1
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Sinigaglia K, Cherian A, Du Q, Lacovich V, Vukić D, Melicherová J, Linhartova P, Zerad L, Stejskal S, Malik R, Prochazka J, Bondurand N, Sedláček R, O'Connell MA, Keegan LP. An ADAR1 dsRBD3-PKR kinase domain interaction on dsRNA inhibits PKR activation. Cell Rep 2024; 43:114618. [PMID: 39146181 DOI: 10.1016/j.celrep.2024.114618] [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: 12/04/2023] [Revised: 05/30/2024] [Accepted: 07/25/2024] [Indexed: 08/17/2024] Open
Abstract
Adar null mutant mouse embryos die with aberrant double-stranded RNA (dsRNA)-driven interferon induction, and Adar Mavs double mutants, in which interferon induction is prevented, die soon after birth. Protein kinase R (Pkr) is aberrantly activated in Adar Mavs mouse pup intestines before death, intestinal crypt cells die, and intestinal villi are lost. Adar Mavs Eifak2 (Pkr) triple mutant mice rescue all defects and have long-term survival. Adenosine deaminase acting on RNA 1 (ADAR1) and PKR co-immunoprecipitate from cells, suggesting PKR inhibition by direct interaction. AlphaFold studies on an inhibitory PKR dsRNA binding domain (dsRBD)-kinase domain interaction before dsRNA binding and on an inhibitory ADAR1 dsRBD3-PKR kinase domain interaction on dsRNA provide a testable model of the inhibition. Wild-type or editing-inactive human ADAR1 expressed in A549 cells inhibits activation of endogenous PKR. ADAR1 dsRNA binding is required for, but is not sufficient for, PKR inhibition. Mutating the ADAR1 dsRBD3-PKR contact prevents co-immunoprecipitation, ADAR1 inhibition of PKR activity, and co-localization of ADAR1 and PKR in cells.
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Affiliation(s)
- Ketty Sinigaglia
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Anna Cherian
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Qiupei Du
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Valentina Lacovich
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia
| | - Dragana Vukić
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Janka Melicherová
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Pavla Linhartova
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia
| | - Lisa Zerad
- Laboratory of Embryology and Genetics of Human Malformation, Imagine Institute, INSERM UMR 1163, Université de Paris Cité, 75015 Paris, France
| | - Stanislav Stejskal
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia
| | - Radek Malik
- Laboratory of Epigenetic Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czechia
| | - Jan Prochazka
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czechia
| | - Nadège Bondurand
- Laboratory of Embryology and Genetics of Human Malformation, Imagine Institute, INSERM UMR 1163, Université de Paris Cité, 75015 Paris, France
| | - Radislav Sedláček
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czechia
| | - Mary A O'Connell
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia.
| | - Liam P Keegan
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia.
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2
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Hesler S, Angeliadis M, Husain B, Cole JL. Contribution of dsRBD2 to PKR Activation. ACS OMEGA 2021; 6:11367-11374. [PMID: 34056292 PMCID: PMC8153938 DOI: 10.1021/acsomega.1c00343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
Protein kinase R (PKR) is a key pattern recognition receptor of the innate immune pathway. PKR is activated by double-stranded RNA (dsRNA) that is often produced during viral genome replication and transcription. PKR contains two tandem double-stranded RNA binding domains at the N-terminus, dsRBD1 and dsRBD2, and a C-terminal kinase domain. In the canonical model for activation, RNAs that bind multiple PKRs induce dimerization of the kinase domain that promotes an active conformation. However, there is evidence that dimerization of the kinase domain is not sufficient to mediate activation and PKR activation is modulated by the RNA-binding mode. dsRBD2 lacks most of the consensus RNA-binding residues, and it has been suggested to function as a modulator of PKR activation. Here, we demonstrate that dsRBD2 regulates PKR activation and identify the N-terminal helix as a critical region for modulating kinase activity. Mutations in dsRBD2 that have minor effects on overall dsRNA-binding affinity strongly inhibit the activation of PKR by dsRNA. These mutations also inhibit RNA-independent PKR activation. These data support a model where dsRBD2 has evolved to function as a regulator of the kinase.
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Affiliation(s)
- Stephen Hesler
- Department
of Molecular and Cell Biology, University
of Connecticut, Storrs 06269, Connecticut, United States
| | - Matthew Angeliadis
- Department
of Molecular and Cell Biology, University
of Connecticut, Storrs 06269, Connecticut, United States
| | - Bushra Husain
- Department
of Molecular and Cell Biology, University
of Connecticut, Storrs 06269, Connecticut, United States
| | - James L. Cole
- Department
of Molecular and Cell Biology, University
of Connecticut, Storrs 06269, Connecticut, United States
- Department
of Chemistry, University of Connecticut, Storrs 06269, Connecticut, United States
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3
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Tong MHG, Jeeves M, Rajesh S, Ludwig C, Lenoir M, Kumar J, McClelland DM, Berditchevski F, Hubbard JA, Kenyon C, Butterworth S, Knapp S, Overduin M. Backbone resonance assignments of the catalytic and regulatory domains of Ca 2+/calmodulin-dependent protein kinase 1D. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:221-225. [PMID: 32535836 PMCID: PMC7462902 DOI: 10.1007/s12104-020-09950-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/21/2020] [Indexed: 06/11/2023]
Abstract
The CaMK subfamily of Ser/Thr kinases are regulated by calmodulin interactions with their C-terminal regions. They are exemplified by Ca2+/calmodulin dependent protein kinase 1δ which is known as CaMK1D, CaMKIδ or CKLiK. CaMK1D mediates intracellular signalling downstream of Ca2+ influx and thereby exhibits amplifications of Ca2+signals and polymorphisms that have been implicated in breast cancer and diabetes. Here we report the backbone 1H, 13C, 15N assignments of the 38 kDa human CaMK1D protein in its free state, including both the canonical bi-lobed kinase fold as well as the autoinhibitory and calmodulin binding domains.
