Influence of Phylogeny on Posttranscriptional Modification of rRNA in Thermophilic Prokaryotes: The Complete Modification Map of 16S rRNA of Thermus thermophilus

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Abstract
Posttranscriptional modification in RNA generally serves to fine-tune and regulate RNA structure and, in many cases, is relatively conserved and phylogenetically distinct. We report the complete modification map for SSU rRNA from Thermusthermophilus, determined primarily by HPLC/electrospray ionization MS-based methods. Thermus modification levels are significantly lower, and structures at the nucleoside level are very different from those of the archaeal thermophile Sulfolobussolfataricus growing in the same temperature range [Noon, K. R., et al. (1998) J. Bacteriol. 180, 2883−2888]. The Thermus modification map is unexpectedly similar to that of Escherichiacoli (11 modified sites), with which it shares identity in 8 of the 14 modifications. Unlike the heavily methylated Sulfolobus SSU RNA, Thermus contains a single ribose-methylated residue, N4,2‘-O-dimethylcytidine-1402, suggesting that O-2‘-ribose methylation in this bacterial thermophile plays a reduced role in thermostabilization compared with the thermophilic archaea. Adjacent pseudouridine residues were found in the single-stranded 3‘ tail of Thermus 16S rRNA at residues 1540 and 1541 (E. coli numbering) in the anti-Shine−Dalgarno mRNA binding sequence. The present results provide an example of the potential of LC/MS for extensive modification mapping in large RNAs.

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