OpenLB
Open Library of Bioscience
Advanced Search
Nature
01, 2021;589 (7840): 125-130.

The coding capacity of SARS-CoV-2.

Yaara Finkel, Orel Mizrahi, Aharon Nachshon, Shira Weingarten-Gabbay, David Morgenstern, Yfat Yahalom-Ronen, Hadas Tamir, Hagit Achdout, Dana Stein, Ofir Israeli, Adi Beth-Din, Sharon Melamed, Shay Weiss, Tomer Israely, Nir Paran, Michal Schwartz, Noam Stern-Ginossar
Author Information
  1. Yaara Finkel: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel. ORCID
  2. Orel Mizrahi: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
  3. Aharon Nachshon: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
  4. Shira Weingarten-Gabbay: Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  5. David Morgenstern: de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalised Medicine, Weizmann Institute of Science, Rehovot, Israel.
  6. Yfat Yahalom-Ronen: Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.
  7. Hadas Tamir: Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.
  8. Hagit Achdout: Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.
  9. Dana Stein: Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel.
  10. Ofir Israeli: Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel.
  11. Adi Beth-Din: Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel.
  12. Sharon Melamed: Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.
  13. Shay Weiss: Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.
  14. Tomer Israely: Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.
  15. Nir Paran: Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.
  16. Michal Schwartz: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel. ORCID
  17. Noam Stern-Ginossar: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel. noam.stern-ginossar@weizmann.ac.il. ORCID
PMID: 32906143 DOI: 10.1038/s41586-020-2739-1

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 2019 (COVID-19) pandemic. To understand the pathogenicity and antigenic potential of SARS-CoV-2 and to develop therapeutic tools, it is essential to profile the full repertoire of its expressed proteins. The current map of SARS-CoV-2 coding capacity is based on computational predictions and relies on homology with other coronaviruses. As the protein complement varies among coronaviruses, especially in regard to the variety of accessory proteins, it is crucial to characterize the specific range of SARS-CoV-2 proteins in an unbiased and open-ended manner. Here, using a suite of ribosome-profiling techniques, we present a high-resolution map of coding regions in the SARS-CoV-2 genome, which enables us to accurately quantify the expression of canonical viral open reading frames (ORFs) and to identify 23 unannotated viral ORFs. These ORFs include upstream ORFs that are likely to have a regulatory role, several in-frame internal ORFs within existing ORFs, resulting in N-terminally truncated products, as well as internal out-of-frame ORFs, which generate novel polypeptides. We further show that viral mRNAs are not translated more efficiently than host mRNAs; instead, virus translation dominates host translation because of the high levels of viral transcripts. Our work provides a resource that will form the basis of future functional studies.

