1
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Hasegawa S, Yoshida M, Nagao H, Sugiyama H, Sawa M, Kinoshita T. Distinct binding modes of a benzothiazole derivative confer structural bases for increasing ERK2 or p38α MAPK selectivity. Biochem Biophys Res Commun 2024; 704:149707. [PMID: 38428305 DOI: 10.1016/j.bbrc.2024.149707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/03/2024]
Abstract
Mitogen-activated protein kinases (MAPKs), including extracellular signal-regulated kinase 2 (ERK2) and p38α MAP kinase (p38α MAPK), regulate various cellular responses. ERK2 is a drug target for treating many diseases, such as cancer, whereas p38α has attracted much attention as a promising drug target for treating inflammatory disorders. ERK2 is a critical off-target for p38α MAPK and vice versa. In this study, an allosteric ERK2 inhibitor with a benzothiazole moiety (compound 1) displayed comparable inhibitory activity against p38α MAPK. Crystal structures of these MAPKs showed that compound 1 bound to the allosteric site of ERK2 and p38α MAPK in distinct manners. Compound 1 formed a covalent bond with Cys162 of p38α MAPK, whereas this covalent bond was absent in the ERK2 complex even though the corresponding cysteine is conserved in ERK2. Structural dissection combined with computational simulations indicated that an amino acid difference in the allosteric site is responsible for the distinct binding modes of compound 1 with ERK2 and p38α MAPK. These structural insights underline the feasibility of developing highly selective and potent ERK2 and p38α MAPK inhibitors.
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Affiliation(s)
- Seisuke Hasegawa
- Graduate School of Science, Osaka Metropolitan University, Osaka, 599-8570, Japan
| | - Mayu Yoshida
- Graduate School of Science, Osaka Metropolitan University, Osaka, 599-8570, Japan
| | | | | | | | - Takayoshi Kinoshita
- Graduate School of Science, Osaka Metropolitan University, Osaka, 599-8570, Japan.
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2
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Li L, Zhang G, Yang Z, Kang X. Stress-Activated Protein Kinases in Intervertebral Disc Degeneration: Unraveling the Impact of JNK and p38 MAPK. Biomolecules 2024; 14:393. [PMID: 38672411 PMCID: PMC11047866 DOI: 10.3390/biom14040393] [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: 02/22/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Intervertebral disc degeneration (IDD) is a major cause of lower back pain. The pathophysiological development of IDD is closely related to the stimulation of various stressors, including proinflammatory cytokines, abnormal mechanical stress, oxidative stress, metabolic abnormalities, and DNA damage, among others. These factors prevent normal intervertebral disc (IVD) development, reduce the number of IVD cells, and induce senescence and apoptosis. Stress-activated protein kinases (SAPKs), particularly, c-Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase (p38 MAPK), control cell signaling in response to cellular stress. Previous studies have shown that these proteins are highly expressed in degenerated IVD tissues and are involved in complex biological signal-regulated processes. Therefore, we summarize the research reports on IDD related to JNK and p38 MAPK. Their structure, function, and signal regulation mechanisms are comprehensively and systematically described and potential therapeutic targets are proposed. This work could provide a reference for future research and help improve molecular therapeutic strategies for IDD.
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Affiliation(s)
- Lei Li
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou 730030, China; (L.L.); (G.Z.); (Z.Y.)
- The Second Clinical Medical College, Lanzhou University, Lanzhou 730030, China
- Key Laboratory of Orthopedics Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou 730030, China
- The International Cooperation Base of Gansu Province for the Pain Research in Spinal Disorders, Lanzhou 730030, China
| | - Guangzhi Zhang
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou 730030, China; (L.L.); (G.Z.); (Z.Y.)
- The Second Clinical Medical College, Lanzhou University, Lanzhou 730030, China
- Key Laboratory of Orthopedics Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou 730030, China
- The International Cooperation Base of Gansu Province for the Pain Research in Spinal Disorders, Lanzhou 730030, China
| | - Zhili Yang
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou 730030, China; (L.L.); (G.Z.); (Z.Y.)
- The Second Clinical Medical College, Lanzhou University, Lanzhou 730030, China
- Key Laboratory of Orthopedics Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou 730030, China
- The International Cooperation Base of Gansu Province for the Pain Research in Spinal Disorders, Lanzhou 730030, China
| | - Xuewen Kang
- Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou 730030, China; (L.L.); (G.Z.); (Z.Y.)
- The Second Clinical Medical College, Lanzhou University, Lanzhou 730030, China
- Key Laboratory of Orthopedics Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou 730030, China
- The International Cooperation Base of Gansu Province for the Pain Research in Spinal Disorders, Lanzhou 730030, China
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3
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Morgos DT, Stefani C, Miricescu D, Greabu M, Stanciu S, Nica S, Stanescu-Spinu II, Balan DG, Balcangiu-Stroescu AE, Coculescu EC, Georgescu DE, Nica RI. Targeting PI3K/AKT/mTOR and MAPK Signaling Pathways in Gastric Cancer. Int J Mol Sci 2024; 25:1848. [PMID: 38339127 PMCID: PMC10856016 DOI: 10.3390/ijms25031848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
Gastric cancer (GC) is the fourth leading cause of death worldwide, with more than 1 million cases diagnosed every year. Helicobacter pylori represents the main risk factor, being responsible for 78% of the cases. Increased amounts of salt, pickled food, red meat, alcohol, smoked food, and refined sugars negatively affect the stomach wall, contributing to GC development. Several gene mutations, including PIK3CA, TP53, ARID1A, CDH1, Ras, Raf, and ERBB3 are encountered in GC pathogenesis, leading to phosphatidylinositol 3-kinase (PI3K) protein kinase B (AKT)/mammalian target of rapamycin (mTOR)-PI3K/AKT/mTOR-and mitogen-activated protein kinase (MAPK) signaling pathway activation and promoting tumoral activity. Helicobacter pylori, growth factors, cytokines, hormones, and oxidative stress also activate both pathways, enhancing GC development. In clinical trials, promising results have come from monoclonal antibodies such as trastuzumab and ramucirumab. Dual inhibitors targeting the PI3K/AKT/mTOR and MAPK signaling pathways were used in vitro studies, also with promising results. The main aim of this review is to present GC incidence and risk factors and the dysregulations of the two protein kinase complexes together with their specific inhibitors.
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Affiliation(s)
- Diana-Theodora Morgos
- Discipline of Anatomy, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Constantin Stefani
- Department I of Family Medicine and Clinical Base, “Dr. Carol Davila” Central Military Emergency University Hospital, 010825 Bucharest, Romania
| | - Daniela Miricescu
- Discipline of Biochemistry, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Maria Greabu
- Discipline of Biochemistry, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Silviu Stanciu
- Department of Internal Medicine and Gastroenterology, Carol Davila University of Medicine and Pharmacy, Central Military Emergency University Hospital, 010825 Bucharest, Romania;
| | - Silvia Nica
- Emergency Discipline, University Hospital of Bucharest, 050098 Bucharest, Romania;
| | - Iulia-Ioana Stanescu-Spinu
- Discipline of Physiology, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (I.-I.S.-S.); (D.G.B.); (A.-E.B.-S.)
| | - Daniela Gabriela Balan
- Discipline of Physiology, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (I.-I.S.-S.); (D.G.B.); (A.-E.B.-S.)
| | - Andra-Elena Balcangiu-Stroescu
- Discipline of Physiology, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (I.-I.S.-S.); (D.G.B.); (A.-E.B.-S.)
| | - Elena-Claudia Coculescu
- Discipline of Oral Pathology, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania;
| | - Dragos-Eugen Georgescu
- Department of General Surgery, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 50474 Bucharest, Romania;
- Department of General Surgery, “Dr. Ion Cantacuzino” Clinical Hospital, 020475 Bucharest, Romania
| | - Remus Iulian Nica
- Central Military Emergency University Hospital “Dr. Carol Davila”, 010825 Bucharest, Romania;
- Discipline of General Surgery, Faculty of Midwifery and Nursing, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
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4
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Torres Robles J, Lou HJ, Shi G, Pan PL, Turk BE. Linear motif specificity in signaling through p38α and ERK2 mitogen-activated protein kinases. Proc Natl Acad Sci U S A 2023; 120:e2316599120. [PMID: 37988460 PMCID: PMC10691213 DOI: 10.1073/pnas.2316599120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK) cascades are essential for eukaryotic cells to integrate and respond to diverse stimuli. Maintaining specificity in signaling through MAPK networks is key to coupling distinct inputs to appropriate cellular responses. Docking sites-short linear motifs found in MAPK substrates, regulators, and scaffolds-can promote signaling specificity through selective interactions, but how they do so remains unresolved. Here, we screened a proteomic library for sequences interacting with the MAPKs extracellular signal-regulated kinase 2 (ERK2) and p38α, identifying selective and promiscuous docking motifs. Sequences specific for p38α had high net charge and lysine content, and selective binding depended on a pair of acidic residues unique to the p38α docking interface. Finally, we validated a set of full-length proteins harboring docking sites selected in our screens to be authentic MAPK interactors and substrates. This study identifies features that help define MAPK signaling networks and explains how specific docking motifs promote signaling integrity.
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Affiliation(s)
- Jaylissa Torres Robles
- Department of Chemistry, Yale University, New Haven, CT06520
- Department of Pharmacology, Yale School of Medicine, New Haven, CT06520
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT06520
| | - Guangda Shi
- Department of Pharmacology, Yale School of Medicine, New Haven, CT06520
| | | | - Benjamin E. Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT06520
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5
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Yajnik KN, Gupta SRR, Taneja M, Singh IK, Singh A. Deciphering mitogen activated protein kinase pathway activated during insect attack in Nicotiana attenuata. J Biomol Struct Dyn 2023:1-17. [PMID: 37811559 DOI: 10.1080/07391102.2023.2263795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023]
Abstract
Plant yields are compromised due to abiotic and biotic stresses. A crucial biotic stress instigated by insect attack, is a major concern that limits crop production. To overcome the deleterious effect of herbivory, pesticides are used but long-term usage of pesticides can be harmful to the environment and human health. Understanding the plants' inherent defense mechanism by interpreting the interaction pattern of defense-related proteins and signalling components and manipulating them to strengthen defense status, is one of the alternative approaches of green biotechnology. During insect attack, host plants initiate innumerable signalling pathways to activate defense response; Mitogen Activated Protein Kinase (MAPK) Pathway is a crucial component of signalling pathway that regulate the expression of downstream defense-related genes. MAPK pathway has three components: MAPKKK, MAPKK and MAPK. Earlier studies have shown participation of SIPK and WIPK (MAPKs) as well as MEK2 (MAPKK) during insect infestation and its association with plant defense. However, information on the third component and elucidation of the complete MAPK pathway are still elusive. Therefore, this study aims to identify the unknown component and decipher MAPK pathway in Nicotiana attenuata involved in plant defense against herbivory by identifying herbivory-inducible MAPKKKs and and their interaction with known partners of the MAPK pathway by docking and MD simulation. The possible pathway was predicted to be MAPKKK Na12134/Na04522-MEK2-SIPK/WIPK. Further, validation of the above interaction by in vitro and in vivo methods is highly recommended.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kalpesh Nath Yajnik
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- J C Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
| | - Shradheya R R Gupta
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Delhi, India
| | - Mansi Taneja
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- J C Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
- Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, Delhi, India
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6
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Shi G, Song C, Torres Robles J, Salichos L, Lou HJ, Lam TT, Gerstein M, Turk BE. Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors. Sci Signal 2023; 16:eabm5518. [PMID: 36626580 PMCID: PMC9995140 DOI: 10.1126/scisignal.abm5518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Essential functions of mitogen-activated protein kinases (MAPKs) depend on their capacity to selectively phosphorylate a limited repertoire of substrates. MAPKs harbor a conserved groove located outside of the catalytic cleft that binds to short linear sequence motifs found in substrates and regulators. However, the weak and transient nature of these "docking" interactions poses a challenge to defining MAPK interactomes and associated sequence motifs. Here, we describe a yeast-based genetic screening pipeline to evaluate large collections of MAPK docking sequences in parallel. Using this platform, we analyzed a combinatorial library based on the docking sequences from the MAPK kinases MKK6 and MKK7, defining features critical for binding to the stress-activated MAPKs JNK1 and p38α. Our screen of a library consisting of ~12,000 sequences from the human proteome revealed multiple MAPK-selective interactors, including many that did not conform to previously defined docking motifs. Analysis of p38α/JNK1 exchange mutants identified specific docking groove residues that mediate selective binding. Last, we verified that docking sequences identified in the screen functioned in substrate recruitment in vitro and in cultured cells. Together, these studies establish an approach to characterize MAPK docking sequences and provide a resource for future investigation of signaling downstream of p38 and JNK.
