2'-O-Methylation of Ribosomal RNA: Towards an Epitranscriptomic Control of Translation?

Abstract

Ribosomal RNA (rRNA) undergoes post-transcriptional modification of over 200 nucleotides, predominantly 2'-O-methylation (2'-O-Me). 2'-O-Methylation protects RNA from hydrolysis and modifies RNA strand flexibility but does not contribute to Watson-Crick base pairing. The contribution of 2'-O-Me to the translational capacity of ribosomes has been established. Yet, how 2'-O-Me participates in ribosome biogenesis and ribosome functioning remains unclear. The development of 2'-O-Me quantitative mapping methods has contributed to the demonstration that these modifications are not constitutive but rather provide heterogeneity to the ribosomal population. Moreover, recent advances in ribosome structure analysis and in vitro translation assays have proven, for the first time, that 2'-O-Me contributes to regulating protein synthesis. This review highlights the recent data exploring the impact of 2'-O-Me on ribosome structure and function, and the emerging idea that the rRNA epitranscriptome is involved in translational control.

Keywords: 2′-O-methylation; fibrillarin; mRNA translation; ribosomal RNA; ribosome heterogeneity; snoRNP.

Figure 1

Schematic representation of the C/D box snoRNP complex, depicting the main features of the complex according to both biochemical data and structural studies using an archaeal complex. The C and D boxes are depicted with their consensus sequence. The substrate ribosomal RNA (rRNA, red) forms an RNA:RNA duplex with the snoRNA along 10–21 nucleotides (nt). The catalytic site of fibrillarin (FBL) faces the fifth nucleotide downstream of the D or D′ boxes (yellow star). The 15.5K protein specifically binds a k-turn motif. The NOP56:NOP58 heterodimer (which is a homodimer in archaea) forms two long alpha helices that are placed across the snoRNA:rRNA complex and contribute to locking FBL in its active position. rRNA: ribosomal RNA; snoRNA: small nucleolar ribonucleoprotein.

Figure 2

Model of 2′-O-methylation (2′-O-Me) profile modulation and its consequence on the intrinsic translational activity of ribosomes. In this model, we represent two possible states: a steady state and a modified state. Following a change in C/D box snoRNP activity (e.g., change in FBL or SNORD expression) during ribosome biogenesis, 2′-O-Me levels change in a site-specific manner as revealed in [30,31] (unchanged level: blue dots; decreased level: red dots; increased level: purple dots). 2′-O-Me is altered in key functional regions of the ribosome, including the inter-subunit bridges, the decoding center (DC), and the peptidyl-transferase center (PTC), the latter being located close to the transfer RNA (tRNA) binding sites (A: aminoacyl-tRNA binding site; P: peptidyl-tRNA binding site; and E: exit site) [25,26]. The ribosomal population changes in its composition and variety (gray, orange, and purple ribosomes). When tested in an in vitro cell-free translation assay, these ribosomal populations exhibit a differential translational activity [25]. mRNA: messenger RNA; snoRNA: small nucleolar ribonucleoprotein; SNORD: C/D box snoRNA gene.