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Affiliation(s)
- Michael H G Tong
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Sundaresan Rajesh
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Christian Ludwig
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Marc Lenoir
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Jitendra Kumar
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Darren M McClelland
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Fedor Berditchevski
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Julia A Hubbard
- Computational, Analytical and Structural Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Colin Kenyon
- Faculty of Medicine and Health Sciences, Stellenbosch University, Francie Van Zijl Dr, Parow, Cape Town, 7505, South Africa
| | - Sam Butterworth
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, M13 9PL, UK
| | - Stefan Knapp
- Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences, Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
| | - Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada.
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4
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Bou-Nader C, Gordon JM, Henderson FE, Zhang J. The search for a PKR code-differential regulation of protein kinase R activity by diverse RNA and protein regulators. RNA (NEW YORK, N.Y.) 2019; 25:539-556. [PMID: 30770398 PMCID: PMC6467004 DOI: 10.1261/rna.070169.118] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The interferon-inducible protein kinase R (PKR) is a key component of host innate immunity that restricts viral replication and propagation. As one of the four eIF2α kinases that sense diverse stresses and direct the integrated stress response (ISR) crucial for cell survival and proliferation, PKR's versatile roles extend well beyond antiviral defense. Targeted by numerous host and viral regulators made of RNA and proteins, PKR is subject to multiple layers of endogenous control and external manipulation, driving its rapid evolution. These versatile regulators include not only the canonical double-stranded RNA (dsRNA) that activates the kinase activity of PKR, but also highly structured viral, host, and artificial RNAs that exert a full spectrum of effects. In this review, we discuss our deepening understanding of the allosteric mechanism that connects the regulatory and effector domains of PKR, with an emphasis on diverse structured RNA regulators in comparison to their protein counterparts. Through this analysis, we conclude that much of the mechanistic details that underlie this RNA-regulated kinase await structural and functional elucidation, upon which we can then describe a "PKR code," a set of structural and chemical features of RNA that are both descriptive and predictive for their effects on PKR.
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Affiliation(s)
- Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | - Jackson M Gordon
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | - Frances E Henderson
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
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5
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Abstract
Detection of double-stranded RNAs (dsRNAs) is a central mechanism of innate immune defense in many organisms. We here discuss several families of dsRNA-binding proteins involved in mammalian antiviral innate immunity. These include RIG-I-like receptors, protein kinase R, oligoadenylate synthases, adenosine deaminases acting on RNA, RNA interference systems, and other proteins containing dsRNA-binding domains and helicase domains. Studies suggest that their functions are highly interdependent and that their interdependence could offer keys to understanding the complex regulatory mechanisms for cellular dsRNA homeostasis and antiviral immunity. This review aims to highlight their interconnectivity, as well as their commonalities and differences in their dsRNA recognition mechanisms.
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Affiliation(s)
- Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA; .,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
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6
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Yefidoff-Freedman R, Fan J, Yan L, Zhang Q, Dos Santos GRR, Rana S, Contreras JI, Sahoo R, Wan D, Young J, Dias Teixeira KL, Morisseau C, Halperin J, Hammock B, Natarajan A, Wang P, Chorev M, Aktas BH. Development of 1-((1,4-trans)-4-Aryloxycyclohexyl)-3-arylurea Activators of Heme-Regulated Inhibitor as Selective Activators of the Eukaryotic Initiation Factor 2 Alpha (eIF2α) Phosphorylation Arm of the Integrated Endoplasmic Reticulum Stress Response. J Med Chem 2017; 60:5392-5406. [PMID: 28590739 DOI: 10.1021/acs.jmedchem.7b00059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Heme-regulated inhibitor (HRI), an eukaryotic translation initiation factor 2 alpha (eIF2α) kinase, plays critical roles in cell proliferation, differentiation, adaptation to stress, and hemoglobin disorders. HRI phosphorylates eIF2α, which couples cellular signals, including endoplasmic reticulum (ER) stress, to translation. We previously identified 1,3-diarylureas and 1-((1,4-trans)-4-aryloxycyclohexyl)-3-arylureas (cHAUs) as specific activators of HRI that trigger the eIF2α phosphorylation arm of ER stress response as molecular probes for studying HRI biology and its potential as a druggable target. To develop drug-like cHAUs needed for in vivo studies, we undertook bioassay-guided structure-activity relationship studies and tested them in the surrogate eIF2α phosphorylation and cell proliferation assays. We further evaluated some of these cHAUs in endogenous eIF2α phosphorylation and in the expression of the transcription factor C/EBP homologous protein (CHOP) and its mRNA, demonstrating significantly improved solubility and/or potencies. These cHAUs are excellent candidates for lead optimization for development of investigational new drugs that potently and specifically activate HRI.
