Damien Brégeon and Anais Mounier (Oxford Nanopore)

Title: Bacterial dihydrouridine synthases

Damien Brégeon
Dihydrouridine (D), a hallmark RNA modification classically associated with RNA flexibility, is undergoing a renaissance. Once thought confined to transfer RNAs, D now emerges as a broader regulatory mark across the transcriptome, intricately linked to stress responses, ribosome biogenesis, and metabolic state1,2. In this seminar, I will present our recent discoveries that reframe our understanding of dihydrouridine biology and the enzymes that install it. We reveal that beyond the canonical Dus enzymes acting on tRNAs, bacteria possess a distinct class of flavin-dependent enzymes capable of modifying ribosomal RNA3. This enzyme, named RdsA, introduces D2449 at the heart of the 23S rRNA peptidyl transferase center, an early and conserved event in ribosome assembly. This discovery expands the known scope of dihydrouridine synthases and uncovers a new functional layer of ribosome maturation. Through genetic and biochemical analysis, we further show how redundant classical Dus enzymes with overlapping specificities collaboratively shape the tRNA modification landscape, influencing growth and adaptation at suboptimal temperatures4. In parallel, we demonstrate how environmental redox changes dynamically tune Dus activity, linking dihydrouridylation to NADPH levels and cellular stress responses5. Strikingly, whether targeting tRNA or rRNA, all known dihydrouridine synthases rely on reduced flavin cofactors, FMN or FAD, suggesting that nature has converged on a single biochemical strategy for uridine reduction. This evolutionary constraint highlights the three ring of flavin isoalloxazine as essential molecular tools in the post-transcriptional control of RNA function. Together, these findings position dihydrouridine not merely as a static mark, but as a dynamic, environmentally responsive modification, woven into the fundamental logic of bacterial gene expression.

References 1-Dihydrouridine in the Transcriptome: New Life for This Ancient RNA Chemical Modification. Brégeon D et al. ACS Chem Biol. 2022;17(7):1638-1657. 2-Integrative Approach to Probe Alternative Redox Mechanisms in RNA Modifications. Bou-Nader C, et al. Acc Chem Res. 2023;56(22):3142-3152. 3-Exploring a unique class of flavoenzymes: Identification and biochemical characterization of ribosomal RNA dihydrouridine synthase. Toubdji S, et al. PNAS. 2024;121(32):e2401981121. 4-Functional redundancy in tRNA dihydrouridylation. et al Nucleic Acids Res. 2024;52(10):5880-5894. 5-Differential redox sensitivity of tRNA dihydrouridylation. et al. Nucleic Acids Res. 2024;52(21):12784-12797.

Anaïs Mounier - Oxford Nanopore

Title:
Décrypter l’ARN dans sa complexité : l’apport du séquençage Nanopore

Abstract:
Présentation de la technologie Nanopore ainsi que de ses applications et avantages pour le séquençage de l’ARN, stratégies de séquençage possible (natif, cDNA, whole transcriptome, ciblé, Single Cell) ainsi que les solutions d’analyse associées.