Structural basis of transfer RNA processing by bacterial minimal RNase P
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...
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| Format: | Article |
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Nature Portfolio
2025-07-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-60002-1 |
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| author | Takamasa Teramoto Takeshi Koyasu Takashi Yokogawa Naruhiko Adachi Kouta Mayanagi Takahiro Nakamura Toshiya Senda Yoshimitsu Kakuta |
| author_facet | Takamasa Teramoto Takeshi Koyasu Takashi Yokogawa Naruhiko Adachi Kouta Mayanagi Takahiro Nakamura Toshiya Senda Yoshimitsu Kakuta |
| author_sort | Takamasa Teramoto |
| collection | DOAJ |
| description | 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). |
| format | Article |
| id | doaj-art-36e636f35488409ca24e17c5e10ab3ab |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-36e636f35488409ca24e17c5e10ab3ab2025-08-20T03:37:37ZengNature PortfolioNature Communications2041-17232025-07-0116111510.1038/s41467-025-60002-1Structural basis of transfer RNA processing by bacterial minimal RNase PTakamasa Teramoto0Takeshi Koyasu1Takashi Yokogawa2Naruhiko Adachi3Kouta Mayanagi4Takahiro Nakamura5Toshiya Senda6Yoshimitsu Kakuta7Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu UniversityLaboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu UniversityFaculty of Engineering, Gifu UniversityStructural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK)Department of Drug Discovery Structural Biology, Faculty of Pharmaceutical Sciences, Kyushu UniversityLaboratory of Genome Chemistry and Engineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu UniversityStructural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK)Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu UniversityAbstract 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).https://doi.org/10.1038/s41467-025-60002-1 |
| spellingShingle | Takamasa Teramoto Takeshi Koyasu Takashi Yokogawa Naruhiko Adachi Kouta Mayanagi Takahiro Nakamura Toshiya Senda Yoshimitsu Kakuta Structural basis of transfer RNA processing by bacterial minimal RNase P Nature Communications |
| title | Structural basis of transfer RNA processing by bacterial minimal RNase P |
| title_full | Structural basis of transfer RNA processing by bacterial minimal RNase P |
| title_fullStr | Structural basis of transfer RNA processing by bacterial minimal RNase P |
| title_full_unstemmed | Structural basis of transfer RNA processing by bacterial minimal RNase P |
| title_short | Structural basis of transfer RNA processing by bacterial minimal RNase P |
| title_sort | structural basis of transfer rna processing by bacterial minimal rnase p |
| url | https://doi.org/10.1038/s41467-025-60002-1 |
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