1
|
Piserchio A, Dalby KN, Ghose R. Revealing eEF-2 kinase: recent structural insights into function. Trends Biochem Sci 2024; 49:169-182. [PMID: 38103971 PMCID: PMC10950556 DOI: 10.1016/j.tibs.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023]
Abstract
The α-kinase eukaryotic elongation factor 2 kinase (eEF-2K) regulates translational elongation by phosphorylating its ribosome-associated substrate, the GTPase eEF-2. eEF-2K is activated by calmodulin (CaM) through a distinctive mechanism unlike that in other CaM-dependent kinases (CAMK). We describe recent structural insights into this unique activation process and examine the effects of specific regulatory signals on this mechanism. We also highlight key unanswered questions to guide future structure-function studies. These include structural mechanisms which enable eEF-2K to interact with upstream/downstream partners and facilitate its integration of diverse inputs, including Ca2+ transients, phosphorylation mediated by energy/nutrient-sensing pathways, pH changes, and metabolites. Answering these questions is key to establishing how eEF-2K harmonizes translation with cellular requirements within the boundaries of its molecular landscape.
Collapse
Affiliation(s)
- Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas, Austin, TX 78712, USA.
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA; The Graduate Center of The City University of New York (CUNY), New York, NY 10016, USA.
| |
Collapse
|
2
|
Stephenson EH, Higgins JMG. Pharmacological approaches to understanding protein kinase signaling networks. Front Pharmacol 2023; 14:1310135. [PMID: 38164473 PMCID: PMC10757940 DOI: 10.3389/fphar.2023.1310135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
Protein kinases play vital roles in controlling cell behavior, and an array of kinase inhibitors are used successfully for treatment of disease. Typical drug development pipelines involve biological studies to validate a protein kinase target, followed by the identification of small molecules that effectively inhibit this target in cells, animal models, and patients. However, it is clear that protein kinases operate within complex signaling networks. These networks increase the resilience of signaling pathways, which can render cells relatively insensitive to inhibition of a single kinase, and provide the potential for pathway rewiring, which can result in resistance to therapy. It is therefore vital to understand the properties of kinase signaling networks in health and disease so that we can design effective multi-targeted drugs or combinations of drugs. Here, we outline how pharmacological and chemo-genetic approaches can contribute to such knowledge, despite the known low selectivity of many kinase inhibitors. We discuss how detailed profiling of target engagement by kinase inhibitors can underpin these studies; how chemical probes can be used to uncover kinase-substrate relationships, and how these tools can be used to gain insight into the configuration and function of kinase signaling networks.
Collapse
Affiliation(s)
| | - Jonathan M. G. Higgins
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle uponTyne, United Kingdom
| |
Collapse
|
3
|
Kim J, Chun Y, Ramirez CB, Hoffner LA, Jung S, Jang KH, Rubtsova VI, Jang C, Lee G. MAPK13 stabilization via m 6A mRNA modification limits anticancer efficacy of rapamycin. J Biol Chem 2023; 299:105175. [PMID: 37599001 PMCID: PMC10511813 DOI: 10.1016/j.jbc.2023.105175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 08/10/2023] [Accepted: 08/12/2023] [Indexed: 08/22/2023] Open
Abstract
N6-adenosine methylation (m6A) is the most abundant mRNA modification that controls gene expression through diverse mechanisms. Accordingly, m6A-dependent regulation of oncogenes and tumor suppressors contributes to tumor development. However, the role of m6A-mediated gene regulation upon drug treatment or resistance is poorly understood. Here, we report that m6A modification of mitogen-activated protein kinase 13 (MAPK13) mRNA determines the sensitivity of cancer cells to the mechanistic target of rapamycin complex 1 (mTORC1)-targeting agent rapamycin. mTORC1 induces m6A modification of MAPK13 mRNA at its 3' untranslated region through the methyltransferase-like 3 (METTL3)-METTL14-Wilms' tumor 1-associating protein(WTAP) methyltransferase complex, facilitating its mRNA degradation via an m6A reader protein YTH domain family protein 2. Rapamycin blunts this process and stabilizes MAPK13. On the other hand, genetic or pharmacological inhibition of MAPK13 enhances rapamycin's anticancer effects, which suggests that MAPK13 confers a progrowth signal upon rapamycin treatment, thereby limiting rapamycin efficacy. Together, our data indicate that rapamycin-mediated MAPK13 mRNA stabilization underlies drug resistance, and it should be considered as a promising therapeutic target to sensitize cancer cells to rapamycin.
Collapse
Affiliation(s)
- Joohwan Kim
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Yujin Chun
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Cuauhtemoc B Ramirez
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA; Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Lauren A Hoffner
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Sunhee Jung
- Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Ki-Hong Jang
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Varvara I Rubtsova
- Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA; School of Biological Sciences, University of California Irvine, Irvine, California, USA
| | - Cholsoon Jang
- Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA
| | - Gina Lee
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, California, USA.
| |
Collapse
|
4
|
Piserchio A, Long K, Browning L, Bohanon A, Isiorho E, Dalby K, Ghose R. ADP enhances the allosteric activation of eukaryotic elongation factor 2 kinase by calmodulin. Proc Natl Acad Sci U S A 2023; 120:e2300902120. [PMID: 37068230 PMCID: PMC10151598 DOI: 10.1073/pnas.2300902120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/06/2023] [Indexed: 04/19/2023] Open
Abstract
Protein translation, one of the most energy-consumptive processes in a eukaryotic cell, requires robust regulation, especially under energy-deprived conditions. A critical component of this regulation is the suppression of translational elongation through reduced ribosome association of the GTPase eukaryotic elongation factor 2 (eEF-2) resulting from its specific phosphorylation by the calmodulin (CaM)-activated α-kinase eEF-2 kinase (eEF-2K). It has been suggested that the eEF-2K response to reduced cellular energy levels is indirect and mediated by the universal energy sensor AMP-activated protein kinase (AMPK) through direct stimulatory phosphorylation and/or downregulation of the eEF-2K-inhibitory nutrient-sensing mTOR pathway. Here, we provide structural, biochemical, and cell-biological evidence of a direct energy-sensing role of eEF-2K through its stimulation by ADP. A crystal structure of the nucleotide-bound complex between CaM and the functional core of eEF-2K phosphorylated at its primary stimulatory site (T348) reveals ADP bound at a unique pocket located on the face opposite that housing the kinase active site. Within this basic pocket (BP), created at the CaM/eEF-2K interface upon complex formation, ADP is stabilized through numerous interactions with both interacting partners. Biochemical analyses using wild-type eEF-2K and specific BP mutants indicate that ADP stabilizes CaM within the active complex, increasing the sensitivity of the kinase to CaM. Induction of energy stress through glycolysis inhibition results in significantly reduced enhancement of phosphorylated eEF-2 levels in cells expressing ADP-binding compromised BP mutants compared to cells expressing wild-type eEF-2K. These results suggest a direct energy-sensing role for eEF-2K through its cooperative interaction with CaM and ADP.
Collapse
Affiliation(s)
- Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY10031
| | - Kimberly J. Long
- Division of Chemical Biology and Medicinal Chemistry, the University of Texas, Austin, TX78712
| | - Luke S. Browning
- Interdisciplinary Life Sciences Graduate Program, the University of Texas, Austin, TX78712
| | - Amanda L. Bohanon
- Interdisciplinary Life Sciences Graduate Program, the University of Texas, Austin, TX78712
| | - Eta A. Isiorho
- Macromolecular Crystallization Facility CUNY Advanced Science Research Center, New York, NY10031
| | - Kevin N. Dalby
- Division of Chemical Biology and Medicinal Chemistry, the University of Texas, Austin, TX78712
- Interdisciplinary Life Sciences Graduate Program, the University of Texas, Austin, TX78712
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY10031
- PhD Program in Biochemistry, The Graduate Center of CUNY, New York, NY10016
- PhD Program in Chemistry, The Graduate Center of CUNY, New York, NY10016
- PhD Program in Physics, The Graduate Center of CUNY, New York, NY10016
| |
Collapse
|
5
|
Díaz-Mora E, González-Romero D, Meireles-da-Silva M, Sanz-Ezquerro JJ, Cuenda A. p38δ controls Mitogen- and Stress-activated Kinase-1 (MSK1) function in response to toll-like receptor activation in macrophages. Front Cell Dev Biol 2023; 11:1083033. [PMID: 36846591 PMCID: PMC9946961 DOI: 10.3389/fcell.2023.1083033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/27/2023] [Indexed: 02/11/2023] Open
Abstract
Mitogen- and Stress-activated Kinase (MSK) 1 is a nuclear protein, activated by p38α Mitogen-Activated Kinase (MAPK) and extracellular signal-regulated kinase (ERK1/2), that modulate the production of certain cytokines in macrophages. Using knockout cells and specific kinase inhibitors, we show that, besides p38α and ERK1/2, another p38MAPK, p38δ, mediates MSK phosphorylation and activation, in LPS-stimulated macrophages. Additionally, recombinant MSK1 was phosphorylated and activated by recombinant p38δ, to the same extent than by p38α, in in vitro experiments. Moreover, the phosphorylation of the transcription factors CREB and ATF1, that are MSK physiological substrates, and the expression of the CREB-dependent gene encoding DUSP1, were impaired in p38δ-deficient macrophages. Also, the transcription of IL-1Ra mRNA, that is MSK-dependent, was reduced. Our results indicate that MSK activation can be one possible mechanism by which p38δ regulates the production of a variety of inflammatory molecules involved in immune innate response.
