1
|
Allen MC, Karplus PA, Mehl RA, Cooley RB. Genetic Encoding of Phosphorylated Amino Acids into Proteins. Chem Rev 2024; 124:6592-6642. [PMID: 38691379 DOI: 10.1021/acs.chemrev.4c00110] [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: 05/03/2024]
Abstract
Reversible phosphorylation is a fundamental mechanism for controlling protein function. Despite the critical roles phosphorylated proteins play in physiology and disease, our ability to study individual phospho-proteoforms has been hindered by a lack of versatile methods to efficiently generate homogeneous proteins with site-specific phosphoamino acids or with functional mimics that are resistant to phosphatases. Genetic code expansion (GCE) is emerging as a transformative approach to tackle this challenge, allowing direct incorporation of phosphoamino acids into proteins during translation in response to amber stop codons. This genetic programming of phospho-protein synthesis eliminates the reliance on kinase-based or chemical semisynthesis approaches, making it broadly applicable to diverse phospho-proteoforms. In this comprehensive review, we provide a brief introduction to GCE and trace the development of existing GCE technologies for installing phosphoserine, phosphothreonine, phosphotyrosine, and their mimics, discussing both their advantages as well as their limitations. While some of the technologies are still early in their development, others are already robust enough to greatly expand the range of biologically relevant questions that can be addressed. We highlight new discoveries enabled by these GCE approaches, provide practical considerations for the application of technologies by non-GCE experts, and also identify avenues ripe for further development.
Collapse
Affiliation(s)
- Michael C Allen
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| |
Collapse
|
2
|
González L, Díaz L, Pous J, Baginski B, Duran-Corbera A, Scarpa M, Brun-Heath I, Igea A, Martin-Malpartida P, Ruiz L, Pallara C, Esguerra M, Colizzi F, Mayor-Ruiz C, Biondi RM, Soliva R, Macias MJ, Orozco M, Nebreda AR. Characterization of p38α autophosphorylation inhibitors that target the non-canonical activation pathway. Nat Commun 2023; 14:3318. [PMID: 37308482 DOI: 10.1038/s41467-023-39051-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/26/2023] [Indexed: 06/14/2023] Open
Abstract
p38α is a versatile protein kinase that can control numerous processes and plays important roles in the cellular responses to stress. Dysregulation of p38α signaling has been linked to several diseases including inflammation, immune disorders and cancer, suggesting that targeting p38α could be therapeutically beneficial. Over the last two decades, numerous p38α inhibitors have been developed, which showed promising effects in pre-clinical studies but results from clinical trials have been disappointing, fueling the interest in the generation of alternative mechanisms of p38α modulation. Here, we report the in silico identification of compounds that we refer to as non-canonical p38α inhibitors (NC-p38i). By combining biochemical and structural analyses, we show that NC-p38i efficiently inhibit p38α autophosphorylation but weakly affect the activity of the canonical pathway. Our results demonstrate how the structural plasticity of p38α can be leveraged to develop therapeutic opportunities targeting a subset of the functions regulated by this pathway.
Collapse
Affiliation(s)
- Lorena González
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Lucía Díaz
- Nostrum Biodiscovery, 08034, Barcelona, Spain
| | - Joan Pous
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Blazej Baginski
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Anna Duran-Corbera
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Margherita Scarpa
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Isabelle Brun-Heath
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Ana Igea
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Pau Martin-Malpartida
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Lidia Ruiz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | | | | | - Francesco Colizzi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
- Department of Marine Biology and Oceanography, Institute of Marine Sciences ICM-CSIC, 08003, Barcelona, Spain
| | - Cristina Mayor-Ruiz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | | | - Maria J Macias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain.
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain.
- Departament de Bioquímica i Biomedicina, Facultat de Biologia, Universitat de Barcelona, 08028, Barcelona, Spain.
| | - Angel R Nebreda
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain.
