Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). SARS-CoV-2 relies on cellular RNA-binding proteins (RBPs) to replicate and spread, although which RBPs control its life cycle remains largely unknown. Here, we employ a multi-omic approach to identify systematically and comprehensively the cellular and viral RBPs that are involved in SARS-CoV-2 infection. We reveal that SARS-CoV-2 infection profoundly remodels the cellular RNA-bound proteome, which includes wide-ranging effects on RNA metabolic pathways, non-canonical RBPs, and antiviral factors. Moreover, we apply a new method to identify the proteins that directly interact with viral RNA, uncovering dozens of cellular RBPs and six viral proteins. Among them are several components of the tRNA ligase complex, which we show regulate SARS-CoV-2 infection. Furthermore, we discover that available drugs targeting host RBPs that interact with SARS-CoV-2 RNA inhibit infection. Collectively, our results uncover a new universe of host-virus interactions with potential for new antiviral therapies against COVID-19.

Abstract licence: CC BY

1. 1.

   HTSeq—a Python framework to work with high-throughput sequencing data · 2014

2. 2.

   Anders S., Reyes A., Huber W. Detecting differential usage of exons from RNA-seq data. Genome Res. 2012;22:2008-2017.

   Not in our library10.1101/gr.133744.111 (opens in a new tab)

3. 3.

   Arif A., Yao P., Terenzi F., Jia J., Ray P.S., Fox P.L. The GAIT translational control system. Wiley Interdiscip. Rev. RNA. 2018;9:e1441.

   Not in our library10.1002/wrna.1441 (opens in a new tab)

4. 4.

   SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses · 2020

5. 5.

   Blanco-Melo D., Nilsson-Payant B.E., Liu W.C., Uhl S., Hoagland D., Møller R., Jordan T.X., Oishi K., Panis M., Sachs D. Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19. Cell. 2020;181:1036-1045.e9.

   Not in our library10.1016/j.cell.2020.04.026 (opens in a new tab)

6. 6.

   Bojkova D., Klann K., Koch B., Widera M., Krause D., Ciesek S., Cinatl J., Münch C. Proteomics of SARS-CoV-2-infected host cells reveals therapy targets. Nature. 2020;583:469-472.

   Not in our library10.1038/s41586-020-2332-7 (opens in a new tab)

7. 7.

   Bouhaddou M., Memon D., Meyer B., White K.M., Rezelj V.V., Correa Marrero M., Polacco B.J., Melnyk J.E., Ulferts S., Kaake R.M. The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell. 2020;182:685-712.e19.

   Not in our library10.1016/j.cell.2020.06.034 (opens in a new tab)

8. 8.

   ‘High vault-age’: non-coding RNA control of autophagy · 2020

   Not checked
9. 9.

   Carlson, M. (2019). GO.db: A set of annotation maps describing the entire Gene Ontology. R package version 3.11.4.

   Not in our library

10. 10.

    Carlson, M. (2019). org.Hs.eg.db: Genome wide annotation for Human. R package version 3.8.2.

    Not in our library

11. 11.

    Carlson, M., Liu, T., Lin, C., Falcon, S., Zhang, J., MacDonald, J.W. (2019). PFAM.db: A set of protein ID mappings for PFAM. R package version 3.11.4.

    Not in our library

12. 12.

    Carrasco L., Sanz M.A., González-Almela E. The Regulation of Translation in Alphavirus-Infected Cells. Viruses. 2018;10:70.

    Not in our library10.3390/v10020070 (opens in a new tab)

13. 13.

    Castello A., Fischer B., Eichelbaum K., Horos R., Beckmann B.M., Strein C., Davey N.E., Humphreys D.T., Preiss T., Steinmetz L.M. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell. 2012;149:1393-1406.

    Not in our library10.1016/j.cell.2012.04.031 (opens in a new tab)

14. 14.

    Castello A., Horos R., Strein C., Fischer B., Eichelbaum K., Steinmetz L.M., Krijgsveld J., Hentze M.W. System-wide identification of RNA-binding proteins by interactome capture. Nat. Protoc. 2013;8:491-500.

    Not in our library10.1038/nprot.2013.020 (opens in a new tab)

15. 15.

    Comprehensive Identification of RNA-Binding Domains in Human Cells · 2016

16. 16.

    Chandel V., Sharma P.P., Raj S., Choudhari R., Rathi B., Kumar D. Structure-based drug repurposing for targeting Nsp9 replicase and spike proteins of severe acute respiratory syndrome coronavirus 2. J. Biomol. Struct. Dyn. 2020.

    Not in our library10.1080/07391102.2020.1811773 (opens in a new tab)

17. 17.

    Chen J., Malone B., Llewellyn E., Grasso M., Shelton P.M.M., Olinares P.D.B., Maruthi K., Eng E.T., Vatandaslar H., Chait B.T. Structural Basis for Helicase-Polymerase Coupling in the SARS-CoV-2 Replication-Transcription Complex. Cell. 2020;182:1560-1573.

    Not in our library10.1016/j.cell.2020.07.033 (opens in a new tab)

18. 18.

    RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination · 2017

19. 19.

    Cotto K.C., Wagner A.H., Feng Y.Y., Kiwala S., Coffman A.C., Spies G., Wollam A., Spies N.C., Griffith O.L., Griffith M. DGIdb 3.0: a redesign and expansion of the drug-gene interaction database. Nucleic Acids Res. 2018;46(D1):D1068-D1073.

    Not in our library10.1093/nar/gkx1143 (opens in a new tab)

20. 20.

    Cox J., Neuhauser N., Michalski A., Scheltema R.A., Olsen J.V., Mann M. Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 2011;10:1794-1805.

    Not in our library10.1021/pr101065j (opens in a new tab)

21. 21.

