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Structural homology screens reveal host-derived poxvirus protein families impacting inflammasome activity
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Abstract
Viruses acquire host genes via horizontal transfer and can express them to manipulate host biology during infections. Some homologs retain sequence identity, but evolutionary divergence can obscure host origins. We use structural modeling to compare vaccinia virus proteins with metazoan proteomes. We identify vaccinia A47L as a homolog of gasdermins, the executioners of pyroptosis. An X-ray crystal structure of A47 confirms this homology, and cell-based assays reveal that A47 interferes with caspase function. We also identify vaccinia C1L as the product of a cryptic gene fusion event coupling a Bcl-2-related fold with a pyrin domain. C1 associates with components of the inflammasome, a cytosolic innate immune sensor involved in pyroptosis, yet paradoxically enhances inflammasome activity, suggesting differential modulation during infections. Our findings demonstrate the increasing power of structural homology screens to reveal proteins with unique combinations of domains that viruses capture from host genes and combine in unique ways.
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Flagged first, then by citations
Research works printed but not linked: 67
- Irwin, 2022, Systematic evaluation of horizontal gene transfer between eukaryotes and viruses, Nat. Microbiol., 7, 327, 10.1038/s41564-021-01026-3 · DOI
- Alcami, 2000, Viral mechanisms of immune evasion, Trends Microbiol., 8, 410, 10.1016/S0966-842X(00)01830-8 · DOI
- Fixsen, 2022, Poxviruses capture host genes by LINE-1 retrotransposition, Elife, 11, e63332, 10.7554/eLife.63332 · DOI
- Rahman, 2022, LINE-1 retrotransposons facilitate horizontal gene transfer into poxviruses, Elife, 11, e63327, 10.7554/eLife.63327 · DOI
- Salomon, 2013, What pathogens have taught us about posttranslational modifications, Cell Host Microbe, 14, 269, 10.1016/j.chom.2013.07.008 · DOI
- Drayman, 2013, Pathogens use structural mimicry of native host ligands as a mechanism for host receptor engagement, Cell Host Microbe, 14, 63, 10.1016/j.chom.2013.05.005 · DOI
- Guven-Maiorov, 2019, Interface-Based Structural Prediction of Novel Host-Pathogen Interactions, Methods Mol. Biol., 1851, 317, 10.1007/978-1-4939-8736-8_18 · DOI
- Lasso, 2021, A Sweep of Earth's Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease, Cell Syst., 12, 82, 10.1016/j.cels.2020.09.006 · DOI
- Seong, 2023, Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses, Nat. Microbiol., 8, 174, 10.1038/s41564-022-01287-6 · DOI
- Huene, 2022, A family of unusual immunoglobulin superfamily genes in an invertebrate histocompatibility complex, Proc. Natl. Acad. Sci. USA, 119, 10.1073/pnas.2207374119 · DOI · Paper page
- Mutz, 2023, Exaptation of Inactivated Host Enzymes for Structural Roles in Orthopoxviruses and Novel Folds of Virus Proteins Revealed by Protein Structure Modeling, mBio, 14, e0040823, 10.1128/mbio.00408-23 · DOI
- Lupfer, 2015, Inflammasome control of viral infection, Curr. Opin. Virol., 12, 38, 10.1016/j.coviro.2015.02.007 · DOI
- Amsler, 2013, The inflammasome as a target of modulation by DNA viruses, Future Virol., 8, 357, 10.2217/fvl.13.22 · DOI
- Senkevich, 2021, Ancient Gene Capture and Recent Gene Loss Shape the Evolution of Orthopoxvirus-Host Interaction Genes, mBio, 12, e0149521, 10.1128/mbio.01495-21 · DOI
- Zhang, 2005, TM-align: a protein structure alignment algorithm based on the TM-score, Nucleic Acids Res., 33, 2302, 10.1093/nar/gki524 · DOI · Paper page
- Lupas, 2001, On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world?, J. Struct. Biol., 134, 191, 10.1006/jsbi.2001.4393 · DOI
- Parkinson, 1995, The vaccinia virus A38L gene product is a 33-kDa integral membrane glycoprotein, Virology, 214, 177, 10.1006/viro.1995.9942 · DOI
- Broz, 2020, The gasdermins, a protein family executing cell death and inflammation, Nat. Rev. Immunol., 20, 143, 10.1038/s41577-019-0228-2 · DOI · Paper page
- Gram, 2012, Inflammasomes and viruses: cellular defence versus viral offence, J. Gen. Virol., 93, 2063, 10.1099/vir.0.042978-0 · DOI
- Lei, 2017, Enterovirus 71 Inhibits Pyroptosis through Cleavage of Gasdermin D, J. Virol., 91, e01069-17, 10.1128/JVI.01069-17 · DOI
