1
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McIvor JAP, Larsen DS, Mercadante D. Charge Relaying within a Phospho-Motif Rescue Binding Competency of a Disordered Transcription Factor. J Chem Inf Model 2024; 64:6041-6052. [PMID: 39074869 DOI: 10.1021/acs.jcim.4c00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Structural disorder in proteins is central to cellular signaling, where conformational plasticity equips molecules to promiscuously interact with different partners. By engaging with multiple binding partners via the rearrangement of its three helices, the nuclear coactivator binding domain (NCBD) of the CBP/p300 transcription factor is a paradigmatic example of promiscuity. Recently, molecular simulations and experiments revealed that, through the establishment of long-range electrostatic interactions, intended as salt-bridges formed between the post-translationally inserted phosphate and positively charged residues in helix H3 of NCBD, phosphorylation triggers NCBD compaction, lowering its affinity for binding partners. By means of extensive molecular simulations, we here investigated the effect of short-range electrostatics on the conformational ensemble of NCBD, by monitoring the interactions between a phosphorylated serine and conserved positively charged residues within the NCBD phospho-motif. We found that empowering proximal electrostatic interactions, as opposed to long-range electrostatics, can reshape the NCBD ensemble rescuing the binding competency of phosphorylated NCBD. Given the conservation of positive charges in phospho-motifs, proximal electrostatic interactions might dampen the effects of phosphorylation and act as a relay to regulate phosphorylated intrinsically disordered proteins, ultimately tuning the binding affinity for different cellular partners.
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Affiliation(s)
- Jordan A P McIvor
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
| | - Danaé S Larsen
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
| | - Davide Mercadante
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
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2
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Heier JL, Boselli DJ, Parker LL. Antibody-free time-resolved terbium luminescence assays designed for cyclin-dependent kinase 5 (CDK5). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590988. [PMID: 38712268 PMCID: PMC11071522 DOI: 10.1101/2024.04.24.590988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Novel time-resolved terbium luminescence assays were developed for CDK5 and CDK2 by designing synthetic substrates which incorporate phospho-inducible terbium sensitizing motifs with kinase substrate consensus sequences. Substrates designed for CDK5 showed no phosphorylation by CDK2, opening the possibility for CDK5-specific assay development for selective drug discovery.
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3
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Javary J, Goupil E, Soulez M, Kanshin E, Bouchard A, Seternes OM, Thibault P, Labbé JC, Meloche S. Phosphoproteomic analysis identifies supervillin as an ERK3 substrate regulating cytokinesis and cell ploidy. J Cell Physiol 2024; 239:e30938. [PMID: 36576983 DOI: 10.1002/jcp.30938] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/29/2022]
Abstract
Extracellular signal-regulated kinase 3 (ERK3) is a poorly characterized member of the mitogen-activated protein (MAP) kinase family. Functional analysis of the ERK3 signaling pathway has been hampered by a lack of knowledge about the substrates and downstream effectors of the kinase. Here, we used large-scale quantitative phosphoproteomics and targeted gene silencing to identify direct ERK3 substrates and gain insight into its cellular functions. Detailed validation of one candidate substrate identified the gelsolin/villin family member supervillin (SVIL) as a bona fide ERK3 substrate. We show that ERK3 phosphorylates SVIL on Ser245 to regulate myosin II activation and cytokinesis completion in dividing cells. Depletion of SVIL or ERK3 leads to increased cytokinesis failure and multinucleation, a phenotype rescued by wild type SVIL but not by the non-phosphorylatable S245A mutant. Our results unveil a new function of the atypical MAP kinase ERK3 in cell division and the regulation of cell ploidy.
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Affiliation(s)
- Joaquim Javary
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
| | - Eugénie Goupil
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
| | - Mathilde Soulez
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
| | - Evgeny Kanshin
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
- NYU Langone Health, New York City, New York, USA
| | - Antoine Bouchard
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
- Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada
| | | | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
- Department of Chemistry, Faculty of Arts and Sciences, Université de Montréal, Montreal, Quebec, Canada
| | - Jean-Claude Labbé
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
- Molecular Biology Program, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Sylvain Meloche
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
- Molecular Biology Program, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
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4
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Hu AJ, Li W, Dinh C, Zhang Y, Hu JK, Daniele SG, Hou X, Yang Z, Asara JM, Hu GF, Farmer SR, Hu MG. CDK6 inhibits de novo lipogenesis in white adipose tissues but not in the liver. Nat Commun 2024; 15:1091. [PMID: 38316780 PMCID: PMC10844593 DOI: 10.1038/s41467-024-45294-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: 11/01/2022] [Accepted: 01/19/2024] [Indexed: 02/07/2024] Open
Abstract
Increased de novo lipogenesis (DNL) in white adipose tissue is associated with insulin sensitivity. Under both Normal-Chow-Diet and High-Fat-Diet, mice expressing a kinase inactive Cyclin-dependent kinase 6 (Cdk6) allele (K43M) display an increase in DNL in visceral white adipose tissues (VAT) as compared to wild type mice (WT), accompanied by markedly increased lipogenic transcriptional factor Carbohydrate-responsive element-binding proteins (CHREBP) and lipogenic enzymes in VAT but not in the liver. Treatment of WT mice under HFD with a CDK6 inhibitor recapitulates the phenotypes observed in K43M mice. Mechanistically, CDK6 phosphorylates AMP-activated protein kinase, leading to phosphorylation and inactivation of acetyl-CoA carboxylase, a key enzyme in DNL. CDK6 also phosphorylates CHREBP thus preventing its entry into the nucleus. Ablation of runt related transcription factor 1 in K43M mature adipocytes reverses most of the phenotypes observed in K43M mice. These results demonstrate a role of CDK6 in DNL and a strategy to alleviate metabolic syndromes.
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Affiliation(s)
- Alexander J Hu
- Department of Medicine, Division of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Wei Li
- Department of Medicine, Division of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, PR China
| | - Calvin Dinh
- Department of Medicine, Division of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA
| | - Yongzhao Zhang
- Department of Medicine, Division of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA
| | - Jamie K Hu
- Department of Medicine, Division of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA
- University of Miami Miller School of Medicine, Dermatology. 1295 NW 14th St. University of Miami Hospital South Bldg. Suites K-M, Miami, FL, USA
| | - Stefano G Daniele
- Yale School of Medicine, MD-PhD program, 333 Cedar St, New Haven, CT, USA
| | - Xiaoli Hou
- Department of Medicine, Division of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA
- Zhejiang Chinese Medical University, Center for Analysis and Testing, 548 Bin-Wen Road, Hangzhou, PR China
| | - Zixuan Yang
- Department of Medicine, Division of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA
- TUFTS University Friedman School of Nutrition Science and Policy, TUFTS University, 150 Harrison Avenue, MA, Boston, USA
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Guo-Fu Hu
- Department of Medicine, Division of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA
| | - Stephen R Farmer
- Boston University School of Medicine, Department of Biochemistry, 72E Concord St, Boston, MA, USA
| | - Miaofen G Hu
- Department of Medicine, Division of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA.
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5
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Kuhn A, Roosjen M, Mutte S, Dubey SM, Carrillo Carrasco VP, Boeren S, Monzer A, Koehorst J, Kohchi T, Nishihama R, Fendrych M, Sprakel J, Friml J, Weijers D. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell 2024; 187:130-148.e17. [PMID: 38128538 PMCID: PMC10783624 DOI: 10.1016/j.cell.2023.11.021] [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: 11/25/2022] [Revised: 06/29/2023] [Accepted: 11/18/2023] [Indexed: 12/23/2023]
Abstract
The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage.
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Affiliation(s)
- Andre Kuhn
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Mark Roosjen
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Sumanth Mutte
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Shiv Mani Dubey
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | | | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Aline Monzer
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Jasper Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Ryuichi Nishihama
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Matyáš Fendrych
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | - Joris Sprakel
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Jiří Friml
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands.
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6
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Latchford LP, Perez LS, Conage-Pough JE, Turk R, Cusimano MA, Vargas VI, Arora S, White FM, Thévenin AF. Differential substrate specificity of ERK, JNK, and p38 MAP kinases toward Connexin 43. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.30.573692. [PMID: 38234737 PMCID: PMC10793482 DOI: 10.1101/2023.12.30.573692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Phosphorylation of connexin 43 (Cx43) is an important regulatory mechanism of gap junction (GJ) function. Cx43 is modified by several kinases on over 15 sites within its ∼140 amino acid-long C-terminus (CT). Phosphorylation of Cx43CT on S255, S262, S279, and S282 by ERK has been widely documented in several cell lines, by many investigators. Phosphorylation of these sites by JNK and p38, on the other hand, is not well-established. Indeed, ERK is a kinase activated by growth factors and is upregulated in diseases, such as cancer. JNK and p38, however, have a largely tumor-suppressive function due to their stress-activated and apoptotic role. We investigated substrate specificity of all three MAPKs toward Cx43CT, both in vitro and in two cell lines (MDCK - non-cancerous, epithelial cells and porcine PAECs - pulmonary artery endothelial cells). Cx43 phosphorylation was monitored through gel-shift assays on an SDS-PAGE, immunodetection with phospho-Cx43 antibodies, and LC-MS/MS phosphoproteomic analyses. Our results demonstrate that p38 and JNK specificity differ from each other and from ERK. JNK has a strong preference for S255 and S279, while p38 readily phosphorylates S279 and S282. In addition, while we confirmed that ERK can phosphorylate all four serines (255, 262, 279, and 282), we identified T290 as a novel ERK phosphorylation site. This work underscores the importance of delineating the effects of ERK, JNK, and p38 signaling pathways on Cx43 and GJ function.
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7
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Nikhil K, Shah K. CDK5: an oncogene or an anti-oncogene: location location location. Mol Cancer 2023; 22:186. [PMID: 37993880 PMCID: PMC10666462 DOI: 10.1186/s12943-023-01895-8] [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: 08/01/2023] [Accepted: 11/03/2023] [Indexed: 11/24/2023] Open
Abstract
Recent studies have uncovered various physiological functions of CDK5 in many nonneuronal tissues. Upregulation of CDK5 and/or its activator p35 in neurons promotes healthy neuronal functions, but their overexpression in nonneuronal tissues is causally linked to cancer of many origins. This review focuses on the molecular mechanisms by which CDK5 recruits diverse tissue-specific substrates to elicit distinct phenotypes in sixteen different human cancers. The emerging theme suggests that CDK5's role as an oncogene or anti-oncogene depends upon its subcellular localization. CDK5 mostly acts as an oncogene, but in gastric cancer, it is a tumor suppressor due to its unique nuclear localization. This indicates that CDK5's access to certain nuclear substrates converts it into an anti-oncogenic kinase. While acting as a bonafide oncogene, CDK5 also activates a few cancer-suppressive pathways in some cancers, presumably due to the mislocalization of nuclear substrates in the cytoplasm. Therefore, directing CDK5 to the nucleus or exporting tumor-suppressive nuclear substrates to the cytoplasm may be promising approaches to combat CDK5-induced oncogenicity, analogous to neurotoxicity triggered by nuclear CDK5. Furthermore, while p35 overexpression is oncogenic, hyperactivation of CDK5 by inducing p25 formation results in apoptosis, which could be exploited to selectively kill cancer cells by dialing up CDK5 activity, instead of inhibiting it. CDK5 thus acts as a molecular rheostat, with different activity levels eliciting distinct functional outcomes. Finally, as CDK5's role is defined by its substrates, targeting them individually or in conjunction with CDK5 should create potentially valuable new clinical opportunities.
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Affiliation(s)
- Kumar Nikhil
- Department of Chemistry, Purdue University Center for Cancer Research, 560 Oval Drive, West Lafayette, IN, 47907, USA
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, 751024, India
| | - Kavita Shah
- Department of Chemistry, Purdue University Center for Cancer Research, 560 Oval Drive, West Lafayette, IN, 47907, USA.