Collapse
Affiliation(s)
- Ester Díaz-Mora
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC (CNB-CSIC), Madrid, Spain
| | - Diego González-Romero
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC (CNB-CSIC), Madrid, Spain
| | - Marta Meireles-da-Silva
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC (CNB-CSIC), Madrid, Spain
| | - Juan José Sanz-Ezquerro
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología/CSIC (CNB-CSIC), Madrid, Spain
| | - Ana Cuenda
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC (CNB-CSIC), Madrid, Spain,*Correspondence: Ana Cuenda,
| |
Collapse
|
6
|
Salimi K, Alvandi M, Saberi Pirouz M, Rakhshan K, Howatson G. Regulating eEF2 and eEF2K in skeletal muscle by exercise. Arch Physiol Biochem 2023:1-12. [PMID: 36633938 DOI: 10.1080/13813455.2023.2164898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/15/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023]
Abstract
Skeletal muscle is a flexible and adaptable tissue that strongly responds to exercise training. The skeletal muscle responds to exercise by increasing muscle protein synthesis (MPS) when energy is available. One of protein synthesis's major rate-limiting and critical regulatory steps is the translation elongation pathway. The process of translation elongation in skeletal muscle is highly regulated. It requires elongation factors that are intensely affected by various physiological stimuli such as exercise and the total available energy of cells. Studies have shown that exercise involves the elongation pathway by numerous signalling pathways. Since the elongation pathway, has been far less studied than the other translation steps, its comprehensive prospect and quantitative understanding remain in the dark. This study highlights the current understanding of the effect of exercise training on the translation elongation pathway focussing on the molecular factors affecting the pathway, including Ca2+, AMPK, PKA, mTORC1/P70S6K, MAPKs, and myostatin. We further discussed the mode and volume of exercise training intervention on the translation elongation pathway.What is the topic of this review? This review summarises the impacts of exercise training on the translation elongation pathway in skeletal muscle focussing on eEF2 and eEF2K.What advances does it highlight? This review highlights mechanisms and factors that profoundly influence the translation elongation pathway and argues that exercise might modulate the response. This review also combines the experimental observations focussing on the regulation of translation elongation during and after exercise. The findings widen our horizon to the notion of mechanisms involved in muscle protein synthesis (MPS) through translation elongation response to exercise training.
Collapse
Affiliation(s)
- Kia Salimi
- Department of Exercise Physiology, Faculty of Sport and Exercise Sciences, University of Tehran, Tehran, Iran
| | - Masoomeh Alvandi
- Department of Biological Science in Sport and Health, University of Shahid Beheshti, Tehran, Iran
| | - Mahdi Saberi Pirouz
- Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Kamran Rakhshan
- Department of Medical Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Electrophysiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Glyn Howatson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
- Water Research Group, North West University, Potchefstroom, South Africa
| |
Collapse
|
7
|
Cai S, Hu T, Venkatesan M, Allam M, Schneider F, Ramalingam SS, Sun SY, Coskun AF. Multiplexed protein profiling reveals spatial subcellular signaling networks. iScience 2022; 25:104980. [PMID: 36093051 PMCID: PMC9460555 DOI: 10.1016/j.isci.2022.104980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 05/25/2022] [Accepted: 08/16/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Shuangyi Cai
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Thomas Hu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Mythreye Venkatesan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Mayar Allam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Frank Schneider
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, GA 30322, USA
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Suresh S. Ramalingam
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Shi-Yong Sun
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ahmet F. Coskun
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Corresponding author
| |
Collapse
|
8
|
Hijazi M, Casado P, Akhtar N, Alvarez-Teijeiro S, Rajeeve V, Cutillas PR. eEF2K Activity Determines Synergy to Cotreatment of Cancer Cells With PI3K and MEK Inhibitors. Mol Cell Proteomics 2022; 21:100240. [PMID: 35513296 PMCID: PMC9184568 DOI: 10.1016/j.mcpro.2022.100240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/17/2022] [Accepted: 04/25/2022] [Indexed: 10/31/2022] Open
Abstract
PI3K-mammalian target of rapamycin and MAPK/ERK kinase (MEK)/mitogen-activated protein kinase (MAPK) are the most frequently dysregulated signaling pathways in cancer. A problem that limits the success of therapies that target individual PI3K-MAPK members is that these pathways converge to regulate downstream functions and often compensate each other, leading to drug resistance and transient responses to therapy. In order to overcome resistance, therapies based on cotreatments with PI3K/AKT and MEK/MAPK inhibitors are now being investigated in clinical trials, but the mechanisms of sensitivity to cotreatment are not fully understood. Using LC-MS/MS-based phosphoproteomics, we found that eukaryotic elongation factor 2 kinase (eEF2K), a key convergence point downstream of MAPK and PI3K pathways, mediates synergism to cotreatment with trametinib plus pictilisib (which target MEK1/2 and PI3Kα/δ, respectively). Inhibition of eEF2K by siRNA or with a small molecule inhibitor reversed the antiproliferative effects of the cotreatment with PI3K plus MEK inhibitors in a cell model-specific manner. Systematic analysis in 12 acute myeloid leukemia cell lines revealed that eEF2K activity was increased in cells for which PI3K plus MEKi cotreatment is synergistic, while PKC potentially mediated resistance to such cotreatment. Together, our study uncovers eEF2K activity as a key mediator of responses to PI3Ki plus MEKi and as a potential biomarker to predict synergy to cotreatment in cancer cells.
Collapse
Affiliation(s)
- Maruan Hijazi
- Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.
| | - Pedro Casado
- Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Nosheen Akhtar
- Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Saul Alvarez-Teijeiro
- Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Vinothini Rajeeve
- Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Pedro R Cutillas
- Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom; The Alan Turing Institute, British Library, London, United Kingdom.
| |
Collapse
|
9
|
Andreev DE, Loughran G, Fedorova AD, Mikhaylova MS, Shatsky IN, Baranov PV. Non-AUG translation initiation in mammals. Genome Biol 2022; 23:111. [PMID: 35534899 PMCID: PMC9082881 DOI: 10.1186/s13059-022-02674-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 04/14/2022] [Indexed: 12/12/2022] Open
Abstract
Recent proteogenomic studies revealed extensive translation outside of annotated protein coding regions, such as non-coding RNAs and untranslated regions of mRNAs. This non-canonical translation is largely due to start codon plurality within the same RNA. This plurality is often due to the failure of some scanning ribosomes to recognize potential start codons leading to initiation downstream—a process termed leaky scanning. Codons other than AUG (non-AUG) are particularly leaky due to their inefficiency. Here we discuss our current understanding of non-AUG initiation. We argue for a near-ubiquitous role of non-AUG initiation in shaping the dynamic composition of mammalian proteomes.
Collapse
|
10
|
Adachi J, Kakudo A, Takada Y, Isoyama J, Ikemoto N, Abe Y, Narumi R, Muraoka S, Gunji D, Hara Y, Katayama R, Tomonaga T. Systematic identification of ALK substrates by integrated phosphoproteome and interactome analysis. Life Sci Alliance 2022; 5:5/8/e202101202. [PMID: 35508387 PMCID: PMC9069051 DOI: 10.26508/lsa.202101202] [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: 08/19/2021] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 11/24/2022] Open
Abstract
Integrated analysis of the phosphoproteome and interactome of anaplastic lymphoma kinase (ALK)-overexpressing HEK 293 cells revealed 37 ALK substrate candidates, contributing to the improvement of kinase activity prediction. The sensitivity of phosphorylation site identification by mass spectrometry has improved markedly. However, the lack of kinase–substrate relationship (KSR) data hinders the improvement of the range and accuracy of kinase activity prediction. In this study, we aimed to develop a method for acquiring systematic KSR data on anaplastic lymphoma kinase (ALK) using mass spectrometry and to apply this method to the prediction of kinase activity. Thirty-seven ALK substrate candidates, including 34 phosphorylation sites not annotated in the PhosphoSitePlus database, were identified by integrated analysis of the phosphoproteome and crosslinking interactome of HEK 293 cells with doxycycline-induced ALK overexpression. Furthermore, KSRs of ALK were validated by an in vitro kinase assay. Finally, using phosphoproteomic data from ALK mutant cell lines and patient-derived cells treated with ALK inhibitors, we found that the prediction of ALK activity was improved when the KSRs identified in this study were used instead of the public KSR dataset. Our approach is applicable to other kinases, and future identification of KSRs will facilitate more accurate estimations of kinase activity and elucidation of phosphorylation signals.
Collapse
Affiliation(s)
- Jun Adachi
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan .,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Laboratory of Proteomics and Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Akemi Kakudo
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Yoko Takada
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Junko Isoyama
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Narumi Ikemoto
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Yuichi Abe
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Ryohei Narumi
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Satoshi Muraoka
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Daigo Gunji
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Department of Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yasuhiro Hara
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Ryohei Katayama
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| |
Collapse
|
11
|
Alagar Boopathy LR, Jacob-Tomas S, Alecki C, Vera M. Mechanisms tailoring the expression of heat shock proteins to proteostasis challenges. J Biol Chem 2022; 298:101796. [PMID: 35248532 PMCID: PMC9065632 DOI: 10.1016/j.jbc.2022.101796] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 12/14/2022] Open
Abstract
All cells possess an internal stress response to cope with environmental and pathophysiological challenges. Upon stress, cells reprogram their molecular functions to activate a survival mechanism known as the heat shock response, which mediates the rapid induction of molecular chaperones such as the heat shock proteins (HSPs). This potent production overcomes the general suppression of gene expression and results in high levels of HSPs to subsequently refold or degrade misfolded proteins. Once the damage or stress is repaired or removed, cells terminate the production of HSPs and resume regular functions. Thus, fulfillment of the stress response requires swift and robust coordination between stress response activation and completion that is determined by the status of the cell. In recent years, single-cell fluorescence microscopy techniques have begun to be used in unravelling HSP-gene expression pathways, from DNA transcription to mRNA degradation. In this review, we will address the molecular mechanisms in different organisms and cell types that coordinate the expression of HSPs with signaling networks that act to reprogram gene transcription, mRNA translation, and decay and ensure protein quality control.
