RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal

Abstract

RNA editing in mitochondria and chloroplasts of land plants alters the coding content of transcripts through site-specific exchanges of cytidines into uridines and vice versa. The abundance of RNA editing in model plant species such as rice or Arabidopsis with some 500 affected sites in their organelle transcripts hinders straightforward approaches to elucidate its mechanisms. The moss Physcomitrella patens is increasingly being appreciated as an alternative plant model system, enhanced by the recent availability of its complete chloroplast, mitochondrial, and nuclear genome sequences. We here report the transcriptomic analysis of Physcomitrella mitochondrial mRNAs as a prerequisite for future studies of mitochondrial RNA editing in this moss. We find a strikingly low frequency of RNA editing affecting only eleven, albeit highly important, sites of C-to-U nucleotide modification in only nine mitochondrial genes. Partial editing was seen for two of these sites but no evidence for any silent editing sites (leaving the identity of the encoded amino acid unchanged) as commonly observed in vascular plants was found in Physcomitrella, indicating a compact and efficient organization of the editing machinery. Furthermore, we here wish to propose a unifying nomenclature to clearly identify and designate RNA editing positions and to facilitate future communication and database annotation.

Extensive Loss of RNA Editing Sites in Rapidly Evolving Silene Mitochondrial Genomes: Selectionvs. Retroprocessing as the Driving Force

“…The extent of editing at these sites is much more likely to vary among individuals and tissue types than at nonsynonymous sites (Bentolila et al 2008), and editing is frequently lost without the C-to-T substitution needed to conserve its effects (Shields and Wolfe 1997;Mower 2008). Overall, synonymous editing has all the hallmarks of a relatively neutral misfiring of the RNA editing machinery (Rü dinger et al 2009). …”

“…The rate of editing in seed plant chloroplast genomes is over an order of magnitude lower (Tillich et al 2006). Outside seed plants, the moss Physcomitrella patens has only 11 edited sites in the mitochondrial genome, and the liverwort Marchantia polymorpha appears to have lost RNA editing altogether (Rü dinger et al 2008(Rü dinger et al , 2009). In contrast, other bryophytes, lycophytes, and ferns exhibit frequent mitochondrial editing (Malek et al 1996;Grewe et al 2009;Li et al 2009), while the only two nonseed plant chloroplast genomes examined (from one hornwort and one fern) also have high levels of editing (Kugita et al 2003;Wolf et al 2004).…”

Can mosses serve as model organisms for forest research?

“…The number of editing sites per gene and specificity of the editing factors, the pentatricopeptide repeat proteins (PPR), can vary between even closely related (moss) species and seems to follow a dynamic evolutionary process (O'Toole et al 2008;Rüdinger et al 2012). In flowering plants, up to 500 RNA editing sites were identified in their organelle transcripts, whereas in contrast only 11 sites were found in P. patens mitochondria (Rüdinger et al 2009). …”

RNA editing in plant mitochondria: 20 years later

“…Of 450 PPR genes identified in the genome of A. thaliana, 200 are PLS class. In contrast, in P. patens, where only 11 mitochondrial and two chloroplast edits have been documented (39), only 10 of 103 identified PPR genes are PLS (all DYW type). These results have focused attention on the PLS class of PPR proteins as key specificity determinants for RNA editing in plant organelles.…”