Structure of the Respiratory Syncytial Virus Polymerase Complex

Overview

Journal Cell

Publisher Cell Press

Specialty Cell Biology

Date 2019 Sep 10

PMID 31495574

Citations 81

Authors

Morgan S A Gilman

Cheng Liu

Amy Fung

Ishani Behera

Paul Jordan

Peter Rigaux

Nina Ysebaert

Sergey Tcherniuk

Julien Sourimant

Jean-Francois Eleouet

Priscila Sutto-Ortiz

Etienne Decroly

Dirk Roymans

Zhinan Jin

Jason S McLellan

Affiliations

Soon will be listed here.

Abstract

Numerous interventions are in clinical development for respiratory syncytial virus (RSV) infection, including small molecules that target viral transcription and replication. These processes are catalyzed by a complex comprising the RNA-dependent RNA polymerase (L) and the tetrameric phosphoprotein (P). RSV P recruits multiple proteins to the polymerase complex and, with the exception of its oligomerization domain, is thought to be intrinsically disordered. Despite their critical roles in RSV transcription and replication, structures of L and P have remained elusive. Here, we describe the 3.2-Å cryo-EM structure of RSV L bound to tetrameric P. The structure reveals a striking tentacular arrangement of P, with each of the four monomers adopting a distinct conformation. The structure also rationalizes inhibitor escape mutants and mutations observed in live-attenuated vaccine candidates. These results provide a framework for determining the molecular underpinnings of RSV replication and transcription and should facilitate the design of effective RSV inhibitors.

Citing Articles

Structural basis of Nipah virus RNA synthesis.

Sala F, Ditter K, Dybkov O, Urlaub H, Hillen H Nat Commun. 2025; 16(1):2261.

PMID: 40050611 PMC: 11885841. DOI: 10.1038/s41467-025-57219-5.

Structural and functional analysis of the Nipah virus polymerase complex.

Hu S, Kim H, Yang P, Yu Z, Ludeke B, Mobilia S Cell. 2025; 188(3):688-703.e18.

PMID: 39837328 PMC: 11813165. DOI: 10.1016/j.cell.2024.12.021.

Structure of the Nipah virus polymerase complex.

Balikci E, Gunl F, Carrique L, Keown J, Fodor E, Grimes J EMBO J. 2024; 44(2):563-586.

PMID: 39739115 PMC: 11730344. DOI: 10.1038/s44318-024-00321-z.

Cryo-EM structure of Nipah virus RNA polymerase complex.

Wang Y, Zhao L, Zhang Y, Wang Y, Tang J, Liu S Sci Adv. 2024; 10(50):eadr7116.

PMID: 39661676 PMC: 11633731. DOI: 10.1126/sciadv.adr7116.

Cryo-EM structure of Nipah virus L-P polymerase complex.

Peng Q, Dong Y, Jia M, Liu Q, Bi Y, Qi J Nat Commun. 2024; 15(1):10524.

PMID: 39627254 PMC: 11615333. DOI: 10.1038/s41467-024-54994-5.

References

Luongo C, Winter C, Collins P, Buchholz U . Increased genetic and phenotypic stability of a promising live-attenuated respiratory syncytial virus vaccine candidate by reverse genetics. J Virol. 2012; 86(19):10792-804. PMC: 3457269. DOI: 10.1128/JVI.01227-12. View

Garcia J, Vivo A, Melero J . Cytoplasmic inclusions of respiratory syncytial virus-infected cells: formation of inclusion bodies in transfected cells that coexpress the nucleoprotein, the phosphoprotein, and the 22K protein. Virology. 1993; 195(1):243-7. DOI: 10.1006/viro.1993.1366. View

Tran T, Castagne N, Dubosclard V, Noinville S, Koch E, Moudjou M . The respiratory syncytial virus M2-1 protein forms tetramers and interacts with RNA and P in a competitive manner. J Virol. 2009; 83(13):6363-74. PMC: 2698528. DOI: 10.1128/JVI.00335-09. View

Lohmann V, KORNER F, Herian U, Bartenschlager R . Biochemical properties of hepatitis C virus NS5B RNA-dependent RNA polymerase and identification of amino acid sequence motifs essential for enzymatic activity. J Virol. 1997; 71(11):8416-28. PMC: 192304. DOI: 10.1128/JVI.71.11.8416-8428.1997. View

Afonso C, Amarasinghe G, Banyai K, Bao Y, Basler C, Bavari S . Taxonomy of the order Mononegavirales: update 2016. Arch Virol. 2016; 161(8):2351-60. PMC: 4947412. DOI: 10.1007/s00705-016-2880-1. View

