Schlafen 11 Restricts Flavivirus Replication

Schlafen 11 (Slfn11) is a ubiquitously expressed interferon stimulating gene (ISG) that controls synthesis of proteins by regulating tRNA abundance. Likely through this mechanism, Slfn11 has previously been shown to impair human immunodeficiency virus 1 (HIV-1) infection and the expression of codon-biased open reading frames. Because replication of positive-sense single-stranded RNA [(+)ssRNA viruses] requires the immediate translation of the incoming viral genome whereas negative sense, single stranded [(-)ssRNA] viruses carry at infection an RNA replicase that makes multiple translation competent copies of the incoming viral genome, we reasoned that (+)ssRNA viruses will be more sensitive to the effect of Slfn11 on protein synthesis than (-)ssRNA viruses. To evaluate this hypothesis, we tested the effects of Slfn11 on the replication of a panel of ssRNA viruses in the human glioblastoma cell line A172, which naturally expresses Slfn11. Depletion of Slfn11 in this cell line significantly increased the replication of (+)ssRNA viruses from the Flavivirus family, including West Nile (WNV), dengue (DENV), and Zika virus (ZIKV) but had no significant effect on the replication of the (-)ssRNA viruses vesicular stomatitis (VSV, Rhabdoviridae family) and Rift Valley fever (RVFV, Phenuiviridae family). Despite that WNV titers in Slfn11-deficient cells were almost 100-fold higher than in cells expressing this protein; they produced approximately two-fold less viral particles, as determined by PCR-based quantification of virion-associated WNV RNA in the cell culture supernatant. These data indicated that Slfn11 impairs WNV fitness but does not affect other steps of the viral life cycle including entry, viral RNA replication and translation, and budding. Similarly to the proposed anti-HIV-1 mechanism of Slfn11, this protein prevented WNV-induced down-regulation of a subset of tRNAs implicated in the translation of 19% of the viral polyprotein. Importantly, we provided evidence suggesting that the broad anti-viral activity of Slfn11 requires other cellular proteins, since overexpression of Slfn11 in cells that naturally lack the expression of this protein, did not impair WNV or HIV-1 infection. In summary, this study demonstrates that Slfn11 restricts flaviviruses replication by impairing viral fitness.\n\nAUTHOR SUMMARYThe host targets mechanisms that viruses have evolved to optimize replication. We provide evidence that the cellular protein Schlafen 11 (Slf11) impairs replication of flaviviruses, including West Nile (WNV), dengue (DENV), and Zika virus (ZIKV). However, replication of single-stranded, negative RNA viruses was not affected. Specifically, Slf11 decreases the fitness of WNV potentially by preventing virus-induced modifications of the host tRNA repertoire that could lead to enhanced viral protein folding. Furthermore, we demonstrated that Slf11 is not the limiting factor of this novel broad anti-viral pathway.