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Affiliation(s)
- Guangda Shi
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Claire Song
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jaylissa Torres Robles
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Leonidas Salichos
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - TuKiet T Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA.,Keck MS and Proteomics Resource, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
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Bardwell AJ, Wu B, Sarin KY, Waterman ML, Atwood SX, Bardwell L. ERK2 MAP kinase regulates SUFU binding by multisite phosphorylation of GLI1. Life Sci Alliance 2022; 5:e202101353. [PMID: 35831023 PMCID: PMC9279676 DOI: 10.26508/lsa.202101353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 01/03/2023] Open
Abstract
Crosstalk between the Hedgehog and MAPK signaling pathways occurs in several types of cancer and contributes to clinical resistance to Hedgehog pathway inhibitors. Here we show that MAP kinase-mediated phosphorylation weakens the binding of the GLI1 transcription factor to its negative regulator SUFU. ERK2 phosphorylates GLI1 on three evolutionarily conserved target sites (S102, S116, and S130) located near the high-affinity binding site for SUFU; these phosphorylations cooperate to weaken the affinity of GLI1-SUFU binding by over 25-fold. Phosphorylation of any one, or even any two, of the three sites does not result in the level of SUFU release seen when all three sites are phosphorylated. Tumor-derived mutations in R100 and S105, residues bordering S102, also diminish SUFU binding, collectively defining a novel evolutionarily conserved SUFU affinity-modulating region. In cultured mammalian cells, GLI1 variants containing phosphomimetic substitutions of S102, S116, and S130 displayed an increased ability to drive transcription. We conclude that multisite phosphorylation of GLI1 by ERK2 or other MAP kinases weakens GLI1-SUFU binding, thereby facilitating GLI1 activation and contributing to both physiological and pathological crosstalk.
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Affiliation(s)
- A Jane Bardwell
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Beibei Wu
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, USA
| | - Kavita Y Sarin
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marian L Waterman
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, USA
| | - Scott X Atwood
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Lee Bardwell
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
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Activation of Host Cellular Signaling and Mechanism of Enterovirus 71 Viral Proteins Associated with Hand, Foot and Mouth Disease. Viruses 2022; 14:v14102190. [PMID: 36298746 PMCID: PMC9609926 DOI: 10.3390/v14102190] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022] Open
Abstract
Enteroviruses are members of the Picornaviridae family consisting of human enterovirus groups A, B, C, and D as well as nonhuman enteroviruses. Human enterovirus type 71 (EV71) has emerged as a major cause of viral encephalitis, known as hand, foot, and mouth disease (HFMD), in children worldwide, especially in the Asia-Pacific region. EV71 and coxsackievirus A16 are the two viruses responsible for HFMD which are members of group A enteroviruses. The identified EV71 receptors provide useful information for understanding viral replication and tissue tropism. Host factors interact with the internal ribosome entry site (IRES) of EV71 to regulate viral translation. However, the specific molecular features of the respective viral genome that determine virulence remain unclear. Although a vaccine is currently approved, there is no effective therapy for treating EV71-infected patients. Therefore, understanding the host-pathogen interaction could provide knowledge in viral pathogenesis and further benefits to anti-viral therapy development. The aim of this study was to investigate the latest findings about the interaction of viral ligands with the host receptors as well as the activation of immunerelated signaling pathways for innate immunity and the involvement of different cytokines and chemokines during host-pathogen interaction. The study also examined the roles of viral proteins, mainly 2A and 3C protease, interferons production and their inhibitory effects.
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Solomon O, Shpilt Z, Sapir H, Marom S, Bibas S, Chen Y, Tshuva EY, Yitzchaik S, Friedler A. Peptide‐Based Inhibitors that Target the Docking Site of ERK2. Isr J Chem 2022. [DOI: 10.1002/ijch.202200041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ohad Solomon
- Institute of Chemistry, T he Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
- Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
| | - Zohar Shpilt
- Institute of Chemistry, T he Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
| | - Hannah Sapir
- Institute of Chemistry, T he Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
- Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
| | - Shir Marom
- Institute of Chemistry, T he Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
- Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
| | - Shai Bibas
- Institute of Chemistry, T he Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
- Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
| | - Yu‐Ju Chen
- Institute of Chemistry Academia Sinica No. 128, Section2, Academia Road Taipei 115 Taiwan
| | - Edit Y. Tshuva
- Institute of Chemistry, T he Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
| | - Shlomo Yitzchaik
- Institute of Chemistry, T he Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
- Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
| | - Assaf Friedler
- Institute of Chemistry, T he Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
- Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Safra Campus, Givat Ram Jerusalem 91904 Israel
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Mitogen-Activated Protein Kinase and Substrate Identification in Plant Growth and Development. Int J Mol Sci 2022; 23:ijms23052744. [PMID: 35269886 PMCID: PMC8911294 DOI: 10.3390/ijms23052744] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/17/2022] [Accepted: 02/28/2022] [Indexed: 02/01/2023] Open
Abstract
Mitogen-activated protein kinases (MAPKs) form tightly controlled signaling cascades that play essential roles in plant growth, development, and defense response. However, the molecular mechanisms underlying MAPK cascades are still very elusive, largely because of our poor understanding of how they relay the signals. The MAPK cascade is composed of MAPK, MAPKK, and MAPKKK. They transfer signals through the phosphorylation of MAPKKK, MAPKK, and MAPK in turn. MAPKs are organized into a complex network for efficient transmission of specific stimuli. This review summarizes the research progress in recent years on the classification and functions of MAPK cascades under various conditions in plants, especially the research status and general methods available for identifying MAPK substrates, and provides suggestions for future research directions.
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Aklilu S, Krakowiak M, Frempong A, Wilson K, Powers C, Fantz D. Nfya-1 functions as a substrate of ERK-MAP kinase during Caenorhabditis elegans vulval development. Cells Dev 2022; 169:203757. [PMID: 34838796 PMCID: PMC8934265 DOI: 10.1016/j.cdev.2021.203757] [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: 08/02/2021] [Revised: 10/18/2021] [Accepted: 11/14/2021] [Indexed: 02/08/2023]
Abstract
A common bridge between a linear cytoplasmic signal and broad nuclear regulation is the family of MAP kinases which can translocate to the nucleus upon activation by the cytoplasmic signal. One pathway which functions to activate the ERK family of MAP kinases is the Ras signaling pathway which functions at multiple times and locations during the development of Caenorhabditis elegans including the development of the excretory cell, germ cells, male tail, and vulva. It has been most extensively characterized during the development of the vulva which is formed from the vulval precursor cells (VPCs), a set of six equivalent, epithelial cells designated P3.p - P8.p. Although LIN-1 appears to be a primary target of ERK MAP kinase during vulval development, it is likely that other developmentally important molecules are also regulated by ERK-mediated phosphorylation. The identification of physiological substrates of MAP kinases has been aided by the identification of docking site domains in substrate proteins that contribute to high-affinity interactions with kinases. Our laboratory has identified the C. elegans protein, T08D10.1/NFYA-1, as a potential ERK MAP kinase substrate in this manner, and we have initiated a characterization of its role during Ras-mediated development. T08D10.1 possesses significant homology to the CCAAT-box DNA-binding domain of the vertebrate nuclear transcription factor-Y, alpha (NF-YA) family of proteins. NF-Y proteins act as part of a complex to regulate the transcription of a large number of genes, in particular, genes that function in the G1/S cell cycle transition. T08D10.1/NFYA-1 is predicted to code for a protein containing multiple potential phosphorylation sites for ERK MAP kinase and a D-domain docking site. We demonstrate through biochemical analysis of purified NFYA-1 protein that it can act in vitro as a high affinity substrate for activated ERK MAP kinase. Growth factor activation of the Ras pathway in a tissue culture system has negligible effect on the protein's transactivation potential, however, the DNA-binding activity of the protein is reduced after treatment with activated ERK-MAP kinase. We demonstrate through mutant analysis that nfya-1 acts to inhibit vulval development and functions downstream or in parallel to let-60/ras. Both the NF-Y complex and the Ras signaling pathway play a fundamental role in cell proliferation and oncogenesis and the connection between the two is an important insight into the mechanisms of cell fate specification and cellular response.
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Affiliation(s)
- Segen Aklilu
- Agnes Scott College, Department of Chemistry, 141 E. College Ave., Decatur, GA 30030, USA
| | - Michelle Krakowiak
- Agnes Scott College, Department of Chemistry, 141 E. College Ave., Decatur, GA 30030, USA
| | - Abena Frempong
- Agnes Scott College, Department of Chemistry, 141 E. College Ave., Decatur, GA 30030, USA
| | - Katherine Wilson
- Agnes Scott College, Department of Chemistry, 141 E. College Ave., Decatur, GA 30030, USA
| | - Christy Powers
- Agnes Scott College, Department of Chemistry, 141 E. College Ave., Decatur, GA 30030, USA
| | - Douglas Fantz
- Agnes Scott College, Department of Chemistry, 141 E. College Ave., Decatur, GA 30030, USA.
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12
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Hwang T, Parker SS, Hill SM, Ilunga MW, Grant RA, Mouneimne G, Keating AE. A distributed residue network permits conformational binding specificity in a conserved family of actin remodelers. eLife 2021; 10:e70601. [PMID: 34854809 PMCID: PMC8639148 DOI: 10.7554/elife.70601] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/08/2021] [Indexed: 11/23/2022] Open
Abstract
Metazoan proteomes contain many paralogous proteins that have evolved distinct functions. The Ena/VASP family of actin regulators consists of three members that share an EVH1 interaction domain with a 100 % conserved binding site. A proteome-wide screen revealed photoreceptor cilium actin regulator (PCARE) as a high-affinity ligand for ENAH EVH1. Here, we report the surprising observation that PCARE is ~100-fold specific for ENAH over paralogs VASP and EVL and can selectively bind ENAH and inhibit ENAH-dependent adhesion in cells. Specificity arises from a mechanism whereby PCARE stabilizes a conformation of the ENAH EVH1 domain that is inaccessible to family members VASP and EVL. Structure-based modeling rapidly identified seven residues distributed throughout EVL that are sufficient to differentiate binding by ENAH vs. EVL. By exploiting the ENAH-specific conformation, we rationally designed the tightest and most selective ENAH binder to date. Our work uncovers a conformational mechanism of interaction specificity that distinguishes highly similar paralogs and establishes tools for dissecting specific Ena/VASP functions in processes including cancer cell invasion.