Grosfeld H, Hill M, Collins P . RNA replication by respiratory syncytial virus (RSV) is directed by the N, P, and L proteins; transcription also occurs under these conditions but requires RSV superinfection for efficient synthesis of full-length mRNA. J Virol. 1995; 69(9):5677-86. PMC: 189426. DOI: 10.1128/JVI.69.9.5677-5686.1995. View

Llorente M, Garcia-Barreno B, Calero M, Camafeita E, Lopez J, Longhi S . Structural analysis of the human respiratory syncytial virus phosphoprotein: characterization of an alpha-helical domain involved in oligomerization. J Gen Virol. 2005; 87(Pt 1):159-169. DOI: 10.1099/vir.0.81430-0. View

Liuzzi M, Mason S, Cartier M, Lawetz C, McCollum R, Dansereau N . Inhibitors of respiratory syncytial virus replication target cotranscriptional mRNA guanylylation by viral RNA-dependent RNA polymerase. J Virol. 2005; 79(20):13105-15. PMC: 1235819. DOI: 10.1128/JVI.79.20.13105-13115.2005. View

DeVincenzo J, McClure M, Symons J, Fathi H, Westland C, Chanda S . Activity of Oral ALS-008176 in a Respiratory Syncytial Virus Challenge Study. N Engl J Med. 2015; 373(21):2048-58. DOI: 10.1056/NEJMoa1413275. View

10.

Lu X, McDonald S, Tortorici M, Tao Y, Vasquez-Del Carpio R, Nibert M . Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1. Structure. 2008; 16(11):1678-88. PMC: 2602806. DOI: 10.1016/j.str.2008.09.006. View

11.

Shahabi A, Peneva D, Incerti D, McLaurin K, Stevens W . Assessing Variation in the Cost of Palivizumab for Respiratory Syncytial Virus Prevention in Preterm Infants. Pharmacoecon Open. 2018; 2(1):53-61. PMC: 5820240. DOI: 10.1007/s41669-017-0042-3. View

12.

Li J, Rahmeh A, Morelli M, Whelan S . A conserved motif in region v of the large polymerase proteins of nonsegmented negative-sense RNA viruses that is essential for mRNA capping. J Virol. 2007; 82(2):775-84. PMC: 2224588. DOI: 10.1128/JVI.02107-07. View

13.

Wahba A, Miller M, Niveleau A, Landers T, Carmichael G, Weber K . Subunit I of G beta replicase and 30 S ribosomal protein S1 of Escherichia coli. Evidence for the identity of the two proteins. J Biol Chem. 1974; 249(10):3314-6. View

14.

Choi K, Groarke J, Young D, Kuhn R, Smith J, Pevear D . The structure of the RNA-dependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation. Proc Natl Acad Sci U S A. 2004; 101(13):4425-30. PMC: 384763. DOI: 10.1073/pnas.0400660101. View

15.

Clarke M, Mackman R, Byun D, Hui H, Barauskas O, Birkus G . Discovery of β-D-2'-deoxy-2'-α-fluoro-4'-α-cyano-5-aza-7,9-dideaza adenosine as a potent nucleoside inhibitor of respiratory syncytial virus with excellent selectivity over mitochondrial RNA and DNA polymerases. Bioorg Med Chem Lett. 2015; 25(12):2484-7. DOI: 10.1016/j.bmcl.2015.04.073. View

16.

Hardy R, Wertz G . The product of the respiratory syncytial virus M2 gene ORF1 enhances readthrough of intergenic junctions during viral transcription. J Virol. 1998; 72(1):520-6. PMC: 109403. DOI: 10.1128/JVI.72.1.520-526.1998. View

17.

Lu B, Brazas R, Ma C, Kristoff T, Cheng X, Jin H . Identification of temperature-sensitive mutations in the phosphoprotein of respiratory syncytial virus that are likely involved in its interaction with the nucleoprotein. J Virol. 2002; 76(6):2871-80. PMC: 135989. DOI: 10.1128/jvi.76.6.2871-2880.2002. View

18.

Rahmeh A, Morin B, Schenk A, Liang B, Heinrich B, Brusic V . Critical phosphoprotein elements that regulate polymerase architecture and function in vesicular stomatitis virus. Proc Natl Acad Sci U S A. 2012; 109(36):14628-33. PMC: 3437890. DOI: 10.1073/pnas.1209147109. View

19.

Pettersen E, Goddard T, Huang C, Couch G, Greenblatt D, Meng E . UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004; 25(13):1605-12. DOI: 10.1002/jcc.20084. View

20.

Deval J, Hong J, Wang G, Taylor J, Smith L, Fung A . Molecular Basis for the Selective Inhibition of Respiratory Syncytial Virus RNA Polymerase by 2'-Fluoro-4'-Chloromethyl-Cytidine Triphosphate. PLoS Pathog. 2015; 11(6):e1004995. PMC: 4476725. DOI: 10.1371/journal.ppat.1004995. View