Dataset Information

The Global Phosphorylation Landscape of SARS-CoV-2 Infection

ABSTRACT: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic, has infected over 3 million people worldwide and caused over 200,000 deaths since it emerged in late 2019. There is an urgent need to develop therapies that can limit SARS-CoV-2 infection, replication, and pathogenesis. Due to the rapid emergence of SARS-CoV-2, there currently exists a lack in the knowledge of the host cellular pathways that sustain infection and contribute to pathogenesis. Here, we present a quantitative proteomics and phosphoproteomics survey of SARS-CoV-2 infection in Vero-E6 cells.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Cercopithecus Aethiops (green Monkey) (grivet)

TISSUE(S): Epithelial Cell

SUBMITTER: Alicia Richards

LAB HEAD: Dr. Nevan J. Krogan

PROVIDER: PXD019113 | Pride | 2020-07-06

REPOSITORIES: Pride

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Publications

The Global Phosphorylation Landscape of SARS-CoV-2 Infection.

Bouhaddou Mehdi M Memon Danish D Meyer Bjoern B White Kris M KM Rezelj Veronica V VV Correa Marrero Miguel M Polacco Benjamin J BJ Melnyk James E JE Ulferts Svenja S Kaake Robyn M RM Batra Jyoti J Richards Alicia L AL Stevenson Erica E Gordon David E DE Rojc Ajda A Obernier Kirsten K Fabius Jacqueline M JM Soucheray Margaret M Miorin Lisa L Moreno Elena E Koh Cassandra C Tran Quang Dinh QD Hardy Alexandra A Robinot Rémy R Vallet Thomas T Nilsson-Payant Benjamin E BE Hernandez-Armenta Claudia C Dunham Alistair A Weigang Sebastian S Knerr Julian J Modak Maya M Quintero Diego D Zhou Yuan Y Dugourd Aurelien A Valdeolivas Alberto A Patil Trupti T Li Qiongyu Q Hüttenhain Ruth R Cakir Merve M Muralidharan Monita M Kim Minkyu M Jang Gwendolyn G Tutuncuoglu Beril B Hiatt Joseph J Guo Jeffrey Z JZ Xu Jiewei J Bouhaddou Sophia S Mathy Christopher J P CJP Gaulton Anna A Manners Emma J EJ Félix Eloy E Shi Ying Y Goff Marisa M Lim Jean K JK McBride Timothy T O'Neal Michael C MC Cai Yiming Y Chang Jason C J JCJ Broadhurst David J DJ Klippsten Saker S De Wit Emmie E Leach Andrew R AR Kortemme Tanja T Shoichet Brian B Ott Melanie M Saez-Rodriguez Julio J tenOever Benjamin R BR Mullins R Dyche RD Fischer Elizabeth R ER Kochs Georg G Grosse Robert R García-Sastre Adolfo A Vignuzzi Marco M Johnson Jeffery R JR Shokat Kevan M KM Swaney Danielle L DL Beltrao Pedro P Krogan Nevan J NJ

Cell 20200628 3

The causative agent of the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected millions and killed hundreds of thousands of people worldwide, highlighting an urgent need to develop antiviral therapies. Here we present a quantitative mass spectrometry-based phosphoproteomics survey of SARS-CoV-2 infection in Vero E6 cells, revealing dramatic rewiring of phosphorylation on host and viral proteins. SARS-CoV-2 infection promoted ca ...[more]

PMID: 32645325

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Project description:Background: Type I interferons (IFNs) are essential to the clearance of viral diseases, in part by initiating upregulation of IFN regulated genes (IRGs). A clear distinction between genes upregulated directly by virus and genes upregulated by secondary IFN production has not been made. Here we investigated the genes regulated by IFN-a2b compared to the genes regulated by SARS-CoV infection in ferrets. Methods: We characterized early host immune responses in peripheral blood and lung necropsies of ferrets injected with IFN-a2b or infected with SARS-CoV/Tor 2 strain, using microarray analysis on the Affymetrix platform. Results: We identified a common IRG signature that was upregulated in both SARS-CoV infected ferrets as well as in ferrets injected with IFN-a2b. We also identified unique patterns of gene expression for leukocyte activation, cell adhesion and complement pathways between IFN-a2b injection and SARS-CoV infection. Conclusions: Our results define the effects of IFN-a2b on the immune system of ferrets highlighting genes regulated by IFN during SARS-CoV infection. We have shown the similarities and differences of top funcional gene groups as well as pathways that play key roles in early immune responses in ferrets in response to IFN-a2b or SARS-CoV. Key words: ferret, gene expression, SARS, interferon. Keywords: time course In experiments with IFN-a2b, for peripheral blood, 15 ferrets were randomly allocated to 3 groups: Day 0, 5 ferrets (no IFN injection), day 1, 6 ferrets (injected), and day 2, 4 ferrets (injected). For lung necropsies of injected ferrets with IFN-a2b, we used 12 ferrets in 3 groups: 4 ferrets, day 0 (no IFN injection), 4 ferrets, day 1 (injected) and 4 ferrets, day 2 (injected). Experimental groups for SARS-CoV infection was as follows: For peripheral blood, 3 and 4 ferrets for day 0 (no infection) and day 2 (infection) respectively. For lung neceropsies, a total of 9 ferrets in 3 groups, each with 3 replicates for day 0 (no infection), day 1 (infection) and day 2 (infection).

Dataset Information

The Global Phosphorylation Landscape of SARS-CoV-2 Infection

Publications

The Global Phosphorylation Landscape of SARS-CoV-2 Infection.

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