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Affiliation(s)
- Revital Yefidoff-Freedman
- Hematology Laboratory for Translational Research, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School , 75 Francis Street, Boston, Massachusetts 02115, United States
| | - Jing Fan
- Hematology Laboratory for Translational Research, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School , 75 Francis Street, Boston, Massachusetts 02115, United States.,Department of Orthopedics, Jiangsu Province Hospital of TCM, Nanjing University of Chinese Medicine , 155 Hanzhong Road, Nanjing, Jiangsu 210029, China
| | - Lu Yan
- Hematology Laboratory for Translational Research, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School , 75 Francis Street, Boston, Massachusetts 02115, United States
| | - Qingwen Zhang
- Hematology Laboratory for Translational Research, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School , 75 Francis Street, Boston, Massachusetts 02115, United States.,Division of Medicinal and Process Chemistry, Shanghai Institute of Pharmaceutical Industry , 1111 Zhongshan North One Road, Hongkou District, Shanghai 200437, China
| | - Guillermo Rodrigo Reis Dos Santos
- Hematology Laboratory for Translational Research, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School , 75 Francis Street, Boston, Massachusetts 02115, United States
| | - Sandeep Rana
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center , Omaha, Nebraska 68198, United States
| | - Jacob I Contreras
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center , Omaha, Nebraska 68198, United States
| | - Rupam Sahoo
- Hematology Laboratory for Translational Research, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School , 75 Francis Street, Boston, Massachusetts 02115, United States
| | - Debin Wan
- Department of Entomology and Nematology, University of California Davis Comprehensive Cancer Center, University of California , One Shields Avenue, Davis, California 95616, United States
| | - Jun Young
- Department of Entomology and Nematology, University of California Davis Comprehensive Cancer Center, University of California , One Shields Avenue, Davis, California 95616, United States
| | - Karina Luiza Dias Teixeira
- Hematology Laboratory for Translational Research, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School , 75 Francis Street, Boston, Massachusetts 02115, United States
| | - Christophe Morisseau
- Department of Entomology and Nematology, University of California Davis Comprehensive Cancer Center, University of California , One Shields Avenue, Davis, California 95616, United States
| | - Jose Halperin
- Hematology Laboratory for Translational Research, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School , 75 Francis Street, Boston, Massachusetts 02115, United States
| | - Bruce Hammock
- Department of Entomology and Nematology, University of California Davis Comprehensive Cancer Center, University of California , One Shields Avenue, Davis, California 95616, United States
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center , Omaha, Nebraska 68198, United States
| | - Peimin Wang
- Department of Orthopedics, Jiangsu Province Hospital of TCM, Nanjing University of Chinese Medicine , 155 Hanzhong Road, Nanjing, Jiangsu 210029, China
| | - Michael Chorev
- Hematology Laboratory for Translational Research, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School , 75 Francis Street, Boston, Massachusetts 02115, United States
| | - Bertal H Aktas
- Hematology Laboratory for Translational Research, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School , 75 Francis Street, Boston, Massachusetts 02115, United States
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7
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Abstract
Although the antiviral kinase PKR was originally characterized as a double-stranded RNA activated enzyme it can be stimulated by RNAs containing limited secondary structure. Single-stranded regions in such RNAs contribute to binding and activation but the mechanism is not understood. Here, we demonstrate that single-stranded RNAs bind to PKR with micromolar dissociation constants and can induce activation. Addition of a 5'-triphosphate slightly enhances binding affinity. Single-stranded RNAs also activate PKR constructs lacking the double-stranded RNA binding domain and bind to a basic region adjacent to the N-terminus of the kinase. However, the isolated kinase is not activated by and does not bind single-stranded RNA. Photocrosslinking measurements demonstrate that that the basic region interacts with RNA in the context of full length PKR. We propose that bivalent interactions with the double stranded RNA binding domain and the basic region underlie the ability of RNAs containing limited structure to activate PKR by enhancing binding affinity and thereby increasing the population of productive complexes containing two PKRs bound to a single RNA.
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8
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Auto-phosphorylation Represses Protein Kinase R Activity. Sci Rep 2017; 7:44340. [PMID: 28281686 PMCID: PMC5345052 DOI: 10.1038/srep44340] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/07/2017] [Indexed: 12/11/2022] Open
Abstract
The central role of protein kinases in controlling disease processes has spurred efforts to develop pharmaceutical regulators of their activity. A rational strategy to achieve this end is to determine intrinsic auto-regulatory processes, then selectively target these different states of kinases to repress their activation. Here we investigate auto-regulation of the innate immune effector protein kinase R, which phosphorylates the eukaryotic initiation factor 2α to inhibit global protein translation. We demonstrate that protein kinase R activity is controlled by auto-inhibition via an intra-molecular interaction. Part of this mechanism of control had previously been reported, but was then controverted. We account for the discrepancy and extend our understanding of the auto-inhibitory mechanism by identifying that auto-inhibition is paradoxically instigated by incipient auto-phosphorylation. Phosphor-residues at the amino-terminus instigate an intra-molecular interaction that enlists both of the N-terminal RNA-binding motifs of the protein with separate surfaces of the C-terminal kinase domain, to co-operatively inhibit kinase activation. These findings identify an innovative mechanism to control kinase activity, providing insight for strategies to better regulate kinase activity.
