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.