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Affiliation(s)
- Theresa Hwang
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Sara S Parker
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of ArizonaTucsonUnited States
| | - Samantha M Hill
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of ArizonaTucsonUnited States
| | - Meucci W Ilunga
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Robert A Grant
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Ghassan Mouneimne
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of ArizonaTucsonUnited States
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biological Engineering and Koch Institue for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
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13
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SUMO enables substrate selectivity by mitogen-activated protein kinases to regulate immunity in plants. Proc Natl Acad Sci U S A 2021; 118:2021351118. [PMID: 33649235 PMCID: PMC7958252 DOI: 10.1073/pnas.2021351118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The versatility of mitogen-activated protein kinases (MAPKs) in translating exogenous and endogenous stimuli into appropriate cellular responses depends on its substrate specificity. In animals, several mechanisms have been proposed about how MAPKs maintain specificity to regulate distinct functional pathways. However, little is known of mechanisms that enable substrate selectivity in plant MAPKs. Small ubiquitin-like modifier (SUMO), a posttranslational modification system, plays an important role in plant development and defense by rapid reprogramming of cellular events. In this study we identified a functional SUMO interaction motif (SIM) in Arabidopsis MPK3 and MPK6 that reveals a mechanism for selective interaction of MPK3/6 with SUMO-conjugated WRKY33, during defense. We show that WRKY33 is rapidly SUMOylated in response to Botrytis cinerea infection and flg22 elicitor treatment. SUMOylation mediates WRKY33 phosphorylation by MPKs and consequent transcription factor activity. Disruption of either WRKY33 SUMO or MPK3/6 SIM sites attenuates their interaction and inactivates WRKY33-mediated defense. However, MPK3/6 SIM mutants show normal interaction with a non-SUMOylated form of another transcription factor, SPEECHLESS, unraveling a role for SUMOylation in differential substrate selectivity by MPKs. We reveal that the SUMO proteases, SUMO PROTEASE RELATED TO FERTILITY1 (SPF1) and SPF2 control WRKY33 SUMOylation and demonstrate a role for these SUMO proteases in defense. Our data reveal a mechanism by which MPK3/6 prioritize molecular pathways by differentially selecting substrates using the SUMO-SIM module during defense responses.
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14
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Enthalpy-Entropy Compensation in the Promiscuous Interaction of an Intrinsically Disordered Protein with Homologous Protein Partners. Biomolecules 2021; 11:biom11081204. [PMID: 34439869 PMCID: PMC8391806 DOI: 10.3390/biom11081204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/01/2021] [Accepted: 08/09/2021] [Indexed: 01/07/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) can engage in promiscuous interactions with their protein targets; however, it is not clear how this feature is encoded in the primary sequence of the IDPs and to what extent the surface properties and the shape of the binding cavity dictate the binding mode and the final bound conformation. Here we show, using a combination of nuclear magnetic resonance (NMR) spectroscopy and isothermal titration calorimetry (ITC), that the promiscuous interaction of the intrinsically disordered regulatory domain of the mitogen-activated protein kinase kinase MKK4 with p38α and JNK1 is facilitated by folding-upon-binding into two different conformations, despite the high sequence conservation and structural homology between p38α and JNK1. Our results support a model whereby the specific surface properties of JNK1 and p38α dictate the bound conformation of MKK4 and that enthalpy–entropy compensation plays a major role in maintaining comparable binding affinities for MKK4 towards the two kinases.
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15
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Nagao H, Kitagawa D, Nakajima F, Sawa M, Kinoshita T. Identification of an allosteric and Smad3-selective inhibitor of p38αMAPK using a substrate-based approach. Bioorg Med Chem Lett 2021; 43:128056. [PMID: 33892104 DOI: 10.1016/j.bmcl.2021.128056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/13/2021] [Accepted: 04/17/2021] [Indexed: 11/26/2022]
Abstract
p38α mitogen activated protein kinase (MAPK) plays important roles in multiple cellular functions by phosphorylating a wide variety of substrates, and therefore, p38α MAPK has been considered as an important drug target. In this study, we designed peptide-based inhibitors for p38α MAPK, which can only inhibit the Smad3 phosphorylation specifically, by targeting the KIM binding site of p38α MAPK. Peptide 6 showed a significant inhibitory potency for the Smad3 phosphorylation by p38α MAPK. Peptide 6 showed no ATP dependency, and did not inhibit the phosphorylation of other substrates by p38α MAPK. The discovery of peptide 6 by targeting the KIM binding site likely provide an opportunity for the discovery of a novel class of allosteric and substrate-specific p38α MAPK inhibitors.
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Affiliation(s)
- Haruna Nagao
- Carna Biosciences, Inc., BMA 3F, 1-5-5 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Daisuke Kitagawa
- Carna Biosciences, Inc., BMA 3F, 1-5-5 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Fumio Nakajima
- Carna Biosciences, Inc., BMA 3F, 1-5-5 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Masaaki Sawa
- Carna Biosciences, Inc., BMA 3F, 1-5-5 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Takayoshi Kinoshita
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai-shi, Osaka 599-8531, Japan
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16
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Lin L, Wu J, Jiang M, Wang Y. Plant Mitogen-Activated Protein Kinase Cascades in Environmental Stresses. Int J Mol Sci 2021; 22:ijms22041543. [PMID: 33546499 PMCID: PMC7913722 DOI: 10.3390/ijms22041543] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 12/17/2022] Open
Abstract
Due to global warming and population growth, plants need to rescue themselves, especially in unfavorable environments, to fulfill food requirements because they are sessile organisms. Stress signal sensing is a crucial step that determines the appropriate response which, ultimately, determines the survival of plants. As important signaling modules in eukaryotes, plant mitogen-activated protein kinase (MAPK) cascades play a key role in regulating responses to the following four major environmental stresses: high salinity, drought, extreme temperature and insect and pathogen infections. MAPK cascades are involved in responses to these environmental stresses by regulating the expression of related genes, plant hormone production and crosstalk with other environmental stresses. In this review, we describe recent major studies investigating MAPK-mediated environmental stress responses. We also highlight the diverse function of MAPK cascades in environmental stress. These findings help us understand the regulatory network of MAPKs under environmental stress and provide another strategy to improve stress resistance in crops to ensure food security.
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Affiliation(s)
- Li Lin
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225000, China;
| | - Jian Wu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225000, China;
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225000, China
- Correspondence: (J.W.); (Y.W.)
| | - Mingyi Jiang
- College of Life Sciences and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China;
| | - Youping Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225000, China;
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225000, China
- Correspondence: (J.W.); (Y.W.)
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17
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He W, Li J, Gong AY, Deng S, Li M, Wang Y, Mathy NW, Feng Y, Xiao L, Chen XM. Cryptosporidial Infection Suppresses Intestinal Epithelial Cell MAPK Signaling Impairing Host Anti-Parasitic Defense. Microorganisms 2021; 9:microorganisms9010151. [PMID: 33445463 PMCID: PMC7826584 DOI: 10.3390/microorganisms9010151] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
Cryptosporidium is a genus of protozoan parasites that infect the gastrointestinal epithelium of a variety of vertebrate hosts. Intestinal epithelial cells are the first line of defense and play a critical role in orchestrating host immunity against Cryptosporidium infection. To counteract host defense response, Cryptosporidium has developed strategies of immune evasion to promote parasitic replication and survival within epithelial cells, but the underlying mechanisms are largely unclear. Using various models of intestinal cryptosporidiosis, we found that Cryptosporidium infection caused suppression of mitogen-activated protein kinase (MAPK) signaling in infected murine intestinal epithelial cells. Whereas expression levels of most genes encoding the key components of the MAPK signaling pathway were not changed in infected intestinal epithelial cells, we detected a significant downregulation of p38/Mapk, MAP kinase-activated protein kinase 2 (Mk2), and Mk3 genes in infected host cells. Suppression of MAPK signaling was associated with an impaired intestinal epithelial defense against C. parvum infection. Our data suggest that cryptosporidial infection may suppress intestinal epithelial cell MAPK signaling associated with the evasion of host antimicrobial defense.
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Affiliation(s)
- Wei He
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (W.H.); (Y.F.); (L.X.)
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68198-5880, USA; (J.L.); (A.-Y.G.); (S.D.); (M.L.); (Y.W.); (N.W.M.)
| | - Juan Li
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68198-5880, USA; (J.L.); (A.-Y.G.); (S.D.); (M.L.); (Y.W.); (N.W.M.)
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Ai-Yu Gong
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68198-5880, USA; (J.L.); (A.-Y.G.); (S.D.); (M.L.); (Y.W.); (N.W.M.)
| | - Silu Deng
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68198-5880, USA; (J.L.); (A.-Y.G.); (S.D.); (M.L.); (Y.W.); (N.W.M.)
| | - Min Li
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68198-5880, USA; (J.L.); (A.-Y.G.); (S.D.); (M.L.); (Y.W.); (N.W.M.)
| | - Yang Wang
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68198-5880, USA; (J.L.); (A.-Y.G.); (S.D.); (M.L.); (Y.W.); (N.W.M.)
| | - Nicholas W. Mathy
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68198-5880, USA; (J.L.); (A.-Y.G.); (S.D.); (M.L.); (Y.W.); (N.W.M.)
| | - Yaoyu Feng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (W.H.); (Y.F.); (L.X.)
| | - Lihua Xiao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (W.H.); (Y.F.); (L.X.)
| | - Xian-Ming Chen
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68198-5880, USA; (J.L.); (A.-Y.G.); (S.D.); (M.L.); (Y.W.); (N.W.M.)
- Correspondence:
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18
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Ma M, Bordignon P, Dotto GP, Pelet S. Visualizing cellular heterogeneity by quantifying the dynamics of MAPK activity in live mammalian cells with synthetic fluorescent biosensors. Heliyon 2020; 6:e05574. [PMID: 33319088 PMCID: PMC7723811 DOI: 10.1016/j.heliyon.2020.e05574] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 10/26/2020] [Accepted: 11/18/2020] [Indexed: 01/19/2023] Open
Abstract
Mitogen-Activated Protein Kinases (MAPKs) control a wide array of cellular functions by transducing extracellular information into defined biological responses. In order to understand how these pathways are regulated, dynamic single cell measurements are highly needed. Fluorescence microscopy is well suited to perform these measurements. However, more dynamic and sensitive biosensors that allow the quantification of signaling activity in living mammalian cells are required. We have engineered a synthetic fluorescent substrate for human MAPKs (ERK, JNK and p38) that relocates from the nucleus to the cytoplasm when phosphorylated by the kinases. We demonstrate that this reporter displays an improved response compared to other relocation biosensors. This assay allows to monitor the heterogeneity in the MAPK response in a population of isogenic cells, revealing pulses of ERK activity upon a physiological EGFR stimulation. We show applicability of this approach to the analysis of multiple cancer cell lines and primary cells as well as its application in vivo to developing tumors. Using this ERK biosensor, dynamic single cell measurements with high temporal resolution can be obtained. These MAPK reporters can be widely applied to the analysis of molecular mechanisms of MAPK signaling in healthy and diseased state, in cell culture assays or in vivo.