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9
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Aktas BH, Bordelois P, Peker S, Merajver S, Halperin JA. Depletion of eIF2·GTP·Met-tRNAi translation initiation complex up-regulates BRCA1 expression in vitro and in vivo. Oncotarget 2016; 6:6902-14. [PMID: 25762631 PMCID: PMC4466658 DOI: 10.18632/oncotarget.3125] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/09/2015] [Indexed: 01/27/2023] Open
Abstract
Most sporadic breast and ovarian cancers express low levels of the breast cancer susceptibility gene, BRCA1. The BRCA1 gene produces two transcripts, mRNAa and mRNAb. mRNAb, present in breast cancer but not in normal mammary epithelial cells, contains three upstream open reading frames (uORFs) in its 5′UTR and is translationally repressed. Comparable tandem uORFs are characteristically seen in mRNAs whose translational efficiency paradoxically increases when the overall translation rate is decreased due to phosphorylation of eukaryotic translation initiation factor 2 α (eIF2α). Here we show fish oil derived eicosopanthenoic acid (EPA) that induces eIF2α phosphorylation translationally up-regulates the expression of BRCA1 in human breast cancer cells. We demonstrate further that a diet rich in EPA strongly induces expression of BRCA1 in human breast cancer xenografts.
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Affiliation(s)
- Bertal H Aktas
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | - Selen Peker
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA.,Ankara University Biotechnology Institute, Ankara, Turkey
| | - Sophia Merajver
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jose A Halperin
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
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10
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Husain B, Mayo C, Cole JL. Role of the Interdomain Linker in RNA-Activated Protein Kinase Activation. Biochemistry 2015; 55:253-61. [PMID: 26678943 DOI: 10.1021/acs.biochem.5b01171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
RNA-activated protein kinase (PKR) is a key component of the interferon-induced antiviral pathway in higher eukaryotes. Upon recognition of viral dsRNA, PKR is activated via dimerization and autophosphorylation. PKR contains two N-terminal dsRNA binding domains (dsRBD) and a C-terminal kinase domain. The dsRBDs and the kinase are separated by a long, unstructured ∼80-amino acid linker in the human enzyme. The length of the N-terminal portion of the linker varies among PKR sequences, and it is completely absent in one ortholog. Here, we characterize the effects of deleting the variable region from the human enzyme to produce PKRΔV. The linker deletion results in quantitative but not qualitative changes in catalytic activity, RNA binding, and conformation. PKRΔV is somewhat more active and exhibits more cooperative RNA binding. As we previously observed for the full-length enzyme, PKRΔV is flexible in solution and adopts a range of compact and extended conformations. The conformational ensemble is biased toward compact states that might be related to weak interactions between the dsRBD and kinase domains. PKR retains RNA-induced autophosphorylation upon complete removal of the linker, indicating that the C-terminal, basic region is also not required for activity.
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Affiliation(s)
- Bushra Husain
- Department of Molecular and Cell Biology and ‡Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Christopher Mayo
- Department of Molecular and Cell Biology and ‡Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - James L Cole
- Department of Molecular and Cell Biology and ‡Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
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11
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Husain B, Hesler S, Cole JL. Regulation of PKR by RNA: formation of active and inactive dimers. Biochemistry 2015; 54:6663-72. [PMID: 26488609 DOI: 10.1021/acs.biochem.5b01046] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
PKR is a member of the eIF2α family of protein kinases that inhibit translational initiation in response to stress stimuli and functions as a key mediator of the interferon-induced antiviral response. PKR contains a dsRNA binding domain that binds to duplex regions present in viral RNAs, resulting in kinase activation and autophosphorylation. An emerging theme in the regulation of protein kinases is the allosteric linkage of dimerization and activation. The PKR kinase domain forms a back-to-back parallel dimer that is implicated in activation. We have developed a sensitive homo-Förster resonance energy transfer assay for kinase domain dimerization to directly probe the relationship among RNA binding, activation, and dimerization. In the case of perfect duplex RNAs, dimerization is correlated with activation and dsRNAs containing 30 bp or more efficiently induce kinase domain dimerization and activation. However, more complex duplex RNAs containing a 10-15 bp 2'-O-methyl RNA barrier produce kinase dimers but do not activate. Similarly, inactivating mutations within the PKR dimer interface that disrupt key electrostatic and hydrogen binding interactions fail to abolish dimerization. Our data support a model in which activating RNAs induce formation of a back-to-back parallel PKR kinase dimer whereas nonactivating RNAs either fail to induce dimerization or produce an alternative, inactive dimer configuration, providing an additional mechanism for distinguishing between host and pathogen RNA.
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Affiliation(s)
- Bushra Husain
- Department of Molecular and Cell Biology and ‡Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Stephen Hesler
- Department of Molecular and Cell Biology and ‡Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - James L Cole
- Department of Molecular and Cell Biology and ‡Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
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12
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Kalaivani R, Srinivasan N. A Gaussian network model study suggests that structural fluctuations are higher for inactive states than active states of protein kinases. MOLECULAR BIOSYSTEMS 2015; 11:1079-95. [DOI: 10.1039/c4mb00675e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein kinases participate extensively in cellular signalling. Using Gaussian normal mode analysis of kinases in active and diverse inactive forms, authors show that structural fluctuations are significantly higher in inactive forms and are localized in functionally sensitive sites.
