Functional redundancy in tRNA dihydrouridylation

• Published in: Nucleic acids research 2024-06, Vol.52 (10), p.5880-5894
• Main Authors: Sudol, Claudia, Kilz, Lea-Marie, Marchand, Virginie, Thullier, Quentin, Guérineau, Vincent, Goyenvalle, Catherine, Faivre, Bruno, Toubdji, Sabrine, Lombard, Murielle, Jean-Jean, Olivier, de Crécy-Lagard, Valérie, Helm, Mark, Motorin, Yuri, Hamdane, Djemel, Brégeon, Damien
• Format: Article
• Language: English
• Subjects: Life Sciences
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkae325

Abstract Dihydrouridine (D) is a common modified base found predominantly in transfer RNA (tRNA). Despite its prevalence, the mechanisms underlying dihydrouridine biosynthesis, particularly in prokaryotes, have remained elusive. Here, we conducted a comprehensive investigation into D biosynthesis in Bacillus subtilis through a combination of genetic, biochemical, and epitranscriptomic approaches. Our findings reveal that B. subtilis relies on two FMN-dependent Dus-like flavoprotein homologs, namely DusB1 and DusB2, to introduce all D residues into its tRNAs. Notably, DusB1 exhibits multisite enzyme activity, enabling D formation at positions 17, 20, 20a and 47, while DusB2 specifically catalyzes D biosynthesis at positions 20 and 20a, showcasing a functional redundancy among modification enzymes. Extensive tRNA-wide D-mapping demonstrates that this functional redundancy impacts the majority of tRNAs, with DusB2 displaying a higher dihydrouridylation efficiency compared to DusB1. Interestingly, we found that BsDusB2 can function like a BsDusB1 when overexpressed in vivo and under increasing enzyme concentration in vitro. Furthermore, we establish the importance of the D modification for B. subtilis growth at suboptimal temperatures. Our study expands the understanding of D modifications in prokaryotes, highlighting the significance of functional redundancy in this process and its impact on bacterial growth and adaptation.