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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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Chrestia JF, Turani O, Araujo NR, Hernando G, Esandi MDC, Bouzat C. Regulation of nicotinic acetylcholine receptors by post-translational modifications. Pharmacol Res 2023; 190:106712. [PMID: 36863428 DOI: 10.1016/j.phrs.2023.106712] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/21/2023] [Accepted: 02/24/2023] [Indexed: 03/04/2023]
Abstract
Nicotinic acetylcholine receptors (nAChRs) comprise a family of pentameric ligand-gated ion channels widely distributed in the central and peripheric nervous system and in non-neuronal cells. nAChRs are involved in chemical synapses and are key actors in vital physiological processes throughout the animal kingdom. They mediate skeletal muscle contraction, autonomic responses, contribute to cognitive processes, and regulate behaviors. Dysregulation of nAChRs is associated with neurological, neurodegenerative, inflammatory and motor disorders. In spite of the great advances in the elucidation of nAChR structure and function, our knowledge about the impact of post-translational modifications (PTMs) on nAChR functional activity and cholinergic signaling has lagged behind. PTMs occur at different steps of protein life cycle, modulating in time and space protein folding, localization, function, and protein-protein interactions, and allow fine-tuned responses to changes in the environment. A large body of evidence demonstrates that PTMs regulate all levels of nAChR life cycle, with key roles in receptor expression, membrane stability and function. However, our knowledge is still limited, restricted to a few PTMs, and many important aspects remain largely unknown. There is thus a long way to go to decipher the association of aberrant PTMs with disorders of cholinergic signaling and to target PTM regulation for novel therapeutic interventions. In this review we provide a comprehensive overview of what is known about how different PTMs regulate nAChR.
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Affiliation(s)
- Juan Facundo Chrestia
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca 8000, Argentina
| | - Ornella Turani
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca 8000, Argentina
| | - Noelia Rodriguez Araujo
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca 8000, Argentina
| | - Guillermina Hernando
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca 8000, Argentina
| | - María Del Carmen Esandi
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca 8000, Argentina
| | - Cecilia Bouzat
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca 8000, Argentina.
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3
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Pascual J, Rahikainen M, Angeleri M, Alegre S, Gossens R, Shapiguzov A, Heinonen A, Trotta A, Durian G, Winter Z, Sinkkonen J, Kangasjärvi J, Whelan J, Kangasjärvi S. ACONITASE 3 is part of theANAC017 transcription factor-dependent mitochondrial dysfunction response. PLANT PHYSIOLOGY 2021; 186:1859-1877. [PMID: 34618107 PMCID: PMC8331168 DOI: 10.1093/plphys/kiab225] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 04/21/2021] [Indexed: 05/26/2023]
Abstract
Mitochondria are tightly embedded within metabolic and regulatory networks that optimize plant performance in response to environmental challenges. The best-known mitochondrial retrograde signaling pathway involves stress-induced activation of the transcription factor NAC DOMAIN CONTAINING PROTEIN 17 (ANAC017), which initiates protective responses to stress-induced mitochondrial dysfunction in Arabidopsis (Arabidopsis thaliana). Posttranslational control of the elicited responses, however, remains poorly understood. Previous studies linked protein phosphatase 2A subunit PP2A-B'γ, a key negative regulator of stress responses, with reversible phosphorylation of ACONITASE 3 (ACO3). Here we report on ACO3 and its phosphorylation at Ser91 as key components of stress regulation that are induced by mitochondrial dysfunction. Targeted mass spectrometry-based proteomics revealed that the abundance and phosphorylation of ACO3 increased under stress, which required signaling through ANAC017. Phosphomimetic mutation at ACO3-Ser91 and accumulation of ACO3S91D-YFP promoted the expression of genes related to mitochondrial dysfunction. Furthermore, ACO3 contributed to plant tolerance against ultraviolet B (UV-B) or antimycin A-induced mitochondrial dysfunction. These findings demonstrate that ACO3 is both a target and mediator of mitochondrial dysfunction signaling, and critical for achieving stress tolerance in Arabidopsis leaves.
