Minimal protein-only RNase P structure reveals insights into tRNA precursor recognition and catalysis

Takamasa Teramoto; Takeshi Koyasu; Naruhiko Adachi; Masato Kawasaki; Toshio Moriya; Tomoyuki Numata; Toshiya Senda; Yoshimitsu Kakuta

doi:10.1016/j.jbc.2021.101028

Minimal protein-only RNase P structure reveals insights into tRNA precursor recognition and catalysis

J Biol Chem. 2021 Sep;297(3):101028. doi: 10.1016/j.jbc.2021.101028. Epub 2021 Jul 31.

Authors

Takamasa Teramoto¹, Takeshi Koyasu², Naruhiko Adachi³, Masato Kawasaki⁴, Toshio Moriya³, Tomoyuki Numata⁵, Toshiya Senda⁴, Yoshimitsu Kakuta⁶

Affiliations

¹ Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Nishi-ku, Fukuoka, Japan. Electronic address: teramotot@agr.kyushu-u.ac.jp.
² Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Nishi-ku, Fukuoka, Japan.
³ Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan.
⁴ Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan; Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), Tsukuba, Ibaraki, Japan.
⁵ Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Nishi-ku, Fukuoka, Japan.
⁶ Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Nishi-ku, Fukuoka, Japan. Electronic address: kakuta@agr.kyushu-u.ac.jp.

Abstract

Ribonuclease P (RNase P) is an endoribonuclease that catalyzes the processing of the 5' leader sequence of precursor tRNA (pre-tRNA). Ribonucleoprotein RNase P and protein-only RNase P (PRORP) in eukaryotes have been extensively studied, but the mechanism by which a prokaryotic nuclease recognizes and cleaves pre-tRNA is unclear. To gain insights into this mechanism, we studied homologs of Aquifex RNase P (HARPs), thought to be enzymes of approximately 23 kDa comprising only this nuclease domain. We determined the cryo-EM structure of Aq880, the first identified HARP enzyme. The structure unexpectedly revealed that Aq880 consists of both the nuclease and protruding helical (PrH) domains. Aq880 monomers assemble into a dimer via the PrH domain. Six dimers form a dodecamer with a left-handed one-turn superhelical structure. The structure also revealed that the active site of Aq880 is analogous to that of eukaryotic PRORPs. The pre-tRNA docking model demonstrated that 5' processing of pre-tRNAs is achieved by two adjacent dimers within the dodecamer. One dimer is responsible for catalysis, and the PrH domains of the other dimer are responsible for pre-tRNA elbow recognition. Our study suggests that HARPs measure an invariant distance from the pre-tRNA elbow to cleave the 5' leader sequence, which is analogous to the mechanism of eukaryotic PRORPs and the ribonucleoprotein RNase P. Collectively, these findings shed light on how different types of RNase P enzymes utilize the same pre-tRNA processing.

Keywords: cryo-EM; molecular evolution; oligomerization; precursor tRNA (pre-tRNA); ribonuclease P (RNase P).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence
Catalysis
Catalytic Domain
Cryoelectron Microscopy
Dimerization
Molecular Docking Simulation
RNA Precursors / metabolism*
RNA, Transfer / metabolism*
Ribonuclease P / chemistry*
Ribonuclease P / metabolism
Sequence Homology, Amino Acid

Substances

RNA Precursors
RNA, Transfer
Ribonuclease P