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| |
Collapse
|
3
|
Burton JC, Okalova J, Grimsey NJ. Fluorescence resonance energy transfer (FRET) spatiotemporal mapping of atypical P38 reveals an endosomal and cytosolic spatial bias. Sci Rep 2023; 13:7477. [PMID: 37156828 PMCID: PMC10167256 DOI: 10.1038/s41598-023-33953-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/21/2023] [Indexed: 05/10/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK) p38 is a central regulator of intracellular signaling, driving physiological and pathological pathways. With over 150 downstream targets, it is predicted that spatial positioning and the availability of cofactors and substrates determines kinase signaling specificity. The subcellular localization of p38 is highly dynamic to facilitate the selective activation of spatially restricted substrates. However, the spatial dynamics of atypical p38 inflammatory signaling are understudied. We utilized subcellular targeted fluorescence resonance energy transfer (FRET) p38 activity biosensors to map the spatial profile of kinase activity. Through comparative analysis of plasma membrane, cytosolic, nuclear, and endosomal compartments, we confirm a characteristic profile of nuclear bias for mitogen-activated kinase kinase 3/6 (MKK3/6) dependent p38 activation. Conversely, atypical p38 activation via thrombin-mediated protease-activated receptor 1 (PAR1) activity led to enhanced p38 activity at the endosome and cytosol, limiting nuclear p38 activity, a profile conserved for prostaglandin E2 activation of p38. Conversely, perturbation of receptor endocytosis led to spatiotemporal switching of thrombin signaling, reducing endosomal and cytosolic p38 activity and increasing nuclear activity. The data presented reveal the spatiotemporal dynamics of p38 activity and provide critical insight into how atypical p38 signaling drives differential signaling responses through spatial sequestration of kinase activity.
Collapse
Affiliation(s)
- Jeremy C Burton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Pharmacy South Rm 414, Athens, 30602, USA
| | - Jennifer Okalova
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Pharmacy South Rm 414, Athens, 30602, USA
- Aflac Cancer and Blood Disorders Center, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Neil J Grimsey
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Pharmacy South Rm 414, Athens, 30602, USA.
| |
Collapse
|
4
|
McClean N, Hasday JD, Shapiro P. Progress in the development of kinase inhibitors for treating asthma and COPD. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2023; 98:145-178. [PMID: 37524486 DOI: 10.1016/bs.apha.2023.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Current therapies to mitigate inflammatory responses involved in airway remodeling and associated pathological features of asthma and chronic obstructive pulmonary disease (COPD) are limited and largely ineffective. Inflammation and the release of cytokines and growth factors activate kinase signaling pathways that mediate changes in airway mesenchymal cells such as airway smooth muscle cells and lung fibroblasts. Proliferative and secretory changes in mesenchymal cells exacerbate the inflammatory response and promote airway remodeling, which is often characterized by increased airway smooth muscle mass, airway hyperreactivity, increased mucus secretion, and lung fibrosis. Thus, inhibition of relevant kinases has been viewed as a potential therapeutic approach to mitigate the debilitating and, thus far, irreversible airway remodeling that occurs in asthma and COPD. Despite FDA approval of several kinase inhibitors for the treatment of proliferative disorders, such as cancer and inflammation associated with rheumatoid arthritis and ulcerative colitis, none of these drugs have been approved to treat asthma or COPD. This review will provide a brief overview of the role kinases play in the pathology of asthma and COPD and an update on the status of kinase inhibitors currently in clinical trials for the treatment of obstructive pulmonary disease. In addition, potential issues associated with the current kinase inhibitors, which have limited their success as therapeutic agents in treating asthma or COPD, and alternative approaches to target kinase functions will be discussed.
Collapse
Affiliation(s)
- Nathaniel McClean
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States
| | - Jeffery D Hasday
- Department of Medicine, Division of Pulmonary Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Paul Shapiro
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States.