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8
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Valverde JM, Dubra G, Phillips M, Haider A, Elena-Real C, Fournet A, Alghoul E, Chahar D, Andrés-Sanchez N, Paloni M, Bernadó P, van Mierlo G, Vermeulen M, van den Toorn H, Heck AJR, Constantinou A, Barducci A, Ghosh K, Sibille N, Knipscheer P, Krasinska L, Fisher D, Altelaar M. A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation. Nat Commun 2023; 14:6316. [PMID: 37813838 PMCID: PMC10562473 DOI: 10.1038/s41467-023-42049-0] [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: 07/05/2023] [Accepted: 09/28/2023] [Indexed: 10/11/2023] Open
Abstract
Cell cycle transitions result from global changes in protein phosphorylation states triggered by cyclin-dependent kinases (CDKs). To understand how this complexity produces an ordered and rapid cellular reorganisation, we generated a high-resolution map of changing phosphosites throughout unperturbed early cell cycles in single Xenopus embryos, derived the emergent principles through systems biology analysis, and tested them by biophysical modelling and biochemical experiments. We found that most dynamic phosphosites share two key characteristics: they occur on highly disordered proteins that localise to membraneless organelles, and are CDK targets. Furthermore, CDK-mediated multisite phosphorylation can switch homotypic interactions of such proteins between favourable and inhibitory modes for biomolecular condensate formation. These results provide insight into the molecular mechanisms and kinetics of mitotic cellular reorganisation.
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Affiliation(s)
- Juan Manuel Valverde
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, 3584 CH, Utrecht, Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, Netherlands
| | - Geronimo Dubra
- IGMM, CNRS, University of Montpellier, INSERM, Montpellier, France
- Equipe Labellisée LIGUE 2018, Ligue Nationale Contre le Cancer, Paris, France
| | - Michael Phillips
- Department of Physics and Astronomy, University of Denver, Denver, Co, 80208, USA
| | - Austin Haider
- Department of Molecular and Cellular Biophysics, University of Denver, 80208, Denver, Co, USA
| | | | - Aurélie Fournet
- CBS, CNRS, University of Montpellier, INSERM, Montpellier, France
| | - Emile Alghoul
- IGH, CNRS, University of Montpellier, Montpellier, France
| | - Dhanvantri Chahar
- IGMM, CNRS, University of Montpellier, INSERM, Montpellier, France
- Equipe Labellisée LIGUE 2018, Ligue Nationale Contre le Cancer, Paris, France
| | - Nuria Andrés-Sanchez
- IGMM, CNRS, University of Montpellier, INSERM, Montpellier, France
- Equipe Labellisée LIGUE 2018, Ligue Nationale Contre le Cancer, Paris, France
| | - Matteo Paloni
- Department of Physics and Astronomy, University of Denver, Denver, Co, 80208, USA
| | - Pau Bernadó
- CBS, CNRS, University of Montpellier, INSERM, Montpellier, France
| | - Guido van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, 6525 GA, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, 6525 GA, The Netherlands
| | - Henk van den Toorn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, 3584 CH, Utrecht, Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, 3584 CH, Utrecht, Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, Netherlands
| | | | | | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, Co, 80208, USA
- Department of Molecular and Cellular Biophysics, University of Denver, 80208, Denver, Co, USA
| | - Nathalie Sibille
- CBS, CNRS, University of Montpellier, INSERM, Montpellier, France
| | - Puck Knipscheer
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center, Utrecht, 3584 CT, Netherlands
| | - Liliana Krasinska
- IGMM, CNRS, University of Montpellier, INSERM, Montpellier, France
- Equipe Labellisée LIGUE 2018, Ligue Nationale Contre le Cancer, Paris, France
| | - Daniel Fisher
- IGMM, CNRS, University of Montpellier, INSERM, Montpellier, France.
- Equipe Labellisée LIGUE 2018, Ligue Nationale Contre le Cancer, Paris, France.
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, 3584 CH, Utrecht, Netherlands.
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, Netherlands.
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9
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Bardwell L, Thorner J. Mitogen-activated protein kinase (MAPK) cascades-A yeast perspective. Enzymes 2023; 54:137-170. [PMID: 37945169 DOI: 10.1016/bs.enz.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Discovery of the class of protein kinase now dubbed a mitogen (or messenger)-activated protein kinase (MAPK) is an illustrative example of how disparate lines of investigation can converge and reveal an enzyme family universally conserved among eukaryotes, from single-celled microbes to humans. Moreover, elucidation of the circuitry controlling MAPK function defined a now overarching principle in enzyme regulation-the concept of an activation cascade mediated by sequential phosphorylation events. Particularly ground-breaking for this field of exploration were the contributions of genetic approaches conducted using several model organisms, but especially the budding yeast Saccharomyces cerevisiae. Notably, examination of how haploid yeast cells respond to their secreted peptide mating pheromones was crucial in pinpointing genes encoding MAPKs and their upstream activators. Fully contemporaneous biochemical analysis of the activities elicited upon stimulation of mammalian cells by insulin and other growth- and differentiation-inducing factors lead eventually to the demonstration that components homologous to those in yeast were involved. Continued studies of these pathways in yeast were integral to other foundational discoveries in MAPK signaling, including the roles of tethering, scaffolding and docking interactions.
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Affiliation(s)
- Lee Bardwell
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, United States
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, College of Letters and Science, University of California, Berkeley, Berkeley, CA, United States.
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10
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Escobedo N, Monzon AM, Fornasari MS, Palopoli N, Parisi G. Combining Protein Conformational Diversity and Phylogenetic Information Using CoDNaS and CoDNaS-Q. Curr Protoc 2023; 3:e764. [PMID: 37184204 DOI: 10.1002/cpz1.764] [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] [Indexed: 05/16/2023]
Abstract
CoDNaS (http://ufq.unq.edu.ar/codnas/) and CoDNaS-Q (http://ufq.unq.edu.ar/codnasq) are repositories of proteins with different degrees of conformational diversity. Following the ensemble nature of the native state, conformational diversity represents the structural differences between the conformers in the ensemble. Each entry in CoDNaS and CoDNaS-Q contains a redundant collection of experimentally determined conformers obtained under different conditions. These conformers represent snapshots of the protein dynamism. While CoDNaS contains examples of conformational diversity at the tertiary level, a recent development, CoDNaS-Q, contains examples at the quaternary level. In the emerging age of accurate protein structure prediction by machine learning approaches, many questions remain open regarding the characterization of protein dynamism. In this context, most bioinformatics resources take advantage of distinct features derived from protein alignments, however, the complexity and heterogeneity of information makes it difficult to recover reliable biological signatures. Here we present five protocols to explore tertiary and quaternary conformational diversity at the individual protein level as well as for the characterization of the distribution of conformational diversity at the protein family level in a phylogenetic context. These protocols can provide curated protein families with experimentally known conformational diversity, facilitating the exploration of sequence determinants of protein dynamism. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Assessing conformational diversity with CoDNaS Alternate Protocol 1: Assessing conformational diversity at the quaternary level with CoDNaS-Q Basic Protocol 2: Exploring conformational diversity in a protein family Alternate Protocol 2: Exploring quaternary conformational diversity in a protein family Basic Protocol 3: Representing conformational diversity in a phylogenetic context.
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Affiliation(s)
- Nahuel Escobedo
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | | | - María Silvina Fornasari
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Nicolas Palopoli
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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11
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Liu X, Wang Y, Weng Z, Xu Q, Zhou C, Tang J, Chen XZ. Inhibition of TRPP3 by calmodulin through Ca 2+/calmodulin-dependent protein kinase II. CELL INSIGHT 2023; 2:100088. [PMID: 37193065 PMCID: PMC10134200 DOI: 10.1016/j.cellin.2023.100088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 05/18/2023]
Abstract
Transient receptor potential (TRP) polycystin-3 (TRPP3) is a non-selective cation channel activated by Ca2+ and protons and is involved in regulating ciliary Ca2+ concentration, hedgehog signaling and sour tasting. The TRPP3 channel function and regulation are still not well understood. Here we investigated regulation of TRPP3 by calmodulin (CaM) by means of electrophysiology and Xenopus oocytes as an expression model. We found that TRPP3 channel function is enhanced by calmidazolium, a CaM antagonist, and inhibited by CaM through binding of the CaM N-lobe to a TRPP3 C-terminal domain not overlapped with the EF-hand. We further revealed that the TRPP3/CaM interaction promotes phosphorylation of TRPP3 at threonine 591 by Ca2+/CaM-dependent protein kinase II, which mediates the inhibition of TRPP3 by CaM.
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Affiliation(s)
- Xiong Liu
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, T6G 2H7, Edmonton, AB, Canada
| | - Yifang Wang
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, T6G 2H7, Edmonton, AB, Canada
- National “111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, Hubei, 430068, China
| | - Ziyi Weng
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, T6G 2H7, Edmonton, AB, Canada
- National “111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, Hubei, 430068, China
| | - Qinyi Xu
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, T6G 2H7, Edmonton, AB, Canada
| | - Cefan Zhou
- National “111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, Hubei, 430068, China
| | - JingFeng Tang
- National “111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, Hubei, 430068, China
| | - Xing-Zhen Chen
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, T6G 2H7, Edmonton, AB, Canada
- National “111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, Hubei, 430068, China
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12
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Xiong Z, Wang M, Wu J, Shi X. Tceal7 Regulates Skeletal Muscle Development through Its Interaction with Cdk1. Int J Mol Sci 2023; 24:ijms24076264. [PMID: 37047236 PMCID: PMC10094454 DOI: 10.3390/ijms24076264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 03/29/2023] Open
Abstract
We have previously reported Tceal7 as a muscle-specific gene that represses myoblast proliferation and promotes myogenic differentiation. The regulatory mechanism of Tceal7 gene expression has been well clarified recently. However, the underlying mechanism of Tceal7 function in skeletal muscle development remains to be elucidated. In the present study, we have generated an MCK 6.5 kb-HA-Tceal7 transgenic model. The transgenic mice are born normally, while they have displayed defects in the growth of body weight and skeletal muscle myofiber during postnatal development. Although four RxL motifs have been identified in the Tceal7 protein sequence, we have not detected any direct protein-protein interaction between Tceal7 and Cyclin A2, Cyclin B1, Cylin D1, or Cyclin E1. Further analysis has revealed the interaction between Tceal7 and Cdk1 instead of Cdk2, Cdk4, or Cdk6. Transgenic overexpression of Tceal7 reduces phosphorylation of 4E-BP1 Ser65, p70S6K1 Thr389, and Cdk substrates in skeletal muscle. In summary, these studies have revealed a novel mechanism of Tceal7 in skeletal muscle development.
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13
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Coste K, Bruet S, Chollat-Namy C, Filhol O, Cochet C, Gallot D, Marceau G, Blanchon L, Sapin V, Belville C. Characterization of RAGE and CK2 Expressions in Human Fetal Membranes. Int J Mol Sci 2023; 24:ijms24044074. [PMID: 36835482 PMCID: PMC9966553 DOI: 10.3390/ijms24044074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/07/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
At the feto-maternal interface, fetal membranes (FM) play a crucial role throughout pregnancy. FM rupture at term implicates different sterile inflammation mechanisms including pathways activated by the transmembrane glycoprotein receptor for advanced glycation end-products (RAGE) belonging to the immunoglobulin superfamily. As the protein kinase CK2 is also implicated in the inflammation process, we aimed to characterize the expressions of RAGE and the protein kinase CK2 as a candidate regulator of RAGE expression. The amnion and choriodecidua were collected from FM explants and/or primary amniotic epithelial cells throughout pregnancy and at term in spontaneous labor (TIL) or term without labor (TNL). The mRNA and protein expressions of RAGE and the CK2α, CK2α', and CK2β subunits were investigated using reverse transcription quantitative polymerase chain reaction and Western blot assays. Their cellular localizations were determined with microscopic analyses, and the CK2 activity level was measured. RAGE and the CK2α, CK2α', and CK2β subunits were expressed in both FM layers throughout pregnancy. At term, RAGE was overexpressed in the amnion from the TNL samples, whereas the CK2 subunits were expressed at the same level in the different groups (amnion/choriodecidua/amniocytes, TIL/TNL), without modification of the CK2 activity level and immunolocalization. This work paves the way for future experiments regarding the regulation of RAGE expression by CK2 phosphorylation.
