The Leader RNA of SARS-CoV-2 Sequesters Polypyrimidine Tract Binding Protein (PTBP1) and Influences Pre-mRNA Splicing in Infected Cells

Overview

Journal Virology

Specialty Microbiology

Date 2024 Jan 30

PMID 38290414

Authors

Noelia H Altina

David G Maranon

John R Anderson

Meghan K Donaldson

Suad Elmegerhi

Laura A St Clair

Rushika Perera

Brian J Geiss

Jeffrey Wilusz

Affiliations

Soon will be listed here.

Abstract

The large amount of viral RNA produced during infections has the potential to interact with and effectively sequester cellular RNA binding proteins, thereby influencing aspects of post-transcriptional gene regulation in the infected cell. Here we demonstrate that the abundant 5' leader RNA region of SARS-CoV-2 viral RNAs can interact with the cellular polypyrimidine tract binding protein (PTBP1). Interestingly, the effect of a knockdown of PTBP1 protein on cellular gene expression is also mimicked during SARS-CoV-2 infection, suggesting that this protein may be functionally sequestered by viral RNAs. Consistent with this model, the alternative splicing of mRNAs that is normally controlled by PTBP1 is dysregulated during SARS-CoV-2 infection. Collectively, these data suggest that the SARS-CoV-2 leader RNA sequesters the cellular PTBP1 protein during infection, resulting in significant impacts on the RNA biology of the host cell. These alterations in post-transcriptional gene regulation may play a role in SARS-CoV-2 mediated molecular pathogenesis.

References

Garcia-Blanco M, Jamison S, Sharp P . Identification and purification of a 62,000-dalton protein that binds specifically to the polypyrimidine tract of introns. Genes Dev. 1989; 3(12A):1874-86. DOI: 10.1101/gad.3.12a.1874. View

Karlebach G, Aronow B, Baylin S, Butler D, Foox J, Levy S . Betacoronavirus-specific alternate splicing. Genomics. 2022; 114(2):110270. PMC: 8782732. DOI: 10.1016/j.ygeno.2022.110270. View

Kim J, Jeong K, Li J, Murphy J, Vukadin L, Stone J . SON drives oncogenic RNA splicing in glioblastoma by regulating PTBP1/PTBP2 switching and RBFOX2 activity. Nat Commun. 2021; 12(1):5551. PMC: 8455679. DOI: 10.1038/s41467-021-25892-x. View

Holste D, Ohler U . Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events. PLoS Comput Biol. 2008; 4(1):e21. PMC: 2217580. DOI: 10.1371/journal.pcbi.0040021. View

Sokoloski K, Dickson A, Chaskey E, Garneau N, Wilusz C, Wilusz J . Sindbis virus usurps the cellular HuR protein to stabilize its transcripts and promote productive infections in mammalian and mosquito cells. Cell Host Microbe. 2010; 8(2):196-207. PMC: 2929003. DOI: 10.1016/j.chom.2010.07.003. View

Davis H, McCorkell L, Vogel J, Topol E . Long COVID: major findings, mechanisms and recommendations. Nat Rev Microbiol. 2023; 21(3):133-146. PMC: 9839201. DOI: 10.1038/s41579-022-00846-2. View

Ge Z, Quek B, Beemon K, Hogg J . Polypyrimidine tract binding protein 1 protects mRNAs from recognition by the nonsense-mediated mRNA decay pathway. Elife. 2016; 5. PMC: 4764554. DOI: 10.7554/eLife.11155. View

Sola I, Almazan F, Zuniga S, Enjuanes L . Continuous and Discontinuous RNA Synthesis in Coronaviruses. Annu Rev Virol. 2016; 2(1):265-88. PMC: 6025776. DOI: 10.1146/annurev-virology-100114-055218. View

Gebauer F, Schwarzl T, Valcarcel J, Hentze M . RNA-binding proteins in human genetic disease. Nat Rev Genet. 2020; 22(3):185-198. DOI: 10.1038/s41576-020-00302-y. View

10.

Kloc M, Uosef A, Wosik J, Kubiak J, Ghobrial R . Virus interactions with the actin cytoskeleton-what we know and do not know about SARS-CoV-2. Arch Virol. 2022; 167(3):737-749. PMC: 8803281. DOI: 10.1007/s00705-022-05366-1. View

11.

Knoch K, Bergert H, Borgonovo B, Saeger H, Altkruger A, Verkade P . Polypyrimidine tract-binding protein promotes insulin secretory granule biogenesis. Nat Cell Biol. 2004; 6(3):207-14. DOI: 10.1038/ncb1099. View

12.

Van Nostrand E, Freese P, Pratt G, Wang X, Wei X, Xiao R . A large-scale binding and functional map of human RNA-binding proteins. Nature. 2020; 583(7818):711-719. PMC: 7410833. DOI: 10.1038/s41586-020-2077-3. View

13.

Ooi Y, Majzoub K, Flynn R, Mata M, Diep J, Li J . An RNA-centric dissection of host complexes controlling flavivirus infection. Nat Microbiol. 2019; 4(12):2369-2382. PMC: 6879806. DOI: 10.1038/s41564-019-0518-2. View

14.

Trefzer R, Elpeleg O, Gabrusskaya T, Stepensky P, Mor-Shaked H, Grosse R . Characterization of a L136P mutation in Formin-like 2 (FMNL2) from a patient with chronic inflammatory bowel disease. PLoS One. 2021; 16(5):e0252428. PMC: 8158924. DOI: 10.1371/journal.pone.0252428. View

15.

Wallar B, Alberts A . The formins: active scaffolds that remodel the cytoskeleton. Trends Cell Biol. 2003; 13(8):435-46. DOI: 10.1016/s0962-8924(03)00153-3. View

16.

Sola I, Galan C, Mateos-Gomez P, Palacio L, Zuniga S, Cruz J . The polypyrimidine tract-binding protein affects coronavirus RNA accumulation levels and relocalizes viral RNAs to novel cytoplasmic domains different from replication-transcription sites. J Virol. 2011; 85(10):5136-49. PMC: 3126201. DOI: 10.1128/JVI.00195-11. View

17.

Westcott C, Qazi S, Maiocco A, Mukhopadhyay S, Sokoloski K . Binding of hnRNP I-vRNA Regulates Sindbis Virus Structural Protein Expression to Promote Particle Infectivity. Viruses. 2022; 14(7). PMC: 9318202. DOI: 10.3390/v14071423. View

18.

Yasunami M, Suzuki K, Ohkubo H . A novel family of TEA domain-containing transcription factors with distinct spatiotemporal expression patterns. Biochem Biophys Res Commun. 1996; 228(2):365-70. DOI: 10.1006/bbrc.1996.1667. View

19.

Ghetti A, Pinol-Roma S, Michael W, Morandi C, Dreyfuss G . hnRNP I, the polypyrimidine tract-binding protein: distinct nuclear localization and association with hnRNAs. Nucleic Acids Res. 1992; 20(14):3671-8. PMC: 334017. DOI: 10.1093/nar/20.14.3671. View

20.

Dai S, Wang C, Zhang C, Feng L, Zhang W, Zhou X . PTB: Not just a polypyrimidine tract-binding protein. J Cell Physiol. 2022; 237(5):2357-2373. DOI: 10.1002/jcp.30716. View