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Scotter EL, Cao MC, Jansson D, Rustenhoven J, Smyth LCD, Aalderink MC, Siemens A, Fan V, Wu J, Mee EW, Faull RLM, Dragunow M. The amyotrophic lateral sclerosis-linked protein TDP-43 regulates interleukin-6 cytokine production by human brain pericytes. Mol Cell Neurosci 2022; 123:103768. [PMID: 36038081 DOI: 10.1016/j.mcn.2022.103768] [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: 04/13/2021] [Revised: 08/02/2022] [Accepted: 08/12/2022] [Indexed: 12/30/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal movement disorder involving degeneration of motor neurons through dysfunction of the RNA-binding protein TDP-43. Pericytes, the perivascular cells of the blood-brain, blood-spinal cord, and blood-CSF barriers also degenerate in ALS. Indeed, pericytes are among the earliest cell types to show gene expression changes in pre-symptomatic animal models of ALS. This suggests that pericyte degeneration precedes neurodegeneration and may involve pericyte cell-autonomous TDP-43 dysfunction. Here we determined the effect of TDP-43 dysfunction in human brain pericytes on interleukin 6 (IL-6), a critical secreted inflammatory mediator reported to be regulated by TDP 43. Primary human brain pericytes were cultured from biopsy tissue from epilepsy surgeries and TDP-43 was silenced using siRNA. TDP-43 silencing of pericytes stimulated with pro-inflammatory cytokines, interleukin-1β or tumour necrosis factor alpha, robustly suppressed the induction of IL-6 transcript and protein. IL-6 regulation by TDP-43 did not involve the assembly of TDP-43 nuclear splicing bodies, and did not occur via altered splicing of IL6. Instead, transcriptome-wide analysis by RNA-Sequencing identified a poison exon in the IL6 destabilising factor HNRNPD (AUF1) as a splicing target of TDP-43. Our data support a model whereby TDP-43 silencing favours destabilisation of IL6 mRNA, via enhanced AU-rich element-mediated decay by HNRNP/AUF1. This suggests that cell-autonomous deficits in TDP-43 function in human brain pericytes would suppress their production of IL-6. Given the importance of the blood-brain and blood-spinal cord barriers in maintaining motor neuron health, TDP-43 in human brain pericytes may represent a cellular target for ALS therapeutics.
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Affiliation(s)
- Emma L Scotter
- Centre for Brain Research, University of Auckland, New Zealand; School of Biological Sciences, University of Auckland, New Zealand; Department of Pharmacology and Clinical Pharmacology, University of Auckland, New Zealand.
| | - Maize C Cao
- Centre for Brain Research, University of Auckland, New Zealand; School of Biological Sciences, University of Auckland, New Zealand; Department of Pharmacology and Clinical Pharmacology, University of Auckland, New Zealand.
| | - Deidre Jansson
- Centre for Brain Research, University of Auckland, New Zealand; School of Biological Sciences, University of Auckland, New Zealand; Department of Pharmacology and Clinical Pharmacology, University of Auckland, New Zealand.
| | - Justin Rustenhoven
- Centre for Brain Research, University of Auckland, New Zealand; Department of Pharmacology and Clinical Pharmacology, University of Auckland, New Zealand.
| | - Leon C D Smyth
- Centre for Brain Research, University of Auckland, New Zealand; Department of Pharmacology and Clinical Pharmacology, University of Auckland, New Zealand.
| | - Miranda C Aalderink
- Centre for Brain Research, University of Auckland, New Zealand; Department of Pharmacology and Clinical Pharmacology, University of Auckland, New Zealand.
| | - Andrew Siemens
- Centre for Brain Research, University of Auckland, New Zealand; Department of Pharmacology and Clinical Pharmacology, University of Auckland, New Zealand.
| | - Vicky Fan
- Bioinformatics Institute, University of Auckland, Auckland, New Zealand.
| | - Jane Wu
- Centre for Brain Research, University of Auckland, New Zealand; Department of Anatomy and Medical Imaging, University of Auckland, New Zealand.
| | - Edward W Mee
- Department of Neurosurgery, Auckland City Hospital, Auckland, New Zealand.
| | - Richard L M Faull
- Centre for Brain Research, University of Auckland, New Zealand; Department of Anatomy and Medical Imaging, University of Auckland, New Zealand.
| | - Mike Dragunow
- Centre for Brain Research, University of Auckland, New Zealand; Department of Pharmacology and Clinical Pharmacology, University of Auckland, New Zealand.
