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Wang Z, Yan S, Ren W, Liu Y, Sun W, Liu M, Lu J, Mi Y, Ma W. Genome-Wide Identification of MAPK, MAPKK, and MAPKKK Gene Families in Fagopyrum tataricum and Analysis of Their Expression Patterns Under Abiotic Stress. Front Genet 2022; 13:894048. [PMID: 35899198 PMCID: PMC9313540 DOI: 10.3389/fgene.2022.894048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
The mitogen-activated protein kinase (MAPK) cascade is a highly conserved signal transduction pathway, ubiquitous in eukaryotes, such as animals and plants. The MAPK cascade has a dominant role in regulating plant adaptation to the environment, such as through stress responses, osmotic adjustment, and processes that modulate pathogenicity. In the present study, the MAPK cascade gene family was identified in Fagopyrum tataricum (Tartary buckwheat), based on complete genome sequence data. Using phylogenetic tree, conservative motif, and chromosome location analyses, a total of 65 FtMAPK cascade genes, distributed on five chromosomes, were classified into three families: MAPK (n = 8), MAPKK (n = 1), and MAPKKK (n = 56). Transcriptome data from Tartary buckwheat seedlings grown under different light conditions demonstrated that, under blue and red light, the expression levels of 18 and 36 FtMAPK cascade genes were up-regulated and down-regulated, respectively. Through qRT-PCR experiments, it was observed that FtMAPK5, FtMAPKK1, FtMAPKKK8, FtMAPKKK10, and FtMAPKKK24 gene expression levels in the Tartary buckwheat seedlings increased under three types of abiotic stress: drought, salt, and high temperature. A co-expression network of FtMAPK cascade genes was constructed, based on gene expression levels under different light conditions, and co-expressed genes annotated by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses, which identified numerous transcription factors related to plant abiotic stress. The authors conclude that FtMAPK cascade genes have important roles in the growth and development of Tartary buckwheat, as well as its responses to abiotic stress.
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Affiliation(s)
- Zhen Wang
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Song Yan
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Weichao Ren
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yan Liu
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Meiqi Liu
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Jiaxin Lu
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yaolei Mi
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Yaolei Mi, ; Wei Ma,
| | - Wei Ma
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin, China
- *Correspondence: Yaolei Mi, ; Wei Ma,
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Buljan M, Ciuffa R, van Drogen A, Vichalkovski A, Mehnert M, Rosenberger G, Lee S, Varjosalo M, Pernas LE, Spegg V, Snijder B, Aebersold R, Gstaiger M. Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases. Mol Cell 2020; 79:504-520.e9. [PMID: 32707033 PMCID: PMC7427327 DOI: 10.1016/j.molcel.2020.07.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 02/14/2020] [Accepted: 06/30/2020] [Indexed: 12/30/2022]
Abstract
Protein kinases are essential for signal transduction and control of most cellular processes, including metabolism, membrane transport, motility, and cell cycle. Despite the critical role of kinases in cells and their strong association with diseases, good coverage of their interactions is available for only a fraction of the 535 human kinases. Here, we present a comprehensive mass-spectrometry-based analysis of a human kinase interaction network covering more than 300 kinases. The interaction dataset is a high-quality resource with more than 5,000 previously unreported interactions. We extensively characterized the obtained network and were able to identify previously described, as well as predict new, kinase functional associations, including those of the less well-studied kinases PIM3 and protein O-mannose kinase (POMK). Importantly, the presented interaction map is a valuable resource for assisting biomedical studies. We uncover dozens of kinase-disease associations spanning from genetic disorders to complex diseases, including cancer.
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Affiliation(s)
- Marija Buljan
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Empa, Swiss Federal Laboratories for Materials Science and Technology, 9014 St. Gallen, Switzerland
| | - Rodolfo Ciuffa
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Audrey van Drogen
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Anton Vichalkovski
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Martin Mehnert
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - George Rosenberger
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Columbia University Department of Systems Biology, New York, NY 10032, USA
| | - Sohyon Lee
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Lucia Espona Pernas
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Berend Snijder
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland.
