Is clustering of plastid RNA editing sites a consequence of transitory loss of gene function? – Implications for past environmental and evolutionary events in plants

Abstract

Abstract Editing changes individual nucleotides in RNA thereby distinguishing the mature transcript sequence from the corresponding genomic sequence. Most editing events in chloroplasts change cytosine to uracil bases at specific positions in transcripts. In hornwort and fern species uracil to cytosine conversions also take place. RNA editing in plastids probably emerged among the first land plants and affects different genes of different plants in different positions. A significant clustering of editing sites in certain genes is found within related taxa. The clustering is particularly evident in ndh genes in angiosperms, where editing sites account for about 50% of total (near 30) editing sites of plastids and are rather similar in a large number of species. In gymnosperms, ndh genes are edited to a much lower extent, and the few editing sites identified in bryophytes are different from those of angiosperms. On the basis of these data and the role of ndh genes in the protection against photooxidative stress, we make the following hypothesis for the origin and evolution of editing sites: (i) primary mutations accumulated in genes which became dispensable for plants in certain ecosystems; (ii) under changing environments, the functionality of these genes was recovered in some of the descendants by transcript editing; and (iii) secondary mutations led to a subsequent and gradual disappearance of editing sites. Evidence and further tests for this hypothesis are discussed.