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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Wu Z, Chu L, Gong Z, Han GZ. The making of a nucleic acid sensor at the dawn of jawed vertebrate evolution. SCIENCE ADVANCES 2024; 10:eado7464. [PMID: 39110805 PMCID: PMC11305385 DOI: 10.1126/sciadv.ado7464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/28/2024] [Indexed: 08/10/2024]
Abstract
Self and nonself discrimination is fundamental to immunity. However, it remains largely enigmatic how the mechanisms of distinguishing nonself from self originated. As an intracellular nucleic acid sensor, protein kinase R (PKR) recognizes double-stranded RNA (dsRNA) and represents a crucial component of antiviral innate immunity. Here, we combine phylogenomic and functional analyses to show that PKR proteins probably originated from a preexisting kinase protein through acquiring dsRNA binding domains at least before the last common ancestor of jawed vertebrates during or before the Silurian period. The function of PKR appears to be conserved across jawed vertebrates. Moreover, we repurpose a protein closely related to PKR proteins into a putative dsRNA sensor, recapturing the making of PKR. Our study illustrates how a nucleic acid sensor might have originated via molecular tinkering with preexisting proteins and provides insights into the origins of innate immunity.
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Affiliation(s)
- Zhiwei Wu
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Lingyu Chu
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Zhen Gong
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Guan-Zhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
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3
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Megawati D, Stroup JN, Park C, Clarkson T, Tazi L, Brennan G, Rothenburg S. Tanapox Virus and Yaba Monkey Tumor Virus K3 Orthologs Inhibit Primate Protein Kinase R in a Species-Specific Fashion. Viruses 2024; 16:1095. [PMID: 39066257 PMCID: PMC11281682 DOI: 10.3390/v16071095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
Yaba monkey tumor virus (YMTV) and Tanapox virus (TPV) are members of the Yatapoxvirus genus and can infect humans and other primates. Despite the threat posed by yatapoxviruses, the factors determining their host range are poorly understood. In this study, we analyzed the ability of YMTV and TPV orthologs of vaccinia virus K3 (called 012 in YMTV and TPV), which share 75% amino acid identity with one another, to inhibit PKR from 15 different primate species. We first used a luciferase-based reporter, and found that YMTV and TPV K3 orthologs inhibited PKR in a species-specific manner and showed distinct PKR inhibition profiles. TPV 012 inhibited PKR from 11 primates, including humans, substantially better than YMTV 012. In contrast, both K3 orthologs inhibited the other four primate PKRs comparably well. Using YMTV 012 and TPV 012 hybrids, we mapped the region responsible for the differential PKR inhibition to the C- terminus of the K3 orthologs. Next, we generated chimeric vaccinia virus strains to investigate whether TPV K3 and YMTV K3 orthologs could rescue the replication of a vaccinia virus strain that lacks PKR inhibitors K3L and E3L. Virus replication in primate-derived cells generally correlated with the patterns observed in the luciferase-based assay. Together, these observations demonstrate that yatapoxvirus K3 orthologs have distinct PKR inhibition profiles and inhibit PKR in a species-specific manner, which may contribute to the differential susceptibility of primate species to yatapoxvirus infections.
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Affiliation(s)
- Dewi Megawati
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA; (D.M.); (J.N.S.); (C.P.); (L.T.)
- Department of Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Warmadewa University, Denpasar 80239, Bali, Indonesia
| | - Jeannine N. Stroup
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA; (D.M.); (J.N.S.); (C.P.); (L.T.)
| | - Chorong Park
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA; (D.M.); (J.N.S.); (C.P.); (L.T.)
| | - Taylor Clarkson
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA; (D.M.); (J.N.S.); (C.P.); (L.T.)
| | - Loubna Tazi
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA; (D.M.); (J.N.S.); (C.P.); (L.T.)
| | - Greg Brennan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA; (D.M.); (J.N.S.); (C.P.); (L.T.)
| | - Stefan Rothenburg
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA; (D.M.); (J.N.S.); (C.P.); (L.T.)
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4
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Uno M, Bono H. Transcriptional Signatures of Domestication Revealed through Meta-Analysis of Pig, Chicken, Wild Boar, and Red Junglefowl Gene Expression Data. Animals (Basel) 2024; 14:1998. [PMID: 38998110 PMCID: PMC11240496 DOI: 10.3390/ani14131998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/25/2024] [Accepted: 07/04/2024] [Indexed: 07/14/2024] Open
Abstract
Domesticated animals have undergone significant changes in their behavior, morphology, and physiological functions during domestication. To identify the changes in gene expression associated with domestication, we collected the RNA-seq data of pigs, chickens, wild boars, and red junglefowl from public databases and performed a meta-analysis. Gene expression was quantified, and the expression ratio between domesticated animals and their wild ancestors (DW-ratio) was calculated. Genes were classified as "upregulated", "downregulated", or "unchanged" based on their DW-ratio, and the DW-score was calculated for each gene. Gene set enrichment analysis revealed that genes upregulated in pigs were related to defense from viral infection, whereas those upregulated in chickens were associated with aminoglycan and carbohydrate derivative catabolic processes. Genes commonly upregulated in pigs and chickens are involved in the immune response, olfactory learning, epigenetic regulation, cell division, and extracellular matrix. In contrast, genes upregulated in wild boar and red junglefowl are related to stress response, cell proliferation, cardiovascular function, neural regulation, and energy metabolism. These findings provide valuable insights into the genetic basis of the domestication process and highlight potential candidate genes for breeding applications.
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Affiliation(s)
- Motoki Uno
- Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima 739-0046, Japan
| | - Hidemasa Bono
- Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima 739-0046, Japan
- Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima 739-0046, Japan
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5
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Gibbs VJ, Lin YH, Ghuge AA, Anderson RA, Schiemann AH, Conaglen L, Sansom BJM, da Silva RC, Sattlegger E. GCN2 in Viral Defence and the Subversive Tactics Employed by Viruses. J Mol Biol 2024; 436:168594. [PMID: 38724002 DOI: 10.1016/j.jmb.2024.168594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/01/2024] [Accepted: 05/01/2024] [Indexed: 06/10/2024]
Abstract
The recent SARS-CoV-2 pandemic and associated COVID19 disease illustrates the important role of viral defence mechanisms in ensuring survival and recovery of the host or patient. Viruses absolutely depend on the host's protein synthesis machinery to replicate, meaning that impeding translation is a powerful way to counteract viruses. One major approach used by cells to obstruct protein synthesis is to phosphorylate the alpha subunit of eukaryotic translation initiation factor 2 (eIF2α). Mammals possess four different eIF2α-kinases: PKR, HRI, PEK/PERK, and GCN2. While PKR is currently considered the principal eIF2α-kinase involved in viral defence, the other eIF2α-kinases have also been found to play significant roles. Unsurprisingly, viruses have developed mechanisms to counteract the actions of eIF2α-kinases, or even to exploit them to their benefit. While some of these virulence factors are specific to one eIF2α-kinase, such as GCN2, others target all eIF2α-kinases. This review critically evaluates the current knowledge of viral mechanisms targeting the eIF2α-kinase GCN2. A detailed and in-depth understanding of the molecular mechanisms by which viruses evade host defence mechanisms will help to inform the development of powerful anti-viral measures.
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Affiliation(s)
- Victoria J Gibbs
- School of Food Technology and Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Yu H Lin
- School of Food Technology and Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Aditi A Ghuge
- School of Food Technology and Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Reuben A Anderson
- School of Food Technology and Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Anja H Schiemann
- School of Food Technology and Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Layla Conaglen
- School of Food Technology and Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Bianca J M Sansom
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - Richard C da Silva
- School of Natural Sciences, Massey University, Auckland, New Zealand; Genome Biology and Epigenetics, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Evelyn Sattlegger
- School of Food Technology and Natural Sciences, Massey University, Palmerston North, New Zealand; School of Natural Sciences, Massey University, Auckland, New Zealand; Maurice Wilkins Centre for Molecular BioDiscovery, Palmerston North, New Zealand.
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6
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Bhattacharjee P, Wang D, Anderson D, Buckler JN, de Geus E, Yan F, Polekhina G, Schittenhelm R, Creek DJ, Harris LD, Sadler AJ. The immune response to RNA suppresses nucleic acid synthesis by limiting ribose 5-phosphate. EMBO J 2024; 43:2636-2660. [PMID: 38778156 PMCID: PMC11217295 DOI: 10.1038/s44318-024-00100-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 02/29/2024] [Accepted: 03/19/2024] [Indexed: 05/25/2024] Open
Abstract
During infection viruses hijack host cell metabolism to promote their replication. Here, analysis of metabolite alterations in macrophages exposed to poly I:C recognises that the antiviral effector Protein Kinase RNA-activated (PKR) suppresses glucose breakdown within the pentose phosphate pathway (PPP). This pathway runs parallel to central glycolysis and is critical to producing NADPH and pentose precursors for nucleotides. Changes in metabolite levels between wild-type and PKR-ablated macrophages show that PKR controls the generation of ribose 5-phosphate, in a manner distinct from its established function in gene expression but dependent on its kinase activity. PKR phosphorylates and inhibits the Ribose 5-Phosphate Isomerase A (RPIA), thereby preventing interconversion of ribulose- to ribose 5-phosphate. This activity preserves redox control but decreases production of ribose 5-phosphate for nucleotide biosynthesis. Accordingly, the PKR-mediated immune response to RNA suppresses nucleic acid production. In line, pharmacological targeting of the PPP during infection decreases the replication of the Herpes simplex virus. These results identify an immune response-mediated control of host cell metabolism and suggest targeting the RPIA as a potential innovative antiviral treatment.
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Affiliation(s)
- Pushpak Bhattacharjee
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia
| | - Die Wang
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia
| | - Dovile Anderson
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Joshua N Buckler
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, 5010, New Zealand
| | - Eveline de Geus
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia
| | - Feng Yan
- Australian Centre for Blood Diseases, Department of Clinical Hematology, Monash University, Clayton, VIC, 3004, Australia
| | - Galina Polekhina
- Department of Epidemiology & Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Ralf Schittenhelm
- Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Lawrence D Harris
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, 5010, New Zealand
| | - Anthony J Sadler
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia.
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7
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Yin JZ, Keszei AFA, Houliston S, Filandr F, Beenstock J, Daou S, Kitaygorodsky J, Schriemer DC, Mazhab-Jafari MT, Gingras AC, Sicheri F. The HisRS-like domain of GCN2 is a pseudoenzyme that can bind uncharged tRNA. Structure 2024; 32:795-811.e6. [PMID: 38531363 DOI: 10.1016/j.str.2024.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 01/09/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024]
Abstract
GCN2 is a stress response kinase that phosphorylates the translation initiation factor eIF2α to inhibit general protein synthesis when activated by uncharged tRNA and stalled ribosomes. The presence of a HisRS-like domain in GCN2, normally associated with tRNA aminoacylation, led to the hypothesis that eIF2α kinase activity is regulated by the direct binding of this domain to uncharged tRNA. Here we solved the structure of the HisRS-like domain in the context of full-length GCN2 by cryoEM. Structure and function analysis shows the HisRS-like domain of GCN2 has lost histidine and ATP binding but retains tRNA binding abilities. Hydrogen deuterium exchange mass spectrometry, site-directed mutagenesis and computational docking experiments support a tRNA binding model that is partially shifted from that employed by bona fide HisRS enzymes. These results demonstrate that the HisRS-like domain of GCN2 is a pseudoenzyme and advance our understanding of GCN2 regulation and function.