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Affiliation(s)
- Jesús Pascual
- Department of Life Technologies, Molecular Plant Biology, University of Turku, Turku FI-20014, Finland
| | - Moona Rahikainen
- Department of Life Technologies, Molecular Plant Biology, University of Turku, Turku FI-20014, Finland
- Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki FI-00014, Finland
| | - Martina Angeleri
- Department of Life Technologies, Molecular Plant Biology, University of Turku, Turku FI-20014, Finland
| | - Sara Alegre
- Department of Life Technologies, Molecular Plant Biology, University of Turku, Turku FI-20014, Finland
| | - Richard Gossens
- Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki FI-00014, Finland
- Viikki Plant Science Center, University of Helsinki, Helsinki FI-00014, Finland
| | - Alexey Shapiguzov
- Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki FI-00014, Finland
- Viikki Plant Science Center, University of Helsinki, Helsinki FI-00014, Finland
- Institute of Plant Physiology, Russian Academy of Sciences, Moscow 127276, Russia
| | - Arttu Heinonen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku FI-20520, Finland
| | - Andrea Trotta
- Department of Life Technologies, Molecular Plant Biology, University of Turku, Turku FI-20014, Finland
- Institute of Biosciences and Bioresources, National Research Council of Italy, Sesto Fiorentino 50019, Italy
| | - Guido Durian
- Department of Life Technologies, Molecular Plant Biology, University of Turku, Turku FI-20014, Finland
| | - Zsófia Winter
- Department of Life Technologies, Molecular Plant Biology, University of Turku, Turku FI-20014, Finland
| | - Jari Sinkkonen
- Department of Chemistry, Instrument Centre, University of Turku, Turku FI-20014, Finland
| | - Jaakko Kangasjärvi
- Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki FI-00014, Finland
- Viikki Plant Science Center, University of Helsinki, Helsinki FI-00014, Finland
| | - James Whelan
- Department of Animal, Plant and Soil Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora 3086, Australia
| | - Saijaliisa Kangasjärvi
- Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki FI-00014, Finland
- Viikki Plant Science Center, University of Helsinki, Helsinki FI-00014, Finland
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki FI-00014, Finland
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4
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Schiapparelli P, Pirman NL, Mohler K, Miranda-Herrera PA, Zarco N, Kilic O, Miller C, Shah SR, Rogulina S, Hungerford W, Abriola L, Hoyer D, Turk BE, Guerrero-Cázares H, Isaacs FJ, Quiñones-Hinojosa A, Levchenko A, Rinehart J. Phosphorylated WNK kinase networks in recoded bacteria recapitulate physiological function. Cell Rep 2021; 36:109416. [PMID: 34289367 PMCID: PMC8379681 DOI: 10.1016/j.celrep.2021.109416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 07/23/2020] [Accepted: 06/28/2021] [Indexed: 12/15/2022] Open
Abstract
Advances in genetic code expansion have enabled the production of proteins containing site-specific, authentic post-translational modifications. Here, we use a recoded bacterial strain with an expanded genetic code to encode phosphoserine into a human kinase protein. We directly encode phosphoserine into WNK1 (with-no-lysine [K] 1) or WNK4 kinases at multiple, distinct sites, which produced activated, phosphorylated WNK that phosphorylated and activated SPAK/OSR kinases, thereby synthetically activating this human kinase network in recoded bacteria. We used this approach to identify biochemical properties of WNK kinases, a motif for SPAK substrates, and small-molecule kinase inhibitors for phosphorylated SPAK. We show that the kinase inhibitors modulate SPAK substrates in cells, alter cell volume, and reduce migration of glioblastoma cells. Our work establishes a protein-engineering platform technology that demonstrates that synthetically active WNK kinase networks can accurately model cellular systems and can be used more broadly to target networks of phosphorylated proteins for research and discovery.
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Affiliation(s)
| | - Natasha L Pirman
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Kyle Mohler
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | | | - Natanael Zarco
- Department of Neurologic Surgery, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Onur Kilic
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Chad Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Sagar R Shah
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Svetlana Rogulina
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - William Hungerford
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA
| | - Denton Hoyer
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | | | - Farren J Isaacs
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | | | - Andre Levchenko
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA; Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA.
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5
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Ai G, Xia Q, Song T, Li T, Zhu H, Peng H, Liu J, Fu X, Zhang M, Jing M, Xia A, Dou D. A Phytophthora sojae CRN effector mediates phosphorylation and degradation of plant aquaporin proteins to suppress host immune signaling. PLoS Pathog 2021; 17:e1009388. [PMID: 33711077 PMCID: PMC7990189 DOI: 10.1371/journal.ppat.1009388] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 03/24/2021] [Accepted: 02/15/2021] [Indexed: 12/31/2022] Open
Abstract
Phytophthora genomes encode a myriad of Crinkler (CRN) effectors, some of which contain putative kinase domains. Little is known about the host targets of these kinase-domain-containing CRNs and their infection-promoting mechanisms. Here, we report the host target and functional mechanism of a conserved kinase CRN effector named CRN78 in a notorious oomycete pathogen, Phytophthora sojae. CRN78 promotes Phytophthora capsici infection in Nicotiana benthamiana and enhances P. sojae virulence on the host plant Glycine max by inhibiting plant H2O2 accumulation and immunity-related gene expression. Further investigation reveals that CRN78 interacts with PIP2-family aquaporin proteins including NbPIP2;2 from N. benthamiana and GmPIP2-13 from soybean on the plant plasma membrane, and membrane localization is necessary for virulence of CRN78. Next, CRN78 promotes phosphorylation of NbPIP2;2 or GmPIP2-13 using its kinase domain in vivo, leading to their subsequent protein degradation in a 26S-dependent pathway. Our data also demonstrates that NbPIP2;2 acts as a H2O2 transporter to positively regulate plant immunity and reactive oxygen species (ROS) accumulation. Phylogenetic analysis suggests that the phosphorylation sites of PIP2 proteins and the kinase domains of CRN78 homologs are highly conserved among higher plants and oomycete pathogens, respectively. Therefore, this study elucidates a conserved and novel pathway used by effector proteins to inhibit host cellular defenses by targeting and hijacking phosphorylation of plant aquaporin proteins. CRN effectors are conserved in diverse pathogens of plants, animals, and insects, and highly expanded in Phytophthora species. Nevertheless, little is known about their functions, targets, and action mechanisms. Here, we characterized a kinase-domain-containing CRN effector (CRN78) in a notorious oomycete pathogen, P. sojae. CRN78 is a virulence-essential effector of P. sojae infection, and acts via suppression of plant H2O2 accumulation and defense gene expressions. We demonstrated that CRN78 might interact with plant PIP2-family aquaporin proteins, including N. benthamiana NbPIP2;2 and soybean GmPIP2-13, and regulate their phosphorylation, resulting in subsequent 26S-dependent protein degradation. Furthermore, we revealed that NbPIP2;2 was an apoplast-to-cytoplast H2O2 transporter and positively regulated plant immunity and ROS accumulation. Importantly, this phosphorylation may be highly conserved in many plant aquaporin proteins. Thus, this study identifies a virulence-related effector from P. sojae and a novel plant immunity-related gene, and reveals a detailed mechanism of effector-mediated phosphorylation and degradation of plant aquaporin proteins.