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Affiliation(s)
- Min Ma
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
- Department of Biochemistry, University of Lausanne, Switzerland
| | - Pino Bordignon
- Department of Biochemistry, University of Lausanne, Switzerland
| | | | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
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19
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Rahman SMT, Zhou W, Deiters A, Haugh JM. Optical control of MAP kinase kinase 6 (MKK6) reveals that it has divergent roles in pro-apoptotic and anti-proliferative signaling. J Biol Chem 2020; 295:8494-8504. [PMID: 32371393 DOI: 10.1074/jbc.ra119.012079] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/21/2020] [Indexed: 12/24/2022] Open
Abstract
The selective pressure imposed by extrinsic death signals and stressors adds to the challenge of isolating and interpreting the roles of proteins in stress-activated signaling networks. By expressing a kinase with activating mutations and a caged lysine blocking the active site, we can rapidly switch on catalytic activity with light and monitor the ensuing dynamics. Applying this approach to MAP kinase 6 (MKK6), which activates the p38 subfamily of MAPKs, we found that decaging active MKK6 in fibroblasts is sufficient to trigger apoptosis in a p38-dependent manner. Both in fibroblasts and in a murine melanoma cell line expressing mutant B-Raf, MKK6 activation rapidly and potently inhibited the pro-proliferative extracellular signal-regulated kinase (ERK) pathway; to our surprise, this negative cross-regulation was equally robust when all p38 isoforms were inhibited. These results position MKK6 as a new pleiotropic signal transducer that promotes both pro-apoptotic and anti-proliferative signaling, and they highlight the utility of caged, light-activated kinases for dissecting stress-activated signaling networks.
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Affiliation(s)
- Shah Md Toufiqur Rahman
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Wenyuan Zhou
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jason M Haugh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
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20
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Abstract
MEK, a central component of the Ras/MAPK cascade, is mutated in human tumors and developmental disorders. Recent studies are beginning to dissect the mechanisms that make these MEK mutants hyperactive.
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Affiliation(s)
- Lee Bardwell
- Department of Developmental and Cell Biology, 2208 Natural Sciences I, University of California, Irvine, CA 92697-2300, USA.
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21
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Koike R, Amano M, Kaibuchi K, Ota M. Protein kinases phosphorylate long disordered regions in intrinsically disordered proteins. Protein Sci 2019; 29:564-571. [PMID: 31724233 DOI: 10.1002/pro.3789] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/09/2019] [Accepted: 11/11/2019] [Indexed: 12/12/2022]
Abstract
Phosphorylation is a major post-translational modification that plays a central role in signaling pathways. Protein kinases phosphorylate substrates (phosphoproteins) by adding phosphate at Ser/Thr or Tyr residues (phosphosites). A large amount of data identifying and describing phosphosites in phosphoproteins has been reported but the specificity of phosphorylation is not fully resolved. In this report, data of kinase-substrate pairs identified by the Kinase-Interacting Substrate Screening (KISS) method were used to analyze phosphosites in intrinsically disordered regions (IDRs) of intrinsically disordered proteins. We compared phosphorylated and nonphosphorylated IDRs and found that the phosphorylated IDRs were significantly longer than nonphosphorylated IDRs. The phosphorylated IDR is often the longest IDR (71%) in a phosphoprotein when only a single phosphosite exists in the IDR, and when the phosphoprotein has multiple phosphosites in an IDR(s), the phosphosites are primarily localized in a single IDR (78%) and this IDR is usually the longest one (81%). We constructed a stochastic model of phosphorylation to estimate the effect of IDR length. The model that accounted for IDR length produced more realistic results when compared with a model that excluded the IDR length. We propose that the IDR length is a significant determinant for locating kinase phosphorylation sites in phosphoproteins.
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Affiliation(s)
- Ryotaro Koike
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | - Mutsuki Amano
- Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Kozo Kaibuchi
- Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Motonori Ota
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
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22
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Mapping low-affinity/high-specificity peptide-protein interactions using ligand-footprinting mass spectrometry. Proc Natl Acad Sci U S A 2019; 116:21001-21011. [PMID: 31578253 DOI: 10.1073/pnas.1819533116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Short linear peptide motifs that are intracellular ligands of folded proteins are a modular, incompletely understood molecular interaction language in signaling systems. Such motifs, which frequently occur in intrinsically disordered protein regions, often bind partner proteins with modest affinity and are difficult to study with conventional structural biology methods. We developed LiF-MS (ligand-footprinting mass spectrometry), a method to map peptide binding sites on folded protein domains that allows consideration of their dynamic disorder, and used it to analyze a set of D-motif peptide-mitogen-activated protein kinase (MAPK) associations to validate the approach and define unknown binding structures. LiF-MS peptide ligands carry a short-lived, indiscriminately reactive cleavable crosslinker that marks contacts close to ligand binding sites with high specificity. Each marked amino acid provides an independent constraint for a set of directed peptide-protein docking simulations, which are analyzed by agglomerative hierarchical clustering. We found that LiF-MS provides accurate ab initio identification of ligand binding surfaces and a view of potential binding ensembles of a set of D-motif peptide-MAPK associations. Our analysis provides an MKK4-JNK1 structural model, which has thus far been crystallographically unattainable, a potential alternate binding mode for part of the NFAT4-JNK interaction, and evidence of bidirectional association of MKK4 peptide with ERK2. Overall, we find that LiF-MS is an effective noncrystallographic way to understand how short linear motifs associate with specific sites on folded protein domains at the level of individual amino acids.
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23
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Olea-Flores M, Zuñiga-Eulogio MD, Mendoza-Catalán MA, Rodríguez-Ruiz HA, Castañeda-Saucedo E, Ortuño-Pineda C, Padilla-Benavides T, Navarro-Tito N. Extracellular-Signal Regulated Kinase: A Central Molecule Driving Epithelial-Mesenchymal Transition in Cancer. Int J Mol Sci 2019; 20:E2885. [PMID: 31200510 PMCID: PMC6627365 DOI: 10.3390/ijms20122885] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 12/18/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a reversible cellular process, characterized by changes in gene expression and activation of proteins, favoring the trans-differentiation of the epithelial phenotype to a mesenchymal phenotype. This process increases cell migration and invasion of tumor cells, progression of the cell cycle, and resistance to apoptosis and chemotherapy, all of which support tumor progression. One of the signaling pathways involved in tumor progression is the MAPK pathway. Within this family, the ERK subfamily of proteins is known for its contributions to EMT. The ERK subfamily is divided into typical (ERK 1/2/5), and atypical (ERK 3/4/7/8) members. These kinases are overexpressed and hyperactive in various types of cancer. They regulate diverse cellular processes such as proliferation, migration, metastasis, resistance to chemotherapy, and EMT. In this context, in vitro and in vivo assays, as well as studies in human patients, have shown that ERK favors the expression, function, and subcellular relocalization of various proteins that regulate EMT, thus promoting tumor progression. In this review, we discuss the mechanistic roles of the ERK subfamily members in EMT and tumor progression in diverse biological systems.
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Affiliation(s)
- Monserrat Olea-Flores
- Laboratorio de Biología Celular del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| | - Miriam Daniela Zuñiga-Eulogio
- Laboratorio de Biología Celular del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| | - Miguel Angel Mendoza-Catalán
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| | - Hugo Alberto Rodríguez-Ruiz
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| | - Eduardo Castañeda-Saucedo
- Laboratorio de Biología Celular del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| | - Carlos Ortuño-Pineda
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| | - Teresita Padilla-Benavides
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.
| | - Napoleón Navarro-Tito
- Laboratorio de Biología Celular del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
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24
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Wang Y, Zhang Y, Lu C, Zhang W, Deng H, Wu J, Wang J, Wang Z. Kinetic and mechanistic studies of p38α
MAP
kinase phosphorylation by
MKK
6. FEBS J 2019; 286:1030-1052. [DOI: 10.1111/febs.14762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/29/2018] [Accepted: 01/17/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Yu‐Lu Wang
- Key Laboratory of Ministry of Education for Protein Science School of Life Sciences Tsinghua University Beijing China
| | - Yuan‐Yuan Zhang
- Key Laboratory of Ministry of Education for Protein Science School of Life Sciences Tsinghua University Beijing China
| | - Chang Lu
- Key Laboratory of Ministry of Education for Protein Science School of Life Sciences Tsinghua University Beijing China
| | - Wenhao Zhang
- Key Laboratory of Ministry of Education for Protein Science School of Life Sciences Tsinghua University Beijing China
| | - Haiteng Deng
- Key Laboratory of Ministry of Education for Protein Science School of Life Sciences Tsinghua University Beijing China
| | - Jia‐Wei Wu
- Key Laboratory of Ministry of Education for Protein Science School of Life Sciences Tsinghua University Beijing China
- Institute of Molecular Enzymology Soochow University Suzhou China
| | - Jue Wang
- Institute of Molecular Enzymology Soochow University Suzhou China
| | - Zhi‐Xin Wang
- Key Laboratory of Ministry of Education for Protein Science School of Life Sciences Tsinghua University Beijing China
- Institute of Molecular Enzymology Soochow University Suzhou China
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25
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Syed A, Lukacsovich T, Pomeroy M, Bardwell AJ, Decker GT, Waymire KG, Purcell J, Huang W, Gui J, Padilla EM, Park C, Paul A, Pham TBT, Rodriguez Y, Wei S, Worthge S, Zebarjedi R, Zhang B, Bardwell L, Marsh JL, MacGregor GR. Miles to go (mtgo) encodes FNDC3 proteins that interact with the chaperonin subunit CCT3 and are required for NMJ branching and growth in Drosophila. Dev Biol 2018; 445:37-53. [PMID: 30539716 DOI: 10.1016/j.ydbio.2018.10.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/01/2018] [Accepted: 10/17/2018] [Indexed: 11/17/2022]
Abstract
Analysis of mutants that affect formation and function of the Drosophila larval neuromuscular junction (NMJ) has provided valuable insight into genes required for neuronal branching and synaptic growth. We report that NMJ development in Drosophila requires both the Drosophila ortholog of FNDC3 genes; CG42389 (herein referred to as miles to go; mtgo), and CCT3, which encodes a chaperonin complex subunit. Loss of mtgo function causes late pupal lethality with most animals unable to escape the pupal case, while rare escapers exhibit an ataxic gait and reduced lifespan. NMJs in mtgo mutant larvae have dramatically reduced branching and growth and fewer synaptic boutons compared with control animals. Mutant larvae show normal locomotion but display an abnormal self-righting response and chemosensory deficits that suggest additional functions of mtgo within the nervous system. The pharate lethality in mtgo mutants can be rescued by both low-level pan- and neuronal-, but not muscle-specific expression of a mtgo transgene, supporting a neuronal-intrinsic requirement for mtgo in NMJ development. Mtgo encodes three similar proteins whose domain structure is most closely related to the vertebrate intracellular cytosolic membrane-anchored fibronectin type-III domain-containing protein 3 (FNDC3) protein family. Mtgo physically and genetically interacts with Drosophila CCT3, which encodes a subunit of the TRiC/CCT chaperonin complex required for maturation of actin, tubulin and other substrates. Drosophila larvae heterozygous for a mutation in CCT3 that reduces binding between CCT3 and MTGO also show abnormal NMJ development similar to that observed in mtgo null mutants. Hence, the intracellular FNDC3-ortholog MTGO and CCT3 can form a macromolecular complex, and are both required for NMJ development in Drosophila.
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Affiliation(s)
- Adeela Syed
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Tamás Lukacsovich
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Miles Pomeroy
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - A Jane Bardwell
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Gentry Thomas Decker
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211-7400, USA
| | - Katrina G Waymire
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Judith Purcell
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Weijian Huang
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - James Gui
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Emily M Padilla
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Cindy Park
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Antor Paul
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Thai Bin T Pham
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Yanete Rodriguez
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Stephen Wei
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Shane Worthge
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Ronak Zebarjedi
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Bing Zhang
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211-7400, USA
| | - Lee Bardwell
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - J Lawrence Marsh
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA.
| | - Grant R MacGregor
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA.