| | - Matthias Gstaiger
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
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Lauenstein JU, Udgata A, Bartram A, De Sutter D, Fisher DI, Halabi S, Eyckerman S, Gay NJ. Phosphorylation of the multifunctional signal transducer B-cell adaptor protein (BCAP) promotes recruitment of multiple SH2/SH3 proteins including GRB2. J Biol Chem 2019; 294:19852-19861. [PMID: 31527084 PMCID: PMC6937578 DOI: 10.1074/jbc.ra119.009931] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/10/2019] [Indexed: 12/21/2022] Open
Abstract
B-cell adaptor protein (BCAP) is a multimodular, multifunctional signal transducer that regulates signal transduction pathways in leukocytes, including macrophages, B-cells, and T-cells. In particular, BCAP suppresses inflammatory signaling by Toll-like receptors (TLRs). However, how BCAP itself is regulated and what its interaction partners are is unclear. Here, using human immune cell lines, including THP-1 cells, we characterized the complex phosphorylation patterns of BCAP and used a novel protein complex trapping strategy, called virotrap, to identify its interaction partners. This analysis identified known interactions of BCAP with phosphoinositide 3-kinase (PI3K) p85 subunit and NCK adaptor protein (NCK), together with previously unknown interactions of BCAP with Src homology 2 (SH2) and SH3 domain-containing adaptor proteins, notably growth factor receptor-bound protein 2 (GRB2) and CRK-like proto-oncogene, adaptor protein (CRKL). We show that the SH3 domain of GRB2 can bind to BCAP independently of BCAP phosphorylation status, suggesting that the SH2 domains mediate interactions with activated receptor tyrosine kinase complexes including the CD19 subunit of the B-cell receptor. Our results also suggested that the PI3K p85 subunit binds to BCAP via SH3 domains forming an inactive complex that is then activated by sequential binding with the SH2 domains. Taken together, our results indicate that BCAP is a complex hub that processes signals from multiple pathways in diverse cell types of the immune system.
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Affiliation(s)
- Johannes U Lauenstein
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Atul Udgata
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Alex Bartram
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Delphine De Sutter
- Department of Biomolecular Medicine, Ghent University, VIB Center for Medical Biotechnology, VIB, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - David I Fisher
- Discovery Sciences, Discovery Biology, IMED Biotech Unit, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Samer Halabi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Sven Eyckerman
- Department of Biomolecular Medicine, Ghent University, VIB Center for Medical Biotechnology, VIB, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Nicholas J Gay
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
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Thrombin-induced IL-8/CXCL8 release is mediated by CK2, MSK1, and NF-κB pathways in human lung epithelial cells. Eur J Pharmacol 2015; 767:135-43. [PMID: 26463037 DOI: 10.1016/j.ejphar.2015.10.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 10/07/2015] [Accepted: 10/08/2015] [Indexed: 12/15/2022]
Abstract
Airway inflammation plays a major role in the pathophysiology of lung inflammatory diseases such as asthma. Thrombin, a serine protease, is known to mediate central functions in thrombosis and hemostasis and also plays a critical role in lung inflammation via producing chemokine release including interleukin (IL)-8/CXCL8. Our previous studies showed that c-Src- and Rac-dependent nuclear factor (NF)-κB signaling pathways participate in thrombin-induced IL-8/CXCL8 release in human lung epithelial cells. In this study, we further investigated the role of casein kinase 2 (CK2)/mitogen stress-activated protein kinase 1 (MSK1)-dependent p65 phosphorylation in thrombin-induced NF-κB activation and IL-8/CXCL8 release. Thrombin-induced IL-8/CXCL8 release was inhibited by CK2 inhibitors (apigenin and tetrabromobenzotriazole, TBB), small interfering RNA of CK2β (CK2β siRNA), and MSK1 siRNA. Treatment of cells with thrombin caused increases in CK2β phosphorylation at Ser209, which was inhibited by a protein kinase C α (PKCα) inhibitor (Ro-32-0432). Thrombin-induced MSK1 phosphorylation at Ser581 and Akt phosphorylation at Ser473 were inhibited by apigenin. Moreover, the thrombin-induced increase in IL-8/CXCL8 release was attenuated by p65 siRNA. Stimulation of cells with thrombin resulted in an increase in p65 phosphorylation at Ser276, which was inhibited by apigenin and MSK1 siRNA. Thrombin-induced κB-luciferase activity was also inhibited by apigenin and MSK1 siRNA. Taken together, these results show that thrombin activates the PKCα/CK2/MSK1 signaling pathways, which in turn initiates p65 phosphorylation and NF-κB activation, and ultimately induces IL-8/CXCL8 release in human lung epithelial cells.
