Adaptive mutations at lysine residues of PRRSV nsp12 enable evasion of host proteasomal and selective autophagic degradation

Ubiquitin signaling in viral infections can either enhance immune responses and degrade viral proteins or be exploited by viruses to target host antiviral factors. Porcine reproductive and respiratory syndrome virus (PRRSV) poses a significant threat to the pig industry, with its non-structural proteins (nsps) critical for virulence and replication. Here, we investigated the role of ubiquitination in the stability of PRRSV-encoded nsps and found that nsp12 was specifically degraded via the ubiquitin-proteasome system. Mechanistically, nsp12 underwent K48- and K63-linked polyubiquitination at lysine residues 89, 91, 127, and 130. RNF114 served as an E3 ubiquitin ligase for nsp12, with its enzymatic activity essential for both nsp12 degradation and viral replication. Additionally, nsp12 underwent ubiquitin-dependent selective autophagy through receptor-mediated recognition, wherein NBR1, SQSTM1, and NDP52 bridged its interaction with LC3 for autophagic degradation. Evolutionary analyses revealed that PRRSV nsp12 acquired non-lysine residues at positions 89, 127, and 130 during viral adaptation. Correspondingly, recombinant PRRSV strains carrying the K91/127/130R mutations within nsp12 exhibited enhanced replication, while a revertant strain with the R89K mutation in nsp12 showed attenuated infectivity. Mass spectrometry analysis further identified significant enrichment of ubiquitination-related modifications among nsp12-interacting proteins. These findings provide valuable insights for anti-PRRSV drug design and highlight the challenge posed by adaptive mutations in viral proteins to the swine industry. Author SummaryUbiquitination plays crucial roles in both proteasomal degradation and selective autophagy during viral infections, yet its impact on the stability of porcine reproductive and respiratory syndrome virus (PRRSV) nonstructural proteins (nsps) remains unexplored. Here, we found that nsp12 was targeted for proteasomal degradation through K48/K63-linked polyubiquitination at lysine residues 89, 91, 127, and 130, which requires the involvement of E3 ubiquitin ligase RNF114. Furthermore, nsp12 underwent receptor-mediated selective autophagic degradation through the action of NBR1, SQSTM1, and NDP52. Using reverse genetics technology, mutations of lysine to arginine in PRRSV nsp12 enhanced viral replication, whereas the reverse mutations reduced its infectivity. Our findings demonstrate that PRRSV evades host degradation by acquiring adaptive mutations within nsp12, which counteract ubiquitin-dependent clearance thus enhancing viral fitness. This novel mechanism illustrates a key viral immune evasion strategy and underlines the challenge in controlling PRRSV.