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U-to-C RNA editing by synthetic PPR-DYW proteins in bacteria and human culture cells

Programmable RNA editing offers significant therapeutic potential for a wide range of genetic diseases. Currently, several deaminase enzymes, including ADAR and APOBEC, can perform programmable adenosine-to-inosine or cytidine-to-uridine RNA correction. However, enzymes to perform guanosine-to-adeno...

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Autores principales: Ichinose, Mizuho, Kawabata, Masuyo, Akaiwa, Yumi, Shimajiri, Yasuka, Nakamura, Izumi, Tamai, Takayuki, Nakamura, Takahiro, Yagi, Yusuke, Gutmann, Bernard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9478123/
https://www.ncbi.nlm.nih.gov/pubmed/36109586
http://dx.doi.org/10.1038/s42003-022-03927-3
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author Ichinose, Mizuho
Kawabata, Masuyo
Akaiwa, Yumi
Shimajiri, Yasuka
Nakamura, Izumi
Tamai, Takayuki
Nakamura, Takahiro
Yagi, Yusuke
Gutmann, Bernard
author_facet Ichinose, Mizuho
Kawabata, Masuyo
Akaiwa, Yumi
Shimajiri, Yasuka
Nakamura, Izumi
Tamai, Takayuki
Nakamura, Takahiro
Yagi, Yusuke
Gutmann, Bernard
author_sort Ichinose, Mizuho
collection PubMed
description Programmable RNA editing offers significant therapeutic potential for a wide range of genetic diseases. Currently, several deaminase enzymes, including ADAR and APOBEC, can perform programmable adenosine-to-inosine or cytidine-to-uridine RNA correction. However, enzymes to perform guanosine-to-adenosine and uridine-to-cytidine (U-to-C) editing are still lacking to complete the set of transition reactions. It is believed that the DYW:KP proteins, specific to seedless plants, catalyze the U-to-C reactions in mitochondria and chloroplasts. In this study, we designed seven DYW:KP domains based on consensus sequences and fused them to a designer RNA-binding pentatricopeptide repeat (PPR) domain. We show that three of these PPR-DYW:KP proteins edit targeted uridine to cytidine in bacteria and human cells. In addition, we show that these proteins have a 5′ but not apparent 3′ preference for neighboring nucleotides. Our results establish the DYW:KP aminase domain as a potential candidate for the development of a U-to-C editing tool in human cells.
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spelling pubmed-94781232022-09-17 U-to-C RNA editing by synthetic PPR-DYW proteins in bacteria and human culture cells Ichinose, Mizuho Kawabata, Masuyo Akaiwa, Yumi Shimajiri, Yasuka Nakamura, Izumi Tamai, Takayuki Nakamura, Takahiro Yagi, Yusuke Gutmann, Bernard Commun Biol Article Programmable RNA editing offers significant therapeutic potential for a wide range of genetic diseases. Currently, several deaminase enzymes, including ADAR and APOBEC, can perform programmable adenosine-to-inosine or cytidine-to-uridine RNA correction. However, enzymes to perform guanosine-to-adenosine and uridine-to-cytidine (U-to-C) editing are still lacking to complete the set of transition reactions. It is believed that the DYW:KP proteins, specific to seedless plants, catalyze the U-to-C reactions in mitochondria and chloroplasts. In this study, we designed seven DYW:KP domains based on consensus sequences and fused them to a designer RNA-binding pentatricopeptide repeat (PPR) domain. We show that three of these PPR-DYW:KP proteins edit targeted uridine to cytidine in bacteria and human cells. In addition, we show that these proteins have a 5′ but not apparent 3′ preference for neighboring nucleotides. Our results establish the DYW:KP aminase domain as a potential candidate for the development of a U-to-C editing tool in human cells. Nature Publishing Group UK 2022-09-15 /pmc/articles/PMC9478123/ /pubmed/36109586 http://dx.doi.org/10.1038/s42003-022-03927-3 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Ichinose, Mizuho
Kawabata, Masuyo
Akaiwa, Yumi
Shimajiri, Yasuka
Nakamura, Izumi
Tamai, Takayuki
Nakamura, Takahiro
Yagi, Yusuke
Gutmann, Bernard
U-to-C RNA editing by synthetic PPR-DYW proteins in bacteria and human culture cells
title U-to-C RNA editing by synthetic PPR-DYW proteins in bacteria and human culture cells
title_full U-to-C RNA editing by synthetic PPR-DYW proteins in bacteria and human culture cells
title_fullStr U-to-C RNA editing by synthetic PPR-DYW proteins in bacteria and human culture cells
title_full_unstemmed U-to-C RNA editing by synthetic PPR-DYW proteins in bacteria and human culture cells
title_short U-to-C RNA editing by synthetic PPR-DYW proteins in bacteria and human culture cells
title_sort u-to-c rna editing by synthetic ppr-dyw proteins in bacteria and human culture cells
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9478123/
https://www.ncbi.nlm.nih.gov/pubmed/36109586
http://dx.doi.org/10.1038/s42003-022-03927-3
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