PXD052138-1

PXD052138 is an original dataset announced via ProteomeXchange.

Title	SARS-CoV-2 Nsp2 recruits GIGYF2 near viral replication sites and supports viral protein production
Description	The SARS-CoV-2 genome encodes 16 non-structural proteins (Nsps), with Nsp2 being the least conserved and least understood. In this study, we found a crucial role of Nsp2 in the SARS-CoV-2 life cycle and demonstrated its interaction with GIGYF2, which causes the relocation of GIGYF2 to near double membrane vesicles (DMVs) and the enhancement of viral protein production. Deletion of the Nsp2-coding region from the viral genome led to a drastic reduction in viral RNA synthesis early in infection (3–4 hours post infection). Through interactome analysis of Nsp2 in virus-infected cells, we identified GIGYF2—a protein involved in translational regulation—as a key partner of Nsp2. We confirm the interaction between GIGYF2 and Nsp2 from both SARS-CoV-1 and SARS-CoV-2. Depleting GIGYF2 or its cofactor ZNF598 phenocopied the replication defects observed with Nsp2 deletion, suggesting their critical roles in viral reproduction. Moreover, GIGYF2 and ZNF598 relocate to areas near DMVs, viral replication sites, upon infection. This relocation does not happen with the Nsp2-deleted virus, indicating Nsp2’s role in directing GIGYF2 to DMVs. Using formaldehyde crosslinking and immunoprecipitation-sequencing experiments (fCLIP-seq), we found that GIGYF2 interacts with viral RNAs, particularly in regions encoding Nsp3, M, and Orf6. Depletion of GIGYF2 resulted in decreased expression of these proteins. Our findings reveal the function of Nsp2 in supporting viral protein production by exploiting GIGYF2 as a host factor.
HostingRepository	PRIDE
AnnounceDate	2025-07-26
AnnouncementXML	Submission_2025-07-26_02:00:16.549.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD052138
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Sunghan Lee
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2024-05-09 01:29:05	ID requested
⏵ 1	2025-07-26 02:00:16	announced

10.1093/NAR/GKAF674;

10.6019/PXD052138;

submitter keyword: SARS-CoV-2, GIGYF2, virus, Nsp2

V. Narry Kim
contact affiliation	Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
contact email	narrykim@snu.ac.kr
lab head
Sunghan Lee
contact affiliation	Seoul National University
contact email	hanbio999@gmail.com
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/2025/07/PXD052138

PRIDE project URI

• PRIDE
  1. PXD052138
     1. Label: PRIDE project
     2. Name: SARS-CoV-2 Nsp2 recruits GIGYF2 near viral replication sites and supports viral protein production