Substitutional RNA Editing in Plant Organelles

Ichinose, Mizuho; Sugita, Mamoru

doi:10.1007/978-1-0716-0787-9_1

Cited by 6 publications

(5 citation statements)

References 23 publications

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“…The recent years have seen much progress towards understanding the molecular machinery behind cytidine-to-uridine RNA editing in plant chloroplasts and mitochondria [1][2][3][4]. Among other insights, very early functional studies on plant RNA editing based on in organello, in vitro or transplastomic studies had already demonstrated that the specificity for identifying cytidine targets largely resides in their immediate sequence environment, mainly within circa 20 upstream nucleotides [5][6][7][8][9][10][11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%

“…In contrast, a much simpler scenario has emerged for C-to-U RNA editing in “early-branching” land plants among which the moss Physcomitrium patens holds a key role as a model organism [ 4 , 21 , 22 ]. All characterized RNA editing factors in Physcomitrium combine a stretch of pentatricopeptide repeats (PPRs) responsible for sequence-specific RNA recognition with a terminal DYW-type cytidine deaminase carrying out the site-specific C-to-U conversion.…”

Section: Introductionmentioning

confidence: 99%

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Beyond a PPR-RNA recognition code: Many aspects matter for the multi-targeting properties of RNA editing factor PPR56

Yang,

Ritzenhofen,

Otrzonsek

et al. 2023

PLoS Genet

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The mitochondrial C-to-U RNA editing factor PPR56 of the moss Physcomitrium patens is an RNA-binding pentatricopeptide repeat protein equipped with a terminal DYW-type cytidine deaminase domain. Transferred into Escherichia coli, PPR56 works faithfully on its two native RNA editing targets, nad3eU230SL and nad4eU272SL, and also converts cytidines into uridines at over 100 off-targets in the bacterial transcriptome. Accordingly, PPR56 is attractive for detailed mechanistic studies in the heterologous bacterial setup, allowing for scoring differential RNA editing activities of many target and protein variants in reasonable time. Here, we report (i) on the effects of numerous individual and combined PPR56 protein and target modifications, (ii) on the spectrum of off-target C-to-U editing in the bacterial background transcriptome for PPR56 and two variants engineered for target re-direction and (iii) on combinations of targets in tandem or separately at the 5’- and 3’-ends of large mRNAs. The latter experimentation finds enhancement of RNA editing at weak targets in many cases, including cox3eU290SF as a new candidate mitogenome target. We conclude that C-to-U RNA editing can be much enhanced by transcript features also outside the region ultimately targeted by PPRs of a plant editing factor, possibly facilitated by its enrichment or scanning along transcripts.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Beyond a PPR-RNA recognition code: Many aspects matter for the multi-targeting properties of RNA editing factor PPR56

Yang,

Ritzenhofen,

Otrzonsek

et al. 2023

PLoS Genet

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show abstract

“…C‐to‐U RNA editing in chloroplasts and mitochondria is universally present in all land plants with the unique exception of the marchantiid subclass of complex‐thalloid liverworts (Freyer et al., 1997; Malek et al., 1996; Rüdinger et al., 2008; Steinhauser et al., 1999). Despite this wide evolutionary conservation, the molecular machinery for the site‐specific deamination of cytidines to create uridines varies in complexity between mosses and seed plants (Ichinose & Sugita, 2021; Knoop, 2023; Small et al., 2020). RNA editing factors in the model moss Physcomitrium patens are single proteins combining the functions of specific RNA target recognition and a cytidine deaminase function (Ichinose et al., 2013; Schallenberg‐Rüdinger & Knoop, 2016).…”

Section: Introductionmentioning

confidence: 99%

DYW cytidine deaminase domains have a long‐range impact on RNA recognition by the PPR array of chimeric plant C‐to‐U RNA editing factors and strongly affect target selection