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In silico-prediction of protein-protein interactions network about MAPKs and PP2Cs reveals a novel docking site variants in Brachypodium distachyon. Sci Rep 2018; 8:15083. [PMID: 30305661 PMCID: PMC6180098 DOI: 10.1038/s41598-018-33428-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/13/2018] [Indexed: 12/26/2022] Open
Abstract
Protein-protein interactions (PPIs) underlie the molecular mechanisms of most biological processes. Mitogen-activated protein kinases (MAPKs) can be dephosphorylated by MAPK-specific phosphatases such as PP2C, which are critical to transduce extracellular signals into adaptive and programmed responses. However, the experimental approaches for identifying PPIs are expensive, time-consuming, laborious and challenging. In response, many computational methods have been developed to predict PPIs. Yet, these methods have inherent disadvantages such as high false positive and negative results. Thus, it is crucial to develop in silico approaches for predicting PPIs efficiently and accurately. In this study, we identified PPIs among 16 BdMAPKs and 86 BdPP2Cs in B. distachyon using a novel docking approach. Further, we systematically investigated the docking site (D-site) of BdPP2C which plays a vital role for recognition and docking of BdMAPKs. D-site analysis revealed that there were 96 pairs of PPIs including all BdMAPKs and most BdPP2Cs, which indicated that BdPP2C may play roles in other signaling networks. Moreover, most BdPP2Cs have a D-site for BdMAPKs in our prediction results, which suggested that our method can effectively predict PPIs, as confirmed by their 3D structure. In addition, we validated this methodology with known Arabidopsis and yeast phosphatase-MAPK interactions from the STRING database. The results obtained provide a vital research resource for exploring an accurate network of PPIs between BdMAPKs and BdPP2Cs.
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Lombard CK, Davis AL, Inukai T, Maly DJ. Allosteric Modulation of JNK Docking Site Interactions with ATP-Competitive Inhibitors. Biochemistry 2018; 57:5897-5909. [PMID: 30211540 DOI: 10.1021/acs.biochem.8b00776] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The c-Jun N-terminal kinases (JNKs) play a wide variety of roles in cellular signaling processes, dictating important, and even divergent, cellular fates. These essential kinases possess docking surfaces distal to their active sites that interact with diverse binding partners, including upstream activators, downstream substrates, and protein scaffolds. Prior studies have suggested that the interactions of certain protein-binding partners with one such JNK docking surface, termed the D-recruitment site (DRS), can allosterically influence the conformational state of the ATP-binding pocket of JNKs. To further explore the allosteric relationship between the ATP-binding pockets and DRSs of JNKs, we investigated how the interactions of the scaffolding protein JIP1, as well as the upstream activators MKK4 and MKK7, are allosterically influenced by the ATP-binding site occupancy of the JNKs. We show that the affinity of the JNKs for JIP1 can be divergently modulated with ATP-competitive inhibitors, with a >50-fold difference in dissociation constant observed between the lowest- and highest-affinity JNK1-inhibitor complexes. Furthermore, we found that we could promote or attenuate phosphorylation of JNK1's activation loop by MKK4 and MKK7, by varying the ATP-binding site occupancy. Given that JIP1, MKK4, and MKK7 all interact with JNK DRSs, these results demonstrate that there is functional allostery between the ATP-binding sites and DRSs of these kinases. Furthermore, our studies suggest that ATP-competitive inhibitors can allosterically influence the intracellular binding partners of the JNKs.
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Affiliation(s)
- Chloe K Lombard
- Department of Chemistry , University of Washington , Seattle , Washington 98117 , United States
| | - Audrey L Davis
- Department of Chemistry , University of Washington , Seattle , Washington 98117 , United States
| | - Takayuki Inukai
- Medicinal Chemistry Research Laboratories , Ono Pharmaceutical Company, Ltd. , 3-1-1 Sakurai , Shimamoto, Mishima, Osaka 618-8585 , Japan
| | - Dustin J Maly
- Department of Chemistry , University of Washington , Seattle , Washington 98117 , United States.,Department of Biochemistry , University of Washington , Seattle , Washington 98117 , United States
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Eblen ST. Extracellular-Regulated Kinases: Signaling From Ras to ERK Substrates to Control Biological Outcomes. Adv Cancer Res 2018; 138:99-142. [PMID: 29551131 DOI: 10.1016/bs.acr.2018.02.004] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The extracellular-regulated kinases ERK1 and ERK2 are evolutionarily conserved, ubiquitous serine-threonine kinases that are involved in regulating cellular signaling in both normal and pathological conditions. Their expression is critical for development and their hyperactivation is a major factor in cancer development and progression. Since their discovery as one of the major signaling mediators activated by mitogens and Ras mutation, we have learned much about their regulation, including their activation, binding partners and substrates. In this review I will discuss some of what has been discovered about the members of the Ras to ERK pathway, including regulation of their activation by growth factors and cell adhesion pathways. Looking downstream of ERK activation I will also highlight some of the many ERK substrates that have been discovered, including those involved in feedback regulation, cell migration and cell cycle progression through the control of transcription, pre-mRNA splicing and protein synthesis.
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Affiliation(s)
- Scott T Eblen
- Medical University of South Carolina, Charleston, SC, United States.
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29
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Delaforge E, Kragelj J, Tengo L, Palencia A, Milles S, Bouvignies G, Salvi N, Blackledge M, Jensen MR. Deciphering the Dynamic Interaction Profile of an Intrinsically Disordered Protein by NMR Exchange Spectroscopy. J Am Chem Soc 2018; 140:1148-1158. [PMID: 29276882 DOI: 10.1021/jacs.7b12407] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Intrinsically disordered proteins (IDPs) display a large number of interaction modes including folding-upon-binding, binding without major structural transitions, or binding through highly dynamic, so-called fuzzy, complexes. The vast majority of experimental information about IDP binding modes have been inferred from crystal structures of proteins in complex with short peptides of IDPs. However, crystal structures provide a mainly static view of the complexes and do not give information about the conformational dynamics experienced by the IDP in the bound state. Knowledge of the dynamics of IDP complexes is of fundamental importance to understand how IDPs engage in highly specific interactions without concomitantly high binding affinity. Here, we combine rotating-frame R1ρ, Carr-Purcell-Meiboom Gill relaxation dispersion as well as chemical exchange saturation transfer to decipher the dynamic interaction profile of an IDP in complex with its partner. We apply the approach to the dynamic signaling complex formed between the mitogen-activated protein kinase (MAPK) p38α and the intrinsically disordered regulatory domain of the MAPK kinase MKK4. Our study demonstrates that MKK4 employs a subtle combination of interaction modes in order to bind to p38α, leading to a complex displaying significantly different dynamics across the bound regions.
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Affiliation(s)
- Elise Delaforge
- Université Grenoble Alpes, CNRS, CEA, IBS , F-38000 Grenoble, France
| | - Jaka Kragelj
- Université Grenoble Alpes, CNRS, CEA, IBS , F-38000 Grenoble, France
| | - Laura Tengo
- Université Grenoble Alpes, CNRS, CEA, IBS , F-38000 Grenoble, France
| | - Andrés Palencia
- Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes , F-38000 Grenoble, France
| | - Sigrid Milles
- Université Grenoble Alpes, CNRS, CEA, IBS , F-38000 Grenoble, France
| | - Guillaume Bouvignies
- Laboratoire des Biomolécules, Département de Chimie, École Normale Supérieur, UPMC Université Paris 06, CNRS, PSL Research University , 24 rue Lhomond, 75005 Paris, France.,Sorbonne Universités, UPMC Université Paris 06 , École Normale Supérieur, CNRS, Laboratoire des Biomolécules (LBM), 75005 Paris, France
| | - Nicola Salvi
- Université Grenoble Alpes, CNRS, CEA, IBS , F-38000 Grenoble, France
| | - Martin Blackledge
- Université Grenoble Alpes, CNRS, CEA, IBS , F-38000 Grenoble, France
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30
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Dory M, Hatzimasoura E, Kállai BM, Nagy SK, Jäger K, Darula Z, Nádai TV, Mészáros T, López‐Juez E, Barnabás B, Palme K, Bögre L, Ditengou FA, Dóczi R. Coevolving MAPK and PID phosphosites indicate an ancient environmental control of PIN auxin transporters in land plants. FEBS Lett 2018; 592:89-102. [PMID: 29197077 PMCID: PMC5814726 DOI: 10.1002/1873-3468.12929] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/22/2017] [Accepted: 11/23/2017] [Indexed: 11/16/2022]
Abstract
Plant growth flexibly adapts to environmental conditions, implying cross-talk between environmental signalling and developmental regulation. Here, we show that the PIN auxin efflux carrier family possesses three highly conserved putative mitogen-activated protein kinase (MAPK) sites adjacent to the phosphorylation sites of the well-characterised AGC kinase PINOID, which regulates the polar localisation of PINs and directional auxin transport, thereby underpinning organ growth. The conserved sites of PIN1 are phosphorylated in vitro by two environmentally activated MAPKs, MPK4 and MPK6. In contrast to AGC kinases, MAPK-mediated phosphorylation of PIN1 at adjacent sites leads to a partial loss of the plasma membrane localisation of PIN1. MAPK-mediated modulation of PIN trafficking may participate in environmental adjustment of plant growth.
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Affiliation(s)
- Magdalena Dory
- Institute of AgricultureCentre for Agricultural ResearchHungarian Academy of SciencesMartonvásárHungary
| | - Elizabeth Hatzimasoura
- School of Biological Sciences and Centre for Systems and Synthetic BiologyRoyal Holloway, University of LondonEghamUK
| | - Brigitta M. Kállai
- Department of Medical ChemistryMolecular Biology and PathobiochemistrySemmelweis UniversityBudapestHungary
| | - Szilvia K. Nagy
- Department of Medical ChemistryMolecular Biology and PathobiochemistrySemmelweis UniversityBudapestHungary
| | - Katalin Jäger
- Institute of AgricultureCentre for Agricultural ResearchHungarian Academy of SciencesMartonvásárHungary
| | - Zsuzsanna Darula
- Laboratory of Proteomics ResearchBiological Research CentreHungarian Academy of SciencesSzegedHungary
| | - Tímea V. Nádai
- Institute of AgricultureCentre for Agricultural ResearchHungarian Academy of SciencesMartonvásárHungary
| | - Tamás Mészáros
- Department of Medical ChemistryMolecular Biology and PathobiochemistrySemmelweis UniversityBudapestHungary
| | - Enrique López‐Juez
- School of Biological Sciences and Centre for Systems and Synthetic BiologyRoyal Holloway, University of LondonEghamUK
| | - Beáta Barnabás
- Institute of AgricultureCentre for Agricultural ResearchHungarian Academy of SciencesMartonvásárHungary
| | - Klaus Palme
- Institute of Biology IIUniversity of FreiburgGermany
- BIOSS Centre for Biological Signalling StudiesUniversity of FreiburgGermany
- Centre for Biological Systems Analysis (ZBSA)University of FreiburgGermany
| | - László Bögre
- School of Biological Sciences and Centre for Systems and Synthetic BiologyRoyal Holloway, University of LondonEghamUK
| | - Franck A. Ditengou
- Institute of Biology IIUniversity of FreiburgGermany
- BIOSS Centre for Biological Signalling StudiesUniversity of FreiburgGermany
- Centre for Biological Systems Analysis (ZBSA)University of FreiburgGermany
| | - Róbert Dóczi
- Institute of AgricultureCentre for Agricultural ResearchHungarian Academy of SciencesMartonvásárHungary
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31
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Bai F, Matton DP. The Arabidopsis Mitogen-Activated Protein Kinase Kinase Kinase 20 (MKKK20) C-terminal domain interacts with MKK3 and harbors a typical DEF mammalian MAP kinase docking site. PLANT SIGNALING & BEHAVIOR 2018; 13:e1503498. [PMID: 30081740 PMCID: PMC6149407 DOI: 10.1080/15592324.2018.1503498] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/05/2018] [Accepted: 07/10/2018] [Indexed: 05/21/2023]
Abstract
Mitogen-activated protein kinase (MAPKs) constitute a major component in plant cellular signaling considering the sheer number of MAPKKKKs, MAPKKKs, MAPKKs and MAPKs when compared to yeast and animal systems. Nevertheless, only few complete MAPK cascades have been deciphered and the same hold true for their substrates. Furthermore, cascades often share kinase components, but little is known about their specific interactions and domains. The Arabidopsis thaliana MAP kinase kinase kinase 20 (MKKK20) was recently showed to interact with MKK3 and MPK18 in two non-complementary signaling cascades involved in root cortical microtubule functions. Here, MKKK20 and MKK3 proteins where dissected and tested in yeast two-hybrid assays followed by an in planta validation through bimolecular fluorescence complementation (BiFC) assays and showed that the MKKK20 C-terminal region interacted with MKK3 that comprised a typical DEF domain akin to MAPKs docking domains.