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Affiliation(s)
- Karen Coste
- iGReD, Team “Translational Approach to Epithelial Injury and Repair”, UMR6293 CNRS-U1103 INSERM, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
- CHU Clermont-Ferrand, Neonatal Intensive Care Department, F-63000 Clermont-Ferrand, France
| | - Shaam Bruet
- CHU Clermont-Ferrand, Neonatal Intensive Care Department, F-63000 Clermont-Ferrand, France
| | - Caroline Chollat-Namy
- CHU Clermont-Ferrand, Neonatal Intensive Care Department, F-63000 Clermont-Ferrand, France
| | - Odile Filhol
- INSERM, CEA, UMR Biosanté, U1292, University Grenoble Alpes, F-38000 Grenoble, France
| | - Claude Cochet
- INSERM, CEA, UMR Biosanté, U1292, University Grenoble Alpes, F-38000 Grenoble, France
| | - Denis Gallot
- iGReD, Team “Translational Approach to Epithelial Injury and Repair”, UMR6293 CNRS-U1103 INSERM, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
- CHU Clermont-Ferrand, Obstetrics and Gynecology Department, F-63000 Clermont-Ferrand, France
| | - Geoffroy Marceau
- iGReD, Team “Translational Approach to Epithelial Injury and Repair”, UMR6293 CNRS-U1103 INSERM, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
- CHU Clermont-Ferrand, Biochemistry and Molecular Genetic Department, F-63000 Clermont-Ferrand, France
| | - Loïc Blanchon
- iGReD, Team “Translational Approach to Epithelial Injury and Repair”, UMR6293 CNRS-U1103 INSERM, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Vincent Sapin
- iGReD, Team “Translational Approach to Epithelial Injury and Repair”, UMR6293 CNRS-U1103 INSERM, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
- CHU Clermont-Ferrand, Biochemistry and Molecular Genetic Department, F-63000 Clermont-Ferrand, France
| | - Corinne Belville
- iGReD, Team “Translational Approach to Epithelial Injury and Repair”, UMR6293 CNRS-U1103 INSERM, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
- Correspondence: ; Tel.: +33-4-7317-8174
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14
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On the Therapeutic Potential of ERK4 in Triple-Negative Breast Cancer. Cancers (Basel) 2022; 15:cancers15010025. [PMID: 36612022 PMCID: PMC9817496 DOI: 10.3390/cancers15010025] [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: 10/28/2022] [Revised: 11/30/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
ERK3 and ERK4 define a distinct and understudied subfamily of mitogen-activated protein kinases (MAPKs). Little is known about the physiological roles of these atypical MAPKs and their association with human diseases. Interestingly, accumulating evidence points towards a role for ERK3 and ERK4 signaling in the initiation and progression of various types of cancer. Notably, a recent study reported that ERK4 is expressed in a subset of triple-negative breast cancer (TNBC) cell lines and that this expression is critical for AKT activation and for sustaining TNBC cell proliferation in vitro and tumor growth in mice. The authors also showed that depletion of ERK4 sensitizes TNBC cells to phosphatidylinositol-3-kinase (PI3K) inhibitors. They concluded that ERK4 is a promising therapeutic target for TNBC and has potential for combination therapy with PI3K inhibitors. Here, we raise concerns about the cellular models and experimental approaches used in this study, which compromise the conclusions on the oncogenic role of ERK4 in TNBC.
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15
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Nicolaou ST, Kannan S, Warwicker J, Verma CS. Activation of p53: How phosphorylated Ser15 triggers sequential phosphorylation of p53 at Thr18 by CK1δ. Proteins 2022; 90:2009-2022. [PMID: 35752942 PMCID: PMC9796392 DOI: 10.1002/prot.26393] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/10/2022] [Accepted: 06/21/2022] [Indexed: 01/01/2023]
Abstract
The N-terminal transactivation domain (TAD) of p53 is a disordered region with multiple phosphorylation sites. Phosphorylation at Thr18 is crucial for the release of p53 from its negative regulator, MDM2. In stressed cells, CK1δ is responsible for phosphorylating Thr18, but requires Ser15 to be phosphorylated. To understand the mechanistic underpinnings of this sequential phosphorylation, molecular modeling and molecular dynamics simulation studies of these phosphorylation events were carried out. Our models suggest that a positively charged region on CK1δ near the adenosine triphosphate (ATP) binding pocket, which is conserved across species, sequesters the negatively charged pSer15, thereby constraining the positioning of the rest of the peptide, such that the side chain of Thr18 is positioned close to the γ-phosphate of ATP. Furthermore, our studies show that the phosphorylated p53 TAD1 (p53pSer15) peptide binds more strongly to CK1δ than does p53. p53 adopts a helical structure when bound to CK1δ, which is lost upon phosphorylation at Ser15, thus gaining higher flexibility and ability to morph into the binding site. We propose that upon phosphorylation at Ser15 the p53 TAD1 peptide binds to CK1δ through an electrostatically driven induced fit mechanism resulting in a flanking fuzzy complex.
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Affiliation(s)
- Sonia T. Nicolaou
- Faculty of Biology, Medicine and Health, School of Biological SciencesManchester Institute of Biotechnology, University of ManchesterManchesterUK,Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR)SingaporeSingapore
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR)SingaporeSingapore
| | - Jim Warwicker
- Faculty of Biology, Medicine and Health, School of Biological SciencesManchester Institute of Biotechnology, University of ManchesterManchesterUK
| | - Chandra S. Verma
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR)SingaporeSingapore,School of Biological SciencesNanyang Technological UniversitySingaporeSingapore,Department of Biological SciencesNational University of SingaporeSingaporeSingapore
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16
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Hassan A, Pollak YE, Kilav-Levin R, Silver J, London N, Nechama M, Ben-Dov IZ, Naveh-Many T. Kidney Failure Alters Parathyroid Pin1 Phosphorylation and Parathyroid Hormone mRNA-Binding Proteins, Leading to Secondary Hyperparathyroidism. J Am Soc Nephrol 2022; 33:1677-1693. [PMID: 35961788 PMCID: PMC9529182 DOI: 10.1681/asn.2022020197] [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: 03/02/2022] [Accepted: 06/01/2022] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Secondary hyperparathyroidism (SHP) is a common complication of CKD that increases morbidity and mortality. In experimental SHP, increased parathyroid hormone (PTH) expression is due to enhanced PTH mRNA stability, mediated by changes in its interaction with stabilizing AUF1 and destabilizing KSRP. The isomerase Pin1 leads to KSRP dephosphorylation, but in SHP parathyroid Pin1 activity is decreased and hence phosphorylated KSRP fails to bind PTH mRNA, resulting in high PTH mRNA stability and levels. The up- and downstream mechanisms by which CKD stimulates the parathyroid glands remain elusive. METHODS Adenine-rich high-phosphate diets induced CKD in rats and mice. Parathyroid organ cultures and transfected cells were incubated with Pin1 inhibitors for their effect on PTH expression. Mass spectrometry was performed on both parathyroid and PTH mRNA pulled-down proteins. RESULTS CKD led to changes in rat parathyroid proteome and phosphoproteome profiles, including KSRP phosphorylation at Pin1 target sites. Furthermore, both acute and chronic kidney failure led to parathyroid-specific Pin1 Ser16 and Ser71 phosphorylation, which disrupts Pin1 activity. Pharmacologic Pin1 inhibition, which mimics the decreased Pin1 activity in SHP, increased PTH expression ex vivo in parathyroid glands in culture and in transfected cells through the PTH mRNA-protein interaction element and KSRP phosphorylation. CONCLUSIONS Kidney failure leads to loss of parathyroid Pin1 activity by inducing Pin1 phosphorylation. This predisposes parathyroids to increase PTH production through impaired PTH mRNA decay that is dependent on KSRP phosphorylation at Pin1-target motifs. Pin1 and KSRP phosphorylation and the Pin1-KSRP-PTH mRNA axis thus drive SHP.
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Affiliation(s)
- Alia Hassan
- Minerva Center for Bone and Mineral Research, Nephrology Services, Hadassah Hebrew University Medical Center and Faculty of Medicine, Jerusalem, Israel
| | - Yael E. Pollak
- Minerva Center for Bone and Mineral Research, Nephrology Services, Hadassah Hebrew University Medical Center and Faculty of Medicine, Jerusalem, Israel
| | - Rachel Kilav-Levin
- Minerva Center for Bone and Mineral Research, Nephrology Services, Hadassah Hebrew University Medical Center and Faculty of Medicine, Jerusalem, Israel
- School of Nursing, Jerusalem College of Technology, Faculty of Life and Health Sciences, Jerusalem, Israel
| | - Justin Silver
- Minerva Center for Bone and Mineral Research, Nephrology Services, Hadassah Hebrew University Medical Center and Faculty of Medicine, Jerusalem, Israel
| | - Nir London
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Morris Nechama
- Department of Pediatric Nephrology, Hadassah Hebrew University Medical Center and Faculty of Medicine, Jerusalem, Israel
- Wohl Institute for Translational Medicine, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Iddo Z. Ben-Dov
- Laboratory of Medical Transcriptomics, Nephrology Services, Hadassah Hebrew University Medical Center and Faculty of Medicine, Jerusalem, Israel
| | - Tally Naveh-Many
- Minerva Center for Bone and Mineral Research, Nephrology Services, Hadassah Hebrew University Medical Center and Faculty of Medicine, Jerusalem, Israel
- Wohl Institute for Translational Medicine, Hadassah Hebrew University Medical Center, Jerusalem, Israel
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17
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Glykofridis IE, Henneman AA, Balk JA, Goeij-de Haas R, Westland D, Piersma SR, Knol JC, Pham TV, Boekhout M, Zwartkruis FJT, Wolthuis RMF, Jimenez CR. Phosphoproteomic analysis of FLCN inactivation highlights differential kinase pathways and regulatory TFEB phosphoserines. Mol Cell Proteomics 2022; 21:100263. [PMID: 35863698 PMCID: PMC9421328 DOI: 10.1016/j.mcpro.2022.100263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 10/26/2022] Open
Abstract
In Birt-Hogg-Dubé (BHD) syndrome, germline mutations in the Folliculin (FLCN) gene lead to an increased risk of renal cancer. To address how FLCN affects cellular kinase signaling pathways, we analyzed comprehensive phosphoproteomic profiles of FLCNPOS and FLCNNEG human renal tubular epithelial cells (RPTEC/TERT1). In total, 15744 phosphorylated peptides were identified from 4329 phosphorylated proteins. INKA analysis revealed that FLCN loss alters the activity of numerous kinases, including tyrosine kinases EGFR, MET and the Ephrin receptor subfamily (EPHA2 and EPHB1), as well their downstream targets MAPK1/3. Validation experiments in the BHD renal tumor cell line UOK257 confirmed that FLCN loss contributes to enhanced MAPK1/3 and downstream RPS6K1/3 signaling. The clinically available MAPK inhibitor Ulixertinib showed enhanced toxicity in FLCNNEG cells. Interestingly, FLCN inactivation induced the phosphorylation of PIK3CD (Tyr524) without altering the phosphorylation of canonical Akt1/Akt2/mTOR/EIF4EBP1 phosphosites. Also, we identified that FLCN inactivation resulted in dephosphorylation of TFEB Ser109, Ser114 and Ser122, which may be caused by fact that FLCNNEG cells experience oxidative stress. Together, our study highlights differential phosphorylation of specific kinases and substrates in FLCNNEG renal cells. This provides insight into BHD-associated renal tumorigenesis and may point to several novel candidates for targeted therapies.
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Affiliation(s)
- Iris E Glykofridis
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Human Genetics, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Alex A Henneman
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Jesper A Balk
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Human Genetics, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Richard Goeij-de Haas
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Denise Westland
- University Medical Center Utrecht, Center for Molecular Medicine, Molecular Cancer Research, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Sander R Piersma
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Jaco C Knol
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Thang V Pham
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Michiel Boekhout
- University Medical Center Utrecht, Center for Molecular Medicine, Molecular Cancer Research, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands; Oncode Institute, Amsterdam, The Netherlands
| | - Fried J T Zwartkruis
- University Medical Center Utrecht, Center for Molecular Medicine, Molecular Cancer Research, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Rob M F Wolthuis
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Human Genetics, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands.
| | - Connie R Jimenez
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands.
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18
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Özden C, Sloutsky R, Mitsugi T, Santos N, Agnello E, Gaubitz C, Foster J, Lapinskas E, Esposito EA, Saneyoshi T, Kelch BA, Garman SC, Hayashi Y, Stratton MM. CaMKII binds both substrates and activators at the active site. Cell Rep 2022; 40:111064. [PMID: 35830796 PMCID: PMC9336311 DOI: 10.1016/j.celrep.2022.111064] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 04/04/2022] [Accepted: 06/16/2022] [Indexed: 11/18/2022] Open
Abstract
Ca2+/calmodulin-dependent protein kinase II (CaMKII) is a signaling protein required for long-term memory. When activated by Ca2+/CaM, it sustains activity even after the Ca2+ dissipates. In addition to the well-known autophosphorylation-mediated mechanism, interaction with specific binding partners also persistently activates CaMKII. A long-standing model invokes two distinct S and T sites. If an interactor binds at the T-site, then it will preclude autoinhibition and allow substrates to be phosphorylated at the S site. Here, we specifically test this model with X-ray crystallography, molecular dynamics simulations, and biochemistry. Our data are inconsistent with this model. Co-crystal structures of four different activators or substrates show that they all bind to a single continuous site across the kinase domain. We propose a mechanistic model where persistent CaMKII activity is facilitated by high-affinity binding partners that kinetically compete with autoinhibition by the regulatory segment to allow substrate phosphorylation.
