Control of nuclear localization of the nucleocapsid protein of SARS-CoV-2

The nucleocapsid (N) protein of coronaviruses is a structural protein that binds viral RNA for assembly into the mature virion, a process that occurs in the cytoplasm. Several coronavirus N proteins also localize to the nucleus. Herein, we identify that two sequences (NLSs) are required for nuclear localization of the SARS-CoV-2 N protein. Deletion or mutation of these two sequences creates an N protein that does not localize to the nucleus in HEK293T cells. Overexpression of both wild-type and NLS-mutated N proteins dysregulate a largely overlapping set of mRNAs in HEK293T cells, suggesting that these N proteins do not have direct nuclear effects on transcription. Consistent with that hypothesis, both N proteins induce nuclear localization of NF-κB p65 and dysregulate a set of previously identified NF-κB-dependent genes. The effects of N on nuclear properties are proposed to alter host cell functions that contribute to viral pathogenesis or replication.