauer S, Mudrak I, Rainey J, Zawacki KP, Suhan TK, Callahan CG, Rebernick R, Natesan R, Siddiqui J, Sauter G, Thomas D, Wang S, Taylor DJ, Simon R, Cieslik M, Chinnaiyan AM, Busino L, Ogris E, Narla G, Asangani IA. Loss of LCMT1 and biased protein phosphatase 2A heterotrimerization drive prostate cancer progression and therapy resistance. Nat Commun 2023; 14:5253. [PMID: 37644036 PMCID: PMC10465527 DOI: 10.1038/s41467-023-40760-6] [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: 01/03/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Loss of the tumor suppressive activity of the protein phosphatase 2A (PP2A) is associated with cancer, but the underlying molecular mechanisms are unclear. PP2A holoenzyme comprises a heterodimeric core, a scaffolding A subunit and a catalytic C subunit, and one of over 20 distinct substrate-directing regulatory B subunits. Methylation of the C subunit regulates PP2A heterotrimerization, affecting B subunit binding and substrate specificity. Here, we report that the leucine carboxy methyltransferase (LCMT1), which methylates the L309 residue of the C subunit, acts as a suppressor of androgen receptor (AR) addicted prostate cancer (PCa). Decreased methyl-PP2A-C levels in prostate tumors is associated with biochemical recurrence and metastasis. Silencing LCMT1 increases AR activity and promotes castration-resistant prostate cancer growth. LCMT1-dependent methyl-sensitive AB56αCme heterotrimers target AR and its critical coactivator MED1 for dephosphorylation, resulting in the eviction of the AR-MED1 complex from chromatin and loss of target gene expression. Mechanistically, LCMT1 is regulated by S6K1-mediated phosphorylation-induced degradation requiring the β-TRCP, leading to acquired resistance to anti-androgens. Finally, feedforward stabilization of LCMT1 by small molecule activator of phosphatase (SMAP) results in attenuation of AR-signaling and tumor growth inhibition in anti-androgen refractory PCa. These findings highlight methyl-PP2A-C as a prognostic marker and that the loss of LCMT1 is a major determinant in AR-addicted PCa, suggesting therapeutic potential for AR degraders or PP2A modulators in prostate cancer treatment.
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Affiliation(s)
- Reyaz Ur Rasool
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA, 19104, USA
| | - Caitlin M O'Connor
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Chandan Kanta Das
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA, 19104, USA
| | - Mohammed Alhusayan
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA, 19104, USA
| | - Brijesh Kumar Verma
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA, 19104, USA
| | - Sehbanul Islam
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA, 19104, USA
| | - Ingrid E Frohner
- Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Dr. Bohr-Gasse 9/2, Vienna, 1030, Austria
| | - Qu Deng
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA, 19104, USA
| | - Erick Mitchell-Velasquez
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA, 19104, USA
| | - Jaya Sangodkar
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Aqila Ahmed
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sarah Linauer
- Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Dr. Bohr-Gasse 9/2, Vienna, 1030, Austria
| | - Ingrid Mudrak
- Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Dr. Bohr-Gasse 9/2, Vienna, 1030, Austria
| | - Jessica Rainey
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA, 19104, USA
| | - Kaitlin P Zawacki
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Tahra K Suhan
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Catherine G Callahan
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ryan Rebernick
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Ramakrishnan Natesan
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA, 19104, USA
| | - Javed Siddiqui
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Dafydd Thomas
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Shaomeng Wang
- Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Derek J Taylor
- Department of Biochemistry Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Marcin Cieslik
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Arul M Chinnaiyan
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Luca Busino
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA, 19104, USA
| | - Egon Ogris
- Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Dr. Bohr-Gasse 9/2, Vienna, 1030, Austria.
| | - Goutham Narla
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Irfan A Asangani
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA, 19104, USA.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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31
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Mansour H, Cabezas-Cruz A, Peucelle V, Farce A, Salomé-Desnoulez S, Metatla I, Guerrera IC, Hollin T, Khalife J. Characterization of GEXP15 as a Potential Regulator of Protein Phosphatase 1 in Plasmodium falciparum. Int J Mol Sci 2023; 24:12647. [PMID: 37628837 PMCID: PMC10454571 DOI: 10.3390/ijms241612647] [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] [Received: 07/04/2023] [Revised: 07/29/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
The Protein Phosphatase type 1 catalytic subunit (PP1c) (PF3D7_1414400) operates in combination with various regulatory proteins to specifically direct and control its phosphatase activity. However, there is little information about this phosphatase and its regulators in the human malaria parasite, Plasmodium falciparum. To address this knowledge gap, we conducted a comprehensive investigation into the structural and functional characteristics of a conserved Plasmodium-specific regulator called Gametocyte EXported Protein 15, GEXP15 (PF3D7_1031600). Through in silico analysis, we identified three significant regions of interest in GEXP15: an N-terminal region housing a PP1-interacting RVxF motif, a conserved domain whose function is unknown, and a GYF-like domain that potentially facilitates specific protein-protein interactions. To further elucidate the role of GEXP15, we conducted in vitro interaction studies that demonstrated a direct interaction between GEXP15 and PP1 via the RVxF-binding motif. This interaction was found to enhance the phosphatase activity of PP1. Additionally, utilizing a transgenic GEXP15-tagged line and live microscopy, we observed high expression of GEXP15 in late asexual stages of the parasite, with localization predominantly in the nucleus. Immunoprecipitation assays followed by mass spectrometry analyses revealed the interaction of GEXP15 with ribosomal- and RNA-binding proteins. Furthermore, through pull-down analyses of recombinant functional domains of His-tagged GEXP15, we confirmed its binding to the ribosomal complex via the GYF domain. Collectively, our study sheds light on the PfGEXP15-PP1-ribosome interaction, which plays a crucial role in protein translation. These findings suggest that PfGEXP15 could serve as a potential target for the development of malaria drugs.
