title: Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata.
abstract: 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.
authors.affiliation: IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115 Bonn, Germany.
authors.forename: Bastian
authors.initials: B
authors.lastname: Oldenkott
authors.affiliation: Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Kanazawa 920-0934, Japan.
authors.forename: Kazuo
authors.initials: K
authors.lastname: Yamaguchi
authors.affiliation: Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Kanazawa 920-0934, Japan.
authors.forename: Sumika
authors.initials: S
authors.lastname: Tsuji-Tsukinoki
authors.affiliation: IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115 Bonn, Germany.
authors.forename: Nils
authors.initials: N
authors.lastname: Knie
authors.affiliation: IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115 Bonn, Germany volker.knoop@uni-bonn.de.
authors.forename: Volker
authors.initials: V
authors.lastname: Knoop
mesh_terms: D001483:Base Sequence; D002736:Chloroplasts / Q000235:genetics*; D003062:Codon / Q000235:genetics*; D007438:Introns / Q000235:genetics*; D008969:Molecular Sequence Data; D017393:RNA Editing / Q000235:genetics*; D018747:RNA, Chloroplast / Q000235:genetics*; D032503:Selaginellaceae / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D003062:Codon; D018747:RNA, Chloroplast
keywords: chloroplast genome; group II introns; lycophyte; plastome; pyrimidine-exchange editing