- Ma, 2021, SARS-CoV-2 nucleocapsid suppresses host pyroptosis by blocking Gasdermin D cleavage, EMBO J., 40, e108249, 10.15252/embj.2021108249 · DOI
- Ding, 2016, Pore-forming activity and structural autoinhibition of the gasdermin family, Nature, 535, 111, 10.1038/nature18590 · DOI · Paper page
- Johnson, 2022, Bacterial gasdermins reveal an ancient mechanism of cell death, Science, 375, 221, 10.1126/science.abj8432 · DOI
- Wang, 2020, Structural Mechanism for GSDMD Targeting by Autoprocessed Caspases in Pyroptosis, Cell, 180, 941, 10.1016/j.cell.2020.02.002 · DOI
- Liu, 2020, Caspase-1 Engages Full-Length Gasdermin D through Two Distinct Interfaces That Mediate Caspase Recruitment and Substrate Cleavage, Immunity, 53, 106, 10.1016/j.immuni.2020.06.007 · DOI
- Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389, 10.1093/nar/25.17.3389 · DOI · Paper page
- Eddy, 2011, Accelerated Profile HMM Searches, PLoS Comput. Biol., 7, e1002195, 10.1371/journal.pcbi.1002195 · DOI · Paper page
- Carulei, 2017, Comparative analysis of avian poxvirus genomes, including a novel poxvirus from lesser flamingos (Phoenicopterus minor), highlights the lack of conservation of the central region, BMC Genom., 18, 947, 10.1186/s12864-017-4315-0 · DOI
- Shi, 2014, Inflammatory caspases are innate immune receptors for intracellular LPS, Nature, 514, 187, 10.1038/nature13683 · DOI · Paper page
- Shi, 2015, Cleavage of GSDMD by inflammatory caspases determines pyroptotic cell death, Nature, 526, 660, 10.1038/nature15514 · DOI · Paper page
- Shi, 2016, Reconstruction of the Mouse Inflammasome System in HEK293T Cells, Bio. Protoc., 6, e1986, 10.21769/BioProtoc.1986 · DOI
- Liu, 2016, Inflammasome-activated gasdermin D causes pyroptosis by forming membrane pores, Nature, 535, 153, 10.1038/nature18629 · DOI · Paper page
- Yuen, 2010, Analysis of A47, an immunoprevalent protein of vaccinia virus, leads to a reevaluation of the total antiviral CD8+ T cell response, J. Virol., 84, 10220, 10.1128/JVI.01281-10 · DOI
- Spriggs, 1992, Vaccinia and cowpox viruses encode a novel secreted interleukin-1-binding protein, Cell, 71, 145, 10.1016/0092-8674(92)90273-F · DOI
- Symons, 2002, The vaccinia virus C12L protein inhibits mouse IL-18 and promotes virus virulence in the murine intranasal model, J. Gen. Virol., 83, 2833, 10.1099/0022-1317-83-11-2833 · DOI
- Gerlic, 2013, Vaccinia virus F1L protein promotes virulence by inhibiting inflammasome activation, Proc. Natl. Acad. Sci. USA, 110, 7808, 10.1073/pnas.1215995110 · DOI
- Kettle, 1997, Vaccinia virus serpin B13R (SPI-2) inhibits interleukin-1beta-converting enzyme and protects virus-infected cells from TNF- and Fas-mediated apoptosis, but does not prevent IL-1beta-induced fever, J. Gen. Virol., 78, 677, 10.1099/0022-1317-78-3-677 · DOI
- González, 2010, A poxvirus Bcl-2-like gene family involved in regulation of host immune response: sequence similarity and evolutionary history, Virol. J., 7, 59, 10.1186/1743-422X-7-59 · DOI
- Holm, 2022, Dali server: structural unification of protein families, Nucleic Acids Res., 50, W210, 10.1093/nar/gkac387 · DOI
- Postigo, 2012, The vaccinia virus-encoded Bcl-2 homologues do not act as direct Bax inhibitors, J. Virol., 86, 203, 10.1128/JVI.05817-11 · DOI
- Schnappauf, 2019, The Pyrin Inflammasome in Health and Disease, Front. Immunol., 10, 1745, 10.3389/fimmu.2019.01745 · DOI
- Rahman, 2009, Co-regulation of NF-kappaB and inflammasome-mediated inflammatory responses by myxoma virus pyrin domain-containing protein M013, PLoS Pathog., 5, e1000635, 10.1371/journal.ppat.1000635 · DOI
- Garg, 2019, Myxoma virus M013 protein antagonizes NF-kappaB and inflammasome pathways via distinct structural motifs, J. Biol. Chem., 294, 8480, 10.1074/jbc.RA118.006040 · DOI
- Johnston, 2005, A poxvirus-encoded pyrin domain protein interacts with ASC-1 to inhibit host inflammatory and apoptotic responses to infection, Immunity, 23, 587, 10.1016/j.immuni.2005.10.003 · DOI
- Dorfleutner, 2007, A Shope Fibroma virus PYRIN-only protein modulates the host immune response, Virus Gene., 35, 685, 10.1007/s11262-007-0141-9 · DOI
- Bratke, 2013, A survey of host range genes in poxvirus genomes, Infect. Genet. Evol., 14, 406, 10.1016/j.meegid.2012.12.002 · DOI
- de Almeida, 2015, The PYRIN Domain-only Protein POP1 Inhibits Inflammasome Assembly and Ameliorates Inflammatory Disease, Immunity, 43, 264, 10.1016/j.immuni.2015.07.018 · DOI
