A microeukaryotic PPR-DYW protein supports multisite C- and A-deamination RNA editing
- 1Department of Biochemistry, Universite de Montreal, Montreal, Quebec, Canada; Robert-Cedergren Centre for Bioinformatics and Genomics, Universite de Montreal, M
Abstract
RNA editing in mitochondria is vital for many eukaryotes. In plants, mitochondrial C-to-U deamination editing is catalyzed by tens to hundreds of PPR-DYW proteins, each typically dedicated to a specific site. Where retained, PPR-DYW family expanded independently in all eukaryotic groups examined here -- except in marine microeukaryotes diplonemids, which encode a single homolog despite deaminating their mitochondrial RNA at more than 100 sites. Here we characterize this unconventional deaminase, PPRD1, from Diplonema papillatum. Native affinity pulldown of the protein identified 20 predominantly sub-stoichiometric partners, including potential RNA-binding helical-repeat proteins. Among them, the divergent PolX-like protein DAPX1 consistently and reciprocally co-purified with PPRD1 in near-equal proportions. Structural modelling suggests that DAPX1 may stabilize the deaminase catalytic domain and expand its interaction interface. Silencing either PPRD1 or DAPX1 inhibited cell growth and reduced in vivo not only C-to-U, but also A-to-I deamination across five mitochondrial RNA-editing clusters encompassing 110 sites. Together, these results support a model of PPRD1 and DAPX1 forming the core of the Diplonema deamination-editing machinery, with sub-stoichiometric partners acting as specificity factors that guide accurate RNA editing with minimal off-target effects.
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BibTeX
@misc{valach2026microeukaryotic,
title = {{A microeukaryotic PPR-DYW protein supports multisite C- and A-deamination RNA editing}},
author = {M. Valach and L. C. Aguilar and N. Kalla and P. Mirzavand Borujeni and B. F. Lang and M. Oeffinger and J. M. Pascal and R. Salavati and G. Burger},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.04.749523},
url = {https://www.biorxiv.org/content/10.64898/2026.09.04.749523v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - A microeukaryotic PPR-DYW protein supports multisite C- and A-deamination RNA editing
AU - M. Valach
AU - L. C. Aguilar
AU - N. Kalla
AU - P. Mirzavand Borujeni
AU - B. F. Lang
AU - M. Oeffinger
AU - J. M. Pascal
AU - R. Salavati
AU - G. Burger
PY - 2026
DA - 2026/09/04
PB - bioRxiv
DO - 10.64898/2026.09.04.749523
UR - https://www.biorxiv.org/content/10.64898/2026.09.04.749523v1
AB - RNA editing in mitochondria is vital for many eukaryotes. In plants, mitochondrial C-to-U deamination editing is catalyzed by tens to hundreds of PPR-DYW proteins, each typically dedicated to a specific site. Where retained, PPR-DYW family expanded independently in all eukaryotic groups examined here -- except in marine microeukaryotes diplonemids, which encode a single homolog despite deaminating their mitochondrial RNA at more than 100 sites. Here we characterize this unconventional deaminase, PPRD1, from Diplonema papillatum. Native affinity pulldown of the protein identified 20 predominantly sub-stoichiometric partners, including potential RNA-binding helical-repeat proteins. Among them, the divergent PolX-like protein DAPX1 consistently and reciprocally co-purified with PPRD1 in near-equal proportions. Structural modelling suggests that DAPX1 may stabilize the deaminase catalytic domain and expand its interaction interface. Silencing either PPRD1 or DAPX1 inhibited cell growth and reduced in vivo not only C-to-U, but also A-to-I deamination across five mitochondrial RNA-editing clusters encompassing 110 sites. Together, these results support a model of PPRD1 and DAPX1 forming the core of the Diplonema deamination-editing machinery, with sub-stoichiometric partners acting as specificity factors that guide accurate RNA editing with minimal off-target effects.
ER -