A protein with an unusually short PPR domain, MEF8, affects editing at over 60 Arabidopsis mitochondrial C targets of RNA editing

Abstract

An RNA-seq approach was used to investigate the role of a PLS-subfamily pentatricopeptide repeat protein, Mitochondrial Editing Factor 8 (MEF8), on editing in Arabidopsis mitochondria and plastids. MEF8 has an intact DYW domain, but possesses an unusually short PLS repeat region of only five repeats. The MEF8 T-DNA insertion (mef8) line exhibited reduced editing at 38 mitochondrial editing sites and increased editing at 24 sites; therefore the absence of MEF8 affects 11% of the mitochondrial editome. Notably, 60% of the matR transcripts' sites showed a decrease of editing extent in the mef8 mutant. An E549A substitution in the MEF8 protein replaced the putatively catalytic glutamate of the HXE motif in the DYW domain. Complementation with MEF8-E549A failed to restore editing at the main target sites but was able to restore editing at the matR transcript; it also decreased the editing extent of most of the C targets exhibiting an increase of editing extent in the mef8 mutant plant. Thus, MEF8 has two antagonistic effects on mitochondrial editing: stimulatory, which requires a catalytic glutamate for most of the targets except for the matR transcript, and inhibitory, for which glutamate is dispensable.

Towards a plant model for enigmatic U‐to‐C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis

“…). In the angiosperm models, such truncations are compensated for by separate DYW domains provided in trans (Boussardon et al , ; Andrés‐Colás et al , ; Diaz et al , ; Guillaumot et al , ). Interestingly, we also identified three small DYW‐only proteins outside of the large PLS‐type PPR gene family in the A. agrestis genome, which feature the conserved cytidine deaminase signatures and a terminal DYW tripeptide (Fig.…”

“…However, the setup of organelle RNA editing is evidently more complex in flowering plants, where truncated proteins require interactions with DYW domains supplied in trans , frequently mediated by extra helper proteins (e.g. NUWA and multiple organellar RNA editing factor (MORF)/RNA‐editing factor interacting protein (RIP) proteins) in much more complex editosomes (Takenaka et al , ; Bentolila et al , ; Boussardon et al , ; Sun et al , , , ; Zehrmann et al , ; Diaz et al , ; Bayer‐Császár et al , ; Andrés‐Colás et al , ; Guillaumot et al , ; Sandoval et al , ).…”

A novel E-Subgroup Pentatricopeptide Repeat Protein DEK55 is Responsible for RNA Editing at 15 Sites and Splicing of nad1 and nad4 in Maize

“…DEK55 is necessary for C-to-U editing of multiple sites in the mitochondrial transcripts of maize PPR proteins, including DYW2, EMP21, NUWA, and MEF8, are involved in C-to-U editing at multiple sites [45][46][47][48]. In this study, DEK55 participated in RNA editing at 15 sites, suggesting it might be a novel Esubgroup PPR protein.…”

“…However, PPR proteins do not share uniform protein features. Among them, DYW2 and MEF8 harbor only ve PPR repeats and belong to an atypical DYW subgroup [45,46]. NUWA belongs to the P-class of PPR proteins [45,47].…”

Non-canonical Features of Pentatricopeptide Repeat Protein-Facilitated RNA Editing in Arabidopsis Chloroplasts

“…PPR editing factors are also involved in the editing reaction, when a deaminase-like DYW domain is located immediately C-terminal to the E2 motif (Wagoner et al, 2015). In some cases, the DYW domain is supplied in trans by other proteins (Boussardon et al, 2012;Andres-Colas et al, 2017;Diaz et al, 2017;Guillaumot et al, 2017). PPR editing factors belong to a larger organellar editosome, where multiple other components have been identified (Sun et al, 2016).…”