CoChat
Sign Up
Cited by 319

The DOI matches its Crossref record; 14 of the 14 references it cites were found in a registry or an index.

The SARS-CoV-2 RNA–protein interactome in infected human cells

Schmidt, Nora, Lareau, Caleb A., Keshishian, Hasmik, Ganskih, Sabina, Schneider, Cornelius, Hennig, Thomas, Melanson, Randy, Werner, Simone, Wei, Yuanjie, Zimmer, Matthias, Ade, Jens, Kirschner, Luisa, Zielinski, Sebastian, Dölken, Lars, Lander, Eric S., Caliskan, Neva, Fischer, Utz, Vogel, Jörg, Carr, Steven A., Bodem, Jochen, Munschauer, Mathias·2020·Nature Microbiology
DOI 10.1038/s41564-020-00846-zPMC PMC7906908

Published version of a preprint

Open this paper in CoChat — free account

Abstract

Characterizing the interactions that SARS-CoV-2 viral RNAs make with host cell proteins during infection can improve our understanding of viral RNA functions and the host innate immune response. Using RNA antisense purification and mass spectrometry, we identified up to 104 human proteins that directly and specifically bind to SARS-CoV-2 RNAs in infected human cells. We integrated the SARS-CoV-2 RNA interactome with changes in proteome abundance induced by viral infection and linked interactome proteins to cellular pathways relevant to SARS-CoV-2 infections. We demonstrated by genetic perturbation that cellular nucleic acid-binding protein (CNBP) and La-related protein 1 (LARP1), two of the most strongly enriched viral RNA binders, restrict SARS-CoV-2 replication in infected cells and provide a global map of their direct RNA contact sites. Pharmacological inhibition of three other RNA interactome members, PPIA, ATP1A1, and the ARP2/3 complex, reduced viral replication in two human cell lines. The identification of host dependency factors and defence strategies as presented in this work will improve the design of targeted therapeutics against SARS-CoV-2.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41564-020-00846-z

Cites

14 of 14 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • A1 cofactors A1CF and RBM47 physically interact with SARS-CoV-2 RNA.

    “Interestingly, both A1 cofactors A1CF and RBM47 were shown to physically interact with SARS-CoV-2 RNA in an interactome study56, offering indirect evidence that these RNA-binding A1-cofactors could recruit A1 to target SARS-CoV-2 RNA for editing in the infected tissue.”

    From The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness (2022) · cites this paper as [56]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 91