| |
Collapse
|
5
|
Yuan L, Bu S, Du M, Wang Y, Ju C, Huang D, Xu W, Tan X, Liang M, Deng S, Yang L, Huang K. RNF207 exacerbates pathological cardiac hypertrophy via post-translational modification of TAB1. Cardiovasc Res 2023; 119:183-194. [PMID: 35352799 DOI: 10.1093/cvr/cvac039] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/14/2022] [Accepted: 03/14/2022] [Indexed: 11/14/2022] Open
Abstract
AIMS The heart undergoes pathological remodelling, featured by the hypertrophic growth of cardiomyocytes and increased cardiac fibrosis, under biomechanical stress such as haemodynamic overload. Ring Finger Protein 207 (RNF207) is an E3 ubiquitin ligase that is predominantly expressed in the heart, but its function remains elusive. In this study, we aimed to explore the role of RNF207 in the development of pathological cardiac hypertrophy and dysfunction. METHODS AND RESULTS Transverse aortic constriction (TAC) surgery was performed on mice to induce cardiac hypertrophy. Cardiac function and remodelling were evaluated by echocardiography, histological assessment, and molecular analyses. Our data indicated that RNF207 overexpression (OE) exacerbated cardiac hypertrophy, fibrosis, and systolic dysfunction. In contrast, TAC-induced cardiac remodelling was profoundly blunted in RNF207 knockdown (KD) hearts. In line with the in vivo findings, RNF207 OE augmented, whereas RNF207 KD alleviated, phenylephrine-induced cardiomyocyte hypertrophy in vitro. Mechanistically, we demonstrated that RNF207 elicited detrimental effects by promoting K63-linked ubiquitination of TAK1-binding protein 1 (TAB1), which triggered the autophosphorylation of transforming growth factor-β activated kinase 1 (TAK1) and the activation of downstream p38 and c-Jun N-terminal kinase (JNK)1/2 signalling pathways. In the TAB1-KD cardiomyocytes, RNF207-OE-induced cell hypertrophy was significantly attenuated, indicating that RNF207-induced hypertrophy is, at least in part, TAB1-dependent. CONCLUSIONS This study demonstrates that RNF207 exacerbates pressure overload-induced cardiac hypertrophy and dysfunction via post-translational modification of TAB1.
Collapse
Affiliation(s)
- Lin Yuan
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
- Department of Cardiology, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), Guangzhou, Guangdong, China
| | - Shichen Bu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Meng Du
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Yilong Wang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Chenhui Ju
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Dandan Huang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Wenjing Xu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Xin Tan
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Minglu Liang
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Shan Deng
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Liu Yang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Kai Huang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
- Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan, Hubei, China
| |
Collapse
|
6
|
Zang Y, Wang H, Kang Y, Zhang J, Li X, Zhang L, Yang Z, Zhang S. TAB1 binding induced p38α conformation change: an accelerated molecular dynamics simulation study. Phys Chem Chem Phys 2022; 24:10506-10513. [PMID: 35441632 DOI: 10.1039/d2cp00144f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
p38α mitogen-activated protein kinase (MAPK) undergoes autophosphorylation induced by the binding of TGFβ-activated kinase 1 binding protein 1 (TAB1) in myocardial ischemia. Investigation of the conformational transformations in p38α triggered by TAB1 binding is motivated by the need to find selective p38α activation inhibitors to treat myocardial ischemia. Herein, the conformational transformations of p38α were studied via all-atom accelerated molecular dynamics simulations and principal component analysis. With the binding of TAB1, the conformational changes of p38α auto-activation were characterized by the movement of the activation loop (A-loop) away from the αG helix toward the αF, αE helixes and L16-loop. In addition, a diverse intermediate state with an extensional and phosphorylated A-loop different from the transition intermediate state was explored. The conformational changes, including the A-loop alpha-structure breaking and the stronger hydrogen bond network formation, are accompanied by the extension of the A-loop and more intramolecular interactions in p38α. TAB1 correlates with other regions of p38α that are distal from the TAB1-binding site, including the A-loop, αC helix, and L16-loop, which regulates the intramolecular correlation of p38α. And, the phosphorylation further enhances the correlations between the A-loop and the other regions of p38α. The correlation results imply the regulation process of p38α conformational transformations. These findings will improve our understanding of the autophosphorylation of kinase and facilitate the development of selective inhibitors for the treatment of ischemic injury.
