摘要The coronavirus disease 2019(COVID-19)caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection is currently a global pandemic.Extensive investigations have been performed to study the clinical and cellular effects of SARS-CoV-2 infection.Mass spectrometry-based proteomics studies have revealed the cellular changes due to the infection and identified a plethora of interactors for all SARS-CoV-2 components,except for the longest non-structural protein 3(NSP3).Here,we expressed the full-length NSP3 proteins of SARS-CoV and SARS-CoV-2 to investigate their unique and shared functions using multi-omics methods.We conducted interactome,phosphoproteome,ubiquitylome,transcriptome,and proteome analy-ses of NSP3-expressing cells.We found that NSP3 plays essential roles in cellular functions such as RNA metabolism and immune response(e.g.,NF-κB signal transduction).Interestingly,we showed that SARS-CoV-2 NSP3 has both endoplasmic reticulum and mitochondrial localizations.In addi-tion,SARS-CoV-2 NSP3 is more closely related to mitochondrial ribosomal proteins,whereas SARS-CoV NSP3 is related to the cytosolic ribosomal proteins.In summary,our integrative multi-omics study of NSP3 improves the understanding of the functions of NSP3 and offers poten-tial targets for the development of anti-SARS strategies.