Collapse
|
12
|
Ballard DJ, Peng HY, Das JK, Kumar A, Wang L, Ren Y, Xiong X, Ren X, Yang JM, Song J. Insights Into the Pathologic Roles and Regulation of Eukaryotic Elongation Factor-2 Kinase. Front Mol Biosci 2021; 8:727863. [PMID: 34532346 PMCID: PMC8438118 DOI: 10.3389/fmolb.2021.727863] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 08/16/2021] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic Elongation Factor-2 Kinase (eEF2K) acts as a negative regulator of protein synthesis, translation, and cell growth. As a structurally unique member of the alpha-kinase family, eEF2K is essential to cell survival under stressful conditions, as it contributes to both cell viability and proliferation. Known as the modulator of the global rate of protein translation, eEF2K inhibits eEF2 (eukaryotic Elongation Factor 2) and decreases translation elongation when active. eEF2K is regulated by various mechanisms, including phosphorylation through residues and autophosphorylation. Specifically, this protein kinase is downregulated through the phosphorylation of multiple sites via mTOR signaling and upregulated via the AMPK pathway. eEF2K plays important roles in numerous biological systems, including neurology, cardiology, myology, and immunology. This review provides further insights into the current roles of eEF2K and its potential to be explored as a therapeutic target for drug development.
Collapse
Affiliation(s)
- Darby J. Ballard
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, United States
| | - Hao-Yun Peng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, United States
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Jugal Kishore Das
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, United States
| | - Anil Kumar
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, United States
| | - Liqing Wang
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, United States
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Yijie Ren
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, United States
| | - Xiaofang Xiong
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, United States
| | - Xingcong Ren
- Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, KY, United States
| | - Jin-Ming Yang
- Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, KY, United States
| | - Jianxun Song
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, United States
| |
Collapse
|
13
|
Niinae T, Imami K, Sugiyama N, Ishihama Y. Identification of Endogenous Kinase Substrates by Proximity Labeling Combined with Kinase Perturbation and Phosphorylation Motifs. Mol Cell Proteomics 2021; 20:100119. [PMID: 34186244 PMCID: PMC8325102 DOI: 10.1016/j.mcpro.2021.100119] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/08/2021] [Accepted: 06/22/2021] [Indexed: 02/08/2023] Open
Abstract
Mass-spectrometry-based phosphoproteomics can identify more than 10,000 phosphorylated sites in a single experiment. But, despite the fact that enormous phosphosite information has been accumulated in public repositories, protein kinase–substrate relationships remain largely unknown. Here, we describe a method to identify endogenous substrates of kinases by using a combination of a proximity-dependent biotin identification method, called BioID, with two other independent methods, kinase-perturbed phosphoproteomics and phosphorylation motif matching. For proof of concept, this approach was applied to casein kinase 2 (CK2) and protein kinase A (PKA), and we identified 24 and 35 putative substrates, respectively. We also show that known cancer-associated missense mutations near phosphosites of substrates affect phosphorylation by CK2 or PKA and thus might alter downstream signaling in cancer cells bearing these mutations. This approach extends our ability to probe physiological kinase–substrate networks by providing new methodology for large-scale identification of endogenous substrates of kinases. Identification of novel kinase interactors by BioID. Applying two orthogonal filters, kinase perturbation and phosphorylation motif. Identification of novel CK2 and PKA substrates. A universal method for the identification of endogenous substrates for all kinases.
Collapse
Affiliation(s)
- Tomoya Niinae
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Koshi Imami
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan; PRESTO, Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, Japan
| | - Naoyuki Sugiyama
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yasushi Ishihama
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan; Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan.
| |
Collapse
|
14
|
An Q, Zhou Z, Xie Y, Sun Y, Zhang H, Cao Y. Knockdown of long non-coding RNA NEAT1 relieves the inflammatory response of spinal cord injury through targeting miR-211-5p/MAPK1 axis. Bioengineered 2021; 12:2702-2712. [PMID: 34151707 PMCID: PMC8806627 DOI: 10.1080/21655979.2021.1930925] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Spinal cord injury (SCI) is a refractory disease often accompanied by inflammation. Long non-coding RNA NEAT1 (lncRNA NEAT1) was reported to be involved in the expression of the inflammasomes, while the regulatory effect of NEAT1 on SCI was poorly investigated. Herein, we carried out further studies on the pathogenesis of SCI. PC-12 cells were incubated with lipopolysaccharide (LPS) to induce inflammation. Western blotting assay was used to measure the protein expression levels. RNA expression levels were analyzed using RT-qPCR. Cell counting kit 8 and flow cytometry assays were used to separately determine the cell viability and apoptosis rate. The targeted relationships were verified by luciferase reporter and RNA pull-down assays. It was found that LPS induced inflammation in the PC-12 cells, leading to significantly higher cell apoptosis rate and lower viability, and the expression level of NEAT1 was elevated by LPS. However, knockdown of NEAT1 partially reversed the effects of LPS. Subsequently, the potential interaction between NEAT1 and miR-211-5p was validated and miR-211-5p inhibitor was further confirmed to antagonize the effects of NEAT knockdown. The downstream target gene of miR-211-5p was predicted and verified to be MAPK1. In addition, overexpression of MAPK1 was proved to antagonize the effects of NEAT1 knockdown. Taken together, the knockdown of NEAT1 remarkably alleviated the inflammation of SCI via miR-211-5p/MAPK1 axis.
Collapse
Affiliation(s)
- Qing An
- Department of Medicine, Soochow university, China.,Hand Surgery Department, The First Affiliated Hospital of JinZhou Medical University, China
| | - Zipeng Zhou
- Department of Medicine, Soochow university, China
| | - Yi Xie
- Department of Medicine, Soochow university, China
| | - Yu Sun
- Bone Trauma Department, The First Affiliated Hospital of JinZhou Medical University, China
| | - Haixiang Zhang
- Bone Trauma Department, The First Affiliated Hospital of JinZhou Medical University, China
| | - Yang Cao
- Department of Medicine, Soochow university, China.,Bone Trauma Department, The First Affiliated Hospital of JinZhou Medical University, China
| |
Collapse
|
15
|
Alboushi L, Hackett AP, Naeli P, Bakhti M, Jafarnejad SM. Multifaceted control of mRNA translation machinery in cancer. Cell Signal 2021; 84:110037. [PMID: 33975011 DOI: 10.1016/j.cellsig.2021.110037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/06/2021] [Indexed: 12/15/2022]
Abstract
The mRNA translation machinery is tightly regulated through several, at times overlapping, mechanisms that modulate its efficiency and accuracy. Due to their fast rate of growth and metabolism, cancer cells require an excessive amount of mRNA translation and protein synthesis. However, unfavorable conditions, such as hypoxia, amino acid starvation, and oxidative stress, which are abundant in cancer, as well as many anti-cancer treatments inhibit mRNA translation. Cancer cells adapt to the various internal and environmental stresses by employing specialised transcript-specific translation to survive and gain a proliferative advantage. We will highlight the major signaling pathways and mechanisms of translation that regulate the global or mRNA-specific translation in response to the intra- or extra-cellular signals and stresses that are key components in the process of tumourigenesis.
Collapse
Affiliation(s)
- Lilas Alboushi
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Angela P Hackett
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Parisa Naeli
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Mostafa Bakhti
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Seyed Mehdi Jafarnejad
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK.
| |
Collapse
|
16
|
Shen Y, Zhang ZC, Cheng S, Liu A, Zuo J, Xia S, Liu X, Liu W, Jia Z, Xie W, Han J. PQBP1 promotes translational elongation and regulates hippocampal mGluR-LTD by suppressing eEF2 phosphorylation. Mol Cell 2021; 81:1425-1438.e10. [PMID: 33662272 DOI: 10.1016/j.molcel.2021.01.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 12/07/2020] [Accepted: 01/21/2021] [Indexed: 10/22/2022]
Abstract
Eukaryotic elongation factor 2 (eEF2) mediates translocation of peptidyl-tRNA from the ribosomal A site to the P site to promote translational elongation. Its phosphorylation on Thr56 by its single known kinase eEF2K inactivates it and inhibits translational elongation. Extensive studies have revealed that different signal cascades modulate eEF2K activity, but whether additional factors regulate phosphorylation of eEF2 remains unclear. Here, we find that the X chromosome-linked intellectual disability protein polyglutamine-binding protein 1 (PQBP1) specifically binds to non-phosphorylated eEF2 and suppresses eEF2K-mediated phosphorylation at Thr56. Loss of PQBP1 significantly reduces general protein synthesis by suppressing translational elongation. Moreover, we show that PQBP1 regulates hippocampal metabotropic glutamate receptor-dependent long-term depression (mGluR-LTD) and mGluR-LTD-associated behaviors by suppressing eEF2K-mediated phosphorylation. Our results identify PQBP1 as a novel regulator in translational elongation and mGluR-LTD, and this newly revealed regulator in the eEF2K/eEF2 pathway is also an excellent therapeutic target for various disease conditions, such as neural diseases, virus infection, and cancer.
Collapse
Affiliation(s)
- Yuqian Shen
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Zi Chao Zhang
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China; Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China.
| | - Shanshan Cheng
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - An Liu
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Jian Zuo
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Shuting Xia
- Institute of Neuroscience, Soochow University, Suzhou 215000, China
| | - Xian Liu
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Wenhua Liu
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Zhengping Jia
- Neurosciences and Mental Health Program, Hospital for Sick Children, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Wei Xie
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China; Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China
| | - Junhai Han
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China; Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China; Department of Neurology, Affiliated ZhongDa Hospital, Institute of Neuropsychiatry, Southeast University, Nanjing, Jiangsu 210009, China.
| |
Collapse
|
17
|
Karakas D, Ozpolat B. The Role of LncRNAs in Translation. Noncoding RNA 2021; 7:16. [PMID: 33672592 PMCID: PMC8005997 DOI: 10.3390/ncrna7010016] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNAs), a group of non-protein coding RNAs with lengths of more than 200 nucleotides, exert their effects by binding to DNA, mRNA, microRNA, and proteins and regulate gene expression at the transcriptional, post-transcriptional, translational, and post-translational levels. Depending on cellular location, lncRNAs are involved in a wide range of cellular functions, including chromatin modification, transcriptional activation, transcriptional interference, scaffolding and regulation of translational machinery. This review highlights recent studies on lncRNAs in the regulation of protein translation by modulating the translational factors (i.e, eIF4E, eIF4G, eIF4A, 4E-BP1, eEF5A) and signaling pathways involved in this process as wells as their potential roles as tumor suppressors or tumor promoters.
