C/D box sRNA-guided 2′-O-methylation patterns of archaeal rRNA molecules

BMC Genomics

Table 3 List of C/D box sRNAs that target distant sites that are close in secondary structure space

Species	sRNA	Subunit	D target	D' target
Iho	sR114	23S	C1961	C2265
Iho	sR114	23S	C2275	D1937
Iho	sR472	23S	C897	G1017
Iho	sR206	16S	G*36 and 505	G482
Iho	sR103	16S	C1045	U1136
Pca	sR53	16S	A509	C34 and 530
Pca	sR56	16S	U894	G1358 and G925
Pca	sR2	23S	G747	C884 and 769
Mka	sR87	23S	A1241	G1385
Neq	sR15	16S	G1217	G930
Neq	sR17	16S	U1370	A915
Tte	sR51	23S	C1947	G2249 and 1980
Tte	sR50	23S	U2883 and 2783	U2753
Tte	sR46	16S	U547 and 984	G924
Tte	sR15	16S	A509	C35 and 530

Five species (Iho, Pca, Mka, Neq, and Tte) have sRNAs that are predicted to target methylation to sites that are distant in the primary rRNA sequence but close in the secondary structure. Two types of interactions are observed. In the first, the D and D′ guides have single targets as exemplified by Neq sR15. In the second, one guide has a single target, whereas the second guide has two targets, one linked and one distant in the primary sequence but close in the secondary structure. An example of this is Tte 509 where the D guide is predicted to modify position 16S A509 and the D′ guide is predicted to modify at the linked position C530 and the distant position C35. In one instance, the Iho sR206 interaction with the distant site at position 16S G36 contains a mismatch base pair at the site of methylation and is predicted not to be modified although the guide-target may well occur. The asterisk (*) indicates a mismatch base pair at the target site in the region of guide-target complementarity

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