Yang,

Oldenkott,

Ramanathan

et al. 2023

The Plant Journal

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SUMMARYThe protein factors for the specific C‐to‐U RNA editing events in plant mitochondria and chloroplasts possess unique arrays of RNA‐binding pentatricopeptide repeats (PPRs) linked to carboxy‐terminal cytidine deaminase DYW domains via the extension motifs E1 and E2. The E1 and E2 motifs have distant similarities to tetratricopeptide repeats known to mediate protein–protein interactions but their precise function is unclear. Here, we investigate the tolerance of PPR56 and PPR65, two functionally characterized RNA editing factors of the moss Physcomitrium patens, for the creation of chimeras by variably replacing their C‐terminal protein regions. Making use of a heterologous RNA editing assay system in Escherichia coli we find that heterologous DYW domains can strongly restrict or widen the spectrum of off‐targets in the bacterial transcriptome for PPR56. Surprisingly, our data suggest that these changes are not only caused by the preference of a given heterologous DYW domain for the immediate sequence environment of the cytidine to be edited but also by a long‐range impact on the nucleotide selectivity of the upstream PPRs.

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“…The recent years have seen much progress towards understanding the molecular machinery behind cytidine-to-uridine RNA editing in plant chloroplasts and mitochondria [1][2][3][4]. The research on RNA editing and other processes of RNA maturation in the two endosymbiotic organelles of plant cells has clearly profited from parallel approaches taken not only with model flowering plants like Arabidopsis, maize or rice but also with bryophyte model organisms [5].…”

Section: Introductionmentioning

confidence: 99%

“…Flowering plants (angiosperms) feature complex RNA editosomes variably composed of numerous and diversely interacting proteins to target specific sites for C-to-U conversion in the organelle transcriptomes [3,[6][7][8]. In contrast, a much simpler scenario has emerged for C-to-U RNA editing in "early-branching" land plants among which the moss Physcomitrium patens holds a key role as a model organism [4,9,10]. All characterized RNA editing factors in Physcomitrium combine a stretch of pentatricopeptide repeats (PPRs) responsible for sequence-specific RNA recognition with a terminal DYW-type cytidine deaminase carrying out the site-specific C-to-U conversion.…”

Section: Introductionmentioning

confidence: 99%

Beyond a PPR-RNA recognition code: Many aspects matter for the multi-targeting properties of RNA editing factor PPR56

Yang

Ritzenhofen

Otrzonsek

et al. 2023

Preprint

View full text Add to dashboard Cite

The mitochondrial C-to-U RNA editing factor PPR56 of the moss Physcomitrium patens is an RNA-binding pentatricopeptide repeat protein equipped with a terminal DYW-type cytidine deaminase domain. Transferred into Escherichia coli, PPR56 works faithfully on its two native RNA editing targets, nad3eU230SL and nad4eU272SL, and also converts cytidines into uridines at over 100 off-targets in the bacterial transcriptome. Accordingly, PPR56 is attractive for detailed mechanistic studies in the heterologous bacterial setup, allowing for scoring differential RNA editing activities of many target and protein variants in reasonable time. Here, we report (i) on the effects of numerous individual and combined PPR56 protein and target modifications, (ii) on the spectrum of off-target C-to-U editing in the bacterial background transcriptome for PPR56 and two variants engineered for target re-direction and (iii) on combinations of targets in tandem or separately at the 5′- and 3′-ends of large mRNAs. The latter experimentation finds enhancement of RNA editing at weak targets in many cases, including cox3eU290SF as a new candidate mitogenome target. We conclude that C-to-U RNA editing can be much enhanced by transcript features also outside the region ultimately targeted by PPRs of a plant editing factor, possibly facilitated by its enrichment or scanning along transcripts.

show abstract

Substitutional RNA Editing in Plant Organelles

Cited by 6 publications

References 23 publications

Beyond a PPR-RNA recognition code: Many aspects matter for the multi-targeting properties of RNA editing factor PPR56

Beyond a PPR-RNA recognition code: Many aspects matter for the multi-targeting properties of RNA editing factor PPR56

DYW cytidine deaminase domains have a long‐range impact on RNA recognition by the PPR array of chimeric plant C‐to‐U RNA editing factors and strongly affect target selection

Beyond a PPR-RNA recognition code: Many aspects matter for the multi-targeting properties of RNA editing factor PPR56

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