A simplified qPCR method revealing tRNAome remodeling upon infection by genotype 3 hepatitis E virus

The landscape of tRNA–viral codons regulates viral adaption at the translational level, presumably through adapting to host codon usage or modulating the host tRNAome. We found that the major zoonotic genotype of hepatitis E virus (HEV) has not adapted to host codon usage, prompting exploration of the effects of HEV infection on the host tRNAome. However, tRNAome quantification is largely impeded by the extremely short sequences of tRNAs and redundancy of tRNA genes. Here, we present a length-extension and stepwise simplified qPCR method that utilizes a universal DNA/RNA hybrid tRNA adaptor and degenerate primers. Using this novel methodology, we observe that HEV infection dramatically reprograms the hepatic tRNAome, which is likely to facilitate translation of viral RNAs. This tRNAome quantification method bears broad implications for future tRNA research and possibly tRNA-based diagnostics

Evolutionarily missing and conserved tRNA genes in human and avian

Viral infection heavily relies on host transfer RNA (tRNA) for viral RNA decoding. Counterintuitively, not all tRNA species based on anticodon are matched to all 64-triplet codons during evolution. Life solves this problem by cognate tRNA species via wobbling decoding. We found that 14 out of 64 tRNA genes in humans and the main avian species (chicken and duck) were parallelly missing, including 8 tRNA-A34NN and 6 tRNA-G34NN species. By analyzing the conservation of key motifs in tRNA genes, we found that box A and B served as intragenic tRNA promoters were evolutionally conserved among human, chicken, and duck. Thus, decoding viral RNA by similar wobbling strategies and tRNA transcripts may be