title: Extra-structural elements in the RNA recognition motif in archaeal Pop5 play a crucial role in the activation of RNase P RNA from Pyrococcus horikoshii OT3.
abstract: Ribonuclease P (RNase P) is a ribonucleoprotein complex essential for the processing of 5' leader sequences of precursor tRNAs (pre-tRNA). PhoPop5 is an archaeal homolog of human RNase P protein hPop5 involved in the activation of RNase P RNA (PhopRNA) in the hyperthermophilic archaeon Pyrococcus horikoshii, probably by promoting RNA annealing (AN) and RNA strand displacement (SD). Although PhoPop5 folds into the RNA recognition motif (RRM), it is distinct from the typical RRM in that it has an insertion of α-helix (α2) between α1 and β2. Biochemical and structural data have shown that the dimerization of PhoPop5 through the loop between α1 and α2 is required for the activation of PhopRNA. In addition, PhoPop5 has additional helices (α4 and α5) at the C-terminus, which pack against one face of the β-sheet. In this study, we examined the contribution of the C-terminal helices to the activation of PhopRNA using mutation analyses. Reconstitution experiments and fluorescence resonance energy transfer (FRET)-based assays indicated that deletion of the C-terminal helices α4 and α5 significantly influenced on the pre-tRNA cleavage activity and abolished AN and SD activities, while that of α5 had little effect on these activities. Moreover, the FRET assay showed that deletion of the loop between α1 and α2 had no influence on the AN and SD activity. Further mutational analyses suggested that basic residues at α4 are involved in interaction with PhopRNA, while hydrophobic residues at α4 participate in interaction with hydrophobic residues at the β-sheet, thereby stabilizing an appropriate orientation of the helix α4. Together, these results indicate that extra-structural elements in the RRM in PhoPop5 play a crucial role in the activation of PhopRNA.
authors.affiliation: Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Graduate School, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Higashi-ku, Fukuoka 812-8581, Japan.
authors.forename: Kohsuke
authors.initials: K
authors.lastname: Hazeyama
authors.forename: Masato
authors.initials: M
authors.lastname: Ishihara
authors.forename: Toshifumi
authors.initials: T
authors.lastname: Ueda
authors.forename: Etsuko
authors.initials: E
authors.lastname: Nishimoto
authors.forename: Takashi
authors.initials: T
authors.lastname: Nakashima
authors.forename: Yoshimitsu
authors.initials: Y
authors.lastname: Kakuta
authors.forename: Makoto
authors.initials: M
authors.lastname: Kimura
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000737:chemistry* / Q000235:genetics; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D043902:Pyrococcus horikoshii; D059367:RNA Cleavage; D012322:RNA Precursors / Q000378:metabolism*; D043262:Ribonuclease P / Q000737:chemistry* / Q000235:genetics
chemical_list: D019843:Archaeal Proteins; D012322:RNA Precursors; D043262:Ribonuclease P
keywords: AN; Archaea; CD; FRET; PhopRNA; Protein–RNA interaction; Pyrococcus horikoshii; RNA annealing; RNA chaperone; RNA recognition motif; RNase P; SD; circular dichroism; fluorescence resonance energy transfer; pre-tRNA; precursor tRNA; ribonuclease P; ribonuclease P RNA from P. horikoshii; strand displacement