The microbiome, consisting of trillions of microorganisms, is tightly linked to human health and disease.[1] Bacteriophages are the dominant gut virome constituents and infect hosts with the standard bacterial code but then utilize suppressor tRNAs to switch to alternative genetic codes.[2] We recently discovered a novel subgroup of minimal hepatitis delta virus (HDV)-like ribozymes[3] – theta ribozymes (Θrz) – potentially involved in the code switch leading to the expression of recoded lysis and structural phage genes.[4] These ribozymes are predominantly found at the 3'-end of freshly transcribed bacteriophage-encoded tRNAs, every fifth associated tRNA being a suppressor tRNA, thus indicating a crucial role of this novel ribozyme in the life cycle regulation of these bacteiophages. They demonstrate HDV-like self-scission behavior in vitro but show a remarkable difference in self-cleavage activity, a distinct dependence on Mg2+, as well as pH. CryoEM and detailed NMR investigations corroborate a classical pseudo-knot structure with a strictly conserved catalytic cytosine crucial for acid-base catalysis; our work constitutes the first NMR structural characterization of a minimal HDV-like ribozyme in general. Theta ribozymes are the first example of small ribozymes used as an alternative to large enzymes that usually process tRNA 3'-ends, expanding the short list of biological functions of small HDV-like ribozymes. They constitute a new player involved in the code switch of certain recoded gut bacteriophages and thereby indirectly affect human well being.
Financial support by the Swiss National Science Foundation and the University of Zurich is gratefully acknowledged.
[1] Duan, Y.; Young, R.; Schnabl, B. Nature Rev. Gastroenterol. Hepatol. 2022, 19, 135.
[2] Peters, S.L. et al. Nature Commun. 2022, 13, 5710.
[3] Webb, C.-H.T.; Lupták, A. RNA Biol. 2011, 8, 719; Riccitelli, N.J.; Delwart, E.; Lupták, A. Biochemistry 2014, 53, 1616.
[4] Kienbeck, K.; Malfertheiner, L.; Zelger-Paulus, S.; Johannsen, S.; von Mering, C.; Sigel, R.K.O. Nature Commun. 2024, 15, 1559.