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Affiliation(s)
- Can Özden
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA; Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Roman Sloutsky
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Tomohiro Mitsugi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Nicholas Santos
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Emily Agnello
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Christl Gaubitz
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Joshua Foster
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Emily Lapinskas
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | | | - Takeo Saneyoshi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Brian A Kelch
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Scott C Garman
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Yasunori Hayashi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Margaret M Stratton
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA.
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19
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Kalyuzhnyy A, Eyers PA, Eyers CE, Bowler-Barnett E, Martin MJ, Sun Z, Deutsch EW, Jones AR. Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation. J Proteome Res 2022; 21:1510-1524. [PMID: 35532924 PMCID: PMC9171898 DOI: 10.1021/acs.jproteome.2c00131] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Public phosphorylation databases such as PhosphoSitePlus (PSP) and PeptideAtlas (PA) compile results from published papers or openly available mass spectrometry (MS) data. However, there is no database-level control for false discovery of sites, likely leading to the overestimation of true phosphosites. By profiling the human phosphoproteome, we estimate the false discovery rate (FDR) of phosphosites and predict a more realistic count of true identifications. We rank sites into phosphorylation likelihood sets and analyze them in terms of conservation across 100 species, sequence properties, and functional annotations. We demonstrate significant differences between the sets and develop a method for independent phosphosite FDR estimation. Remarkably, we report estimated FDRs of 84, 98, and 82% within sets of phosphoserine (pSer), phosphothreonine (pThr), and phosphotyrosine (pTyr) sites, respectively, that are supported by only a single piece of identification evidence─the majority of sites in PSP. We estimate that around 62 000 Ser, 8000 Thr, and 12 000 Tyr phosphosites in the human proteome are likely to be true, which is lower than most published estimates. Furthermore, our analysis estimates that 86 000 Ser, 50 000 Thr, and 26 000 Tyr phosphosites are likely false-positive identifications, highlighting the significant potential of false-positive data to be present in phosphorylation databases.
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Affiliation(s)
- Anton Kalyuzhnyy
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, U.K.,Computational Biology Facility, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, U.K
| | - Patrick A Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, U.K
| | - Claire E Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, U.K.,Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, U.K
| | - Emily Bowler-Barnett
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, U.K
| | - Maria J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, U.K
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Andrew R Jones
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, U.K.,Computational Biology Facility, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, U.K
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20
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Zhang T, Fassl A, Vaites LP, Fu S, Sicinski P, Paulo JA, Gygi SP. Interrogating Kinase-Substrate Relationships with Proximity Labeling and Phosphorylation Enrichment. J Proteome Res 2022; 21:494-506. [PMID: 35044772 PMCID: PMC9142857 DOI: 10.1021/acs.jproteome.1c00865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Kinases govern many cellular responses through the reversible transfer of a phosphate moiety to their substrates. However, pairing a substrate with a kinase is challenging. In proximity labeling experiments, proteins proximal to a target protein are marked by biotinylation, and mass spectrometry can be used for their identification. Here, we combine ascorbate peroxidase (APEX) proximity labeling and a phosphorylation enrichment-based workflow, Phospho-APEX (pAPEX), to rapidly identify phosphorylated and biotinylated neighbor proteins which can be considered for candidate substrates. The pAPEX strategy enriches and quantifies differences in proximity for proteins and phosphorylation sites proximal to an APEX2-tagged kinase under the kinase "ON" and kinase "OFF" conditions. As a proof of concept, we identified candidate substrates of MAPK1 in HEK293T and HCT116 cells and candidate substrates of PKA in HEK293T cells. In addition to many known substrates, C15orf39 was identified and confirmed as a novel MAPK1 substrate. In all, we adapted the proximity labeling-based platform to accommodate phosphorylation analysis for kinase substrate identification.
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Affiliation(s)
- Tian Zhang
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Laura P. Vaites
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sipei Fu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
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21
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Chen Y, Wu X, Zhang J, Pan G, Wang X, Guo X, Wang J, Cui X, Gao H, Cheng M, Yang J, Zhang C, Jiang F. Amino acid starvation-induced LDLR trafficking accelerates lipoprotein endocytosis and LDL clearance. EMBO Rep 2022; 23:e53373. [PMID: 34994492 PMCID: PMC8892268 DOI: 10.15252/embr.202153373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 12/20/2022] Open
Abstract
Mammalian cells utilize Akt‐dependent signaling to deploy intracellular Glut4 toward cell surface to facilitate glucose uptake. Low‐density lipoprotein receptor (LDLR) is the cargo receptor mediating endocytosis of apolipoprotein B‐containing lipoproteins. However, signaling‐controlled regulation of intracellular LDLR trafficking remains elusive. Here, we describe a unique amino acid stress response, which directs the deployment of intracellular LDLRs, causing enhanced LDL endocytosis, likely via Ca2+ and calcium/calmodulin‐dependent protein kinase II‐mediated signalings. This response is independent of induction of autophagy. Amino acid stress‐induced increase in LDL uptake in vitro is comparable to that by pravastatin. In vivo, acute AAS challenge for up to 72 h enhanced the rate of hepatic LDL uptake without changing the total expression level of LDLR. Reducing dietary amino acids by 50% for 2 to 4 weeks ameliorated high fat diet‐induced hypercholesterolemia in heterozygous LDLR‐deficient mice, with reductions in both LDL and VLDL fractions. We suggest that identification of signaling‐controlled regulation of intracellular LDLR trafficking has advanced our understanding of the LDLR biology, and may benefit future development of additional therapeutic strategies for treating hypercholesterolemia.
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Affiliation(s)
- Ye Chen
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Cardiovascular Proteomics of Shandong Province, Department of Geriatrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiao Wu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Jinan, China.,The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Jing Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Guopin Pan
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiaoyun Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiaosun Guo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jianli Wang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, China
| | - Xiaopei Cui
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Department of Geriatrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Haiqing Gao
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Department of Geriatrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Mei Cheng
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Department of Geriatrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jingwen Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Cheng Zhang
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Jinan, China.,The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Fan Jiang
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Department of Geriatrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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22
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Tsai CF, Ogata K, Sugiyama N, Ishihama Y. Motif-centric phosphoproteomics to target kinase-mediated signaling pathways. CELL REPORTS METHODS 2022; 2:100138. [PMID: 35474870 PMCID: PMC9017188 DOI: 10.1016/j.crmeth.2021.100138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/08/2021] [Accepted: 12/13/2021] [Indexed: 12/27/2022]
Abstract
Identifying cellular phosphorylation pathways based on kinase-substrate relationships is a critical step to understanding the regulation of physiological functions in cells. Mass spectrometry-based phosphoproteomics workflows have made it possible to comprehensively collect information on individual phosphorylation sites in a variety of samples. However, there is still no generic approach to uncover phosphorylation networks based on kinase-substrate relationships in rare cell populations. Here, we describe a motif-centric phosphoproteomics approach combined with multiplexed isobaric labeling, in which in vitro kinase reactions are used to generate targeted phosphopeptides, which are spiked into one of the isobaric channels to increase detectability. Proof-of-concept experiments demonstrate selective and comprehensive quantification of targeted phosphopeptides by using multiple kinases for motif-centric channels. More than 7,000 tyrosine phosphorylation sites were quantified from several tens of micrograms of starting materials. This approach enables the quantification of multiple phosphorylation pathways under physiological or pathological regulation in a motif-centric manner.
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Affiliation(s)
- Chia-Feng Tsai
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Kosuke Ogata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Naoyuki Sugiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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23
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Group I Metabotropic Glutamate Receptors and Interacting Partners: An Update. Int J Mol Sci 2022; 23:ijms23020840. [PMID: 35055030 PMCID: PMC8778124 DOI: 10.3390/ijms23020840] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/09/2022] [Accepted: 01/10/2022] [Indexed: 12/21/2022] Open
Abstract
Group I metabotropic glutamate (mGlu) receptors (mGlu1/5 subtypes) are G protein-coupled receptors and are broadly expressed in the mammalian brain. These receptors play key roles in the modulation of normal glutamatergic transmission and synaptic plasticity, and abnormal mGlu1/5 signaling is linked to the pathogenesis and symptomatology of various mental and neurological disorders. Group I mGlu receptors are noticeably regulated via a mechanism involving dynamic protein-protein interactions. Several synaptic protein kinases were recently found to directly bind to the intracellular domains of mGlu1/5 receptors and phosphorylate the receptors at distinct amino acid residues. A variety of scaffolding and adaptor proteins also interact with mGlu1/5. Constitutive or activity-dependent interactions between mGlu1/5 and their interacting partners modulate trafficking, anchoring, and expression of the receptors. The mGlu1/5-associated proteins also finetune the efficacy of mGlu1/5 postreceptor signaling and mGlu1/5-mediated synaptic plasticity. This review analyzes the data from recent studies and provides an update on the biochemical and physiological properties of a set of proteins or molecules that interact with and thus regulate mGlu1/5 receptors.
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24
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Chen JS, Jones CM, Igarashi MG, Ren L, Johnson AE, Gould KL. Localization of the ubiquitin ligase Dma1 to the fission yeast contractile ring is modulated by phosphorylation. FEBS Lett 2021; 595:2781-2792. [PMID: 34674264 PMCID: PMC8721890 DOI: 10.1002/1873-3468.14211] [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: 09/06/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 11/06/2022]
Abstract
The timing of cytokinesis relative to other mitotic events in the fission yeast Schizosaccharomyces pombe is controlled by the septation initiation network (SIN). During a mitotic checkpoint, the SIN is inhibited by the E3 ubiquitin ligase Dma1 to prevent chromosome mis-segregation. Dma1 dynamically localizes to spindle pole bodies (SPBs) and the contractile ring (CR) during mitosis, though its role at the CR is unknown. Here, we examined whether Dma1 phosphorylation affects its localization or function. We found that preventing Dma1 phosphorylation by substituting the six phosphosites with alanines diminished its CR localization but did not affect its mitotic checkpoint function. These studies reinforce the conclusion that Dma1 localization to the SPB is key to its role in the mitotic checkpoint.
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Affiliation(s)
- Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240
| | | | - Maya G. Igarashi
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240
| | - Liping Ren
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240
| | | | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240
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25
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Structural Insights into Protein Regulation by Phosphorylation and Substrate Recognition of Protein Kinases/Phosphatases. Life (Basel) 2021; 11:life11090957. [PMID: 34575106 PMCID: PMC8467178 DOI: 10.3390/life11090957] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/05/2021] [Accepted: 09/10/2021] [Indexed: 12/30/2022] Open
Abstract
Protein phosphorylation is one of the most widely observed and important post-translational modification (PTM) processes. Protein phosphorylation is regulated by protein kinases, each of which covalently attaches a phosphate group to an amino acid side chain on a serine (Ser), threonine (Thr), or tyrosine (Tyr) residue of a protein, and by protein phosphatases, each of which, conversely, removes a phosphate group from a phosphoprotein. These reversible enzyme activities provide a regulatory mechanism by activating or deactivating many diverse functions of proteins in various cellular processes. In this review, their structures and substrate recognition are described and summarized, focusing on Ser/Thr protein kinases and protein Ser/Thr phosphatases, and the regulation of protein structures by phosphorylation. The studies reviewed here and the resulting information could contribute to further structural, biochemical, and combined studies on the mechanisms of protein phosphorylation and to drug discovery approaches targeting protein kinases or protein phosphatases.
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26
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Najar MA, Aravind A, Dagamajalu S, Sidransky D, Ashktorab H, Smoot DT, Gowda H, Prasad TSK, Modi PK, Chatterjee A. Hyperactivation of MEK/ERK pathway by Ca 2+ /calmodulin-dependent protein kinase kinase 2 promotes cellular proliferation by activating cyclin-dependent kinases and minichromosome maintenance protein in gastric cancer cells. Mol Carcinog 2021; 60:769-783. [PMID: 34437731 DOI: 10.1002/mc.23343] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 01/04/2023]
Abstract
Although CAMKK2 is overexpressed in several cancers, its role and relevant downstream signaling pathways in gastric cancer (GC) are poorly understood. Treatment of AGS GC cells with a CAMKK2 inhibitor, STO-609, resulted in decreased cell proliferation, cell migration, invasion, colony-forming ability, and G1/S-phase arrest. Quantitative phosphoproteomics in AGS cells with the CAMKK2 inhibitor led to the identification of 9603 unique phosphosites mapping to 3120 proteins. We observed decreased phosphorylation of 1101 phosphopeptides (1.5-fold) corresponding to 752 proteins upon CAMKK2 inhibition. Bioinformatics analysis of hypo-phosphorylated proteins revealed enrichment of MAPK1/MAPK3 signaling. Kinase enrichment analysis of hypo-phosphorylated proteins using the X2K Web tool identified ERK1, cyclin-dependant kinase 1 (CDK1), and CDK2 as downstream substrates of CAMKK2. Moreover, inhibition of CAMKK2 and MEK1 resulted in decreased phosphorylation of ERK1, CDK1, MCM2, and MCM3. Immunofluorescence results were in concordance with our mass spectroscopy data and Western blot analysis results. Taken together, our data reveal the essential role of CAMKK2 in the pathobiology of GC through the activation of the MEK/ERK1 signaling cascade.
