Posttranscriptional Modifications in 16S and 23S rRNAs of the Archaeal Hyperthermophile Sulfolobus solfataricus

Abstract

Posttranscriptional modification is common to many types of RNA, but the majority of information concerning structure and function of modification is derived principally from tRNA. By contrast, less is known about modification in rRNA in spite of accumulating evidence for its direct participation in translation. The structural identities and approximate molar levels of modifications have been established for 16S and 23S rRNAs of the archaeal hyperthermophile Sulfolobus solfactaricus by using combined chromatography-mass spectrometry-based methods. Modification levels are exceptionally high for prokaryotic organisms, with approximately 38 modified sites in 16S rRNA and 50 in 23S rRNA for cells cultured at 75°C, compared with 11 and 23 sites, respectively, in Escherichia coli. We structurally characterized 10 different modified nucleosides in 16S rRNA, 64% (24 residues) of which are methylated at O-2′ of ribose, and 8 modified species in 23S rRNA, 86% (43 residues) of which are ribose methylated, a form of modification shown in earlier studies to enhance stability of the polynucleotide chain. From cultures grown at progressively higher temperatures, 60, 75, and 83°C, a slight trend toward increased ribose methylation levels was observed, with greatest net changes over the 23°C range shown for 2′-O-methyladenosine in 16S rRNA (21% increase) and for 2′-O-methylcytidine (24%) and 2′-O-methylguanosine (22%) in 23S rRNA. These findings are discussed in terms of the potential role of modification in stabilization of rRNA in the thermal environment.

The first determination of pseudouridine residues in 23S ribosomal RNA from hyperthermophilic Archaea Sulfolobus acidocaldarius

“…In this paper we report the mapping of 8 residues in the LSU rRNA of a hyperthermophile Archaea, Sulfolobus acidocaldarius. Six 8 residues were detected in the studied rRNA regions, which is slightly higher than the 3.7 þ 0.1 mol/mol of 8 residues detected by chromatography/mass spectrometry in the S. sulfolobus LSU rRNA [40] and the four 8 residues localised in the H. halobium LSU rRNA. Only a few modi¢cation positions are conserved between Bacteria and Archaea, while the others seem to be speci¢c for Archaea or common to Archaea and Eucarya.…”

The Sso7d DNA‐binding protein from Sulfolobus solfataricus has ribonuclease activity

“…Our observations raise the issue of whether Sso7d exhibits any speci¢city in vivo. Although we do not have any de¢nite answer at present, it should be pointed out that RNAs from S. solfataricus have been reported to have exceptionally high modi¢cation levels: for instance, in both 16S and 23S rRNAs several residues are methylated at O-2P of ribose, a modi¢ca- tion that enhances the stability of the polynucleotide chain at high temperatures [31]. These modi¢cations may therefore lead to a more restricted in vivo speci¢city of Sso7d.…”

RNAs in Extreme Environments

“…Archaeal rRNAs are rich in post-transcriptionally modified nucleotides. Examination of the extent of rRNA modifications in the hyperthermophilic archaeon Sulfolobus solfataricus revealed an exceptionally high proportion of modifications as compared to prokaryotic organisms, with 38 modified sites in the 16S rRNA and 50 in the 23S rRNA for the archaeon, compared with 11 and 23 sites, respectively, in Escherichia coli [33]. The principal modifications in S. solfataricus 16S and 23S rRNAs are methylation of the 2'-OH group of sugar residues (2'-O-methylation).…”

“…The principal modifications in S. solfataricus 16S and 23S rRNAs are methylation of the 2'-OH group of sugar residues (2'-O-methylation). It has been suggested that the 2'-O-Me groups act to stabilize RNA stems by maintaining the sugar residues in the more rigid C(3')-endo-conformation [33]. Moreover, an increase in ribose methylation was observed in rRNAs of S. solfataricus (21 -24% increase) with progressive temperature increase of the culture [33].…”

“…It has been suggested that the 2'-O-Me groups act to stabilize RNA stems by maintaining the sugar residues in the more rigid C(3')-endo-conformation [33]. Moreover, an increase in ribose methylation was observed in rRNAs of S. solfataricus (21 -24% increase) with progressive temperature increase of the culture [33]. It is, however, still not clear whether this increase in modifications reflects regulated activation of the methylation machinery at high temperature or simply unregulated inhibition at low temperature.…”