Modomics - A Database of RNA Modifications

Published on April 6, 2018 in Angew. Chem. Int. Ed. volume .

PubMed ID: 29624844

DOI: 10.1002/anie.201713188


Recently discovered new chemical entities in RNA modifications have provided surprises with respect to functional groups that enlarge the chemical space of RNA. Using LC‐MS, we found over one hundred signals of RNA constituents that contained a ribose moiety in tRNAs from E. coli. Feeding experiments with variegated stable isotope labeled compounds identified 37 compounds, representing new structures of RNA modifications. One structure was elucidated by deuterium exchange and high resolution mass spectrometry. The structure of msms2i6A (2‐methylthiomethylenethio‐N6‐isopentenyl‐adenosine) was confirmed by methione‐D3 feeding experiments and finally by synthesis of the nucleobase. The msms2i6A contains a thioacetal, which we demonstrated in vitro to be biosynthetically derived from ms2i6A by the action of the radical‐SAM enzyme MiaB. This enzyme performs thiomethylation, forming ms2i6A from i6A in a first turnover. The newly discovered thioacetal is formed by a second turnover, now involving hydrogen abstraction from the previously introduced methyl group. Not only are thioacetals extremely rare in natural product chemistry, but also does this constitute a novel enzymatic mechanism for their formation. In conjunction with the pool of 36 new modification, this work describes a new layer of RNA modification chemistry.