Expanding the nucleotide repertoire of the ribosome with post-transcriptional modifications

Abstract

In all kingdoms of life, RNAs undergo specific post-transcriptional modifications. More than 100 different analogues of the four standard RNA nucleosides have been identified. Modifications in ribosomal RNAs (rRNAs) are highly prevalent and cluster in regions of the ribosome that have functional importance, have a high level of nucleotide conservation, and typically lack proteins. Modifications also play roles in determining antibiotic resistance or sensitivity. A wide spectrum of chemical diversity from the modifications provides the ribosome with a broader range of possible interactions between rRNA regions, transfer RNA, messenger RNA, proteins, or ligands by influencing local rRNA folds and fine-tuning the translation process. The collective importance of the modified nucleosides in ribosome function has been demonstrated for a number of organisms, and further studies may reveal how the individual players regulate these functions through synergistic or cooperative effects.

Figure 1

The four major types of rRNA modification are shown: a) isomerization of uridine to pseudouridine (Ψ); b) base modification of C and G to m⁵C and m²G, respectively; c) 2′-O-methylation of uridine to 2′-O-methyluridine (Um); and d) multiple modification of pseudouridine to m¹acp³Ψ.

Figure 2

The distribution of the 36 naturally occurring modified nucleotides from E. coli rRNA is shown on the crystal structure of the 70S ribosome (Protein Data Bank ID: 2avy-30S subunit and 2aw4-50S subunit) (7). The left side shows the clustering of modified nucleotides on the large (50S, light brown) and small (30S, light blue) subunits. The functionally important regions are highlighted: a) the peptidyl-transferase center, b) the subunit interface, and c) the decoding region. The expanded region to the right highlights specific residues (E. coli numbering) that are discussed in the text. The color scheme for the 36 modified nucleotides is as follows: Ψ, m³Ψ (red); m⁵U, m³U, D (yellow); m²G, m⁷G, m¹G (blue); m⁵C, s²C (green); m⁴Cm (orange); m⁶A, m²A, m₂⁶A (white); and Cm, Um, Gm (magenta) (note that not all 36 modified residues are visible from this perspective). This figure was generated with PyMOL software.

Figure 3

The eukaryotic C/D and H/ACA box snoRNPs are represented. The binding of proteins to the snoRNAs (black) and target RNAs (red) are depicted in which the C/D box class (panel a) binds to Nop1p/fibrillarin, Nop56p, Nop58p, and Snu13p/Nhpx, and the H/ACA box class (panel b) interacts with Cbf5p/dyskerin, Gar1p, Nhp2p, and Nop10p. The conserved box C, D, and H elements are highlighted, and N represents a conserved nucleotide that is located next to the target Ψ (panel b).