Nucleic Acids Research, 2002, Vol. 30, No. 4 921-930
© 2002 Oxford University Press
RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing
1Institut für Experimentelle Pathologie/Molekulare Neurobiologie (ZMBE), Universität Münster, D-48149 Münster, Germany, 2Chemistry Department, Moscow State University, 119899 Moscow, Russian Federation, 3Laboratoire de Biologie Moleculaire Eucaryote du CNRS, Université Paul-Sabatier, F-31062 Toulouse, France, 4Lehrstuhl für Mikrobiologie, Universität Regensburg, D-93053 Regensburg, Germany and 5UMR 7567 CNRS, Université Henri Poincaré, F-54506 Vandoeuvre-les-Nancy, France
The bulge–helix–bulge (BHB) motif recognised by the archaeal splicing endonuclease is also found in the long processing stems of archaeal rRNA precursors in which it is cleaved to generate pre-16S and pre-23S rRNAs. We show that in two species, Archaeoglobus fulgidus and Sulfolobus solfataricus, representatives from the two major archaeal kingdoms Euryarchaeota and Crenarchaeota, respectively, the pre-rRNA spacers cleaved at the BHB motifs surrounding pre-16S and pre-23S rRNAs subsequently become ligated. In addition, we present evidence that this is accompanied by circularisation of ribosomal pre-16S and pre-23S rRNAs in both species. These data reveal a further link between intron splicing and pre-rRNA processing in Archaea, which might reflect a common evolutionary origin of the two processes. One spliced RNA species designated 16S-D RNA, resulting from religation at the BHB motif of 16S pre-rRNA, is a highly abundant and stable RNA which folds into a three-stem structure interrupted by two single-stranded regions as assessed by chemical probing. It spans a region of the pre-rRNA 5' external transcribed spacer exhibiting a highly conserved folding pattern in Archaea. Surprisingly, 16S-D RNA contains structural motifs found in archaeal C/D box small RNAs and binds to the L7Ae protein, a core component of archaeal C/D box RNPs. This supports the notion that it might have an important but still unknown role in pre-rRNA biogenesis or might even target RNA molecules other than rRNA.
* To whom correspondence should be addressed. Tel: +49 251 8352136; Fax: +49 251 8352134; Email: huttenh{at}uni-muenster.de Correspondence may also be addressed to Jean-Pierre Bachellerie. Tel: +33 561 335934; Fax: +33 561 335886; Email: bachel{at}ibcg.biotoul.fr
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