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2
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Pellegrini E, Palencia A, Braun L, Kapp U, Bougdour A, Belrhali H, Bowler MW, Hakimi MA. Structural Basis for the Subversion of MAP Kinase Signaling by an Intrinsically Disordered Parasite Secreted Agonist. Structure 2016; 25:16-26. [PMID: 27889209 PMCID: PMC5222587 DOI: 10.1016/j.str.2016.10.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/21/2016] [Accepted: 10/25/2016] [Indexed: 01/07/2023]
Abstract
The causative agent of toxoplasmosis, the intracellular parasite Toxoplasma gondii, delivers a protein, GRA24, into the cells it infects that interacts with the mitogen-activated protein (MAP) kinase p38α (MAPK14), leading to activation and nuclear translocation of the host kinase and a subsequent inflammatory response that controls the progress of the parasite. The purification of a recombinant complex of GRA24 and human p38α has allowed the molecular basis of this activation to be determined. GRA24 is shown to be intrinsically disordered, binding two kinases that act independently, and is the only factor required to bypass the canonical mitogen-activated protein kinase activation pathway. An adapted kinase interaction motif (KIM) forms a highly stable complex that competes with cytoplasmic regulatory partners. In addition, the recombinant complex forms a powerful in vitro tool to evaluate the specificity and effectiveness of p38α inhibitors that have advanced to clinical trials, as it provides a hitherto unavailable stable and highly active form of p38α. Toxoplasmosis controls its host immune response via a protein effector, GRA24 A recombinant complex of GRA24 and MAPK p38α demonstrates how the protein works An adapted KIM domain ensures activation and a sustained inflammatory response The recombinant complex is useful in the evaluation of p38 inhibitors
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Affiliation(s)
- Erika Pellegrini
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France; Unit for Virus Host Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Andrés Palencia
- IAB, Team Host-Pathogen Interactions & Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38700 Grenoble, France
| | - Laurence Braun
- IAB, Team Host-Pathogen Interactions & Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38700 Grenoble, France
| | - Ulrike Kapp
- Structural Biology Group, European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Alexandre Bougdour
- IAB, Team Host-Pathogen Interactions & Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38700 Grenoble, France
| | - Hassan Belrhali
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France; Unit for Virus Host Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France.
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France; Unit for Virus Host Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France.
| | - Mohamed-Ali Hakimi
- IAB, Team Host-Pathogen Interactions & Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38700 Grenoble, France.
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Strigolactones: a novel class of phytohormones that inhibit the growth and survival of breast cancer cells and breast cancer stem-like enriched mammosphere cells. Breast Cancer Res Treat 2012; 134:1041-55. [PMID: 22476848 DOI: 10.1007/s10549-012-1992-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 02/09/2012] [Indexed: 01/12/2023]
Abstract
Several naturally occurring phytohormones have shown enormous potential in the prevention and treatment of variety of different type of cancers. Strigolactones (SLs) are a novel class of plant hormones produced in roots and regulate new above ground shoot branching, by inhibiting self-renewal of undifferentiated meristem cells. Here, we study the effects of six synthetic SL analogs on breast cancer cell lines growth and survival. We show that SL analogs are able to inhibit proliferation and induce apoptosis of breast cancer cells but to a much lesser extent "non-cancer" lines. Given the therapeutic problem of cancer recurrence which is hypothesized to be due to drug resistant cancer stem cells, we also tested the ability of SL analogs to inhibit the growth of mammosphere cultures that are typically enriched with cancer stem-like cells. We show that SLs are potent inhibitors of self-renewal and survival of breast cancer cell lines grown as mammospheres and even a short exposure leads to irreversible effects on mammosphere dissociation and cell death. Immunoblot analysis revealed that SLs analogs induce activation of the stress response mediated by both P38 and JNK1/2 MAPK modules and inhibits PI3K/AKT activation. Taken together this study indicates that SLs may be promising anticancer agents whose activities may be achieved through modulation of stress and survival signaling pathways.
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Pillai VB, Sundaresan NR, Samant SA, Wolfgeher D, Trivedi CM, Gupta MP. Acetylation of a conserved lysine residue in the ATP binding pocket of p38 augments its kinase activity during hypertrophy of cardiomyocytes. Mol Cell Biol 2011; 31:2349-63. [PMID: 21444723 PMCID: PMC3133249 DOI: 10.1128/mcb.01205-10] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Accepted: 03/04/2011] [Indexed: 12/22/2022] Open
Abstract
Like phosphorylation, acetylation of lysine residues within a protein is considered a biologically relevant modification that controls the activity of target proteins. During stress of cells, massive protein acetylation takes place. Here, we show that p38 mitogen-activated protein kinase (MAPK), which controls many biological functions during stress, is reversibly acetylated by PCAF/p300 and HDAC3. We identified two acetylated lysine residues, K152 and K53, located in the substrate binding domain and in the ATP-binding pocket of p38, respectively. Acetylation of lysine 53 enhanced the activity of p38 by increasing its affinity for ATP binding. The enhanced acetylation and activation of p38 were found to be in parallel with reduced intracellular ATP levels in cardiomyocytes under stress, as well as in vivo models of cardiac hypertrophy. Thus, our data show, for the first time, that p38 activity is critically regulated by, in addition to phosphorylation, reversible acetylation of a lysine residue, which is conserved in other kinases, implying the possibility of a similar mechanism regulating their activity.
