Dihydrouridine in the Transcriptome: New Life for This Ancient RNA Chemical Modification

Abstract

Until recently, post-transcriptional modifications of RNA were largely restricted to noncoding RNA species. However, this belief seems to have quickly dissipated with the growing number of new modifications found in mRNA that were originally thought to be primarily tRNA-specific, such as dihydrouridine. Recently, transcriptomic profiling, metabolic labeling, and proteomics have identified unexpected dihydrouridylation of mRNAs, greatly expanding the catalog of novel mRNA modifications. These data also implicated dihydrouridylation in meiotic chromosome segregation, protein translation rates, and cell proliferation. Dihydrouridylation of tRNAs and mRNAs are introduced by flavin-dependent dihydrouridine synthases. In this review, we will briefly outline the current knowledge on the distribution of dihydrouridines in the transcriptome, their chemical labeling, and highlight structural and mechanistic aspects regarding the dihydrouridine synthases enzyme family. A special emphasis on important research directions to be addressed will also be discussed. This new entry of dihydrouridine into mRNA modifications has definitely added a new layer of information that controls protein synthesis.

Evolutionary Diversity of Dus2 Enzymes Reveals Novel Structural and Functional Features among Members of the RNA Dihydrouridine Synthases Family

“…Dihydrouridine (D) is one of the most abundant post-transcriptional modified bases in the transcriptome [ 1 , 2 , 3 ]. Present mainly in transfer RNA (tRNA) and occasionally in bacterial ribosomal RNA (rRNA), D has recently entered the messenger RNA (mRNA) world [ 1 , 2 ].…”

“…Dihydrouridine (D) is one of the most abundant post-transcriptional modified bases in the transcriptome [ 1 , 2 , 3 ]. Present mainly in transfer RNA (tRNA) and occasionally in bacterial ribosomal RNA (rRNA), D has recently entered the messenger RNA (mRNA) world [ 1 , 2 ]. Indeed, this modification was recently detected in fission yeast mRNAs, including those encoding cytoskeleton-related proteins (2), in Saccharomyces cerevisiae mRNAs [ 4 ], but also in human mRNAs [ 5 , 6 ].…”

“…D is often present at multiple positions in bacterial and eukaryotic tRNAs, and its abundance varies with both organism and tRNA type. In prokaryotes, D can be present at five positions of the tRNA ( Figure 1 B), namely positions 16, 17, 20 and 20a, all located in the D loop, but also at position 47 in the variable loop (V loop) [ 2 ], which has so far only been observed in Bacillus subtilis tRNA Met (CAU). In eukaryotes, D is observed in as many as six sites, including five in the D-loop (D16, D17, D20, D20a, and D20b) and one in the variable loop (D47) [ 3 ] ( Figure 1 B), with D20 being the most frequent D-modification in tRNAs [ 2 ].…”

“…In prokaryotes, D can be present at five positions of the tRNA ( Figure 1 B), namely positions 16, 17, 20 and 20a, all located in the D loop, but also at position 47 in the variable loop (V loop) [ 2 ], which has so far only been observed in Bacillus subtilis tRNA Met (CAU). In eukaryotes, D is observed in as many as six sites, including five in the D-loop (D16, D17, D20, D20a, and D20b) and one in the variable loop (D47) [ 3 ] ( Figure 1 B), with D20 being the most frequent D-modification in tRNAs [ 2 ]. D residues are introduced in tRNAs and mRNAs by a set of conserved dihydrouridine synthases (Dus) that are members of the Cluster of Orthologous Group family COG0042 [ 2 , 15 , 16 , 17 ].…”

“…In eukaryotes, D is observed in as many as six sites, including five in the D-loop (D16, D17, D20, D20a, and D20b) and one in the variable loop (D47) [ 3 ] ( Figure 1 B), with D20 being the most frequent D-modification in tRNAs [ 2 ]. D residues are introduced in tRNAs and mRNAs by a set of conserved dihydrouridine synthases (Dus) that are members of the Cluster of Orthologous Group family COG0042 [ 2 , 15 , 16 , 17 ]. These flavoenzymes catalyze an NADPH-dependent reduction of specific uridines using the flavin mononucleotide (FMN) as a tRNA-reducing coenzyme ( Figure 1 A) [ 2 , 15 , 16 , 18 , 19 ].…”