Collapse
Affiliation(s)
- Didem Karakas
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Istinye University, Istanbul 34010, Turkey;
| | - Bulent Ozpolat
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
18
|
Wei TH, Hsieh CL. Effect of Acupuncture on the p38 Signaling Pathway in Several Nervous System Diseases: A Systematic Review. Int J Mol Sci 2020; 21:E4693. [PMID: 32630156 PMCID: PMC7370084 DOI: 10.3390/ijms21134693] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/26/2020] [Accepted: 06/28/2020] [Indexed: 12/16/2022] Open
Abstract
Acupuncture is clinically used to treat various diseases and exerts positive local and systemic effects in several nervous system diseases. Advanced molecular and clinical studies have continually attempted to decipher the mechanisms underlying these effects of acupuncture. While a growing understanding of the pathophysiology underlying several nervous system diseases shows it to be related to inflammation and impair cell regeneration after ischemic events, the relationship between the therapeutic mechanism of acupuncture and the p38 MAPK signal pathway has yet to be elucidated. This review discusses the latest advancements in the identification of the effect of acupuncture on the p38 signaling pathway in several nervous system diseases. We electronically searched databases including PubMed, Embase, and the Cochrane Library from their inception to April 2020, using the following keywords alone or in various combinations: "acupuncture", "p38 MAPK pathway", "signaling", "stress response", "inflammation", "immune", "pain", "analgesic", "cerebral ischemic injury", "epilepsy", "Alzheimer's disease", "Parkinson's disease", "dementia", "degenerative", and "homeostasis". Manual acupuncture and electroacupuncture confer positive therapeutic effects by regulating proinflammatory cytokines, ion channels, scaffold proteins, and transcription factors including TRPV1/4, Nav, BDNF, and NADMR1; consequently, p38 regulates various phenomena including cell communication, remodeling, regeneration, and gene expression. In this review article, we found the most common acupoints for the relief of nervous system disorders including GV20, GV14, ST36, ST37, and LI4. Acupuncture exhibits dual regulatory functions of activating or inhibiting different p38 MAPK pathways, contributing to an overall improvement of clinical symptoms and function in several nervous system diseases.
Collapse
Affiliation(s)
- Tzu-Hsuan Wei
- Department of Chinese Medicine, China Medical University Hospital, Taichung 40447, Taiwan;
| | - Ching-Liang Hsieh
- Department of Chinese Medicine, China Medical University Hospital, Taichung 40447, Taiwan;
- Chinese Medicine Research Center, China Medical University, Taichung 40402, Taiwan
- Graduate Institute of Acupuncture Science, College of Chinese Medicine, China Medical University, Taichung 40402, Taiwan
| |
Collapse
|
19
|
Sugiyama N. Mass Spectrometry-Based Discovery of in vitro Kinome Substrates. ACTA ACUST UNITED AC 2020; 9:A0082. [PMID: 32547896 PMCID: PMC7242781 DOI: 10.5702/massspectrometry.a0082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/10/2020] [Indexed: 12/28/2022]
Abstract
Protein phosphorylation mediated by protein kinases is one of the most significant posttranslational modifications in many biological events. The function and physiological substrates of specific protein kinases, which are highly associated with known signal transduction elements or therapeutic targets, have been extensively studied using various approaches; however, most protein kinases have not yet been characterized. In recent decades, many techniques have been developed for the identification of in vitro and physiological substrates of protein kinases. In this review, I summarize recent studies profiling the characteristics of kinases using mass spectrometry-based proteomics, focusing on the large-scale identification of in vitro substrates of the human kinome using a quantitative phosphoproteomics approach.
Collapse
Affiliation(s)
- Naoyuki Sugiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| |
Collapse
|
20
|
Baros SS, Blackburn JM, Soares NC. Phosphoproteomic Approaches to Discover Novel Substrates of Mycobacterial Ser/Thr Protein Kinases. Mol Cell Proteomics 2020; 19:233-244. [PMID: 31839597 PMCID: PMC7000118 DOI: 10.1074/mcp.r119.001668] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/15/2019] [Indexed: 12/21/2022] Open
Abstract
Mycobacterial Ser/Thr protein kinases (STPKs) play a critical role in signal transduction pathways that ultimately determine mycobacterial growth and metabolic adaptation. Identification of key physiological substrates of these protein kinases is, therefore, crucial to better understand how Ser/Thr phosphorylation contributes to mycobacterial environmental adaptation, including response to stress, cell division, and host-pathogen interactions. Various substrate detection methods have been employed with limited success, with direct targets of STPKs remaining elusive. Recently developed mass spectrometry (MS)-based phosphoproteomic approaches have expanded the list of potential STPK substrate identifications, yet further investigation is required to define the most functionally significant phosphosites and their physiological importance. Prior to the application of MS workflows, for instance, GarA was the only known and validated physiological substrate for protein kinase G (PknG) from pathogenic mycobacteria. A subsequent list of at least 28 candidate PknG substrates has since been reported with the use of MS-based analyses. Herein, we integrate and critically review MS-generated datasets available on novel STPK substrates and report new functional and subcellular localization enrichment analyses on novel candidate protein kinase A (PknA), protein kinase B (PknB) and PknG substrates to deduce the possible physiological roles of these kinases. In addition, we assess substrate specificity patterns across different mycobacterial STPKs by analyzing reported sets of phosphopeptides, in order to determine whether novel motifs or consensus regions exist for mycobacterial Ser/Thr phosphorylation sites. This review focuses on MS-based techniques employed for STPK substrate identification in mycobacteria, while highlighting the advantages and challenges of the various applications.
Collapse
Affiliation(s)
- Seanantha S Baros
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Jonathan M Blackburn
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa; Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Nelson C Soares
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates.
| |
Collapse
|
21
|
Suzuki K, Monteggia LM. The role of eEF2 kinase in the rapid antidepressant actions of ketamine. RAPID ACTING ANTIDEPRESSANTS 2020; 89:79-99. [DOI: 10.1016/bs.apha.2020.04.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
22
|
Chowdhury D, Singh A, Gupta A, Tulsawani R, Meena RC, Chakrabarti A. p38 MAPK pathway-dependent SUMOylation of Elk-1 and phosphorylation of PIAS2 correlate with the downregulation of Elk-1 activity in heat-stressed HeLa cells. Cell Stress Chaperones 2019; 24:393-407. [PMID: 30783905 PMCID: PMC6439063 DOI: 10.1007/s12192-019-00974-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 01/10/2019] [Accepted: 01/15/2019] [Indexed: 01/01/2023] Open
Abstract
Stress-activated and mitogen-activated protein kinases (MAPKs) regulate gene expression by post-translational modifications of transcription factors. Elk-1, a transcription factor that regulates the expression of immediate early genes, is amenable to regulation by all the three mammalian MAPKs. In the present report, using inhibitors specific for different MAPK pathways, we show that during exposure of HeLa cells to heat stress, Elk-1 is SUMOylated with SUMO1 by p38 MAPK pathway-dependent mechanisms. Elk-1-phosphorylation levels were significantly reduced under similar conditions. We also show that transcriptional activity of Elk-1 as assessed by luciferase reporter expression and qPCR estimation of the expression of genes regulated by Elk-1 was downregulated upon exposure to heat stress; this downregulation was reversed when heat exposure was performed in the presence of either SB203580 (p38 MAPK inhibitor) or ginkgolic acid (inhibitor of SUMOylation). Elk-1 induced transcription is also regulated by PIAS2 which acts as a coactivator upon the activation of extracellular signal-regulated kinases (ERKs) and as a corepressor upon its phosphorylation by p38 MAPK. Since heat stress activates the p38 MAPK pathway, we determined if PIAS2 was phosphorylated in heat-stressed HeLa cells. Our studies indicate that in HeLa cells exposed to heat stress, PIAS2 is phosphorylated by p38 MAPK pathway-dependent mechanisms. Collectively, the results presented demonstrate that in heat-stressed HeLa cells, p38 MAPK pathway-dependent SUMOylation of Elk-1 and phosphorylation of PIAS2 correlate with the downregulation of transactivation by Elk-1.
Collapse
Affiliation(s)
- Daipayan Chowdhury
- Department of Molecular Biology, Defence Institute of Physiology and Allied Sciences, Lucknow Road, Timarpur, Delhi, 110054, India
| | - Ajeet Singh
- Department of Molecular Biology, Defence Institute of Physiology and Allied Sciences, Lucknow Road, Timarpur, Delhi, 110054, India
| | - Avinash Gupta
- Department of Molecular Biology, Defence Institute of Physiology and Allied Sciences, Lucknow Road, Timarpur, Delhi, 110054, India
| | - Rajkumar Tulsawani
- Department of Chemistry, Defence Institute of Physiology and Allied Sciences, Lucknow Road, Timarpur, Delhi, 110054, India
| | - Ramesh Chand Meena
- Department of Molecular Biology, Defence Institute of Physiology and Allied Sciences, Lucknow Road, Timarpur, Delhi, 110054, India.
| | - Amitabha Chakrabarti
- Department of Molecular Biology, Defence Institute of Physiology and Allied Sciences, Lucknow Road, Timarpur, Delhi, 110054, India.
| |
Collapse
|
23
|
Liong S, Lappas M. Markers of protein synthesis are increased in fetal membranes and myometrium after human labour and delivery. Reprod Fertil Dev 2018; 30:313-329. [PMID: 28701259 DOI: 10.1071/rd17081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/12/2017] [Indexed: 12/21/2022] Open
Abstract
Preterm birth remains one of the leading causes of neonatal death. Inflammation and maternal infection are two of the leading aetiological factors for preterm birth. Labour is associated with increased production of proinflammatory cytokines, chemokines and prolabour mediators in human gestational tissues. In non-gestational tissues, synthesis of proinflammatory and prolabour mediators is regulated by components of the protein synthesis machinery. Therefore, in the present study we investigated the effect of human labour on the expression of three protein synthesis markers, namely eukaryotic elongation factor 2 kinase (EEF2K), mitogen-activated protein kinase interacting protein kinase 1 (MKNK1) and eukaryotic translation initiation factor 4E (EIF4E), and their role in regulating inflammation in human gestational tissues. In fetal membranes and myometrium, EEF2K expression was significantly lower, whereas MKNK1 expression was significantly higher withterm and preterm labourcompared to term nolabour. In contrast, EIF4E expression did not change in fetal membranes or myometrium with labour. In primary myometrial cells, loss-of-function studies using specific chemical inhibitors of EEF2K (A484954) and MKNK1 (CGP57380) demonstrated that MKNK1, but not EEF2K, was required for polyinosinic-polycytidylic acid (poly(I:C); a viral double-stranded RNA mimetic) and interleukin (IL)-1β-induced production of IL6, C-X-C motif chemokine ligand 8 (CXCL8), prostaglandin-endoperoxide synthase 2 (PTGS2) and prostaglandin F2α. In conclusion, spontaneous term and preterm labour is associated with decreased EEF2K and increased MKNK1 expression in fetal membranes and myometrium. Moreover, MKNK1 is involved in the genesis of proinflammatory and prolabour mediators that is mediated by inflammation or infection. However, further studies are required to elucidate the role of EEF2K in human labour.
