Crystal structure of "PPR-DYW protein" elucidated by Kyushu University — Moment of target recognition by plant RNA Editing enzyme captured

A joint research group consisting of Assistant Professor Takamasa Teramoto, Professor Yoshimitsu Kakuta, and Technical Staff Ayumi Okada of the Faculty of Agriculture, Graduate Student Ryota Urushihara and Undergraduate Student Reiya Aoyama (at the time of the research) of the Department of Bioscience and Biotechnology, Faculty of Agriculture, in collaboration with Professor Takahiro Nakamura of the Faculty of Agriculture at Kyushu University together with EditForce Inc., has elucidated the crystal structure of the plant-specific RNA editing enzyme "PPR-DYW protein" at the exact moment it recognizes and edits target RNA. This achievement is expected to find applications in the design and development of tools capable of editing targeted RNA sequences.

The results were published in Nature Communications on April 27. (Left) Three-dimensional structure of the PPR-DYW protein bound to its target RNA.(Upper right) Measurement of editing efficiency using the PPR-DYW protein.

(Lower right) Enlarged view of the active site of the DYW domain.Provided by Kyushu University In living organisms, DNA serves as the blueprint and RNA acts as the transcript of information to carry genetic data and produce proteins. However, there are cases where "RNA editing" occurs, rewriting the information of the blueprint after the DNA has been transcribed into RNA.

Particularly in plant chloroplasts and mitochondria, RNA editing takes place at hundreds to thousands of sites, and a specific PPR-DYW protein exists for each corresponding editing site. The PPR-DYW protein is composed of two domains: a PPR domain that reads the target RNA sequence and a DYW domain that converts a cytosine (C) base into a uracil (U) base. For the normal growth of plants, it is essential that each protein accurately edits its assigned site to be edited.

On the other hand, exactly how both domains cooperate to achieve this precise editing, as well as the crystal structure of the PPR-DYW protein, had remained unknown. Therefore, the group designed and prepared a consensus PPR-DYW protein possessing RNA editing activity. First, they confirmed in an experimental system using E.

coli that this protein edited the target C base of the targeted RNA sequence with a high efficiency of approximately 90% and did not erroneously edit the surrounding C bases. Next, utilizing X-ray crystallography at the large synchrotron radiation facility SPring-8, they determined two crystal structures of this protein: one prior to RNA binding and one after RNA binding. By comparing these two crystal structures, they revealed that upon RNA binding, the two domains adopt an appropriate positional relationship, forming a structure that fits the target C base precisely into the catalytic center.

Furthermore, by combining this with biochemical analysis, they elucidated the editing mechanism: the PPR domain recognizes the upstream sequence of the target C base, and as the two domains take on the appropriate positional relationship, the DYW domain accurately converts the target C base into a U base. This clarified the overall picture of the molecular mechanism by which the PPR-DYW protein achieves RNA editing. This protein holds the potential to freely alter its target RNA sequence through the sequence design of its PPR domain.

Moving forward, the group plans to advance the design and development of more efficient and highly precise RNA editing tools. Teramoto stated: "We have demonstrated for the first time the structural foundation that supports the precision with which plants accurately rewrite just one targeted site out of tens of thousands of bases. This achievement was made possible by the strength of the students and collaborators who diligently carried out the experiments.

I hope to continue deciphering the exquisite mechanisms of proteins that support life from the perspective of their structures." Journal Information Publication: Nature Communications Title: Structural basis of plant organelle C-to-U RNA editing by PPR-DYW proteins DOI: 10.1038/s41467-026-72391-y Biology 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. 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.