ARF6 is a host factor for SARS-CoV-2 infection<i>in vitro</i>

Mirabelli, Carmen; Sherman, Emily J.; Wotring, Jesse W; Saghir, Jamal El; Cunha, Juliana Bragazzi; Harder, Jennifer L.; Sexton, Jonathan Z.; Emmer, Brian T.; Wobus, Christiane E.

doi:10.1101/2022.06.09.495482

Cited by 4 publications

(4 citation statements)

References 23 publications

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“…Other genes are involved in cell processes that are hijacked by the virus during infection. For example, ARF6 was identified as involved in exocytosis, but is used by the virus to infiltrate and infect the cell [114]. Overall, the findings of our functional analysis highlight some key mechanisms involved in the viral response to COVID-19.…”

Section: Pathway Enrichment Analysesmentioning

confidence: 75%

Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics

Waman,

Ashford,

Lam

et al. 2023

Preprint

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The COVID-19 disease is an ongoing global health concern. Although vaccination provides some protection, people are still susceptible to re-infection. Ostensibly, certain populations or clinical groups may be more vulnerable. Factors causing these differences are unclear and whilst socioeconomic and cultural differences are likely to be important, human genetic factors could influence susceptibility. Experimental studies indicate SARS-CoV-2 uses innate immune suppression as a strategy to speed-up entry and replication into the host cell. Therefore, it is necessary to understand the impact of variants in immunity-associated human proteins on susceptibility to COVID-19.In this work, we analysed missense coding variants in several SARS-CoV-2 proteins and its human protein interactors that could enhance binding affinity to SARS-CoV-2. We curated a dataset of 19 SARS-CoV-2: human protein 3D-complexes, from the experimentally determined structures in the Protein Data Bank and models built using AlphaFold2-multimer, and analysed impact of missense variants occurring in the protein-protein interface region. We analysed 468 missense variants from human proteins and 212 variants from SARS-CoV-2 proteins and computationally predicted their impacts on binding affinities to SARS-CoV-2 proteins, using 3D-complexes.We predicted a total of 26 affinity-enhancing variants from 14 human proteins implicated in increased binding affinity to SARS-CoV-2. These include key-immunity associated genes (TOMM70, ISG15, IFIH1, IFIT2, RPS3, PALS1, NUP98, RAE1, AXL, ARF6, TRIMM, TRIM25) as well as important spike receptors (KREMEN1, AXL and ACE2). We report both common (e.g., Y13N in IFIH1) and rare variants in these proteins and discuss their likely structural and functional impact, using information on known and predicted functional sites. Potential mechanisms associated with immune suppression implicated by these variants are discussed.Occurrence of certain predicted affinity-enhancing variants should be monitored as they could lead to increased susceptibility and reduced immune response to SARS-CoV-2 infection in individuals/populations carrying them. Our analyses aid in understanding the potential impact of genetic variation in immunity-associated proteins on COVID-19 susceptibility and help guide drug-repurposing strategies.

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Section: Pathway Enrichment Analysesmentioning

confidence: 75%

Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics

Waman,

Ashford,

Lam

et al. 2023

Preprint

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“…Since SARS-CoV-2 requires ACE2 and ARF6 to enter human cells [ 43 , 44 ], we assessed where ACE2 expression and ARF6 activation are altered in SARS-CoV-2 spike S1 RBD- stimulated EA.hy 296 Cells. For this purpose, we lysed EA.hy 296 cells treated with 0–10 μg/mL of the RBD for 72 h and used the cell lysates for analyzing the expression of ACE2 expression and ARF6 activation.…”

Section: Resultsmentioning

confidence: 99%

“…Guanine nucleotide exchange factors (GEFs) activate ARFs whereas GTPase activating proteins (GAPs) inactive them ( Figure 4 b) [ 45 ]. Since ARF6 is considered a potential target in SARS-CoV-2 infection [ 44 ], we used the GST-GGA3 PBD pulldown assay to assess if the SARS-CoV-2 spike protein S1 RBD treatment of EA.hy 296 cells causes ARF6 activation. The GST-GGA3 PBD specifically binds to the GTP-bound form of ARF and, therefore, the fusion protein coupled to glutathione beads along with an ARF1- or ARF6-specific antibody has been used to detect activated ARF1 or ARF6 in cell lysates [ 46 ].…”

Section: Resultsmentioning

confidence: 99%

Molecular Analysis of SARS-CoV-2 Spike Protein-Induced Endothelial Cell Permeability and vWF Secretion

Guo

Kanamarlapudi

2023

IJMS

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Coronavirus disease COVID-19, which is caused by severe acute respiratory syndrome coronavirus SARS-CoV-2, has become a worldwide pandemic in recent years. In addition to being a respiratory disease, COVID-19 is a ‘vascular disease’ since it causes a leaky vascular barrier and increases blood clotting by elevating von Willebrand factor (vWF) levels in the blood. In this study, we analyzed in vitro how the SARS-CoV-2 spike protein S1 induces endothelial cell (EC) permeability and its vWF secretion, and the underlying molecular mechanism for it. We showed that the SARS-CoV-2 spike protein S1 receptor-binding domain (RBD) is sufficient to induce endothelial permeability and vWF-secretion through the angiotensin-converting enzyme (ACE)2 in an ADP-ribosylation factor (ARF)6 activation-dependent manner. However, the mutants, including those in South African and South Californian variants of SARS-CoV-2, in the spike protein did not affect its induced EC permeability and vWF secretion. In addition, we have identified a signaling cascade downstream of ACE2 for the SARS-CoV-2 spike protein-induced EC permeability and its vWF secretion by using pharmacological inhibitors. The knowledge gained from this study could be useful in developing novel drugs or repurposing existing drugs for treating infections of SARS-CoV-2, particularly those strains that respond poorly to the existing vaccines.

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“…ARFs are also hijacked by pathogens, including bacteria, that directly subvert ARFs or their cognate effectors (Jimenez et al, 2016). ARF6 has been identified as an important host factor for the cellular entry of the SARS-CoV-2 (Zhou et al, 2022, Mirabelli et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways

Quirion

Ahrends

Boulais

et al. 2023

Preprint

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The ADP-ribosylation factor (ARF) family of GTPases are essential molecular switches that control a large variety of cellular processes. Here, we used classical proximity-dependent biotin identification (BioID) to comprehensively define the interactome of 28 out of 29 ARF proteins in two cell lines. The identification of ∼3000 high-confidence interactors allowed us to assign specific subcellular localization to the family members, uncovering previously undefined localization for ARL4D and ARL10. Clusterization analysis further showed the uniqueness in the set of interactors identified with these two ARF GTPases. We found that the expression of the understudied member ARL14 is restricted to the stomach and intestines and have identified phospholipase D1 (PLD1) and the ESCPE-1 complex, more precisely SNX1, as effectors. We showed that ARL14 can activate PLD1in celluloand is involved in the trafficking of cargosviathe ESCPE-1 complex. Thus, the BioID data generated in this study represent a useful tool to dissect the intricacies of ARF signaling and its spatial organization.

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ARF6 is a host factor for SARS-CoV-2 infectionin vitro

Cited by 4 publications

References 23 publications

Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics

Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics

Molecular Analysis of SARS-CoV-2 Spike Protein-Induced Endothelial Cell Permeability and vWF Secretion

Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways

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