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Affiliation(s)
- Gan Ai
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Qingyue Xia
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Tianqiao Song
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Institute of plant protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Tianli Li
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Hai Zhu
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Hao Peng
- Department of Crop and Soil Sciences, Washington State University, Pullman, United States of America
| | - Jin Liu
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Xiaowei Fu
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ming Zhang
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Maofeng Jing
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ai Xia
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Daolong Dou
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- * E-mail:
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6
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Losev Y, Frenkel-Pinter M, Abu-Hussien M, Viswanathan GK, Elyashiv-Revivo D, Geries R, Khalaila I, Gazit E, Segal D. Differential effects of putative N-glycosylation sites in human Tau on Alzheimer's disease-related neurodegeneration. Cell Mol Life Sci 2021; 78:2231-2245. [PMID: 32926180 PMCID: PMC11072875 DOI: 10.1007/s00018-020-03643-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/13/2020] [Accepted: 09/04/2020] [Indexed: 12/21/2022]
Abstract
Amyloid assemblies of Tau are associated with Alzheimer's disease (AD). In AD Tau undergoes several abnormal post-translational modifications, including hyperphosphorylation and glycosylation, which impact disease progression. N-glycosylated Tau was reported to be found in AD brain tissues but not in healthy counterparts. This is surprising since Tau is a cytosolic protein whereas N-glycosylation occurs in the ER-Golgi. Previous in vitro studies indicated that N-glycosylation of Tau facilitated its phosphorylation and contributed to maintenance of its Paired Helical Filament structure. However, the specific Tau residue(s) that undergo N-glycosylation and their effect on Tau-engendered pathology are unknown. High-performance liquid chromatography and mass spectrometry (LC-MS) analysis indicated that both N359 and N410 were N-glycosylated in wild-type (WT) human Tau (hTau) expressed in human SH-SY5Y cells. Asparagine to glutamine mutants, which cannot undergo N-glycosylation, at each of three putative N-glycosylation sites in hTau (N167Q, N359Q, and N410Q) were generated and expressed in SH-SY5Y cells and in transgenic Drosophila. The mutants modulated the levels of hTau phosphorylation in a site-dependent manner in both cell and fly models. Additionally, N359Q ameliorated, whereas N410Q exacerbated various aspects of hTau-engendered neurodegeneration in transgenic flies.
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Affiliation(s)
- Yelena Losev
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel
| | - Moran Frenkel-Pinter
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel
| | - Malak Abu-Hussien
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel
| | - Guru Krishnakumar Viswanathan
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel
| | - Donna Elyashiv-Revivo
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel
| | - Rana Geries
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel
| | - Isam Khalaila
- Department of Biotechnology Engineering, Ben-Gurion University of Negev, 84105, Beer Sheva, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel
- Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel
| | - Daniel Segal
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel.
- Sagol Interdisciplinary School of Neuroscience, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel.
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7
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RORα phosphorylation by casein kinase 1α as glucose signal to regulate estrogen sulfation in human liver cells. Biochem J 2021; 477:3583-3598. [PMID: 32686824 PMCID: PMC7527261 DOI: 10.1042/bcj20200427] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 12/24/2022]
Abstract
Estrogen sulfotransferase (SULT1E1) metabolically inactivates estrogen and SULT1E1 expression is tightly regulated by multiple nuclear receptors. Human fetal, but not adult, livers express appreciable amounts of SULT1E1 protein, which is mimicked in human hepatoma-derived HepG2 cells cultured in high glucose (450 mg/dl) medium. Here, we have investigated this glucose signal that leads to phosphorylation of nuclear receptor RORα (NR1F1) at Ser100 and the transcription mechanism by which phosphorylated RORα transduces this signal to nuclear receptor HNF4α, activating the SULT1E1 promoter. The promoter is repressed by non-phosphorylated RORα which binds a distal enhancer (−943/−922 bp) and interacts with and represses HNF4α-mediated transcription. In response to high glucose, RORα becomes phosphorylated at Ser100 and reverses its repression of HNF4α promoter activation. Moreover, the casein kinase CK1α, which is identified in an enhancer-bound nuclear protein complex, phosphorylates Ser100 in in vitro kinase assays. During these dynamic processes, both RORα and HNF4α remain on the enhancer. Thus, RORα utilizes phosphorylation to integrate HNF4α and transduces the glucose signal to regulate the SULT1E1 gene in HepG2 cells and this phosphorylation-mediated mechanism may also regulate SULT1E1 expressions in the human liver.