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Affiliation(s)
- Jay Z Yin
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alexander F A Keszei
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Scott Houliston
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Frantisek Filandr
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jonah Beenstock
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Salima Daou
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Julia Kitaygorodsky
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Mohammad T Mazhab-Jafari
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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8
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Chambers MJ, Scobell SB, Sadhu MJ. Systematic genetic characterization of the human PKR kinase domain highlights its functional malleability to escape a viral substrate mimic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596416. [PMID: 38903081 PMCID: PMC11188142 DOI: 10.1101/2024.05.29.596416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Evolutionary arms races can arise at the contact surfaces between host and viral proteins, producing dynamic spaces in which genetic variants are continually pursued. However, the sampling of genetic variation must be balanced with the need to maintain protein function. A striking case is given by protein kinase R (PKR), a member of the mammalian innate immune system. PKR detects viral replication within the host cell and halts protein synthesis to prevent viral replication by phosphorylating eIF2α, a component of the translation initiation machinery. PKR is targeted by many viral antagonists, including poxvirus pseudosubstrate antagonists that inhibit PKR by interacting with the same binding surface as eIF2α. Remarkably, PKR has several rapidly evolving residues at this interface, suggesting it is engaging in an evolutionary arms race, despite the surface's critical role in phosphorylating eIF2α. To systematically explore the evolutionary opportunities available at this dynamic interface, we generated and characterized a library of 426 SNP-accessible nonsynonymous variants of human PKR for their ability to escape inhibition by the model pseudosubstrate inhibitor K3 from vaccinia virus. We identified key sites in the PKR kinase domain that harbor K3-resistant variants, as well as critical sites where variation leads to loss of function. We find K3-resistant variants are readily available throughout the interface and are enriched at sites under positive selection. Moreover, variants beneficial against K3 were also beneficial against an enhanced variant of K3, indicating resilience to viral adaptation. Overall, we find that the eIF2α-binding surface of PKR is highly malleable, potentiating its evolutionary ability to combat viral inhibition.
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Affiliation(s)
- Michael J Chambers
- Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
- Department of Microbiology & Immunology, Georgetown University, Washington DC, USA
| | - Sophia B Scobell
- Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Meru J Sadhu
- Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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9
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Haller SL, Park C, Bruneau RC, Megawati D, Zhang C, Vipat S, Peng C, Senkevich TG, Brennan G, Tazi L, Rothenburg S. Molecular basis for the host range function of the poxvirus PKR inhibitor E3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594589. [PMID: 38798513 PMCID: PMC11118487 DOI: 10.1101/2024.05.16.594589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The antiviral protein kinase R (PKR) is activated by viral double-stranded RNA and phosphorylates translation initiation factor eIF2α, thereby inhibiting translation and virus replication. Most poxviruses contain two PKR inhibitors, called E3 and K3 in vaccinia virus (VACV), which are determinants of viral host range. The prevailing model for E3 function is that it inhibits PKR through the non-specific sequestration of double-stranded (ds) RNA. Our data revealed that Syrian hamster PKR was resistant to E3, which is at odds with the sequestration model. However, Syrian hamster PKR was still sensitive to K3 inhibition. In contrast, Armenian hamster PKR showed opposite sensitivities, being sensitive to E3 and resistant to K3 inhibition. Mutational analyses of hamster PKRs showed that sensitivity to E3 inhibition was largely determined by the region linking the dsRNA-binding domains and the kinase domain of PKR, whereas two amino acid residues in the kinase domain (helix αG) determined sensitivity to K3. Expression of PKRs in congenic cells showed that Syrian hamster PKR containing the two Armenian hamster PKR residues in helix-αG was resistant to wild type VACV infection, and that cells expressing either hamster PKR recapitulated the phenotypes observed in species-derived cell lines. The observed resistance of Syrian hamster PKR to E3 explains its host range function and challenges the paradigm that dsRNA-binding PKR inhibitors mainly act by the sequestration of dsRNA. Significance The molecular mechanisms that govern the host range of viruses are incompletely understood. A small number of poxvirus genes have been identified that influence the host range of poxviruses. We show that the host range functions of E3 and K3, two host range factors from vaccinia virus, are a result of species-specific interactions with the antiviral protein kinase R (PKR) and that PKR from closely related species displayed dramatic differences in their sensitivities to these viral inhibitors. While there is a substantial body of work demonstrating host-specific interactions with K3, the current model for E3-mediated PKR inhibition is that E3 non-specifically sequesters dsRNA to prevent PKR activation. This model does not predict species-specific sensitivity to E3; therefore, our data suggest that the current model is incomplete, and that dsRNA sequestration is not the primary mechanism for E3 activity.
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10
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Feinstein AG, Cole JL, May ER. The α C helix is a central regulator of PKR activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591909. [PMID: 38746189 PMCID: PMC11092653 DOI: 10.1101/2024.04.30.591909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Protein kinase R (PKR) functions in the eukaryotic innate immune system as a first-line defense against viral infections. PKR binds viral dsRNA, leading to autophosphorylation and activation. In its active state, PKR can phosphorylate its primary substrate, eIF2 α , which blocks initiation of translation in the infected cell. It has been established that PKR activation occurs when the kinase domain dimerizes in a back-to-back configuration. However, the mechanism by which dimerization leads to enzymatic activation is not fully understood. Here, we investigate the structural mechanistic basis and energy landscape for PKR activation, with a focus on the α C helix - a kinase activation and signal integration hub - using all-atom equilibrium and enhanced sampling molecular dynamics simulations. By employing window-exchange umbrella sampling, we compute free energy profiles of activation which show that back-to-back dimerization stabilizes a catalytically competent conformation of PKR. Key hydrophobic residues in the homodimer interface contribute to stabilization of the α C helix in an active conformation and the position of its glutamate residue. Using linear mutual information analysis, we analyze allosteric communication connecting the protomers' N-lobes and the α C helix dimer interface with the α C helix.
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11
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Solorio-Kirpichyan K, Fan X, Golovenko D, Korostelev AA, Yan N, Korennykh A. Cryo-EM Structure of HRSL Domain Reveals Activating Crossed Helices at the Core of GCN2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.591037. [PMID: 38712127 PMCID: PMC11071503 DOI: 10.1101/2024.04.24.591037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
GCN2 is a conserved receptor kinase activating the Integrated Stress Response (ISR) in eukaryotic cells. The ISR kinases detect accumulation of stress molecules and reprogram translation from basal tasks to preferred production of cytoprotective proteins. GCN2 stands out evolutionarily among all protein kinases due to the presence of a h istidyl t R NA s ynthetase-like (HRSL) domain, which arises only in GCN2 and is located next to the kinase domain. How HRSL contributes to GCN2 signaling remains unknown. Here we report a 3.2 Å cryo-EM structure of HRSL from thermotolerant yeast Kluyveromyces marxianus . This structure shows a constitutive symmetrical homodimer featuring a compact helical-bundle structure at the junction between HRSL and kinase domains, in the core of the receptor. Mutagenesis demonstrates that this junction structure activates GCN2 and indicates that our cryo-EM structure captures the active signaling state of HRSL. Based on these results, we put forward a GCN2 regulation mechanism, where HRSL drives the formation of activated kinase dimers. Remaining domains of GCN2 have the opposite role and in the absence of stress they help keep GCN2 basally inactive. This autoinhibitory activity is relieved upon stress ligand binding. We propose that the opposing action of HRSL and additional GCN2 domains thus yields a regulated ISR receptor. Significance statement Regulation of protein synthesis (translation) is a central mechanism by which eukaryotic cells adapt to stressful conditions. In starving cells, this translational adaptation is achieved via the receptor kinase GCN2, which stays inactive under normal conditions, but is switched on under stress. The molecular mechanism of GCN2 switching is not well understood due to the presence of a structurally and biochemically uncharacterized h istidyl t R NA s ynthetase-like domain (HRSL) at the core of GCN2. Here we use single-particle cryo-EM and biochemistry to elucidate the structure and function of HRSL. We identify a structure at the kinase/HRSL interface, which forms crossed helices and helps position GCN2 kinase domains for activation. These data clarify the molecular mechanism of GCN2 regulation.
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12
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Vu GT, Awad V, Norberto MF, Bowman TV, Trompouki E. Nucleic acid-induced inflammation on hematopoietic stem cells. Exp Hematol 2024; 131:104148. [PMID: 38151171 PMCID: PMC11061806 DOI: 10.1016/j.exphem.2023.104148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
Hematopoiesis, the process of generating blood cells, starts during development with the primitive, pro-definitive, and definitive hematopoietic waves. The first two waves will generate erythrocytes and myeloid cells, although the definitive wave will give rise to hematopoietic stem cells (HSCs) that are multipotent and can produce most of the blood cells in an adult. Although HSCs are highly proliferative during development, during adulthood they remain quiescent in the bone marrow. Inflammatory signaling in the form of interferons, interleukins, tumor necrosis factors, and others is well-established to influence both developmental and adult hematopoiesis. Here we discuss the role of specific inflammatory pathways that are induced by sensing nucleic acids. We discuss the role of RNA-sensing members of the Toll-like, Rig-I-like, nucleotide-binding oligomerization domain (NOD)-like, and AIM2-like protein kinase receptors and the DNA-sensing receptors, DEAD-Box helicase 41 (DDX41) and cGAS. The main downstream pathways of these receptors are discussed, as well as their influence on developmental and adult hematopoiesis, including hematopoietic pathologies.
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Affiliation(s)
- Giang To Vu
- IRCAN Institute for Research on Cancer and Aging, INSERM Unité 1081, CNRS UMR 7284, Université Côte d'Azur, Nice, France
| | - Valerie Awad
- Department of Developmental and Molecular Biology and Gottesman Institute of Stem Cell Biology and Regenerative Medicine Bronx, Albert Einstein College of Medicine, NY
| | - Maria Feliz Norberto
- Department of Developmental and Molecular Biology and Gottesman Institute of Stem Cell Biology and Regenerative Medicine Bronx, Albert Einstein College of Medicine, NY
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology and Gottesman Institute of Stem Cell Biology and Regenerative Medicine Bronx, Albert Einstein College of Medicine, NY; Department of Oncology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY.
| | - Eirini Trompouki
- IRCAN Institute for Research on Cancer and Aging, INSERM Unité 1081, CNRS UMR 7284, Université Côte d'Azur, Nice, France.
