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TitleStructural basis of transfer RNA processing by bacterial minimal RNase P.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 5456, Year 2025
Publish dateJul 1, 2025
AuthorsTakamasa Teramoto / Takeshi Koyasu / Takashi Yokogawa / Naruhiko Adachi / Kouta Mayanagi / Takahiro Nakamura / Toshiya Senda / Yoshimitsu Kakuta /
PubMed AbstractPrecursor tRNAs (pre-tRNAs) require nucleolytic removal of 5'-leader and 3'-trailer sequences for maturation, which is essential for proper tRNA function. The endoribonuclease RNase P exists in ...Precursor tRNAs (pre-tRNAs) require nucleolytic removal of 5'-leader and 3'-trailer sequences for maturation, which is essential for proper tRNA function. The endoribonuclease RNase P exists in diverse forms, including RNA- and protein-based RNase P, and removes 5'-leader sequences from pre-tRNAs. Some bacteria and archaea possess a unique minimal protein-based RNase P enzyme, HARP, which forms dodecamers with twelve active sites. Here, we present cryogenic electron microscopy structures of HARP dodecamers complexed with five pre-tRNAs, and we show that HARP oligomerization enables specific recognition of the invariant distance between the acceptor stem 5'-end and the TψC-loop, functioning as a molecular ruler-a feature representing convergent evolution among RNase P enzymes. The HARP dodecamer uses only five active sites for 5'-leader cleavage, while we identify a 3'-trailer cleavage activity in the remaining seven sites. This elucidation reveals how small proteins evolve through oligomerization to adapt a pivotal biological function (5'-leader processing) and acquire a novel function (3'-trailer processing).
External linksNat Commun / PubMed:40593470 / PubMed Central
MethodsEM (single particle)
Resolution2.87 - 3.19 Å
Structure data

37128

8kd9

EMDB-37128, PDB-8kd9:
Cryo-EM structure of Aquifex aeolicus minimal protein-only RNase P (HARP) in complex with pre-tRNAs
Method: EM (single particle) / Resolution: 2.87 Å

37129

8kda

EMDB-37129, PDB-8kda:
Cryo-EM structure of Hydrogenobacter thermophilus minimal protein-only RNase P (HARP) in complex with pre-tRNAs
Method: EM (single particle) / Resolution: 3.19 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • aquifex aeolicus (bacteria)
  • aquifex aeolicus vf5 (bacteria)
  • Hydrogenobacter thermophilus (bacteria)
  • hydrogenobacter thermophilus dsm 653 (bacteria)
KeywordsHYDROLASE-RNA COMPLEX / pre-tRNA processing / tRNA / pre-tRNA complex / RNA-free ribonuclease P / ribonuclease / HYDROLASE/RNA / ribonuclease P

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