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Affiliation(s)
- Hala Mansour
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000 Lille, France; (H.M.); (V.P.)
| | - Alejandro Cabezas-Cruz
- ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700 Maisons-Alfort, France;
| | - Véronique Peucelle
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000 Lille, France; (H.M.); (V.P.)
| | - Amaury Farce
- Univ. Lille, Inserm, CHU Lille, U1286–Infinite–Institute for Translational Research in Inflammation, 59000 Lille, France;
| | - Sophie Salomé-Desnoulez
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41–UAR 2014–PLBS, 59000 Lille, France;
| | - Ines Metatla
- Proteomics Platform Necker, Université Paris Cité–Structure Fédérative de Recherche Necker, INSERM US24/CNRS UAR3633, 75015 Paris, France; (I.M.); (I.C.G.)
| | - Ida Chiara Guerrera
- Proteomics Platform Necker, Université Paris Cité–Structure Fédérative de Recherche Necker, INSERM US24/CNRS UAR3633, 75015 Paris, France; (I.M.); (I.C.G.)
| | - Thomas Hollin
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000 Lille, France; (H.M.); (V.P.)
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Jamal Khalife
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000 Lille, France; (H.M.); (V.P.)
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32
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Mariano NC, Rusin SF, Nasa I, Kettenbach AN. Inducible Protein Degradation as a Strategy to Identify Phosphoprotein Phosphatase 6 Substrates in RAS-Mutant Colorectal Cancer Cells. Mol Cell Proteomics 2023; 22:100614. [PMID: 37392812 PMCID: PMC10400926 DOI: 10.1016/j.mcpro.2023.100614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 06/13/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023] Open
Abstract
Protein phosphorylation is an essential regulatory mechanism that controls most cellular processes, including cell cycle progression, cell division, and response to extracellular stimuli, among many others, and is deregulated in many diseases. Protein phosphorylation is coordinated by the opposing activities of protein kinases and protein phosphatases. In eukaryotic cells, most serine/threonine phosphorylation sites are dephosphorylated by members of the Phosphoprotein Phosphatase (PPP) family. However, we only know for a few phosphorylation sites which specific PPP dephosphorylates them. Although natural compounds such as calyculin A and okadaic acid inhibit PPPs at low nanomolar concentrations, no selective chemical PPP inhibitors exist. Here, we demonstrate the utility of endogenous tagging of genomic loci with an auxin-inducible degron (AID) as a strategy to investigate specific PPP signaling. Using Protein Phosphatase 6 (PP6) as an example, we demonstrate how rapidly inducible protein degradation can be employed to identify dephosphorylation sites and elucidate PP6 biology. Using genome editing, we introduce AID-tags into each allele of the PP6 catalytic subunit (PP6c) in DLD-1 cells expressing the auxin receptor Tir1. Upon rapid auxin-induced degradation of PP6c, we perform quantitative mass spectrometry-based proteomics and phosphoproteomics to identify PP6 substrates in mitosis. PP6 is an essential enzyme with conserved roles in mitosis and growth signaling. Consistently, we identify candidate PP6c-dependent dephosphorylation sites on proteins implicated in coordinating the mitotic cell cycle, cytoskeleton, gene expression, and mitogen-activated protein kinase (MAPK) and Hippo signaling. Finally, we demonstrate that PP6c opposes the activation of large tumor suppressor 1 (LATS1) by dephosphorylating Threonine 35 (T35) on Mps One Binder (MOB1), thereby blocking the interaction of MOB1 and LATS1. Our analyses highlight the utility of combining genome engineering, inducible degradation, and multiplexed phosphoproteomics to investigate signaling by individual PPPs on a global level, which is currently limited by the lack of tools for specific interrogation.
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Affiliation(s)
- Natasha C Mariano
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Scott F Rusin
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Isha Nasa
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA; Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA; Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA.
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33
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Nguyen H, Kettenbach AN. Substrate and phosphorylation site selection by phosphoprotein phosphatases. Trends Biochem Sci 2023; 48:713-725. [PMID: 37173206 PMCID: PMC10523993 DOI: 10.1016/j.tibs.2023.04.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/15/2023]
Abstract
Dynamic protein phosphorylation and dephosphorylation are essential regulatory mechanisms that ensure proper cellular signaling and biological functions. Deregulation of either reaction has been implicated in several human diseases. Here, we focus on the mechanisms that govern the specificity of the dephosphorylation reaction. Most cellular serine/threonine dephosphorylation is catalyzed by 13 highly conserved phosphoprotein phosphatase (PPP) catalytic subunits, which form hundreds of holoenzymes by binding to regulatory and scaffolding subunits. PPP holoenzymes recognize phosphorylation site consensus motifs and interact with short linear motifs (SLiMs) or structural elements distal to the phosphorylation site. We review recent advances in understanding the mechanisms of PPP site-specific dephosphorylation preference and substrate recruitment and highlight examples of their interplay in the regulation of cell division.
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Affiliation(s)
- Hieu Nguyen
- Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Arminja N Kettenbach
- Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA; Dartmouth Cancer Center, Lebanon, NH 03756, USA.
