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Osawa J, Karakawa M, Taniguchi A, Inui Y, Usuki C, Ishida A, Kameshita I, Sueyoshi N. Functional regulation of the protein phosphatase PPM1M by phosphorylation at multiple sites with Ser/Thr-Pro motifs. Arch Biochem Biophys 2024; 753:109887. [PMID: 38224862 DOI: 10.1016/j.abb.2024.109887] [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: 11/03/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 01/17/2024]
Abstract
The imbalance in the phosphorylation and the dephosphorylation of proteins leads to various diseases. Therefore, in vivo, the functions of protein kinases and protein phosphatases are strictly regulated. Mg2+/Mn2+-dependent protein phosphatase PPM1M has been implicated in immunity and cancer; however, the regulation mechanism remains unknown. In this study, we show that PPM1M is regulated in different ways by multiple phosphorylation. PPM1M has four Ser/Thr-Pro motifs (Ser27, Ser43, Ser60, and Thr254) that are recognized by proline-directed kinases, and Ser60 was found to be phosphorylated by cyclin-dependent kinase 5 (CDK5) in the cell. The phospho-mimetic mutation of Ser27 and Ser43 in the N-terminal domain suppresses the nuclear localization of PPM1M and promotes its accumulation in the cytoplasm. The phospho-mimetic mutation of Ser60 decreases PPM1M activity; conversely, the phospho-mimetic mutation of Thr254 increases PPM1M activity. These results suggest that the subcellular localization and phosphatase activity of PPM1M are regulated by protein kinases, including CDK5, via phosphorylation at multiple sites. Thus, PPM1M is differentially regulated by proline-directed kinases, including CDK5.
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Affiliation(s)
- Jin Osawa
- Department of Life Sciences, Faculty of Agriculture, Kagawa University, Kagawa, 761-0795, Japan
| | - Masataka Karakawa
- Department of Life Sciences, Faculty of Agriculture, Kagawa University, Kagawa, 761-0795, Japan
| | - Aoi Taniguchi
- Department of Life Sciences, Faculty of Agriculture, Kagawa University, Kagawa, 761-0795, Japan
| | - Yuiko Inui
- Department of Life Sciences, Faculty of Agriculture, Kagawa University, Kagawa, 761-0795, Japan
| | - Chika Usuki
- Department of Life Sciences, Faculty of Agriculture, Kagawa University, Kagawa, 761-0795, Japan
| | - Atsuhiko Ishida
- Laboratory of Molecular Brain Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8521, Japan.
| | - Isamu Kameshita
- Department of Life Sciences, Faculty of Agriculture, Kagawa University, Kagawa, 761-0795, Japan
| | - Noriyuki Sueyoshi
- Department of Life Sciences, Faculty of Agriculture, Kagawa University, Kagawa, 761-0795, Japan.
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2
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Heo S, Kang T, Bygrave AM, Larsen MR, Huganir RL. Experience-Induced Remodeling of the Hippocampal Post-synaptic Proteome and Phosphoproteome. Mol Cell Proteomics 2023; 22:100661. [PMID: 37806341 PMCID: PMC10652125 DOI: 10.1016/j.mcpro.2023.100661] [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: 02/03/2023] [Revised: 09/25/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023] Open
Abstract
The postsynaptic density (PSD) of excitatory synapses contains a highly organized protein network with thousands of proteins and is a key node in the regulation of synaptic plasticity. To gain new mechanistic insight into experience-induced changes in the PSD, we examined the global dynamics of the hippocampal PSD proteome and phosphoproteome in mice following four different types of experience. Mice were trained using an inhibitory avoidance (IA) task and hippocampal PSD fractions were isolated from individual mice to investigate molecular mechanisms underlying experience-dependent remodeling of synapses. We developed a new strategy to identify and quantify the relatively low level of site-specific phosphorylation of PSD proteome from the hippocampus, by using a modified iTRAQ-based TiSH protocol. In the PSD, we identified 3938 proteins and 2761 phosphoproteins in the sequential strategy covering a total of 4968 unique protein groups (at least two peptides including a unique peptide). On the phosphoproteins, we identified a total of 6188 unambiguous phosphosites (75%
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Affiliation(s)
- Seok Heo
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, Maryland, USA
| | - Taewook Kang
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Alexei M Bygrave
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, Maryland, USA
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
| | - Richard L Huganir
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, Maryland, USA.
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Yeshaw WM, Adhikari A, Chiang CY, Dhekne HS, Wawro PS, Pfeffer SR. Localization of PPM1H phosphatase tunes Parkinson's disease-linked LRRK2 kinase-mediated Rab GTPase phosphorylation and ciliogenesis. Proc Natl Acad Sci U S A 2023; 120:e2315171120. [PMID: 37889931 PMCID: PMC10622911 DOI: 10.1073/pnas.2315171120] [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: 08/31/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
PPM1H phosphatase reverses Parkinson's disease-associated, Leucine Rich Repeat Kinase 2-mediated Rab GTPase phosphorylation. We show here that PPM1H relies on an N-terminal amphipathic helix for Golgi localization. The amphipathic helix enables PPM1H to bind to liposomes in vitro, and small, highly curved liposomes stimulate PPM1H activity. We artificially anchored PPM1H to the Golgi, mitochondria, or mother centriole. Our data show that regulation of Rab10 GTPase phosphorylation requires PPM1H access to Rab10 at or near the mother centriole. Moreover, poor colocalization of Rab12 explains in part why it is a poor substrate for PPM1H in cells but not in vitro. These data support a model in which localization drives PPM1H substrate selection and centriolar PPM1H is critical for regulation of Rab GTPase-regulated ciliogenesis. Moreover, Golgi localized PPM1H may maintain active Rab GTPases on the Golgi to carry out their nonciliogenesis-related functions in membrane trafficking.