- Byrd, 2014, Primary human macrophages serve as vehicles for vaccinia virus replication and dissemination, J. Virol., 88, 6819, 10.1128/JVI.03726-13 · DOI
- Davies, 2017, A systemic macrophage response is required to contain a peripheral poxvirus infection, PLoS Pathog., 13, e1006435, 10.1371/journal.ppat.1006435 · DOI
- Holm, 2023, DALI shines a light on remote homologs: One hundred discoveries, Protein Sci., 32, e4519, 10.1002/pro.4519 · DOI
- Sanchez-Pulido, 2022, OAF: a new member of the BRICHOS family, Bioinform. Adv., 2, vbac087, 10.1093/bioadv/vbac087 · DOI
- Zhang, 2023, DPAM: A domain parser for AlphaFold models, Protein Sci., 32, e4548, 10.1002/pro.4548 · DOI
- Goebel, 1990, The complete DNA sequence of vaccinia virus, Virology, 179, 247-66, 10.1016/0042-6822(90)90294-2 · DOI
- Scott, 2018, A Novel Ultra-Stable, Monomeric Green Fluorescent Protein For Direct Volumetric Imaging of Whole Organs Using CLARITY, Sci. Rep., 8, 667, 10.1038/s41598-017-18045-y · DOI
- Tamura, 2021, MEGA11: Molecular Evolutionary Genetics Analysis Version 11, Mol. Biol. Evol., 38, 3022, 10.1093/molbev/msab120 · DOI
- Nguyen, 2015, IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol. Biol. Evol., 32, 268, 10.1093/molbev/msu300 · DOI · Paper page
- Camacho, 2009, BLAST+: architecture and applications, BMC Bioinf., 10, 421, 10.1186/1471-2105-10-421 · DOI · Paper page
- Heinig, 2004, STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins, Nucleic Acids Res., 32, W500, 10.1093/nar/gkh429 · DOI · Paper page
- Li, 2018, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, 34, 3094, 10.1093/bioinformatics/bty191 · DOI · Paper page
- Li, 2009, The Sequence Alignment/Map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352 · DOI · Paper page
- Kolmogorov, 2019, Assembly of long, error-prone reads using repeat graphs, Nat. Biotechnol., 37, 540, 10.1038/s41587-019-0072-8 · DOI · Paper page
- Kabsch, 2010, Integration, scaling, space-group assignment and post-refinement, Acta Crystallogr. D Biol. Crystallogr., 66, 133, 10.1107/S0907444909047374 · DOI
- Adams, 2010, PHENIX: a comprehensive Python-based system for macromolecular structure solution, Acta Crystallogr. D Biol. Crystallogr., 66, 213, 10.1107/S0907444909052925 · DOI · Paper page
- Liebschner, 2019, Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix, Acta Crystallogr. D Struct. Biol., 75, 861, 10.1107/S2059798319011471 · DOI · Paper page
- Emsley, 2004, Coot: model-building tools for molecular graphics, Acta Crystallogr. D Biol. Crystallogr., 60, 2126, 10.1107/S0907444904019158 · DOI · Paper page
- Chen, 2010, MolProbity: all-atom structure validation for macromolecular crystallography, Acta Crystallogr. D Biol. Crystallogr., 66, 12, 10.1107/S0907444909042073 · DOI · Paper page
- Weiss, 2001, Global indicators of X-ray data quality, J. Appl. Crystallogr., 34, 130, 10.1107/S0021889800018227 · DOI
Metadata
- Authors
- Boys, I. N., Johnson, A. G., Quinlan, M. R., Kranzusch, P. J., & Elde, N. C.
- Affiliations
- Howard Hughes Medical Institute (US)
- Harvard University (US)
- Corresponding author
- Elde, Nels C.
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2023-08
- Volume
- 42
- Issue
- 8
- Pages
- 112878
- ISSN
- 2211-1247 (ISSN-L)
- PMC
- PMC10715236
- OpenAlex
- W4385252366
- Cited by
- 23
- References
- 7
- Citations by year
- 2026: 7 · 2025: 3 · 2024: 12 · 2023: 1
- FWCI
- 3.02
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Cell Reports (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion, cc-by)
- PubMed Central (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Burroughs Wellcome Fund
- University of Utah
- Life Sciences Research Foundation
- G. Harold and Leila Y. Mathers Foundation
- Open Philanthropy Project
- National Institutes of Health
- Center for High Performance Computing
- National Cancer Institute (R01CA260414)
- National Institute of General Medical Sciences (R35GM134936)
- Topics
- Life Sciences › Immunology and Microbiology › Virology › Poxvirus research and outbreaks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Inflammasome and immune disorders
- Life Sciences › Immunology and Microbiology › Immunology › interferon and immune responses
- Keywords
- vaccinia virus, pyroptosis, inflammasome, caspase inhibition, horizontal gene transfer, pyrin domain, innate immunity
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