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34
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Heidari B, Nemie-Feyissa D, Lillo C. Distinct Clades of Protein Phosphatase 2A Regulatory B'/B56 Subunits Engage in Different Physiological Processes. Int J Mol Sci 2023; 24:12255. [PMID: 37569631 PMCID: PMC10418862 DOI: 10.3390/ijms241512255] [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: 06/30/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Protein phosphatase 2A (PP2A) is a strongly conserved and major protein phosphatase in all eukaryotes. The canonical PP2A complex consists of a catalytic (C), scaffolding (A), and regulatory (B) subunit. Plants have three groups of evolutionary distinct B subunits: B55, B' (B56), and B''. Here, the Arabidopsis B' group is reviewed and compared with other eukaryotes. Members of the B'α/B'β clade are especially important for chromatid cohesion, and dephosphorylation of transcription factors that mediate brassinosteroid (BR) signaling in the nucleus. Other B' subunits interact with proteins at the cell membrane to dampen BR signaling or harness immune responses. The transition from vegetative to reproductive phase is influenced differentially by distinct B' subunits; B'α and B'β being of little importance, whereas others (B'γ, B'ζ, B'η, B'θ, B'κ) promote transition to flowering. Interestingly, the latter B' subunits have three motifs in a conserved manner, i.e., two docking sites for protein phosphatase 1 (PP1), and a POLO consensus phosphorylation site between these motifs. This supports the view that a conserved PP1-PP2A dephosphorelay is important in a variety of signaling contexts throughout eukaryotes. A profound understanding of these regulators may help in designing future crops and understand environmental issues.
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Affiliation(s)
| | | | - Cathrine Lillo
- IKBM, Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, 4036 Stavanger, Norway; (B.H.); (D.N.-F.)
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35
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Vertyshev AY, Akberdin IR, Kolpakov FA. Numerous Trigger-like Interactions of Kinases/Protein Phosphatases in Human Skeletal Muscles Can Underlie Transient Processes in Activation of Signaling Pathways during Exercise. Int J Mol Sci 2023; 24:11223. [PMID: 37446402 DOI: 10.3390/ijms241311223] [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: 01/27/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Optimizing physical training regimens to increase muscle aerobic capacity requires an understanding of the internal processes that occur during exercise that initiate subsequent adaptation. During exercise, muscle cells undergo a series of metabolic events that trigger downstream signaling pathways and induce the expression of many genes in working muscle fibers. There are a number of studies that show the dependence of changes in the activity of AMP-activated protein kinase (AMPK), one of the mediators of cellular signaling pathways, on the duration and intensity of single exercises. The activity of various AMPK isoforms can change in different directions, increasing for some isoforms and decreasing for others, depending on the intensity and duration of the load. This review summarizes research data on changes in the activity of AMPK, Ca2+/calmodulin-dependent protein kinase II (CaMKII), and other components of the signaling pathways in skeletal muscles during exercise. Based on these data, we hypothesize that the observed changes in AMPK activity may be largely related to metabolic and signaling transients rather than exercise intensity per se. Probably, the main events associated with these transients occur at the beginning of the exercise in a time window of about 1-10 min. We hypothesize that these transients may be partly due to putative trigger-like kinase/protein phosphatase interactions regulated by feedback loops. In addition, numerous dynamically changing factors, such as [Ca2+], metabolite concentration, and reactive oxygen and nitrogen species (RONS), can shift the switching thresholds and change the states of these triggers, thereby affecting the activity of kinases (in particular, AMPK and CaMKII) and phosphatases. The review considers the putative molecular mechanisms underlying trigger-like interactions. The proposed hypothesis allows for a reinterpretation of the experimental data available in the literature as well as the generation of ideas to optimize future training regimens.
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Affiliation(s)
| | - Ilya R Akberdin
- Department of Computational Biology, Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, 354340 Sochi, Russia
- Biosoft.Ru, Ltd., 630058 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Fedor A Kolpakov
- Department of Computational Biology, Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, 354340 Sochi, Russia
- Biosoft.Ru, Ltd., 630058 Novosibirsk, Russia
- Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
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36
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Kieft R, Zhang Y, Yan H, Schmitz RJ, Sabatini R. Knockout of protein phosphatase 1 in Leishmania major reveals its role during RNA polymerase II transcription termination. Nucleic Acids Res 2023; 51:6208-6226. [PMID: 37194692 PMCID: PMC10325913 DOI: 10.1093/nar/gkad394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/26/2023] [Accepted: 05/04/2023] [Indexed: 05/18/2023] Open
Abstract
The genomes of kinetoplastids are organized into polycistronic transcription units that are flanked by a modified DNA base (base J, beta-D-glucosyl-hydroxymethyluracil). Previous work established a role of base J in promoting RNA polymerase II (Pol II) termination in Leishmania major and Trypanosoma brucei. We recently identified a PJW/PP1 complex in Leishmania containing a J-binding protein (JBP3), PP1 phosphatase 1, PP1 interactive-regulatory protein (PNUTS) and Wdr82. Analyses suggested the complex regulates transcription termination by recruitment to termination sites via JBP3-base J interactions and dephosphorylation of proteins, including Pol II, by PP1. However, we never addressed the role of PP1, the sole catalytic component, in Pol II transcription termination. We now demonstrate that deletion of the PP1 component of the PJW/PP1 complex in L. major, PP1-8e, leads to readthrough transcription at the 3'-end of polycistronic gene arrays. We show PP1-8e has in vitro phosphatase activity that is lost upon mutation of a key catalytic residue and associates with PNUTS via the conserved RVxF motif. Additionally, purified PJW complex with associated PP1-8e, but not complex lacking PP1-8e, led to dephosphorylation of Pol II, suggesting a direct role of PNUTS/PP1 holoenzymes in regulating transcription termination via dephosphorylating Pol II in the nucleus.