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8
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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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9
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Komolov KE, Sulon SM, Bhardwaj A, van Keulen SC, Duc NM, Laurinavichyute DK, Lou HJ, Turk BE, Chung KY, Dror RO, Benovic JL. Structure of a GRK5-Calmodulin Complex Reveals Molecular Mechanism of GRK Activation and Substrate Targeting. Mol Cell 2020; 81:323-339.e11. [PMID: 33321095 DOI: 10.1016/j.molcel.2020.11.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 09/15/2020] [Accepted: 11/12/2020] [Indexed: 10/22/2022]
Abstract
The phosphorylation of G protein-coupled receptors (GPCRs) by GPCR kinases (GRKs) facilitates arrestin binding and receptor desensitization. Although this process can be regulated by Ca2+-binding proteins such as calmodulin (CaM) and recoverin, the molecular mechanisms are poorly understood. Here, we report structural, computational, and biochemical analysis of a CaM complex with GRK5, revealing how CaM shapes GRK5 response to calcium. The CaM N and C domains bind independently to two helical regions at the GRK5 N and C termini to inhibit GPCR phosphorylation, though only the C domain interaction disrupts GRK5 membrane association, thereby facilitating cytoplasmic translocation. The CaM N domain strongly activates GRK5 via ordering of the amphipathic αN-helix of GRK5 and allosteric disruption of kinase-RH domain interaction for phosphorylation of cytoplasmic GRK5 substrates. These results provide a framework for understanding how two functional effects, GRK5 activation and localization, can cooperate under control of CaM for selective substrate targeting by GRK5.
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Affiliation(s)
- Konstantin E Komolov
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Sarah M Sulon
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Anshul Bhardwaj
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Siri C van Keulen
- Department of Computer Science, Department of Molecular and Cellular Physiology, Department of Structural Biology, and Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Nguyen Minh Duc
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea; Division of Precision Medicine, Research Institute, National Cancer Center, Goyang, South Korea
| | - Daniela K Laurinavichyute
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea
| | - Ron O Dror
- Department of Computer Science, Department of Molecular and Cellular Physiology, Department of Structural Biology, and Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA; Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Jeffrey L Benovic
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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10
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Kimura S, Hunter K, Vaahtera L, Tran HC, Citterico M, Vaattovaara A, Rokka A, Stolze SC, Harzen A, Meißner L, Wilkens MMT, Hamann T, Toyota M, Nakagami H, Wrzaczek M. CRK2 and C-terminal Phosphorylation of NADPH Oxidase RBOHD Regulate Reactive Oxygen Species Production in Arabidopsis. THE PLANT CELL 2020; 32:1063-1080. [PMID: 32034035 PMCID: PMC7145479 DOI: 10.1105/tpc.19.00525] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 01/13/2020] [Accepted: 02/06/2020] [Indexed: 05/18/2023]
Abstract
Reactive oxygen species (ROS) are important messengers in eukaryotic organisms, and their production is tightly controlled. Active extracellular ROS production by NADPH oxidases in plants is triggered by receptor-like protein kinase-dependent signaling networks. Here, we show that CYSTEINE-RICH RLK2 (CRK2) kinase activity is required for plant growth and CRK2 exists in a preformed complex with the NADPH oxidase RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD) in Arabidopsis (Arabidopsis thaliana). Functional CRK2 is required for the full elicitor-induced ROS burst, and consequently the crk2 mutant is impaired in defense against the bacterial pathogen Pseudomonas syringae pv tomato DC3000. Our work demonstrates that CRK2 regulates plant innate immunity. We identified in vitro CRK2-dependent phosphorylation sites in the C-terminal region of RBOHD. Phosphorylation of S703 RBOHD is enhanced upon flg22 treatment, and substitution of S703 with Ala reduced ROS production in Arabidopsis. Phylogenetic analysis suggests that phospho-sites in the C-terminal region of RBOHD are conserved throughout the plant lineage and between animals and plants. We propose that regulation of NADPH oxidase activity by phosphorylation of the C-terminal region might be an ancient mechanism and that CRK2 is an important element in regulating microbe-associated molecular pattern-triggered ROS production.