    Cvitkovic I., Jurica M.S. Spliceosome database: a tool for tracking components of the spliceosome. Nucleic Acids Res. 2013;41:D132-D141.

    Not in our library10.1093/nar/gks999 (opens in a new tab)

22. 22.

    Dawar F.U., Tu J., Khattak M.N., Mei J., Lin L. Cyclophilin A: A Key Factor in Virus Replication and Potential Target for Anti-viral Therapy. Curr. Issues Mol. Biol. 2017;21:1-20.

    Not in our library10.21775/cimb.021.001 (opens in a new tab)

23. 23.

    Di Giorgio S., Martignano F., Torcia M.G., Mattiuz G., Conticello S.G. Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2. Sci. Adv. 2020;6:eabb5813.

    Not in our library10.1126/sciadv.abb5813 (opens in a new tab)

24. 24.

    Dicker K., Jarvelin A.I., Garcia-Moreno M., Castello A. The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity. Semin. Cell Dev. Biol. 2021;111:108-118.

    Not in our library10.1016/j.semcdb.2020.08.002 (opens in a new tab)

25. 25.

    Dobin A., Davis C.A., Schlesinger F., Drenkow J., Zaleski C., Jha S., Batut P., Chaisson M., Gingeras T.R. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15-21.

    Not in our library10.1093/bioinformatics/bts635 (opens in a new tab)

26. 26.

    Dong E., Du H., Gardner L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect. Dis. 2020;20:533-534.

    Not in our library10.1016/s1473-3099(20)30120-1 (opens in a new tab)

27. 27.

    Egloff M.P., Ferron F., Campanacci V., Longhi S., Rancurel C., Dutartre H., Snijder E.J., Gorbalenya A.E., Cambillau C., Canard B. The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world. Proc. Natl. Acad. Sci. USA. 2004;101:3792-3796.

    Not in our library10.1073/pnas.0307877101 (opens in a new tab)

28. 28.

    Fox A.H., Nakagawa S., Hirose T., Bond C.S. Paraspeckles: Where Long Noncoding RNA Meets Phase Separation. Trends Biochem. Sci. 2018;43:124-135.

    Not in our library10.1016/j.tibs.2017.12.001 (opens in a new tab)

29. 29.

    Gack M.U., Shin Y.C., Joo C.H., Urano T., Liang C., Sun L., Takeuchi O., Akira S., Chen Z., Inoue S., Jung J.U. TRIM25 RING-finger E3 ubiquitin ligase is essential for RIG-I-mediated antiviral activity. Nature. 2007;446:916-920.

    Not in our library10.1038/nature05732 (opens in a new tab)

30. 30.

    Galluzzi L., Diotallevi A., Magnani M. Endoplasmic reticulum stress and unfolded protein response in infection by intracellular parasites. Future Sci. OA. 2017;3:FSO198.

    Not in our library10.4155/fsoa-2017-0020 (opens in a new tab)

31. 31.

    Garcia-Moreno M., Järvelin A.I., Castello A. Unconventional RNA-binding proteins step into the virus-host battlefront. Wiley Interdiscip. Rev. RNA. 2018;9:e1498.

    Not in our library10.1002/wrna.1498 (opens in a new tab)

32. 32.

    System-wide Profiling of RNA-Binding Proteins Uncovers Key Regulators of Virus Infection · 2019

33. 33.

    Garnier S.

    Not in our library

34. 34.

    Gehring N.H., Lamprinaki S., Kulozik A.E., Hentze M.W. Disassembly of exon junction complexes by PYM. Cell. 2009;137:536-548.

    Not in our library10.1016/j.cell.2009.02.042 (opens in a new tab)

35. 35.

    Gordon D.E., Jang G.M., Bouhaddou M., Xu J., Obernier K., White K.M., O’Meara M.J., Rezelj V.V., Guo J.Z., Swaney D.L. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020;583:459-468.

    Not in our library10.1038/s41586-020-2286-9 (opens in a new tab)

36. 36.

    Habjan M., Pichlmair A. Cytoplasmic sensing of viral nucleic acids. Curr. Opin. Virol. 2015;11:31-37.

    Not in our library10.1016/j.coviro.2015.01.012 (opens in a new tab)

37. 37.

    Hentze M.W., Castello A., Schwarzl T., Preiss T. A brave new world of RNA-binding proteins. Nat. Rev. Mol. Cell Biol. 2018;19:327-341.

    Not in our library10.1038/nrm.2017.130 (opens in a new tab)

38. 38.

    Horos R., Büscher M., Kleinendorst R., Alleaume A.M., Tarafder A.K., Schwarzl T., Dziuba D., Tischer C., Zielonka E.M., Adak A. The Small Non-coding Vault RNA1-1 Acts as a Riboregulator of Autophagy. Cell. 2019;176:1054-1067.e12.

    Not in our library10.1016/j.cell.2019.01.030 (opens in a new tab)

39. 39.

    Huber W., von Heydebreck A., Sültmann H., Poustka A., Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics. 2002;18(Suppl 1):S96-S104.

    Not in our library10.1093/bioinformatics/18.suppl_1.s96 (opens in a new tab)

40. 40.

    Hughes C.S., Moggridge S., Müller T., Sorensen P.H., Morin G.B., Krijgsveld J. Single-pot, solid-phase-enhanced sample preparation for proteomics experiments. Nat. Protoc. 2019;14:68-85.

    Not in our library10.1038/s41596-018-0082-x (opens in a new tab)

• Cytoplasmic ribonucleoprotein complexes, RNA helicases and coronavirus infection · 2022

  Not checked

• The short isoform of the host antiviral protein ZAP acts as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting · 2021

  Not checked

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.