  1. Sola, I., Almazán, F., Zúñiga, S. & Enjuanes, L. Continuous and discontinuous RNA synthesis in coronaviruses. Ann. Rev. Virol. 2, 265–288 (2015). · DOI · Paper page
  2. Chan, Y. K. & Gack, M. U. Viral evasion of intracellular DNA and RNA sensing. Nat. Rev. Microbiol. 14, 360–373 (2016). · DOI
  3. Blanco-Melo, D. et al. Imbalanced host response to SARS-CoV-2 drives development of COVID-19. Cell 181, 1036–1045 (2020). · DOI · Paper page
  4. Emanuel, W. et al. Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention. Preprint at bioRxiv https://www.biorxiv.org/content/10.1101/2020.05.05.079194v1 (2020). · DOI
  5. Bouhaddou, M. et al. The global phosphorylation landscape of SARS-CoV-2 infection. Cell 182, 685–712 (2020). · DOI
  6. Klann, K. et al. Growth factor receptor signaling inhibition prevents SARS-CoV-2 replication. Mol. Cell 80, 164–174 (2020). · DOI
  7. Gordon, D. E. et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 583, 459–468 (2020). · DOI · Paper page
  8. Gordon, D. E. et al. Comparative host–coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science 370, eabe9403 (2020). · DOI
  9. Eckhardt, M., Hultquist, J. F., Kaake, R. M., Hüttenhain, R. & Krogan, N. J. A systems approach to infectious disease. Nat. Rev. Genet. 21, 339–354 (2020). · DOI
  10. Maranon, D. G., Anderson, J. R., Maranon, A. G. & Wilusz, J. The interface between coronaviruses and host cell RNA biology: novel potential insights for future therapeutic intervention. Wiley Interdiscip. Rev. RNA 11, e1614 (2020). · DOI
  11. McHugh, C. A. et al. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature 521, 232–236 (2015). · DOI
  12. Munschauer, M. et al. The NORAD lncRNA assembles a topoisomerase complex critical for genome stability. Nature 561, 132–136 (2018). · DOI
  13. Chu, C. et al. Systematic discovery of Xist RNA binding proteins. Cell 161, 404–416 (2015). · DOI
  14. Minajigi, A. et al. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. Science 349, aab2276 (2015). · DOI
  15. Ramanathan, M., Porter, D. F. & Khavari, P. A. Methods to study RNA–protein interactions. Nat. Methods 16, 225–234 (2019). · DOI
  16. Lee, F. C. Y. & Ule, J. Advances in CLIP technologies for studies of protein–RNA interactions. Mol. Cell 69, 354–369 (2018). · DOI
  17. Nie, Y. et al. Highly infectious SARS-CoV pseudotyped virus reveals the cell tropism and its correlation with receptor expression. Biochem. Biophys. Res. Commun. 321, 994–1000 (2004). · DOI
  18. Harcourt, J. et al. Severe acute respiratory syndrome coronavirus 2 from patient with coronavirus disease, United States. Emerg. Infect. Dis. 26, 1266–1273 (2020). · DOI
  19. Wang, Y. et al. SARS-CoV-2 infection of the liver directly contributes to hepatic impairment in patients with COVID-19. J. Hepatol. 73, 807–816 (2020). · DOI
  20. Perederina, A. et al. Cryo-EM structure of catalytic ribonucleoprotein complex RNase MRP. Nat. Commun. 11, 3474 (2020). · DOI
  21. Snijder, E. J., Decroly, E. & Ziebuhr, J. The nonstructural proteins directing coronavirus RNA synthesis and processing. Adv. Virus Res. 96, 59–126 (2016). · DOI
  22. Kim, Y. et al. Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2. Protein Sci. 29, 1596–1605 (2020). · DOI
  23. Hillen, H. S. et al. Structure of replicating SARS-CoV-2 polymerase. Nature 584, 154–156 (2020). · DOI
  24. Viswanathan, T. et al. Structural basis of RNA cap modification by SARS-CoV-2. Nat. Commun. 11, 3718 (2020).
  25. Sutton, G. et al. The nsp9 replicase protein of SARS-coronavirus, structure and functional insights. Structure 12, 341–353 (2004). · DOI
  26. Tanaka, T., Kamitani, W., DeDiego, M. L., Enjuanes, L. & Matsuura, Y. Severe acute respiratory syndrome coronavirus nsp1 facilitates efficient propagation in cells through a specific translational shutoff of host mRNA. J. Virol. 86, 11128–11137 (2012). · DOI