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Affiliation(s)
| | | | | | - Don Wolfgeher
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois
| | - Chinmay M. Trivedi
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Mahesh P. Gupta
- Department of Surgery
- Committee on Cellular and Molecular Physiology, University of Chicago Medical Center, Chicago, Illinois 60637
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Akella R, Min X, Wu Q, Gardner KH, Goldsmith EJ. The third conformation of p38α MAP kinase observed in phosphorylated p38α and in solution. Structure 2011; 18:1571-8. [PMID: 21134636 DOI: 10.1016/j.str.2010.09.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2010] [Revised: 09/01/2010] [Accepted: 09/22/2010] [Indexed: 01/22/2023]
Abstract
MAPKs engage substrates, MAP2Ks, and phosphatases via a docking groove in the C-terminal domain of the kinase. Prior crystallographic studies on the unphosphorylated MAPKs p38α and ERK2 defined the docking groove and revealed long-range conformational changes affecting the activation loop and active site of the kinase induced by peptide. Solution NMR data presented here for unphosphorylated p38α with a MEK3b-derived peptide (p38α/pepMEK3b) validate these findings. Crystallograhic data from doubly phosphorylated active p38α (p38α/T∗GY∗/pepMEK3b) reveal a structure similar to unphosphorylated p38α/MEK3b, and distinct from phosphorylated p38γ (p38γ/T∗GY∗) and ERK2 (ERK2/T∗EY∗). The structure supports the idea that MAP kinases adopt three distinct conformations: unphosphorylated, phosphorylated, and a docking peptide-induced form.
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Affiliation(s)
- Radha Akella
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
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6
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Moïse N, Dingar D, Mamarbachi AM, Villeneuve LR, Farhat N, Gaestel M, Khairallah M, Allen BG. Characterization of a novel MK3 splice variant from murine ventricular myocardium. Cell Signal 2010; 22:1502-12. [PMID: 20570725 PMCID: PMC5300773 DOI: 10.1016/j.cellsig.2010.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 05/14/2010] [Accepted: 05/29/2010] [Indexed: 11/30/2022]
Abstract
p38 MAP kinase (MAPK) isoforms alpha, beta, and gamma, are expressed in the heart. p38alpha appears pro-apoptotic whereas p38beta is pro-hypertrophic. The mechanisms mediating these divergent effects are unknown; hence elucidating the downstream signaling of p38 should further our understanding. Downstream effectors include MAPK-activated protein kinase (MK)-3, which is expressed in many tissues including skeletal muscles and heart. We cloned full-length MK3 (MK3.1, 384 aa) and a novel splice variant (MK3.2, 266 aa) from murine heart. For MK3.2, skipping of exons 8 and 9 resulted in a frame-shift in translation of the first 85 base pairs of exon 10 followed by an in-frame stop codon. Of 3 putative phosphorylation sites for p38 MAPK, only Thr-203 remained functional in MK3.2. In addition, MK3.2 lacked nuclear localization and export signals. Quantitative real-time PCR confirmed the presence of these mRNA species in heart and skeletal muscle; however, the relative abundance of MK3.2 differed. Furthermore, whereas total MK3 mRNA was increased, the relative abundance of MK3.2 mRNA decreased in MK2(-/-) mice. Immunoblotting revealed 2 bands of MK3 immunoreactivity in ventricular lysates. Ectopically expressed MK3.1 localized to the nucleus whereas MK3.2 was distributed throughout the cell; however, whereas MK3.1 translocated to the cytoplasm in response to osmotic stress, MK3.2 was degraded. The p38alpha/beta inhibitor SB203580 prevented the degradation of MK3.2. Furthermore, replacing Thr-203 with alanine prevented the loss of MK3.2 following osmotic stress, as did pretreatment with the proteosome inhibitor MG132. In vitro, GST-MK3.1 was strongly phosphorylated by p38alpha and p38beta, but a poor substrate for p38delta and p38gamma. GST-MK3.2 was poorly phosphorylated by p38alpha and p38beta and not phosphorylated by p38delta and p38gamma. Hence, differential regulation of MKs may, in part, explain diverse downstream effects mediated by p38 signaling.