Collapse
Affiliation(s)
- Yongjian Zang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| | - He Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Ying Kang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Jianwen Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| |
Collapse
|
7
|
Molinar-Inglis O, Wozniak JM, Grimsey NJ, Orduña-Castillo L, Cheng N, Lin Y, Gonzalez Ramirez ML, Birch CA, Lapek JD, Gonzalez DJ, Trejo J. Phosphoproteomic analysis of thrombin- and p38 MAPK-regulated signaling networks in endothelial cells. J Biol Chem 2022; 298:101801. [PMID: 35257745 PMCID: PMC8987612 DOI: 10.1016/j.jbc.2022.101801] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 01/11/2023] Open
Abstract
Endothelial dysfunction is a hallmark of inflammation and is mediated by inflammatory factors that signal through G protein–coupled receptors including protease-activated receptor-1 (PAR1). PAR1, a receptor for thrombin, signals via the small GTPase RhoA and myosin light chain intermediates to facilitate endothelial barrier permeability. PAR1 also induces endothelial barrier disruption through a p38 mitogen-activated protein kinase–dependent pathway, which does not integrate into the RhoA/MLC pathway; however, the PAR1-p38 signaling pathways that promote endothelial dysfunction remain poorly defined. To identify effectors of this pathway, we performed a global phosphoproteome analysis of thrombin signaling regulated by p38 in human cultured endothelial cells using multiplexed quantitative mass spectrometry. We identified 5491 unique phosphopeptides and 2317 phosphoproteins, four distinct dynamic phosphoproteome profiles of thrombin-p38 signaling, and an enrichment of biological functions associated with endothelial dysfunction, including modulators of endothelial barrier disruption and a subset of kinases predicted to regulate p38-dependent thrombin signaling. Using available antibodies to detect identified phosphosites of key p38-regulated proteins, we discovered that inhibition of p38 activity and siRNA-targeted depletion of the p38α isoform increased basal phosphorylation of extracellular signal–regulated protein kinase 1/2, resulting in amplified thrombin-stimulated extracellular signal–regulated protein kinase 1/2 phosphorylation that was dependent on PAR1. We also discovered a role for p38 in the phosphorylation of α-catenin, a component of adherens junctions, suggesting that this phosphorylation may function as an important regulatory process. Taken together, these studies define a rich array of thrombin- and p38-regulated candidate proteins that may serve important roles in endothelial dysfunction.
Collapse
|
8
|
Atypical p38 Signaling, Activation, and Implications for Disease. Int J Mol Sci 2021; 22:ijms22084183. [PMID: 33920735 PMCID: PMC8073329 DOI: 10.3390/ijms22084183] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/29/2021] [Accepted: 04/13/2021] [Indexed: 02/07/2023] Open
Abstract
The mitogen-activated protein kinase (MAPK) p38 is an essential family of kinases, regulating responses to environmental stress and inflammation. There is an ever-increasing plethora of physiological and pathophysiological conditions attributed to p38 activity, ranging from cell division and embryonic development to the control of a multitude of diseases including retinal, cardiovascular, and neurodegenerative diseases, diabetes, and cancer. Despite the decades of intense investigation, a viable therapeutic approach to disrupt p38 signaling remains elusive. A growing body of evidence supports the pathological significance of an understudied atypical p38 signaling pathway. Atypical p38 signaling is driven by a direct interaction between the adaptor protein TAB1 and p38α, driving p38 autophosphorylation independent from the classical MKK3 and MKK6 pathways. Unlike the classical MKK3/6 signaling pathway, atypical signaling is selective for just p38α, and at present has only been characterized during pathophysiological stimulation. Recent studies have linked atypical signaling to dermal and vascular inflammation, myocardial ischemia, cancer metastasis, diabetes, complications during pregnancy, and bacterial and viral infections. Additional studies are required to fully understand how, when, where, and why atypical p38 signaling is induced. Furthermore, the development of selective TAB1-p38 inhibitors represents an exciting new opportunity to selectively inhibit pathological p38 signaling in a wide array of diseases.
Collapse
|
9
|
Canovas B, Nebreda AR. Diversity and versatility of p38 kinase signalling in health and disease. Nat Rev Mol Cell Biol 2021; 22:346-366. [PMID: 33504982 PMCID: PMC7838852 DOI: 10.1038/s41580-020-00322-w] [Citation(s) in RCA: 234] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2020] [Indexed: 02/06/2023]
Abstract
The ability of cells to deal with different types of stressful situations in a precise and coordinated manner is key for survival and involves various signalling networks. Over the past 25 years, p38 kinases — in particular, p38α — have been implicated in the cellular response to stress at many levels. These span from environmental and intracellular stresses, such as hyperosmolarity, oxidative stress or DNA damage, to physiological situations that involve important cellular changes such as differentiation. Given that p38α controls a plethora of functions, dysregulation of this pathway has been linked to diseases such as inflammation, immune disorders or cancer, suggesting the possibility that targeting p38α could be of therapeutic interest. In this Review, we discuss the organization of this signalling pathway focusing on the diversity of p38α substrates, their mechanisms and their links to particular cellular functions. We then address how the different cellular responses can be generated depending on the signal received and the cell type, and highlight the roles of this kinase in human physiology and in pathological contexts. p38α — the best-characterized member of the p38 kinase family — is a key mediator of cellular stress responses. p38α is activated by a plethora of signals and functions through a multitude of substrates to regulate different cellular behaviours. Understanding context-dependent p38α signalling provides important insights into p38α roles in physiology and pathology.