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Affiliation(s)
- Rudo Kieft
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA30602, USA
| | - Yang Zhang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA30602, USA
| | - Haidong Yan
- Department of Genetics, University of Georgia, Athens, GA30602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA30602, USA
| | - Robert Sabatini
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA30602, USA
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Patil RS, Kovacs-Kasa A, Gorshkov BA, Fulton DJR, Su Y, Batori RK, Verin AD. Serine/Threonine Protein Phosphatases 1 and 2A in Lung Endothelial Barrier Regulation. Biomedicines 2023; 11:1638. [PMID: 37371733 PMCID: PMC10296329 DOI: 10.3390/biomedicines11061638] [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: 05/04/2023] [Revised: 05/28/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Vascular barrier dysfunction is characterized by increased permeability and inflammation of endothelial cells (ECs), which are prominent features of acute lung injury (ALI), acute respiratory distress syndrome (ARDS), and sepsis, and a major complication of the SARS-CoV-2 infection and COVID-19. Functional impairment of the EC barrier and accompanying inflammation arises due to microbial toxins and from white blood cells of the lung as part of a defensive action against pathogens, ischemia-reperfusion or blood product transfusions, and aspiration syndromes-based injury. A loss of barrier function results in the excessive movement of fluid and macromolecules from the vasculature into the interstitium and alveolae resulting in pulmonary edema and collapse of the architecture and function of the lungs, and eventually culminates in respiratory failure. Therefore, EC barrier integrity, which is heavily dependent on cytoskeletal elements (mainly actin filaments, microtubules (MTs), cell-matrix focal adhesions, and intercellular junctions) to maintain cellular contacts, is a critical requirement for the preservation of lung function. EC cytoskeletal remodeling is regulated, at least in part, by Ser/Thr phosphorylation/dephosphorylation of key cytoskeletal proteins. While a large body of literature describes the role of phosphorylation of cytoskeletal proteins on Ser/Thr residues in the context of EC barrier regulation, the role of Ser/Thr dephosphorylation catalyzed by Ser/Thr protein phosphatases (PPases) in EC barrier regulation is less documented. Ser/Thr PPases have been proposed to act as a counter-regulatory mechanism that preserves the EC barrier and opposes EC contraction. Despite the importance of PPases, our knowledge of the catalytic and regulatory subunits involved, as well as their cellular targets, is limited and under-appreciated. Therefore, the goal of this review is to discuss the role of Ser/Thr PPases in the regulation of lung EC cytoskeleton and permeability with special emphasis on the role of protein phosphatase 1 (PP1) and protein phosphatase 2A (PP2A) as major mammalian Ser/Thr PPases. Importantly, we integrate the role of PPases with the structural dynamics of the cytoskeleton and signaling cascades that regulate endothelial cell permeability and inflammation.
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Affiliation(s)
- Rahul S. Patil
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Anita Kovacs-Kasa
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Boris A. Gorshkov
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - David J. R. Fulton
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Department of Pharmacology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Yunchao Su
- Department of Pharmacology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Robert K. Batori
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Alexander D. Verin
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
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Zhang M, Liu C, Zhao L, Zhang X, Su Y. The Emerging Role of Protein Phosphatase in Regeneration. Life (Basel) 2023; 13:life13051216. [PMID: 37240861 DOI: 10.3390/life13051216] [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: 03/31/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Maintaining normal cellular behavior is essential for the survival of organisms. One of the main mechanisms to control cellular behavior is protein phosphorylation. The process of protein phosphorylation is reversible under the regulation of protein kinases and protein phosphatases. The importance of kinases in numerous cellular processes has been well recognized. In recent years, protein phosphatases have also been demonstrated to function actively and specifically in various cellular processes and thus have gained more and more attention from researchers. In the animal kingdom, regeneration frequently occurs to replace or repair damaged or missing tissues. Emerging evidence has revealed that protein phosphatases are crucial for organ regeneration. In this review, after providing a brief overview of the classification of protein phosphatases and their functions in several representative developmental processes, we highlight the critical roles that protein phosphatases play in organ regeneration by summarizing the most recent research on the function and underlying mechanism of protein phosphatase in the regeneration of the liver, bone, neuron, and heart in vertebrates.
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Affiliation(s)
- Meiling Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Chenglin Liu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Long Zhao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Xuejiao Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Ying Su
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
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Srivastava G, Choy MS, Bolik-Coulon N, Page R, Peti W. Inhibitor-3 inhibits Protein Phosphatase 1 via a metal binding dynamic protein-protein interaction. Nat Commun 2023; 14:1798. [PMID: 37002212 PMCID: PMC10066265 DOI: 10.1038/s41467-023-37372-5] [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: 09/01/2022] [Accepted: 02/21/2023] [Indexed: 04/03/2023] Open
Abstract
To achieve substrate specificity, protein phosphate 1 (PP1) forms holoenzymes with hundreds of regulatory and inhibitory proteins. Inhibitor-3 (I3) is an ancient inhibitor of PP1 with putative roles in PP1 maturation and the regulation of PP1 activity. Here, we show that I3 residues 27-68 are necessary and sufficient for PP1 binding and inhibition. In addition to a canonical RVxF motif, which is shared by nearly all PP1 regulators and inhibitors, and a non-canonical SILK motif, I3 also binds PP1 via multiple basic residues that bind directly in the PP1 acidic substrate binding groove, an interaction that provides a blueprint for how substrates bind this groove for dephosphorylation. Unexpectedly, this interaction positions a CCC (cys-cys-cys) motif to bind directly across the PP1 active site. Using biophysical and inhibition assays, we show that the I3 CCC motif binds and inhibits PP1 in an unexpected dynamic, fuzzy manner, via transient engagement of the PP1 active site metals. Together, these data not only provide fundamental insights into the mechanisms by which IDP protein regulators of PP1 achieve inhibition, but also shows that fuzzy interactions between IDPs and their folded binding partners, in addition to enhancing binding affinity, can also directly regulate enzyme activity.
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Affiliation(s)
- Gautam Srivastava
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Meng S Choy
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Nicolas Bolik-Coulon
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Rebecca Page
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Wolfgang Peti
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA.
