Functional characterization of archaeal homologs of human nuclear RNase P proteins Rpp21 and Rpp29 provides insights into the molecular basis of their cooperativity in catalysis
Ribonuclease P (RNase P) is a ribonucleoprotein that catalyzes the processing of 5′ leader sequences of precursor tRNAs (pre-tRNA). RNase P proteins PhoRpp21 and PhoRpp29 in the hyperthermophilic archaeon Pyrococcus horikoshii, homologs of human nuclear RNase P proteins Rpp21 and Rpp29 respectively, fold into a heterodimeric structure and synergistically function in the activation of the specificity domain (S-domain) in RNase P RNA (PhopRNA). To elucidate the molecular basis for their cooperativity, we first analyzed binding ability to PhopRNA using a pull-down assay. The result showed that PhoRpp21 is able to bind to PhopRNA in the absence of PhoRpp29, whereas PhoRpp29 alone has reduced affinity to PhopRNA, suggesting that PhoRpp21 primarily functions as a binding element for PhopRNA in the PhoRpp21-PhoRpp29 complex. Mutational analyses suggested that although individual positively charged clusters contribute little to the PhopRNA binding, Lys53, Lys54, and Lys56 at the N-terminal helix (α2) in PhoRpp21 and 10 C-terminal residues in PhoRpp29 are essential for PhopRNA activation. Moreover, deletion of a single stranded loop linking P11 and P12 helices in the PhopRNA S-domain impaired the PhoRpp21-PhoRpp29 complex binding to PhopRNA. Collectively, the present results suggest that PhoRpp21 binds the loop between P11 and P12 helices through overall positively charged clusters on the surface of the complex and serves as a scaffold for PhoRpp29 to optimize structural conformation of its N-terminal helix (α2) in PhoRpp21, as well as C-terminal residues in PhoRpp29, for RNase P activity. - Graphical abstract: A mechanistic model for the synergistic activation of PhopRNA by PhoRpp21 and PhoRpp29. PhoRpp21 binds to the loop between P11 and P12 helices in PhopRNA and serves as a scaffold for PhoRpp29 to optimize a structural conformation of a positively charged edge composed of lysine residues (●) at α2 in PhoRpp21and C-terminal residues (â–‹) in PhoRpp29 on the protein complex which probably stabilize stacking interactions between PhopRNA and pre-tRNA. ▲ indicates the processing site in pre-tRNA. Display Omitted - Highlights: • RNase P proteins PhoRpp21 and PhoRpp29 synergistically function in RNase P catalysis. • PhoRpp21 functions as an RNA-binding element in the PhoRpp21-PhoRpp29 complex. • PhoRpp21 serves as a scaffold for PhoRpp29 in RNase P. • PhoRpp21 binds the loop between P11 and P12 helices in the PhopRNA S-domain. • The molecular basis for the cooperativity of PhoRpp21 and PhoRpp29 is presented.