Dengue virus exploits the host tRNA epitranscriptome to promote viral replication

The 40–50 RNA modifications of the epitranscriptome regulate posttranscriptional gene expression. Here we show that flaviviruses hijack the host tRNA epitranscriptome to promote expression of pro-viral proteins, with tRNA-modifying ALKBH1 acting as a host restriction factor in dengue virus infection. Early in the infection of human Huh-7 cells, ALKBH1 and its tRNA products 5-formylcytidine (f(5)C) and 2’-O-methyl-5-formylcytidine (f(5)Cm) were reduced. ALKBH1 knockdown mimicked viral infection, but caused increased viral NS3 protein levels during infection, while ALKBH1 overexpression reduced NS3 levels and viral replication, and increased f(5)C and f(5)Cm. Viral NS5, but not host FTSJ1, increased f(5)Cm levels late in infection. Consistent with reports of impaired decoding of leucine UUA codon by f(5)Cm-modified tRNA(Leu(CAA)), ALKBH1 knockdown induced translation of UUA-deficient transcripts, most having pro-viral functions. Our findings support a dynamic ALKBH1/f(5)Cm axis during dengue infection, with virally-induced remodeling of the proteome by tRNA reprogramming and codon-biased translation.