The Global Phosphorylation Landscape of SARS-CoV-2 Infection

Bouhaddou, Mehdi; Memon, Danish; Meyer, Björn; White, Kris M.; Rezelj, Veronica V.; Marrero, Miguel; Polacco, Benjamin J.; Melnyk, James E.; Ulferts, Svenja; Kaake, Robyn M.; Batra, Jyoti; Richards, Alicia; Stevenson, Erica; Gordon, David E.; Rojc, Ajda; Obernier, Kirsten; Fabius, Jacqueline M.; Soucheray, Margaret; Miorin, Lisa; Moreno, Elena; Koh, Cassandra; Tran, Quang; Hardy, Alexandra; Robinot, Rémy; Vallet, Thomas; Nilsson-Payant, Benjamin E.; Hernández-Armenta, Claudia; Dunham, Alistair S.; Weigang, Sebastian; Knerr, Julian; Modak, Maya; Quintero, Diego; Zhou, Yuan; Dugourd, Aurélien; Valdeolivas, Alberto; Patil, Trupti; Li, Qiongyu; Hüttenhain, Ruth; Çakır, Merve; Muralidharan, Monita; Kim, Minkyu; Jang, Gwendolyn Μ.; Tutuncuoglu, Beril; Hiatt, Joseph; Guo, Jeffrey Z.; Xu, Jiewei; Bouhaddou, Sophia; Mathy, Christopher J.P.; Gaulton, Anna; Manners, Emma; Félix, Eloy; Shi, Ying; Goff, Marisa; Lim, Jean K.; McBride, Timothy P.; O’Neal, Michael C.; Cai, Yiming; Chang, Jason C.; Broadhurst, David J.; Klippsten, Saker; Wit, Emmie de; Leach, Andrew R.; Kortemme, Tanja; Shoichet, Brian K.; Ott, Mélanie; Sáez-Rodríguez, Julio; tenOever, Benjamin R.; Mullins, R. Dyche; Fischer, Elizabeth R.; Kochs, Georg; Grosse, Robert; García‐Sastre, Adolfo; Vignuzzi, Marco; Johnson, Jeffrey R.; Shokat, Kevan M.; Swaney, Danielle L.; Beltrão, Pedro; Krogan, Nevan J.

doi:10.1016/j.cell.2020.06.034

Cited by 947 publications

(1,403 citation statements)

References 439 publications

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“…ORF9b appears in UniProt annotations and was detected by Bojkova et al 14 infected cells 14,15 did not detect peptides that originate from the out-of-frame ORFs we annotated, likely due to challenges in detecting trypsin-digested products from short coding regions 24 . Indeed, two canonical SARS-CoV-2 proteins, ORF7b (43aa) and ORF-E (75aa) were also not detected by mass-spectrometry 14,15,26,27 , and our ribosome profiling data is the first to show these SARS-CoV-2 proteins are indeed expressed.…”

Section: Mainmentioning

confidence: 61%

The coding capacity of SARS-CoV-2

Finkel

Mizrahi

Nachshon

et al. 2020

Preprint

107

166

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SARS-CoV-2 is a coronavirus responsible for the COVID-19 pandemic. In order to understand its pathogenicity, antigenic potential and to develop diagnostic and therapeutic tools, it is essential to portray the full repertoire of its expressed proteins. The SARS-CoV-2 coding capacity map is currently based on computational predictions and relies on homology to other coronaviruses. Since coronaviruses differ in their protein array, especially in the variety of accessory proteins, it is crucial to characterize the specific collection of SARS-CoV-2 translated open reading frames (ORF)s in an unbiased and open-ended manner. Utilizing a suit of ribosome profiling techniques, we present a high-resolution map of the SARS-CoV-2 coding regions, allowing us to accurately quantify the expression of canonical viral ORFs and to identify 23 novel unannotated viral ORFs. These ORFs include several in-frame internal ORFs lying within existing ORFs, resulting in N-terminally truncated products, as well as internal out-of-frameORFs, which generate novel polypeptides. Finally, we detected a prominent initiation at a CUG codon located in the 5'UTR. Although this codon is shared by all SARS-CoV-2 transcripts, the initiation was specific to the genomic RNA, indicating that the genomic RNA harbors unique features that may affect ribosome engagement. Overall, our work reveals the full coding capacity of SARS-CoV-2 genome, providing a rich resource, which will form the basis of future functional studies and diagnostic efforts.