Collapse
Affiliation(s)
- Stella Liong
- Mercy Perinatal Research Centre, Mercy Hospital for Women, 4th Floor, 163 Studley Road, Heidelberg, Vic. 3084, Australia
| | - Martha Lappas
- Mercy Perinatal Research Centre, Mercy Hospital for Women, 4th Floor, 163 Studley Road, Heidelberg, Vic. 3084, Australia
| |
Collapse
|
24
|
Abstract
Translation is a key step in the regulation of gene expression and one of the most energy-consuming processes in the cell. In response to various stimuli, multiple signaling pathways converge on the translational machinery to regulate its function. To date, the roles of phosphoinositide 3-kinase (PI3K)/AKT and the mitogen-activated protein kinase (MAPK) pathways in the regulation of translation are among the best understood. Both pathways engage the mechanistic target of rapamycin (mTOR) to regulate a variety of components of the translational machinery. While these pathways regulate protein synthesis in homeostasis, their dysregulation results in aberrant translation leading to human diseases, including diabetes, neurological disorders, and cancer. Here we review the roles of the PI3K/AKT and MAPK pathways in the regulation of mRNA translation. We also highlight additional signaling mechanisms that have recently emerged as regulators of the translational apparatus.
Collapse
|
25
|
Anisomycin prevents OGD-induced necroptosis by regulating the E3 ligase CHIP. Sci Rep 2018; 8:6379. [PMID: 29686306 PMCID: PMC5913227 DOI: 10.1038/s41598-018-24414-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 03/23/2018] [Indexed: 01/02/2023] Open
Abstract
Necroptosis is an essential pathophysiological process in cerebral ischemia-related diseases. Therefore, targeting necroptosis may prevent cell death and provide a much-needed therapy. Ansiomycin is an inhibitor of protein synthesis which can also activate c-Jun N-terminal kinases. The present study demonstrated that anisomycin attenuated necroptosis by upregulating CHIP (carboxyl terminus of Hsc70-interacting protein) leading to the reduced levels of receptor-interacting protein kinase 1 (RIPK1) and receptor-interacting protein kinase 3 (RIPK3) proteins in two in vitro models of cerebral ischemia. Further exploration in this research revealed that losing neither the co-chaperone nor the ubiquitin E3 ligase function of CHIP could abolish its ability to reduce necroptosis. Collectively, this study identifies a novel means of preventing necroptosis in two in vitro models of cerebral ischemia injury through activating the expression of CHIP, and it may provide a potential target for the further study of the disease.
Collapse
|
26
|
Abstract
Traditional pharmacological treatments for depression have a delayed therapeutic onset, ranging from several weeks to months, and there is a high percentage of individuals who never respond to treatment. In contrast, ketamine produces rapid-onset antidepressant, anti-suicidal, and anti-anhedonic actions following a single administration to patients with depression. Proposed mechanisms of the antidepressant action of ketamine include N-methyl-D-aspartate receptor (NMDAR) modulation, gamma aminobutyric acid (GABA)-ergic interneuron disinhibition, and direct actions of its hydroxynorketamine (HNK) metabolites. Downstream actions include activation of the mechanistic target of rapamycin (mTOR), deactivation of glycogen synthase kinase-3 and eukaryotic elongation factor 2 (eEF2), enhanced brain-derived neurotrophic factor (BDNF) signaling, and activation of α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid receptors (AMPARs). These putative mechanisms of ketamine action are not mutually exclusive and may complement each other to induce potentiation of excitatory synapses in affective-regulating brain circuits, which results in amelioration of depression symptoms. We review these proposed mechanisms of ketamine action in the context of how such mechanisms are informing the development of novel putative rapid-acting antidepressant drugs. Such drugs that have undergone pre-clinical, and in some cases clinical, testing include the muscarinic acetylcholine receptor antagonist scopolamine, GluN2B-NMDAR antagonists (i.e., CP-101,606, MK-0657), (2R,6R)-HNK, NMDAR glycine site modulators (i.e., 4-chlorokynurenine, pro-drug of the glycineB NMDAR antagonist 7-chlorokynurenic acid), NMDAR agonists [i.e., GLYX-13 (rapastinel)], metabotropic glutamate receptor 2/3 (mGluR2/3) antagonists, GABAA receptor modulators, and drugs acting on various serotonin receptor subtypes. These ongoing studies suggest that the future acute treatment of depression will typically occur within hours, rather than months, of treatment initiation.
Collapse
Affiliation(s)
- Panos Zanos
- Department of Psychiatry, University of Maryland School of Medicine, Rm. 934F MSTF, 685 W. Baltimore St., Baltimore, MD, 21201, USA.
| | - Scott M Thompson
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Physiology, University of Maryland School of Medicine, St. BRB 5-007, 655 W. Baltimore St., Baltimore, MD, 21201, USA, Baltimore, MD, 21201, USA
| | - Ronald S Duman
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Carlos A Zarate
- Experimental Therapeutics and Pathophysiology Branch, Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Todd D Gould
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Psychiatry, University of Maryland School of Medicine, Rm. 936 MSTF, 685 W. Baltimore St., Baltimore, MD, 21201, USA
| |
Collapse
|
27
|
Deng Z, Luo P, Lai W, Song T, Peng J, Wei HK. Myostatin inhibits eEF2K-eEF2 by regulating AMPK to suppress protein synthesis. Biochem Biophys Res Commun 2017; 494:278-284. [DOI: 10.1016/j.bbrc.2017.10.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 10/07/2017] [Indexed: 02/07/2023]
|
28
|
Eukaryotic Elongation Factor 2 Kinase (eEF2K) in Cancer. Cancers (Basel) 2017; 9:cancers9120162. [PMID: 29186827 PMCID: PMC5742810 DOI: 10.3390/cancers9120162] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/24/2017] [Accepted: 11/25/2017] [Indexed: 12/31/2022] Open
Abstract
Eukaryotic elongation factor 2 kinase (eEF2K) is a highly unusual protein kinase that negatively regulates the elongation step of protein synthesis. This step uses the vast majority of the large amount of energy and amino acids required for protein synthesis. eEF2K activity is controlled by an array of regulatory inputs, including inhibition by signalling through mammalian target of rapamycin complex 1 (mTORC1). eEF2K is activated under conditions of stress, such as energy depletion or nutrient deprivation, which can arise in poorly-vascularised tumours. In many such stress conditions, eEF2K exerts cytoprotective effects. A growing body of data indicates eEF2K aids the growth of solid tumours in vivo. Since eEF2K is not essential (in mice) under ‘normal’ conditions, eEF2K may be a useful target in the treatment of solid tumours. However, some reports suggest that eEF2K may actually impair tumorigenesis in some situations. Such a dual role of eEF2K in cancer would be analogous to the situation for other pathways involved in cell metabolism, such as autophagy and mTORC1. Further studies are needed to define the role of eEF2K in different tumour types and at differing stages in tumorigenesis, and to assess its utility as a therapeutic target in oncology.
Collapse
|
29
|
Li CW, Chu YH, Chen BS. Construction and Clarification of Dynamic Gene Regulatory Network of Cancer Cell Cycle via Microarray Data. Cancer Inform 2017. [DOI: 10.1177/117693510600200008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Background Cell cycle is an important clue to unravel the mechanism of cancer cells. Recently, expression profiles of cDNA microarray data of Cancer cell cycle are available for the information of dynamic interactions among Cancer cell cycle related genes. Therefore, it is more appealing to construct a dynamic model for gene regulatory network of Cancer cell cycle to gain more insight into the infrastructure of gene regulatory mechanism of cancer cell via microarray data. Results Based on the gene regulatory dynamic model and microarray data, we construct the whole dynamic gene regulatory network of Cancer cell cycle. In this study, we trace back upstream regulatory genes of a target gene to infer the regulatory pathways of the gene network by maximum likelihood estimation method. Finally, based on the dynamic regulatory network, we analyze the regulatory abilities and sensitivities of regulatory genes to clarify their roles in the mechanism of Cancer cell cycle. Conclusions Our study presents a systematically iterative approach to discern and characterize the transcriptional regulatory network in Hela cell cycle from the raw expression profiles. The transcription regulatory network in Hela cell cycle can also be confirmed by some experimental reviews. Based on our study and some literature reviews, we can predict and clarify the E2F target genes in G1/S phase, which are crucial for regulating cell cycle progression and tumorigenesis. From the results of the network construction and literature confirmation, we infer that MCM4, MCM5, CDC6, CDC25A, UNG and E2F2 are E2F target genes in Hela cell cycle.
