Discovery of Theta Ribozymes in Gut Phages–Implications for tRNA and Alternative Genetic Coding

Ribozymes, 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, coined theta ribozymes. Hundreds of unique examples were found adjacent to viral tRNAs within Caudoviricetes bacteriophages of the mammalian gut virome. In vitro experiments confirm site-specific self-scission activity, suggesting their involvement in processing tRNA 3’-trailers. Intriguingly, a significant fraction of theta ribozymes 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 Summary Newly unveiled theta ribozymes associate with suppressor tRNAs of alternatively coded gut phages: a potential lytic switch. ### Competing Interest Statement The authors have declared no competing interest.