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Affiliation(s)
- Sachie Kimura
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Kerri Hunter
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Lauri Vaahtera
- Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Huy Cuong Tran
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Matteo Citterico
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Aleksia Vaattovaara
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Anne Rokka
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku FI-20520, Finland
| | - Sara Christina Stolze
- Protein Mass Spectrometry Group, Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Anne Harzen
- Protein Mass Spectrometry Group, Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Lena Meißner
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Maya Melina Tabea Wilkens
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Thorsten Hamann
- Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Masatsugu Toyota
- Department of Biochemistry and Molecular Biology, Saitama University, Saitama 338-8570, Japan
- Department of Botany, University of Wisconsin, Madison, WI 53593, USA
| | - Hirofumi Nakagami
- Protein Mass Spectrometry Group, Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Michael Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
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11
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McCormick JW, Pincus D, Resnekov O, Reynolds KA. Strategies for Engineering and Rewiring Kinase Regulation. Trends Biochem Sci 2019; 45:259-271. [PMID: 31866305 DOI: 10.1016/j.tibs.2019.11.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 12/31/2022]
Abstract
Eukaryotic protein kinases (EPKs) catalyze the transfer of a phosphate group onto another protein in response to appropriate regulatory cues. In doing so, they provide a primary means for cellular information transfer. Consequently, EPKs play crucial roles in cell differentiation and cell-cycle progression, and kinase dysregulation is associated with numerous disease phenotypes including cancer. Nonnative cues for synthetically regulating kinases are thus much sought after, both for dissecting cell signaling pathways and for pharmaceutical development. In recent years advances in protein engineering and sequence analysis have led to new approaches for manipulating kinase activity, localization, and in some instances specificity. These tools have revealed fundamental principles of intracellular signaling and suggest paths forward for the design of therapeutic allosteric kinase regulators.
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Affiliation(s)
- James W McCormick
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David Pincus
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA; Center for Physics of Evolving Systems, University of Chicago, Chicago, IL 60637, USA
| | | | - Kimberly A Reynolds
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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12
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Miller CJ, Lou HJ, Simpson C, van de Kooij B, Ha BH, Fisher OS, Pirman NL, Boggon TJ, Rinehart J, Yaffe MB, Linding R, Turk BE. Comprehensive profiling of the STE20 kinase family defines features essential for selective substrate targeting and signaling output. PLoS Biol 2019; 17:e2006540. [PMID: 30897078 PMCID: PMC6445471 DOI: 10.1371/journal.pbio.2006540] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 04/02/2019] [Accepted: 03/14/2019] [Indexed: 12/14/2022] Open
Abstract
Specificity within protein kinase signaling cascades is determined by direct and indirect interactions between kinases and their substrates. While the impact of localization and recruitment on kinase-substrate targeting can be readily assessed, evaluating the relative importance of direct phosphorylation site interactions remains challenging. In this study, we examine the STE20 family of protein serine-threonine kinases to investigate basic mechanisms of substrate targeting. We used peptide arrays to define the phosphorylation site specificity for the majority of STE20 kinases and categorized them into four distinct groups. Using structure-guided mutagenesis, we identified key specificity-determining residues within the kinase catalytic cleft, including an unappreciated role for the kinase β3-αC loop region in controlling specificity. Exchanging key residues between the STE20 kinases p21-activated kinase 4 (PAK4) and Mammalian sterile 20 kinase 4 (MST4) largely interconverted their phosphorylation site preferences. In cells, a reprogrammed PAK4 mutant, engineered to recognize MST substrates, failed to phosphorylate PAK4 substrates or to mediate remodeling of the actin cytoskeleton. In contrast, this mutant could rescue signaling through the Hippo pathway in cells lacking multiple MST kinases. These observations formally demonstrate the importance of catalytic site specificity for directing protein kinase signal transduction pathways. Our findings further suggest that phosphorylation site specificity is both necessary and sufficient to mediate distinct signaling outputs of STE20 kinases and imply broad applicability to other kinase signaling systems.
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Affiliation(s)
- Chad J. Miller
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Craig Simpson
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bert van de Kooij
- Departments of Biological Engineering and Biology, MIT Center for Precision Cancer Medicine and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Byung Hak Ha
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Oriana S. Fisher
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Natasha L. Pirman
- Department of Cellular and Molecular Physiology and Systems Biology Institute, Yale University, New Haven, Connecticut, United States of America
| | - Titus J. Boggon
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Jesse Rinehart
- Department of Cellular and Molecular Physiology and Systems Biology Institute, Yale University, New Haven, Connecticut, United States of America
| | - Michael B. Yaffe
- Departments of Biological Engineering and Biology, MIT Center for Precision Cancer Medicine and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Rune Linding
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin E. Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
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13
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Shi J, Ruijtenbeek R, Pieters RJ. Demystifying O-GlcNAcylation: hints from peptide substrates. Glycobiology 2019; 28:814-824. [PMID: 29635275 DOI: 10.1093/glycob/cwy031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
O-GlcNAcylation, analogous to phosphorylation, is an essential post-translational modification of proteins at Ser/Thr residues with a single β-N-acetylglucosamine moiety. This dynamic protein modification regulates many fundamental cellular processes and its deregulation has been linked to chronic diseases such as cancer, diabetes and neurodegenerative disorders. Reversible attachment and removal of O-GlcNAc is governed only by O-GlcNAc transferase and O-GlcNAcase, respectively. Peptide substrates, derived from natural O-GlcNAcylation targets, function in the catalytic cores of these two enzymes by maintaining interactions between enzyme and substrate, which makes them ideal models for the study of O-GlcNAcylation and deglycosylation. These peptides provide valuable tools for a deeper understanding of O-GlcNAc processing enzymes. By taking advantage of peptide chemistry, recent progress in the study of activity and regulatory mechanisms of these two enzymes has advanced our understanding of their fundamental specificities as well as their potential as therapeutic targets. Hence, this review summarizes the recent achievements on this modification studied at the peptide level, focusing on enzyme activity, enzyme specificity, direct function, site-specific antibodies and peptide substrate-inspired inhibitors.