Collapse
Affiliation(s)
- Cheng-Wei Li
- Lab. of Systems biology, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Yung-Hsiang Chu
- Lab. of Systems biology, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Bor-Sen Chen
- Lab. of Systems biology, National Tsing Hua University, Hsinchu, 300, Taiwan
| |
Collapse
|
30
|
|
31
|
Cuenda A, Sanz-Ezquerro JJ. p38γ and p38δ: From Spectators to Key Physiological Players. Trends Biochem Sci 2017; 42:431-442. [PMID: 28473179 DOI: 10.1016/j.tibs.2017.02.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/14/2017] [Accepted: 02/22/2017] [Indexed: 12/20/2022]
Abstract
Although the physiological roles of p38γ and p38δ signalling pathways are largely unknown, new genetic and pharmacological tools are providing groundbreaking information on the function of these two stress-activated protein kinases. Recent studies show the importance of p38γ and p38δ in the regulation of processes as diverse as cytokine production, protein synthesis, exocytosis, cell migration, gene expression, and neuron activity, which have an acute impact on the development of pathologies related to inflammation, diabetes, neurodegeneration, and cancer. These recent breakthroughs are resolving some of the questions that have long been asked regarding the function of p38γ and p38δ in biology and pathology.
Collapse
Affiliation(s)
- Ana Cuenda
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Juan José Sanz-Ezquerro
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Identification of mycobacterial GarA as a substrate of protein kinase G from M. tuberculosis using a KESTREL-based proteome wide approach. J Microbiol Methods 2017; 136:34-39. [PMID: 28249794 DOI: 10.1016/j.mimet.2017.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/19/2017] [Accepted: 02/24/2017] [Indexed: 11/22/2022]
Abstract
Signal transduction in bacteria is generally mediated via two-component systems. These systems depend on the transfer of a phosphate molecule from a donor to an acceptor by histidine kinases, thereby activating the acceptor to allow downstream signaling/activation. Several bacterial genomes, including the genome of M. tuberculosis, were shown to encode eukaryotic-like kinases. To better understand the function of these kinases and the regulatory networks within which they operate, identification of downstream targets is essential. We here present a straightforward approach for the identification of bacterial Ser/Thr-kinase substrates. This approach is based on the KESTREL (Kinase Tracking and Substrate Elucidation) procedure combined with reversed-phase chromatography and two-dimensional gel electrophoresis. Using this method, GarA was identified as one potential substrate for the mycobacterial Ser/Thr-protein kinase G (PknG). These results show that the modified KESTREL approach can be successfully employed for the identification of substrates for bacterial Ser/Thr-kinases.
Collapse
|
34
|
Sugiyama N, Ishihama Y. Large-scale profiling of protein kinases for cellular signaling studies by mass spectrometry and other techniques. J Pharm Biomed Anal 2016; 130:264-272. [DOI: 10.1016/j.jpba.2016.05.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/26/2016] [Accepted: 05/27/2016] [Indexed: 01/26/2023]
|
35
|
miR-625-3p regulates oxaliplatin resistance by targeting MAP2K6-p38 signalling in human colorectal adenocarcinoma cells. Nat Commun 2016; 7:12436. [PMID: 27526785 PMCID: PMC4990699 DOI: 10.1038/ncomms12436] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/01/2016] [Indexed: 12/14/2022] Open
Abstract
Oxaliplatin resistance in colorectal cancers (CRC) is a major medical problem, and predictive markers are urgently needed. Recently, miR-625-3p was reported as a promising predictive marker. Herein, we show that miR-625-3p functionally induces oxaliplatin resistance in CRC cells, and identify the signalling networks affected by miR-625-3p. We show that the p38 MAPK activator MAP2K6 is a direct target of miR-625-3p, and, accordingly, is downregulated in non-responder patients of oxaliplatin therapy. miR-625-3p-mediated resistance is reversed by anti-miR-625-3p treatment and ectopic expression of a miR-625-3p insensitive MAP2K6 variant. In addition, reduction of p38 signalling by using siRNAs, chemical inhibitors or expression of a dominant-negative MAP2K6 protein induces resistance to oxaliplatin. Transcriptome, proteome and phosphoproteome profiles confirm inactivation of MAP2K6-p38 signalling as one likely mechanism of oxaliplatin resistance. Our study shows that miR-625-3p induces oxaliplatin resistance by abrogating MAP2K6-p38-regulated apoptosis and cell cycle control networks, and corroborates the predictive power of miR-625-3p.
Collapse
|
36
|
Circadian clock regulation of mRNA translation through eukaryotic elongation factor eEF-2. Proc Natl Acad Sci U S A 2016; 113:9605-10. [PMID: 27506798 DOI: 10.1073/pnas.1525268113] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The circadian clock has a profound effect on gene regulation, controlling rhythmic transcript accumulation for up to half of expressed genes in eukaryotes. Evidence also exists for clock control of mRNA translation, but the extent and mechanisms for this regulation are not known. In Neurospora crassa, the circadian clock generates daily rhythms in the activation of conserved mitogen-activated protein kinase (MAPK) pathways when cells are grown in constant conditions, including rhythmic activation of the well-characterized p38 osmosensing (OS) MAPK pathway. Rhythmic phosphorylation of the MAPK OS-2 (P-OS-2) leads to temporal control of downstream targets of OS-2. We show that osmotic stress in N. crassa induced the phosphorylation of a eukaryotic elongation factor-2 (eEF-2) kinase, radiation sensitivity complementing kinase-2 (RCK-2), and that RCK-2 is necessary for high-level phosphorylation of eEF-2, a key regulator of translation elongation. The levels of phosphorylated RCK-2 and phosphorylated eEF-2 cycle in abundance in wild-type cells but not in cells deleted for OS-2 or the core clock component FREQUENCY (FRQ). Translation extracts from cells grown in constant conditions show decreased translational activity in the late subjective morning, coincident with the peak in eEF-2 phosphorylation, and rhythmic translation of glutathione S-transferase (GST-3) from constitutive mRNA levels in vivo is dependent on circadian regulation of eEF-2 activity. In contrast, rhythms in phosphorylated eEF-2 levels are not necessary for rhythms in accumulation of the clock protein FRQ, indicating that clock control of eEF-2 activity promotes rhythmic translation of specific mRNAs.
Collapse
|
37
|
Müller AC, Giambruno R, Weißer J, Májek P, Hofer A, Bigenzahn JW, Superti-Furga G, Jessen HJ, Bennett KL. Identifying Kinase Substrates via a Heavy ATP Kinase Assay and Quantitative Mass Spectrometry. Sci Rep 2016; 6:28107. [PMID: 27346722 PMCID: PMC4921819 DOI: 10.1038/srep28107] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 05/31/2016] [Indexed: 01/17/2023] Open
Abstract
Mass spectrometry-based in vitro kinase screens play an essential role in the discovery of kinase substrates, however, many suffer from biological and technical noise or necessitate genetically-altered enzyme-cofactor systems. We describe a method that combines stable γ-[(18)O2]-ATP with classical in vitro kinase assays within a contemporary quantitative proteomic workflow. Our approach improved detection of known substrates of the non-receptor tyrosine kinase ABL1; and identified potential, new in vitro substrates.
Collapse
Affiliation(s)
- André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Roberto Giambruno
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Juliane Weißer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Peter Májek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexandre Hofer
- University of Zurich, Department of Chemistry, Zurich, Switzerland
| | - Johannes W Bigenzahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Henning J Jessen
- University of Zurich, Department of Chemistry, Zurich, Switzerland
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| |
Collapse
|
38
|
Escós A, Risco A, Alsina-Beauchamp D, Cuenda A. p38γ and p38δ Mitogen Activated Protein Kinases (MAPKs), New Stars in the MAPK Galaxy. Front Cell Dev Biol 2016; 4:31. [PMID: 27148533 PMCID: PMC4830812 DOI: 10.3389/fcell.2016.00031] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/28/2016] [Indexed: 01/04/2023] Open
Abstract
The protein kinases p38γ and p38δ belong to the p38 mitogen-activated protein kinase (MAPK) family. p38MAPK signaling controls many cellular processes and is one of the most conserved mechanisms in eukaryotes for the cellular response to environmental stress and inflammation. Although p38γ and p38δ are widely expressed, it is likely that they perform specific functions in different tissues. Their involvement in human pathologies such as inflammation-related diseases or cancer is starting to be uncovered. In this article we give a general overview and highlight recent advances made in defining the functions of p38γ and p38δ, focusing in innate immunity and inflammation. We consider the potential of the pharmacological targeting of MAPK pathways to treat autoimmune and inflammatory diseases and cancer.
Collapse
Affiliation(s)
- Alejandra Escós
- Department of Immunology and Oncology, Centro Nacional de Biotecnología, Spanish National Research Council (CSIC) Madrid, Spain
| | - Ana Risco
- Department of Immunology and Oncology, Centro Nacional de Biotecnología, Spanish National Research Council (CSIC) Madrid, Spain
| | - Dayanira Alsina-Beauchamp
- Department of Immunology and Oncology, Centro Nacional de Biotecnología, Spanish National Research Council (CSIC) Madrid, Spain
| | - Ana Cuenda
- Department of Immunology and Oncology, Centro Nacional de Biotecnología, Spanish National Research Council (CSIC) Madrid, Spain
| |
Collapse
|
39
|
Abstract
Obesity is a new global pandemic, with growing incidence and prevalence. This disease is associated with increased risk of several pathologies, including diabetes, cardiovascular diseases, and cancer. The mechanisms underlying obesity-associated metabolic changes are the focus of efforts to identify new therapies. Stress-activated protein kinases (SAPK), including cJun N-terminal kinases (JNKs) and p38, are required for cellular responses to metabolic stress and therefore might contribute to the pathogenesis of obesity. Tissue-specific knockout models support a cell-type-specific role for JNK isoforms, in particular JNK1, highlighting its importance in cell homeostasis and organ crosstalk. However, more efforts are needed to elucidate the specific roles of other JNK isoforms and p38 family members in metabolism and obesity. This review provides an overview of the role of SAPKs in the regulation of metabolism.