Collapse
Affiliation(s)
- Begoña Canovas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Angel R Nebreda
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain. .,ICREA, Barcelona, Spain.
| |
Collapse
|
10
|
Birch CA, Molinar-Inglis O, Trejo J. Subcellular hot spots of GPCR signaling promote vascular inflammation. ACTA ACUST UNITED AC 2020; 16:37-42. [PMID: 32838054 PMCID: PMC7431397 DOI: 10.1016/j.coemr.2020.07.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
G-coupled protein receptors (GPCRs) comprise the largest class of druggable targets. Signaling by GPCRs is initiated from subcellular hot spots including the plasma membrane, signalosomes, and endosomes to contribute to vascular inflammation. GPCR-G protein signaling at the plasma membrane causes endothelial barrier disruption and also cross-talks with growth factor receptors to promote proinflammatory signaling. A second surge of GPCR signaling is initiated by cytoplasmic NFκB activation mediated by β-arrestins and CARMA-BCL10-MALT1 signalosomes. Once internalized, ubiquitinated GPCRs initiate signaling from endosomes via assembly of the transforming growth factor-β-activated kinase binding protein-1 (TAB1)-TAB2-p38 MAPK complex to promote vascular inflammation. Understanding the complexities of GPCR signaling is critical for development of new strategies to treat vascular inflammation such as that associated with COVID-19.
Collapse
Key Words
- Arrestins
- B-cell lymphoma protein 10, (BCL10)
- COVID-19
- Endosomes
- Endothelial
- G protein-coupled receptor, GPCR
- JAK-STAT
- Janus kinase, JAK
- MALT1
- NFκB
- adherens junctions, AJ
- angiotensin II type 1 receptor, AT1
- angiotensin converting enzyme-2, ACE2
- caspase recruitment domain-containing protein, CARMA
- coronavirus disease of 2019, COVID-19
- fibroblast-growth-factor, FGF
- inhibitor of NFκB kinase, IKK
- mitogen-activated protein kinase, MAPK
- mucosa-associated lymphoid tissue lymphoma translocation protein 1, (MALT1)
- neural precursor cell expressed developmentally downregulated protein 4, NEDD4
- nuclear factor kappa-light-chain-enhancer of activated B cells, NFκB
- p38 MAPK
- platelet activating factor, PAF
- protease-activated receptor-1, PAR1
- severe acute respiratory syndrome coronavirus 2, SARS-CoV-2
- signal transducer and activator of transcription, STAT
- transforming growth factor-α-activated kinase binding protein-1, TAB1
Collapse
Affiliation(s)
- Cierra A Birch
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Olivia Molinar-Inglis
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - JoAnn Trejo
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| |
Collapse
|
11
|
Nichols C, Ng J, Keshu A, Kelly G, Conte MR, Marber MS, Fraternali F, De Nicola GF. Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1β-IL1R and p38α-TAB1 Complexes. J Med Chem 2020; 63:7559-7568. [PMID: 32543856 DOI: 10.1021/acs.jmedchem.0c00403] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nowadays, it is possible to combine X-ray crystallography and fragment screening in a medium throughput fashion to chemically probe the surfaces used by proteins to interact and use the outcome of the screens to systematically design protein-protein inhibitors. To prove it, we first performed a bioinformatics analysis of the Protein Data Bank protein complexes, which revealed over 400 cases where the crystal lattice of the target in the free form is such that large portions of the interacting surfaces are free from lattice contacts and therefore accessible to fragments during soaks. Among the tractable complexes identified, we then performed single fragment crystal screens on two particular interesting cases: the Il1β-ILR and p38α-TAB1 complexes. The result of the screens showed that fragments tend to bind in clusters, highlighting the small-molecule hotspots on the surface of the target protein. In most of the cases, the hotspots overlapped with the binding sites of the interacting proteins.