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Affiliation(s)
- Jie Shi
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, TB Utrecht, The Netherlands
| | - Rob Ruijtenbeek
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, TB Utrecht, The Netherlands.,PamGene International BV, HH's-Hertogenbosch, The Netherlands
| | - Roland J Pieters
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, TB Utrecht, The Netherlands
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14
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Barber KW, Miller CJ, Jun JW, Lou HJ, Turk BE, Rinehart J. Kinase Substrate Profiling Using a Proteome-wide Serine-Oriented Human Peptide Library. Biochemistry 2018; 57:4717-4725. [PMID: 29920078 DOI: 10.1021/acs.biochem.8b00410] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human proteome encodes >500 protein kinases and hundreds of thousands of potential phosphorylation sites. However, the identification of kinase-substrate pairs remains an active area of research because the relationships between individual kinases and these phosphorylation sites remain largely unknown. Many techniques have been established to discover kinase substrates but are often technically challenging to perform. Moreover, these methods frequently rely on substrate reagent pools that do not reflect human protein sequences or are biased by human cell line protein expression profiles. Here, we describe a new approach called SERIOHL-KILR (serine-oriented human library-kinase library reactions) to profile kinase substrate specificity and to identify candidate substrates for serine kinases. Using a purified library of >100000 serine-oriented human peptides expressed heterologously in Escherichia coli, we perform in vitro kinase reactions to identify phosphorylated human peptide sequences by liquid chromatography and tandem mass spectrometry. We compare our results for protein kinase A to those of a well-established positional scanning peptide library method, certifying that SERIOHL-KILR can identify the same predominant motif elements as traditional techniques. We then interrogate a small panel of cancer-associated PKCβ mutants using our profiling protocol and observe a shift in substrate specificity likely attributable to the loss of key polar contacts between the kinase and its substrates. Overall, we demonstrate that SERIOHL-KILR can rapidly identify candidate kinase substrates that can be directly mapped to human sequences for pathway analysis. Because this technique can be adapted for various kinase studies, we believe that SERIOHL-KILR will have many new victims in the future.
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Affiliation(s)
- Karl W Barber
- Department of Cellular & Molecular Physiology , Yale University , New Haven , Connecticut 06520 , United States.,Systems Biology Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - Chad J Miller
- Department of Pharmacology , Yale University , New Haven , Connecticut 06520 , United States
| | - Jay W Jun
- Division of Nutritional Sciences , Cornell University , Ithaca , New York 14850 , United States.,The Cancer Systems Biology Consortium Research Center , Yale University , West Haven , Connecticut 06516 , United States
| | - Hua Jane Lou
- Department of Pharmacology , Yale University , New Haven , Connecticut 06520 , United States
| | - Benjamin E Turk
- Department of Pharmacology , Yale University , New Haven , Connecticut 06520 , United States
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology , Yale University , New Haven , Connecticut 06520 , United States.,Systems Biology Institute , Yale University , West Haven , Connecticut 06516 , United States.,The Cancer Systems Biology Consortium Research Center , Yale University , West Haven , Connecticut 06516 , United States
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15
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Baltussen LL, Rosianu F, Ultanir SK. Kinases in synaptic development and neurological diseases. Prog Neuropsychopharmacol Biol Psychiatry 2018; 84:343-352. [PMID: 29241837 DOI: 10.1016/j.pnpbp.2017.12.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 12/08/2017] [Accepted: 12/09/2017] [Indexed: 10/18/2022]
Abstract
Neuronal morphogenesis and synapse development is essential for building a functioning nervous system, and defects in these processes are associated with neurological disorders. Our understanding of molecular components and signalling events that contribute to neuronal development and pathogenesis is limited. Genes associated with neurodevelopmental and neurodegenerative diseases provide entry points for elucidating molecular events that contribute to these conditions. Several protein kinases, enzymes that regulate protein function by phosphorylating their substrates, are genetically linked to neurological disorders. Identifying substrates of these kinases is key to discovering their function and providing insight for possible therapies. In this review, we describe how various methods for kinase-substrate identification helped elucidate kinase signalling pathways important for neuronal development and function. We describe recent advances on roles of kinases TAOK2, TNIK and CDKL5 in neuronal development and the converging pathways of LRRK2, PINK1 and GAK in Parkinson's Disease.
