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Influence of Phylogeny on Posttranscriptional Modification of rRNA in Thermophilic Prokaryotes: The Complete Modification Map of 16S rRNA of Thermus thermophilus†
journal contribution
posted on 2006-04-18, 00:00 authored by Rebecca Guymon, Steven C. Pomerantz, Pamela F. Crain, James A. McCloskeyPosttranscriptional 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 Thermus thermophilus, 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 Sulfolobus solfataricus 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 Escherichia coli (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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archaeal thermophile Sulfolobus solfataricusHPLCRNA structureThermus thermophilus14 modificationsComplete Modification Mapnucleoside levelThermus modification levelsthermophilic archaeashares identityAdjacent pseudouridine residuesPosttranscriptional Modificationtemperature rangemodification mapmethylated Sulfolobus SSU RNAThermus modification mapSSU rRNAresidues 1540Thermus 16 S rRNALCmodification mapping16 S rRNA
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