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Affiliation(s)
- Fangwen Bai
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, Canada
| | - Daniel P. Matton
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, Canada
- CONTACT Daniel P. Matton Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, Canada
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32
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Transcriptional and Post-Translational Targeting of Myocyte Stress Protein 1 (MS1) by the JNK Pathway in Cardiac Myocytes. J Mol Signal 2017; 12:3. [PMID: 30210579 PMCID: PMC5853832 DOI: 10.5334/1750-2187-12-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Myocyte Stress Protein 1 (MS1) is a muscle-specific, stress-responsive, regulator of gene expression. It was originally identified in embryonic mouse heart which showed increased expression in a rat model of left ventricular hypertrophy. To determine if MS1 was responsive to other stresses relevant to cardiac myocyte function, we tested if it could be induced by the metabolic stresses associated with ischaemia/reperfusion injury in cardiac myocytes. We found that metabolic stress increased MS1 expression, both at the mRNA and protein level, concurrent with activation of the c-Jun N-terminal Kinase (JNK) signalling pathway. MS1 induction by metabolic stress was blocked by both the transcription inhibitor actinomycin D and a JNK inhibitor, suggesting that activation of the JNK pathway during metabolic stress in cardiac myocytes leads to transcriptional induction of MS1. MS1 was also found to be an efficient JNK substrate in vitro, with a major JNK phosphorylation site identified at Thr-62. In addition, MS1 was found to co-precipitate with JNK, and inspection of the amino acid sequence upstream of the phosphorylation site, at Thr-62, revealed a putative Mitogen-Activated Protein Kinase (MAPK) binding site. Taken together, these data identify MS1 as a likely transcriptional and post-translational target for the JNK pathway in cardiac myocytes subjected to metabolic stress.
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33
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Wang Y, Cui R, Zhang X, Qiao Y, Liu X, Chang Y, Yu Y, Sun F, Wang J. SIRT1 increases YAP- and MKK3-dependent p38 phosphorylation in mouse liver and human hepatocellular carcinoma. Oncotarget 2017; 7:11284-98. [PMID: 26824501 PMCID: PMC4905473 DOI: 10.18632/oncotarget.7022] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/13/2016] [Indexed: 12/19/2022] Open
Abstract
Both oncoprotein and tumor-suppressor activity have been reported for SIRTUIN1 (SIRT1) and p38 in many types of cancer. The effect of SIRT1 on p38 phosphorylation (p-p38) remains controversial and may be organ- and cell-specific. We found that SIRT1 is essential for maintaining liver size and weight in mice. SIRT1 levels were elevated in human HCC compared to adjacent normal liver tissue, and its expression correlated positively with p-p38 levels. Additionally, SIRT1-activated p38 increased liver cancer malignancy. SIRT1 increased phosphorylation and nuclear accumulation of p38, possibly by increasing MKK3 expression. SIRT1 also induced YAP expression, which in turn increased MKK3 transcription. Positive correlations between SIRT1, YAP, MKK3, and p-p38 levels indicate that blocking their activity may prove helpful in treating HCC.
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Affiliation(s)
- Yulan Wang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Ran Cui
- Department of Oncology, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Xiao Zhang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Yongxia Qiao
- School of Public Health, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Xiangfan Liu
- Faculty of Medical Laboratory Science, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Yefei Chang
- Department of Clinical Laboratory Medicine, Third People's Hospital of Yunnan Province, Kunming, 650011, Yunnan Province, China
| | - Yongchun Yu
- Shanghai Municipal Hospital of Traditional Chinese Medicine Affiliated to Shanghai TCM University, Shanghai, 200071, China
| | - Fenyong Sun
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Jiayi Wang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China.,Advanced Institute of Translational Medicine, Tongji University, Shanghai, 200092, China
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34
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Han MS, Lee YM, Kim SW, Kim KM, Lee T, Lee W, Kwon OK, Lee S, Bae JS. Role of moesin in HMGB1-stimulated severe inflammatory responses. Thromb Haemost 2017; 114:350-63. [DOI: 10.1160/th14-11-0969] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 02/25/2015] [Indexed: 11/05/2022]
Abstract
SummarySepsis is a life-threatening condition that arises when the body’s response to infection causes systemic inflammation. High-mobility group box 1 (HMGB1), as a late mediator of sepsis, enhances hyper-permeability, and it is therefore a therapeutic target. Despite extensive research into the underlying mechanisms of sepsis, the target molecules controlling vascular leakage remain largely unknown. Moesin is a cytoskeletal protein involved in cytoskeletal changes and para-cellular gap formation. The objectives of this study were to determine the roles of moesin in HMGB1-mediated vascular hyperpermeability and inflammatory responses and to investigate the mechanisms of action underlying these responses. Using siRNA knockdown of moesin expression in primary human umbilical vein endothelial cells (HUVECs), moesin was found to be required in HMGB1-induced F-actin rearrangement, hyperpermeability, and inflammatory responses. The mechanisms involved in moesin phosphorylation were analysed by blocking the binding of the HMGB1 receptor (RAGE) and inhibiting the Rho and MAPK pathways. HMGB1-treated HUVECs exhibited an increase in Thr558 phosphorylation of moesin. Circulating levels of moesin were measured in patients admitted to the intensive care unit with sepsis, severe sepsis, and septic shock; these patients showed significantly higher levels of moesin than healthy controls, which was strongly correlated with disease severity. High blood moesin levels were also observed in cecal ligation and puncture (CLP)-induced sepsis in mice. Administration of blocking moesin antibodies attenuated CLP-induced septic death. Collectively, our findings demonstrate that the HMGB1-RAGE-moesin axis can elicit severe inflammatory responses, suggesting it to be a potential target for the development of diagnostics and therapeutics for sepsis.
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35
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Chen Q, Wang Y, Chen B, Zhang C, Wang L, Li J. Using propensity scores to predict the kinases of unannotated phosphopeptides. Knowl Based Syst 2017. [DOI: 10.1016/j.knosys.2017.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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36
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Enders TA, Frick EM, Strader LC. An Arabidopsis kinase cascade influences auxin-responsive cell expansion. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:68-81. [PMID: 28710770 PMCID: PMC5605409 DOI: 10.1111/tpj.13635] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 06/27/2017] [Accepted: 06/30/2017] [Indexed: 05/02/2023]
Abstract
Mitogen-activated protein kinase (MPK) cascades are conserved mechanisms of signal transduction across eukaryotes. Despite the importance of MPK proteins in signaling events, specific roles for many Arabidopsis MPK proteins remain unknown. Multiple studies have suggested roles for MPK signaling in a variety of auxin-related processes. To identify MPK proteins with roles in auxin response, we screened mpk insertional alleles and identified mpk1-1 as a mutant that displays hypersensitivity in auxin-responsive cell expansion assays. Further, mutants defective in the upstream MAP kinase kinase MKK3 also display hypersensitivity in auxin-responsive cell expansion assays, suggesting that this MPK cascade affects auxin-influenced cell expansion. We found that MPK1 interacts with and phosphorylates ROP BINDING PROTEIN KINASE 1 (RBK1), a protein kinase that interacts with members of the Rho-like GTPases from Plants (ROP) small GTPase family. Similar to mpk1-1 and mkk3-1 mutants, rbk1 insertional mutants display auxin hypersensitivity, consistent with a possible role for RBK1 downstream of MPK1 in influencing auxin-responsive cell expansion. We found that RBK1 directly phosphorylates ROP4 and ROP6, supporting the possibility that RBK1 effects on auxin-responsive cell expansion are mediated through phosphorylation-dependent modulation of ROP activity. Our data suggest a MKK3 • MPK1 • RBK1 phosphorylation cascade that may provide a dynamic module for altering cell expansion.
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Affiliation(s)
| | | | - Lucia C. Strader
- Correspondence: Lucia Strader (), Department of Biology; Washington University in St. Louis; 1 Brookings Drive; St. Louis, MO 63130; USA, Phone: 314-935-3298, Fax: 314-935-4432
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37
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Gomez-Gutierrez P, Rubio-Martinez J, Perez JJ. Identification of Potential Small Molecule Binding Pockets in p38α MAP Kinase. J Chem Inf Model 2017; 57:2566-2574. [DOI: 10.1021/acs.jcim.7b00439] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Patricia Gomez-Gutierrez
- Allinky
Biopharma, Madrid Scientific Park, Faraday, 7, 28049 Madrid, Spain
- Department
of Chemical Engineering, Universitat Politecnica de Catalunya, ETSEIB. Av. Diagonal, 647, 08028 Barcelona, Spain
| | - Jaime Rubio-Martinez
- Department
of Physical Chemistry, Faculty of Chemistry, Universitat de Barcelona and Institut de Recerca en Quimica Teorica i Computacional (IQTCUB), Marti i Franques 1-3, 08028 Barcelona, Spain
| | - Juan J. Perez
- Department
of Chemical Engineering, Universitat Politecnica de Catalunya, ETSEIB. Av. Diagonal, 647, 08028 Barcelona, Spain
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A simple optogenetic MAPK inhibitor design reveals resonance between transcription-regulating circuitry and temporally-encoded inputs. Nat Commun 2017; 8:15017. [PMID: 28497795 PMCID: PMC5437309 DOI: 10.1038/ncomms15017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 02/20/2017] [Indexed: 12/31/2022] Open
Abstract
Engineering light-sensitive protein regulators has been a tremendous multidisciplinary challenge. Optogenetic regulators of MAPKs, central nodes of cellular regulation, have not previously been described. Here we present OptoJNKi, a light-regulated JNK inhibitor based on the AsLOV2 light-sensor domain using the ubiquitous FMN chromophore. OptoJNKi gene-transfer allows optogenetic applications, whereas protein delivery allows optopharmacology. Development of OptoJNKi suggests a design principle for other optically regulated inhibitors. From this, we generate Optop38i, which inhibits p38MAPK in intact illuminated cells. Neurons are known for interpreting temporally-encoded inputs via interplay between ion channels, membrane potential and intracellular calcium. However, the consequences of temporal variation of JNK-regulating trophic inputs, potentially resulting from synaptic activity and reversible cellular protrusions, on downstream targets are unknown. Using OptoJNKi, we reveal maximal regulation of c-Jun transactivation can occur at unexpectedly slow periodicities of inhibition depending on the inhibitor's subcellular location. This provides evidence for resonance in metazoan JNK-signalling circuits. Light-sensitive regulators of protein kinases could offer valuable insights into intracellular signalling. Here the authors design an optogenetic inhibitor of c-Jun N-terminal kinase (JNK) and show evidence for resonance in JNK signalling circuits in neurons, and use the same design principle to develop an inhibitor for p38MAPK.