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Affiliation(s)
- Mohd A Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Anjana Aravind
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hassan Ashktorab
- Department of Medicine, Howard University, Washington, District of Columbia, USA
| | - Duane T Smoot
- Department of Medicine, Meharry Medical Center, Nashville, Tennessee, USA
| | - Harsha Gowda
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.,Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Prashant K Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Aditi Chatterjee
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.,Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
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27
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Phosphatase and Kinase Substrate Specificity Profiling with Pooled Synthetic Peptides and Mass Spectrometry. Methods Mol Biol 2021. [PMID: 34085215 DOI: 10.1007/978-1-0716-1538-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Reversible phosphorylation is a pervasive regulatory event in cellular physiology controlled by reciprocal actions of protein kinases and phosphatases. Determining the inherent substrate specificity of kinases and phosphatases is essential for understanding their cellular roles. Synthetic peptides have long served as substrate proxies for defining intrinsic kinase and phosphatase specificities. Here, we describe a high throughput protocol to simultaneously measure specificity constants (kcat/KM) of many synthetic peptide substrates in a single pool using label-free quantitative mass spectrometry. The generation of specificity constants from a single pooled reaction provides a rigorous and rapid comparison of substrate variants to help define an enzyme's specificity. Equally applicable to kinases and phosphatases, as well as other enzyme classes, the protocol consists of three general steps: (1) reaction of enzyme with pooled peptide substrates, each ideally with a unique mass and at concentrations well below KM, (2) analysis of reaction products using liquid chromatography-coupled mass spectrometry (LC-MS), and (3) automated extraction and integration of elution peaks for each substrate/product pair. We incorporate an ionization correction strategy allowing direct calculation of reaction progress, and subsequently kcat/KM, from substrate and product peak areas in a single sample, obviating the need for stable isotope labeling. Peptide consumption is minimal, and high peptide purity and accurate concentrations are not required. Access to a high-resolution LC-MS system is the only nonstandard equipment need. We present an analysis pipeline consisting entirely of established open-source software tools, and demonstrate proof of principle with the highly selective cell cycle phosphatase Cdc14 from Saccharomyces cerevisiae.
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28
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Longhena F, Faustini G, Brembati V, Pizzi M, Benfenati F, Bellucci A. An updated reappraisal of synapsins: structure, function and role in neurological and psychiatric disorders. Neurosci Biobehav Rev 2021; 130:33-60. [PMID: 34407457 DOI: 10.1016/j.neubiorev.2021.08.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/29/2021] [Accepted: 08/09/2021] [Indexed: 01/02/2023]
Abstract
Synapsins (Syns) are phosphoproteins strongly involved in neuronal development and neurotransmitter release. Three distinct genes SYN1, SYN2 and SYN3, with elevated evolutionary conservation, have been described to encode for Synapsin I, Synapsin II and Synapsin III, respectively. Syns display a series of common features, but also exhibit distinctive localization, expression pattern, post-translational modifications (PTM). These characteristics enable their interaction with other synaptic proteins, membranes and cytoskeletal components, which is essential for the proper execution of their multiple functions in neuronal cells. These include the control of synapse formation and growth, neuron maturation and renewal, as well as synaptic vesicle mobilization, docking, fusion, recycling. Perturbations in the balanced expression of Syns, alterations of their PTM, mutations and polymorphisms of their encoding genes induce severe dysregulations in brain networks functions leading to the onset of psychiatric or neurological disorders. This review presents what we have learned since the discovery of Syn I in 1977, providing the state of the art on Syns structure, function, physiology and involvement in central nervous system disorders.
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Affiliation(s)
- Francesca Longhena
- Division of Pharmacology, Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy.
| | - Gaia Faustini
- Division of Pharmacology, Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy.
| | - Viviana Brembati
- Division of Pharmacology, Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy.
| | - Marina Pizzi
- Division of Pharmacology, Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy.
| | - Fabio Benfenati
- Italian Institute of Technology, Via Morego 30, Genova, Italy; IRCSS Policlinico San Martino Hospital, Largo Rosanna Benzi 10, 16132, Genova, Italy.
| | - Arianna Bellucci
- Division of Pharmacology, Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy; Laboratory for Preventive and Personalized Medicine, Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy.
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29
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Abstract
The chronification of pain can be attributed to changes in membrane receptors and channels underlying neuronal plasticity and signal transduction largely within nociceptive neurons that initiate and maintain pathological pain states. These proteins are subject to dynamic modification by posttranslational modifications, creating a code that controls protein function in time and space. Phosphorylation is an important posttranslational modification that affects ∼30% of proteins in vivo. Increased phosphorylation of various nociceptive ion channels and of their modulators underlies sensitization of different pain states. Cyclin-dependent kinases are proline-directed serine/threonine kinases that impact various biological and cellular systems. Cyclin-dependent kinase 5 (Cdk5), one member of this kinase family, and its activators p35 and p39 are expressed in spinal nerves, dorsal root ganglia, and the dorsal horn of the spinal cord. In neuropathic pain conditions, expression and/or activity of Cdk5 is increased, implicating Cdk5 in nociception. Experimental evidence suggests that Cdk5 is regulated through its own phosphorylation, through increasing p35's interaction with Cdk5, and through cleavage of p35 into p25. This narrative review discusses the molecular mechanisms of Cdk5-mediated regulation of target proteins involved in neuropathic pain. We focus on Cdk5 substrates that have been linked to nociceptive pathways, including channels (eg, transient receptor potential cation channel and voltage-gated calcium channel), proteins involved in neurotransmitter release (eg, synaptophysin and collapsin response mediator protein 2), and receptors (eg, glutamate, purinergic, and opioid). By altering the phosphoregulatory "set point" of proteins involved in pain signaling, Cdk5 thus appears to be an attractive target for treating neuropathic pain conditions.
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30
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Zhang Z, Tian S, Wu C, Yan L, Wan J, Zhang J, Liu X, Zhang W. Comprehensive bioinformatics analysis reveals kinase activity profiling associated with heart failure. J Cell Biochem 2021; 122:1126-1140. [PMID: 33899242 DOI: 10.1002/jcb.29935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/22/2021] [Indexed: 01/27/2023]
Abstract
Heart failure is a complex clinical syndrome originating from cardiac injury, which leads to considerable morbidity and mortality. Among the dynamic molecular adaptations occurring in heart failure development, aggravation of the disease is often attributed to global or local abnormality of the kinase. Therefore, the overall monitoring of kinase activity is indispensable. In this study, a bioinformatics analysis method was developed to conduct deep mining of transcriptome and phosphoproteome in failing heart tissue. A total of 982 differentially expressed genes and 9781 phosphorylation sites on 3252 proteins were identified. Via upstream regulator relations and kinase-substrate relations, a dendrogram of kinases can be constructed to monitor its abnormality. The results show that, on the dendrogram, the distribution of kinases demonstrated complex kinase activity changes and certain rules that occur during heart failure. Finally, we also identified the hub kinases in heart failure and verified the expression of these kinases by reverse-transcription polymerase chain reaction and Western blot analysis. In conclusion, for the first time, we have systematically analyzed the differences in kinases during heart failure and provided an unprecedented breadth of multi-omics data. These results can bring about a sufficient data foundation and novel research perspectives.
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Affiliation(s)
- Zhen Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Saisai Tian
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Chennan Wu
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Li Yan
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Jingjing Wan
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Jinbo Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Xia Liu
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Weidong Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China
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31
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Borgo C, D'Amore C, Cesaro L, Sarno S, Pinna LA, Ruzzene M, Salvi M. How can a traffic light properly work if it is always green? The paradox of CK2 signaling. Crit Rev Biochem Mol Biol 2021; 56:321-359. [PMID: 33843388 DOI: 10.1080/10409238.2021.1908951] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
CK2 is a constitutively active protein kinase that assuring a constant level of phosphorylation to its numerous substrates supports many of the most important biological functions. Nevertheless, its activity has to be controlled and adjusted in order to cope with the varying needs of a cell, and several examples of a fine-tune regulation of its activity have been described. More importantly, aberrant regulation of this enzyme may have pathological consequences, e.g. in cancer, chronic inflammation, neurodegeneration, and viral infection. Our review aims at summarizing our current knowledge about CK2 regulation. In the first part, we have considered the most important stimuli shown to affect protein kinase CK2 activity/expression. In the second part, we focus on the molecular mechanisms by which CK2 can be regulated, discussing controversial aspects and future perspectives.
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Affiliation(s)
- Christian Borgo
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Claudio D'Amore
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Luca Cesaro
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Stefania Sarno
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Lorenzo A Pinna
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,CNR Institute of Neurosciences, Padova, Italy
| | - Maria Ruzzene
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,CNR Institute of Neurosciences, Padova, Italy
| | - Mauro Salvi
- Department of Biomedical Sciences, University of Padova, Padova, Italy
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32
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Jafari S, Farsani FM, Ganji M, Ganjalikhany MR. The functional regulatory details of ERK2 in complex with RSK1: an in silico insight. RSC Adv 2021; 11:11048-11056. [PMID: 35423626 PMCID: PMC8695832 DOI: 10.1039/d1ra01020d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 03/01/2021] [Indexed: 12/12/2022] Open
Abstract
Protein kinases play a significant role in cellular activation procedures by exhibiting a vivid selection in the target, as well as recognizing and phosphorylating them. Extracellular signal-regulated kinase 2 (ERK2) is one of the main kinases in the mitogen-activated protein kinase (MAPK) signaling cascade and engages in dynamically regulating the activities of signaling proteins and physiological processes, including cell proliferation, differentiation, adhesion, migration, and survival. Predicting collective dynamic and structural motions in biological macromolecules is pivotal to obtain a better understanding of the majority of biological processes. Here, through molecular dynamic simulation and normal mode analysis, we investigated ERK2 conformations, in the forms of active (phosphorylated), inactive (unphosphorylated), and in a complex with its substrate, ribosomal protein S6 kinase alpha-1 (RSK1), to determine functional characteristics. Our finding demonstrated that ERK2 plays a switch role in the regulation of pathways. In the case that this protein kinase is in the active form, all critical regions shift to be prepared to accept the substrate and catalytic action. Meanwhile, inactive ERK2 shows contrasting results in which all motions tend to close the catalytic site and cease the phosphorylation action in the MAPK cascade. These findings are in line with those from other similar studies and provide us with novel molecular target regions and recent details on how this mechanism works. DFG, αC-helix orientation regarding the active site position and distance between K54 and Glu71 in the active and inactive states of ERK2.![]()
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Affiliation(s)
- Sepideh Jafari
- Department of Cell and Molecular Biology, Faculty of Biological Science and Technology, University of Isfahan Isfahan Iran +98-31-37932250 +98-31-37932250
| | - Farzaneh Mohamadi Farsani
- Department of Cell and Molecular Biology, Faculty of Biological Science and Technology, University of Isfahan Isfahan Iran +98-31-37932250 +98-31-37932250
| | - Maziar Ganji
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences Tehran Iran
| | - Mohamad Reza Ganjalikhany
- Department of Cell and Molecular Biology, Faculty of Biological Science and Technology, University of Isfahan Isfahan Iran +98-31-37932250 +98-31-37932250
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33
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Gubas A, Karantanou C, Popovic D, Tascher G, Hoffmann ME, Platzek A, Dawe N, Dikic I, Krause DS, McEwan DG. The endolysosomal adaptor PLEKHM1 is a direct target for both mTOR and MAPK pathways. FEBS Lett 2021; 595:864-880. [PMID: 33452816 DOI: 10.1002/1873-3468.14041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 12/21/2022]
Abstract
The lysosome is a cellular signalling hub at the point of convergence of endocytic and autophagic pathways, where the contents are degraded and recycled. Pleckstrin homology domain-containing family member 1 (PLEKHM1) acts as an adaptor to facilitate the fusion of endocytic and autophagic vesicles with the lysosome. However, it is unclear how PLEKHM1 function at the lysosome is controlled. Herein, we show that PLEKHM1 coprecipitates with, and is directly phosphorylated by, mTOR. Using a phosphospecific antibody against Ser432/S435 of PLEKHM1, we show that the same motif is a direct target for ERK2-mediated phosphorylation in a growth factor-dependent manner. This dual regulation of PLEKHM1 at a highly conserved region points to a convergence of both growth factor- and amino acid-sensing pathways, placing PLEKHM1 at a critical juncture of cellular metabolism.