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Affiliation(s)
- Raju Kalaivani
- Molecular Biophysics Unit
- Indian Institute of Science
- Bangalore 560012
- India
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13
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Abstract
Translation initiation plays a critical role in the regulation of cell growth and tumorigenesis. We report here that inhibiting translation initiation through induction of eIF2α phosphorylation by small-molecular-weight compounds restricts the availability of the eIF2·GTP·Met-tRNAi ternary complex and abrogates the proliferation of cancer cells in vitro and tumor growth in vivo. Restricting the availability of the ternary complex preferentially down-regulates the expression of growth-promoting proteins and up-regulates the expression of ER stress response genes in cancer cells as well as in tumors excised from either animal models of human cancer or cancer patients. These findings provide the first direct evidence for translational control of gene-specific expression by small molecules in vivo and indicate that translation initiation factors are bona fide targets for development of mechanism-specific anti-cancer agents.
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14
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Luna RE, Akabayov SR, Ziarek JJ, Wagner G. Examining weak protein-protein interactions in start codon recognition via NMR spectroscopy. FEBS J 2014; 281:1965-73. [PMID: 24393460 DOI: 10.1111/febs.12667] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 11/28/2013] [Indexed: 12/01/2022]
Abstract
Weak protein-protein interactions are critical in numerous biological processes. Unfortunately, they are difficult to characterize due to the high concentrations required for the production and detection of the complex population. The inherent sensitivity of NMR spectroscopy to the chemical environment makes it an excellent tool to tackle this problem. NMR permits the exploration of interactions over a range of affinities, yielding essential insights into dynamic biological processes. The conversion of messanger RNA to protein is one such process that requires the coordinated association of many low-affinity proteins. During start codon recognition, eukaryotic initiation factors assemble into high-order complexes that bind messanger RNA and bring it to the ribosome for decoding. Many of the structures of the eukaryotic initiation factors have been determined; however, little is known regarding the weak binary complexes formed and their structure-function mechanisms. Herein, we use start codon recognition as a model system to review the relevant NMR methods for the characterization of weak interactions and the development of small molecule inhibitors.
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Affiliation(s)
- Rafael E Luna
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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15
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Dey M, Mann BR, Anshu A, Mannan MAU. Activation of protein kinase PKR requires dimerization-induced cis-phosphorylation within the activation loop. J Biol Chem 2013; 289:5747-57. [PMID: 24338483 DOI: 10.1074/jbc.m113.527796] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Protein kinase R (PKR) functions in a plethora of cellular processes, including viral and cellular stress responses, by phosphorylating the translation initiation factor eIF2α. The minimum requirements for PKR function are homodimerization of its kinase and RNA-binding domains, and autophosphorylation at the residue Thr-446 in a flexible loop called the activation loop. We investigated the interdependence between dimerization and Thr-446 autophosphorylation using the yeast Saccharomyces cerevisiae model system. We showed that an engineered PKR that bypassed the need for Thr-446 autophosphorylation (PKR(T446∼P)-bypass mutant) could function without a key residue (Asp-266 or Tyr-323) that is essential for PKR dimerization, suggesting that dimerization precedes and stimulates activation loop autophosphorylation. We also showed that the PKR(T446∼P)-bypass mutant was able to phosphorylate eIF2α even without its RNA-binding domains. These two significant findings reveal that PKR dimerization and activation loop autophosphorylation are mutually exclusive yet interdependent processes. Also, we provide evidence that Thr-446 autophosphorylation during PKR activation occurs in a cis mechanism following dimerization.
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Affiliation(s)
- Madhusudan Dey
- From the Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211
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16
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Chen L, Aktas BH, Wang Y, He X, Sahoo R, Zhang N, Denoyelle S, Kabha E, Yang H, Freedman RY, Supko JG, Chorev M, Wagner G, Halperin JA. Tumor suppression by small molecule inhibitors of translation initiation. Oncotarget 2013; 3:869-81. [PMID: 22935625 PMCID: PMC3478463 DOI: 10.18632/oncotarget.598] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Translation initiation factors are over-expressed and/or activated in many human cancers and may contribute to their genesis and/or progression. Removal of physiologic restraints on translation initiation causes malignant transformation. Conversely, restoration of physiological restrains on translation initiation reverts malignant phenotypes. Here, we extensively characterize the anti-cancer activity of two small molecule inhibitors of translation initiation: #1181, which targets the eIF2-GTP-Met-tRNAi ternary complex, and 4EGI-1, which targets the eIF4F complex. In vitro, both molecules inhibit translation initiation, abrogate preferentially translation of mRNAs coding for oncogenic proteins, and inhibit proliferation of human cancer cells. In vivo, both #1181 and 4EGI-1 strongly inhibit growth of human breast and melanoma cancer xenografts without any apparent macroscopic- or microscopic-toxicity. Mechanistically, #1181 phosphorylates eIF2α while 4EGI-1 disrupts eIF4G/eIF4E interaction in the tumors excised from mice treated with these agents. These data indicate that inhibition of translation initiation is a new paradigm in cancer therapy.
