PXD036206-3

PXD036206 is an original dataset announced via ProteomeXchange.

Title	Identification of host dependency factors involved in SARS-CoV-2 replication organelle formation through proteomics and ultrastructural analysis
Description	Positive-strand RNA viruses subvert the cellular endomembrane system for the generation of distinct compartments termed replication organelles (ROs) that harbor the site where viral RNAs are generated. In this study, we corroborate that the SARS-CoV-2 non-structural proteins 3 and 4 (nsp3 and nsp4) suffice to remodel the endoplasmic reticulum to form double membrane vesicles similar to ROs observed in viral infection. Cellular membrane alterations induced by nsp3/4 expression were evaluated through electron tomography and confocal microscopy and nsp3/4 associated host factors were identified using mass spectrometry. The role of these host factors in virus infection was determined using gene silencing, identifying several host proteins involved in the SARS-CoV-2 replication cycle. Combining the gene silencing approach with ultrastructural analysis of nsp3/4-expressing cells, we found that the host dependency factors FAM149B1, CCAR2 and ZC3HAV1 play a role in the formation of double membrane vesicles in a replication-independent manner.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:06:56.980.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pietro Scaturro
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2022-08-21 07:19:04	ID requested
1	2023-10-23 04:02:48	announced
2	2023-11-14 07:59:33	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 06:06:57	announced	2024-10-22: Updated project metadata.

10.1128/JVI.00878-23;

submitter keyword: FAM149B1, SARS-CoV-2, Interaction, label-free,AP-MS/MS, nsp3, nsp4

Pietro Scaturro
contact affiliation	Systems Arbovirology, Leibniz Institute of Virology, Hamburg, Germany
contact email	pietro.scaturro@leibniz-liv.de
lab head
Pietro Scaturro
contact affiliation	Systems Arbovirology, Leibniz Institute of Virology
contact email	pietro.scaturro@tum.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/10/PXD036206

PRIDE project URI

• PRIDE
  1. PXD036206
     1. Label: PRIDE project
     2. Name: Identification of host dependency factors involved in SARS-CoV-2 replication organelle formation through proteomics and ultrastructural analysis