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Affiliation(s)
- Wondwossen M. Yeshaw
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305-5307
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Ayan Adhikari
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305-5307
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Claire Y. Chiang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305-5307
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Herschel S. Dhekne
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305-5307
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Paulina S. Wawro
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305-5307
| | - Suzanne R. Pfeffer
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305-5307
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
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4
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Onyedibe KI, Mohallem R, Wang M, Aryal UK, Sintim HO. Proteomic and phosphoproteomic analyses of Jurkat T-cell treated with 2'3' cGAMP reveals various signaling axes impacted by cyclic dinucleotides. J Proteomics 2023; 279:104869. [PMID: 36889538 DOI: 10.1016/j.jprot.2023.104869] [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: 06/19/2022] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023]
Abstract
Cyclic dinucleotides (CDNs), such as 2'3'-cGAMP, bind to STING to trigger the production of cytokines and interferons, mainly via activation of TBK1. STING activation by CDN also leads to the release and activation of Nuclear Factor Kappa-light-chain-enhancer of activated B cells (NF-κB) via the phosphorylation of Inhibitor of NF-κB (IκB)-alpha (IκBα) by IκB Kinase (IKK). Beyond the canonical TBK1 or IKK phosphorylations, little is known about how CDNs broadly affect the phosphoproteome and/or other signaling axes. To fill this gap, we performed an unbiased proteome and phosphoproteome analysis of Jurkat T-cell treated with 2'3'-cGAMP or vehicle control to identify proteins and phosphorylation sites that are differentially modulated by 2'3'-cGAMP. We uncovered different classes of kinase signatures associated with cell response to 2'3'-cGAMP. 2'3'-cGAMP upregulated Arginase 2 (Arg2) and the antiviral innate immune response receptor RIG-I as well as proteins involved in ISGylation, E3 ISG15-protein ligase HERC5 and ubiquitin-like protein ISG15, while downregulating ubiquitin-conjugating enzyme UBE2C. Kinases that play a role in DNA double strand break repair, apoptosis, and cell cycle regulation were differentially phosphorylated. Overall, this work demonstrates that 2'3'-cGAMP has a much broader effects on global phosphorylation events than currently appreciated, beyond the canonical TBK1/IKK signaling. SIGNIFICANCE: The host cyclic dinucleotide, 2'3'-cGAMP is known to bind to Stimulator of Interferon Genes (STING) to trigger the production of cytokines and interferons in immune cells via STING-TBK1-IRF3 pathway. Beyond the canonical phosphorelay via the STING-TBK1-IRF3 pathway, little is known about how this second messenger broadly affects the global proteome. Using an unbiased phosphoproteomics, this study identifies several kinases and phosphosites that are modulated by cGAMP. The study expands our knowledge about how cGAMP modulates global proteome and also global phosphorylations.
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Affiliation(s)
- Kenneth I Onyedibe
- Department of Chemistry, Purdue University, West Lafayette, IN, USA; Purdue Institute for Drug Discovery and Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Rodrigo Mohallem
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA; Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA
| | - Modi Wang
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Uma K Aryal
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA; Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA
| | - Herman O Sintim
- Department of Chemistry, Purdue University, West Lafayette, IN, USA; Purdue Institute for Drug Discovery and Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA.
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5
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Analysis of protein phosphorylation using Phos-tag gels. J Proteomics 2022; 259:104558. [DOI: 10.1016/j.jprot.2022.104558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/18/2022]
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Waschbüsch D, Berndsen K, Lis P, Knebel A, Lam YPY, Alessi DR, Khan AR. Structural basis for the specificity of PPM1H phosphatase for Rab GTPases. EMBO Rep 2021; 22:e52675. [PMID: 34580980 PMCID: PMC8567228 DOI: 10.15252/embr.202152675] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 08/16/2021] [Accepted: 08/27/2021] [Indexed: 12/17/2022] Open
Abstract
LRRK2 serine/threonine kinase is associated with inherited Parkinson's disease. LRRK2 phosphorylates a subset of Rab GTPases within their switch 2 motif to control their interactions with effectors. Recent work has shown that the metal-dependent protein phosphatase PPM1H counteracts LRRK2 by dephosphorylating Rabs. PPM1H is highly selective for LRRK2 phosphorylated Rabs, and closely related PPM1J exhibits no activity towards substrates such as Rab8a phosphorylated at Thr72 (pThr72). Here, we have identified the molecular determinant of PPM1H specificity for Rabs. The crystal structure of PPM1H reveals a structurally conserved phosphatase fold that strikingly has evolved a 110-residue flap domain adjacent to the active site. The flap domain distantly resembles tudor domains that interact with histones in the context of epigenetics. Cellular assays, crosslinking and 3-D modelling suggest that the flap domain encodes the docking motif for phosphorylated Rabs. Consistent with this hypothesis, a PPM1J chimaera with the PPM1H flap domain dephosphorylates pThr72 of Rab8a both in vitro and in cellular assays. Therefore, PPM1H has acquired a Rab-specific interaction domain within a conserved phosphatase fold.