Collapse
Affiliation(s)
- Charlie Nichols
- British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St Thomas' Hospital, King's College London, London SE1 7EH, U.K.,The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Joseph Ng
- The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Annika Keshu
- The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Geoff Kelly
- NMR Facility, The Francis Crick Institute, London NW1 1AT, U.K
| | - Maria R Conte
- The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Michael S Marber
- British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St Thomas' Hospital, King's College London, London SE1 7EH, U.K
| | - Franca Fraternali
- The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Gian F De Nicola
- British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St Thomas' Hospital, King's College London, London SE1 7EH, U.K.,The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| |
Collapse
|
12
|
Authier F, Muha V, van Aalten DMF. A mouse model for functional dissection of TAB1 O-GlcNAcylation. Wellcome Open Res 2020; 4:128. [PMID: 32676538 PMCID: PMC7333360 DOI: 10.12688/wellcomeopenres.15394.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2020] [Indexed: 01/02/2023] Open
Abstract
Background: O-GlcNAcylation is a posttranslational modification associated with various physiological and pathophysiological processes including diabetes, cancer, neurodegeneration and inflammation. However, the biological mechanisms underlying the role of specific O-GlcNAc sites and their link to phenotypes remain largely unexplored due to lack of suitable
in vivo models. TGF-β activated kinase-1 binding protein-1 (TAB1) is a scaffolding protein required for TGF-β activated kinase-1 (TAK1) mediated signalling. A single O-GlcNAc site has been identified on human TAB1 that modulates TAK1-mediated cytokine release in cells. Methods: Here, we report the generation of the
Tab1
S393A mouse model using a constitutive knock-in strategy. The
Tab1
S393A mice carry a Ser393Ala (S393A) mutation that leads to loss of O-GlcNAcylation site on TAB1. Results: We did not observe any obvious phenotype in
Tab1
S393A mice. Loss of O-GlcNAcylation on TAB1 has no consequences on TAB1 protein level or on TAB1-TAK1 interaction. Conclusions: The homozygous
Tab1
S393A mice are viable and develop with no obvious abnormalities, providing a powerful tool to further investigate the role of O-GlcNAc on TAB1 in the inflammatory response in the context of a whole organism.
Collapse
Affiliation(s)
- Florence Authier
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Villő Muha
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Daan M F van Aalten
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| |
Collapse
|
13
|
Authier F, Muha V, van Aalten DM. A mouse model for functional dissection of TAB1 O-GlcNAcylation. Wellcome Open Res 2019; 4:128. [DOI: 10.12688/wellcomeopenres.15394.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2019] [Indexed: 11/20/2022] Open
Abstract
Background: O-GlcNAcylation is a posttranslational modification associated with various physiological and pathophysiological processes including diabetes, cancer, neurodegeneration and inflammation. However, the biological mechanisms underlying the role of specific O-GlcNAc sites and their link to phenotypes remain largely unexplored due to lack of suitable in vivo models. TGF-β activated kinase-1 binding protein-1 (TAB1) is a scaffolding protein required for TGF-β activated kinase-1 (TAK1) mediated signalling. A single O-GlcNAc site has been identified on TAB1 that modulates TAK1-mediated cytokine release in cells. Methods: Here, we report the generation of the Tab1S393A mouse model using a constitutive knock-in strategy. The Tab1S393A mice carry a Ser393Ala (S393A) mutation that leads to loss of the single O-GlcNAcylation site on TAB1. Results: We did not observe any obvious phenotype in Tab1S393A mice. Loss of O-GlcNAcylation on TAB1 has no consequences on TAB1 protein level or on TAB1-TAK1 interaction. Conclusions: The homozygous Tab1S393A mice are viable and develop with no obvious abnormalities, providing a powerful tool to further investigate the role of O-GlcNAc on TAB1 in the inflammatory response in the context of a whole organism.
Collapse
|
14
|
Burton JC, Grimsey NJ. Ubiquitination as a Key Regulator of Endosomal Signaling by GPCRs. Front Cell Dev Biol 2019; 7:43. [PMID: 30984758 PMCID: PMC6449645 DOI: 10.3389/fcell.2019.00043] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/11/2019] [Indexed: 12/14/2022] Open
Abstract
G protein-coupled receptors (GPCRs) represent the largest family of therapeutic targets for FDA approved drugs. Therefore, understanding the molecular regulation of their signaling pathways is of paramount importance. Similarly, the mitogen activated protein kinase (MAPK) p38 is a critical mediator of proinflammatory disease. Yet despite decades of intense investigation, therapeutically viable inhibitors have struggled to make it into the clinic. New studies describing the regulation and activation of a GPCR dependent atypical p38 signaling pathway represents a novel therapeutic avenue to the treatment of many proinflammatory disorders. These recent studies have defined how thrombin and ADP can induce Src dependent activation of the E3 ubiquitin ligase NEDD4-2. Src dependent phosphorylation of a 2,3-linker peptide releases NEDD4-2 auto-inhibition and triggers the induction of proinflammatory atypical p38 signaling from the endosome. Activation of the atypical p38 pathway requires the direct interaction between an adaptor protein TAB1 and p38, that bypasses the requirement for the classical MKK3/6 dependent activation of p38. Therefore, providing a mechanism to specifically block proinflammatory GPCR atypical p38 activation while leaving basic p38 activity intact. Critically, new studies demonstrated that disruption of the TAB1-p38 interface is a druggable target, that would enable the selective inhibition of proinflammatory p38 signaling and ischemic injury. Atypical p38 signaling is linked to multiple clinically relevant pathologies including inflammation, cardiotoxicity, myocardial ischemia and ischemia reperfusion injury. Therefore, GPCR induced endosomal p38 signaling represents a novel understudied branch of proinflammatory p38 signaling and an ideal potential therapeutic target that warrants further investigation.