  27. Angelini, M. M., Akhlaghpour, M., Neuman, B. W. & Buchmeier, M. J. Severe acute respiratory syndrome coronavirus nonstructural proteins 3, 4, and 6 induce double-membrane vesicles. mBio 4, e00524-13 (2013). · DOI
  28. Wolff, G. et al. A molecular pore spans the double membrane of the coronavirus replication organelle. Science 369, 1395–1398 (2020). · DOI
  29. Sharma, K. et al. The 3a accessory protein of SARS coronavirus specifically interacts with the 5′UTR of its genomic RNA, using a unique 75 amino acid interaction domain. Biochemistry 46, 6488–6499 (2007). · DOI
  30. Masters, P. S. Coronavirus genomic RNA packaging. Virology 537, 198–207 (2019). · DOI
  31. Caudron-Herger, M. & Jansen, R. E. & Wassmer, E. & Diederichs, S. RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions. Nucleic Acids Res. https://doi.org/10.1093/nar/gkaa1040 (2020). · DOI
  32. Beckmann, B. M. et al. The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs. Nat. Commun. 6, 10127 (2015). · DOI
  33. Ooi, Y. S. et al. An RNA-centric dissection of host complexes controlling flavivirus infection. Nat. Microbiol. 4, 2369–2382 (2019). · DOI
  34. V’kovski, P. et al. Determination of host proteins composing the microenvironment of coronavirus replicase complexes by proximity-labeling. eLife 8, e42037 (2019). · DOI · Paper page
  35. Miller, S. & Krijnse-Locker, J. Modification of intracellular membrane structures for virus replication. Nat. Rev. Microbiol. 6, 363–374 (2008). · DOI
  36. Wada, M., Lokugamage, K. G., Nakagawa, K., Narayanan, K. & Makino, S. Interplay between coronavirus, a cytoplasmic RNA virus, and nonsense-mediated mRNA decay pathway. Proc. Natl Acad. Sci. USA 115, E10157–E10166 (2018).
  37. Ramírez-Valle, F., Braunstein, S., Zavadil, J., Formenti, S. C. & Schneider, R. J. eIF4GI links nutrient sensing by mTOR to cell proliferation and inhibition of autophagy. J. Cell Biol. 181, 293–307 (2008). · DOI
  38. Shahbazian, D. et al. The mTOR/PI3K and MAPK pathways converge on eIF4B to control its phosphorylation and activity. EMBO J. 25, 2781–2791 (2006). · DOI
  39. Cotto, K. C. et al. DGIdb 3.0: a redesign and expansion of the drug–gene interaction database. Nucleic Acids Res. 46, D1068–D1073 (2018). · DOI
  40. Narita, R. et al. A novel function of human Pumilio proteins in cytoplasmic sensing of viral infection. PLoS Pathog. 10, e1004417 (2014). · DOI
  41. Takeuchi, A. et al. YB-1 suppression induces STAT3 proteolysis and sensitizes renal cancer to interferon-α. Cancer Immunol. Immunother. 62, 517–527 (2013). · DOI
  42. Alam, U. & Kennedy, D. G3BP1 and G3BP2 regulate translation of interferon-stimulated genes: IFITM1, IFITM2 and IFITM3 in the cancer cell line MCF7. Mol. Cell. Biochem. 459, 189–204 (2019). · DOI
  43. Bidet, K., Dadlani, D. & Garcia-Blanco, M. A. G3BP1, G3BP2 and CAPRIN1 are required for translation of interferon stimulated mRNAs and are targeted by a dengue virus non-coding RNA. PLoS Pathog. 10, e1004242 (2014). · DOI
  44. Kroczynska, B. et al. Interferon-dependent engagement of eukaryotic initiation factor 4B via S6 kinase (S6K)- and ribosomal protein S6K-mediated signals. Mol. Cell. Biol. 29, 2865–2875 (2009). · DOI
  45. Cuevas, R. A. et al. MOV10 provides antiviral activity against RNA viruses by enhancing RIG-I-MAVS-independent IFN induction. J. Immunol. 196, 3877–3886 (2016). · DOI
  46. Soulat, D. et al. The DEAD-box helicase DDX3X is a critical component of the TANK-binding kinase 1-dependent innate immune response. EMBO J. 27, 2135–2146 (2008). · DOI
  47. Li, Y. et al. LSm14A is a processing body-associated sensor of viral nucleic acids that initiates cellular antiviral response in the early phase of viral infection. Proc. Natl Acad. Sci. USA 109, 11770–11775 (2012). · DOI