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Affiliation(s)
- Andrea Gubas
- Faculty of Medicine, Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Christina Karantanou
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Medicine, Frankfurt, Germany.,Goethe University Frankfurt, Frankfurt, Germany
| | - Doris Popovic
- Faculty of Medicine, Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Georg Tascher
- Faculty of Medicine, Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marina E Hoffmann
- Faculty of Medicine, Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anna Platzek
- Faculty of Medicine, Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Nina Dawe
- Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, UK
| | - Ivan Dikic
- Faculty of Medicine, Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany.,Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Daniela S Krause
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Medicine, Frankfurt, Germany.,Goethe University Frankfurt, Frankfurt, Germany
| | - David G McEwan
- Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, UK.,Cancer Research UK Beatson Institute, Garscube Estate, Glasgow, UK
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Rosales M, Rodríguez-Ulloa A, Besada V, Ramón AC, Pérez GV, Ramos Y, Guirola O, González LJ, Zettl K, Wiśniewski JR, Perera Y, Perea SE. Phosphoproteomic Landscape of AML Cells Treated with the ATP-Competitive CK2 Inhibitor CX-4945. Cells 2021; 10:cells10020338. [PMID: 33562780 PMCID: PMC7915770 DOI: 10.3390/cells10020338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/30/2021] [Accepted: 02/02/2021] [Indexed: 12/13/2022] Open
Abstract
Casein kinase 2 (CK2) regulates a plethora of proteins with pivotal roles in solid and hematological neoplasia. Particularly, in acute myeloid leukemia (AML) CK2 has been pointed as an attractive therapeutic target and prognostic marker. Here, we explored the impact of CK2 inhibition over the phosphoproteome of two cell lines representing major AML subtypes. Quantitative phosphoproteomic analysis was conducted to evaluate changes in phosphorylation levels after incubation with the ATP-competitive CK2 inhibitor CX-4945. Functional enrichment, network analysis, and database mining were performed to identify biological processes, signaling pathways, and CK2 substrates that are responsive to CX-4945. A total of 273 and 1310 phosphopeptides were found differentially modulated in HL-60 and OCI-AML3 cells, respectively. Despite regulated phosphopeptides belong to proteins involved in multiple biological processes and signaling pathways, most of these perturbations can be explain by direct CK2 inhibition rather than off-target effects. Furthermore, CK2 substrates regulated by CX-4945 are mainly related to mRNA processing, translation, DNA repair, and cell cycle. Overall, we evidenced that CK2 inhibitor CX-4945 impinge on mediators of signaling pathways and biological processes essential for primary AML cells survival and chemosensitivity, reinforcing the rationale behind the pharmacologic blockade of protein kinase CK2 for AML targeted therapy.
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Affiliation(s)
- Mauro Rosales
- Department of Animal and Human Biology, Faculty of Biology, University of Havana (UH), Havana 10400, Cuba;
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (A.C.R.); (G.V.P.)
| | - Arielis Rodríguez-Ulloa
- Mass Spectrometry Laboratory, Proteomics Group, Department of Systems Biology, Biomedical Research Division, CIGB, Havana 10600, Cuba; (A.R.-U.); (V.B.); (Y.R.); (L.J.G.)
| | - Vladimir Besada
- Mass Spectrometry Laboratory, Proteomics Group, Department of Systems Biology, Biomedical Research Division, CIGB, Havana 10600, Cuba; (A.R.-U.); (V.B.); (Y.R.); (L.J.G.)
| | - Ailyn C. Ramón
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (A.C.R.); (G.V.P.)
| | - George V. Pérez
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (A.C.R.); (G.V.P.)
| | - Yassel Ramos
- Mass Spectrometry Laboratory, Proteomics Group, Department of Systems Biology, Biomedical Research Division, CIGB, Havana 10600, Cuba; (A.R.-U.); (V.B.); (Y.R.); (L.J.G.)
| | - Osmany Guirola
- Bioinformatics Group, Department of Systems Biology, Biomedical Research Division, CIGB, Havana 10600, Cuba;
| | - Luis J. González
- Mass Spectrometry Laboratory, Proteomics Group, Department of Systems Biology, Biomedical Research Division, CIGB, Havana 10600, Cuba; (A.R.-U.); (V.B.); (Y.R.); (L.J.G.)
| | - Katharina Zettl
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, 82152 Munich, Germany; (K.Z.); (J.R.W.)
| | - Jacek R. Wiśniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, 82152 Munich, Germany; (K.Z.); (J.R.W.)
| | - Yasser Perera
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (A.C.R.); (G.V.P.)
- China-Cuba Biotechnology Joint Innovation Center (CCBJIC), Yongzhou Zhong Gu Biotechnology Co., Ltd, Lengshuitan District, Yongzhou 425000, China
- Correspondence: (Y.P.); (S.E.P.)
| | - Silvio E. Perea
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (A.C.R.); (G.V.P.)
- Correspondence: (Y.P.); (S.E.P.)
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35
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Singh P, Pesenti ME, Maffini S, Carmignani S, Hedtfeld M, Petrovic A, Srinivasamani A, Bange T, Musacchio A. BUB1 and CENP-U, Primed by CDK1, Are the Main PLK1 Kinetochore Receptors in Mitosis. Mol Cell 2021; 81:67-87.e9. [PMID: 33248027 PMCID: PMC7837267 DOI: 10.1016/j.molcel.2020.10.040] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 09/08/2020] [Accepted: 10/28/2020] [Indexed: 02/02/2023]
Abstract
Reflecting its pleiotropic functions, Polo-like kinase 1 (PLK1) localizes to various sub-cellular structures during mitosis. At kinetochores, PLK1 contributes to microtubule attachments and mitotic checkpoint signaling. Previous studies identified a wealth of potential PLK1 receptors at kinetochores, as well as requirements for various mitotic kinases, including BUB1, Aurora B, and PLK1 itself. Here, we combine ectopic localization, in vitro reconstitution, and kinetochore localization studies to demonstrate that most and likely all of the PLK1 is recruited through BUB1 in the outer kinetochore and centromeric protein U (CENP-U) in the inner kinetochore. BUB1 and CENP-U share a constellation of sequence motifs consisting of a putative PP2A-docking motif and two neighboring PLK1-docking sites, which, contingent on priming phosphorylation by cyclin-dependent kinase 1 and PLK1 itself, bind PLK1 and promote its dimerization. Our results rationalize previous observations and describe a unifying mechanism for recruitment of PLK1 to human kinetochores.
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Affiliation(s)
- Priyanka Singh
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Marion E Pesenti
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Stefano Maffini
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Sara Carmignani
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Marius Hedtfeld
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Arsen Petrovic
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Anupallavi Srinivasamani
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Tanja Bange
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany; Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitätsstrasse, 45141 Essen, Germany.
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36
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Bradley D, Viéitez C, Rajeeve V, Selkrig J, Cutillas PR, Beltrao P. Sequence and Structure-Based Analysis of Specificity Determinants in Eukaryotic Protein Kinases. Cell Rep 2021; 34:108602. [PMID: 33440154 PMCID: PMC7809594 DOI: 10.1016/j.celrep.2020.108602] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/03/2020] [Accepted: 12/14/2020] [Indexed: 01/04/2023] Open
Abstract
Protein kinases lie at the heart of cell-signaling processes and are often mutated in disease. Kinase target recognition at the active site is in part determined by a few amino acids around the phosphoacceptor residue. However, relatively little is known about how most preferences are encoded in the kinase sequence or how these preferences evolved. Here, we used alignment-based approaches to predict 30 specificity-determining residues (SDRs) for 16 preferences. These were studied with structural models and were validated by activity assays of mutant kinases. Cancer mutation data revealed that kinase SDRs are mutated more frequently than catalytic residues. We have observed that, throughout evolution, kinase specificity has been strongly conserved across orthologs but can diverge after gene duplication, as illustrated by the G protein-coupled receptor kinase family. The identified SDRs can be used to predict kinase specificity from sequence and aid in the interpretation of evolutionary or disease-related genomic variants.
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Affiliation(s)
- David Bradley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Cristina Viéitez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Vinothini Rajeeve
- Integrative Cell Signalling & Proteomics, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Joel Selkrig
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Pedro R Cutillas
- Integrative Cell Signalling & Proteomics, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK.
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37
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Mullin NP, Varghese J, Colby D, Richardson JM, Findlay GM, Chambers I. Phosphorylation of NANOG by casein kinase I regulates embryonic stem cell self-renewal. FEBS Lett 2021; 595:14-25. [PMID: 33107035 PMCID: PMC7839479 DOI: 10.1002/1873-3468.13969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022]
Abstract
The self-renewal efficiency of mouse embryonic stem cells (ESCs) is determined by the concentration of the transcription factor NANOG. While NANOG binds thousands of sites in chromatin, the regulatory systems that control DNA binding are poorly characterised. Here, we show that NANOG is phosphorylated by casein kinase I, and identify target residues. Phosphomimetic substitutions at phosphorylation sites within the homeodomain (S130 and S131) have site-specific functional effects. Phosphomimetic substitution of S130 abolishes DNA binding by NANOG and eliminates LIF-independent self-renewal. In contrast, phosphomimetic substitution of S131 enhances LIF-independent self-renewal, without influencing DNA binding. Modelling the DNA-homeodomain complex explains the disparate effects of these phosphomimetic substitutions. These results indicate how phosphorylation may influence NANOG homeodomain interactions that underpin ESC self-renewal.
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Affiliation(s)
- Nicholas P. Mullin
- Centre for Regenerative MedicineInstitute for Stem Cell ResearchSchool of Biological SciencesUniversity of EdinburghUK
| | - Joby Varghese
- Protein Phosphorylation and Ubiquitylation UnitJames Black CentreSchool of Life SciencesDundeeUK
| | - Douglas Colby
- Centre for Regenerative MedicineInstitute for Stem Cell ResearchSchool of Biological SciencesUniversity of EdinburghUK
| | - Julia M. Richardson
- Institute of Quantitative Biology, Biochemistry and BiotechnologyEdinburghUK
| | - Greg M. Findlay
- Protein Phosphorylation and Ubiquitylation UnitJames Black CentreSchool of Life SciencesDundeeUK
| | - Ian Chambers
- Centre for Regenerative MedicineInstitute for Stem Cell ResearchSchool of Biological SciencesUniversity of EdinburghUK
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38
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Zhou Y, Pozo PN, Oh S, Stone HM, Cook JG. Distinct and sequential re-replication barriers ensure precise genome duplication. PLoS Genet 2020; 16:e1008988. [PMID: 32841231 PMCID: PMC7473519 DOI: 10.1371/journal.pgen.1008988] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 09/04/2020] [Accepted: 07/12/2020] [Indexed: 01/19/2023] Open
Abstract
Achieving complete and precise genome duplication requires that each genomic segment be replicated only once per cell division cycle. Protecting large eukaryotic genomes from re-replication requires an overlapping set of molecular mechanisms that prevent the first DNA replication step, the DNA loading of MCM helicase complexes to license replication origins, after S phase begins. Previous reports have defined many such origin licensing inhibition mechanisms, but the temporal relationships among them are not clear, particularly with respect to preventing re-replication in G2 and M phases. Using a combination of mutagenesis, biochemistry, and single cell analyses in human cells, we define a new mechanism that prevents re-replication through hyperphosphorylation of the essential MCM loading protein, Cdt1. We demonstrate that Cyclin A/CDK1 can hyperphosphorylate Cdt1 to inhibit MCM re-loading in G2 phase. The mechanism of inhibition is to block Cdt1 binding to MCM independently of other known Cdt1 inactivation mechanisms such as Cdt1 degradation during S phase or Geminin binding. Moreover, our findings suggest that Cdt1 dephosphorylation at the mitosis-to-G1 phase transition re-activates Cdt1. We propose that multiple distinct, non-redundant licensing inhibition mechanisms act in a series of sequential relays through each cell cycle phase to ensure precise genome duplication. The initial step of DNA replication is loading the DNA helicase, MCM, onto DNA during the first phase of the cell division cycle. If MCM loading occurs inappropriately onto DNA that has already been replicated, then cells risk DNA re-replication, a source of endogenous DNA damage and genome instability. How mammalian cells prevent any sections of their very large genomes from re-replicating is still not fully understood. We found that the Cdt1 protein, one of the critical MCM loading factors, is inhibited specifically in late cell cycle stages through a mechanism involving protein phosphorylation. This phosphorylation prevents Cdt1 from binding MCM; when Cdt1 cannot be phosphorylated MCM is inappropriately re-loaded onto DNA and cells are prone to re-replication. When cells divide and transition into G1 phase, Cdt1 is then dephosphorylated to re-activate it for MCM loading. Based on these findings we assert that the different mechanisms that cooperate to avoid re-replication are not redundant. Instead, different cell cycle phases are dominated by different re-replication control mechanisms. These findings have implications for understanding how genomes are duplicated precisely once per cell cycle and shed light on how that process is perturbed by changes in Cdt1 levels or phosphorylation activity.
