Host tRNA modifications drive efficient translation of influenza A virus genome and impact host antiviral stress responses

Abstract Influenza A virus (IAV), as all other viruses, is completely dependent on the host translation machinery components, including host transfer RNAs (tRNAs), to effectively decode its genome. However, while the human genome is biased towards cytosine (C) and guanosine (G)-ending codons, the IAV genome is skewed towards adenine (A) and uridine (U)-ending codons. Nevertheless, translation of IAV’s RNA genome is highly efficient. Here we show that host tRNA and tRNA epitranscriptome dynamics are important regulators of IAV RNA translation and host antiviral responses. We show that the levels of several tRNA modifications, including 5-methylcarboxymethyluridine (mcm5U34) and 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U34), and their cognate writers, vary over the course of IAV infection. Additionally, we demonstrate that a set of tRNAs are preferentially recruited to ribosomes upon IAV infection, in line with IAV codon usage requirements. We further show that loss of ELP3, the catalytic subunit of the elongator complex, which is involved in the catalysis of mcm5U34 and of mcm5s2U34, induces tRNA hypomodifications, impairs translation of codon biased IAV genes and triggers the integrated stress response (ISR), interfering with IAV propagation. Taken together, our results uncover the relevance of host tRNAs and their modifications for optimal expression of viral genomes and host antiviral responses, setting the tRNA epitranscriptome as a promising target for the development of host-based antiviral therapies. Competing Interest Statement MM has received travel bursaries from Oxford Nanopore Technologies (ONT) to present her results at research conferences. EMN has received travel and accommodation expenses to speak at ONT conferences. EMN is listed as inventor in the patent describing the Nano-tRNAseq method (PCT/IB2023/059599, publication WO2024/069467). The remaining authors declare that they have no conflict of interest. Footnotes ↵* Co-senior authors