Evidence map›Paper›PMID 40593470›Full record

ArticleNature communications2025

Structural basis of transfer RNA processing by bacterial minimal RNase P.

Takamasa Teramoto, Takeshi Koyasu, Takashi Yokogawa, Naruhiko Adachi, Kouta Mayanagi, Takahiro Nakamura, Toshiya Senda, Yoshimitsu Kakuta

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Takamasa Teramoto *Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan. teramotot@agr.kyushu-u.ac.jp.ORCID http://orcid.org/0000-0003-1555-5394
Takeshi Koyasu *Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.
Takashi YokogawaFaculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
Naruhiko AdachiStructural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.ORCID http://orcid.org/0000-0003-1539-6696
Kouta MayanagiDepartment of Drug Discovery Structural Biology, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka, 812-8582, Japan.
Takahiro NakamuraLaboratory of Genome Chemistry and Engineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.ORCID http://orcid.org/0000-0002-5387-6538
Toshiya SendaStructural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.ORCID http://orcid.org/0000-0002-5153-928X
Yoshimitsu KakutaLaboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan. kakuta@agr.kyushu-u.ac.jp.ORCID http://orcid.org/0000-0002-0781-2074

Funding

Japan Agency for Medical Research and Development (AMED) JP21am0101071Japan Agency for Medical Research and Development (AMED) JP21am0101091Japan Society for the Promotion of Science London (JSPS London) 21K06032Japan Society for the Promotion of Science London (JSPS London) JPMJSP2136
6 · The paper itself

Abstract

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).

Indexed as

Ribonuclease PRNA PrecursorsRNA Processing, Post-TranscriptionalRNA, TransferCatalytic DomainCryoelectron MicroscopyEscherichia coliModels, MolecularNucleic Acid ConformationProtein MultimerizationRibonuclease PRNA PrecursorsRNA, Transfer

Identifiers

PMID40593470
PMCPMC12217051

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.