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Affiliation(s)
- Yizhuo Zhou
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United State of America
| | - Pedro N. Pozo
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United State of America
| | - Seeun Oh
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute and the Research Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United State of America
| | - Haley M. Stone
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United State of America
| | - Jeanette Gowen Cook
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United State of America
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United State of America
- Lineberger Comprehensive Cancer, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United State of America
- * E-mail:
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39
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Nitika, Porter CM, Truman AW, Truttmann MC. Post-translational modifications of Hsp70 family proteins: Expanding the chaperone code. J Biol Chem 2020; 295:10689-10708. [PMID: 32518165 PMCID: PMC7397107 DOI: 10.1074/jbc.rev120.011666] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/08/2020] [Indexed: 02/01/2023] Open
Abstract
Cells must be able to cope with the challenge of folding newly synthesized proteins and refolding those that have become misfolded in the context of a crowded cytosol. One such coping mechanism that has appeared during evolution is the expression of well-conserved molecular chaperones, such as those that are part of the heat shock protein 70 (Hsp70) family of proteins that bind and fold a large proportion of the proteome. Although Hsp70 family chaperones have been extensively examined for the last 50 years, most studies have focused on regulation of Hsp70 activities by altered transcription, co-chaperone "helper" proteins, and ATP binding and hydrolysis. The rise of modern proteomics has uncovered a vast array of post-translational modifications (PTMs) on Hsp70 family proteins that include phosphorylation, acetylation, ubiquitination, AMPylation, and ADP-ribosylation. Similarly to the pattern of histone modifications, the histone code, this complex pattern of chaperone PTMs is now known as the "chaperone code." In this review, we discuss the history of the Hsp70 chaperone code, its currently understood regulation and functions, and thoughts on what the future of research into the chaperone code may entail.
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Affiliation(s)
- Nitika
- Department of Biological Sciences, University of North Carolina, Charlotte, North Carolina, USA
| | - Corey M Porter
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew W Truman
- Department of Biological Sciences, University of North Carolina, Charlotte, North Carolina, USA
| | - Matthias C Truttmann
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
- Geriatrics Center, University of Michigan, Ann Arbor, Michigan, USA
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40
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Kasarpalkar N, Deb B, Kumar P, Bhor VM. The Role of Integrin α 4β 7 Signaling in Human Immunodeficiency Virus-1 Pathogenesis and Viral Entry in Primary CD4 + T Cells As Revealed by Comparative Phosphoproteomic Signatures. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 24:437-450. [PMID: 32522079 DOI: 10.1089/omi.2019.0196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Integrin α4β7, a CD4 independent receptor of human immunodeficiency virus-1 (HIV-1) gp120, defines a subset of CD4+T cells preferentially targeted by HIV. It is also considered as a promising therapeutic target for HIV-1 infection. Despite its role in HIV acquisition and disease progression, HIV-1-mediated integrin α4β7 signaling has not been elucidated so far. In view of this, we determined phosphoproteomic signatures of HIV-1 gp120 signaling as well as signaling mediated by the integrin α4β7 ligand, mucosal vascular addressin cell adhesion molecule-1 (MAdCAM-1), in primary CD4+ T cells. This is the first comprehensive report on MAdCAM-1 signaling, which is believed to enhance HIV-1 replication. Importantly, we identified proteins associated with both classical and nonclassical integrin functions. We observed that HIV-1 gp120 signaling is associated with proteins that have previously not been associated with HIV-1 pathogenesis and thus, need to be explored further. There was a significant overlap in proteins identified by both MAdCAM-1 and HIV-1 gp120 signaling, which most likely represents cellular processes triggered upon interaction of HIV-1 gp120 with integrin α4β7. Pathway analysis revealed enrichment of processes that could facilitate viral replication as well as viral entry through endocytosis. Although these results warrant independent replication and further validation, they suggest the presence of additional potential therapeutic targets. These results also suggest that combinatorial approaches for targeting both HIV-1 gp120 and MAdCAM-1 signaling may be necessary for efficient control of HIV-1 infection as well as novel innovation strategies in HIV therapeutics.
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Affiliation(s)
- Nandini Kasarpalkar
- Department of Molecular Immunology and Microbiology, Indian Council of Medical Research-National Institute for Research in Reproductive Health (ICMR-NIRRH), Mumbai, India
| | - Barnali Deb
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Vikrant M Bhor
- Department of Molecular Immunology and Microbiology, Indian Council of Medical Research-National Institute for Research in Reproductive Health (ICMR-NIRRH), Mumbai, India
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41
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Cyclin-Dependent Kinase-Like 5 (CDKL5): Possible Cellular Signalling Targets and Involvement in CDKL5 Deficiency Disorder. Neural Plast 2020; 2020:6970190. [PMID: 32587608 PMCID: PMC7293752 DOI: 10.1155/2020/6970190] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 12/29/2022] Open
Abstract
Cyclin-dependent kinase-like 5 (CDKL5, also known as STK9) is a serine/threonine protein kinase originally identified in 1998 during a transcriptional mapping project of the human X chromosome. Thereafter, a mutation in CDKL5 was reported in individuals with the atypical Rett syndrome, a neurodevelopmental disorder, suggesting that CDKL5 plays an important regulatory role in neuronal function. The disease associated with CDKL5 mutation has recently been recognised as CDKL5 deficiency disorder (CDD) and has been distinguished from the Rett syndrome owing to its symptomatic manifestation. Because CDKL5 mutations identified in patients with CDD cause enzymatic loss of function, CDKL5 catalytic activity is likely strongly associated with the disease. Consequently, the exploration of CDKL5 substrate characteristics and regulatory mechanisms of its catalytic activity are important for identifying therapeutic target molecules and developing new treatment. In this review, we summarise recent findings on the phosphorylation of CDKL5 substrates and the mechanisms of CDKL5 phosphorylation and dephosphorylation. We also discuss the relationship between changes in the phosphorylation signalling pathways and the Cdkl5 knockout mouse phenotype and consider future prospects for the treatment of mental and neurological disease associated with CDKL5 mutations.
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42
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Quirion B, Bergeron F, Blais V, Gendron L. The Delta-Opioid Receptor; a Target for the Treatment of Pain. Front Mol Neurosci 2020; 13:52. [PMID: 32431594 PMCID: PMC7214757 DOI: 10.3389/fnmol.2020.00052] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/13/2020] [Indexed: 12/15/2022] Open
Abstract
Nowadays, pain represents one of the most important societal burdens. Current treatments are, however, too often ineffective and/or accompanied by debilitating unwanted effects for patients dealing with chronic pain. Indeed, the prototypical opioid morphine, as many other strong analgesics, shows harmful unwanted effects including respiratory depression and constipation, and also produces tolerance, physical dependence, and addiction. The urgency to develop novel treatments against pain while minimizing adverse effects is therefore crucial. Over the years, the delta-opioid receptor (DOP) has emerged as a promising target for the development of new pain therapies. Indeed, targeting DOP to treat chronic pain represents a timely alternative to existing drugs, given the weak unwanted effects spectrum of DOP agonists. Here, we review the current knowledge supporting a role for DOP and its agonists for the treatment of pain. More specifically, we will focus on the cellular and subcellular localization of DOP in the nervous system. We will also discuss in further detail the molecular and cellular mechanisms involved in controlling the cellular trafficking of DOP, known to differ significantly from most G protein-coupled receptors. This review article will allow a better understanding of how DOP represents a promising target to develop new treatments for pain management as well as where we stand as of our ability to control its cellular trafficking and cell surface expression.
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Affiliation(s)
- Béatrice Quirion
- Faculté de Médecine et des Sciences de la Santé, Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Francis Bergeron
- Faculté de Médecine et des Sciences de la Santé, Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Véronique Blais
- Faculté de Médecine et des Sciences de la Santé, Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Louis Gendron
- Faculté de Médecine et des Sciences de la Santé, Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC, Canada
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Zhou J, Chow HM, Liu Y, Wu D, Shi M, Li J, Wen L, Gao Y, Chen G, Zhuang K, Lin H, Zhang G, Xie W, Li H, Leng L, Wang M, Zheng N, Sun H, Zhao Y, Zhang Y, Xue M, Huang TY, Bu G, Xu H, Yuan Z, Herrup K, Zhang J. Cyclin-Dependent Kinase 5-Dependent BAG3 Degradation Modulates Synaptic Protein Turnover. Biol Psychiatry 2020; 87:756-769. [PMID: 31955914 DOI: 10.1016/j.biopsych.2019.11.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 11/28/2022]
Abstract
BACKGROUND Synaptic protein dyshomeostasis and functional loss is an early invariant feature of Alzheimer's disease (AD), yet the unifying etiological pathway remains largely unknown. Knowing that cyclin-dependent kinase 5 (CDK5) plays critical roles in synaptic formation and degeneration, its phosphorylation targets were reexamined in search of candidates with direct global impacts on synaptic protein dynamics, and the associated regulatory network was also analyzed. METHODS Quantitative phosphoproteomics and bioinformatics analyses were performed to identify top-ranked candidates. A series of biochemical assays was used to investigate the associated regulatory signaling networks. Histological, electrochemical, and behavioral assays were performed in conditional knockout, small hairpin RNA-mediated knockdown, and AD-related mice models to evaluate the relevance of CDK5 to synaptic homeostasis and functions. RESULTS Among candidates with known implications in synaptic modulations, BAG3 ranked the highest. CDK5-mediated phosphorylation on S297/S291 (mouse/human) destabilized BAG3. Loss of BAG3 unleashed the selective protein degradative function of the HSP70 machinery. In neurons, this resulted in enhanced degradation of a number of glutamatergic synaptic proteins. Conditional neuronal knockout of Bag3 in vivo led to impairment of learning and memory functions. In human AD and related mouse models, aberrant CDK5-mediated loss of BAG3 yielded similar effects on synaptic homeostasis. Detrimental effects of BAG3 loss on learning and memory functions were confirmed in these mice, and such effects were reversed by ectopic BAG3 reexpression. CONCLUSIONS Our results highlight that the neuronal CDK5-BAG3-HSP70 signaling axis plays a critical role in modulating synaptic homeostasis. Dysregulation of the signaling pathway directly contributes to synaptic dysfunction and AD pathogenesis.
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Affiliation(s)
- Jiechao Zhou
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Hei-Man Chow
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong.
| | - Yan Liu
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China; Department of Traditional Chinese Medicine, Medical College, Xiamen University, Xiamen, Fujian, China
| | - Di Wu
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Meng Shi
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Jieyin Li
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Lei Wen
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China; Department of Traditional Chinese Medicine, Medical College, Xiamen University, Xiamen, Fujian, China
| | - Yuehong Gao
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Guimiao Chen
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Kai Zhuang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Hui Lin
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Guanyun Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Wenting Xie
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Huifang Li
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Lige Leng
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Mengdan Wang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Naizhen Zheng
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Hao Sun
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yingjun Zhao
- Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Yunwu Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Maoqiang Xue
- Department of Basic Medical Science, Medical College, Xiamen University, Xiamen, Fujian, China
| | - Timothy Y Huang
- Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida
| | - Huaxi Xu
- Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Zengqiang Yuan
- The Brain Science Center, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Karl Herrup
- Department of Neurobiology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jie Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, Fujian, China.