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KA S, CM P, Swingle MR, A M, C L, AD C, RE H, AN K. Quantitative proteomics and phosphoproteomics of PPP2R5D variants reveal deregulation of RPS6 phosphorylation through converging signaling cascades. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.534397. [PMID: 37034727 PMCID: PMC10081281 DOI: 10.1101/2023.03.27.534397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Variants in the phosphoprotein phosphatase-2 regulatory protein-5D gene ( PPP2R5D ) cause the clinical phenotype of Jordan's Syndrome (PPP2R5D-related disorder), which includes intellectual disability, hypotonia, seizures, macrocephaly, autism spectrum disorder and delayed motor skill development. The disorder originates from de novo single nucleotide mutations, generating missense variants that act in a dominant manner. Pathogenic mutations altering 13 different amino acids have been identified, with the E198K variant accounting for ∼40% of reported cases. Here, we use CRISPR-PRIME genomic editing to introduce a transition (c.592G>A) in the PPP2R5D allele in a heterozygous manner in HEK293 cells, generating E198K-heterozygous lines to complement existing E420K variant lines. We generate global protein and phosphorylation profiles of wild-type, E198K, and E420K cell lines and find unique and shared changes between variants and wild-type cells in kinase- and phosphatase-controlled signaling cascades. As shared signaling alterations, we observed ribosomal protein S6 (RPS6) hyperphosphorylation, indicative of increased ribosomal protein S6-kinase activity. Rapamycin treatment suppressed RPS6 phosphorylation in both, suggesting activation of mTORC1. Intriguingly, our data suggest AKT-dependent (E420K) and -independent (E198K) activation of mTORC1. Thus, although upstream activation of mTORC1 differs between PPP2R5D-related disorder genotypes, treatment with rapamycin or a p70S6K inhibitor warrants further investigation as potential therapeutic strategies for patients.
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Affiliation(s)
- Smolen KA
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Papke CM
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - MR Swingle
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Musiyenko A
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Li C
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Camp AD
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Honkanen RE
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Kettenbach AN
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
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41
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Mariano NC, Rusin SF, Nasa I, Kettenbach AN. Inducible protein degradation as a strategy to identify Phosphoprotein Phosphatase 6 substrates in RAS-mutant colorectal cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.25.534211. [PMID: 36993243 PMCID: PMC10055397 DOI: 10.1101/2023.03.25.534211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Protein phosphorylation is an essential regulatory mechanism that controls most cellular processes, including cell cycle progression, cell division, and response to extracellular stimuli, among many others, and is deregulated in many diseases. Protein phosphorylation is coordinated by the opposing activities of protein kinases and protein phosphatases. In eukaryotic cells, most serine/threonine phosphorylation sites are dephosphorylated by members of the Phosphoprotein Phosphatase (PPP) family. However, we only know for a few phosphorylation sites which specific PPP dephosphorylates them. Although natural compounds such as calyculin A and okadaic acid inhibit PPPs at low nanomolar concentrations, no selective chemical PPP inhibitors exist. Here, we demonstrate the utility of endogenous tagging of genomic loci with an auxin-inducible degron (AID) as a strategy to investigate specific PPP signaling. Using Protein Phosphatase 6 (PP6) as an example, we demonstrate how rapidly inducible protein degradation can be employed to identify dephosphorylation SITES and elucidate PP6 biology. Using genome editing, we introduce AID-tags into each allele of the PP6 catalytic subunit (PP6c) in DLD-1 cells expressing the auxin receptor Tir1. Upon rapid auxin-induced degradation of PP6c, we perform quantitative mass spectrometry-based proteomics and phosphoproteomics to identify PP6 substrates in mitosis. PP6 is an essential enzyme with conserved roles in mitosis and growth signaling. Consistently, we identify candidate PP6c-dependent phosphorylation sites on proteins implicated in coordinating the mitotic cell cycle, cytoskeleton, gene expression, and mitogen-activated protein kinase (MAPK) and Hippo signaling. Finally, we demonstrate that PP6c opposes the activation of large tumor suppressor 1 (LATS1) by dephosphorylating Threonine 35 (T35) on Mps One Binder (MOB1), thereby blocking the interaction of MOB1 and LATS1. Our analyses highlight the utility of combining genome engineering, inducible degradation, and multiplexed phosphoproteomics to investigate signaling by individual PPPs on a global level, which is currently limited by the lack of tools for specific interrogation.
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42
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Arribas RL, Viejo L, Bravo I, Martínez M, Ramos E, Romero A, García-Frutos EM, Janssens V, Montiel C, de Los Ríos C. C-glycosides analogues of the okadaic acid central fragment exert neuroprotection via restoration of PP2A-phosphatase activity: A rational design of potential drugs for Alzheimer's disease targeting tauopathies. Eur J Med Chem 2023; 251:115245. [PMID: 36905916 DOI: 10.1016/j.ejmech.2023.115245] [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] [Received: 10/31/2022] [Revised: 01/24/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
Protein phosphatase 2A (PP2A) is an important Ser/Thr phosphatase that participates in the regulation of multiple cellular processes. This implies that any deficient activity of PP2A is the responsible of severe pathologies. For instance, one of the main histopathological features of Alzheimer's disease is neurofibrillary tangles, which are mainly comprised by hyperphosphorylated forms of tau protein. This altered rate of tau phosphorylation has been correlated with PP2A depression AD patients. With the goal of preventing PP2A inactivation in neurodegeneration scenarios, we have aimed to design, synthesize and evaluate new ligands of PP2A capable of preventing its inhibition. To achieve this goal, the new PP2A ligands present structural similarities with the central fragment C19-C27 of the well-established PP2A inhibitor okadaic acid (OA). Indeed, this central moiety of OA does not exert inhibitory actions. Hence, these compounds lack PP2A-inhibiting structural motifs but, in contrast, compete with PP2A inhibitors, thus recovering phosphatase activity. Proving this hypothesis, most compounds showed a good neuroprotective profile in neurodegeneration models related to PP2A impairment, highlighting derivative 10, named ITH12711, as the most promising one. This compound (1) restored in vitro and cellular PP2A catalytic activity, measured on a phospho-peptide substrate and by western-blot analyses, (2) proved good brain penetration measured by PAMPA, and (3) prevented LPS-induced memory impairment of mice in the object recognition test. Thus, the promising outcomes of the compound 10 validate our rational approach to design new PP2A-activating drugs based on OA central fragment.