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17
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Pindel A, Sadler A. The Role of Protein Kinase R in the Interferon Response. J Interferon Cytokine Res 2011; 31:59-70. [DOI: 10.1089/jir.2010.0099] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Agnieszka Pindel
- Centre for Cancer Research, Monash Institute of Medical Research, Monash University, Melbourne, Australia
| | - Anthony Sadler
- Centre for Cancer Research, Monash Institute of Medical Research, Monash University, Melbourne, Australia
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18
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Sadler AJ. Orchestration of the activation of protein kinase R by the RNA-binding motif. J Interferon Cytokine Res 2010; 30:195-204. [PMID: 20377414 DOI: 10.1089/jir.2010.0005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The protein kinase R (PKR) constitutes part of the host antiviral response. PKR activation is regulated by the N-terminus of protein, which encodes tandem RNA-binding motifs (RBMs). The full capabilities of RBMs from PKR and other proteins have surpassed the narrow specificities initially determined as merely binding double-stranded RNA. Recognition of the increased affinity of the RBM for additional RNA species has established an immunological distinction by which PKR can detect exogenous RNAs, as well as identified PKR-mediated expression of specific endogenous genes. Furthermore, as RBMs also mediate interactions with other proteins, including PKR itself, this motif connects PKR to the broader RNA metabolism. Given the fundamental importance of protein-RNA interactions, not only in the innate immune response to intracellular pathogens, but also to coordinate the cellular replication machinery, there is considerable interest in the mechanisms by which proteins recognize and respond to RNA. This review appraises our understanding of how PKR activity is modulated by the RBMs.
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Affiliation(s)
- Anthony J Sadler
- Monash Institute of Medical Research, Monash University, Melbourne, Australia
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19
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Abstract
The lack of an efficacious HIV-1 vaccine and the continued emergence of drug-resistant HIV-1 strains have pushed the research community to explore novel avenues for AIDS therapy. Over the last decade, one new avenue that has been realized involves cellular HIV-1 restriction factors, defined as host cellular proteins or factors that restrict or inhibit HIV-1 replication. Many of these factors are interferon-induced and inhibit specific stages of the HIV-1 lifecycle that are not targeted by current AIDS therapies. Our understanding of the molecular mechanisms underlying HIV-1 restriction is far from complete, but our current knowledge of these factors offers hope for the future development of novel therapeutic ideas.
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Affiliation(s)
- Stephen D Barr
- Department of Microbiology & Immunology, The University of Western Ontario, London, ON, Canada
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20
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VanOudenhove J, Anderson E, Kreuger S, Cole JL. Analysis of PKR structure by small-angle scattering. J Mol Biol 2009; 387:910-20. [PMID: 19232355 PMCID: PMC2663012 DOI: 10.1016/j.jmb.2009.02.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Revised: 02/05/2009] [Accepted: 02/10/2009] [Indexed: 11/20/2022]
Abstract
Protein kinase R (PKR) is a key component of the interferon antiviral defense pathway. Upon binding double-stranded RNA, PKR undergoes autophosphorylation reactions that activate the kinase. PKR contains an N-terminal double-stranded RNA binding domain, which consists of two tandem double-stranded RNA binding motifs, and a C-terminal kinase domain. We have used small-angle X-ray scattering and small-angle neutron scattering to define the conformation of latent PKR in solution. Guinier analysis indicates a radius of gyration of about 35 A. The p(r) distance distribution function exhibits a peak near 30 A, with a broad shoulder extending to longer distances. Good fits to the scattering data require models that incorporate multiple compact and extended conformations of the two interdomain linker regions. Thus, PKR belongs to the growing family of proteins that contain intrinsically unstructured regions. We propose that the flexible linkers may allow PKR to productively dimerize upon interaction with RNA activators that have diverse structures.
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Affiliation(s)
- Jennifer VanOudenhove
- Department of Molecular and Cell Biology, University of Connecticut Storrs, Connecticut 06269, USA
| | - Eric Anderson
- Department of Molecular and Cell Biology, University of Connecticut Storrs, Connecticut 06269, USA
| | - Susan Kreuger
- NIST Center for Neutron Research National Institutes of Standards and Technology Gaithersburg, MD 21702-1201, USA
| | - James L. Cole
- Department of Molecular and Cell Biology, University of Connecticut Storrs, Connecticut 06269, USA
- Deparment of Chemistry University of Connecticut Storrs, Connecticut 06269, USA
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21
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Hu J, Sharma M, Qin H, Gao FP, Cross TA. Ligand binding in the conserved interhelical loop of CorA, a magnesium transporter from Mycobacterium tuberculosis. J Biol Chem 2009; 284:15619-28. [PMID: 19346249 DOI: 10.1074/jbc.m901581200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CorA is a constitutively expressed magnesium transporter in many bacteria. The crystal structures of Thermotoga maritima CorA provide an excellent structural framework for continuing studies. Here, the ligand binding properties of the conserved interhelical loop, the only portion of the protein exposed to the periplasmic space, are characterized by solution nuclear magnetic resonance spectroscopy. Through titration experiments performed on the isolated transmembrane domain of Mycobacterium tuberculosis CorA, it was found that two CorA substrates (Mg2+ and Co2+) and the CorA-specific inhibitor (Co(III) hexamine chloride) bind in the loop at the same binding site. This site includes the glutamic acid residue from the conserved "MPEL" motif. The relatively large dissociation constants indicate that such interactions are weak but not atypical for channels. The present data support the hypothesis that the negatively charged loop could act as an electrostatic ring, increasing local substrate concentrations before transport across the membrane.
