Effect of CHIKV capsid protein nucleolar localisation on host gene modulation

Host cell nuclear localisation of alphaviral proteins has been shown to be important for host transcriptional shut off, antagonising type I interferon induction and inhibiting the antiviral response. Our previous studies demonstrate that mutation of the nucleolar localisation sequence (NoLS) of chikungunya virus (CHIKV) capsid protein significantly attenuates CHIKV replication. However, the reason for this attenuation remains unclear. In this study we investigated the impact of CHIKV capsid protein on host gene expression using Nanostring analysis and determined whether nucleolar localisation of capsid protein is required for host gene modulation. Little significant change in differential gene expression (adjusted p value <0.05) was observed in Capsid-WT-EGFP and mutant Capsid-NoLS-EGFP transfected HEK293T cells compared to mock EGFP transfected cells. To explore minor changes to host gene modulation in response to capsid protein, differential gene expression analysis was performed under a reduced arbitrary threshold (unadjusted P value < 0.01). Results suggest that, expressed as a recombinant protein, CHIKV capsid has limited impact on host gene expression, regardless of its ability to localise to the nucleolus. Results further suggest that attenuation of CHIKV resulting from mutation of the capsid protein NoLS is largely dependent on viral rather than host factors.