show abstract

Section: Mainmentioning

confidence: 61%

The coding capacity of SARS-CoV-2

Finkel

Mizrahi

Nachshon

et al. 2020

Preprint

107

166

View full text Add to dashboard Cite

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“…They also indicate that it will not be trivial to identify the essential targets that mediate thapsigargin's antiviral effects. Our data provide a rich resource for further drug target analysis, also in conjunction with the few deep protein sequencing studies available for SARS-CoV-2 (but not MERS-CoV) (Bojkova et al, 2020;Bouhaddou et al, 2020;Grenga et al, 2020;Stukalov et al, 2020). Our study fills an important knowledge gap by providing a direct side-by-side comparison of pharmacologically targeted cells infected with two highly pathogenic human coronaviruses.…”

Section: Discussionmentioning

confidence: 88%

Inhibiting coronavirus replication in cultured cells by chemical ER stress

Shaban

Müller

Mayr-Buro

et al. 2020

Preprint

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Coronaviruses (CoVs) are important human pathogens for which no specific treatment is available. Here, we provide evidence that pharmacological reprogramming of ER stress pathways can be exploited to suppress CoV replication. We found that the ER stress inducer thapsigargin efficiently inhibits coronavirus (HCoV-229E, MERS-CoV, SARS-CoV-2) replication in different cell types, (partially) restores the virus-induced translational shut-down, and counteracts the CoV-mediated downregulation of IRE1α and the ER chaperone BiP. Proteome-wide data sets revealed specific pathways, protein networks and components that likely mediate the thapsigargin-induced antiviral state, including HERPUD1, an essential factor of ER quality control, and ER-associated protein degradation complexes. The data show that thapsigargin hits a central mechanism required for CoV replication, suggesting that thapsigargin (or derivatives thereof) may be developed into broad-spectrum anti-CoV drugs.One Sentence Summary / Running titleSuppression of coronavirus replication through thapsigargin-regulated ER stress, ERQC / ERAD and metabolic pathways

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“…AVEN, TP53BP2, AREL1, BAG3, ZAK, CASP8). Multiple kinases were also identified (see 18 ), suggesting that NSP2 is an important signaling perturbator in infected cells. NSP2 could thus play a role in modulating cellular response to infection and death signals.…”

Section: Nsp2 Uniquely Interacts With Rig-i and Stat1 And Appears Asmentioning

confidence: 99%

Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms

Laurent

Sofianatos

Komarova

et al. 2020

Preprint

128

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The worldwide SARS-CoV-2 outbreak poses a serious challenge to human societies and economies. SARS-CoV-2 proteins orchestrate complex pathogenic mechanisms that underlie COVID-19 disease. Thus, understanding how viral polypeptides rewire host protein networks enables better-founded therapeutic research. In complement to existing proteomic studies, in this study we define the first proximal interaction network of SARS-CoV-2 proteins, at the whole proteome level in human cells. Applying a proximity-dependent biotinylation (BioID)-based approach greatly expanded the current knowledge by detecting interactions within poorly soluble compartments, transient, and/or of weak affinity in living cells. Our BioID study was complemented by a stringent filtering and uncovered 2,128 unique cellular targets (1,717 not previously associated with SARS-CoV-1 or 2 proteins) connected to the N- and C-ter BioID-tagged 28 SARS-CoV-2 proteins by a total of 5,415 (5,236 new) proximal interactions. In order to facilitate data exploitation, an innovative interactive 3D web interface was developed to allow customized analysis and exploration of the landscape of interactions (accessible at http://www.sars-cov-2-interactome.org/). Interestingly, 342 membrane proteins including interferon and interleukin pathways factors, were associated with specific viral proteins. We uncovered ORF7a and ORF7b protein proximal partners that could be related to anosmia and ageusia symptoms. Moreover, comparing proximal interactomes in basal and infection-mimicking conditions (poly(I:C) treatment) allowed us to detect novel links with major antiviral response pathway components, such as ORF9b with MAVS and ISG20; N with PKR and TARB2; NSP2 with RIG-I and STAT1; NSP16 with PARP9-DTX3L. Altogether, our study provides an unprecedented comprehensive resource for understanding how SARS-CoV-2 proteins orchestrate host proteome remodeling and innate immune response evasion, which can inform development of targeted therapeutic strategies.

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The Global Phosphorylation Landscape of SARS-CoV-2 Infection

Cited by 947 publications

References 439 publications

The coding capacity of SARS-CoV-2

The coding capacity of SARS-CoV-2

Inhibiting coronavirus replication in cultured cells by chemical ER stress

Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms

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