The structural basis of mRNA recognition and binding by eukaryotic pseudouridine synthase PUS1

Abstract

ABSTRACTThe chemical modification of RNA bases represents a ubiquitous activity that spans all domains of life. The formation of pseudouridine is the most common RNA modification and is observed within tRNA, rRNA, ncRNA and mRNAs. The catalysts of pseudouridylation, termed pseudouridine synthase or ‘PUS’ enzymes, include those that rely on guide RNA molecules and others that function as ‘stand-alone’ enzymes. Among the latter, up to ten are encoded in eukaryotic genomes, including several that modify uracil within mRNA transcripts. Neither the biological purpose of mRNA pseudouridylation, nor the mechanism by which individual mRNA bases are targeted, are well understood. In this study, we describe the high-resolution crystal structure of yeast PUS1 bound to an RNA target that we identified as being a hot spot for recognition, binding, and activity within a model mRNA. The enzyme recognizes RNA structural features corresponding to a base-paired duplex, which appears to act as a docking site leading to subsequent modification of the transcript. The study also allows us to visualize the divergence of related PUS-1 enzymes and their corresponding RNA target specificities, and to speculate on the basis by which this single PUS enzyme can bind and modify mRNA or tRNA substrates.