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Takla M, Huang CLH, Jeevaratnam K. The cardiac CaMKII-Na v1.5 relationship: From physiology to pathology. J Mol Cell Cardiol 2020; 139:190-200. [PMID: 31958466 DOI: 10.1016/j.yjmcc.2019.12.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/20/2019] [Accepted: 12/30/2019] [Indexed: 12/19/2022]
Abstract
The SCN5A gene encodes Nav1.5, which, as the cardiac voltage-gated Na+ channel's pore-forming α subunit, is crucial for the initiation and propagation of atrial and ventricular action potentials. The arrhythmogenic propensity of inherited SCN5A mutations implicates the Na+ channel in determining cardiomyocyte excitability under normal conditions. Cytosolic kinases have long been known to alter the kinetic profile of Nav1.5 inactivation via phosphorylation of specific residues. Recent substantiation of both the role of calmodulin-dependent kinase II (CaMKII) in modulating the properties of the Nav1.5 inactivation gate and the significant rise in oxidation-dependent autonomous CaMKII activity in structural heart disease has raised the possibility of a novel pathway for acquired arrhythmias - the CaMKII-Nav1.5 relationship. The aim of this review is to: (1) outline the relationship's translation from physiological adaptation to pathological vicious circle; and (2) discuss the relative merits of each of its components as pharmacological targets.
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Affiliation(s)
- Michael Takla
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7AL, United Kingdom
| | - Christopher L-H Huang
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7AL, United Kingdom; Physiological Laboratory, University of Cambridge, Downing Street, Cambridge, CB2 3EG, United Kingdom
| | - Kamalan Jeevaratnam
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7AL, United Kingdom; Physiological Laboratory, University of Cambridge, Downing Street, Cambridge, CB2 3EG, United Kingdom.
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45
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Sharma S, Sicinski P. A kinase of many talents: non-neuronal functions of CDK5 in development and disease. Open Biol 2020; 10:190287. [PMID: 31910742 PMCID: PMC7014686 DOI: 10.1098/rsob.190287] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The cyclin-dependent kinase 5 (CDK5) represents an unusual member of the family of cyclin-dependent kinases, which is activated upon binding to non-cyclin p35 and p39 proteins. The role of CDK5 in the nervous system has been very well established. In addition, there is growing evidence that CDK5 is also active in non-neuronal tissues, where it has been postulated to affect a variety of functions such as the immune response, angiogenesis, myogenesis, melanogenesis and regulation of insulin levels. Moreover, high levels of CDK5 have been observed in different tumour types, and CDK5 was proposed to play various roles in the tumorigenic process. In this review, we discuss these various CDK5 functions in normal physiology and disease, and highlight the therapeutic potential of targeting CDK5.
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Affiliation(s)
- Samanta Sharma
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
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Li Y, Xiang Q, Yao YH, Li JJ, Wang Y, Li XH. Inactivated AMPK-α2 promotes the progression of diabetic brain damage by Cdk5 phosphorylation at Thr485 site. Biochimie 2019; 168:277-284. [PMID: 31786229 DOI: 10.1016/j.biochi.2019.11.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 11/18/2019] [Indexed: 02/01/2023]
Abstract
Changes in brain energy metabolism in diabetes mellitus, including increased insulin resistance and mitochondrial dysfunction, are critically involved in diabetes-related neurodegeneration, and associate with early cognitive impairment as well. The aim of this study is to detect the specific phosphorylated-Thr485- AMP-activated protein kinase (AMPK-α2), regulated by cyclin-dependent kinase 5 (Cdk5) paly the inhibitory functional role of AMPK-α2, Which is maybe the link to the accelerated diabetic brain damage progression. Here, we used GK rats, the type 2 diabetic animal model for in vivo studies and performed In vitro kinase assay, high glucose treatment, -phosphorylated mutation and protein expression in both HEK-293T and HT-22 cell lines. In vitro, the results show that murine wild-type AMPK-α2 was phosphorylated by Cdk5 at a (S/T)PX(K/H/R) phosphorylation consensus sequence, which was associated with decreased AMPK-α2 activity. Surprisingly, mutation of Thr485 to alanine in AMPK-α2 results in the abolished Cdk5 effects, demonstrating that Thr485-phosphorylation is critical to AMPK-α2 inhibition by Cdk5. In addition, these alterations in AMPK-α2-phosphorylation and -activity induced by Cdk5 is specific at Thr485. Furthermore, in GK rats, the increased phosphorylated- Thr 485 of AMPK-α2 results in the decreased AMPK-α2 activity, which is correlated with the apoptosis of neurons in hippocamps. After high glucose treatment, the decreased survival showed in AMPK-α2T485A HT-22 cells compared to AMPK-α2WT. The down-regulated of p-CREB, SNAP25, synaptophysin as well as synapsin-1were shown in both GK rats and HT-22 cell line. Meanwhile, pre-treated with either the specific Cdk5-inhibitor (roscovitine) or the antidiabetic AMPK-α2-inhibitor (metformin) could restore the alterations in neuronal protein expression. Our results suggest that Cdk5-mediated phosphorylated- Thr485 in AMPK-α2 may be involved in the pathogenesis of diabetic brain damage.
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Affiliation(s)
- Yan Li
- College of Medicine, Jishou University, Hunan Province, PR China
| | - Qiong Xiang
- Institute of Medicine, Medical Research Center, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, Jishou University, Hunan Province, PR China
| | - Yu-Han Yao
- College of Medicine, Jishou University, Hunan Province, PR China
| | - Jing-Jing Li
- College of Medicine, Jishou University, Hunan Province, PR China
| | - Yan Wang
- Pharmacy Department, The First People's Hospital of Foshan, Foshan City, Guang Dong Province, PR China
| | - Xian-Hui Li
- Institute of Medicine, Medical Research Center, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, Jishou University, Hunan Province, PR China.
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T cell receptor signaling results in ERK-dependent Ser163 phosphorylation of lymphocyte phosphatase-associated phosphoprotein. Biochem Biophys Res Commun 2019; 519:559-565. [PMID: 31537385 DOI: 10.1016/j.bbrc.2019.09.041] [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: 08/07/2019] [Accepted: 09/11/2019] [Indexed: 11/22/2022]
Abstract
Lymphocyte phosphatase-associated phosphoprotein (LPAP) is a transmembrane protein tightly associated with the phosphatase CD45, which regulates antigen specific lymphocyte activation. Although LPAP is positioned in close proximity to key signaling molecules, its function remains unknown. In this study, we investigated signaling pathways involved in LPAP phosphorylation. Using phosphospecific antibodies generated in our laboratory, we analyzed changes in LPAP phosphorylation in response to various stimuli. Cross-linking with antibodies against TCR or BCR, as well as ionophores and Thapsigargin, resulted in rapid dephosphorylation at Ser172 and Ser99 followed by phosphorylation at Ser163. A panel of inhibitors allowed us to show that PMA and TCR cross-linkage engages the MEK-ERK pathway to drive phosphorylation of LPAP at Ser163. The ERK1/2 kinase was the most distal element in the cascade, which when inhibited prevented changes in LPAP phosphorylation. Supporting this, we found that ERK1 is capable of phosphorylating LPAP at Ser163 in vitro. Although the functional role of this event is yet to be revealed, we provide evidence for a new ERK1/2 target in lymphocytes, namely LPAP, representing a potential regulatory mechanism in the signaling cascade.
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Rahm M, Merl-Pham J, Adamski J, Hauck SM. Time-resolved phosphoproteomic analysis elucidates hepatic 11,12-Epoxyeicosatrienoic acid signaling pathways. Prostaglandins Other Lipid Mediat 2019; 146:106387. [PMID: 31669255 DOI: 10.1016/j.prostaglandins.2019.106387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/24/2019] [Accepted: 10/16/2019] [Indexed: 01/20/2023]
Abstract
Epoxyeicosatrienoic acids (EETs) are potent lipid mediators with well-established effects in vascular tissues. Recent studies indicated an emerging role of these eicosanoids in metabolic diseases and the EET signaling pathway was shown to be involved in hepatic insulin sensitivity. However, compared to vascular tissues, there is only limited knowledge about the underlying signaling pathways in the liver. Therefore, we employed an LC-MS/MS-based time-resolved phosphoproteomics approach to characterize 11,12-EET-mediated signaling events in the liver cell line Hepa 1-6. 11,12-EET treatment resulted in the time-dependent regulation of phosphopeptides involved in processes as yet unknown to be affected by EETs, including RNA processing, splicing and translation regulation. Pathway analysis combined with western blot-based validation revealed enhanced AKT/mTOR/p70S6K signaling as demonstrated by increased acute phosphorylation of AKT (Ser473) and p70S6K (Thr389). In addition, 11,12-EET treatment led to differential regulation of phosphopeptides including important mediators of the DNA damage response and we observed a prolonged induction of the etoposide-induced DNA damage marker γH2AX in response to 11,12-EET. In summary, our findings extend current knowledge of 11,12-EET signaling events and emphasize the importance of the AKT/mTOR/p70S6K pathway in hepatic 11,12-EET signaling. Based on the results presented in this study, we furthermore propose a novel role of EET signaling in the regulation of the DNA damage response.
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Affiliation(s)
- Marco Rahm
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Juliane Merl-Pham
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany.
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Alkozi HA, Navarro G, Franco R, Pintor J. Melatonin and the control of intraocular pressure. Prog Retin Eye Res 2019; 75:100798. [PMID: 31560946 DOI: 10.1016/j.preteyeres.2019.100798] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 12/15/2022]
Abstract
Melatonin is not only synthesized by the pineal gland but by several ocular structures. This natural indoleamine is of great importance for regulating several eye processes, among which pressure homeostasis is included. Glaucoma, the most prevalent eye disease, also known as the silent thief of vision, is a multifactorial pathology that is associated to age and, often, to intraocular hypertension (IOP). Indeed IOP is the only modifiable risk factor and as such medications are available to control it; however, novel medications are sought to minimize undesirable side effects. Melatonin and analogues decrease IOP in both normotensive and hypertensive eyes. Melatonin activates its cognate membrane receptors, MT1 and MT2, which are present in numerous ocular tissues, including the aqueous-humor-producing ciliary processes. Melatonin receptors belong to the superfamily of G-protein-coupled receptors and their activation would lead to different signalling pathways depending on the tissue. This review describes the molecular mechanisms underlying differential functionalities that are attributed to melatonin receptors. Accordingly, the current work highlights the important role of melatonin and its analogues in the healthy and in the glaucomatous eyes, with special attention to the control of intraocular pressure.
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Affiliation(s)
- Hanan Awad Alkozi
- Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, University Complutense of Madrid, Madrid, Spain
| | - Gemma Navarro
- Centro de Investigación en Red, Enfermedades Neurodegeneratives (CiberNed), Instituto de Salud Carlos III, Sinesio Delgado 6, 28029, Madrid, Spain; Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Universitat de Barcelona, Avda. Juan XXIII, 27, 08027, Barcelona, Spain
| | - Rafael Franco
- Centro de Investigación en Red, Enfermedades Neurodegeneratives (CiberNed), Instituto de Salud Carlos III, Sinesio Delgado 6, 28029, Madrid, Spain; Department of Biochemistry and Molecular Biomedicine, School of Biology, Universitat de Barcelona, Diagonal 643, 08028, Barcelona, Barcelona, Spain.
| | - Jesus Pintor
- Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, University Complutense of Madrid, Madrid, Spain; Real Academia Nacional de Farmacia, Calle Farmacia 11, 28004, Madrid, Spain.
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Tunicamycin Sensitivity-Suppression by High Gene Dosage Reveals New Functions of the Yeast Hog1 MAP Kinase. Cells 2019; 8:cells8070710. [PMID: 31336877 PMCID: PMC6678945 DOI: 10.3390/cells8070710] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/03/2019] [Accepted: 07/09/2019] [Indexed: 01/10/2023] Open
Abstract
In the yeast Saccharomyces cerevisiae, components of the High Osmolarity Glycerol (HOG) pathway are important for the response to diverse stresses including response to endoplasmic reticulum stress (ER stress), which is produced by the accumulation of unfolded proteins in the lumen of this organelle. Accumulation of unfolded proteins may be due to the inhibition of protein N-glycosylation, which can be achieved by treatment with the antibiotic tunicamycin (Tn). In this work we were interested in finding proteins involved in the ER stress response regulated by Hog1, the mitogen activated protein kinase (MAPK) of the HOG pathway. A high gene dosage suppression screening allowed us to identify genes that suppressed the sensitivity to Tn shown by a hog1Δ mutant. The suppressors participate in a limited number of cellular processes, including lipid/carbohydrate biosynthesis and protein glycosylation, vesicle-mediated transport and exocytosis, cell wall organization and biogenesis, and cell detoxification processes. The finding of suppressors Rer2 and Srt1, which participate in the dolichol biosynthesis pathway revealed that the hog1Δ strain has a defective polyprenol metabolism. This work uncovers new genetic and functional interactors of Hog1 and contributes to a better understanding of the participation of this MAPK in the ER stress response.
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