Archaeal homologs of human RNase P protein pairs Pop5 with Rpp30 and Rpp21 with Rpp29 work on distinct functional domains of the RNA subunit.

We examined the functional equivalency between Escherichia coli RNase P protein (C5) and Pyrococcus horikoshii RNase P proteins (PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, and PhoRpp38) for RNase P activity. The C5 protein and P. horikoshii RNase P proteins were unable to activate non-congnate RNase P RNAs, P. horikoshii RNase P RNA (PhopRNA) and E. coli RNase P RNA (M1 RNA) respectively. Two chimeric RNAs, in which functional C- and S-domains of M1 RNA and PhopRNA were exchanged, were prepared and characterized with respect to the cleavage of P. horikoshii pre-tRNA(Tyr) in the presence of C5 or P. horikoshii proteins. The results suggest that PhoPop5 and PhoRpp30 function equivalently to the C5 protein in the E. coli RNase P, being involved in activation of the PhopRNA C-domain. On the other hand, PhoRpp21 and PhoRpp29 are implicated in stabilization of the PhopRNA S-domain.