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Affiliation(s)
- Nadège Moïse
- Montreal Heart Institute, Université de Montréal, Montreal, Quebec, Canada H3C 3J7
- Department of Biochemistry, Université de Montréal, Montreal, Quebec, Canada H3C 3J7
| | - Dharmendra Dingar
- Montreal Heart Institute, Université de Montréal, Montreal, Quebec, Canada H3C 3J7
- Department of Biochemistry, Université de Montréal, Montreal, Quebec, Canada H3C 3J7
| | - Aida M. Mamarbachi
- Montreal Heart Institute, Université de Montréal, Montreal, Quebec, Canada H3C 3J7
| | - Louis R. Villeneuve
- Montreal Heart Institute, Université de Montréal, Montreal, Quebec, Canada H3C 3J7
| | - Nada Farhat
- Montreal Heart Institute, Université de Montréal, Montreal, Quebec, Canada H3C 3J7
| | - Matthias Gaestel
- Institute of Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Maya Khairallah
- Montreal Heart Institute, Université de Montréal, Montreal, Quebec, Canada H3C 3J7
- Department of Biochemistry, Université de Montréal, Montreal, Quebec, Canada H3C 3J7
| | - Bruce G. Allen
- Montreal Heart Institute, Université de Montréal, Montreal, Quebec, Canada H3C 3J7
- Department of Biochemistry, Université de Montréal, Montreal, Quebec, Canada H3C 3J7
- Department of Medicine, Université de Montréal, Montreal, Quebec, Canada H3C 3J7
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada H3G 1Y6
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7
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Xu F, Du P, Shen H, Hu H, Wu Q, Xie J, Yu L. Correlated mutation analysis on the catalytic domains of serine/threonine protein kinases. PLoS One 2009; 4:e5913. [PMID: 19526051 PMCID: PMC2690836 DOI: 10.1371/journal.pone.0005913] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2009] [Accepted: 05/11/2009] [Indexed: 01/15/2023] Open
Abstract
Background Protein kinases (PKs) have emerged as the largest family of signaling proteins in eukaryotic cells and are involved in every aspect of cellular regulation. Great progresses have been made in understanding the mechanisms of PKs phosphorylating their substrates, but the detailed mechanisms, by which PKs ensure their substrate specificity with their structurally conserved catalytic domains, still have not been adequately understood. Correlated mutation analysis based on large sets of diverse sequence data may provide new insights into this question. Methodology/Principal Findings Statistical coupling, residue correlation and mutual information analyses along with clustering were applied to analyze the structure-based multiple sequence alignment of the catalytic domains of the Ser/Thr PK family. Two clusters of highly coupled sites were identified. Mapping these positions onto the 3D structure of PK catalytic domain showed that these two groups of positions form two physically close networks. We named these two networks as θ-shaped and γ-shaped networks, respectively. Conclusions/Significance The θ-shaped network links the active site cleft and the substrate binding regions, and might participate in PKs recognizing and interacting with their substrates. The γ-shaped network is mainly situated in one side of substrate binding regions, linking the activation loop and the substrate binding regions. It might play a role in supporting the activation loop and substrate binding regions before catalysis, and participate in product releasing after phosphoryl transfer. Our results exhibit significant correlations with experimental observations, and can be used as a guide to further experimental and theoretical studies on the mechanisms of PKs interacting with their substrates.
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Affiliation(s)
- Feng Xu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
- * E-mail: (FX); (LY)
| | - Pan Du
- Biomedical Informatics Center, Northwestern University, Chicago, Illinois, United States of America
| | - Hongbo Shen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Hairong Hu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Qi Wu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jun Xie
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Long Yu
- Institute of Biomedical Sciences, Fudan University, Shanghai, China
- * E-mail: (FX); (LY)
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Akella R, Moon TM, Goldsmith EJ. Unique MAP Kinase binding sites. BIOCHIMICA ET BIOPHYSICA ACTA 2008; 1784:48-55. [PMID: 18068683 PMCID: PMC2266891 DOI: 10.1016/j.bbapap.2007.09.016] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Revised: 08/22/2007] [Accepted: 09/21/2007] [Indexed: 12/20/2022]
Abstract
Map kinases are drug targets for autoimmune disease, cancer, and apoptosis-related diseases. Drug discovery efforts have developed MAP kinase inhibitors directed toward the ATP binding site and neighboring "DFG-out" site, both of which are targets for inhibitors of other protein kinases. On the other hand, MAP kinases have unique substrate and small molecule binding sites that could serve as inhibition sites. The substrate and processing enzyme D-motif binding site is present in all MAP kinases, and has many features of a good small molecule binding site. Further, the MAP kinase p38alpha has a binding site near its C-terminus discovered in crystallographic studies. Finally, the MAP kinases ERK2 and p38alpha have a second substrate binding site, the FXFP binding site that is exposed in active ERK2 and the D-motif peptide induced conformation of MAP kinases. Crystallographic evidence of these latter two binding sites is presented.
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Affiliation(s)
- Radha Akella
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-8816, USA
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Goldsmith EJ, Akella R, Min X, Zhou T, Humphreys JM. Substrate and docking interactions in serine/threonine protein kinases. Chem Rev 2007; 107:5065-81. [PMID: 17949044 PMCID: PMC4012561 DOI: 10.1021/cr068221w] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Elizabeth J Goldsmith
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8816, USA.