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Influence of Nitric Oxide generated through microwave plasma on L6 skeletal muscle cell myogenesis via oxidative signaling pathways. Sci Rep 2017; 7:542. [PMID: 28373641 PMCID: PMC5427886 DOI: 10.1038/s41598-017-00154-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 02/13/2017] [Indexed: 02/04/2023] Open
Abstract
Myogenic precursors are myoblasts that have a potency to differentiate into muscle fibers on injury and maintain the regenerative power of skeletal muscle. However, the roles of exogenous nitric oxide (NO) in muscle development and myoblast differentiation are largely unknown. Therefore, in this study, we examined the effects of exogenous NO generated by a microwave plasma torch on rat myoblastic L6 cell proliferation and differentiation. We observed that the differentiation of L6 myogenic precursor cells into myotubes was significantly enhanced after NO treatment. The expression of the myogenesis marker proteins and mRNA level, such as myoD, myogenin, and myosin heavy chain (MHC), as well as the cyclic guanosine monophosphate (cGMP) level, were significantly increased after the NO treatment, without creating toxicity. Moreover, we observed that the oxidative stress signaling [extracellular-signal-regulated kinase (Erks), and Adenosine monophosphate-activated protein kinase (AMPK)] phosphorylation was higher in NO treated cells than in the control cells [without NO treatment]. Therefore, these results reveal the exogenous NO role in regulating myoblast differentiation through the oxidative stress signaling pathway. Through this work, we can suggest that exogenous NO can help in cell differentiation and tissue regeneration, which provides new possibilities for plasma medicine.
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40
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Jung H, Kim DO, Byun JE, Kim WS, Kim MJ, Song HY, Kim YK, Kang DK, Park YJ, Kim TD, Yoon SR, Lee HG, Choi EJ, Min SH, Choi I. Thioredoxin-interacting protein regulates haematopoietic stem cell ageing and rejuvenation by inhibiting p38 kinase activity. Nat Commun 2016; 7:13674. [PMID: 27929088 PMCID: PMC5155146 DOI: 10.1038/ncomms13674] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 10/25/2016] [Indexed: 01/11/2023] Open
Abstract
Ageing is a natural process in living organisms throughout their lifetime, and most elderly people suffer from ageing-associated diseases. One suggested way to tackle such diseases is to rejuvenate stem cells, which also undergo ageing. Here we report that the thioredoxin-interacting protein (TXNIP)-p38 mitogen-activated protein kinase (p38) axis regulates the ageing of haematopoietic stem cells (HSCs), by causing a higher frequency of long-term HSCs, lineage skewing, a decrease in engraftment, an increase in reactive oxygen species and loss of Cdc42 polarity. TXNIP inhibits p38 activity via direct interaction in HSCs. Furthermore, cell-penetrating peptide (CPP)-conjugated peptide derived from the TXNIP-p38 interaction motif inhibits p38 activity via this docking interaction. This peptide dramatically rejuvenates aged HSCs in vitro and in vivo. Our findings suggest that the TXNIP-p38 axis acts as a regulatory mechanism in HSC ageing and indicate the potent therapeutic potential of using CPP-conjugated peptide to rejuvenate aged HSCs.
The processes regulating the ageing of stem cells are not clearly defined. Here, the authors report that in haematopoietic stem cells (HSC) thioredoxin-interacting protein, known to regulate the cell cycle, binds to p38 mitogen-activated protein kinase and regulates HSC ageing and rejuvenation.
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Affiliation(s)
- Haiyoung Jung
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Dong Oh Kim
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Jae-Eun Byun
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Biochemistry, School of Life Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Won Sam Kim
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Mi Jeong Kim
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Hae Young Song
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Young Kwan Kim
- Scripps Korea Antibody Institute, 1 Kangwondaehak-gil, Chuncheon 24341, Republic of Korea
| | - Du-Kyeong Kang
- Bioenergy and Biochemical Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Young-Jun Park
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Tae-Don Kim
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Suk Ran Yoon
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Hee Gu Lee
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Biomolecular Science, University of Science and Technology, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Eun-Ji Choi
- Department of Hematology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Sang-Hyun Min
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), 80 Chumbokro Dong-gu 41061, Daegu, Republic of Korea
| | - Inpyo Choi
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Yuseong-gu, Daejeon 34113, Republic of Korea
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41
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Dory M, Doleschall Z, Nagy SK, Ambrus H, Mészáros T, Barnabás B, Dóczi R. Kinase-Associated Phosphoisoform Assay: a novel candidate-based method to detect specific kinase-substrate phosphorylation interactions in vivo. BMC PLANT BIOLOGY 2016; 16:204. [PMID: 27655033 PMCID: PMC5031308 DOI: 10.1186/s12870-016-0894-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/12/2016] [Indexed: 05/30/2023]
Abstract
BACKGROUND Protein kinases are important components of signalling pathways, and kinomes have remarkably expanded in plants. Yet, our knowledge of kinase substrates in plants is scarce, partly because tools to analyse protein phosphorylation dynamically are limited. Here we describe Kinase-Associated Phosphoisoform Assay, a flexible experimental method for directed experiments to study specific kinase-substrate interactions in vivo. The concept is based on the differential phosphoisoform distribution of candidate substrates transiently expressed with or without co-expression of activated kinases. Phosphorylation status of epitope-tagged proteins is subsequently detected by high-resolution capillary isoelectric focusing coupled with nanofluidic immunoassay, which is capable of detecting subtle changes in isoform distribution. RESULTS The concept is validated by showing phosphorylation of the known mitogen-activated protein kinase (MAPK) substrate, ACS6, by MPK6. Next, we demonstrate that two transcription factors, WUS and AP2, both of which are shown to be master regulators of plant development by extensive genetic studies, exist in multiple isoforms in plant cells and are phosphorylated by activated MAPKs. CONCLUSION As plant development flexibly responds to environmental conditions, phosphorylation of developmental regulators by environmentally-activated kinases may participate in linking external cues to developmental regulation. As a counterpart of advances in unbiased screening methods to identify potential protein kinase substrates, such as phosphoproteomics and computational predictions, our results expand the candidate-based experimental toolkit for kinase research and provide an alternative in vivo approach to existing in vitro methodologies.
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Affiliation(s)
- Magdalena Dory
- Department of Plant Cell Biology, Centre for Agricultural Research of the Hungarian Academy of Sciences, H-2462, Brunszvik u. 2, Martonvásár, Hungary
| | - Zoltán Doleschall
- Department of Pathogenetics, National Institute of Oncology, H-1122, Ráth György u. 7-9, Budapest, Hungary
| | - Szilvia K. Nagy
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, H-1094, Tűzoltó u. 37-47, Budapest, Hungary
| | - Helga Ambrus
- Department of Plant Cell Biology, Centre for Agricultural Research of the Hungarian Academy of Sciences, H-2462, Brunszvik u. 2, Martonvásár, Hungary
| | - Tamás Mészáros
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, H-1094, Tűzoltó u. 37-47, Budapest, Hungary
- Research Group for Technical Analytical Chemistry, Hungarian Academy of Sciences - Budapest University of Technology and Economics, H-1111, Szt. Gellért tér 4, Budapest, Hungary
| | - Beáta Barnabás
- Department of Plant Cell Biology, Centre for Agricultural Research of the Hungarian Academy of Sciences, H-2462, Brunszvik u. 2, Martonvásár, Hungary
| | - Róbert Dóczi
- Department of Plant Cell Biology, Centre for Agricultural Research of the Hungarian Academy of Sciences, H-2462, Brunszvik u. 2, Martonvásár, Hungary
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42
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Xu H, Watanabe KA, Zhang L, Shen QJ. WRKY transcription factor genes in wild rice Oryza nivara. DNA Res 2016; 23:311-23. [PMID: 27345721 PMCID: PMC4991837 DOI: 10.1093/dnares/dsw025] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 05/18/2016] [Indexed: 11/26/2022] Open
Abstract
The WRKY transcription factor family is one of the largest gene families involved in plant development and stress response. Although many WRKY genes have been studied in cultivated rice (Oryza sativa), the WRKY genes in the wild rice species Oryza nivara, the direct progenitor of O. sativa, have not been studied. O. nivara shows abundant genetic diversity and elite drought and disease resistance features. Herein, a total of 97 O. nivara WRKY (OnWRKY) genes were identified. RNA-sequencing demonstrates that OnWRKY genes were generally expressed at higher levels in the roots of 30-day-old plants. Bioinformatic analyses suggest that most of OnWRKY genes could be induced by salicylic acid, abscisic acid, and drought. Abundant potential MAPK phosphorylation sites in OnWRKYs suggest that activities of most OnWRKYs can be regulated by phosphorylation. Phylogenetic analyses of OnWRKYs support a novel hypothesis that ancient group IIc OnWRKYs were the original ancestors of only some group IIc and group III WRKYs. The analyses also offer strong support that group IIc OnWRKYs containing the HVE sequence in their zinc finger motifs were derived from group Ia WRKYs. This study provides a solid foundation for the study of the evolution and functions of WRKY genes in O. nivara.
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Affiliation(s)
- Hengjian Xu
- School of Life Sciences, Shandong University of Technology, Zibo 255000, Shandong Province, People's Republic of China School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Kenneth A Watanabe
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Liyuan Zhang
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Qingxi J Shen
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
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43
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Carey HA, Bronisz A, Cabrera J, Hildreth BE, Cuitiño M, Fu Q, Ahmad A, Toribio RE, Ostrowski MC, Sharma SM. Failure to Target RANKL Signaling Through p38-MAPK Results in Defective Osteoclastogenesis in the Microphthalmia Cloudy-Eyed Mutant. J Cell Physiol 2016. [PMID: 26218069 DOI: 10.1002/jcp.25108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Microphthalmia-associated transcription factor (MITF) is a basic helix-loop-helix leucine zipper family factor that is essential for terminal osteoclast differentiation. Previous work demonstrates that phosphorylation of MITF by p38 MAPK downstream of Receptor Activator of NFkB Ligand (RANKL) signaling is necessary for MITF activation in osteoclasts. The spontaneous Mitf cloudy eyed (ce) allele results in production of a truncated MITF protein that lacks the leucine zipper and C-terminal end. Here we show that the Mitf(ce) allele leads to a dense bone phenotype in neonatal mice due to defective osteoclast differentiation. In response to RANKL stimulation, in vitro osteoclast differentiation was impaired in myeloid precursors derived from neonatal or adult Mitf(ce/ce) mice. The loss of the leucine zipper domain in Mitf(ce/ce) mice does not interfere with the recruitment of MITF/PU.1 complexes to target promoters. Further, we have mapped the p38 MAPK docking site within the region deleted in Mitf(ce). This interaction is necessary for the phosphorylation of MITF by p38 MAPK. Site-directed mutations in the docking site interfered with the interaction between MITF and its co-factors FUS and BRG1. MITF-ce fails to recruit FUS and BRG1 to target genes, resulting in decreased expression of target genes and impaired osteoclast function. These results highlight the crucial role of signaling dependent MITF/p38 MAPK interactions in osteoclast differentiation.
