Molecular Analysis Of An Rna Editing Cis-Element And Its Trans-Acting Factor

In angiosperm organelles, RNA editing alters specific cytidines to uridines. The mechanism involves recognition of cis-sequences surrounding specific Cs by nuclear-encoded proteins, but the particular molecular interactions and catalytic activities remain unclear. Functional analyses of the cis-elements suggest the upstream sequences act as binding sites for editing trans-factors. One trans-factor, REQUIRED FOR ACCD RNA EDITING 1 (RARE1), is essential for RNA editing in the chloroplast accD transcript. This study examines 19 Brassicaceae species for editing patterns in the accD transcripts and utilizes comprehensive sequence analysis of RARE1 homologs to analyze the evolutionary interaction between the cis-elements and trans-factors. The overall Ka/Ks ratio suggests all orthologous RARE1 genes undergo negative selection although the varying Ka/Ks ratios for individual motifs indicate certain motifs are more conserved. In Brassicaceae species lacking editing at the accD site, RARE1 orthologs show significant sequence variation indicating possible lost editing function or an alternate function