Discovery ofThetaRibozymes in Gut Phages–Implications for tRNA and Alternative Genetic Coding

Abstract

AbstractRibozymes, relics of the “RNA world”, are essential across all domains of life. Nonetheless, the functions and genomic contexts of recently discovered small ribozymes, such as minimal hepatitis delta virus (HDV)-like ribozymes, remain elusive. Using bioinformatic analyses, we identified a novel subfamily of minimal HDV-like ribozymes, coinedthetaribozymes. Hundreds of unique examples were found adjacent to viral tRNAs withinCaudoviricetesbacteriophages of the mammalian gut virome.In vitroexperiments confirm site-specific self-scission activity, suggesting their involvement in processing tRNA 3’-trailers.Intriguingly, a significant fraction ofthetaribozymes is associated with viral suppressor tRNAs, potentially regulating the late-stage assembly of recoded bacteriophages. These findings advance the understanding of RNA-based mechanisms underlying the intricate interplay between the bacterial and viral parts of the mammalian gut microbiome.One-Sentence SummaryNewly unveiledthetaribozymes associate with suppressor tRNAs of alternatively coded gut phages: a potential lytic switch.