Structure and Function of Archaeal Ribonuclease P

Ribonuclease P (RNase P) is a ribonucleoprotein complex involved in the processing of the 5′-leader sequence of precursor tRNA (pre-tRNA) and other small RNAs in all phylogenetic domains. A characteristic feature of archaeal RNase P RNAs is that they alone have, unlike bacterial counterparts, little pre-tRNA cleavage activity, but the interaction with protein components activates their catalytic activity. In addition, it has not yet been confirmed whether archaeal RNase P, like its bacterial and eukaryotic counterparts, has additional substrates in vivo. We have found that RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of RNase P RNA (PhopRNA) and five protein cofactors designated PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, and PhoRpp38. Biochemical and structural studies over the past 10 years have revealed that PhoPop5 and PhoRpp30 form a heterotetrameric complex and cooperatively activates a catalytic domain (C-domain), while PhoRpp21 and PhoRpp29 form a heterodimer and function together to activate a specificity domain (S-domain) in PhopRNA. As for the fifth protein, PhoRpp38 is involved in elevation of the optimum temperature of RNase P activity, binding to two peripheral stem-loops, including helices P12.1/12.2 and P16. Moreover, comparative analysis of the RNase P RNA sequences and existing crystallographic structural information of the bacterial RNase P RNAs were combined to generate a phylogenetically supported three-dimensional (3D) model of PhopRNA. Recent biochemical data on the protein-PhopRNA interactions localized the protein binding sites on PhopRNA. Moreover, a comparative transcriptome on the hyperthermophilic archaeon Thermococcus kodakarensis suggested the presence of additional substrates for archaeal RNase Ps. Here, we review biochemical information on archaeal RNase Ps, mainly focusing on recent studies that allow us to generate a structural and mechanistic model for the PhopRNA activation by the protein cofactors.