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Affiliation(s)
- Lucas L Baltussen
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Flavia Rosianu
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom.
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16
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Miller CJ, Muftuoglu Y, Turk BE. A high throughput assay to identify substrate-selective inhibitors of the ERK protein kinases. Biochem Pharmacol 2017. [PMID: 28647489 DOI: 10.1016/j.bcp.2017.06.127] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Extracellular signal-regulated kinases 1 and 2 (ERK1/2) phosphorylate a variety of substrates important for survival and proliferation, and their activity is frequently deregulated in tumors. ERK pathway inhibitors have shown clinical efficacy as anti-cancer drugs, but most patients eventually relapse due to reactivation of the pathway. One factor limiting the efficacy of current therapeutics is the difficulty in reaching clinically effective inhibition of the ERK pathway in the absence of on-target toxicities. Here, we describe an assay suitable for high throughput screening to discover substrate selective ERK1/2 inhibitors, which may have a larger therapeutic window than conventional inhibitors. Specifically, we aim to target a substrate-binding pocket within the ERK1/2 catalytic domain outside of the catalytic cleft. The assay uses an AlphaScreen format to detect phosphorylation of a high-efficiency substrate harboring an essential docking site motif. Pilot screening established that the assay is suitably robust for high-throughput screening. Importantly, the assay can be conducted at high ATP concentrations, which we show reduces the discovery of conventional ATP-competitive inhibitors. These studies provide the basis for high-throughput screens to discover new classes of non-conventional ERK1/2 inhibitors.
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Affiliation(s)
- Chad J Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Yagmur Muftuoglu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, United States.
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17
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Jayaraman D, Richards AL, Westphall MS, Coon JJ, Ané JM. Identification of the phosphorylation targets of symbiotic receptor-like kinases using a high-throughput multiplexed assay for kinase specificity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:1196-1207. [PMID: 28267253 PMCID: PMC5461195 DOI: 10.1111/tpj.13529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 02/17/2017] [Accepted: 03/01/2017] [Indexed: 05/29/2023]
Abstract
Detecting the phosphorylation substrates of multiple kinases in a single experiment is a challenge, and new techniques are being developed to overcome this challenge. Here, we used a multiplexed assay for kinase specificity (MAKS) to identify the substrates directly and to map the phosphorylation site(s) of plant symbiotic receptor-like kinases. The symbiotic receptor-like kinases nodulation receptor-like kinase (NORK) and lysin motif domain-containing receptor-like kinase 3 (LYK3) are indispensable for the establishment of root nodule symbiosis. Although some interacting proteins have been identified for these symbiotic receptor-like kinases, very little is known about their phosphorylation substrates. Using this high-throughput approach, we identified several other potential phosphorylation targets for both these symbiotic receptor-like kinases. In particular, we also discovered the phosphorylation of LYK3 by NORK itself, which was also confirmed by pairwise kinase assays. Motif analysis of potential targets for these kinases revealed that the acidic motif xxxsDxxx was common to both of them. In summary, this high-throughput technique catalogs the potential phosphorylation substrates of multiple kinases in a single efficient experiment, the biological characterization of which should provide a better understanding of phosphorylation signaling cascade in symbiosis.
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Affiliation(s)
- Dhileepkumar Jayaraman
- Department of Agronomy, 1575 Linden Drive, University of Wisconsin–Madison, WI 53706, USA
| | - Alicia L. Richards
- Department of Chemistry, 1101 University Avenue, University of Wisconsin–Madison, WI 53706, USA
- Genome Center of Wisconsin, University of Wisconsin–Madison, 425 Henry Mall, WI 53706, USA
| | - Michael S. Westphall
- Department of Chemistry, 1101 University Avenue, University of Wisconsin–Madison, WI 53706, USA
- Genome Center of Wisconsin, University of Wisconsin–Madison, 425 Henry Mall, WI 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, 420 Henry Mall, WI 53706, USA
| | - Joshua J. Coon
- Department of Chemistry, 1101 University Avenue, University of Wisconsin–Madison, WI 53706, USA
- Genome Center of Wisconsin, University of Wisconsin–Madison, 425 Henry Mall, WI 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, 420 Henry Mall, WI 53706, USA
| | - Jean-Michel Ané
- Department of Agronomy, 1575 Linden Drive, University of Wisconsin–Madison, WI 53706, USA
- Department of Bacteriology, 1550 Linden Drive, University of Wisconsin–Madison, WI 53706, USA
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18
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Cann ML, McDonald IM, East MP, Johnson GL, Graves LM. Measuring Kinase Activity-A Global Challenge. J Cell Biochem 2017; 118:3595-3606. [PMID: 28464261 DOI: 10.1002/jcb.26103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 12/22/2022]
Abstract
The kinase enzymes within a cell, known collectively as the kinome, play crucial roles in many signaling pathways, including survival, motility, differentiation, stress response, and many more. Aberrant signaling through kinase pathways is often linked to cancer, among other diseases. A major area of scientific research involves understanding the relationships between kinases, their targets, and how the kinome adapts to perturbations of the cellular system. This review will discuss many of the current and developing methods for studying kinase activity, and evaluate their applications, advantages, and disadvantages. J. Cell. Biochem. 118: 3595-3606, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Marissa L Cann
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Ian M McDonald
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Michael P East