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13
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Suskiewicz MJ. The logic of protein post-translational modifications (PTMs): Chemistry, mechanisms and evolution of protein regulation through covalent attachments. Bioessays 2024; 46:e2300178. [PMID: 38247183 DOI: 10.1002/bies.202300178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
Protein post-translational modifications (PTMs) play a crucial role in all cellular functions by regulating protein activity, interactions and half-life. Despite the enormous diversity of modifications, various PTM systems show parallels in their chemical and catalytic underpinnings. Here, focussing on modifications that involve the addition of new elements to amino-acid sidechains, I describe historical milestones and fundamental concepts that support the current understanding of PTMs. The historical survey covers selected key research programmes, including the study of protein phosphorylation as a regulatory switch, protein ubiquitylation as a degradation signal and histone modifications as a functional code. The contribution of crucial techniques for studying PTMs is also discussed. The central part of the essay explores shared chemical principles and catalytic strategies observed across diverse PTM systems, together with mechanisms of substrate selection, the reversibility of PTMs by erasers and the recognition of PTMs by reader domains. Similarities in the basic chemical mechanism are highlighted and their implications are discussed. The final part is dedicated to the evolutionary trajectories of PTM systems, beginning with their possible emergence in the context of rivalry in the prokaryotic world. Together, the essay provides a unified perspective on the diverse world of major protein modifications.
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Affiliation(s)
- Marcin J Suskiewicz
- Centre de Biophysique Moléculaire, CNRS - Orléans, UPR 4301, affiliated with Université d'Orléans, Orléans, France
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14
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Fatalska A, Hodgson G, Freund SMV, Maslen SL, Morgan T, Thorkelsson SR, van Slegtenhorst M, Lorenz S, Andreeva A, Kaat LD, Bertolotti A. Recruitment of trimeric eIF2 by phosphatase non-catalytic subunit PPP1R15B. Mol Cell 2024; 84:506-521.e11. [PMID: 38159565 PMCID: PMC7615683 DOI: 10.1016/j.molcel.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 09/06/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
Regulated protein phosphorylation controls most cellular processes. The protein phosphatase PP1 is the catalytic subunit of many holoenzymes that dephosphorylate serine/threonine residues. How these enzymes recruit their substrates is largely unknown. Here, we integrated diverse approaches to elucidate how the PP1 non-catalytic subunit PPP1R15B (R15B) captures its full trimeric eIF2 substrate. We found that the substrate-recruitment module of R15B is largely disordered with three short helical elements, H1, H2, and H3. H1 and H2 form a clamp that grasps the substrate in a region remote from the phosphorylated residue. A homozygous N423D variant, adjacent to H1, reducing substrate binding and dephosphorylation was discovered in a rare syndrome with microcephaly, developmental delay, and intellectual disability. These findings explain how R15B captures its 125 kDa substrate by binding the far end of the complex relative to the phosphosite to present it for dephosphorylation by PP1, a paradigm of broad relevance.
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Affiliation(s)
- Agnieszka Fatalska
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - George Hodgson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Stefan M V Freund
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Sarah L Maslen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Tomos Morgan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Sigurdur R Thorkelsson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Sonja Lorenz
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Antonina Andreeva
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Laura Donker Kaat
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Anne Bertolotti
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
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15
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Chambers MJ, Scobell S, Sadhu MJ. Systematic characterization of the local evolutionary space available to human PKR and vaccinia virus K3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568178. [PMID: 38076952 PMCID: PMC10705557 DOI: 10.1101/2023.11.21.568178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The interfaces between host and viral proteins can be dynamic spaces in which genetic variants are continually pursued, giving rise to evolutionary arms races. One such scenario is found between the mammalian innate immunity protein PKR (protein kinase R) and the poxvirus antagonist K3. Once activated, PKR phosphorylates the natural substrate eIF2α, which halts protein synthesis within the cell and prevents viral replication. K3 acts as a pseudosubstrate antagonist against PKR by directly antagonizing this halt in protein synthesis, enabling poxviruses to replicate in the cell. Exploring the impact of genetic variants in both PKR and K3 is necessary not only to highlight residues of evolutionary constraint and opportunity but also to elucidate the mechanism by which human PKR is able to subvert a rapidly evolving viral antagonist. To systematically explore this dynamic interface, we have generated a combinatorial library of PKR and K3 missense variants to be co-expressed and characterized in a high-throughput yeast selection assay. This assay allows us to characterize hundreds of thousands of unique PKR-K3 genetic combinations in a single pooled experiment. Our results highlight specific missense variants available to PKR that subvert the K3 antagonist. We find that improved PKR variants are readily available at sites under positive selection, with limited opportunity at sites interfacing with K3 and eIF2α. Additionally, we find many variants that improve and disable K3 antagonism, suggesting a pliable interface. We reason that this approach can be leveraged to explore the evolutionary plasticity of many other host-virus interfaces.
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Affiliation(s)
- Michael J Chambers
- Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
- Department of Microbiology & Immunology, Georgetown University, Washington DC, USA
| | - Sophia Scobell
- Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Meru J Sadhu
- Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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16
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Ito T, Wuerth JD, Weber F. Protection of eIF2B from inhibitory phosphorylated eIF2: A viral strategy to maintain mRNA translation during the PKR-triggered integrated stress response. J Biol Chem 2023; 299:105287. [PMID: 37742919 PMCID: PMC10616414 DOI: 10.1016/j.jbc.2023.105287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023] Open
Abstract
The integrated stress response (ISR) protects cells from a variety of insults. Once elicited (e.g., by virus infections), it eventually leads to the block of mRNA translation. Central to the ISR are the interactions between translation initiation factors eIF2 and eIF2B. Under normal conditions, eIF2 drives the initiation of protein synthesis through hydrolysis of GTP, which becomes replenished by the guanine nucleotide exchange factor eIF2B. The antiviral branch of the ISR is activated by the RNA-activated kinase PKR which phosphorylates eIF2, thereby converting it into an eIF2B inhibitor. Here, we describe the recently solved structures of eIF2B in complex with eIF2 and a novel escape strategy used by viruses. While unphosphorylated eIF2 interacts with eIF2B in its "productive" conformation, phosphorylated eIF2 [eIF2(αP)] engages a different binding cavity on eIF2B and forces it into the "nonproductive" conformation that prohibits guanine nucleotide exchange factor activity. It is well established that viruses express so-called PKR antagonists that interfere with double-strand RNA, PKR itself, or eIF2. However recently, three taxonomically unrelated viruses were reported to encode antagonists targeting eIF2B instead. For one antagonist, the S segment nonstructural protein of Sandfly fever Sicilian virus, atomic structures showed that it occupies the eIF2(αP)-binding cavity on eIF2B without imposing a switch to the nonproductive conformation. S segment nonstructural protein thus antagonizes the activity of PKR by protecting eIF2B from inhibition by eIF2(αP). As the ISR and specifically eIF2B are central to neuroprotection and a wide range of genetic and age-related diseases, these developments may open new possibilities for treatments.
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Affiliation(s)
- Takuhiro Ito
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | | | - Friedemann Weber
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany.
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17
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Pennisi R, Maria Teresa S. HSV-1 Triggers an Antiviral Transcriptional Response during Viral Replication That Is Completely Abrogated in PKR -/- Cells. Pathogens 2023; 12:1126. [PMID: 37764935 PMCID: PMC10536113 DOI: 10.3390/pathogens12091126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/29/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
The activation of the innate immune response during HSV-1 infection stimulates several transcription factors, such as NF-κB and IRF3, which are critical regulators of IFN-β expression. The released IFN-β activates the ISGs, which encode antiviral effectors such as the PKR. We found that HSV-1 triggers an antiviral transcriptional response during viral replication by activating TBK1-IRF3-NF-κB network kinetically. In contrast, we reported that infected PKR-/- cells fail to activate the transcription of TBK1. Downstream, TBK1 was unable to activate the transcription of IRF3 and NF-κB. These data suggested that in PKR-/- cells, HSV-1 replication counteracts TBK1-IRF3-NF-κB network. In this scenario, a combined approach of gene knockout and gene silencing was used to determine how the lack of PKR facilitates HSV-1 replication. We reported that in HEp-2-infected cells, PKR can influence the TBK1-IRF3-NF-κB network, consequently interfering with viral replication. Otherwise, an abrogated PKR-mediated signaling sustains the HSV-1 replication. Our result allows us to add additional information on the complex HSV-host interaction network by reinforcing the concept of the PKR role in the innate response-related networks during HSV replication in an in vitro model.
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Affiliation(s)
- Rosamaria Pennisi
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Sciortino Maria Teresa
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy
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18
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Yang J, Baron KR, Pride DE, Schneemann A, Guo X, Chen W, Song AS, Aviles G, Kampmann M, Wiseman RL, Lander GC. DELE1 oligomerization promotes integrated stress response activation. Nat Struct Mol Biol 2023; 30:1295-1302. [PMID: 37550454 PMCID: PMC10528447 DOI: 10.1038/s41594-023-01061-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 07/11/2023] [Indexed: 08/09/2023]
Abstract
Mitochondria are dynamic organelles that continually respond to cellular stress. Recent studies have demonstrated that mitochondrial stress is relayed from mitochondria to the cytosol by the release of a proteolytic fragment of DELE1 that binds to the eIF2α kinase HRI to initiate integrated stress response (ISR) signaling. We report the cryo-electron microscopy structure of the C-terminal cleavage product of human DELE1, which assembles into a high-order oligomer. The oligomer consists of eight DELE1 monomers that assemble with D4 symmetry via two sets of hydrophobic inter-subunit interactions. We identified the key residues involved in DELE1 oligomerization, and confirmed their role in stabilizing the octamer in vitro and in cells using mutagenesis. We further show that assembly-impaired DELE1 mutants are compromised in their ability to induce HRI-dependent ISR activation in cell culture models. Together, our findings provide molecular insights into the activity of DELE1 and how it signals to promote ISR activity following mitochondrial insult.
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Affiliation(s)
- Jie Yang
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Kelsey R Baron
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Daniel E Pride
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Anette Schneemann
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Xiaoyan Guo
- Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Genetics and Genome Science, University of Connecticut Health Center, Farmington, CT, USA
| | - Wenqian Chen
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Albert S Song
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Giovanni Aviles
- Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - R Luke Wiseman
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA.
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19
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Reinhardt R, Leonard TA. A critical evaluation of protein kinase regulation by activation loop autophosphorylation. eLife 2023; 12:e88210. [PMID: 37470698 PMCID: PMC10359097 DOI: 10.7554/elife.88210] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023] Open
Abstract
Phosphorylation of proteins is a ubiquitous mechanism of regulating their function, localization, or activity. Protein kinases, enzymes that use ATP to phosphorylate protein substrates are, therefore, powerful signal transducers in eukaryotic cells. The mechanism of phosphoryl-transfer is universally conserved among protein kinases, which necessitates the tight regulation of kinase activity for the orchestration of cellular processes with high spatial and temporal fidelity. In response to a stimulus, many kinases enhance their own activity by autophosphorylating a conserved amino acid in their activation loop, but precisely how this reaction is performed is controversial. Classically, kinases that autophosphorylate their activation loop are thought to perform the reaction in trans, mediated by transient dimerization of their kinase domains. However, motivated by the recently discovered regulation mechanism of activation loop cis-autophosphorylation by a kinase that is autoinhibited in trans, we here review the various mechanisms of autoregulation that have been proposed. We provide a framework for critically evaluating biochemical, kinetic, and structural evidence for protein kinase dimerization and autophosphorylation, and share some thoughts on the implications of these mechanisms within physiological signaling networks.
