Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV

Stukalov, Alexey; Girault, Virginie; Grass, Vincent; Karayel, Özge; Bergant, Valter; Urban, Christian; Haas, Darya A.; Huang, Yiqi; Oubraham, Lila; Wang, Anqi; Hamad, Mohammad; Piras, Antonio; Hansen, Fynn M.; Tanzer, Maria C.; Paron, Igor; Zinzula, Luca; Engleitner, Thomas; Reinecke, Maria; Lavacca, Teresa M.; Ehmann, Rosina; Wölfel, Roman; Jores, Joerg; Küster, Bernhard; Protzer, Ulrike; Rad, Roland; Ziebuhr, John; Thiel, Volker; Scaturro, Pietro; Mann, Matthias; Pichlmair, Andreas

doi:10.1038/s41586-021-03493-4

Cited by 590 publications

(729 citation statements)

References 85 publications

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“…The fact that ATP8B1 was important for both SARS-CoV-2 and MERS-CoV replication highlighted a potentially conserved role for coronaviruses and it would be of high interest to understand the underlying molecular mechanisms. Interestingly, ATP8B1 and its homologous ATP8B2 were recently identified as bindingpartners of SARS-CoV-2 ORF3 and M, respectively 67 , suggesting that the virus might subvert their functions. Of note, TMEM41B, an integral protein of the endoplasmic reticulum known to regulate the formation of autophagosomes, lipid droplets and lipoproteins, was recently shown to be both an essential coronavirus cofactor 25 and a phospholipid scramblase whose deficiency impaired the normal cellular distribution of cholesterol and phosphatidylserine 68 .…”

Section: Discussionmentioning

confidence: 99%

Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal HCoVs

Goujon¹,

Rebendenne²,

Roy

et al. 2021

Preprint

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Several genome-wide CRISPR knockout screens have been conducted to identify host factors regulating SARS-CoV-2 replication, but the models used have often relied on overexpression of ACE2 receptor. Additionally, such screens have yet to identify the protease TMPRSS2, known to be important for viral entry at the plasma membrane. Here, we conducted a meta-analysis of these screens and showed a high level of cell-type specificity of the identified hits, arguing for the necessity of additional models to uncover the full landscape of SARS-CoV-2 host factors. We performed genome-wide knockout and activation CRISPR screens in Calu-3 lung epithelial cells, as well as knockout screens in Caco-2 intestinal cells. In addition to identifying ACE2 and TMPRSS2 as top hits, our study reveals a series of so far unidentified and critical host-dependency factors, including the Adaptins AP1G1 and AP1B1 and the flippase ATP8B1. Moreover, new anti-SARS-CoV-2 proteins with potent activity, including several membrane-associated Mucins, IL6R, and CD44 were identified. We further observed that these genes mostly acted at the critical step of viral entry, with the notable exception of ATP8B1, the knockout of which prevented late stages of viral replication. Exploring the pro- and anti-viral breadth of these genes using highly pathogenic MERS-CoV, seasonal HCoV-NL63 and -229E and influenza A orthomyxovirus, we reveal that some genes such as AP1G1 and ATP8B1 are general coronavirus cofactors. In contrast, Mucins recapitulated their known role as a general antiviral defense mechanism. These results demonstrate the value of considering multiple cell models and perturbational modalities for understanding SARS-CoV-2 replication and provide a list of potential new targets for therapeutic interventions.

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Section: Discussionmentioning

confidence: 99%

Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal HCoVs

Goujon¹,

Rebendenne²,

Roy

et al. 2021

Preprint

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“…Nonetheless, it is worth noting that the ERM proteins anchor plasma membrane proteins to the actin cytoskeleton and hence can direct their accumulation at specific regions of the cell surface, and also that cell fusion proteins expressed by reoviruses have been found to direct actin filament formation to drive cell fusion 49,50 . Two recent studies have reported interaction screens of all proteins expressed by SARS-CoV-2, looking for host proteins that co-precipitate with each viral protein when expressed individually in cultured cells 51,52 . In both cases, the only interaction partners identified for S were the palmitoyltransferase subunits ZDHHC5 and GOLGA7.…”

Section: Discussionmentioning

confidence: 99%

Sequences in the cytoplasmic tail of SARS-CoV-2 Spike facilitate expression at the cell surface and syncytia formation

Cattin‐Ortolá

Welch

Skehel

et al. 2020

Preprint

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The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds the cell surface protein ACE2 to mediate fusion of the viral membrane with target cells. S comprises a large external domain, a transmembrane domain (TMD) and a short cytoplasmic tail. To elucidate the intracellular trafficking of S protein in host cells we applied proteomics to identify cellular factors that interact with its cytoplasmic tail. We confirm interactions with components of the COPI, COPII and SNX27/retromer vesicle coats, and with FERM domain actin regulators and the WIPI3 autophagy component. The interaction with COPII promotes efficient exit from the endoplasmic reticulum (ER), and although COPI-binding should retain S in the early Golgi system where viral budding occurs, the binding is weakened by a suboptimal histidine residue in the recognition motif. As a result, S leaks to the surface where it accumulates as it lacks an endocytosis motif of the type found in many other coronaviruses. It is known that when at the surface S can direct cell:cell fusion leading to the formation of multinucleate syncytia. Thus, the trafficking signals in the cytoplasmic tail of S protein indicate that syncytia formation is not an inadvertent by-product of infection but rather a key aspect of the replicative cycle of SARS-CoV-2 and potential cause of pathological symptoms.

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“…The coronaviruses are the largest single stranded RNA viruses known and their genomic RNA encodes around 30 viral proteins 1 . During infection each viral protein performs unique functions and interacts with a range of cellular protein host factors to allow viral proliferation and immune escape [2][3][4][5] . Precise disruption of viral-host factor interactions is an attractive strategy for developing novel antiviral reagents.…”

mentioning

confidence: 99%

Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities

Kruse

Benz

Garvanska

et al. 2021

Preprint

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Viral proteins make extensive use of short peptide interaction motifs to hijack cellular host factors. However, most current large-scale methods do not identify this important class of protein-protein interactions. Uncovering peptide mediated interactions provides both a molecular understanding of viral interactions with their host and the foundation for developing novel antiviral reagents. Here we describe a scalable viral peptide discovery approach covering 229 RNA viruses that provides high resolution information on direct virus-host interactions. We identify 269 peptide-based interactions for 18 coronaviruses including a specific interaction between the human G3BP1/2 proteins and an [FILV]xFG peptide motif in the SARS-CoV-2 nucleocapsid (N) protein. This interaction supports viral replication and through its [FILV]xFG motif N rewires the G3BP1/2 interactome to disrupt stress granules. A peptide-based inhibitor disrupting the G3BP1/2-N interaction blocks SARS-CoV-2 infection showing that our results can be directly translated into novel specific antiviral reagents.

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Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV

Cited by 590 publications

References 85 publications

Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal HCoVs

Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal HCoVs

Sequences in the cytoplasmic tail of SARS-CoV-2 Spike facilitate expression at the cell surface and syncytia formation

Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities

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