A research group led by Assistant Professor Takamasa Teramoto, Professor Yoshimitsu Kakuta and Graduate Student Takeshi Koyasu from Kyushu University, conducted joint research with Professor Takashi Yokogawa from Gifu University, Associate Professor Naruhiko Adachi from the University of Tsukuba (KEK Institute of Materials Structure Science at the time of research), Lecturer Kouta Mayanagi from Kyushu University, and Professor Toshiya Senda from KEK, and elucidated a new mechanism by which twelve bacterial small ribonuclease P (RNase P) enzymes called HARP assemble to form a star-shaped structure and cleave both ends (5' and 3' termini) of precursor tRNA. Their research was published in Nature Communications.
Provided by Kyushu University
tRNA, which is essential for protein synthesis, is produced in cells in an immature state called precursor tRNA. This precursor contains extra sequences at the 5' and 3' termini that are not needed for the original tRNA function. When both of its ends are accurately cut and trimmed, it becomes a mature molecule capable of fulfilling its original function. In other words, the cleavage of both 5' and 3' termini is a finishing process necessary for tRNA to function and is an essential reaction for life activities.
In recent years, the RNase P enzyme HARP, which is the smallest among various types of RNase P, has been identified in some bacteria and archaea, and its structural characteristics and evolutionary significance have attracted attention. HARP forms a dodecamer (12-mer) composed of twelve enzymes that create a star-shaped three-dimensional structure. However, how HARP recognizes and cleaves precursor tRNA and why it forms the unique dodecameric structure had not been sufficiently clarified.
The research group conducted structural analysis of HARP using cryo-electron microscopy at Kyushu University's Structural Drug Discovery Center via Green-Pharma and KEK. They found that the HARP dodecamer forms a complex with five precursor tRNA molecules, and among these, five active sites are involved in cleaving 5' excess sequences. Furthermore, through biochemical analysis, it was suggested that the remaining seven active sites are responsible for cleaving 3' excess sequences, an activity not seen in conventional RNase P enzymes. In other words, it was revealed that HARP is a "dual-sword" enzyme with dual functions that cleave both the 5' and 3' termini of precursor tRNA through multimerization.
Notably, HARP functions as a molecular ruler that accurately measures the distance between the 5' terminus and the tRNA-specific elbow region within the tRNA molecule to determine the cleavage position. Since different types of RNase P enzymes share this common function, this can be considered an example of convergent evolution.
This research reveals the evolutionary mechanism by which proteins acquire new functions (3' terminal processing) while maintaining basic functions (5' terminal processing) through multimerization, providing new perspectives for understanding tRNA maturation.
In the future, detailed analysis of how HARP switches between active sites and the molecular mechanism and physiological significance of 3' terminal cleavage activity is expected to deepen our understanding of the diversity of RNA processing and its evolution. Furthermore, by applying the principles of the molecular ruler function revealed in this study to the design of artificial enzymes and RNA processing tools, spillover effects into synthetic biology and biotechnology fields are anticipated.
Journal Information
Publication: Nature Communications
Title: Structural basis of transfer RNA processing by bacterial minimal RNase P
DOI: 10.1038/s41467-025-60002-1
This article has been translated by JST with permission from The Science News Ltd. (https://sci-news.co.jp/). Unauthorized reproduction of the article and photographs is prohibited.