Cargando…

Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata

RNA editing in chloroplasts and mitochondria of land plants differs significantly in abundance. For example, some 200–500 sites of cytidine-to-uridine RNA editing exist in flowering plant mitochondria as opposed to only 30–50 such C-to-U editing events in their chloroplasts. In contrast, we predicte...

Descripción completa

Detalles Bibliográficos
Autores principales: Oldenkott, Bastian, Yamaguchi, Kazuo, Tsuji-Tsukinoki, Sumika, Knie, Nils, Knoop, Volker
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4174432/
https://www.ncbi.nlm.nih.gov/pubmed/25142065
http://dx.doi.org/10.1261/rna.045575.114
_version_ 1782336347212611584
author Oldenkott, Bastian
Yamaguchi, Kazuo
Tsuji-Tsukinoki, Sumika
Knie, Nils
Knoop, Volker
author_facet Oldenkott, Bastian
Yamaguchi, Kazuo
Tsuji-Tsukinoki, Sumika
Knie, Nils
Knoop, Volker
author_sort Oldenkott, Bastian
collection PubMed
description RNA editing in chloroplasts and mitochondria of land plants differs significantly in abundance. For example, some 200–500 sites of cytidine-to-uridine RNA editing exist in flowering plant mitochondria as opposed to only 30–50 such C-to-U editing events in their chloroplasts. In contrast, we predicted significantly more chloroplast RNA editing for the protein-coding genes in the available complete plastome sequences of two species of the spike moss genus Selaginella (Lycopodiophyta). To evaluate these predictions we investigated the Selaginella uncinata chloroplast transcriptome. Our exhaustive cDNA studies identified the extraordinary number of 3415 RNA-editing events, exclusively of the C-to-U type, in the 74 mRNAs encoding intact reading frames in the S. uncinata chloroplast. We find the overwhelming majority (61%) of the 428 silent editing events leaving codon meanings unaltered directly neighboring other editing events, possibly suggesting a sterically more flexible RNA-editing deaminase activity in Selaginella. No evidence of RNA editing was found for tRNAs or rRNAs but we identified a total of 74 editing sites in cDNA sequences of four group II introns (petBi6g2, petDi8g2, ycf3i124g2, and ycf3i354g2) retained in partially matured transcripts, which strongly contribute to improved base-pairing in the intron secondary structures as a likely prerequisite for their splicing.
format Online
Article
Text
id pubmed-4174432
institution National Center for Biotechnology Information
language English
publishDate 2014
publisher Cold Spring Harbor Laboratory Press
record_format MEDLINE/PubMed
spelling pubmed-41744322015-10-01 Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata Oldenkott, Bastian Yamaguchi, Kazuo Tsuji-Tsukinoki, Sumika Knie, Nils Knoop, Volker RNA Letter to the Editor RNA editing in chloroplasts and mitochondria of land plants differs significantly in abundance. For example, some 200–500 sites of cytidine-to-uridine RNA editing exist in flowering plant mitochondria as opposed to only 30–50 such C-to-U editing events in their chloroplasts. In contrast, we predicted significantly more chloroplast RNA editing for the protein-coding genes in the available complete plastome sequences of two species of the spike moss genus Selaginella (Lycopodiophyta). To evaluate these predictions we investigated the Selaginella uncinata chloroplast transcriptome. Our exhaustive cDNA studies identified the extraordinary number of 3415 RNA-editing events, exclusively of the C-to-U type, in the 74 mRNAs encoding intact reading frames in the S. uncinata chloroplast. We find the overwhelming majority (61%) of the 428 silent editing events leaving codon meanings unaltered directly neighboring other editing events, possibly suggesting a sterically more flexible RNA-editing deaminase activity in Selaginella. No evidence of RNA editing was found for tRNAs or rRNAs but we identified a total of 74 editing sites in cDNA sequences of four group II introns (petBi6g2, petDi8g2, ycf3i124g2, and ycf3i354g2) retained in partially matured transcripts, which strongly contribute to improved base-pairing in the intron secondary structures as a likely prerequisite for their splicing. Cold Spring Harbor Laboratory Press 2014-10 /pmc/articles/PMC4174432/ /pubmed/25142065 http://dx.doi.org/10.1261/rna.045575.114 Text en © 2014 Oldenkott et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Letter to the Editor
Oldenkott, Bastian
Yamaguchi, Kazuo
Tsuji-Tsukinoki, Sumika
Knie, Nils
Knoop, Volker
Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata
title Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata
title_full Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata
title_fullStr Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata
title_full_unstemmed Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata
title_short Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata
title_sort chloroplast rna editing going extreme: more than 3400 events of c-to-u editing in the chloroplast transcriptome of the lycophyte selaginella uncinata
topic Letter to the Editor
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4174432/
https://www.ncbi.nlm.nih.gov/pubmed/25142065
http://dx.doi.org/10.1261/rna.045575.114
work_keys_str_mv AT oldenkottbastian chloroplastrnaeditinggoingextrememorethan3400eventsofctoueditinginthechloroplasttranscriptomeofthelycophyteselaginellauncinata
AT yamaguchikazuo chloroplastrnaeditinggoingextrememorethan3400eventsofctoueditinginthechloroplasttranscriptomeofthelycophyteselaginellauncinata
AT tsujitsukinokisumika chloroplastrnaeditinggoingextrememorethan3400eventsofctoueditinginthechloroplasttranscriptomeofthelycophyteselaginellauncinata
AT knienils chloroplastrnaeditinggoingextrememorethan3400eventsofctoueditinginthechloroplasttranscriptomeofthelycophyteselaginellauncinata
AT knoopvolker chloroplastrnaeditinggoingextrememorethan3400eventsofctoueditinginthechloroplasttranscriptomeofthelycophyteselaginellauncinata