Expanding paradigms of RNA modifications: from evolutionary adaptation to human diseases

Abstract

RNA undergoes a variety of chemical modifications after transcription, which are essential for RNA maturation and function. Over 150 RNA modifications have been identified to date, yet only about 16% of them are conserved across all three domains of life—eukaryotes, archaea, and bacteria. The vast majority of RNA modifications are domain- or species-specific, suggesting that RNA modifications have been independently acquired and fixed during evolution to meet diverse environmental challenges. We are engaged in a project to identify novel RNA modifications from various sources, and have reported 18 modifications so far. Taking advantage of mass spec analysis of RNA modifications, we identified more than 50 genes responsible for tRNA modifications, rRNA modifications as well as mRNA modification.
Ribosomal RNAs (rRNAs) contain a wide variety of post-transcriptional modifications which play critical roles in ribosome assembly and function. Recently we discovered two stereoselective rRNA methylations in the peptidyl-transferase center (PTC) of 50S ribosomal subunit in Escherichia coli cultured under anaerobic conditions. We also identified the rlmX gene which encodes a cobalamin-dependent radical SAM methyltransferase responsible for these methylations. Double knockout strain of rlmX and rlhA (responsible for ho5C2501) exhibited anaerobic growth reduction. Biochemical studies showed that protein synthesis and peptide bond formation were promoted by these rRNA modifications. Cryogenic electron microscopy (cryo-EM) structure of E. coli 70S ribosome indicated that these hypoxia-induced rRNA modifications stabilize the P-site and the PTC. These findings demonstrated that ribosomes are activated by the hypoxia-induced rRNA modifications to enhance translational capability, thereby surviving in anaerobic conditions.
The physiological importance of RNA modification is highlighted by human diseases caused by aberrant RNA modification. We previously reported a severe reduction in the frequency of tRNA modifications in mitochondrial disease patients, like MELAS and MERRF. These findings provided the first evidence of RNA modification disorder. We call “RNA modopathy” as a new category of human diseases. Recently, we successfully introduced tRNA modifications into mutant tRNAs by expressing tRNA-modifying enzymes in the MELAS patient cells. In this presentation, I am gonna talk on our efforts toward future gene therapy.