Pseudouridine synthase 7 is an opportunistic enzyme that binds and modifies substrates with diverse sequences and structures

• DOI: 10.1073/pnas.2109708119
• Publication Date: 2022-01-20T22:00:13Z
• Authors: Meredith K. Purchal; Daniel E. Eyler; Mehmet Tardu; Monika K. Franco; Megan M. Korn; Taslima Khan; Ryan McNassor; Rachel Giles; Katherine Lev; Hari Sharma; Jeremy Monroe; Leena Mallik; Markos Koutmos; Kristin S. Koutmou
• Keywords: Models, Molecular; 0301 basic medicine; Binding Sites; Saccharomyces cerevisiae Proteins; Protein Conformation; Temperature; RNA, Fungal; Biological Sciences; Substrate Specificity; Structure-Activity Relationship; 03 medical and health sciences; Stress, Physiological; Catalytic Domain; Thermodynamics; Protein Interaction Domains and Motifs; Amino Acid Sequence; RNA, Messenger; Protein Binding

Significance

Pseudouridine is among the most-abundant RNA modifications. We present a framework for conceptualizing how eukaryotic pseudouridine synthases select their substrates. This work reveals the structure of yeast pseudouridine synthase 7 (Pus7) and presents cell-based and biochemical investigations of enzyme binding and activity. We demonstrate that Pus7 interacts promiscuously with RNAs containing UG U AR sequences. Our observations raise the question of why these enzymes only modify <5% of UG U AR sequences in the transcriptome, suggesting that factors beyond inherent enzyme properties—such as protein localization, local RNA structure, and RNA–protein interactions—principally shape Pus7 substrate selection. These findings support a role for Pus7 in providing cells with a mechanism to rapidly alter protein synthesis in response to cellular conditions.