Collapse
Affiliation(s)
- Elisa Manieri
- Myocardial Pathophysiology AreaFundación Centro Nacional de Investigaciones Cardiovasculares Carlos III, CNIC, C/Melchor Fernandez Almagro, 2, 28029 Madrid, SpainDepartment of Immunology and OncologyCentro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, Madrid, Spain Myocardial Pathophysiology AreaFundación Centro Nacional de Investigaciones Cardiovasculares Carlos III, CNIC, C/Melchor Fernandez Almagro, 2, 28029 Madrid, SpainDepartment of Immunology and OncologyCentro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Guadalupe Sabio
- Myocardial Pathophysiology AreaFundación Centro Nacional de Investigaciones Cardiovasculares Carlos III, CNIC, C/Melchor Fernandez Almagro, 2, 28029 Madrid, SpainDepartment of Immunology and OncologyCentro Nacional de Biotecnología/CSIC, Campus de Cantoblanco, Madrid, Spain
| |
Collapse
|
40
|
Regulated stability of eukaryotic elongation factor 2 kinase requires intrinsic but not ongoing activity. Biochem J 2015; 467:321-31. [DOI: 10.1042/bj20150089] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Eukaryotic elongation factor 2 kinase (eEF2K) is an atypical protein kinase which negatively regulates protein synthesis, is activated under stress conditions and plays a role in cytoprotection, e.g. in cancer cells. It is regarded as a possible target for therapeutic intervention in solid tumours. Earlier studies showed that eEF2K is degraded by a proteasome-dependent pathway in response to genotoxic stress and that this requires a phosphodegron that includes an autophosphorylation site. Thus, application of eEF2K inhibitors would stabilize eEF2K, partially negating the effects of inhibiting its activity. In the present study, we show that under a range of other stress conditions, including acidosis or treatment of cells with 2-deoxyglucose, eEF2K is also degraded. However, in these settings, the previously identified phosphodegron is not required for its degradation. Nevertheless, kinase-dead and other activity-deficient mutants of eEF2K are stabilized, as is a mutant lacking a critical autophosphorylation site (Thr348 in eEF2K), which is thought to be required for eEF2K and other α-kinases to achieve their active conformations. In contrast, application of small-molecule eEF2K inhibitors does not stabilize the protein. Our data suggest that achieving an active conformation, rather than eEF2K activity per se, is required for its susceptibility to degradation. Additional degrons and E3 ligases beyond those already identified are probably involved in regulating eEF2K levels. Our findings have significant implications for therapeutic targeting of eEF2K, e.g. in oncology.
Collapse
|
41
|
Molecular Mechanism for the Control of Eukaryotic Elongation Factor 2 Kinase by pH: Role in Cancer Cell Survival. Mol Cell Biol 2015; 35:1805-24. [PMID: 25776553 DOI: 10.1128/mcb.00012-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/03/2015] [Indexed: 01/09/2023] Open
Abstract
Acidification of the extracellular and/or intracellular environment is involved in many aspects of cell physiology and pathology. Eukaryotic elongation factor 2 kinase (eEF2K) is a Ca(2+)/calmodulin-dependent kinase that regulates translation elongation by phosphorylating and inhibiting eEF2. Here we show that extracellular acidosis elicits activation of eEF2K in vivo, leading to enhanced phosphorylation of eEF2. We identify five histidine residues in eEF2K that are crucial for the activation of eEF2K during acidosis. Three of them (H80, H87, and H94) are in its calmodulin-binding site, and their protonation appears to enhance the ability of calmodulin to activate eEF2K. The other two histidines (H227 and H230) lie in the catalytic domain of eEF2K. We also identify His108 in calmodulin as essential for activation of eEF2K. Acidification of cancer cell microenvironments is a hallmark of malignant solid tumors. Knocking down eEF2K in cancer cells attenuated the decrease in global protein synthesis when cells were cultured at acidic pH. Importantly, activation of eEF2K is linked to cancer cell survival under acidic conditions. Inhibition of eEF2K promotes cancer cell death under acidosis.
Collapse
|
42
|
Elongation Factor 2 Kinase Is Regulated by Proline Hydroxylation and Protects Cells during Hypoxia. Mol Cell Biol 2015; 35:1788-804. [PMID: 25755286 DOI: 10.1128/mcb.01457-14] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 03/01/2015] [Indexed: 12/19/2022] Open
Abstract
Protein synthesis, especially translation elongation, requires large amounts of energy, which is often generated by oxidative metabolism. Elongation is controlled by phosphorylation of eukaryotic elongation factor 2 (eEF2), which inhibits its activity and is catalyzed by eEF2 kinase (eEF2K), a calcium/calmodulin-dependent α-kinase. Hypoxia causes the activation of eEF2K and induces eEF2 phosphorylation independently of previously known inputs into eEF2K. Here, we show that eEF2K is subject to hydroxylation on proline-98. Proline hydroxylation is catalyzed by proline hydroxylases, oxygen-dependent enzymes which are inactivated during hypoxia. Pharmacological inhibition of proline hydroxylases also stimulates eEF2 phosphorylation. Pro98 lies in a universally conserved linker between the calmodulin-binding and catalytic domains of eEF2K. Its hydroxylation partially impairs the binding of calmodulin to eEF2K and markedly limits the calmodulin-stimulated activity of eEF2K. Neuronal cells depend on oxygen, and eEF2K helps to protect them from hypoxia. eEF2K is the first example of a protein directly involved in a major energy-consuming process to be regulated by proline hydroxylation. Since eEF2K is cytoprotective during hypoxia and other conditions of nutrient insufficiency, it may be a valuable target for therapy of poorly vascularized solid tumors.
Collapse
|
43
|
Iliuk AB, Arrington JV, Tao WA. Analytical challenges translating mass spectrometry-based phosphoproteomics from discovery to clinical applications. Electrophoresis 2014; 35:3430-40. [PMID: 24890697 PMCID: PMC4250476 DOI: 10.1002/elps.201400153] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/29/2014] [Accepted: 05/12/2014] [Indexed: 12/21/2022]
Abstract
Phosphoproteomics is the systematic study of one of the most common protein modifications in high throughput with the aim of providing detailed information of the control, response, and communication of biological systems in health and disease. Advances in analytical technologies and strategies, in particular the contributions of high-resolution mass spectrometers, efficient enrichments of phosphopeptides, and fast data acquisition and annotation, have catalyzed dramatic expansion of signaling landscapes in multiple systems during the past decade. While phosphoproteomics is an essential inquiry to map high-resolution signaling networks and to find relevant events among the apparently ubiquitous and widespread modifications of proteome, it presents tremendous challenges in separation sciences to translate it from discovery to clinical practice. In this mini-review, we summarize the analytical tools currently utilized for phosphoproteomic analysis (with focus on MS), progresses made on deciphering clinically relevant kinase-substrate networks, MS uses for biomarker discovery and validation, and the potential of phosphoproteomics for disease diagnostics and personalized medicine.
Collapse
Affiliation(s)
- Anton B. Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | | | - Weiguo Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
44
|
Zhang P, Riazy M, Gold M, Tsai SH, McNagny K, Proud C, Duronio V. Impairing eukaryotic elongation factor 2 kinase activity decreases atherosclerotic plaque formation. Can J Cardiol 2014; 30:1684-8. [PMID: 25475470 PMCID: PMC4424975 DOI: 10.1016/j.cjca.2014.09.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 09/23/2014] [Accepted: 09/23/2014] [Indexed: 01/16/2023] Open
Abstract
We tested whether loss of eukaryotic elongation factor 2 kinase (eEF2K) activity in macrophages suppresses development of atherosclerosis by transplanting bone marrow from mice with mutant eEF2K into ldlr−/− mice. Sixteen weeks after high-fat diet feeding, mutant eEF2K hematopoietic chimeras had a dramatically reduced level of atherosclerotic plaque formation. M1-skewed macrophages from eEF2K knock-in mice have less tumour necrosis factor-α release and a lesser ability to induce expression of endothelial cell markers, providing a potential explanation for the role of eEF2K. Because eEF2K activity in cells of the hematopoietic compartment contributes to atherosclerosis development, drugs inhibiting eEF2K might have a beneficial effect in treatment of atherosclerosis.
Collapse
Affiliation(s)
- Peng Zhang
- Department of Medicine, University of British Columbia and Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
| | - Maziar Riazy
- Department of Medicine, University of British Columbia and Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
| | - Matthew Gold
- Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shu-Huei Tsai
- Department of Medicine, University of British Columbia and Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
| | - Kelly McNagny
- Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher Proud
- Centre for Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Vincent Duronio
- Department of Medicine, University of British Columbia and Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada.
| |
Collapse
|
45
|
Fonseca BD, Smith EM, Yelle N, Alain T, Bushell M, Pause A. The ever-evolving role of mTOR in translation. Semin Cell Dev Biol 2014; 36:102-12. [PMID: 25263010 DOI: 10.1016/j.semcdb.2014.09.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 09/12/2014] [Accepted: 09/15/2014] [Indexed: 02/06/2023]
Abstract
Control of translation allows for the production of stoichiometric levels of each protein in the cell. Attaining such a level of fine-tuned regulation of protein production requires the coordinated temporal and spatial control of numerous cellular signalling cascades impinging on the various components of the translational machinery. Foremost among these is the mTOR signalling pathway. The mTOR pathway regulates both the initiation and elongation steps of protein synthesis through the phosphorylation of numerous translation factors, while simultaneously ensuring adequate folding of nascent polypeptides through co-translational degradation of misfolded proteins. Perhaps most remarkably, mTOR is also a key regulator of the synthesis of ribosomal proteins and translation factors themselves. Two seminal studies have recently shown in translatome analysis that the mTOR pathway preferentially regulates the translation of mRNAs encoding ribosomal proteins and translation factors. Therefore, the role of the mTOR pathway in the control of protein synthesis extends far beyond immediate translational control. By controlling ribosome production (and ultimately ribosome availability), mTOR is a master long-term controller of protein synthesis. Herein, we review the literature spanning the early discoveries of mTOR on translation to the latest advances in our understanding of how the mTOR pathway controls the synthesis of ribosomal proteins.