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Affiliation(s)
- Raquel L Arribas
- Instituto-Fundación Teófilo Hernando, Universidad Autónoma de Madrid, 28029, Madrid, Spain; Departamento de Ciencias Básicas de la Salud, Universidad Rey Juan Carlos, 28922, Alcorcón, Spain
| | - Lucía Viejo
- Instituto-Fundación Teófilo Hernando, Universidad Autónoma de Madrid, 28029, Madrid, Spain; Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, C/ Diego de León, 62, 28006, Madrid, Spain
| | - Isaac Bravo
- Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, C/ Diego de León, 62, 28006, Madrid, Spain; Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | - Minerva Martínez
- Instituto-Fundación Teófilo Hernando, Universidad Autónoma de Madrid, 28029, Madrid, Spain
| | - Eva Ramos
- Departamento de Farmacología y Toxicología, Facultad de Veterinaria, Universidad Complutense, 28040, Madrid, Spain
| | - Alejandro Romero
- Departamento de Farmacología y Toxicología, Facultad de Veterinaria, Universidad Complutense, 28040, Madrid, Spain
| | - Eva M García-Frutos
- Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain; Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Ctra. Madrid-Barcelona Km.33,600, 28871, Alcalá de Henares, Madrid, Spain
| | - Veerle Janssens
- Department of Cellular & Molecular Medicine, Laboratory of Protein Phosphorylation and Proteomics, KU Leuven, B-3000, Leuven, Belgium; LBI (KU Leuven Brain Institute), B-3000, Leuven, Belgium
| | - Carmen Montiel
- Instituto-Fundación Teófilo Hernando, Universidad Autónoma de Madrid, 28029, Madrid, Spain
| | - Cristóbal de Los Ríos
- Instituto-Fundación Teófilo Hernando, Universidad Autónoma de Madrid, 28029, Madrid, Spain; Departamento de Ciencias Básicas de la Salud, Universidad Rey Juan Carlos, 28922, Alcorcón, Spain; Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, C/ Diego de León, 62, 28006, Madrid, Spain.
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Phosphorylated Peptide Derived from the Myosin Phosphatase Target Subunit Is a Novel Inhibitor of Protein Phosphatase-1. Int J Mol Sci 2023; 24:ijms24054789. [PMID: 36902219 PMCID: PMC10003451 DOI: 10.3390/ijms24054789] [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: 01/19/2023] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Identification of specific protein phosphatase-1 (PP1) inhibitors is of special importance regarding the study of its cellular functions and may have therapeutic values in diseases coupled to signaling processes. In this study, we prove that a phosphorylated peptide of the inhibitory region of myosin phosphatase (MP) target subunit (MYPT1), R690QSRRS(pT696)QGVTL701 (P-Thr696-MYPT1690-701), interacts with and inhibits the PP1 catalytic subunit (PP1c, IC50 = 3.84 µM) and the MP holoenzyme (Flag-MYPT1-PP1c, IC50 = 3.84 µM). Saturation transfer difference NMR measurements established binding of hydrophobic and basic regions of P-Thr696-MYPT1690-701 to PP1c, suggesting interactions with the hydrophobic and acidic substrate binding grooves. P-Thr696-MYPT1690-701 was dephosphorylated by PP1c slowly (t1/2 = 81.6-87.9 min), which was further impeded (t1/2 = 103 min) in the presence of the phosphorylated 20 kDa myosin light chain (P-MLC20). In contrast, P-Thr696-MYPT1690-701 (10-500 µM) slowed down the dephosphorylation of P-MLC20 (t1/2 = 1.69 min) significantly (t1/2 = 2.49-10.06 min). These data are compatible with an unfair competition mechanism between the inhibitory phosphopeptide and the phosphosubstrate. Docking simulations of the PP1c-P-MYPT1690-701 complexes with phosphothreonine (PP1c-P-Thr696-MYPT1690-701) or phosphoserine (PP1c-P-Ser696-MYPT1690-701) suggested their distinct poses on the surface of PP1c. In addition, the arrangements and distances of the surrounding coordinating residues of PP1c around the phosphothreonine or phosphoserine at the active site were distinct, which may account for their different hydrolysis rate. It is presumed that P-Thr696-MYPT1690-701 binds tightly at the active center but the phosphoester hydrolysis is less preferable compared to P-Ser696-MYPT1690-701 or phosphoserine substrates. Moreover, the inhibitory phosphopeptide may serve as a template to synthesize cell permeable PP1-specific peptide inhibitors.
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Simpson LM, Fulcher LJ, Sathe G, Brewer A, Zhao JF, Squair DR, Crooks J, Wightman M, Wood NT, Gourlay R, Varghese J, Soares RF, Sapkota GP. An affinity-directed phosphatase, AdPhosphatase, system for targeted protein dephosphorylation. Cell Chem Biol 2023; 30:188-202.e6. [PMID: 36720221 DOI: 10.1016/j.chembiol.2023.01.003] [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: 01/13/2022] [Revised: 11/07/2022] [Accepted: 01/10/2023] [Indexed: 02/02/2023]
Abstract
Reversible protein phosphorylation, catalyzed by protein kinases and phosphatases, is a fundamental process that controls protein function and intracellular signaling. Failure of phospho-control accounts for many human diseases. While a kinase phosphorylates multiple substrates, a substrate is often phosphorylated by multiple kinases. This renders phospho-control at the substrate level challenging, as it requires inhibition of multiple kinases, which would thus affect other kinase substrates. Here, we describe the development and application of the affinity-directed phosphatase (AdPhosphatase) system for targeted dephosphorylation of specific phospho-substrates. By deploying the Protein Phosphatase 1 or 2A catalytic subunits conjugated to an antigen-stabilized anti-GFP nanobody, we can promote the dephosphorylation of two independent phospho-proteins, FAM83D or ULK1, knocked in with GFP-tags using CRISPR-Cas9, with exquisite specificity. By redirecting protein phosphatases to neo-substrates through nanobody-mediated proximity, AdPhosphatase can alter the phospho-status and function of target proteins and thus, offers a new modality for potential drug discovery approaches.