  48. Suzuki, Y. et al. Characterization of RyDEN (C19orf66) as an interferon-stimulated cellular inhibitor against Dengue virus replication. PLoS Pathog. 12, e1005357 (2016). · DOI
  49. Wang, X. et al. Regulation of HIV-1 Gag-Pol expression by Shiftless, an inhibitor of programmed-1 ribosomal frameshifting. Cell 176, 625–635 (2019). · DOI
  50. Huh, H. D., Lee, E., Shin, J., Park, B. & Lee, S. STRAP positively regulates TLR3-triggered signaling pathway. Cell Immunol. 318, 55–60 (2017). · DOI
  51. Bist, P. et al. Annexin-A1 regulates TLR-mediated IFN-β production through an interaction with TANK-binding kinase 1. J. Immunol. 191, 4375–4382 (2013). · DOI
  52. Zhou, Y. et al. Cellular RNA helicase DDX1 is involved in transmissible gastroenteritis virus nsp14-induced interferon-beta production. Front. Immunol. 8, 940 (2017). · DOI
  53. Xin, Z. et al. PCBP2 enhances the antiviral activity of IFN-α against HCV by stabilizing the mRNA of STAT1 and STAT2. PLoS ONE 6, e25419 (2011). · DOI
  54. Wang, L., Wen, M. & Cao, X. Nuclear hnRNPA2B1 initiates and amplifies the innate immune response to DNA viruses. Science 365, eaav0758 (2019). · DOI
  55. Han, X., Han, Y., Jiao, H. & Jie, Y. 14-3-3ζ regulates immune response through Stat3 signaling in oral squamous cell carcinoma. Mol. Cells 38, 112–121 (2015). · DOI
  56. Moore, M. J. From birth to death: the complex lives of eukaryotic mRNAs. Science 309, 1514–1518 (2005). · DOI
  57. Díaz-Muñoz, M. D. & Turner, M. Uncovering the role of RNA-binding proteins in gene expression in the immune system. Front. Immunol. 9, 1094 (2018). · DOI
  58. Garcia-Moreno, M., Järvelin, A. I. & Castello, A. Unconventional RNA-binding proteins step into the virus–host battlefront. Wiley Interdiscip. Rev. RNA 9, e1498 (2018). · DOI
  59. Wei, J. et al. Genome-wide CRISPR screens reveal host factors critical for SARS-CoV-2 infection. Cell https://doi.org/10.1016/j.cell.2020.10.028 (2020). · DOI
  60. Hoffmann, H.-H. et al. Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors. Preprint at bioRxiv https://www.biorxiv.org/content/10.1101/2020.09.11.291716v1 (2020). · DOI
  61. Chen, Y. et al. CNBP controls IL-12 gene transcription and Th1 immunity. J. Exp. Med. 215, 3136–3150 (2018). · DOI
  62. Lee, E. et al. CNBP acts as a key transcriptional regulator of sustained expression of interleukin-6. Nucleic Acids Res. 45, 3280–3296 (2017). · DOI
  63. Van Nostrand, E. L. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat. Methods 13, 508–514 (2016). · DOI · Paper page
  64. Benhalevy, D. et al. The Human CCHC-type zinc finger nucleic acid-binding protein binds G-rich elements in target mRNA coding sequences and promotes translation. Cell Rep. 18, 2979–2990 (2017). · DOI
  65. Hong, S. et al. LARP1 functions as a molecular switch for mTORC1-mediated translation of an essential class of mRNAs. eLife 6, e25237 (2017). · DOI
  66. Fonseca, B. D. et al. La-related protein 1 (LARP1) represses terminal oligopyrimidine (TOP) mRNA translation downstream of mTOR complex 1 (mTORC1). J. Biol. Chem. 290, 15996–16020 (2015). · DOI
  67. Lahr, R. M. et al. La-related protein 1 (LARP1) binds the mRNA cap, blocking eIF4F assembly on TOP mRNAs. eLife 6, e24146 (2017). · DOI
  68. Philippe, L., van den Elzen, A. M. G., Watson, M. J. & Thoreen, C. C. Global analysis of LARP1 translation targets reveals tunable and dynamic features of 5′ TOP motifs. Proc. Natl Acad. Sci. USA 117, 5319–5328 (2020). · DOI
  69. Kim, D. et al. The architecture of SARS-CoV-2 transcriptome. Cell 181, 914–921 (2020). · DOI · Paper page
  70. Plant, E. P. & Dinman, J. D. The role of programmed-1 ribosomal frameshifting in coronavirus propagation. Front. Biosci. 13, 4873–4881 (2008). · DOI
