| RRC ID |
84962
|
| Author |
Toubdji S, Thullier Q, Kilz LM, Marchand V, Yuan Y, Sudol C, Goyenvalle C, Jean-Jean O, Rose S, Douthwaite S, Hardy L, Baharoglu Z, de Crécy-Lagard V, Helm M, Motorin Y, Hamdane D, Brégeon D.
|
| Title |
Exploring a unique class of flavoenzymes: Identification and biochemical characterization of ribosomal RNA dihydrouridine synthase.
|
| Journal |
Proc Natl Acad Sci U S A
|
| Abstract |
Dihydrouridine (D), a prevalent and evolutionarily conserved base in the transcriptome, primarily resides in tRNAs and, to a lesser extent, in mRNAs. Notably, this modification is found at position 2449 in the Escherichia coli 23S rRNA, strategically positioned near the ribosome's peptidyl transferase site. Despite the prior identification, in E. coli genome, of three dihydrouridine synthases (DUS), a set of NADPH and FMN-dependent enzymes known for introducing D in tRNAs and mRNAs, characterization of the enzyme responsible for D2449 deposition has remained elusive. This study introduces a rapid method for detecting D in rRNA, involving reverse transcriptase-blockage at the rhodamine-labeled D2449 site, followed by PCR amplification (RhoRT-PCR). Through analysis of rRNA from diverse E. coli strains, harboring chromosomal or single-gene deletions, we pinpoint the yhiN gene as the ribosomal dihydrouridine synthase, now designated as RdsA. Biochemical characterizations uncovered RdsA as a unique class of flavoenzymes, dependent on FAD and NADH, with a complex structural topology. In vitro assays demonstrated that RdsA dihydrouridylates a short rRNA transcript mimicking the local structure of the peptidyl transferase site. This suggests an early introduction of this modification before ribosome assembly. Phylogenetic studies unveiled the widespread distribution of the yhiN gene in the bacterial kingdom, emphasizing the conservation of rRNA dihydrouridylation. In a broader context, these findings underscore nature's preference for utilizing reduced flavin in the reduction of uridines and their derivatives.
|
| Volume |
121(32)
|
| Pages |
e2401981121
|
| Published |
2024-8-6
|
| DOI |
10.1073/pnas.2401981121
|
| PMID |
39078675
|
| PMC |
PMC11317573
|
| MeSH |
Escherichia coli* / genetics
Escherichia coli* / metabolism
Escherichia coli Proteins / chemistry
Escherichia coli Proteins / genetics
Escherichia coli Proteins / metabolism
RNA, Bacterial / chemistry
RNA, Bacterial / genetics
RNA, Bacterial / metabolism
RNA, Ribosomal, 23S / chemistry
RNA, Ribosomal, 23S / genetics
RNA, Ribosomal, 23S / metabolism
Uridine / analogs & derivatives
Uridine / chemistry
Uridine / metabolism
|
| IF |
9.412
|
| Resource |
| Prokaryotes E. coli |
ME5125
ME5079
ME5081
ME5082
ME5085
ME5086
ME5088
ME5091
ME5092
ME5094
ME5099
ME5102
ME5106
ME5108
ME5110 |