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Affiliation(s)
- Jian Hu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
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22
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Abstract
Since the discovery of interferons (IFNs), considerable progress has been made in describing the nature of the cytokines themselves, the signalling components that direct the cell response and their antiviral activities. Gene targeting studies have distinguished four main effector pathways of the IFN-mediated antiviral response: the Mx GTPase pathway, the 2',5'-oligoadenylate-synthetase-directed ribonuclease L pathway, the protein kinase R pathway and the ISG15 ubiquitin-like pathway. As discussed in this Review, these effector pathways individually block viral transcription, degrade viral RNA, inhibit translation and modify protein function to control all steps of viral replication. Ongoing research continues to expose additional activities for these effector proteins and has revealed unanticipated functions of the antiviral response.
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Affiliation(s)
- Anthony J. Sadler
- Monash Institute of Medical Research, Monash University, Clayton, 3168 Victoria Australia
| | - Bryan R. G. Williams
- Monash Institute of Medical Research, Monash University, Clayton, 3168 Victoria Australia
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23
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Mechanism of PKR Activation by dsRNA. J Mol Biol 2008; 381:351-60. [PMID: 18599071 DOI: 10.1016/j.jmb.2008.05.056] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 05/20/2008] [Accepted: 05/23/2008] [Indexed: 01/20/2023]
Abstract
Protein kinase R (PKR) is a central component of the interferon antiviral defense pathway. Upon binding double-stranded RNA (dsRNA), PKR undergoes autophosphorylation reactions that activate the kinase. PKR then phosphorylates eukaryotic initiation factor 2alpha, thus inhibiting protein synthesis in virally infected cells. Using a series of dsRNAs of increasing length, we define the mechanism of PKR activation. A minimal dsRNA of 30 bp is required to bind two PKR monomers and 30 bp is the smallest dsRNA that elicits autophosphorylation activity. Thus, the ability of dsRNAs to function as PKR activators is correlated with binding of two or more PKR monomers. Sedimentation velocity data fit a model where PKR monomers sequentially attach to a single dsRNA. These results support an activation mechanism where the role of the dsRNA is to bring two or more PKR monomers in close proximity to enhance dimerization via the kinase domain. This model explains the inhibition observed at high dsRNA concentrations and the strong dependence of maximum activation on dsRNA binding affinity. Binding affinities increase dramatically upon reducing the salt concentration from 200 to 75 mM NaCl and we observe that a second PKR can bind to the 20-bp dsRNA. Nonspecific assembly of PKR on dsRNA occurs stochastically without apparent cooperativity.
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24
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Anderson E, Cole JL. Domain stabilities in protein kinase R (PKR): evidence for weak interdomain interactions. Biochemistry 2008; 47:4887-97. [PMID: 18393532 DOI: 10.1021/bi702211j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
PKR (protein kinase R) is induced by interferon and is a key component of the innate immunity antiviral pathway. Upon binding dsRNA, PKR undergoes autophosphorylation reactions that activate the kinase, leading it to phosphorylate eIF2alpha, thus inhibiting protein synthesis in virally infected cells. PKR contains a dsRNA-binding domain (dsRBD) and a kinase domain. The dsRBD is composed of two tandem dsRNA-binding motifs. An autoinhibition model for PKR has been proposed, whereby dsRNA binding activates the enzyme by inducing a conformational change that relieves the latent enzyme of the inhibition that is mediated by the interaction of the dsRBD with the kinase. However, recent biophysical data support an open conformation for the latent enzyme, where activation is mediated by dimerization of PKR induced upon binding dsRNA. We have probed the importance of interdomain contacts by comparing the relative stabilities of isolated domains with the same domain in the context of the intact enzyme using equilibrium chemical denaturation experiments. The two dsRNA-binding motifs fold independently, with the C-terminal motif exhibiting greater stability. The kinase domain is stabilized by about 1.5 kcal/mol in the context of the holenzyme, and we detect low-affinity binding of the kinase and dsRBD constructs in solution, indicating that these domains interact weakly. Limited proteolysis measurements confirm the expected domain boundaries and reveal that the activation loop in the kinase is accessible to cleavage and unstructured. Autophosphorylation induces a conformation change that blocks proteolysis of the activation loop.
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Affiliation(s)
- Eric Anderson
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269-3125, USA
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25
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McKenna SA, Lindhout DA, Shimoike T, Puglisi JD. Biophysical and biochemical investigations of dsRNA-activated kinase PKR. Methods Enzymol 2008; 430:373-96. [PMID: 17913645 DOI: 10.1016/s0076-6879(07)30014-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Protein kinase RNA-activated (PKR) is a serine/threonine kinase that contains an N-terminal RNA-binding domain (dsRNA) and a C-terminal kinase domain. On binding viral dsRNA molecules, PKR can become activated and phosphorylate cellular targets, such as eukaryotic translation initiation factor 2alpha (eIF-2alpha). Phosphorylation of eIF-2alpha results in attenuation of protein translation initiation. Therefore, PKR plays an integral role in the antiviral response to cellular infection. Here we provide a methodological framework for probing PKR function by use of assays for phosphorylation, RNA-protein stability, PKR dimerization, and in vitro translation. These methods are complemented by nuclear magnetic resonance approaches for probing structural features of PKR activation. Considerations required for both PKR and dsRNA sample preparation are also discussed.