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Affiliation(s)
- Ronja Reinhardt
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- Medical University of Vienna, Center for Medical BiochemistryViennaAustria
| | - Thomas A Leonard
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- Medical University of Vienna, Center for Medical BiochemistryViennaAustria
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20
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Lu J, Zhang C, Wang W, Xu W, Chen W, Tao L, Li Z, Zhang Y, Cheng J. Exposure to environmental concentrations of glyphosate induces cardiotoxicity through cellular senescence and reduced cell proliferation capacity. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 261:115112. [PMID: 37290295 DOI: 10.1016/j.ecoenv.2023.115112] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/01/2023] [Accepted: 06/04/2023] [Indexed: 06/10/2023]
Abstract
Glyphosate (GLY), the preeminent herbicide utilized globally, is known to be exposed to the environment and population on a chronic basis. Exposure to GLY and the consequent health risks are alarming public health problems that are attracting international attention. However, the cardiotoxicity of GLY has been a matter of dispute and uncertainty. Here, AC16 cardiomyocytes and zebrafish were exposed to GLY. This study found that low concentrations of GLY lead to morphological enlargement of AC16 human cardiomyocytes, indicating a senescent state. The increased expression of P16, P21, and P53 following exposure to GLY demonstrated that GLY causes senescence in AC16. Moreover, it was mechanistically confirmed that GLY-induced senescence in AC16 cardiomyocytes was produced by ROS-mediated DNA damage. In terms of in vivo cardiotoxicity, GLY decreased the proliferative capacity of cardiomyocytes in zebrafish through the notch signaling pathway, resulting in a reduction of cardiomyocytes. It was also found that GLY caused zebrafish cardiotoxicity associated with DNA damage and mitochondrial damage. KEGG analysis after RNA-seq shows a significant enrichment of protein processing pathways in the endoplasmic reticulum (ER) after GLY exposure. Importantly, GLY induced ER stress in AC16 cells and zebrafish by activating PERK-eIF2α-ATF4 pathway. Our study has thus provided the first novel insights into the mechanism underlying GLY-induced cardiotoxicity. Furthermore, our findings emphasize the need for increased attention to the potential cardiotoxic effects of GLY.
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Affiliation(s)
- Jian Lu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Cheng Zhang
- Department of Pathology,UT southwestern Medical Center, Dallas, TX 75390, United States
| | - Weiguo Wang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Wenping Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weidong Chen
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Liming Tao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhong Li
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yang Zhang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
| | - Jiagao Cheng
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
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21
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Straub S, Sampaio NG. Activation of cytosolic RNA sensors by endogenous ligands: roles in disease pathogenesis. Front Immunol 2023; 14:1092790. [PMID: 37292201 PMCID: PMC10244536 DOI: 10.3389/fimmu.2023.1092790] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/15/2023] [Indexed: 06/10/2023] Open
Abstract
Early detection of infection is a central and critical component of our innate immune system. Mammalian cells have developed specialized receptors that detect RNA with unusual structures or of foreign origin - a hallmark of many virus infections. Activation of these receptors induces inflammatory responses and an antiviral state. However, it is increasingly appreciated that these RNA sensors can also be activated in the absence of infection, and that this 'self-activation' can be pathogenic and promote disease. Here, we review recent discoveries in sterile activation of the cytosolic innate immune receptors that bind RNA. We focus on new aspects of endogenous ligand recognition uncovered in these studies, and their roles in disease pathogenesis.
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Affiliation(s)
- Sarah Straub
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, School of Clinical Sciences, Monash University, Clayton, VIC, Australia
| | - Natalia G. Sampaio
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, School of Clinical Sciences, Monash University, Clayton, VIC, Australia
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22
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Morales C, Fernandez M, Ferrer R, Raimunda D, Carrer DC, Bollo M. Ursodeoxycholic Acid Binds PERK and Ameliorates Neurite Atrophy in a Cellular Model of GM2 Gangliosidosis. Int J Mol Sci 2023; 24:7209. [PMID: 37108372 PMCID: PMC10138647 DOI: 10.3390/ijms24087209] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 04/29/2023] Open
Abstract
The Unfolded protein response (UPR), triggered by stress in the endoplasmic reticulum (ER), is a key driver of neurodegenerative diseases. GM2 gangliosidosis, which includes Tay-Sachs and Sandhoff disease, is caused by an accumulation of GM2, mainly in the brain, that leads to progressive neurodegeneration. Previously, we demonstrated in a cellular model of GM2 gangliosidosis that PERK, a UPR sensor, contributes to neuronal death. There is currently no approved treatment for these disorders. Chemical chaperones, such as ursodeoxycholic acid (UDCA), have been found to alleviate ER stress in cell and animal models. UDCA's ability to move across the blood-brain barrier makes it interesting as a therapeutic tool. Here, we found that UDCA significantly diminished the neurite atrophy induced by GM2 accumulation in primary neuron cultures. It also decreased the up-regulation of pro-apoptotic CHOP, a downstream PERK-signaling component. To explore its potential mechanisms of action, in vitro kinase assays and crosslinking experiments were performed with different variants of recombinant protein PERK, either in solution or in reconstituted liposomes. The results suggest a direct interaction between UDCA and the cytosolic domain of PERK, which promotes kinase phosphorylation and dimerization.
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Affiliation(s)
| | | | | | | | | | - Mariana Bollo
- Instituto de Investigación Médica M y M Ferreyra, INIMEC-CONICET, Universidad Nacional de Córdoba, Córdoba 5016, Argentina
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23
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Cusack KP, Argiriadi MA, Gordon TD, Harris CM, Herold JM, Hoemann MZ, Yestrepsky BD. Identification of potent and selective inhibitors of PKR via virtual screening and traditional design. Bioorg Med Chem Lett 2023; 79:129047. [PMID: 36400288 DOI: 10.1016/j.bmcl.2022.129047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/05/2022] [Accepted: 11/03/2022] [Indexed: 11/17/2022]
Abstract
Protein Kinase RNA-activated (PKR) inhibition is thought to be relevant for immunology due to the potential to reduce macrophage and dendritic cell responses to bacteria and its signaling downstream of TNFα. PKR is also associated with neuroscience indications such as Alzheimer's disease due to its activation by the double stranded DNA (dsDNA) virus HSV1, a virus suggested to be important in the development of AD. Studies exploring the mechanistic role of PKR with existing tool molecules such as the tricyclic oxindole C16 are clouded by the poor selectivity profile of this ATP-competitive, Type I kinase inhibitor. Type II kinase leads such as the benzothiophene or pyrazolopyrimidine scaffolds from literature are equally poor in their selectivity profiles. As such, it became necessary to identify more potent and selective chemical matter to better understand PKR biology. A dual approach was taken. The first step of the strategy included virtual screening of the AbbVie compound collection. A combination of pharmacophore-based and GPU shape-based screening was pursued to identify selective chemical matter from promiscuous leads. The second step of the strategy followed traditional compound design. This step initiated from a literature lead with PKR cross reactivity. Combined, the two parallel efforts led to identification of more selective leads for investigation of PKR biology.
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Affiliation(s)
- K P Cusack
- AbbVie Bioresearch Center, 381 Plantation Street, Worcester, MA 01605, United States.
| | - M A Argiriadi
- AbbVie Bioresearch Center, 381 Plantation Street, Worcester, MA 01605, United States
| | | | - C M Harris
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, MA 01605, United States
| | - J M Herold
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, MA 01605, United States
| | - M Z Hoemann
- AbbVie Bioresearch Center, 381 Plantation Street, Worcester, MA 01605, United States
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24
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Zhou L, Cheng A, Wang M, Wu Y, Yang Q, Tian B, Ou X, Sun D, Zhang S, Mao S, Zhao XX, Huang J, Gao Q, Zhu D, Jia R, Liu M, Chen S. Mechanism of herpesvirus protein kinase UL13 in immune escape and viral replication. Front Immunol 2022; 13:1088690. [PMID: 36531988 PMCID: PMC9749954 DOI: 10.3389/fimmu.2022.1088690] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/15/2022] [Indexed: 12/05/2022] Open
Abstract
Upon infection, the herpes viruses create a cellular environment suitable for survival, but innate immunity plays a vital role in cellular resistance to viral infection. The UL13 protein of herpesviruses is conserved among all herpesviruses and is a serine/threonine protein kinase, which plays a vital role in escaping innate immunity and promoting viral replication. On the one hand, it can target various immune signaling pathways in vivo, such as the cGAS-STING pathway and the NF-κB pathway. On the other hand, it phosphorylates regulatory many cellular and viral proteins for promoting the lytic cycle. This paper reviews the research progress of the conserved herpesvirus protein kinase UL13 in immune escape and viral replication to provide a basis for elucidating the pathogenic mechanism of herpesviruses, as well as providing insights into the potential means of immune escape and viral replication of other herpesviruses that have not yet resolved the function of it.
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Affiliation(s)
- Lin Zhou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China,*Correspondence: Mingshu Wang,
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xin-Xin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
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25
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Fahie KMM, Papanicolaou KN, Zachara NE. Integration of O-GlcNAc into Stress Response Pathways. Cells 2022; 11:3509. [PMID: 36359905 PMCID: PMC9654274 DOI: 10.3390/cells11213509] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
The modification of nuclear, mitochondrial, and cytosolic proteins by O-linked βN-acetylglucosamine (O-GlcNAc) has emerged as a dynamic and essential post-translational modification of mammalian proteins. O-GlcNAc is cycled on and off over 5000 proteins in response to diverse stimuli impacting protein function and, in turn, epigenetics and transcription, translation and proteostasis, metabolism, cell structure, and signal transduction. Environmental and physiological injury lead to complex changes in O-GlcNAcylation that impact cell and tissue survival in models of heat shock, osmotic stress, oxidative stress, and hypoxia/reoxygenation injury, as well as ischemic reperfusion injury. Numerous mechanisms that appear to underpin O-GlcNAc-mediated survival include changes in chaperone levels, impacts on the unfolded protein response and integrated stress response, improvements in mitochondrial function, and reduced protein aggregation. Here, we discuss the points at which O-GlcNAc is integrated into the cellular stress response, focusing on the roles it plays in the cardiovascular system and in neurodegeneration.
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Affiliation(s)
- Kamau M. M. Fahie
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kyriakos N. Papanicolaou
- Department of Medicine, Division of Cardiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Natasha E. Zachara
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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26
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Crocodilepox Virus Protein 157 Is an Independently Evolved Inhibitor of Protein Kinase R. Viruses 2022; 14:v14071564. [PMID: 35891544 PMCID: PMC9318007 DOI: 10.3390/v14071564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 02/05/2023] Open
Abstract
Crocodilepox virus (CRV) belongs to the Poxviridae family and mainly infects hatchling and juvenile Nile crocodiles. Most poxviruses encode inhibitors of the host antiviral protein kinase R (PKR), which is activated by viral double-stranded (ds) RNA formed during virus replication, resulting in the phosphorylation of eIF2α and the subsequent shutdown of general mRNA translation. Because CRV lacks orthologs of known poxviral PKR inhibitors, we experimentally characterized one candidate (CRV157), which contains a predicted dsRNA-binding domain. Bioinformatic analyses indicated that CRV157 evolved independently from other poxvirus PKR inhibitors. CRV157 bound to dsRNA, co-localized with PKR in the cytosol, and inhibited PKR from various species. To analyze whether CRV157 could inhibit PKR in the context of a poxvirus infection, we constructed recombinant vaccinia virus strains that contain either CRV157, or a mutant CRV157 deficient in dsRNA binding in a strain that lacks PKR inhibitors. The presence of wild-type CRV157 rescued vaccinia virus replication, while the CRV157 mutant did not. The ability of CRV157 to inhibit PKR correlated with virus replication and eIF2α phosphorylation. The independent evolution of CRV157 demonstrates that poxvirus PKR inhibitors evolved from a diverse set of ancestral genes in an example of convergent evolution.