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Affiliation(s)
- Luke M Simpson
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Luke J Fulcher
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Gajanan Sathe
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Abigail Brewer
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Jin-Feng Zhao
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Daniel R Squair
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Jennifer Crooks
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Melanie Wightman
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Nicola T Wood
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Robert Gourlay
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Joby Varghese
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Renata F Soares
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Gopal P Sapkota
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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Wada R, Fujinuma S, Nakatsumi H, Matsumoto M, Nakayama KI. Phosphorylation of PBX2, a novel downstream target of mTORC1, is determined by GSK3 and PP1. J Biochem 2023; 173:129-138. [PMID: 36477205 DOI: 10.1093/jb/mvac094] [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: 09/06/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022] Open
Abstract
Mechanistic target of rapamycin complex 1 (mTORC1) is a serine-threonine kinase that is activated by extracellular signals, such as nutrients and growth factors. It plays a key role in the control of various biological processes, such as protein synthesis and energy metabolism by mediating or regulating the phosphorylation of multiple target molecules, some of which remain to be identified. We have here reanalysed a large-scale phosphoproteomics data set for mTORC1 target molecules and identified pre-B cell leukemia transcription factor 2 (PBX2) as such a novel target that is dephosphorylated downstream of mTORC1. We confirmed that PBX2, but not other members of the PBX family, is dephosphorylated in an mTORC1 activity-dependent manner. Furthermore, pharmacological and gene knockdown experiments revealed that glycogen synthase kinase 3 (GSK3) and protein phosphatase 1 (PP1) are responsible for the phosphorylation and dephosphorylation of PBX2, respectively. Our results thus suggest that the balance between the antagonistic actions of GSK3 and PP1 determines the phosphorylation status of PBX2 and its regulation by mTORC1.
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Key Words
- glycogen synthase kinase 3 (GSK3)
Abbreviations: DAPI, 4′,6-diamidino-2-phenylindole; DMSO, dimethyl sulfoxide; ERK, extracellular signal–regulated kinase; FOXK1, forkhead box K1;
GSK3, glycogen synthase kinase 3; HA, hemagglutinin; LARP1, La-related protein 1; MEK, ERK kinase; mTORC1, mechanistic target of rapamycin complex 1; PBS, phosphate-buffered saline; PBX2, pre–B cell leukemia transcription factor 2; PI3K, phosphoinositide 3-kinase; PDK1, phosphoinositide-dependent protein kinase 1; PP1, protein phosphatase 1;
PP2A, protein phosphatase 2A; RAG, RAS-related GTP-binding protein; RHEB, Ras homolog enriched in Brain; shRNA, short hairpin RNA; siRNA, small interfering RNA; TBC1D7, TBC1 (TRE2-BUB2-CDC16) domain family member 7; TSC2, tuberous sclerosis complex 2; WT, wild-type
- mechanistic target of rapamycin complex 1 (mTORC1)
- phosphorylation
- pre–B cell leukemia transcription factor 2 (PBX2)
- protein phosphatase 1 (PP1)
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Affiliation(s)
- Reona Wada
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Shun Fujinuma
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Hirokazu Nakatsumi
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan.,Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, 757 Ichibancho, Asahimachi-dori, Chuo-ku, Niigata City, Niigata 951-8510, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
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46
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Targeting protein phosphatases in cancer immunotherapy and autoimmune disorders. Nat Rev Drug Discov 2023; 22:273-294. [PMID: 36693907 PMCID: PMC9872771 DOI: 10.1038/s41573-022-00618-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2022] [Indexed: 01/25/2023]
Abstract
Protein phosphatases act as key regulators of multiple important cellular processes and are attractive therapeutic targets for various diseases. Although extensive effort has been dedicated to phosphatase-targeted drug discovery, early expeditions for competitive phosphatase inhibitors were plagued by druggability issues, leading to the stigmatization of phosphatases as difficult targets. Despite challenges, persistent efforts have led to the identification of several drug-like, non-competitive modulators of some of these enzymes - including SH2 domain-containing protein tyrosine phosphatase 2, protein tyrosine phosphatase 1B, vascular endothelial protein tyrosine phosphatase and protein phosphatase 1 - reigniting interest in therapeutic targeting of phosphatases. Here, we discuss recent progress in phosphatase drug discovery, with emphasis on the development of selective modulators that exhibit biological activity. The roles and regulation of protein phosphatases in immune cells and their potential as powerful targets for immuno-oncology and autoimmunity indications are assessed.
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47
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Zhang K, Da Silva F, Seidl C, Wilsch-Bräuninger M, Herbst J, Huttner WB, Niehrs C. Primary cilia are WNT-transducing organelles whose biogenesis is controlled by a WNT-PP1 axis. Dev Cell 2023; 58:139-154.e8. [PMID: 36693320 DOI: 10.1016/j.devcel.2022.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 10/18/2022] [Accepted: 12/19/2022] [Indexed: 01/24/2023]
Abstract
WNT signaling is important in development, stem cell maintenance, and disease. WNT ligands typically signal via receptor activation across the plasma membrane to induce β-catenin-dependent gene activation. Here, we show that in mammalian primary cilia, WNT receptors relay a WNT/GSK3 signal that β-catenin-independently promotes ciliogenesis. Characterization of a LRP6 ciliary targeting sequence and monitoring of acute WNT co-receptor activation (phospho-LRP6) support this conclusion. Ciliary WNT signaling inhibits protein phosphatase 1 (PP1) activity, a negative regulator of ciliogenesis, by preventing GSK3-mediated phosphorylation of the PP1 regulatory inhibitor subunit PPP1R2. Concordantly, deficiency of WNT/GSK3 signaling by depletion of cyclin Y and cyclin-Y-like protein 1 induces primary cilia defects in mouse embryonic neuronal precursors, kidney proximal tubules, and adult mice preadipocytes.
