Hammerhead Ribozymes in Archaeal Genomes: A Computational Hunt

Hammerhead ribozymes (HHRs) are small self-cleaving RNAs, first discovered in viroids and satellite RNAs of plant viruses. They are composed of a catalytic core of conserved nucleotides flanked by three helices. More recently, hammerhead-encoding sequences have been identified in the genomes of many eukaryotes, prokaryotes and other non-viral species regulating various functions. In this study we have explored the Archaeal domain to identify HHRs using three different bioinformatics approach. Our study reveals four putative hits of HHRs type I and type II in the group Thaumarchaeota and Euryarchaeota in the Archaeal domain, one of which is the instance of HHR 1 in C. symbiosum A, already identified in a previous study. These HHRs are very similar to those previously described in terms of the conservation of their catalytic core. Based on 3-D structure analysis and free energy, these instances were concluded as putative HHRs. Our findings reveal that the catalytic core contains the conserved motifs that are essential for cleavage activity, but there are some instances in which compensatory core variations are present. However, no instances of HHRs have been found in Crenarchaeota. This study reveals a very scarce presence of HHRs in Archaea which suggests the involvement of other ncRNA elements in gene regulatory system like RNase P which are abundantly found in the Archaeal domain.