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Affiliation(s)
- Sean A McKenna
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA
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26
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Lunde BM, Moore C, Varani G. RNA-binding proteins: modular design for efficient function. Nat Rev Mol Cell Biol 2007; 8:479-90. [PMID: 17473849 PMCID: PMC5507177 DOI: 10.1038/nrm2178] [Citation(s) in RCA: 906] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Many RNA-binding proteins have modular structures and are composed of multiple repeats of just a few basic domains that are arranged in various ways to satisfy their diverse functional requirements. Recent studies have investigated how different modules cooperate in regulating the RNA-binding specificity and the biological activity of these proteins. They have also investigated how multiple modules cooperate with enzymatic domains to regulate the catalytic activity of enzymes that act on RNA. These studies have shown how, for many RNA-binding proteins, multiple modules define the fundamental structural unit that is responsible for biological function.
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Affiliation(s)
- Bradley M Lunde
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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27
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Kalai M, Suin V, Festjens N, Meeus A, Bernis A, Wang XM, Saelens X, Vandenabeele P. The caspase-generated fragments of PKR cooperate to activate full-length PKR and inhibit translation. Cell Death Differ 2007; 14:1050-9. [PMID: 17318221 DOI: 10.1038/sj.cdd.4402110] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We have studied the involvement of receptor interacting protein kinase-1 (RIP1) and dsRNA-activated protein kinase (PKR) in external dsRNA-induced apoptotic and necrotic cell death in Jurkat T cell lymphoma. Our results suggest that RIP1 plays an imported role in dsRNA-induced apoptosis and necrosis. We demonstrated that contrary to necrosis, protein synthesis is inhibited in apoptosis. Here, we show that phosphorylation of translation initiation factor 2-alpha (eukaryotic initiation factor 2-alpha (eIF2-alpha)) and its kinase, PKR, occur in dsRNA-induced apoptosis but not in necrosis. These events are caspase-dependent and coincide with the appearance of the caspase-mediated PKR fragments, N-terminal domain (ND) and kinase domain (KD). Our immunoprecipitation experiments demonstrated that both fragments could independently co-precipitate with full-length PKR. Expression of PKR-KD leads to PKR and eIF2-alpha phosphorylation and inhibits protein translation, whereas that of PKR-ND does not. Co-expression of PKR-ND and PKR-KD promotes their interaction with PKR, PKR and eIF2-alpha phosphorylation and suppresses protein translation better than PKR-KD alone. Our findings suggest a caspase-dependent mode of activation of PKR in apoptosis in which the PKR-KD fragment interacts with and activates intact PKR. PKR-ND facilitates the interaction of PKR-KD with full-length PKR and thus the activation of the kinase and amplifies the translation inhibitory signal.
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Affiliation(s)
- M Kalai
- Laboratory of Cellular Microbiology, Pasteur Institute, Rue Engeland, Brussels, Belgium.
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28
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McKenna SA, Lindhout DA, Kim I, Liu CW, Gelev VM, Wagner G, Puglisi JD. Molecular framework for the activation of RNA-dependent protein kinase. J Biol Chem 2007; 282:11474-86. [PMID: 17284445 DOI: 10.1074/jbc.m700301200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RNA-dependent protein kinase (PKR) plays an integral role in the antiviral response to cellular infection. PKR contains three distinct domains consisting of two conserved N-terminal double-stranded RNA (dsRNA)-binding domains, a C-terminal Ser-Thr kinase domain, and a central 80-residue linker. Despite rich structural and biochemical data, a detailed mechanistic explanation of PKR activation remains unclear. Here we provide a framework for understanding dsRNA-dependent activation of PKR using nuclear magnetic resonance spectroscopy, dynamic light scattering, gel filtration, and autophosphorylation kinetics. In the latent state, PKR exists as an extended monomer, with an increase in self-affinity upon dsRNA association. Subsequent phosphorylation leads to efficient release of dsRNA followed by a greater increase in self-affinity. Activated PKR displays extensive conformational perturbations within the kinase domain. We propose an updated model for PKR activation in which the communication between RNA binding, central linker, and kinase domains is critical in the propagation of the activation signal and for PKR dimerization.
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Affiliation(s)
- Sean A McKenna
- Department of Structural Biology and Stanford Magnetic Resonance Laboratory, Stanford University School of Medicine, Stanford, California 94305-5126, USA
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29
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Cole JL. Activation of PKR: an open and shut case? Trends Biochem Sci 2006; 32:57-62. [PMID: 17196820 PMCID: PMC2703476 DOI: 10.1016/j.tibs.2006.12.003] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 11/16/2006] [Accepted: 12/18/2006] [Indexed: 11/15/2022]
Abstract
The double-stranded (ds) RNA-activated protein kinase, PKR, has a key role in the innate immunity response to viral infection in higher eukaryotes. PKR contains an N-terminal dsRNA-binding domain and a C-terminal kinase domain. In the prevalent autoinhibition model for PKR activation, dsRNA binding induces a conformational change that leads to the release of the dsRNA-binding domain from the kinase, thus relieving the inhibition of the latent enzyme. Structural and biophysical data now favor a model whereby dsRNA principally functions to induce dimerization of PKR via the kinase domain. This dimerization model has implications for other PKR regulatory mechanisms and represents a new structural paradigm for control of protein kinase activity.
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Affiliation(s)
- James L Cole
- Department of Molecular and Cell Biology, 91 N. Eagleville Road, U-3125 University of Connecticut, Storrs, CT 06269, USA.
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