PXD050159-1

PXD050159 is an original dataset announced via ProteomeXchange.

Title	An Integrated Proteomics Approach Identifies Phosphorylation Sites on Host and Viral Proteins that Regulate West Nile Virus Infection
Description	Upon infection, viruses remodel host cells to create an environment hospitable to viral replication. In response, host cells have evolved to sense infection and rapidly induce pathways to limit viral replication. One strategy used by both players is to regulate the host cell proteome for their benefit. To characterize these changes, we used a mass spectrometry strategy to define alterations in the viral and host proteome during infection of human cells with West Nile virus (WNV). Our studies reveal previously uncharacterized post-translational modifications (PTMs) on viral proteins, including phosphorylation sites on the WNV nonstructural proteins, NS3 and NS5, that impact viral RNA replication. Additionally, we monitored changes in host protein abundance and found that while 82 proteins had increased expression upon WNV infection, only five of these are canonical interferon stimulated genes (ISGs). Our data suggests that the majority of the upregulated non-ISGs are regulated at the translational, rather than transcriptional level, defining a new group of virus-induced proteins (VIPs). HERPUD1 is a stress-response protein that was induced at both the transcriptional and translational level. We show HERPUD1 restricts WNV replication, likely through a mechanism independent of its previously defined role in ER-associated degradation (ERAD). Our phosphoproteomics studies revealed eight phosphorylation sites on viral proteins, including a site on the WNV helicase/protease NS3 that is important for viral replication. Further, we identified XXX phosphorylation sites on host proteins with increased abundance and XXX sites with decreased abundance during WNV infection. We used bioinformatics to identify phosphosites predicted to increase host protein activity and found two antiviral host kinases that are activated by phosphorylation during WNV infection. First, we identified a phosphorylation site at S108 of AMPKβ1, a non-catalytic subunit that is thought to regulate activity of the AMPK complex. We also found that a group I p21-activated kinase, PAK2, is phosphorylated at S141. This phosphorylation event in the autoinhibitory domain activates PAK2, which restricts viral protein translation. Altogether, our work contributes to our understanding of the interplay between host and virus while providing a resource to define the changes to the proteome that regulate viral infection.
HostingRepository	PRIDE
AnnounceDate	2025-04-29
AnnouncementXML	Submission_2025-04-29_10:14:04.778.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jeffrey Johnson
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2024-02-26 13:37:36	ID requested
⏵ 1	2025-04-29 10:14:05	announced

Dataset with its publication pending

submitter keyword: WNV,West Nile virus, flavivirus

Jeffrey Johnson
contact affiliation	Department of Microbiology Icahn School of Medicine at Mount Sinai
contact email	jeffrey.johnson@mssm.edu
lab head
Jeffrey Johnson
contact affiliation	Icahn School of Medicine at Mount Sinai
contact email	jeffrey.johnson@mssm.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD050159
     1. Label: PRIDE project
     2. Name: An Integrated Proteomics Approach Identifies Phosphorylation Sites on Host and Viral Proteins that Regulate West Nile Virus Infection