The extensive m5C epitranscriptome of Thermococcus kodakarensis is generated by a suite of RNA methyltransferases that support thermophily

Comprehensive nucleoside analysis of archaeal RNA modification profiles reveals an m7G in the conserved P loop of 23S rRNA

Extremophilic Archaea employ diverse RNA modifications for survival. Our understanding of the modified nucleosides and their functions in Archaea is far from complete. Here, we establish an extensive profile of nucleoside modifications in thermophilic and mesophilic Archaea. Through liquid chromatography-tandem mass spectrometry (LC-MS/MS) and rigorous non-coding RNA depletion, we identify four previously unannotated modifications in archaeal mRNA. Nucleoside analysis conducted on total, large, small, and mRNA-enriched subfractions of hyperthermophile Thermococcus kodakarensis reveals modifications whose relative abundance is dynamically responsive to growth temperatures. To predict archaeal RNA-modifying enzymes, we leverage open-access databases to compare putative functional domains with previously annotated enzymes. Our approach leads to the discovery of a methyltransferase responsible for the installation of m7G in the P loop of 23S rRNA peptidyl transferase center in T. kodakarensis. The methyltransferase activity is confirmed in vitro with synthetic substrates and in vivo by assessing the presence of the m7G modification in a genetic deletion strain.

A novel N4,N4-dimethylcytidine in the archaeal ribosome enhances hyperthermophily

Ribosome structure and activity are challenged at high temperatures, often demanding modifications to ribosomal RNAs (rRNAs) to retain translation fidelity. LC-MS/MS, bisulfite-sequencing, and high-resolution cryo-EM structures of the archaeal ribosome identified an RNA modification, N4,N4-dimethylcytidine (m42C), at the universally conserved C918 in the 16S rRNA helix 31 loop. Here, we characterize and structurally resolve a class of RNA methyltransferase that generates m42C whose function is critical for hyperthermophilic growth. m42C is synthesized by the activity of a unique family of RNA methyltransferase containing a Rossman-fold that targets only intact ribosomes. The phylogenetic distribution of the newly identified m42C synthase family implies that m42C is biologically relevant in each domain. Resistance of m42C to bisulfite-driven deamination suggests that efforts to capture m5C profiles via bisulfite sequencing are also capturing m42C.