Structural Basis for the Inactivation of Cytosolic DNA Sensing by the Vaccinia Virus

Overview

Journal Nat Commun

Specialty Biology

Date 2022 Nov 18

PMID 36400800

Authors

Angel Rivera-Calzada

Raquel Arribas-Bosacoma

Alba Ruiz-Ramos

Paloma Escudero-Bravo

Jasminka Boskovic

Rafael Fernandez-Leiro

Antony W Oliver

Laurence H Pearl

Oscar Llorca

Affiliations

Soon will be listed here.

Abstract

Detection of cytosolic DNA is a central element of the innate immunity system against viral infection. The Ku heterodimer, a component of the NHEJ pathway of DNA repair in the nucleus, functions as DNA sensor that detects dsDNA of viruses that replicate in the cytoplasm. Vaccinia virus expresses two proteins, C4 and C16, that inactivate DNA sensing and enhance virulence. The structural basis for this is unknown. Here we determine the structure of the C16 - Ku complex using cryoEM. Ku binds dsDNA by a preformed ring but C16 sterically blocks this access route, abrogating binding to a dsDNA end and its insertion into DNA-PK, thereby averting signalling into the downstream innate immunity system. C4 replicates these activities using a domain with 54% identity to C16. Our results reveal how vaccinia virus subverts the capacity of Ku to recognize viral DNA.

Citing Articles

The monkeypox virus-host interplays.

Yi X, Lei Y, Li M, Zhong L, Li S Cell Insight. 2024; 3(5):100185.

PMID: 39144256 PMC: 11321328. DOI: 10.1016/j.cellin.2024.100185.

Filamin B restricts vaccinia virus spread and is targeted by vaccinia virus protein C4.

Georgana I, Scutts S, Gao C, Lu Y, Torres A, Ren H J Virol. 2024; 98(3):e0148523.

PMID: 38412044 PMC: 10949515. DOI: 10.1128/jvi.01485-23.

HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search.

Lee Y, Guler M, Chigumba D, Wang S, Mittal N, Miller C Nat Commun. 2023; 14(1):4219.

PMID: 37452020 PMC: 10349150. DOI: 10.1038/s41467-023-39905-4.

Selective events at individual sites underlie the evolution of monkeypox virus clades.

Molteni C, Forni D, Cagliani R, Arrigoni F, Pozzoli U, De Gioia L Virus Evol. 2023; 9(1):vead031.

PMID: 37305708 PMC: 10256197. DOI: 10.1093/ve/vead031.

Exaptation of Inactivated Host Enzymes for Structural Roles in Orthopoxviruses and Novel Folds of Virus Proteins Revealed by Protein Structure Modeling.

Mutz P, Resch W, Faure G, Senkevich T, Koonin E, Moss B mBio. 2023; 14(2):e0040823.

PMID: 37017580 PMC: 10128050. DOI: 10.1128/mbio.00408-23.

References

Scutts S, Ember S, Ren H, Ye C, Lovejoy C, Mazzon M . DNA-PK Is Targeted by Multiple Vaccinia Virus Proteins to Inhibit DNA Sensing. Cell Rep. 2018; 25(7):1953-1965.e4. PMC: 6250978. DOI: 10.1016/j.celrep.2018.10.034. View

Sri Krishna S, Aravind L . The bridge-region of the Ku superfamily is an atypical zinc ribbon domain. J Struct Biol. 2010; 172(3):294-9. PMC: 2964384. DOI: 10.1016/j.jsb.2010.05.011. View

Chen X, Xu X, Chen Y, Cheung J, Wang H, Jiang J . Structure of an activated DNA-PK and its implications for NHEJ. Mol Cell. 2021; 81(4):801-810.e3. PMC: 7897279. DOI: 10.1016/j.molcel.2020.12.015. View

Walker J, Corpina R, Goldberg J . Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. Nature. 2001; 412(6847):607-14. DOI: 10.1038/35088000. View

Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O . Highly accurate protein structure prediction with AlphaFold. Nature. 2021; 596(7873):583-589. PMC: 8371605. DOI: 10.1038/s41586-021-03819-2. View