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Affiliation(s)
- Heather A Carey
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Agnieszka Bronisz
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jennifer Cabrera
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Blake E Hildreth
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, Ohio.,College of Veterinary Medicine, The Ohio State University, Columbus, Ohio
| | - Maria Cuitiño
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Qi Fu
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Asrar Ahmad
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Ramiro E Toribio
- College of Veterinary Medicine, The Ohio State University, Columbus, Ohio
| | - Michael C Ostrowski
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Sudarshana M Sharma
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, Ohio
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44
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Wei G, Xi W, Nussinov R, Ma B. Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell. Chem Rev 2016; 116:6516-51. [PMID: 26807783 DOI: 10.1021/acs.chemrev.5b00562] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
All soluble proteins populate conformational ensembles that together constitute the native state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the distributions of the states on the energy landscape are determined by statistical thermodynamics; however, they are optimized to perform their biological functions. In this review we briefly describe advances in free energy landscape studies of protein conformational ensembles. Experimental (nuclear magnetic resonance, small-angle X-ray scattering, single-molecule spectroscopy, and cryo-electron microscopy) and computational (replica-exchange molecular dynamics, metadynamics, and Markov state models) approaches have made great progress in recent years. These address the challenging characterization of the highly flexible and heterogeneous protein ensembles. We focus on structural aspects of protein conformational distributions, from collective motions of single- and multi-domain proteins, intrinsically disordered proteins, to multiprotein complexes. Importantly, we highlight recent studies that illustrate functional adjustment of protein conformational ensembles in the crowded cellular environment. We center on the role of the ensemble in recognition of small- and macro-molecules (protein and RNA/DNA) and emphasize emerging concepts of protein dynamics in enzyme catalysis. Overall, protein ensembles link fundamental physicochemical principles and protein behavior and the cellular network and its regulation.
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Affiliation(s)
- Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University , Shanghai, P. R. China
| | - Wenhui Xi
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University , Shanghai, P. R. China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute , Frederick, Maryland 21702, United States.,Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University , Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute , Frederick, Maryland 21702, United States
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45
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Oruganty K, Talevich EE, Neuwald AF, Kannan N. Identification and classification of small molecule kinases: insights into substrate recognition and specificity. BMC Evol Biol 2016; 16:7. [PMID: 26738562 PMCID: PMC4702295 DOI: 10.1186/s12862-015-0576-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 12/21/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Many prokaryotic kinases that phosphorylate small molecule substrates, such as antibiotics, lipids and sugars, are evolutionarily related to Eukaryotic Protein Kinases (EPKs). These Eukaryotic-Like Kinases (ELKs) share the same overall structural fold as EPKs, but differ in their modes of regulation, substrate recognition and specificity-the sequence and structural determinants of which are poorly understood. RESULTS To better understand the basis for ELK specificity, we applied a Bayesian classification procedure designed to identify sequence determinants responsible for functional divergence. This reveals that a large and diverse family of aminoglycoside kinases, characterized members of which are involved in antibiotic resistance, fall into major sub-groups based on differences in putative substrate recognition motifs. Aminoglycoside kinase substrate specificity follows simple rules of alternating hydroxyl and amino groups that is strongly correlated with variations at the DFG + 1 position. CONCLUSIONS Substrate specificity determining features in small molecule kinases are mostly confined to the catalytic core and can be identified based on quantitative sequence and crystal structure comparisons.
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Affiliation(s)
- Krishnadev Oruganty
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
| | - Eric E Talevich
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA.
| | - Andrew F Neuwald
- Institute for Genome Sciences and Department of Biochemistry & Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD, 21201, USA.
| | - Natarajan Kannan
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.
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46
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Ras oncogene-mediated progressive silencing of extracellular superoxide dismutase in tumorigenesis. BIOMED RESEARCH INTERNATIONAL 2015; 2015:780409. [PMID: 26550576 PMCID: PMC4624945 DOI: 10.1155/2015/780409] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/31/2015] [Indexed: 02/03/2023]
Abstract
Extracellular superoxide dismutase (SOD3) is a secreted enzyme that uses superoxide anion as a substrate in a dismutase reaction that results in the formation of hydrogen peroxide. Both of these reactive oxygen species affect growth signaling in cells. Although SOD3 has growth-supporting characteristics, the expression of SOD3 is downregulated in epithelial cancer cells. In the current work, we studied the mechanisms regulating SOD3 expression in vitro using thyroid cell models representing different stages of thyroid cancer. We demonstrate that a low level of RAS activation increases SOD3 mRNA synthesis that then gradually decreases with increasing levels of RAS activation and the decreasing degree of differentiation of the cancer cells. Our data indicate that SOD3 regulation can be divided into two classes. The first class involves RAS–driven reversible regulation of SOD3 expression that can be mediated by the following mechanisms: RAS GTPase regulatory genes that are responsible for SOD3 self-regulation; RAS-stimulated p38 MAPK activation; and RAS-activated increased expression of the mir21 microRNA, which inversely correlates with sod3 mRNA expression. The second class involves permanent silencing of SOD3 mediated by epigenetic DNA methylation in cells that represent more advanced cancers. Therefore, the work suggests that SOD3 belongs to the group of ras oncogene-silenced genes.
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47
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Bardwell AJ, Bardwell L. Two hydrophobic residues can determine the specificity of mitogen-activated protein kinase docking interactions. J Biol Chem 2015; 290:26661-74. [PMID: 26370088 DOI: 10.1074/jbc.m115.691436] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Indexed: 11/06/2022] Open
Abstract
MAPKs bind to many of their upstream regulators and downstream substrates via a short docking motif (the D-site) on their binding partner. MAPKs that are in different families (e.g. ERK, JNK, and p38) can bind selectively to D-sites in their authentic substrates and regulators while discriminating against D-sites in other pathways. Here we demonstrate that the short hydrophobic region at the distal end of the D-site plays a critical role in determining the high selectivity of JNK MAPKs for docking sites in their cognate MAPK kinases. Changing just 1 or 2 key hydrophobic residues in this submotif is sufficient to turn a weak JNK-binding D-site into a strong one, or vice versa. These specificity-determining differences are also found in the D-sites of the ETS family transcription factors Elk-1 and Net. Moreover, swapping two hydrophobic residues between these D-sites switches the relative efficiency of Elk-1 and Net as substrates for ERK versus JNK, as predicted. These results provide new insights into docking specificity and suggest that this specificity can evolve rapidly by changes to just 1 or 2 amino acids.
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Affiliation(s)
- A Jane Bardwell
- From the Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, California 92697
| | - Lee Bardwell
- From the Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, California 92697
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48
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Tian T, Harding A. How MAP kinase modules function as robust, yet adaptable, circuits. Cell Cycle 2015; 13:2379-90. [PMID: 25483189 DOI: 10.4161/cc.29349] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Genetic and biochemical studies have revealed that the diversity of cell types and developmental patterns evident within the animal kingdom is generated by a handful of conserved, core modules. Core biological modules must be robust, able to maintain functionality despite perturbations, and yet sufficiently adaptable for random mutations to generate phenotypic variation during evolution. Understanding how robust, adaptable modules have influenced the evolution of eukaryotes will inform both evolutionary and synthetic biology. One such system is the MAP kinase module, which consists of a 3-tiered kinase circuit configuration that has been evolutionarily conserved from yeast to man. MAP kinase signal transduction pathways are used across eukaryotic phyla to drive biological functions that are crucial for life. Here we ask the fundamental question, why do MAPK modules follow a conserved 3-tiered topology rather than some other number? Using computational simulations, we identify a fundamental 2-tiered circuit topology that can be readily reconfigured by feedback loops and scaffolds to generate diverse signal outputs. When this 2-kinase circuit is connected to proximal input kinases, a 3-tiered modular configuration is created that is both robust and adaptable, providing a biological circuit that can regulate multiple phenotypes and maintain functionality in an uncertain world. We propose that the 3-tiered signal transduction module has been conserved through positive selection, because it facilitated the generation of phenotypic variation during eukaryotic evolution.
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Affiliation(s)
- Tianhai Tian
- a School of Mathematical Science; Monash University; Victoria, Australia
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49
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Fang L, Lu W, Choi HH, Yeung SCJ, Tung JY, Hsiao CD, Fuentes-Mattei E, Menter D, Chen C, Wang L, Wang J, Lee MH. ERK2-Dependent Phosphorylation of CSN6 Is Critical in Colorectal Cancer Development. Cancer Cell 2015; 28:183-97. [PMID: 26267535 PMCID: PMC4560098 DOI: 10.1016/j.ccell.2015.07.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 01/17/2015] [Accepted: 07/10/2015] [Indexed: 12/25/2022]
Abstract
Biomarkers for predicting prognosis are critical to treating colorectal cancer (CRC) patients. We found that CSN6, a subunit of COP9 signalosome, is overexpressed in CRC samples and that CSN6 overexpression is correlated with poor patient survival. Mechanistic studies revealed that CSN6 is deregulated by epidermal growth factor receptor (EGFR) signaling, in which ERK2 binds directly to CSN6 Leu163/Val165 and phosphorylates CSN6 at Ser148. Furthermore, CSN6 regulated β-Trcp and stabilized β-catenin expression by blocking the ubiquitin-proteasome pathway, thereby promoting CRC development. High CSN6 expression was positively correlated with ERK2 activation and β-catenin overexpression in CRC samples, and inhibiting CSN6 stability with cetuximab reduced colon cancer growth. Taken together, our study's findings indicate that the deregulation of β-catenin by ERK2-activated CSN6 is important for CRC development.
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Affiliation(s)
- Lekun Fang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Weisi Lu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China; Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Program in Genes and Development, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA
| | - Hyun Ho Choi
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sai-Ching J Yeung
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jung-Yu Tung
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Enrique Fuentes-Mattei
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chuangqi Chen
- Department of Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Lei Wang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Jianping Wang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China.
| | - Mong-Hong Lee
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Program in Cancer Biology, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA; Program in Genes and Development, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA.
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Piala AT, Humphreys JM, Goldsmith EJ. MAP kinase modules: the excursion model and the steps that count. Biophys J 2015; 107:2006-15. [PMID: 25418086 DOI: 10.1016/j.bpj.2014.09.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/12/2014] [Accepted: 09/16/2014] [Indexed: 01/04/2023] Open
Abstract
MAP kinase modules propagate diverse extracellular signals to downstream effectors. The two dual phosphorylation reactions catalyzed by the modules are thought to control the switch behavior of the pathway. Here we review recent approaches to understand these pathways through signal-to-response studies in cells and in vitro. These data are reconciled with physical models as well as predictions made on mathematical and theoretical grounds. Biochemical analysis has shown recently that the dual phosphorylation reactions catalyzed by MAP kinase modules are sequential at both levels of the cascade. The observed order of phosphorylation events suggests an excursion from the Ser/Thr kinase activity of the MAP3K into Tyr kinase activity of the central dual specificity MAP2K. How the order of events might be encoded in the structures and interactions is discussed. The ordered mechanism confirms predictions that reactions should be sequential to generate the steep signal-to-response curves and delayed responses observed in cells.
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Affiliation(s)
- Alexander T Piala
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - John M Humphreys
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Elizabeth J Goldsmith
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.
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