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10
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Abramczyk O, Rainey MA, Barnes R, Martin L, Dalby KN. Expanding the repertoire of an ERK2 recruitment site: cysteine footprinting identifies the D-recruitment site as a mediator of Ets-1 binding. Biochemistry 2007; 46:9174-86. [PMID: 17658891 PMCID: PMC2897722 DOI: 10.1021/bi7002058] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many substrates of ERK2 contain a D-site, a sequence recognized by ERK2 that is used to promote catalysis. Despite lacking a canonical D-site, the substrate Ets-1 is displaced from ERK2 by peptides containing one. This suggests that Ets-1 may contain a novel or cryptic D-site. To investigate this possibility a protein footprinting strategy was developed to elucidate ERK2-ligand interactions. Using this approach, single cysteine reporters were placed in the D-recruitment site (DRS) of ERK2 and the resulting ERK2 proteins subjected to alkylation by iodoacetamide. The ability of residues 1-138 of Ets-1 to protect the cysteines from alkylation was determined. The pattern of protection observed is consistent with Ets-1 occupying a hydrophobic binding site within the DRS of ERK2. Significantly, a peptide derived from the D-site of Elk-1, which is known to bind the DRS, exhibits a similar pattern of cysteine protection. This analysis expands the repertoire of the DRS on ERK2 and suggests that other targeting sequences remain to be identified. Furthermore, cysteine-footprinting is presented as a useful way to interrogate protein-ligand interactions at the resolution of a single amino acid.
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Affiliation(s)
- Olga Abramczyk
- Division of Medicinal Chemistry, University of Texas at Austin, Texas 78712
| | - Mark A. Rainey
- Graduate Program in Molecular Biology, University of Texas at Austin, Texas 78712
| | - Richard Barnes
- Graduate Program in Biochemistry, University of Texas at Austin, Texas 78712
| | - Lance Martin
- Department of Biochemistry, Stanford University, Stanford, California 94305
| | - Kevin N. Dalby
- Division of Medicinal Chemistry, University of Texas at Austin, Texas 78712
- Graduate Program in Molecular Biology, University of Texas at Austin, Texas 78712
- Graduate Program in Biochemistry, University of Texas at Austin, Texas 78712
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11
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Callaway KA, Rainey MA, Riggs AF, Abramczyk O, Dalby KN. Properties and Regulation of a Transiently Assembled ERK2·Ets-1 Signaling Complex†. Biochemistry 2006; 45:13719-33. [PMID: 17105191 DOI: 10.1021/bi0610451] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ERK2 is a proline-directed protein kinase that displays a high specificity for a single threonine (Thr-38) on the substrate Ets-1, which lies within the consensus sequence 36phi-chi-Thr-Pro39 (where phi is typically a small hydrophobic residue and chi appears to be unrestricted). Thr-38 lies in a long flexible N-terminal tail (residues 1-52), which also contains a second potential phosphorylation site, Ser-26. How Ets-1 binds ERK2 to promote the phosphorylation of Thr-38 while simultaneously discriminating against the phosphorylation of Ser-26 is unclear. To delineate the details of the molecular recognition of Ets-1 by ERK2, the binding of various mutants and truncations of Ets-1 were analyzed by fluorescence anisotropy. The data that were obtained support the notion that the N-terminal tail contains a previously unrecognized docking site that promotes the phosphorylation of Thr-38. This new docking site helps assemble the complex of Ets-1 and ERK2 and makes a similar contribution to the stabilization of the complex as does the pointed domain of Ets-1. The in vitro activation of ERK2 by MKK1 induces a large conformational transition of the activation segment (DFG-APE), but neither induces self-association of ERK2 nor destabilizes the stability of the ERK2.Ets-1 complex. This latter observation suggests that interactions intrinsic to the active site are not important for complex assembly, a notion further supported by the observation that the substitution of a number of different amino acids for Pro-39 does not destabilize the complex. Mutagenesis of ERK2 within loop 13 suggests that Ets-1 binds the substrate-binding groove. These data suggest that ERK2 uses two weak docking interactions to specifically assemble the complex, perhaps in doing so denying Ser-26 access to the active site. Displacement of residues 1-138 of Ets-1 (EtsDelta138) from ERK2 by the peptide N-QKGKPRDLELPLSPSL-C, derived from Elk-1, suggests that Ets-1 engages the D-recruitment site (beta7-beta8 reverse turn and the alphaD-alphaE helix) of ERK2. Displacement of EtsDelta138 from ERK2 by the peptide N-AKLSFQFPS-C derived from Elk-1 shows that EtsDelta138 communicates with the F-recruitment site of ERK2 also.
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Affiliation(s)
- Kari A Callaway
- Graduate Program in Biochemistry, University of Texas, Austin, Texas 78712-0252, USA
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Zhou T, Sun L, Humphreys J, Goldsmith EJ. Docking interactions induce exposure of activation loop in the MAP kinase ERK2. Structure 2006; 14:1011-9. [PMID: 16765894 DOI: 10.1016/j.str.2006.04.006] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Revised: 04/17/2006] [Accepted: 04/19/2006] [Indexed: 01/28/2023]
Abstract
MAP kinases bind activating kinases, phosphatases, and substrates through docking interactions. Here, we report a 1.9 A crystallographic analysis of inactive ERK2 bound to a "D motif" docking peptide (pepHePTP) derived from hematopoietic tyrosine phosphatase, a negative regulator of ERK2. In this complex, the complete D motif interaction defined by mutagenic analysis is observed, including extensive electrostatic interactions with the "CD" site of the kinase. Large conformational changes occur in the activation loop where the dual phosphorylation sites, which are buried in the inactive form of ERK2, become exposed to solvent in the complex. Similar conformational changes occur in a complex between ERK2 and a MEK2 (MAP/ERK kinase-2)-derived D motif peptide (pepMEK2). D motif peptides are known to bind homologous loci in the MAP kinases p38alpha and JNK1, also inducing conformational changes in these enzymes. However, the binding interactions and conformational changes are unique to each, thus contributing to specificity among MAP kinases.