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Affiliation(s)
- Dieter Waschbüsch
- School of Biochemistry and ImmunologyTrinity College DublinDublin 2Ireland
| | - Kerryn Berndsen
- MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research NetworkChevy ChaseMDUSA
| | - Pawel Lis
- MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research NetworkChevy ChaseMDUSA
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Yuko PY Lam
- MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research NetworkChevy ChaseMDUSA
| | - Dario R Alessi
- MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research NetworkChevy ChaseMDUSA
| | - Amir R Khan
- School of Biochemistry and ImmunologyTrinity College DublinDublin 2Ireland
- Division of Newborn MedicineBoston Children's HospitalBostonMAUSA
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7
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Beavo JA, Golkowski M, Shimizu-Albergine M, Beltejar MC, Bornfeldt KE, Ong SE. Phosphoproteomic Analysis as an Approach for Understanding Molecular Mechanisms of cAMP-Dependent Actions. Mol Pharmacol 2021; 99:342-357. [PMID: 33574048 PMCID: PMC8058506 DOI: 10.1124/molpharm.120.000197] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/23/2020] [Indexed: 12/26/2022] Open
Abstract
In recent years, highly sensitive mass spectrometry-based phosphoproteomic analysis is beginning to be applied to identification of protein kinase substrates altered downstream of increased cAMP. Such studies identify a very large number of phosphorylation sites regulated in response to increased cAMP. Therefore, we now are tasked with the challenge of determining how many of these altered phosphorylation sites are relevant to regulation of function in the cell. This minireview describes the use of phosphoproteomic analysis to monitor the effects of cyclic nucleotide phosphodiesterase (PDE) inhibitors on cAMP-dependent phosphorylation events. More specifically, it describes two examples of this approach carried out in the authors' laboratories using the selective PDE inhibitor approach. After a short discussion of several likely conclusions suggested by these analyses of cAMP function in steroid hormone-producing cells and also in T-cells, it expands into a discussion about some newer and more speculative interpretations of the data. These include the idea that multiple phosphorylation sites and not a single rate-limiting step likely regulate these and, by analogy, many other cAMP-dependent pathways. In addition, the idea that meaningful regulation requires a high stoichiometry of phosphorylation to be important is discussed and suggested to be untrue in many instances. These new interpretations have important implications for drug design, especially for targeting pathway agonists. SIGNIFICANCE STATEMENT: Phosphoproteomic analyses identify thousands of altered phosphorylation sites upon drug treatment, providing many possible regulatory targets but also highlighting questions about which phosphosites are functionally important. These data imply that multistep processes are regulated by phosphorylation at not one but rather many sites. Most previous studies assumed a single step or very few rate-limiting steps were changed by phosphorylation. This concept should be changed. Previous interpretations also assumed substoichiometric phosphorylation was not of regulatory importance. This assumption also should be changed.
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Affiliation(s)
- Joseph A Beavo
- Departments of Pharmacology and Medicine (J.A.B., M.G., M.S.-A., M.-C.B., S.-E.O.), and Division of Metabolism, Endocrinology and Nutrition (K.E.B.), University of Washington, Seattle, Washington
| | - Martin Golkowski
- Departments of Pharmacology and Medicine (J.A.B., M.G., M.S.-A., M.-C.B., S.-E.O.), and Division of Metabolism, Endocrinology and Nutrition (K.E.B.), University of Washington, Seattle, Washington
| | - Masami Shimizu-Albergine
- Departments of Pharmacology and Medicine (J.A.B., M.G., M.S.-A., M.-C.B., S.-E.O.), and Division of Metabolism, Endocrinology and Nutrition (K.E.B.), University of Washington, Seattle, Washington
| | - Michael-Claude Beltejar
- Departments of Pharmacology and Medicine (J.A.B., M.G., M.S.-A., M.-C.B., S.-E.O.), and Division of Metabolism, Endocrinology and Nutrition (K.E.B.), University of Washington, Seattle, Washington
| | - Karin E Bornfeldt
- Departments of Pharmacology and Medicine (J.A.B., M.G., M.S.-A., M.-C.B., S.-E.O.), and Division of Metabolism, Endocrinology and Nutrition (K.E.B.), University of Washington, Seattle, Washington
| | - Shao-En Ong
- Departments of Pharmacology and Medicine (J.A.B., M.G., M.S.-A., M.-C.B., S.-E.O.), and Division of Metabolism, Endocrinology and Nutrition (K.E.B.), University of Washington, Seattle, Washington
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