Collapse
Affiliation(s)
- Jeremy C Burton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, United States
| | - Neil J Grimsey
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, United States
| |
Collapse
|
15
|
Grimsey NJ, Lin Y, Narala R, Rada CC, Mejia-Pena H, Trejo J. G protein-coupled receptors activate p38 MAPK via a non-canonical TAB1-TAB2- and TAB1-TAB3-dependent pathway in endothelial cells. J Biol Chem 2019; 294:5867-5878. [PMID: 30760523 DOI: 10.1074/jbc.ra119.007495] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/07/2019] [Indexed: 01/03/2023] Open
Abstract
Endothelial dysfunction is induced by inflammatory mediators including multiple G protein-coupled receptor (GPCR) agonists. However, the GPCR signaling pathways that promote endothelial dysfunction are incompletely understood. We previously showed that thrombin promotes endothelial barrier disruption through autophosphorylation and activation of p38 mitogen-activated protein kinase (MAPK) via a non-canonical transforming growth factor-β-activated protein kinase-1-binding protein-1 (TAB1) and TAB2-dependent pathway rather than the canonical three-tiered kinase cascade. Here, we sought to determine whether other GPCR agonists stimulate p38 MAPK activation via this non-canonical pathway in human endothelial cells derived from different vascular beds. Using primary human umbilical vein endothelial cells (HUVECs), HUVEC-derived EA.hy926 cells, and human dermal microvascular endothelial cells (HDMECs), we found that both non-canonical and canonical p38 activation pathways components are expressed in these various endothelial cell types, including TAB3, a structurally-related TAB2 homolog. Moreover, multiple GPCRs agonists, including thrombin, histamine, prostaglandin E2, and ADP, stimulated robust p38 autophosphorylation, whereas phosphorylation of the upstream MAPKs MAP kinase kinase 3 (MKK3) and MKK6, was virtually undetectable, indicating that non-canonical p38 activation may exist for other GPCRs. Indeed, in EA.hy926 cells, thrombin- and histamine-stimulated p38 activation depended on TAB1-TAB2, whereas in primary HUVECs, both TAB1-TAB2 and TAB1-TAB3 were required for p38 activation. In HDMECs, thrombin-induced p38 activation depended on TAB1-TAB3, but histamine-induced p38 activation required TAB1-TAB2. Moreover, thrombin- and histamine-stimulated interleukin-6 production required both TAB1-TAB2 and TAB1-TAB3 in HUVEC. We conclude that multiple GPCR agonists utilize non-canonical TAB1-TAB2 and TAB1-TAB3-dependent p38 activation to promote endothelial inflammatory responses.
Collapse
Affiliation(s)
- Neil J Grimsey
- From the Department of Pharmacology, University of California, San Diego, La Jolla, California 92093
| | - Ying Lin
- From the Department of Pharmacology, University of California, San Diego, La Jolla, California 92093
| | - Rachan Narala
- From the Department of Pharmacology, University of California, San Diego, La Jolla, California 92093
| | - Cara C Rada
- From the Department of Pharmacology, University of California, San Diego, La Jolla, California 92093; Biomedical Sciences Graduate Program, School of Medicine, University of California, San Diego, La Jolla, California 92093
| | - Hilda Mejia-Pena
- From the Department of Pharmacology, University of California, San Diego, La Jolla, California 92093
| | - JoAnn Trejo
- From the Department of Pharmacology, University of California, San Diego, La Jolla, California 92093.
| |
Collapse
|