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Affiliation(s)
- Tianjun Zhou
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
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13
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Zhou H, Zheng M, Chen J, Xie C, Kolatkar AR, Zarubin T, Ye Z, Akella R, Lin S, Goldsmith EJ, Han J. Determinants that control the specific interactions between TAB1 and p38alpha. Mol Cell Biol 2006; 26:3824-34. [PMID: 16648477 PMCID: PMC1489000 DOI: 10.1128/mcb.26.10.3824-3834.2006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous studies have revealed that transforming growth factor-beta-activated protein kinase 1 (TAB1) interacts with p38alpha and induces p38alpha autophosphorylation. Here, we examine the sequence requirements in TAB1 and p38alpha that drive their interaction. Deletion and point mutations in TAB1 reveal that a proline residue in the C terminus of TAB1 (Pro412) is necessary for its interaction with p38alpha. Furthermore, a cryptic D-domain-like docking site was identified adjacent to the N terminus of Pro412, putting Pro412 in the phi(B)+3 position of the docking site. Through mutational analysis, we found that the previously identified hydrophobic docking groove in p38alpha is involved in this interaction, whereas the CD domain and ED domain are not. Furthermore, chimeric analysis with p38beta (which does not bind to TAB1) revealed a previously unidentified locus of p38alpha comprising Thr218 and Ile275 that is essential for specific binding of p38alpha to TAB1. Converting either of these residues to the corresponding amino acid of p38beta abolishes p38alpha interaction with TAB1. These p38alpha mutants still can be fully activated by p38alpha upstream activating kinase mitogen-activated protein kinase kinase 6, but their basal activity and activation in response to some extracellular stimuli are reduced. Adjacent to Thr218 and Ile275 is a site where large conformational changes occur in the presence of docking-site peptides derived from p38alpha substrates and activators. This suggests that TAB1-induced autophosphorylation of p38alpha results from conformational changes that are similar but unique to those seen in p38alpha interactions with its substrates and activating kinases.
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Affiliation(s)
- Huamin Zhou
- The Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, Fujian, China
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14
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Lukas SM, Kroe RR, Wildeson J, Peet GW, Frego L, Davidson W, Ingraham RH, Pargellis CA, Labadia ME, Werneburg BG. Catalysis and function of the p38 alpha.MK2a signaling complex. Biochemistry 2004; 43:9950-60. [PMID: 15287722 DOI: 10.1021/bi049508v] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The p38 mitogen-activated protein kinase (p38) pathway is required for the production of proinflammatory cytokines (TNFalpha and IL-1) that mediate the chronic inflammatory phases of several autoimmune diseases. Potent p38 inhibitors, such as the slow tight-binding inhibitor BIRB 796, have recently been reported to block the production of TNFalpha and IL-1beta. Here we analyze downstream signaling complexes and molecular mechanisms, to provide new insight into the function of p38 signaling complexes and the development of novel inhibitors of the p38 pathway. Catalysis, signaling functions, and molecular interactions involving p38alpha and one of its downstream signaling partners, mitogen-activated protein kinase-activated protein kinase 2 (MK2), have been explored by steady-state kinetics, surface plasmon resonance, isothermal calorimetry, and stopped-flow fluorescence. Functional 1/1 signaling complexes (Kd = 1-100 nM) composed of activated and nonactivated forms of p38alpha and a splice variant of MK2 (MK2a) were characterized. Catalysis of MK2a phosphorylation and activation by p38alpha was observed to be efficient under conditions where substrate is saturating (kcat(app) = 0.05-0.3 s(-1)) and nonsaturating (kcat(app)/KM(app) = 1-3 x 10(6) M(-1) s(-1)). Specific interactions between the carboxy-terminal residues of MK2a (370-400) and p38alpha precipitate formation of a high-affinity complex (Kd = 20 nM); the p38alpha-dependent MK2a phosphorylation reaction was inhibited by the 30-amino acid docking domain peptide of MK2a (IC50 = 60 nM). The results indicate that the 30-amino acid docking domain peptide of MK2a is required for the formation of a tight, functional p38alpha.MK2a complex, and that perturbation of the tight-docking interaction between these signaling partners prevents the phosphorylation of MK2a. The thermodynamic and steady-state kinetic characterization of the p38alpha.MK2a signaling complex has led to a clear understanding of complex formation, catalysis, and function on the molecular level.