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Affiliation(s)
- Kaiqing Zhang
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Fabio Da Silva
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Carina Seidl
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Michaela Wilsch-Bräuninger
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraβe 108, 01307 Dresden, Germany
| | - Jessica Herbst
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraβe 108, 01307 Dresden, Germany
| | - Christof Niehrs
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Institute of Molecular Biology (IMB), 55128 Mainz, Germany.
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48
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Brauer BL, Wiredu K, Gerber SA, Kettenbach AN. Evaluation of Quantification and Normalization Strategies for Phosphoprotein Phosphatase Affinity Proteomics: Application to Breast Cancer Signaling. J Proteome Res 2023; 22:47-61. [PMID: 36448918 PMCID: PMC10625046 DOI: 10.1021/acs.jproteome.2c00465] [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] [Indexed: 12/02/2022]
Abstract
Accurate quantification of proteomics data is essential for revealing and understanding biological signaling processes. We have recently developed a chemical proteomic strategy termed phosphatase inhibitor beads and mass spectrometry (PIB-MS) to investigate endogenous phosphoprotein phosphatase (PPP) dephosphorylation signaling. Here, we compare the robustness and reproducibility of status quo quantification methods for optimal performance and ease of implementation. We then apply PIB-MS to an array of breast cancer cell lines to determine differences in PPP signaling between subtypes. Breast cancer, a leading cause of cancer death in women, consists of three main subtypes: estrogen receptor-positive (ER+), human epidermal growth factor receptor two positive (HER2+), and triple-negative (TNBC). Although there are effective treatment strategies for ER+ and HER2+ subtypes, tumors become resistant and progress. Furthermore, TNBC has few targeted therapies. Therefore, there is a need to identify new approaches for treating breast cancers. Using PIB-MS, we distinguished TNBC from non-TNBC based on subtype-specific PPP holoenzyme composition. In addition, we identified an increase in PPP interactions with Hippo pathway proteins in TNBC. These interactions suggest that phosphatases in TNBC play an inhibitory role on the Hippo pathway and correlate with increased expression of YAP/TAZ target genes both in TNBC cell lines and in TNBC patients.
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Affiliation(s)
- Brooke L. Brauer
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Kwame Wiredu
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Scott A. Gerber
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Arminja N. Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH
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49
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Keefe JA, Moore OM, Ho KS, Wehrens XHT. Role of Ca 2+ in healthy and pathologic cardiac function: from normal excitation-contraction coupling to mutations that cause inherited arrhythmia. Arch Toxicol 2023; 97:73-92. [PMID: 36214829 PMCID: PMC10122835 DOI: 10.1007/s00204-022-03385-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/15/2022] [Indexed: 01/19/2023]
Abstract
Calcium (Ca2+) ions are a key second messenger involved in the rhythmic excitation and contraction of cardiomyocytes throughout the heart. Proper function of Ca2+-handling proteins is required for healthy cardiac function, whereas disruption in any of these can cause cardiac arrhythmias. This comprehensive review provides a broad overview of the roles of Ca2+-handling proteins and their regulators in healthy cardiac function and the mechanisms by which mutations in these proteins contribute to inherited arrhythmias. Major Ca2+ channels and Ca2+-sensitive regulatory proteins involved in cardiac excitation-contraction coupling are discussed, with special emphasis on the function of the RyR2 macromolecular complex. Inherited arrhythmia disorders including catecholaminergic polymorphic ventricular tachycardia, long QT syndrome, Brugada syndrome, short QT syndrome, and arrhythmogenic right-ventricular cardiomyopathy are discussed with particular emphasis on subtypes caused by mutations in Ca2+-handling proteins.
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Affiliation(s)
- Joshua A Keefe
- Cardiovascular Research Institute, Baylor College of Medicine, One Baylor Plaza, BCM335, Houston, TX, 77030, USA.,Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Oliver M Moore
- Cardiovascular Research Institute, Baylor College of Medicine, One Baylor Plaza, BCM335, Houston, TX, 77030, USA.,Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kevin S Ho
- Cardiovascular Research Institute, Baylor College of Medicine, One Baylor Plaza, BCM335, Houston, TX, 77030, USA.,Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xander H T Wehrens
- Cardiovascular Research Institute, Baylor College of Medicine, One Baylor Plaza, BCM335, Houston, TX, 77030, USA. .,Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Center for Space Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
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50
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Ulengin-Talkish I, Cyert MS. A cellular atlas of calcineurin signaling. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119366. [PMID: 36191737 PMCID: PMC9948804 DOI: 10.1016/j.bbamcr.2022.119366] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Intracellular Ca2+ signals are temporally controlled and spatially restricted. Signaling occurs adjacent to sites of Ca2+ entry and/or release, where Ca2+-dependent effectors and their substrates co-localize to form signaling microdomains. Here we review signaling by calcineurin, the Ca2+/calmodulin regulated protein phosphatase and target of immunosuppressant drugs, Cyclosporin A and FK506. Although well known for its activation of the adaptive immune response via NFAT dephosphorylation, systematic mapping of human calcineurin substrates and regulators reveals unexpected roles for this versatile phosphatase throughout the cell. We discuss calcineurin function, with an emphasis on where signaling occurs and mechanisms that target calcineurin and its substrates to signaling microdomains, especially binding of cognate short linear peptide motifs (SLiMs). Calcineurin is ubiquitously expressed and regulates events at the plasma membrane, other intracellular membranes, mitochondria, the nuclear pore complex and centrosomes/cilia. Based on our expanding knowledge of localized CN actions, we describe a cellular atlas of Ca2+/calcineurin signaling.
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Affiliation(s)
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, CA 94035, United States.
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