Evidence map›Paper›PMID 33655243›Full record

ArticlebioRxiv : the preprint server for biology2021

The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation.

Jordan M Meyers, Muthukumar Ramanathan, Ronald L Shanderson, Laura Donohue, Ian Ferguson, Margaret G Guo, Deepti S Rao, Weili Miao, David Reynolds, Xue Yang and 4 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 10 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

14 authors at 2 institutions in 1 country.

Jordan M MeyersProgram in Epithelial Biology, Stanford University, Stanford, CA 94305, USA.
Muthukumar RamanathanProgram in Epithelial Biology, Stanford University, Stanford, CA 94305, USA.
Ronald L ShandersonProgram in Epithelial Biology, Stanford University, Stanford, CA 94305, USA.
Laura DonohueProgram in Epithelial Biology, Stanford University, Stanford, CA 94305, USA.
Ian FergusonProgram in Epithelial Biology, Stanford University, Stanford, CA 94305, USA.
Margaret G GuoProgram in Epithelial Biology, Stanford University, Stanford, CA 94305, USA.
Deepti S RaoProgram in Epithelial Biology, Stanford University, Stanford, CA 94305, USA.
Weili MiaoProgram in Epithelial Biology, Stanford University, Stanford, CA 94305, USA.
David ReynoldsProgram in Epithelial Biology, Stanford University, Stanford, CA 94305, USA.
Xue YangProgram in Epithelial Biology, Stanford University, Stanford, CA 94305, USA.
Yang ZhaoProgram in Epithelial Biology, Stanford University, Stanford, CA 94305, USA.
Yen-Yu YangDepartment of Chemistry, University of California, Riverside, CA, 92521, USA.
Yinsheng WangDepartment of Chemistry, University of California, Riverside, CA, 92521, USA.
Paul A KhavariProgram in Epithelial Biology, Stanford University, Stanford, CA 94305, USA.
Stanford University · USUniversity of California, Riverside · US

Funding

REGULATORS OF EPIDERMAL GENE EXPRESSIONR01AR045192 · NIAMS · STANFORD UNIVERSITY · PI PAUL KHAVARI · 1999 to 2026
$9.9M
NIAMS NIH HHS R01 AR045192
6 · The paper itself

Abstract

Viral proteins localize within subcellular compartments to subvert host machinery and promote pathogenesis. To study SARS-CoV-2 biology, we generated an atlas of 2422 human proteins vicinal to 17 SARS-CoV-2 viral proteins using proximity proteomics. This identified viral proteins at specific intracellular locations, such as association of accessary proteins with intracellular membranes, and projected SARS-CoV-2 impacts on innate immune signaling, ER-Golgi transport, and protein translation. It identified viral protein adjacency to specific host proteins whose regulatory variants are linked to COVID-19 severity, including the TRIM4 interferon signaling regulator which was found proximal to the SARS-CoV-2 M protein. Viral NSP1 protein adjacency to the EIF3 complex was associated with inhibited host protein translation whereas ORF6 localization with MAVS was associated with inhibited RIG-I 2CARD-mediated AUTHOR SUMMARY: SARS-CoV-2 is the latest pathogenic coronavirus to emerge as a public health threat. We create a database of proximal host proteins to 17 SARS-CoV-2 viral proteins. We validate that NSP1 is proximal to the EIF3 translation initiation complex and is a potent inhibitor of translation. We also identify ORF6 antagonism of RNA-mediate innate immune signaling. We produce a database of potential host targets of the viral protease NSP5, and create a fluorescence-based assay to screen cleavage of peptide sequences. We believe that this data will be useful for identifying roles for many of the uncharacterized SARS-CoV-2 proteins and provide insights into the pathogenicity of new or emerging coronaviruses.

Identifiers

PMID33655243
PMCPMC7924263
OpenAlexW3126405788

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.