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Affiliation(s)
- Susan M Lukas
- Department of Immunology and Inflammation, Research and Development Center, Boehringer Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, Connecticut 06877, USA
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15
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Zhang J, Zhou B, Zheng CF, Zhang ZY. A bipartite mechanism for ERK2 recognition by its cognate regulators and substrates. J Biol Chem 2003; 278:29901-12. [PMID: 12754209 DOI: 10.1074/jbc.m303909200] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mitogen-activated protein (MAP) kinases control gene expression in response to extracellular stimuli and exhibit exquisite specificity for their cognate regulators and substrates. We performed a structure-based mutational analysis of ERK2 to identify surface areas that are important for recognition of its interacting proteins. We show that binding and activation of MKP3 by ERK2 involve two distinct protein-protein interaction sites in ERK2. Thus, the common docking (CD) site composed of Glu-79, Tyr-126, Arg-133, Asp-160, Tyr-314, Asp-316, and Asp-319 are important for high affinity MKP3 binding but not essential for ERK2-induced MKP3 activation. MKP3 activation requires residues Tyr-111, Thr-116, Leu-119, Lys-149, Arg-189, Trp-190, Glu-218, Arg-223, Lys-229, and His-230 in the ERK2 substrate-binding region, located distal to the common docking site. Interestingly, many of the residues important for MKP3 recognition are also used for Elk1 binding and phosphorylation. In addition to the shared residues, there are also residues that are unique to each target recognition. There is evidence indicating that the CD site and the substrate-binding region defined here are also utilized for MEK1 recognition, and indeed, we demonstrate that the binding of MKP3, Elk1, and MEK1 to ERK2 is mutually exclusive. Taken together, our data suggest that the efficiency and fidelity of ERK2 signaling is achieved by a bipartite recognition process. In this model, one part of the ERK2-binding proteins (e.g. the kinase interaction motif sequence) docks to the CD site located on the back side of the ERK2 catalytic pocket for high affinity association, whereas the interaction of the substrate-binding region with another structural element (e.g. the FXFP motif in MKP3 and Elk1) may not only stabilize binding but also provide contacts crucial for modulating the activity and/or specificity of ERK2 target molecules.
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Affiliation(s)
- Jialin Zhang
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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16
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Shi Y, Gaestel M. In the cellular garden of forking paths: how p38 MAPKs signal for downstream assistance. Biol Chem 2002; 383:1519-36. [PMID: 12452429 DOI: 10.1515/bc.2002.173] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitogen-activated protein kinases (MAPKs) are evolutionarily conserved enzymes which connect cell-surface receptors to regulatory targets within cells and convert receptor signals into various outputs. In mammalian cells, four distinct MAPKs have been identified: the extracellular signal-related kinases (ERK)-1/2, the c-jun N-terminal kinases or stress-activated protein kinases 1 (JNK1/2/3, or SAPK1s), the p38 MAPKs (p38 alpha/beta/gamma/delta, or SAPK2s), and the ERK5 or big MAP kinase 1 (BMK1). The p38 MAPK cascade is activated by stress or cytokines and leads to phosphorylation of its central elements, the p38 MAPKs. Downstream of p38 MAPKs there is a diversification and extensive branching of signalling pathways. For that reason, we will focus in this review on the different signalling events that are triggered by p38 activity, and analyse how these events contribute to specific gene expression and cellular responses.
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Affiliation(s)
- Yu Shi
- Hannover Medical School, Institute of Biochemistry, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany
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17
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Adams JL, Badger AM, Kumar S, Lee JC. p38 MAP kinase: molecular target for the inhibition of pro-inflammatory cytokines. PROGRESS IN MEDICINAL CHEMISTRY 2002; 38:1-60. [PMID: 11774793 DOI: 10.1016/s0079-6468(08)70091-2] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- J L Adams
- Smith Kline Beecham Pharmaceuticals, 709 Swedeland Road, King of Prussia, PA 19406, USA
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18
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19
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Hannigan MO, Zhan L, Ai Y, Kotlyarov A, Gaestel M, Huang CK. Abnormal migration phenotype of mitogen-activated protein kinase-activated protein kinase 2-/- neutrophils in Zigmond chambers containing formyl-methionyl-leucyl-phenylalanine gradients. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2001; 167:3953-61. [PMID: 11564814 DOI: 10.4049/jimmunol.167.7.3953] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Time-lapsed video microscopy and confocal imaging were used to study the migration of wild-type (WT) and mitogen-activated protein kinase-activated protein kinase 2 (MK2-/-) mouse neutrophils in Zigmond chambers containing fMLP gradients. Confocal images of polarized WT neutrophils showed an intracellular gradient of phospho-MK2 from the anterior to the posterior region of the neutrophils. Compared with WT neutrophils, MK2-/- neutrophils showed a partial loss of directionality but higher migration speed. Immunoblotting experiments showed a lower protein level of p38 mitogen-activated protein kinase and a loss of fMLP-induced extracellular signal-related kinase phosphorylation in MK2-/- neutrophils. These results suggest that MK2 plays an important role in the regulation of neutrophil migration and may also affect other signaling molecules.
