Specific Recognition of a Stem-Loop RNA Structure by the Alphavirus Capsid Protein

Overview

Journal Viruses

Publisher MDPI

Specialty Microbiology

Date 2021 Aug 28

PMID 34452382

Citations 4

Authors

Rebecca S Brown

Lisa Kim

Margaret Kielian

Affiliations

Soon will be listed here.

Abstract

Alphaviruses are small enveloped viruses with positive-sense RNA genomes. During infection, the alphavirus capsid protein (Cp) selectively packages and assembles with the viral genomic RNA to form the nucleocapsid core, a process critical to the production of infectious virus. Prior studies of the alphavirus Semliki Forest virus (SFV) showed that packaging and assembly are promoted by Cp binding to multiple high affinity sites on the genomic RNA. Here, we developed an in vitro Cp binding assay based on fluorescently labeled RNA oligos. We used this assay to explore the RNA sequence and structure requirements for Cp binding to site #1, the top binding site identified on the genomic RNA during all stages of virus assembly. Our results identify a stem-loop structure that promotes specific binding of the SFV Cp to site #1 RNA. This structure is also recognized by the Cps of the related alphaviruses chikungunya virus and Ross River virus.

Citing Articles

DDX RNA helicases: key players in cellular homeostasis and innate antiviral immunity.

Tapescu I, Cherry S J Virol. 2024; 98(10):e0004024.

PMID: 39212449 PMC: 11494928. DOI: 10.1128/jvi.00040-24.

Pathogenicity and virulence of chikungunya virus.

Freppel W, Silva L, Stapleford K, Herrero L Virulence. 2024; 15(1):2396484.

PMID: 39193780 PMC: 11370967. DOI: 10.1080/21505594.2024.2396484.

Virus (SFV) Self-Amplifying RNA Delivered to J774A.1 Macrophage Lineage by Its Association with a Purified Recombinant SFV Capsid Protein.

Gomes R, Barbosa F, Toledo M, Jorge S, Astray R Int J Mol Sci. 2024; 25(14).

PMID: 39063100 PMC: 11276834. DOI: 10.3390/ijms25147859.

The RNA helicase DDX39A binds a conserved structure in chikungunya virus RNA to control infection.

Tapescu I, Taschuk F, Pokharel S, Zginnyk O, Ferretti M, Bailer P Mol Cell. 2023; 83(22):4174-4189.e7.

PMID: 37949067 PMC: 10722560. DOI: 10.1016/j.molcel.2023.10.008.

References

Weaver S, Osorio J, Livengood J, Chen R, Stinchcomb D . Chikungunya virus and prospects for a vaccine. Expert Rev Vaccines. 2012; 11(9):1087-101. PMC: 3562718. DOI: 10.1586/erv.12.84. View

Baxter V, Heise M . Immunopathogenesis of alphaviruses. Adv Virus Res. 2020; 107:315-382. PMC: 8224468. DOI: 10.1016/bs.aivir.2020.06.002. View

Weaver S, Winegar R, Manger I, Forrester N . Alphaviruses: population genetics and determinants of emergence. Antiviral Res. 2012; 94(3):242-57. PMC: 3737490. DOI: 10.1016/j.antiviral.2012.04.002. View

Kim D, Firth A, Atasheva S, Frolova E, Frolov I . Conservation of a packaging signal and the viral genome RNA packaging mechanism in alphavirus evolution. J Virol. 2011; 85(16):8022-36. PMC: 3147971. DOI: 10.1128/JVI.00644-11. View

Brown R, Wan J, Kielian M . The Alphavirus Exit Pathway: What We Know and What We Wish We Knew. Viruses. 2018; 10(2). PMC: 5850396. DOI: 10.3390/v10020089. View

Button J, Mukhopadhyay S . Removing the Polyanionic Cargo Requirement for Assembly of Alphavirus Core-Like Particles to Make an Empty Alphavirus Core. Viruses. 2020; 12(8). PMC: 7472333. DOI: 10.3390/v12080846. View