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Gary L Johnson
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Lee M Graves
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
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19
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Meyer NO, O'Donoghue AJ, Schulze-Gahmen U, Ravalin M, Moss SM, Winter MB, Knudsen GM, Craik CS. Multiplex Substrate Profiling by Mass Spectrometry for Kinases as a Method for Revealing Quantitative Substrate Motifs. Anal Chem 2017; 89:4550-4558. [PMID: 28322550 DOI: 10.1021/acs.analchem.6b05002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The more than 500 protein kinases comprising the human kinome catalyze hundreds of thousands of phosphorylation events to regulate a diversity of cellular functions; however, the extended substrate specificity is still unknown for many of these kinases. We report here a method for quantitatively describing kinase substrate specificity using an unbiased peptide library-based approach with direct measurement of phosphorylation by tandem liquid chromatography-tandem mass spectrometry (LC-MS/MS) peptide sequencing (multiplex substrate profiling by mass spectrometry, MSP-MS). This method can be deployed with as low as 10 nM enzyme to determine activity against S/T/Y-containing peptides; additionally, label-free quantitation is used to ascertain catalytic efficiency values for individual peptide substrates in the multiplex assay. Using this approach we developed quantitative motifs for a selection of kinases from each branch of the kinome, with and without known substrates, highlighting the applicability of the method. The sensitivity of this approach is evidenced by its ability to detect phosphorylation events from nanogram quantities of immunoprecipitated material, which allows for wider applicability of this method. To increase the information content of the quantitative kinase motifs, a sublibrary approach was used to expand the testable sequence space within a peptide library of approximately 100 members for CDK1, CDK7, and CDK9. Kinetic analysis of the HIV-1 Tat (transactivator of transcription)-positive transcription elongation factor b (P-TEFb) interaction allowed for localization of the P-TEFb phosphorylation site as well as characterization of the stimulatory effect of Tat on P-TEFb catalytic efficiency.
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Affiliation(s)
- Nicole O Meyer
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| | - Anthony J O'Donoghue
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| | - Ursula Schulze-Gahmen
- Department of Molecular and Cell Biology, University of California Berkeley , Berkeley, California 94720, United States
| | - Matthew Ravalin
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| | - Steven M Moss
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| | - Michael B Winter
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| | - Giselle M Knudsen
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
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20
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Mathea S, Abdul Azeez KR, Salah E, Tallant C, Wolfreys F, Konietzny R, Fischer R, Lou HJ, Brennan PE, Schnapp G, Pautsch A, Kessler BM, Turk BE, Knapp S. Structure of the Human Protein Kinase ZAK in Complex with Vemurafenib. ACS Chem Biol 2016; 11:1595-602. [PMID: 26999302 DOI: 10.1021/acschembio.6b00043] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The mixed lineage kinase ZAK is a key regulator of the MAPK pathway mediating cell survival and inflammatory response. ZAK is targeted by several clinically approved kinase inhibitors, and inhibition of ZAK has been reported to protect from doxorubicin-induced cardiomyopathy. On the other hand, unintended targeting of ZAK has been linked to severe adverse effects such as the development of cutaneous squamous cell carcinoma. Therefore, both specific inhibitors of ZAK, as well as anticancer drugs lacking off-target activity against ZAK, may provide therapeutic benefit. Here, we report the first crystal structure of ZAK in complex with the B-RAF inhibitor vemurafenib. The cocrystal structure displayed a number of ZAK-specific features including a highly distorted P loop conformation enabling rational inhibitor design. Positional scanning peptide library analysis revealed a unique substrate specificity of the ZAK kinase including unprecedented preferences for histidine residues at positions -1 and +2 relative to the phosphoacceptor site. In addition, we screened a library of clinical kinase inhibitors identifying several inhibitors that potently inhibit ZAK, demonstrating that this kinase is commonly mistargeted by currently used anticancer drugs.
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Affiliation(s)
- Sebastian Mathea
- Structural
Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX37DQ, United Kingdom
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Kamal R. Abdul Azeez
- Structural
Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX37DQ, United Kingdom
| | - Eidarus Salah
- Structural
Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX37DQ, United Kingdom
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Cynthia Tallant
- Structural
Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX37DQ, United Kingdom
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Finn Wolfreys
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Rebecca Konietzny
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Roman Fischer
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Hua Jane Lou
- Department
of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Paul E. Brennan
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Gisela Schnapp
- Lead Discovery and Optimisation Support, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, 88400, Germany
| | - Alexander Pautsch
- Lead Discovery and Optimisation Support, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, 88400, Germany
| | - Benedikt M. Kessler
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Benjamin E. Turk
- Department
of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Stefan Knapp
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
- Institute
for Pharmaceutical Chemistry and Buchmann Institute for Molecular
Life Sciences (BMLS), Johann Wolfgang Goethe University, Frankfurt am Main, 60438, Germany
| |
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