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Chomwisarutkun K, Murani E, Ponsuksili S, Wimmers K. Microarray analysis reveals genes and functional networks relevant to the predisposition to inverted teats in pigs1. J Anim Sci 2012; 90:1-15. [DOI: 10.2527/jas.2011-4269] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- K. Chomwisarutkun
- Leibniz Institute for Farm Animal Biology, Research Unit Molecular Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - E. Murani
- Leibniz Institute for Farm Animal Biology, Research Unit Molecular Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - S. Ponsuksili
- Leibniz Institute for Farm Animal Biology, Research Group Functional Genome Analysis, Dummerstorf, Germany
| | - K. Wimmers
- Leibniz Institute for Farm Animal Biology, Research Unit Molecular Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
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6
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Activation and function of the MAPKs and their substrates, the MAPK-activated protein kinases. Microbiol Mol Biol Rev 2011; 75:50-83. [PMID: 21372320 DOI: 10.1128/mmbr.00031-10] [Citation(s) in RCA: 2158] [Impact Index Per Article: 166.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The mitogen-activated protein kinases (MAPKs) regulate diverse cellular programs by relaying extracellular signals to intracellular responses. In mammals, there are more than a dozen MAPK enzymes that coordinately regulate cell proliferation, differentiation, motility, and survival. The best known are the conventional MAPKs, which include the extracellular signal-regulated kinases 1 and 2 (ERK1/2), c-Jun amino-terminal kinases 1 to 3 (JNK1 to -3), p38 (α, β, γ, and δ), and ERK5 families. There are additional, atypical MAPK enzymes, including ERK3/4, ERK7/8, and Nemo-like kinase (NLK), which have distinct regulation and functions. Together, the MAPKs regulate a large number of substrates, including members of a family of protein Ser/Thr kinases termed MAPK-activated protein kinases (MAPKAPKs). The MAPKAPKs are related enzymes that respond to extracellular stimulation through direct MAPK-dependent activation loop phosphorylation and kinase activation. There are five MAPKAPK subfamilies: the p90 ribosomal S6 kinase (RSK), the mitogen- and stress-activated kinase (MSK), the MAPK-interacting kinase (MNK), the MAPK-activated protein kinase 2/3 (MK2/3), and MK5 (also known as p38-regulated/activated protein kinase [PRAK]). These enzymes have diverse biological functions, including regulation of nucleosome and gene expression, mRNA stability and translation, and cell proliferation and survival. Here we review the mechanisms of MAPKAPK activation by the different MAPKs and discuss their physiological roles based on established substrates and recent discoveries.
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Cargnello M, Roux PP. Activation and Function of the MAPKs and Their Substrates, the MAPK-Activated Protein Kinases. Microbiol Mol Biol Rev 2011. [DOI: 78495111110.1128/mmbr.00031-10' target='_blank'>'"<>78495111110.1128/mmbr.00031-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [78495111110.1128/mmbr.00031-10','', '10.5483/bmbrep.2009.42.12.840')">Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
78495111110.1128/mmbr.00031-10" />
Abstract
SUMMARYThe mitogen-activated protein kinases (MAPKs) regulate diverse cellular programs by relaying extracellular signals to intracellular responses. In mammals, there are more than a dozen MAPK enzymes that coordinately regulate cell proliferation, differentiation, motility, and survival. The best known are the conventional MAPKs, which include the extracellular signal-regulated kinases 1 and 2 (ERK1/2), c-Jun amino-terminal kinases 1 to 3 (JNK1 to -3), p38 (α, β, γ, and δ), and ERK5 families. There are additional, atypical MAPK enzymes, including ERK3/4, ERK7/8, and Nemo-like kinase (NLK), which have distinct regulation and functions. Together, the MAPKs regulate a large number of substrates, including members of a family of protein Ser/Thr kinases termed MAPK-activated protein kinases (MAPKAPKs). The MAPKAPKs are related enzymes that respond to extracellular stimulation through direct MAPK-dependent activation loop phosphorylation and kinase activation. There are five MAPKAPK subfamilies: the p90 ribosomal S6 kinase (RSK), the mitogen- and stress-activated kinase (MSK), the MAPK-interacting kinase (MNK), the MAPK-activated protein kinase 2/3 (MK2/3), and MK5 (also known as p38-regulated/activated protein kinase [PRAK]). These enzymes have diverse biological functions, including regulation of nucleosome and gene expression, mRNA stability and translation, and cell proliferation and survival. Here we review the mechanisms of MAPKAPK activation by the different MAPKs and discuss their physiological roles based on established substrates and recent discoveries.
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Affiliation(s)
- Marie Cargnello
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
- Molecular Biology Program, Université de Montréal, Montreal, Quebec, Canada
| | - Philippe P. Roux
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
- Molecular Biology Program, Université de Montréal, Montreal, Quebec, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
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Hyun TK, Kim JS, Kwon SY, Kim SH. Comparative genomic analysis of mitogen activated protein kinase gene family in grapevine. Genes Genomics 2010. [DOI: 10.1007/s13258-010-0010-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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