Resurrecting an ancestral protein as a novel tool to study RNA biology

By deducing the possible ancient forms of a bacterial enzyme, OIST scientists have resurrected one of its ancestral versions, with a comparably higher ability to chemically modify RNA. In the Protein Engineering and Evolution Unit's latest publication in Nucleic Acids Research, the team presents an engineered RNA methyltransferase, which can be used to study the role of RNA modifications in cells. 

With RNA modifications affecting stability, promoting translation, and influencing its location within the cell, such modifications play an important role in the cell’s health and in diseases.

Mr. Yoshiki Ochiai, the paper’s first author and PhD student in the Protein Engineering and Evolution Unit, tried to improve RNA methylation activity of a bacterial non-site-specific DNA methyltransferase M.EcoGII with a residual activity for RNA methylation. The team then investigated its history using bioinformatical analysis to understand if its ancestors were RNA or DNA methyltransferases.

After inferring sequences of the protein’s ancestors, the team tested proteins which might have had a higher RNA methyltransferase activity. Among these candidates, the team found a variant that preferentially modified RNA and named it SUPer RNA EcoGII Methyltransferase (SUPREM). This enzyme's selectivity for RNA, its high methylation activity, and the fact that it could be active in the mammalian cell suggested that SUPREM could be used to develop new tools to investigate RNA modifications in various diseases.