Plant Mitochondrial RNA Editing

Abstract

RNA editing affects messenger RNAs and transfer RNAs in plant mitochondria by site-specific exchange of cytidine and uridine bases in both seed and nonseed plants. Distribution of the phenomenon among bryophytes has been unclear since RNA editing has been detected in some but not all liverworts and mosses. A more detailed understanding of RNA editing in plants required extended data sets for taxa and sequences investigated. Toward this aim an internal region of the mitochondrial nad5 gene (1104 nt) was analyzed in a large collection of bryophytes and green algae (Charles). The genomic nad5 sequences predict editing in 30 mosses, 2 hornworts, and 7 simple thalloid and leafy liverworts (Jungermanniidae). No editing is, however, required in seven species of the complex thalloid liverworts (Marchantiidae) and the algae. RNA editing among the Jungermanniidae, on the other hand, reaches frequencies of up to 6% of codons being modified. Predictability of RNA editing from the genomic sequences was confirmed by cDNA analysis in the mosses Schistostega pennata and Rhodobryum roseum, the hornworts Anthoceros husnotii and A. punctatus, and the liverworts Metzgeria conjugata and Moerckia flotoviana. All C-to-U nucleotide exchanges predicted to reestablish conserved codons were confirmed. Editing in the hornworts includes the removal of genomic stop codons by frequent reverse U-to-C edits. Expectedly, no RNA editing events were identified by cDNA analysis in the marchantiid liverworts Ricciocarpos natans, Corsinia coriandra, and Lunularia cruciata. The findings are discussed in relation to models on the phylogeny of land plants.

The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum : Insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants

“…The distribution patterns of mitochondrial introns among basal land plants are consistent with this hypothesis and also indicate that all five trans-spliced introns conserved among angiosperm mtDNAs arose from cis-spliced intron homologs (21)(22)(23)(24)(25). RNA-editing events involving mainly the conversions of cytidine into uridine have been observed in the mitochondria of basal land plants and angiosperms (26)(27)(28)(29) as well as in their chloro-plasts (26,(30)(31)(32) but appear to be absent in both organelles of Marchantia and the few algae examined thus far. These events are more frequent in mitochondria, where they affect essentially every protein-encoding mRNA in angiosperms.…”

Phylogenetic Analyses of Basal Angiosperms Based on Nine Plastid, Mitochondrial, and Nuclear Genes

“…For an issue as critical as the rooting of angiosperm phylogeny, merely having high bootstrap numbers from an analysis is not enough to gain confidence in the result ). Some poorly understood molecular evolutionary phenomena, such as RNA editing (Steinhauser et al 1999;Kugita et al 2003;Dombrovska and Qiu 2004) and GC-content bias (Steel et al 1993), both of which can occur in a genome-wide, lineagespecific fashion, can generate substitutions that lead to spurious groupings in phylogenetic analyses. Hence, it is important that we understand the types of substitutions that are behind those high bootstrap percentages.…”

Diversity and Evolution of Mitochondrial RNA Editing Systems

“…Compared to the situation in plant mitochondria, editing in chloroplasts is much more limited in extent (only 31 edits in tobacco chloroplasts, all C-to-U (24)), even though chloroplast DNA encodes a substantially larger number of ORFs than does plant mitochondrial DNA. Whereas organellar U-to-C editing events are rare or entirely absent in angiosperms and gymnosperms, they are comparatively much more abundant in both mitochondria and chloroplasts of certain primitive land plants, such as the hornwort Anthoceros (25,26).…”