Mass Spectrometry-Based Proteomic Analysis of Porcine Reproductive and Respiratory Syndrome Virus NSP9 Protein with Host Proteins

Porcine reproductive and respiratory syndrome virus (PRRSV) nonstructural protein 9 (NSP9), the viral RNA-dependent RNA polymerase (RdRp), is essential for viral replication but its comprehensive host interactome remains uncharacterized. This study employed co-immunoprecipitation coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to systematically identify NSP9-associated host proteins. We identified 222 high-confidence host interactors, with Gene Ontology and KEGG pathway analyses revealing significant enrichment in RNA/DNA-binding proteins, ubiquitin-proteasome pathways, metabolic regulators (amino acid/lipid biosynthesis), endoplasmic reticulum processing, and cell cycle components. Protein-protein interaction network analysis further delineated six functional modules involved in RNA processing, vesicular transport, and innate immunity. Crucially, validation studies confirmed direct binding between NSP9 and key candidates (CAPZ1, PSMA3, CDK1, USP48). Functional assessment demonstrated that CDK1 overexpression significantly inhibited PRRSV replication, implicating CDK1 as a host restriction factor. These findings collectively unveil the multifaceted role of NSP9 in subverting host machinery while identifying novel host defense mechanisms and potential targets for antiviral development against PRRSV.