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27
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Olson AT, Child SJ, Geballe AP. Antagonism of Protein Kinase R by Large DNA Viruses. Pathogens 2022; 11:pathogens11070790. [PMID: 35890034 PMCID: PMC9319463 DOI: 10.3390/pathogens11070790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/02/2022] Open
Abstract
Decades of research on vaccinia virus (VACV) have provided a wealth of insights and tools that have proven to be invaluable in a broad range of studies of molecular virology and pathogenesis. Among the challenges that viruses face are intrinsic host cellular defenses, such as the protein kinase R pathway, which shuts off protein synthesis in response to the dsRNA that accumulates during replication of many viruses. Activation of PKR results in phosphorylation of the α subunit of eukaryotic initiation factor 2 (eIF2α), inhibition of protein synthesis, and limited viral replication. VACV encodes two well-characterized antagonists, E3L and K3L, that can block the PKR pathway and thus enable the virus to replicate efficiently. The use of VACV with a deletion of the dominant factor, E3L, enabled the initial identification of PKR antagonists encoded by human cytomegalovirus (HCMV), a prevalent and medically important virus. Understanding the molecular mechanisms of E3L and K3L function facilitated the dissection of the domains, species-specificity, and evolutionary potential of PKR antagonists encoded by human and nonhuman CMVs. While remaining cognizant of the substantial differences in the molecular virology and replication strategies of VACV and CMVs, this review illustrates how VACV can provide a valuable guide for the study of other experimentally less tractable viruses.
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Affiliation(s)
- Annabel T. Olson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, 1100 Fairview Ave N Seattle, P.O. Box 19024, Seattle, WA 98109, USA; (A.T.O.); (S.J.C.)
- Departments of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Stephanie J. Child
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, 1100 Fairview Ave N Seattle, P.O. Box 19024, Seattle, WA 98109, USA; (A.T.O.); (S.J.C.)
| | - Adam P. Geballe
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, 1100 Fairview Ave N Seattle, P.O. Box 19024, Seattle, WA 98109, USA; (A.T.O.); (S.J.C.)
- Departments of Microbiology, University of Washington, Seattle, WA 98195, USA
- Departments of Medicine, University of Washington, Seattle, WA 98195, USA
- Correspondence:
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28
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Zappa F, Muniozguren NL, Wilson MZ, Costello MS, Ponce-Rojas JC, Acosta-Alvear D. Signaling by the integrated stress response kinase PKR is fine-tuned by dynamic clustering. J Cell Biol 2022; 221:213199. [PMID: 35522180 PMCID: PMC9086502 DOI: 10.1083/jcb.202111100] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/15/2022] [Accepted: 04/05/2022] [Indexed: 12/16/2022] Open
Abstract
The double-stranded RNA sensor kinase PKR is one of four integrated stress response (ISR) sensor kinases that phosphorylate the α subunit of eukaryotic initiation factor 2 (eIF2α) in response to stress. The current model of PKR activation considers the formation of back-to-back PKR dimers as a prerequisite for signal propagation. Here we show that PKR signaling involves the assembly of dynamic PKR clusters. PKR clustering is driven by ligand binding to PKR’s sensor domain and by front-to-front interfaces between PKR’s kinase domains. PKR clusters are discrete, heterogeneous, autonomous coalescences that share some protein components with processing bodies. Strikingly, eIF2α is not recruited to PKR clusters, and PKR cluster disruption enhances eIF2α phosphorylation. Together, these results support a model in which PKR clustering may limit encounters between PKR and eIF2α to buffer downstream signaling and prevent the ISR from misfiring.
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Affiliation(s)
- Francesca Zappa
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA
| | - Nerea L Muniozguren
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA
| | - Maxwell Z Wilson
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA
| | - Michael S Costello
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA
| | - Jose Carlos Ponce-Rojas
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA
| | - Diego Acosta-Alvear
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA
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29
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The role of eIF2 phosphorylation in cell and organismal physiology: new roles for well-known actors. Biochem J 2022; 479:1059-1082. [PMID: 35604373 DOI: 10.1042/bcj20220068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 02/06/2023]
Abstract
Control of protein synthesis (mRNA translation) plays key roles in shaping the proteome and in many physiological, including homeostatic, responses. One long-known translational control mechanism involves phosphorylation of initiation factor, eIF2, which is catalysed by any one of four protein kinases, which are generally activated in response to stresses. They form a key arm of the integrated stress response (ISR). Phosphorylated eIF2 inhibits eIF2B (the protein that promotes exchange of eIF2-bound GDP for GTP) and thus impairs general protein synthesis. However, this mechanism actually promotes translation of certain mRNAs by virtue of specific features they possess. Recent work has uncovered many previously unknown features of this regulatory system. Several studies have yielded crucial insights into the structure and control of eIF2, including that eIF2B is regulated by several metabolites. Recent studies also reveal that control of eIF2 and the ISR helps determine organismal lifespan and surprising roles in sensing mitochondrial stresses and in controlling the mammalian target of rapamycin (mTOR). The latter effect involves an unexpected role for one of the eIF2 kinases, HRI. Phosphoproteomic analysis identified new substrates for another eIF2 kinase, Gcn2, which senses the availability of amino acids. Several genetic disorders arise from mutations in genes for eIF2α kinases or eIF2B (i.e. vanishing white matter disease, VWM and microcephaly, epileptic seizures, microcephaly, hypogenitalism, diabetes and obesity, MEHMO). Furthermore, the eIF2-mediated ISR plays roles in cognitive decline associated with Alzheimer's disease. New findings suggest potential therapeutic value in interfering with the ISR in certain settings, including VWM, for example by using compounds that promote eIF2B activity.
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Maladaptation after a virus host switch leads to increased activation of the pro-inflammatory NF-κB pathway. Proc Natl Acad Sci U S A 2022; 119:e2115354119. [PMID: 35549551 PMCID: PMC9171774 DOI: 10.1073/pnas.2115354119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Myxoma virus (MYXV) is benign in the natural brush rabbit host but causes a fatal disease in European rabbits. Here, we demonstrate that MYXV M156 inhibited brush rabbit protein kinase R (bPKR) more efficiently than European rabbit PKR (ePKR). Because ePKR was not completely inhibited by M156, there was a depletion of short–half-life proteins like the nuclear factor kappa B (NF-κB) inhibitor IκBα, concomitant NF-κB activation and NF-κB target protein expression in ePKR-expressing cells. NF-κB pathway activation was blocked by either hypoactive or hyperactive M156 mutants. This demonstrates that maladaptation of viral immune antagonists can result in substantially different immune responses in aberrant hosts. These different host responses may contribute to altered viral dissemination and may influence viral pathogenesis. Myxoma virus (MYXV) causes localized cutaneous fibromas in its natural hosts, tapeti and brush rabbits; however, in the European rabbit, MYXV causes the lethal disease myxomatosis. Currently, the molecular mechanisms underlying this increased virulence after cross-species transmission are poorly understood. In this study, we investigated the interaction between MYXV M156 and the host protein kinase R (PKR) to determine their crosstalk with the proinflammatory nuclear factor kappa B (NF-κB) pathway. Our results demonstrated that MYXV M156 inhibits brush rabbit PKR (bPKR) more strongly than European rabbit PKR (ePKR). This moderate ePKR inhibition could be improved by hyperactive M156 mutants. We hypothesized that the moderate inhibition of ePKR by M156 might incompletely suppress the signal transduction pathways modulated by PKR, such as the NF-κB pathway. Therefore, we analyzed NF-κB pathway activation with a luciferase-based promoter assay. The moderate inhibition of ePKR resulted in significantly higher NF-κB–dependent reporter activity than complete inhibition of bPKR. We also found a stronger induction of the NF-κB target genes TNFα and IL-6 in ePKR-expressing cells than in bPKR-expressing cells in response to M156 in both transfection and infections assays. Furthermore, a hyperactive M156 mutant did not cause ePKR-dependent NF-κB activation. These observations indicate that M156 is maladapted for ePKR inhibition, only incompletely blocking translation in these hosts, resulting in preferential depletion of short–half-life proteins, such as the NF-κB inhibitor IκBα. We speculate that this functional activation of NF-κB induced by the intermediate inhibition of ePKR by M156 may contribute to the increased virulence of MYXV in European rabbits.
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Papendorf JJ, Krüger E, Ebstein F. Proteostasis Perturbations and Their Roles in Causing Sterile Inflammation and Autoinflammatory Diseases. Cells 2022; 11:cells11091422. [PMID: 35563729 PMCID: PMC9103147 DOI: 10.3390/cells11091422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/04/2022] [Accepted: 04/14/2022] [Indexed: 12/17/2022] Open
Abstract
Proteostasis, a portmanteau of the words protein and homeostasis, refers to the ability of eukaryotic cells to maintain a stable proteome by acting on protein synthesis, quality control and/or degradation. Over the last two decades, an increasing number of disorders caused by proteostasis perturbations have been identified. Depending on their molecular etiology, such diseases may be classified into ribosomopathies, proteinopathies and proteasomopathies. Strikingly, most—if not all—of these syndromes exhibit an autoinflammatory component, implying a direct cause-and-effect relationship between proteostasis disruption and the initiation of innate immune responses. In this review, we provide a comprehensive overview of the molecular pathogenesis of these disorders and summarize current knowledge of the various mechanisms by which impaired proteostasis promotes autoinflammation. We particularly focus our discussion on the notion of how cells sense and integrate proteostasis perturbations as danger signals in the context of autoinflammatory diseases to provide insights into the complex and multiple facets of sterile inflammation.
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Levina A, Fleming KD, Burke JE, Leonard TA. Activation of the essential kinase PDK1 by phosphoinositide-driven trans-autophosphorylation. Nat Commun 2022; 13:1874. [PMID: 35387990 PMCID: PMC8986801 DOI: 10.1038/s41467-022-29368-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 03/08/2022] [Indexed: 12/18/2022] Open
Abstract
3-phosphoinositide-dependent kinase 1 (PDK1) is an essential serine/threonine protein kinase, which plays a crucial role in cell growth and proliferation. It is often referred to as a 'master' kinase due to its ability to activate at least 23 downstream protein kinases implicated in various signaling pathways. In this study, we have elucidated the mechanism of phosphoinositide-driven PDK1 auto-activation. We show that PDK1 trans-autophosphorylation is mediated by a PIP3-mediated face-to-face dimer. We report regulatory motifs in the kinase-PH interdomain linker that allosterically activate PDK1 autophosphorylation via a linker-swapped dimer mechanism. Finally, we show that PDK1 is autoinhibited by its PH domain and that positive cooperativity of PIP3 binding drives switch-like activation of PDK1. These results imply that the PDK1-mediated activation of effector kinases, including Akt, PKC, Sgk, S6K and RSK, many of whom are not directly regulated by phosphoinositides, is also likely to be dependent on PIP3 or PI(3,4)P2.
