Abstract
Bulge-helix-bulge (BHB) elements guide the enzymatic splicing machinery that in Archaea excises introns from tRNAs, rRNAs from their primary precursor, and accounts for the assembly of piece-wise encoded tRNAs. This processing pathway renders the intronic sequences as circularized RNA species. Although archaeal transcriptomes harbor a large number of circular small RNAs, it remains unknown whether most or all of them are produced through BHB-dependent splicing. We therefore conduct a genome-wide survey of BHB elements of a phylogenetically diverse set of archaeal species and complement this approach by searching for BHB-like structures in the vicinity of circularized transcripts. We find that besides tRNA introns, the majority of box C/D snoRNAs is associated with BHB elements. Not all circularized sRNAs, however, can be explained by BHB elements, suggesting that there is at least one other mechanism of RNA circularization at work in Archaea. Pattern search methods were unable, however, to identify common sequence and/or secondary structure features that could be characteristic for such a mechanism.
Highlights
The small non-coding RNAs of Archaea are much less understood than their eubacterial counterparts
We obtained a recall of 85% for the transfer RNAs (tRNAs) with introns of Methanopyrus kandleri (6/7), Sulfolobus solfataricus (14/16), and Sulfolobus acidocaldarius (15/18)
A positive signal was recovered for 9 of the remaining 11 N. equitans [39] box C/D snoRNAs not already included in MSA2, for 112 of the 126 sequences from M. kandleri, for 7 of 20 loci in S. solfataricus [9] and 22 of the 24 box C/D snoRNAs reported for S. acidocaldarius [41], see Table 2
Summary
The small non-coding RNAs (sRNAs) of Archaea are much less understood than their eubacterial counterparts. A large number of other sRNAs has been described for individual species, only three RNA classes are unambiguously recognizable within this diversity: Archaea and Eubacteria share CRISPR-Cas adaptive immune systems [1], and two classes of guide RNAs direct chemical modifications of rRNAs and other noncoding RNAs in both Eukarya and Archaea [2]. Both the Archaeal box C/D and the box H/ACA ribonucleoproteins (RNPs) contain core proteins clearly homologous to those of the Eukaryotic snoRNPs (reviewed in [3, 4]). Beyond the canonical forms, recently several pseudouridylation guide RNAs with divergent secondary structures have been reported [8]
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