  71. Backlund, M. et al. Plasticity of nuclear and cytoplasmic stress responses of RNA-binding proteins. Nucleic Acids Res. 48, 4725–4740 (2020). · DOI
  72. Zhou, D., Mei, Q., Li, J. & He, H. Cyclophilin A and viral infections. Biochem. Biophys. Res. Commun. 424, 647–650 (2012). · DOI
  73. Pfefferle, S. et al. The SARS-coronavirus-host interactome: identification of cyclophilins as target for pan-coronavirus inhibitors. PLoS Pathog. 7, e1002331 (2011). · DOI
  74. Pawlotsky, J. M. COVID-19 pandemic: time to revive the cyclophilin inhibitor alisporivir. Clin. Infect. Dis. 71, 2191–2194 (2020). · DOI
  75. Lingemann, M. et al. The alpha-1 subunit of the Na+,K+-ATPase (ATP1A1) is required for macropinocytic entry of respiratory syncytial virus (RSV) in human respiratory epithelial cells. PLoS Pathog. 15, e1007963 (2019). · DOI
  76. Burkard, C. et al. ATP1A1-mediated Src signaling inhibits coronavirus entry into host cells. J. Virol. 89, 4434–4448 (2015). · DOI
  77. Mehedi, M. et al. Actin-related protein 2 (ARP2) and virus-induced filopodia facilitate human respiratory syncytial virus spread. PLoS Pathog. 12, e1006062 (2016). · DOI
  78. Peterhoff, D. et al. A highly specific and sensitive serological assay detects SARS-CoV-2 antibody levels in COVID-19 patients that correlate with neutralization. Infection https://doi.org/10.1007/s15010-020-01503-7 (2020). · DOI
  79. Engreitz, J. M. et al. RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent pre-mRNAs and chromatin sites. Cell 159, 188–199 (2014). · DOI
  80. Engreitz, J. M. et al. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 341, 1237973 (2013). · DOI
  81. Li, J. et al. Cell-surface proteomic profiling in the fly brain uncovers wiring regulators. Cell 180, 373–386 (2020). · DOI · Paper page
  82. Mertins, P. et al. Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry. Nat. Protoc. 13, 1632–1661 (2018). · DOI
  83. Zecha, J. et al. TMT labeling for the masses: a robust and cost-efficient, in-solution labeling approach. Mol. Cell. Proteomics 18, 1468–1478 (2019). · DOI
  84. Finkel, Y. et al. The coding capacity of SARS-CoV-2. Nature https://doi.org/10.1038/s41586-020-2739-1 (2020). · DOI · Paper page
  85. Szklarczyk, D. et al. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47, D607–D613 (2019). · DOI · Paper page
  86. Yu, G., Wang, L.-G., Han, Y. & He, Q.-Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284–287 (2012). · DOI · Paper page
  87. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009). · DOI · Paper page
  88. Zhang, Y. et al. Model-based analysis of ChIP–Seq (MACS). Genome Biol. 9, R137 (2008).
  89. Lawrence, M. et al. Software for computing and annotating genomic ranges. PLoS Comput. Biol. 9, e1003118 (2013). · DOI
  90. Ramírez, F., Dündar, F., Diehl, S., Grüning, B. A. & Manke, T. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42, W187–W191 (2014). · DOI · Paper page
  91. Bailey, T. L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202–W208 (2009). · DOI · Paper page

Cited by

Sorted by citations

Metadata

Authors
Schmidt, N., Lareau, C. A., Keshishian, H., Ganskih, S., Schneider, C., Hennig, T., Melanson, R., Werner, S., Wei, Y., Zimmer, M., Ade, J., Kirschner, L., Zielinski, S., Dölken, L., Lander, E. S., Caliskan, N., Fischer, U., Vogel, J., Carr, S. A., Bodem, J., & Munschauer, M.
ORCID
Venue
Nature Microbiology
Publisher
Springer Science and Business Media LLC
Published
2020-12-21
Volume
6
Issue
3
Pages
339-353
ISSN
2058-5276
DOI
10.1038/s41564-020-00846-z
PMC
PMC7906908
Cited by
319
References
14
Language
en
Licence
Funders
Helmholtz Association (VH-NG-1428)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review