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Affiliation(s)
- Aleksandra Levina
- Department of Structural and Computational Biology, Max Perutz Labs, Campus Vienna Biocenter 5, 1030, Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, 1090, Vienna, Austria
| | - Kaelin D Fleming
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max Perutz Labs, Campus Vienna Biocenter 5, 1030, Vienna, Austria.
- Department of Medical Biochemistry, Medical University of Vienna, 1090, Vienna, Austria.
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Chan CP, Jin DY. Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations. RNA (NEW YORK, N.Y.) 2022; 28:449-477. [PMID: 35031583 PMCID: PMC8925969 DOI: 10.1261/rna.079016.121] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Sensing of pathogen-associated molecular patterns including viral RNA by innate immunity represents the first line of defense against viral infection. In addition to RIG-I-like receptors and NOD-like receptors, several other RNA sensors are known to mediate innate antiviral response in the cytoplasm. Double-stranded RNA-binding protein PACT interacts with prototypic RNA sensor RIG-I to facilitate its recognition of viral RNA and induction of host interferon response, but variations of this theme are seen when the functions of RNA sensors are modulated by other RNA-binding proteins to impinge on antiviral defense, proinflammatory cytokine production and cell death programs. Their discrete and coordinated actions are crucial to protect the host from infection. In this review, we will focus on cytoplasmic RNA sensors with an emphasis on their interplay with RNA-binding partners. Classical sensors such as RIG-I will be briefly reviewed. More attention will be brought to new insights on how RNA-binding partners of RNA sensors modulate innate RNA sensing and how viruses perturb the functions of RNA-binding partners.
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Affiliation(s)
- Chi-Ping Chan
- School of Biomedical Sciences and State Key Laboratory of Liver Research, Faculty of Medicine Building, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences and State Key Laboratory of Liver Research, Faculty of Medicine Building, Pokfulam, Hong Kong
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34
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Klein P, Kallenberger SM, Roth H, Roth K, Ly-Hartig TBN, Magg V, Aleš J, Talemi SR, Qiang Y, Wolf S, Oleksiuk O, Kurilov R, Di Ventura B, Bartenschlager R, Eils R, Rohr K, Hamprecht FA, Höfer T, Fackler OT, Stoecklin G, Ruggieri A. Temporal control of the integrated stress response by a stochastic molecular switch. SCIENCE ADVANCES 2022; 8:eabk2022. [PMID: 35319985 PMCID: PMC8942376 DOI: 10.1126/sciadv.abk2022] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Stress granules (SGs) are formed in the cytosol as an acute response to environmental cues and activation of the integrated stress response (ISR), a central signaling pathway controlling protein synthesis. Using chronic virus infection as stress model, we previously uncovered a unique temporal control of the ISR resulting in recurrent phases of SG assembly and disassembly. Here, we elucidate the molecular network generating this fluctuating stress response by integrating quantitative experiments with mathematical modeling and find that the ISR operates as a stochastic switch. Key elements controlling this switch are the cooperative activation of the stress-sensing kinase PKR, the ultrasensitive response of SG formation to the phosphorylation of the translation initiation factor eIF2α, and negative feedback via GADD34, a stress-induced subunit of protein phosphatase 1. We identify GADD34 messenger RNA levels as the molecular memory of the ISR that plays a central role in cell adaptation to acute and chronic stress.
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Affiliation(s)
- Philipp Klein
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg University, Heidelberg, Germany
| | - Stefan M. Kallenberger
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin, Germany
- Medical Oncology, National Center for Tumor Diseases, Heidelberg University, Heidelberg, Germany
| | - Hanna Roth
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg University, Heidelberg, Germany
| | - Karsten Roth
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg University, Heidelberg, Germany
| | - Thi Bach Nga Ly-Hartig
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Vera Magg
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg University, Heidelberg, Germany
| | - Janez Aleš
- HCI/IWR, Heidelberg University, Heidelberg, Germany
| | - Soheil Rastgou Talemi
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yu Qiang
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University, Heidelberg, Germany
| | - Steffen Wolf
- HCI/IWR, Heidelberg University, Heidelberg, Germany
| | - Olga Oleksiuk
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg University, Heidelberg, Germany
| | - Roma Kurilov
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Di Ventura
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg University, Heidelberg, Germany
- Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin, Germany
| | - Karl Rohr
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University, Heidelberg, Germany
| | | | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver T. Fackler
- Department of Infectious Diseases, Integrative Virology, Center for Integrative Infectious Diseases Research, Heidelberg University, Heidelberg, Germany
| | - Georg Stoecklin
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg University, Heidelberg, Germany
- Corresponding author.
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35
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Chen YG, Hur S. Cellular origins of dsRNA, their recognition and consequences. Nat Rev Mol Cell Biol 2021; 23:286-301. [PMID: 34815573 DOI: 10.1038/s41580-021-00430-1] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2021] [Indexed: 01/02/2023]
Abstract
Double-stranded RNA (dsRNA) is associated with most viral infections - it either constitutes the viral genome (in the case of dsRNA viruses) or is generated in host cells during viral replication. Hence, nearly all organisms have the capability of recognizing dsRNA and mounting a response, the primary aim of which is to mitigate the potential infection. In vertebrates, a set of innate immune receptors for dsRNA induce a multitude of cell-intrinsic and cell-extrinsic immune responses upon dsRNA recognition. Notably, recent studies showed that vertebrate cells can accumulate self-derived dsRNAs or dsRNA-like species upon dysregulation of several cellular processes, activating the very same immune pathways as in infected cells. On the one hand, such aberrant immune activation in the absence of infection can lead to pathogenesis of immune disorders, such as Aicardi-Goutières syndrome. On the other hand, the same innate immune reaction can be induced in a controlled setting for a therapeutic benefit, as occurs in immunotherapies. In this Review, we describe mechanisms by which immunostimulatory dsRNAs are generated in mammalian cells, either by viruses or by the host cells, and how cells respond to them, with the focus on recent developments regarding the role of cellular dsRNAs in immune modulation.
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Affiliation(s)
- Y Grace Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
| | - Sun Hur
- Harvard Medical School & Boston Children's Hospital, Boston, MA, USA.
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36
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Chitrakar A, Solorio-Kirpichyan K, Prangley E, Rath S, Du J, Korennykh A. Introns encode dsRNAs undetected by RIG-I/MDA5/interferons and sensed via RNase L. Proc Natl Acad Sci U S A 2021; 118:e2102134118. [PMID: 34772806 PMCID: PMC8609619 DOI: 10.1073/pnas.2102134118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2021] [Indexed: 12/24/2022] Open
Abstract
Double-stranded RNA (dsRNA), a hallmark viral material that activates antiviral interferon (IFN) responses, can appear in human cells also in the absence of viruses. We identify phosphorothioate DNAs (PS DNAs) as triggers of such endogenous dsRNA (endo-dsRNA). PS DNAs inhibit decay of nuclear RNAs and induce endo-dsRNA via accumulation of high levels of intronic and intergenic inverted retroelements (IIIR). IIIRs activate endo-dsRNA responses distinct from antiviral defense programs. IIIRs do not turn on transcriptional RIG-I/MDA5/IFN signaling, but they trigger the dsRNA-sensing pathways of OAS3/RNase L and PKR. Thus, nuclear RNA decay and nuclear-cytosolic RNA sorting actively protect from these innate immune responses to self. Our data suggest that the OAS3/RNase L and PKR arms of innate immunity diverge from antiviral IFN responses and monitor nuclear RNA decay by sensing cytosolic escape of IIIRs. OAS3 provides a receptor for IIIRs, whereas RNase L cleaves IIIR-carrying introns and intergenic RNAs.
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Affiliation(s)
- Alisha Chitrakar
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | | | - Eliza Prangley
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Sneha Rath
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Jin Du
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Alexei Korennykh
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
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37
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Beenstock J, Sicheri F. The structural and functional workings of KEOPS. Nucleic Acids Res 2021; 49:10818-10834. [PMID: 34614169 PMCID: PMC8565320 DOI: 10.1093/nar/gkab865] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/09/2021] [Accepted: 10/04/2021] [Indexed: 11/14/2022] Open
Abstract
KEOPS (Kinase, Endopeptidase and Other Proteins of Small size) is a five-subunit protein complex that is highly conserved in eukaryotes and archaea and is essential for the fitness of cells and for animal development. In humans, mutations in KEOPS genes underlie Galloway-Mowat syndrome, which manifests in severe microcephaly and renal dysfunction that lead to childhood death. The Kae1 subunit of KEOPS catalyzes the universal and essential tRNA modification N6-threonylcarbamoyl adenosine (t6A), while the auxiliary subunits Cgi121, the kinase/ATPase Bud32, Pcc1 and Gon7 play a supporting role. Kae1 orthologs are also present in bacteria and mitochondria but function in distinct complexes with proteins that are not related in structure or function to the auxiliary subunits of KEOPS. Over the past 15 years since its discovery, extensive study in the KEOPS field has provided many answers towards understanding the roles that KEOPS plays in cells and in human disease and how KEOPS carries out these functions. In this review, we provide an overview into recent advances in the study of KEOPS and illuminate exciting future directions.
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Affiliation(s)
- Jonah Beenstock
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Frank Sicheri
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Ontario, M5S 1A8, Canada.,Department of Biochemistry, University of Toronto, Ontario, M5S 1A8, Canada
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38
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Chukwurah E, Farabaugh KT, Guan BJ, Ramakrishnan P, Hatzoglou M. A tale of two proteins: PACT and PKR and their roles in inflammation. FEBS J 2021; 288:6365-6391. [PMID: 33387379 PMCID: PMC9248962 DOI: 10.1111/febs.15691] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/14/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022]
Abstract
Inflammation is a pathological hallmark associated with bacterial and viral infections, autoimmune diseases, genetic disorders, obesity and diabetes, as well as environmental stresses including physical and chemical trauma. Among numerous proteins regulating proinflammatory signaling, very few such as Protein kinase R (PKR), have been shown to play an all-pervading role in inflammation induced by varied stimuli. PKR was initially characterized as an interferon-inducible gene activated by viral double-stranded RNA with a role in protein translation inhibition. However, it has become increasingly clear that PKR is involved in multiple pathways that promote inflammation in response to stress activation, both dependent on and independent of its cellular protein activator of PKR (PACT). In this review, we discuss the signaling pathways that contribute to the initiation of inflammation, including Toll-like receptor, interferon, and RIG-I-like receptor signaling, as well as inflammasome activation. We go on to discuss the specific roles that PKR and PACT play in such proinflammatory signaling, as well as in metabolic syndrome- and environmental stress-induced inflammation.