Eaglesham J, Pan Y, Kupper T, Kranzusch P . Viral and metazoan poxins are cGAMP-specific nucleases that restrict cGAS-STING signalling. Nature. 2019; 566(7743):259-263. PMC: 6640140. DOI: 10.1038/s41586-019-0928-6. View

Punjani A, Fleet D . 3D variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM. J Struct Biol. 2021; 213(2):107702. DOI: 10.1016/j.jsb.2021.107702. View

Emsley P, Lohkamp B, Scott W, Cowtan K . Features and development of Coot. Acta Crystallogr D Biol Crystallogr. 2010; 66(Pt 4):486-501. PMC: 2852313. DOI: 10.1107/S0907444910007493. View

Hnizda A, Tesina P, Nguyen T, Kukacka Z, Kater L, Chaplin A . SAP domain forms a flexible part of DNA aperture in Ku70/80. FEBS J. 2021; 288(14):4382-4393. PMC: 8653891. DOI: 10.1111/febs.15732. View

10.

Fahy A, Clark R, Glyde E, Smith G . Vaccinia virus protein C16 acts intracellularly to modulate the host response and promote virulence. J Gen Virol. 2008; 89(Pt 10):2377-2387. PMC: 2885005. DOI: 10.1099/vir.0.2008/004895-0. View

11.

Zivanov J, Nakane T, Forsberg B, Kimanius D, Hagen W, Lindahl E . New tools for automated high-resolution cryo-EM structure determination in RELION-3. Elife. 2018; 7. PMC: 6250425. DOI: 10.7554/eLife.42166. View

12.

Kimanius D, Dong L, Sharov G, Nakane T, Scheres S . New tools for automated cryo-EM single-particle analysis in RELION-4.0. Biochem J. 2021; 478(24):4169-4185. PMC: 8786306. DOI: 10.1042/BCJ20210708. View

13.

Chaplin A, Hardwick S, Kefala Stavridi A, Buehl C, Goff N, Ropars V . Cryo-EM of NHEJ supercomplexes provides insights into DNA repair. Mol Cell. 2021; 81(16):3400-3409.e3. PMC: 9006396. DOI: 10.1016/j.molcel.2021.07.005. View

14.

El-Jesr M, Teir M, Maluquer de Motes C . Vaccinia Virus Activation and Antagonism of Cytosolic DNA Sensing. Front Immunol. 2020; 11:568412. PMC: 7559579. DOI: 10.3389/fimmu.2020.568412. View

15.

DiMaio D . Viruses, masters at downsizing. Cell Host Microbe. 2012; 11(6):560-1. DOI: 10.1016/j.chom.2012.05.004. View

16.

Bepler T, Morin A, Rapp M, Brasch J, Shapiro L, Noble A . Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat Methods. 2019; 16(11):1153-1160. PMC: 6858545. DOI: 10.1038/s41592-019-0575-8. View

17.

Ferguson B, Mansur D, Peters N, Ren H, Smith G . DNA-PK is a DNA sensor for IRF-3-dependent innate immunity. Elife. 2012; 1:e00047. PMC: 3524801. DOI: 10.7554/eLife.00047. View

18.

Zahid A, Ismail H, Li B, Jin T . Molecular and Structural Basis of DNA Sensors in Antiviral Innate Immunity. Front Immunol. 2020; 11:613039. PMC: 7734173. DOI: 10.3389/fimmu.2020.613039. View

19.

Mazzon M, Castro C, Roberts L, Griffin J, Smith G . A role for vaccinia virus protein C16 in reprogramming cellular energy metabolism. J Gen Virol. 2014; 96(Pt 2):395-407. PMC: 4298679. DOI: 10.1099/vir.0.069591-0. View

20.

Peters N, Ferguson B, Mazzon M, Fahy A, Krysztofinska E, Arribas-Bosacoma R . A mechanism for the inhibition of DNA-PK-mediated DNA sensing by a virus. PLoS Pathog. 2013; 9(10):e1003649. PMC: 3789764. DOI: 10.1371/journal.ppat.1003649. View