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Abstract

XRN1 is a key regulator of mRNA degradation, with proposed roles in viral infection. However, the exact function of XRN1 in infection remains poorly understood due to antagonistic results. We recently showed that Sindbis virus (SINV, alphavirus genus) causes a global downregulation of host gene expression through a pervasive degradation of cellular mRNA. This is concomitant with an increased association of XRN1 with cellular RNA and the emergence of viral RNA. Nevertheless, the link between XRN1, cellular mRNA degradation, and SINV replication remains mysterious. Here, we show that XRN1 and other members of the 5’-to-3’ mRNA decay pathway, such as DCP1 and DCP2, are essential for alphaviruses replication. Rescue of XRN1 knock out cells with XRN1-WT, but not with a catalytically inactive mutant, partially restores infection, highlighting the importance of the exonuclease activity in the regulation of viral infection. iCLIP analysis revealed that XRN1 predominantly engages with the cellular transcripts that are unstable in infected cells, suggesting a link between its enzymatic activity and the degradation process. Furthermore, the RNA decay machinery localizes to viral replication centres by the interaction of XRN1 with the viral protein nsP1, physically bridging the fast degradation of cellular RNA with the viral replication machinery. This, together with the detection of nucleotide kinases accumulating at the viral replication factories, suggests that XRN1 may produce free nucleotides that are locally phosphorylated to nucleotides triphosphate to feed replication. Supporting this hypothesis, the addition of nucleosides to XRN1-KO rescued cells enhances SINV infection. In summary, our data support a model in which XRN1 sustains viral replication by degrading cellular mRNA to increase the local pool of free nucleotides.