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Affiliation(s)
- Evelyn Chukwurah
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106
| | - Kenneth T. Farabaugh
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106
| | - Bo-Jhih Guan
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106
| | | | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106
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39
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Dwivedy A, Mariadasse R, Ahmad M, Chakraborty S, Kar D, Tiwari S, Bhattacharyya S, Sonar S, Mani S, Tailor P, Majumdar T, Jeyakanthan J, Biswal BK. Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2. PLoS Comput Biol 2021; 17:e1009384. [PMID: 34516563 PMCID: PMC8478224 DOI: 10.1371/journal.pcbi.1009384] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 09/28/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, a well-known kinase inhibitor- Sorafenib showed a significant inhibition and dampened viral load in SARS-CoV-2 infected cells. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2. The on-going coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is significantly affecting the world health. Unfortunately, over 180 million cases of COVID-19 resulting in nearly 4 million deaths have been reported till June, 2021. In this study, using a combination of bioinformatics, biochemical and mass spectrometry methods, we show that the Nidovirus RdRp associated Nucleotidyl transferase (NiRAN) domain of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 exhibits a kinase like activity. Additionally, we also show that few broad spectrum anti-cancer and anti-microbial drugs dampen this kinase like activity. Of note, Sorafenib, an FDA approved anti-cancer kinase inhibiting drug significantly reduces the SARS-CoV-2 load in cell lines. Our study suggests that NiRAN domain of the SARS-CoV-2 RdRp is indispensible for the successful viral life cycle and shows that abolishing this enzymatic function of RdRp by small molecule inhibitors may open novel avenues for COVID-19 therapeutics.
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Affiliation(s)
| | | | | | | | | | | | | | - Sudipta Sonar
- Translational Health Science and Technology Institute, Faridabad, India
| | - Shailendra Mani
- Translational Health Science and Technology Institute, Faridabad, India
| | | | - Tanmay Majumdar
- National Institute of Immunology, New Delhi, India
- * E-mail: (TM); (JJ); (BKB)
| | - Jeyaraman Jeyakanthan
- Department of Bioinformatics, Alagappa University, Tamil Nadu, India
- * E-mail: (TM); (JJ); (BKB)
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40
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Dwivedy A, Mariadasse R, Ahmad M, Chakraborty S, Kar D, Tiwari S, Bhattacharyya S, Sonar S, Mani S, Tailor P, Majumdar T, Jeyakanthan J, Biswal BK. Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2. PLoS Comput Biol 2021. [DOI: https://doi.org/10.1371/journal.pcbi.1009384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, a well-known kinase inhibitor- Sorafenib showed a significant inhibition and dampened viral load in SARS-CoV-2 infected cells. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2.
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41
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Muñoz C, González-Lorca J, Parra M, Soto S, Valdes N, Sandino AM, Vargas R, González A, Tello M. Lactococcus lactis Expressing Type I Interferon From Atlantic Salmon Enhances the Innate Antiviral Immune Response In Vivo and In Vitro. Front Immunol 2021; 12:696781. [PMID: 34475871 PMCID: PMC8406758 DOI: 10.3389/fimmu.2021.696781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
In salmon farming, viruses are responsible for outbreaks that produce significant economic losses for which there is a lack of control tools other than vaccines. Type I interferon has been successfully used for treating some chronic viral infections in humans. However, its application in salmonids depends on the proper design of a vehicle that allows its massive administration, ideally orally. In mammals, administration of recombinant probiotics capable of expressing cytokines has shown local and systemic therapeutic effects. In this work, we evaluate the use of Lactococcus lactis as a type I Interferon expression system in Atlantic salmon, and we analyze its ability to stimulate the antiviral immune response against IPNV, in vivo and in vitro. The interferon expressed in L. lactis, even though it was located mainly in the bacterial cytoplasm, was functional, stimulating Mx and PKR expression in CHSE-214 cells, and reducing the IPNV viral load in SHK-1 cells. In vivo, the oral administration of this L. lactis producer of Interferon I increases Mx and PKR expression, mainly in the spleen, and to a lesser extent, in the head kidney. The oral administration of this strain also reduces the IPNV viral load in Atlantic salmon specimens challenged with this pathogen. Our results show that oral administration of L. lactis producing Interferon I induces systemic effects in Atlantic salmon, allowing to stimulate the antiviral immune response. This probiotic could have effects against a wide variety of viruses that infect Atlantic salmon and also be effective in other salmonids due to the high identity among their type I interferons.
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Affiliation(s)
- Carlos Muñoz
- Laboratorio de Metagenómica Bacteriana, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Josue González-Lorca
- Laboratorio de Metagenómica Bacteriana, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Mick Parra
- Laboratorio de Metagenómica Bacteriana, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Sarita Soto
- Laboratorio de Metagenómica Bacteriana, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Natalia Valdes
- Laboratorio de Metagenómica Bacteriana, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Ana María Sandino
- Laboratorio de Virología, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,ActivaQ S.A., Santiago, Chile
| | - Rodrigo Vargas
- Laboratorio de Metagenómica Bacteriana, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Alex González
- Laboratorio de Microbiología Ambiental y Extremófilos, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de los Lagos, Osorno, Chile
| | - Mario Tello
- Laboratorio de Metagenómica Bacteriana, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,IctioBiotic SpA, Santiago, Chile
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42
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Truebestein L, Hornegger H, Anrather D, Hartl M, Fleming KD, Stariha JTB, Pardon E, Steyaert J, Burke JE, Leonard TA. Structure of autoinhibited Akt1 reveals mechanism of PIP 3-mediated activation. Proc Natl Acad Sci U S A 2021; 118:e2101496118. [PMID: 34385319 PMCID: PMC8379990 DOI: 10.1073/pnas.2101496118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The protein kinase Akt is one of the primary effectors of growth factor signaling in the cell. Akt responds specifically to the lipid second messengers phosphatidylinositol-3,4,5-trisphosphate [PI(3,4,5)P3] and phosphatidylinositol-3,4-bisphosphate [PI(3,4)P2] via its PH domain, leading to phosphorylation of its activation loop and the hydrophobic motif of its kinase domain, which are critical for activity. We have now determined the crystal structure of Akt1, revealing an autoinhibitory interface between the PH and kinase domains that is often mutated in cancer and overgrowth disorders. This interface persists even after stoichiometric phosphorylation, thereby restricting maximum Akt activity to PI(3,4,5)P3- or PI(3,4)P2-containing membranes. Our work helps to resolve the roles of lipids and phosphorylation in the activation of Akt and has wide implications for the spatiotemporal control of Akt and potentially lipid-activated kinase signaling in general.
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Affiliation(s)
- Linda Truebestein
- Department of Structural and Computational Biology, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, 1090 Vienna, Austria
| | - Harald Hornegger
- Department of Structural and Computational Biology, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, 1090 Vienna, Austria
| | - Dorothea Anrather
- Mass Spectrometry Core Facility, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria
| | - Markus Hartl
- Mass Spectrometry Core Facility, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria
| | - Kaelin D Fleming
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Jordan T B Stariha
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria;
- Department of Medical Biochemistry, Medical University of Vienna, 1090 Vienna, Austria
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43
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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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44
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Padariya M, Sznarkowska A, Kote S, Gómez-Herranz M, Mikac S, Pilch M, Alfaro J, Fahraeus R, Hupp T, Kalathiya U. Functional Interfaces, Biological Pathways, and Regulations of Interferon-Related DNA Damage Resistance Signature (IRDS) Genes. Biomolecules 2021; 11:622. [PMID: 33922087 PMCID: PMC8143464 DOI: 10.3390/biom11050622] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/15/2021] [Accepted: 04/20/2021] [Indexed: 12/14/2022] Open
Abstract
Interferon (IFN)-related DNA damage resistant signature (IRDS) genes are a subgroup of interferon-stimulated genes (ISGs) found upregulated in different cancer types, which promotes resistance to DNA damaging chemotherapy and radiotherapy. Along with briefly discussing IFNs and signalling in this review, we highlighted how different IRDS genes are affected by viruses. On the contrary, different strategies adopted to suppress a set of IRDS genes (STAT1, IRF7, OAS family, and BST2) to induce (chemo- and radiotherapy) sensitivity were deliberated. Significant biological pathways that comprise these genes were classified, along with their frequently associated genes (IFIT1/3, IFITM1, IRF7, ISG15, MX1/2 and OAS1/3/L). Major upstream regulators from the IRDS genes were identified, and different IFN types regulating these genes were outlined. Functional interfaces of IRDS proteins with DNA/RNA/ATP/GTP/NADP biomolecules featured a well-defined pharmacophore model for STAT1/IRF7-dsDNA and OAS1/OAS3/IFIH1-dsRNA complexes, as well as for the genes binding to GDP or NADP+. The Lys amino acid was found commonly interacting with the ATP phosphate group from OAS1/EIF2AK2/IFIH1 genes. Considering the premise that targeting IRDS genes mediated resistance offers an efficient strategy to resensitize tumour cells and enhances the outcome of anti-cancer treatment, this review can add some novel insights to the field.
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Affiliation(s)
- Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Alicja Sznarkowska
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Maria Gómez-Herranz
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Sara Mikac
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Magdalena Pilch
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Javier Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, F-75010 Paris, France
- Department of Medical Biosciences, Building 6M, Umeå University, 901 85 Umeå, Sweden
- RECAMO, Masaryk Memorial Cancer Institute, Zlutykopec 7, 65653 Brno, Czech Republic
| | - Ted Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
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McKellar J, Rebendenne A, Wencker M, Moncorgé O, Goujon C. Mammalian and Avian Host Cell Influenza A Restriction Factors. Viruses 2021; 13:522. [PMID: 33810083 PMCID: PMC8005160 DOI: 10.3390/v13030522] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/27/2022] Open
Abstract
The threat of a new influenza pandemic is real. With past pandemics claiming millions of lives, finding new ways to combat this virus is essential. Host cells have developed a multi-modular system to detect incoming pathogens, a phenomenon called sensing. The signaling cascade triggered by sensing subsequently induces protection for themselves and their surrounding neighbors, termed interferon (IFN) response. This response induces the upregulation of hundreds of interferon-stimulated genes (ISGs), including antiviral effectors, establishing an antiviral state. As well as the antiviral proteins induced through the IFN system, cells also possess a so-called intrinsic immunity, constituted of antiviral proteins that are constitutively expressed, creating a first barrier preceding the induction of the interferon system. All these combined antiviral effectors inhibit the virus at various stages of the viral lifecycle, using a wide array of mechanisms. Here, we provide a review of mammalian and avian influenza A restriction factors, detailing their mechanism of action and in vivo relevance, when known. Understanding their mode of action might help pave the way for the development of new influenza treatments, which are absolutely required if we want to be prepared to face a new pandemic.
