Analysis of the Porcine Reproductive and Respiratory Syndrome Virus Nucleocapsid Interactome

Porcine reproductive and respiratory syndrome virus (PRRSV) is a major swine pathogen that causes significant economic losses worldwide. The nucleocapsid (N) protein, the most abundant viral protein in infected cells, plays roles beyond its structural function, influencing various host cellular processes. Here, we report the identification of 301 cellular protein candidates interacting with PRRSV N using EGFP immunoprecipitation combined with label-free quantitative mass spectrometry. The analysis underscores the versatile nature of the N protein in targeting a wide range of cellular proteins and processes across multiple subcellular compartments. We observed strong enrichment of ribosomal proteins, nucleolar proteins involved in ribosome biogenesis, splicing factors, RNA helicases, and DNA-binding proteins involved in chromatin remodeling and DNA damage response. Additionally, we identified proteins involved in viral RNA sensing and intrinsic antiviral mechanisms that may contribute to the immunosuppressive properties of the viral protein. Several interactions were validated and further characterized for RNA dependence, including MYBBP1A, NCL, IGF2BP1, UPF3B, G3BP1, EIF2S1, RFC4, ABCF1, PPM1G, NSUN2, and NOP2. Notably, RTCB and MYBBP1A were identified as host dependency factors for PRRSV infection. Our findings expand the current understanding of PRRSV-host interactions and reveal novel N-interacting proteins that may contribute to viral pathogenesis and immune evasion.