Fig. 3

Complexes between sRNA guides and targets at sites of conserved 2′-O-ribose methylation in rRNA. a Conserved methyl modification of position 23S rRNA C/U2880. The complementarities between the D' and D guide regions of Pca sR30, Tte sR152, Sac sR13, Mka sR3, Neq sR10 and Iho sR6 with the 23S rRNA region around position C/U2880 (Eco position C2606; see Additional file 3) are illustrated with position 2880 aligned in the middle and labelled in red. The sRNA sequences for each species are listed below the rRNA sequences with the C and C' boxes outlined with blue and the D' and D box sequences outlined with green. The predicted positions of methyl modification are indicated by “Me” in red within the rRNA sequences. The D' guide of Tte sR112 has no significant complementarity to rRNA (empty guide). The D' guide-target complementarity of Sac sR13 exhibits a mismatch basepair at the predicted site of modification (C2847; MM:mismatch) and is likely not modified. b Conserved methyl modifications at positions 16S A512 and G491. The complementarities between the D' and D guide regions of Tte sR114, Iho sR21, Pca sR28 and Sac sR115 to the regions around 16S A512 (left of center) and G491 (right of center) are illustrated. These modification sites correspond to positions A535 and G515 in helix 18 of Eco 16S rRNA (Additional file 3). The sRNA C and C', and D' and D boxes are outlined with blue and green respectively. The predicted sites of methyl modification are indicated by (Me) in red. The sequence complementarity between the D guide of Iho sR21 and the region of around 16S G491 is disrupted by three GU base pairs (0) which likely compromises methylation activity; this Iho sR21 site was not considered to be a robust prediction in our analysis