Processed Small RNAs in Archaea and BHB Elements

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 piecewise 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.

Plasticity of archaeal C/D box sRNA biogenesis

“…Consequently, sequence‐ or structure‐specific endoribonucleases that recognize motifs outside of the C/D box sRNA sequence are not involved in their maturation process. Recently, relaxed structure motifs for the tRNA splicing endonuclease were identified computationally in the vicinity of some C/D box sRNA genes (Berkemer et al ., ). Our results indicate that C/D box maturation is feasible without the presence of splicing endonuclease motifs.…”