Brown R, Anastasakis D, Hafner M, Kielian M . Multiple capsid protein binding sites mediate selective packaging of the alphavirus genomic RNA. Nat Commun. 2020; 11(1):4693. PMC: 7499256. DOI: 10.1038/s41467-020-18447-z. View

Mendes A, Kuhn R . Alphavirus Nucleocapsid Packaging and Assembly. Viruses. 2018; 10(3). PMC: 5869531. DOI: 10.3390/v10030138. View

Madden E, Plante K, Morrison C, Kutchko K, Sanders W, Long K . Using SHAPE-MaP To Model RNA Secondary Structure and Identify 3'UTR Variation in Chikungunya Virus. J Virol. 2020; 94(24). PMC: 7925192. DOI: 10.1128/JVI.00701-20. View

10.

Frolov I, Frolova E . Molecular Virology of Chikungunya Virus. Curr Top Microbiol Immunol. 2019; 435:1-31. DOI: 10.1007/82_2018_146. View

11.

Liljestrom P . M-X-I motif of semliki forest virus capsid protein affects nucleocapsid assembly. J Virol. 2001; 75(10):4625-32. PMC: 114215. DOI: 10.1128/JVI.75.10.4625-4632.2001. View

12.

Zaid A, Burt F, Liu X, Poo Y, Zandi K, Suhrbier A . Arthritogenic alphaviruses: epidemiological and clinical perspective on emerging arboviruses. Lancet Infect Dis. 2020; 21(5):e123-e133. DOI: 10.1016/S1473-3099(20)30491-6. View

13.

Rumenapf T, Strauss E, Strauss J . Subgenomic mRNA of Aura alphavirus is packaged into virions. J Virol. 1994; 68(1):56-62. PMC: 236263. DOI: 10.1128/JVI.68.1.56-62.1994. View

14.

Warrier R, Linger B, Golden B, Kuhn R . Role of sindbis virus capsid protein region II in nucleocapsid core assembly and encapsidation of genomic RNA. J Virol. 2008; 82(9):4461-70. PMC: 2293040. DOI: 10.1128/JVI.01936-07. View

15.

Chen G, Coates E, Plummer S, Carter C, Berkowitz N, Conan-Cibotti M . Effect of a Chikungunya Virus-Like Particle Vaccine on Safety and Tolerability Outcomes: A Randomized Clinical Trial. JAMA. 2020; 323(14):1369-1377. PMC: 7156994. DOI: 10.1001/jama.2020.2477. View

16.

Kim B, Arcos S, Rothamel K, Jian J, L Rose K, McDonald W . Discovery of Widespread Host Protein Interactions with the Pre-replicated Genome of CHIKV Using VIR-CLASP. Mol Cell. 2020; 78(4):624-640.e7. PMC: 7263428. DOI: 10.1016/j.molcel.2020.04.013. View

17.

Dykeman E, Stockley P, Twarock R . Solving a Levinthal's paradox for virus assembly identifies a unique antiviral strategy. Proc Natl Acad Sci U S A. 2014; 111(14):5361-6. PMC: 3986145. DOI: 10.1073/pnas.1319479111. View

18.

Wan J, Brown R, Kielian M . Berberine Chloride is an Alphavirus Inhibitor That Targets Nucleocapsid Assembly. mBio. 2020; 11(3). PMC: 7327175. DOI: 10.1128/mBio.01382-20. View

19.

Twarock R, Stockley P . RNA-Mediated Virus Assembly: Mechanisms and Consequences for Viral Evolution and Therapy. Annu Rev Biophys. 2019; 48:495-514. PMC: 7612295. DOI: 10.1146/annurev-biophys-052118-115611. View

20.

Silva L, Dermody T . Chikungunya virus: epidemiology, replication, disease mechanisms, and prospective intervention strategies. J Clin Invest. 2017; 127(3):737-749. PMC: 5330729. DOI: 10.1172/JCI84417. View