References

Zhu, N. et al. A novel coronavirus from patients with pneumonia in China, 2019. N. Engl. J. Med. 382, 727–733 (2020). [DOI: 10.1056/NEJMoa2001017]
Stern-Ginossar, N. et al. Decoding human cytomegalovirus. Science 338, 1088–1093 (2012). [DOI: 10.1126/science.1227919]
Irigoyen, N. et al. High-resolution analysis of coronavirus gene expression by RNA sequencing and ribosome profiling. PLoS Pathog. 12, e1005473 (2016). [DOI: 10.1371/journal.ppat.1005473]
Finkel, Y. et al. Comprehensive annotations of human herpesvirus 6A and 6B genomes reveal novel and conserved genomic features. eLife 9, e50960 (2020). [DOI: 10.7554/eLife.50960]
Sola, I., Almazán, F., Zúñiga, S. & Enjuanes, L. Continuous and discontinuous RNA synthesis in coronaviruses. Annu. Rev. Virol. 2, 265–288 (2015). [DOI: 10.1146/annurev-virology-100114-055218]
Lai, M. M. & Stohlman, S. A. Comparative analysis of RNA genomes of mouse hepatitis viruses. J. Virol. 38, 661–670 (1981). [DOI: 10.1128/JVI.38.2.661-670.1981]
Yogo, Y., Hirano, N., Hino, S., Shibuta, H. & Matumoto, M. Polyadenylate in the virion RNA of mouse hepatitis virus. J. Biochem. 82, 1103–1108 (1977). [DOI: 10.1093/oxfordjournals.jbchem.a131782]
Bojkova, D. et al. Proteomics of SARS-CoV-2-infected host cells reveals therapy targets. Nature 583, 469–472 (2020). [DOI: 10.1038/s41586-020-2332-7]
Davidson, A. D. et al. Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein. Genome Med. 12, 68 (2020). [DOI: 10.1186/s13073-020-00763-0]
Ingolia, N. T. et al. Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. Cell Rep. 8, 1365–1379 (2014). [DOI: 10.1016/j.celrep.2014.07.045]
Dinan, A. M. et al. Comparative analysis of gene expression in virulent and attenuated strains of infectious bronchitis virus at subcodon resolution. J. Virol. 93, 714–733 (2019). [DOI: 10.1128/JVI.00714-19]
Kim, D. et al. The architecture of SARS-CoV-2 transcriptome. Cell 181, 914–921 (2020). [DOI: 10.1016/j.cell.2020.04.011]
Schaecher, S. R., Mackenzie, J. M. & Pekosz, A. The ORF7b protein of severe acute respiratory syndrome coronavirus (SARS-CoV) is expressed in virus-infected cells and incorporated into SARS-CoV particles. J. Virol. 81, 718–731 (2007). [DOI: 10.1128/JVI.01691-06]
Davidson, A. D. et al. Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein. Genome Med. 12, 68 (2020). [DOI: 10.1186/s13073-020-00763-0]
Wu, A. et al. Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China. Cell Host Microbe 27, 325–328 (2020). [DOI: 10.1016/j.chom.2020.02.001]
Erhard, F. et al. Improved Ribo-seq enables identification of cryptic translation events. Nat. Methods 15, 363–366 (2018). [DOI: 10.1038/nmeth.4631]
Fields, A. P. et al. A regression-based analysis of ribosome-profiling data reveals a conserved complexity to mammalian translation. Mol. Cell 60, 816–827 (2015). [DOI: 10.1016/j.molcel.2015.11.013]
Cagliani, R., Forni, D., Clerici, M. & Sironi, M. Coding potential and sequence conservation of SARS-CoV-2 and related animal viruses. Infect. Genet. Evol. 83, 104353 (2020). [DOI: 10.1016/j.meegid.2020.104353]
Firth, A. E. A putative new SARS-CoV protein, 3c, encoded in an ORF overlapping ORF3a. J. Gen. Virol. https://doi.org/10.1099/jgv.0.001469 (2020).
Jungreis, I., Sealfon, R. & Kellis, M. SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Preprint at https://doi.org/10.1101/2020.06.02.130955 (2020).
Gordon, D. E. et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 583, 459–468 (2020). [DOI: 10.1038/s41586-020-2286-9]
Hachim, A. et al. Beyond the spike: identification of viral targets of the antibody response to SARS-CoV-2 in COVID-19 patients. Preprint at https://doi.org/10.1101/2020.04.30.20085670 (2020).
Hadfield, J. et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 34, 4121–4123 (2018). [DOI: 10.1093/bioinformatics/bty407]
Yewdell, J. W. DRiPs solidify: progress in understanding endogenous MHC class I antigen processing. Trends Immunol. 32, 548–558 (2011). [DOI: 10.1016/j.it.2011.08.001]
Abernathy, E. & Glaunsinger, B. Emerging roles for RNA degradation in viral replication and antiviral defense. Virology 479-480, 600–608 (2015). [DOI: 10.1016/j.virol.2015.02.007]
Huang, C. et al. SARS coronavirus nsp1 protein induces template-dependent endonucleolytic cleavage of mRNAs: viral mRNAs are resistant to nsp1-induced RNA cleavage. PLoS Pathog. 7, e1002433 (2011). [DOI: 10.1371/journal.ppat.1002433]
Kamitani, W., Huang, C., Narayanan, K., Lokugamage, K. G. & Makino, S. A two-pronged strategy to suppress host protein synthesis by SARS coronavirus Nsp1 protein. Nat. Struct. Mol. Biol. 16, 1134–1140 (2009). [DOI: 10.1038/nsmb.1680]
Tirosh, O. et al. The transcription and translation landscapes during human cytomegalovirus infection reveal novel host–pathogen interactions. PLoS Pathog. 11, e1005288 (2015). [DOI: 10.1371/journal.ppat.1005288]
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009). [DOI: 10.1186/gb-2009-10-3-r25]
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013). [DOI: 10.1093/bioinformatics/bts635]
Käll, L., Krogh, A. & Sonnhammer, E. L. L. A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol. 338, 1027–1036 (2004). [DOI: 10.1016/j.jmb.2004.03.016]
Yahalom-Ronen, Y. et al. A single dose of recombinant VSV-ΔG-spike vaccine provides protection against SARS-CoV-2 challenge. Preprint at https://doi.org/10.1101/2020.06.18.160655 (2020).

MeSH Term

Animals
Cell Line
Gene Expression Profiling
Genome, Viral
Humans
Molecular Sequence Annotation
Open Reading Frames
Peptides
Protein Biosynthesis
RNA, Messenger
RNA, Viral
Ribosomes
SARS-CoV-2
Viral Proteins

Chemicals

Peptides
RNA, Messenger
RNA, Viral
Viral Proteins
Journal Article Research Support, Non-U.S. Gov't

Word Cloud

Similar Articles

Cited By