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Affiliation(s)
- Joe McKellar
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
| | - Antoine Rebendenne
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
| | - Mélanie Wencker
- Centre International de Recherche en Infectiologie, INSERM/CNRS/UCBL1/ENS de Lyon, 69007 Lyon, France;
| | - Olivier Moncorgé
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
| | - Caroline Goujon
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
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Lange SM, Nelen MI, Cohen P, Kulathu Y. Dimeric Structure of the Pseudokinase IRAK3 Suggests an Allosteric Mechanism for Negative Regulation. Structure 2021; 29:238-251.e4. [PMID: 33238146 PMCID: PMC7955167 DOI: 10.1016/j.str.2020.11.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 10/05/2020] [Accepted: 11/02/2020] [Indexed: 01/26/2023]
Abstract
Interleukin-1 receptor associated kinases (IRAKs) are key players in innate immune signaling that mediate the host response to pathogens. In contrast to the active kinases IRAK1 and IRAK4, IRAK2 and IRAK3 are pseudokinases lacking catalytic activity and their functions are poorly understood. IRAK3 is thought to be a negative regulator of innate immune signaling and mutations in IRAK3 are associated with asthma and cancer. Here, we report the crystal structure of the human IRAK3 pseudokinase domain in a closed, pseudoactive conformation. IRAK3 dimerizes in a unique way through a head-to-head arrangement not observed in any other kinases. Multiple conserved cysteine residues imply a potential redox control of IRAK3 conformation and dimerization. By analyzing asthma-associated mutations, we identify an evolutionarily conserved surface on IRAK3 that could form an interaction interface with IRAK4, suggesting a model for the negative regulation of IRAK4 by IRAK3.
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Affiliation(s)
- Sven M Lange
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, Dow Street, Dundee, Scotland DD1 5EH, UK
| | - Marina I Nelen
- Discovery, Janssen Research and Development, Welsh and McKean Roads, Spring House, PA 19477, USA
| | - Philip Cohen
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, Dow Street, Dundee, Scotland DD1 5EH, UK.
| | - Yogesh Kulathu
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, Dow Street, Dundee, Scotland DD1 5EH, UK.
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Park C, Peng C, Rahman MJ, Haller SL, Tazi L, Brennan G, Rothenburg S. Orthopoxvirus K3 orthologs show virus- and host-specific inhibition of the antiviral protein kinase PKR. PLoS Pathog 2021; 17:e1009183. [PMID: 33444388 PMCID: PMC7840043 DOI: 10.1371/journal.ppat.1009183] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 01/27/2021] [Accepted: 11/25/2020] [Indexed: 01/06/2023] Open
Abstract
The antiviral protein kinase R (PKR) is an important host restriction factor, which poxviruses must overcome to productively infect host cells. To inhibit PKR, many poxviruses encode a pseudosubstrate mimic of the alpha subunit of eukaryotic translation initiation factor 2 (eIF2), designated K3 in vaccinia virus. Although the interaction between PKR and eIF2α is highly conserved, some K3 orthologs from host-restricted poxviruses were previously shown to inhibit PKR in a species-specific manner. To better define this host range function, we compared the sensitivity of PKR from 17 mammals to inhibition by K3 orthologs from closely related orthopoxviruses, a genus with a generally broader host range. The K3 orthologs showed species-specific inhibition of PKR and exhibited three distinct inhibition profiles. In some cases, PKR from closely related species showed dramatic differences in their sensitivity to K3 orthologs. Vaccinia virus expressing the camelpox virus K3 ortholog replicated more than three orders of magnitude better in human and sheep cells than a virus expressing vaccinia virus K3, but both viruses replicated comparably well in cow cells. Strikingly, in site-directed mutagenesis experiments between the variola virus and camelpox virus K3 orthologs, we found that different amino acid combinations were necessary to mediate improved or diminished inhibition of PKR derived from different host species. Because there is likely a limited number of possible variations in PKR that affect K3-interactions but still maintain PKR/eIF2α interactions, it is possible that by chance PKR from some potential new hosts may be susceptible to K3-mediated inhibition from a virus it has never previously encountered. We conclude that neither the sensitivity of host proteins to virus inhibition nor the effectiveness of viral immune antagonists can be inferred from their phylogenetic relatedness but must be experimentally determined. Most virus families are composed of large numbers of virus species. However, in general, only a few prototypic viruses are experimentally studied in-depth, and it is often assumed that the obtained results are representative of other viruses in the same family. In order to test this assumption, we compared the sensitivity of the antiviral protein kinase PKR from various mammals to inhibition by multiple orthologs of K3, a PKR inhibitor expressed by several closely related orthopoxviruses. We found strong differences in PKR inhibition by the K3 orthologs, demonstrating that sensitivity to a specific inhibitor was not indicative of broad sensitivity to orthologs of these inhibitors from closely related viruses. We also show that PKR from even closely related species displayed markedly different sensitivities to these poxvirus inhibitors. Furthermore, we identified amino acid residues in these K3 orthologs that are critical for enhanced or decreased PKR inhibition and found that distinct amino acid combinations affected PKRs from various species differently. Our study shows that even closely related inhibitors of an antiviral protein can vary dramatically in their inhibitory potential, and cautions that results from host-virus interaction studies of a prototypic virus genus member cannot necessarily be extrapolated to other viruses in the same genus without experimental verification.
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Affiliation(s)
- Chorong Park
- School of Medicine, University of California Davis, Department of Medial Microbiology and Immunology, Davis, California, United States of America
| | - Chen Peng
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Laboratory of Viral Diseases, Bethesda, Maryland, United States of America
| | - M. Julhasur Rahman
- School of Medicine, University of California Davis, Department of Medial Microbiology and Immunology, Davis, California, United States of America
| | - Sherry L. Haller
- University of Texas Medical Branch at Galveston, Department of Microbiology and Immunology, Galveston, Texas, United States of America
| | - Loubna Tazi
- School of Medicine, University of California Davis, Department of Medial Microbiology and Immunology, Davis, California, United States of America
| | - Greg Brennan
- School of Medicine, University of California Davis, Department of Medial Microbiology and Immunology, Davis, California, United States of America
| | - Stefan Rothenburg
- School of Medicine, University of California Davis, Department of Medial Microbiology and Immunology, Davis, California, United States of America
- * E-mail:
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48
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Higher-order phosphatase-substrate contacts terminate the integrated stress response. Nat Struct Mol Biol 2021; 28:835-846. [PMID: 34625748 PMCID: PMC8500838 DOI: 10.1038/s41594-021-00666-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/23/2021] [Indexed: 01/09/2023]
Abstract
Many regulatory PPP1R subunits join few catalytic PP1c subunits to mediate phosphoserine and phosphothreonine dephosphorylation in metazoans. Regulatory subunits engage the surface of PP1c, locally affecting flexible access of the phosphopeptide to the active site. However, catalytic efficiency of holophosphatases towards their phosphoprotein substrates remains unexplained. Here we present a cryo-EM structure of the tripartite PP1c-PPP1R15A-G-actin holophosphatase that terminates signaling in the mammalian integrated stress response (ISR) in the pre-dephosphorylation complex with its substrate, translation initiation factor 2α (eIF2α). G-actin, whose essential role in eIF2α dephosphorylation is supported crystallographically, biochemically and genetically, aligns the catalytic and regulatory subunits, creating a composite surface that engages the N-terminal domain of eIF2α to position the distant phosphoserine-51 at the active site. Substrate residues that mediate affinity for the holophosphatase also make critical contacts with eIF2α kinases. Thus, a convergent process of higher-order substrate recognition specifies functionally antagonistic phosphorylation and dephosphorylation in the ISR.
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49
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Yang Y, Xie L, Zhong Y, Zhong X, Meng R, Xue Q, Liang F, Zhao K, Tang Y. Double-Stranded RNA Dependent Kinase R Regulates Antibacterial Immunity in Sepsis. J Innate Immun 2020; 13:26-37. [PMID: 33333514 DOI: 10.1159/000507932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 03/25/2020] [Indexed: 12/13/2022] Open
Abstract
Double-stranded RNA dependent kinase R (PKR) is originally identified as an intracellular sensor of viral infection, but its role in bacterial infection remains largely unknown. Here we report that PKR was an important regulator of antibacterial immunity in sepsis. Genetic deletion of PKR or pharmacological inhibition of its kinase activity markedly increased bacterial loads, organ injury, and mortality in polymicrobial infection induced by cecal ligation and puncture (CLP). In contrast, PKR deficiency or inhibition did not affect bacterial loads, organ injury, or mortality when mice were systemically challenged with Escherichia coli, an abundant microbe in the gastrointestinal tract. PKR deficiency or inhibition markedly decreased the release of interleukin (IL)-1β after CLP. Defect in IL-1 signaling phenocopied PKR deficiency or inhibition in CLP-induced bacterial sepsis. Taken together, these findings identified a critical role of the PKR signaling pathway in antibacterial immunity.
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Affiliation(s)
- Yanliang Yang
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Lingli Xie
- Department of Hematology and Key Laboratory of Non-resolving Inflammation and Cancer of Hunan Province, Central South University, Changsha, China.,Department of Pathophysiology, Medical School, Hunan University of Chinese Medicine, Changsha, China
| | - Yanjun Zhong
- The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoli Zhong
- Department of Hematology and Key Laboratory of Non-resolving Inflammation and Cancer of Hunan Province, Central South University, Changsha, China
| | - Ran Meng
- Department of Hematology and Key Laboratory of Non-resolving Inflammation and Cancer of Hunan Province, Central South University, Changsha, China
| | - Qianqian Xue
- Department of Hematology and Key Laboratory of Non-resolving Inflammation and Cancer of Hunan Province, Central South University, Changsha, China
| | - Fang Liang
- Department of Hematology and Key Laboratory of Non-resolving Inflammation and Cancer of Hunan Province, Central South University, Changsha, China
| | - Kai Zhao
- Department of Hematology and Key Laboratory of Non-resolving Inflammation and Cancer of Hunan Province, Central South University, Changsha, China
| | - Yiting Tang
- Department of Physiology, School of Basic Medical Science, Central South University, Changsha, China,
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50
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Teoh PJ, Koh MY, Chng WJ. ADARs, RNA editing and more in hematological malignancies. Leukemia 2020; 35:346-359. [PMID: 33139858 DOI: 10.1038/s41375-020-01076-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/21/2020] [Accepted: 10/20/2020] [Indexed: 02/08/2023]
Abstract
Adenosine-to-inosine (A-to-I) editing is the most prevalent type of RNA editing in humans, mediated by the adenosine deaminases acting on RNA (ADARs). Physiologically, these enzymes are present in the nucleus and/or the cytoplasm, where they catalyze the conversion of adenosines (A) to inosines (I) on double-stranded mRNA molecules. Aberrant ADAR-mediated-editing is a prominent feature in a variety of cancers. Importantly, the biological functions of ADARs and its functional implications in hematological malignancies have recently been unraveled. In this review, we will highlight the functions of ADARs and their involvements in cancer, specifically in hematological malignancies. RNA editing-independent function of cellular processes by ADARs and the potential of developing novel therapeutic approaches revolving RNA editing will also be discussed.
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Affiliation(s)
- Phaik Ju Teoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, Singapore, Singapore
| | - Mun Yee Koh
- Cancer Science Institute of Singapore, Singapore, Singapore
| | - Wee Joo Chng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Cancer Science Institute of Singapore, Singapore, Singapore. .,Department of Haematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore, Singapore.
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