Collapse
Affiliation(s)
- Bruno D Fonseca
- Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, ON K1H 8L1, Canada.
| | - Ewan M Smith
- MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
| | - Nicolas Yelle
- Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, ON K1H 8L1, Canada
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, ON K1H 8L1, Canada
| | - Martin Bushell
- MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
| | - Arnim Pause
- Goodman Cancer Research Centre, Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada.
| |
Collapse
|
46
|
p38δ MAPK: Emerging Roles of a Neglected Isoform. Int J Cell Biol 2014; 2014:272689. [PMID: 25313309 PMCID: PMC4182853 DOI: 10.1155/2014/272689] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/29/2014] [Accepted: 08/31/2014] [Indexed: 12/19/2022] Open
Abstract
p38δ mitogen activated protein kinase (MAPK) is a unique stress responsive protein kinase. While the p38 MAPK family as a whole has been implicated in a wide variety of biological processes, a specific role for p38δ MAPK in cellular signalling and its contribution to both physiological and pathological conditions are presently lacking. Recent emerging evidence, however, provides some insights into specific p38δ MAPK signalling. Importantly, these studies have helped to highlight functional similarities as well as differences between p38δ MAPK and the other members of the p38 MAPK family of kinases. In this review we discuss the current understanding of the molecular mechanisms underlying p38δ MAPK activity. We outline a role for p38δ MAPK in important cellular processes such as differentiation and apoptosis as well as pathological conditions such as neurodegenerative disorders, diabetes, and inflammatory disease. Interestingly, disparate roles for p38δ MAPK in tumour development have also recently been reported. Thus, we consider evidence which characterises p38δ MAPK as both a tumour promoter and a tumour suppressor. In summary, while our knowledge of p38δ MAPK has progressed somewhat since its identification in 1997, our understanding of this particular isoform in many cellular processes still strikingly lags behind that of its counterparts.
Collapse
|
47
|
Eukaryotic elongation factor 2 kinase activity is controlled by multiple inputs from oncogenic signaling. Mol Cell Biol 2014; 34:4088-103. [PMID: 25182533 DOI: 10.1128/mcb.01035-14] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic elongation factor 2 kinase (eEF2K), an atypical calmodulin-dependent protein kinase, phosphorylates and inhibits eEF2, slowing down translation elongation. eEF2K contains an N-terminal catalytic domain, a C-terminal α-helical region and a linker containing several regulatory phosphorylation sites. eEF2K is expressed at high levels in certain cancers, where it may act to help cell survival, e.g., during nutrient starvation. However, it is a negative regulator of protein synthesis and thus cell growth, suggesting that cancer cells may possess mechanisms to inhibit eEF2K under good growth conditions, to allow protein synthesis to proceed. We show here that the mTORC1 pathway and the oncogenic Ras/Raf/MEK/extracellular signal-regulated kinase (ERK) pathway cooperate to restrict eEF2K activity. We identify multiple sites in eEF2K whose phosphorylation is regulated by mTORC1 and/or ERK, including new ones in the linker region. We demonstrate that certain sites are phosphorylated directly by mTOR or ERK. Our data reveal that glycogen synthase kinase 3 signaling also regulates eEF2 phosphorylation. In addition, we show that phosphorylation sites remote from the N-terminal calmodulin-binding motif regulate the phosphorylation of N-terminal sites that control CaM binding. Mutations in the former sites, which occur in cancer cells, cause the activation of eEF2K. eEF2K is thus regulated by a network of oncogenic signaling pathways.
Collapse
|
48
|
Bigeard J, Rayapuram N, Pflieger D, Hirt H. Phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins. Proteomics 2014; 14:2127-40. [PMID: 24889195 DOI: 10.1002/pmic.201400073] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/28/2014] [Accepted: 05/26/2014] [Indexed: 12/25/2022]
Abstract
In eukaryotes, most of the DNA is located in the nucleus where it is organized with histone proteins in a higher order structure as chromatin. Chromatin and chromatin-associated proteins contribute to DNA-related processes such as replication and transcription as well as epigenetic regulation. Protein functions are often regulated by PTMs among which phosphorylation is one of the most abundant PTM. Phosphorylation of proteins affects important properties, such as enzyme activity, protein stability, or subcellular localization. We here describe the main specificities of protein phosphorylation in plants and review the current knowledge on phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins. We also outline some future challenges to further elucidate protein phosphorylation and chromatin regulation.
Collapse
Affiliation(s)
- Jean Bigeard
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA/CNRS/Université d'Evry Val d'Essonne/Saclay Plant Sciences, Evry, France
| | | | | | | |
Collapse
|
49
|
McDermott MSJ, Browne BC, Conlon NT, O’Brien NA, Slamon DJ, Henry M, Meleady P, Clynes M, Dowling P, Crown J, O’Donovan N. PP2A inhibition overcomes acquired resistance to HER2 targeted therapy. Mol Cancer 2014; 13:157. [PMID: 24958351 PMCID: PMC4230643 DOI: 10.1186/1476-4598-13-157] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 06/12/2014] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND HER2 targeted therapies including trastuzumab and more recently lapatinib have significantly improved the prognosis for HER2 positive breast cancer patients. However, resistance to these agents is a significant clinical problem. Although several mechanisms have been proposed for resistance to trastuzumab, the mechanisms of lapatinib resistance remain largely unknown. In this study we generated new models of acquired resistance to HER2 targeted therapy and investigated mechanisms of resistance using phospho-proteomic profiling. RESULTS Long-term continuous exposure of SKBR3 cells to low dose lapatinib established a cell line, SKBR3-L, which is resistant to both lapatinib and trastuzumab. Phospho-proteomic profiling and immunoblotting revealed significant alterations in phospho-proteins involved in key signaling pathways and molecular events. In particular, phosphorylation of eukaryotic elongation factor 2 (eEF2), which inactivates eEF2, was significantly decreased in SKBR3-L cells compared to the parental SKBR3 cells. SKBR3-L cells exhibited significantly increased activity of protein phosphatase 2A (PP2A), a phosphatase that dephosphorylates eEF2. SKBR3-L cells showed increased sensitivity to PP2A inhibition, with okadaic acid, compared to SKBR3 cells. PP2A inhibition significantly enhanced response to lapatinib in both the SKBR3 and SKBR3-L cells. Furthermore, treatment of SKBR3 parental cells with the PP2A activator, FTY720, decreased sensitivity to lapatinib. The alteration in eEF2 phosphorylation, PP2A activity and sensitivity to okadaic acid were also observed in a second HER2 positive cell line model of acquired lapatinib resistance, HCC1954-L. CONCLUSIONS Our data suggests that decreased eEF2 phosphorylation, mediated by increased PP2A activity, contributes to resistance to HER2 inhibition and may provide novel targets for therapeutic intervention in HER2 positive breast cancer which is resistant to HER2 targeted therapies.
Collapse
Affiliation(s)
- Martina SJ McDermott
- Molecular Therapeutics for Cancer Ireland, National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Brigid C Browne
- Cancer Research Program, The Kinghorn Cancer Centre, Garvan Institute of Medical Research Sydney, Sydney, New South Wales, Australia
| | - Neil T Conlon
- Molecular Therapeutics for Cancer Ireland, National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Neil A O’Brien
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
| | - Dennis J Slamon
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
| | - Michael Henry
- Molecular Therapeutics for Cancer Ireland, National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- Molecular Therapeutics for Cancer Ireland, National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Clynes
- Molecular Therapeutics for Cancer Ireland, National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paul Dowling
- Molecular Therapeutics for Cancer Ireland, National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
- Department of Biology, National University of Ireland, Maynooth, Maynooth, Co, Kildare, Ireland
| | - John Crown
- Molecular Therapeutics for Cancer Ireland, National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
- Department of Medical Oncology, St Vincent’s University Hospital, Elm Park, Dublin 4, Ireland
| | - Norma O’Donovan
- Molecular Therapeutics for Cancer Ireland, National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| |
Collapse
|
50
|
Xie CM, Liu XY, Sham KWY, Lai JMY, Cheng CHK. Silencing of EEF2K (eukaryotic elongation factor-2 kinase) reveals AMPK-ULK1-dependent autophagy in colon cancer cells. Autophagy 2014; 10:1495-508. [PMID: 24955726 PMCID: PMC4206530 DOI: 10.4161/auto.29164] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
EEF2K (eukaryotic elongation factor-2 kinase), also known as Ca2+/calmodulin-dependent protein kinase III, functions in downregulating peptide chain elongation through inactivation of EEF2 (eukaryotic translation elongation factor 2). Currently, there is a limited amount of information on the promotion of autophagic survival by EEF2K in breast and glioblastoma cell lines. However, the precise role of EEF2K in carcinogenesis as well as the underlying mechanism involved is still poorly understood. In this study, contrary to the reported autophagy-promoting activity of EEF2K in certain cancer cells, EEF2K is shown to negatively regulate autophagy in human colon cancer cells as indicated by the increase of LC3-II levels, the accumulation of LC3 dots per cell, and the promotion of autophagic flux in EEF2K knockdown cells. EEF2K negatively regulates cell viability, clonogenicity, cell proliferation, and cell size in colon cancer cells. Autophagy induced by EEF2K silencing promotes cell survival and does not potentiate the anticancer efficacy of the AKT inhibitor MK-2206. In addition, autophagy induced by silencing of EEF2K is attributed to induction of protein synthesis and activation of the AMPK-ULK1 pathway, independent of the suppression of MTOR activity and ROS generation. Knockdown of AMPK or ULK1 significantly abrogates EEF2K silencing-induced increase of LC3-II levels, accumulation of LC3 dots per cell as well as cell proliferation in colon cancer cells. In conclusion, silencing of EEF2K promotes autophagic survival via activation of the AMPK-ULK1 pathway in colon cancer cells. This finding suggests that upregulation of EEF2K activity may constitute a novel approach for the treatment of human colon cancer.
Collapse
Affiliation(s)
- Chuan-Ming Xie
- School of Biomedical Sciences; The Chinese University of Hong Kong; Hong Kong, China
| | - Xiao-Yu Liu
- School of Biomedical Sciences; The Chinese University of Hong Kong; Hong Kong, China
| | - Kathy W Y Sham
- School of Biomedical Sciences; The Chinese University of Hong Kong; Hong Kong, China
| | - Josie M Y Lai
- School of Biomedical Sciences; The Chinese University of Hong Kong; Hong Kong, China
| | - Christopher H K Cheng
- School of Biomedical Sciences; The Chinese University of Hong Kong; Hong Kong, China; Center of Novel Functional Molecules; The Chinese University of Hong Kong; Hong Kong, China
| |
Collapse
|