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Affiliation(s)
- M O Hannigan
- Department of Pathology, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030, USA
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20
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Harper SJ, LoGrasso P. Signalling for survival and death in neurones: the role of stress-activated kinases, JNK and p38. Cell Signal 2001; 13:299-310. [PMID: 11369511 DOI: 10.1016/s0898-6568(01)00148-6] [Citation(s) in RCA: 232] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The pathways involved in neuronal survival or death have been extensively studied mainly in cell lines. Recent evidence has suggested that activation of the stress activated pathways, jun N-terminal kinase (JNK) and p38 may play important roles in neuronal cell death or regeneration. In this review we will discuss these pahtways in detail. We will examine the evidence that these pathways are important in neuronal cell death. Finally we will review the evidence that inhibitors of these pathways have a neuroprotective effect both in vitro and in vivo.
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Affiliation(s)
- S J Harper
- Department of Pharmacology, Merck Sharp and Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Essex CM20 2QR, Harlow, UK.
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21
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Waas WF, Lo HH, Dalby KN. The kinetic mechanism of the dual phosphorylation of the ATF2 transcription factor by p38 mitogen-activated protein (MAP) kinase alpha. Implications for signal/response profiles of MAP kinase pathways. J Biol Chem 2001; 276:5676-84. [PMID: 11069918 DOI: 10.1074/jbc.m008787200] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mitogen-activated protein kinases (MAPKs) are a family of enzymes conserved among eukaryotes that regulate cellular activities in response to numerous external signals. They are the terminal component of a three-kinase cascade that is evolutionarily conserved and whose arrangement appears to offer considerable flexibility in encompassing the diverse biological situations for which they are employed. Although multistep protein phosphorylation within mitogen-activated protein kinase (MAPK) cascades can dramatically influence the sensitivity of signal propagation, an investigation of the mechanism of multisite phosphorylation by a MAPK has not been reported. Here we report a kinetic examination of the phosphorylation of Thr-69 and Thr-71 of the glutathione S-transferase fusion protein of the trans-activation domain of activating transcription factor-2 (GST-ATF2-(1-115)) by p38 MAPKalpha (p38alpha) as a model system for the phosphorylation of ATF2 by p38alpha. Our experiments demonstrated that GST-ATF2-(1-115) is phosphorylated in a two-step distributive mechanism, where p38alpha dissociates from GST-ATF2-(1-115) after the initial phosphorylation of either Thr-69 or Thr-71. Whereas p38alpha showed similar specificity for Thr-71 and Thr-69 in the unphosphorylated protein, it displayed a marked difference in specificity toward the mono-phosphoisomers. Phosphorylation of Thr-71 had no significant effect on the rate of Thr-69 phosphorylation, but Thr-69 phosphorylation reduced the specificity, k(cat)/K(M), of p38alpha for Thr-71 by approximately 40-fold. Computer simulation of the mechanism suggests that the activation of ATF2 by p38alpha in vivo is essentially Michaelian and provides insight into how the kinetics of a two-step distributive mechanism can be adapted to modulate effectively the sensitivity of a signal transduction pathway. This work also suggests that whereas MAPKs utilize docking interactions to bind substrates, they can be weak and transient in nature, providing just enough binding energy to promote the phosphorylation of a specific substrate.
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Affiliation(s)
- W F Waas
- Division of Medicinal Chemistry, University of Texas, Austin, Texas 78712, USA
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22
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Hawkins J, Zheng S, Frantz B, LoGrasso P. p38 map kinase substrate specificity differs greatly for protein and peptide substrates. Arch Biochem Biophys 2000; 382:310-3. [PMID: 11068883 DOI: 10.1006/abbi.2000.2005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- J Hawkins
- Department of Molecular Design and Diversity, Merck Research Laboratories, Rahway, New Jersey 07065, USA
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23
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Sharrocks AD, Yang SH, Galanis A. Docking domains and substrate-specificity determination for MAP kinases. Trends Biochem Sci 2000; 25:448-53. [PMID: 10973059 DOI: 10.1016/s0968-0004(00)01627-3] [Citation(s) in RCA: 367] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Signalling specificity in eukaryotic cells is maintained by several mechanisms. One mechanism by which mitogen-activated protein (MAP) kinases ensure their specificity of action is by interacting with their substrates through docking domains. These docking domains recruit the kinases to the correct substrates and enhance their fidelity and efficiency of action. Additional specificity determinants in the substrates serve to enhance the specificity of substrate phosphorylation by MAP kinases further.
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Affiliation(s)
- A D Sharrocks
- School of Biological Sciences, University of Manchester, 2.205 Stopford Building, Oxford Road, Manchester, UK M13 9PT.
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