Nuclear DYW-Type PPR Gene Families Diversify with Increasing RNA Editing Frequencies in Liverwort and Moss Mitochondria

Abstract

RNA editing in mitochondria and chloroplasts of land plants alters transcript sequences by site-specific conversions of cytidines into uridines. RNA editing frequencies vary extremely between land plant clades, ranging from zero in some liverworts to more than 2,000 sites in lycophytes. Unique pentatricopeptide repeat (PPR) proteins with variable domain extension (E/E+/DYW) have recently been identified as specific editing site recognition factors in model plants. The distinctive functions of these PPR protein domain additions have remained unclear, although deaminase function has been proposed for the DYW domain. To shed light on diversity of RNA editing and DYW proteins at the origin of land plant evolution, we investigated editing patterns of the mitochondrial nad5, nad4, and nad2 genes in a wide sampling of more than 100 liverworts and mosses using the recently developed PREPACT program (www.prepact.de) and exemplarily confirmed predicted RNA editing sites in selected taxa. Extreme variability in RNA editing frequency is seen both in liverworts and mosses. Only few editings exist in the liverwort Lejeunea cavifolia or the moss Pogonatum urnigerum whereas up to 20% of cytidines are edited in the liverwort Haplomitrium mnioides or the moss Takakia lepidozioides. Interestingly, the latter are taxa that branch very early within their respective clades. Amplicons targeting the E/E+/DYW domains and subsequent random clone sequencing show DYW domains among bryophytes to be highly conserved in comparison with their angiosperm counterparts and to correlate well with RNA editing frequencies regarding their diversities. We propose that DYW proteins are the key players of RNA editing at the origin of land plants.

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

“…The PPR arrays of such proteins mediate sequence-specific RNA-binding in a predictable manner (Barkan et al 2012;Takenaka et al 2013;Yagi et al 2013), whereas the carboxy-terminal DYW domain of these proteins has cytidine deaminase similarity (Salone et al 2007;Iyer et al 2011), although a direct biochemical proof for the latter is still lacking. Among land plants, RNA-editing abundance and the diversity of DYWtype PPR gene families appear to correlate well (Rüdinger et al 2008(Rüdinger et al , 2012. Expectedly, the Selaginella moellendorffii genome (Banks et al 2011) features an extended DYW-type PPR protein gene family-however, its ∼200 members are far below numbers of some 4000 to 5000 organellar RNA-editing events.…”

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).…”

Pentatricopeptide repeats

“…Furthermore, and this class includes the PPR RNA editing proteins within chloroplasts and mitochondria of land plants. [45][46][47] The PLS class of PPR proteins contain C-terminal domains required for RNA editing and a distinctive PPR architecture. These editing proteins contain triplet repeats alternating between a typical PPR, a longer PPR of 35 or 36 amino acids and a short PPR of only 31 amino acids (Fig.…”