When you can't trust the DNA: RNA editing changes transcript sequences

Abstract

RNA editing describes targeted sequence alterations in RNAs so that the transcript sequences differ from their DNA template. Since the original discovery of RNA editing in trypanosomes nearly 25 years ago more than a dozen such processes of nucleotide insertions, deletions, and exchanges have been identified in evolutionarily widely separated groups of the living world including plants, animals, fungi, protists, bacteria, and viruses. In many cases gene expression in mitochondria is affected, but RNA editing also takes place in chloroplasts and in nucleocytosolic genetic environments. While some RNA editing systems largely seem to repair defect genes (cryptogenes), others have obvious functions in modulating gene activities. The present review aims for an overview on the current states of research in the different systems of RNA editing by following a historic timeline along the respective original discoveries.

Fig. 1

The term “RNA maturation” is used as an umbrella term for different phenomena of biochemical transformations of RNA transcripts. “RNA processing” is mostly used to describe changes affecting sequence stretches of variable length through cutting and rejoining processes such as intron splicing. It is generally also used for the capping and polyadenylation processes at the 5′ and 3′ ends, respectively, of eukaryotic nucleus-encoded mRNAs. The term “modification” in contrast is best reserved for biochemical alterations resulting in nonstandard nucleotides (mostly identified in tRNAs and rRNAs) such as pseudouridine, dihydrouridine, methylated nucleotides, and many more. Finally, “RNA editing” comprises all sequence changes in the four-letter RNA alphabet relative to the gene template other than splicing and polyadenylation that could in principle be encoded in the DNA directly. Overlaps in terminology exist, however: the capping nucleotide is a methylated guanosine added in inverted orientation, stop codons may emerge only after polyadenylation, and inosine nucleotides (read as guanosine) result from deamination of adenosines

Fig. 2

A highly simplified view of the uridine insertion type of RNA editing in kinetoplastid mitochondria. Small, 3′-oligo-uridylated antisense guide RNAs (gRNAs) pairing with a given pre-mRNA carry information on location and number of uridines to be inserted. The (entirely hypothetical) example shown displays a case for insertion of four uridines into the pre-mRNA that are ultimately complementary to the initially unpaired adenosines of the gRNA. The different enzymatic activities for RNA editing are assembled in 20S editosome multi-protein complexes, which come in at least three different variants of protein composition, also depending on the location and mode (U insertion vs. deletion) of editing. The three major biochemical activities for uridine insertion are an endonuclease activity cleaving the pre-mRNA at the site of editing, a terminal uridylyl transferase adding uridylates from UTPs to the free 3′OH end of the upstream part of the pre-mRNA, and a ligase rejoining the transcript ends after editing. In the case of uridine deletion editing, a 3′-uridine-exonuclease of the ~20S editosome comes into play that removes unpaired “extra” uridines from the pre-mRNA, which remained unpaired in the hybrid with the respective gRNA

Fig. 3

Modern insights on plant phylogeny place liverworts as the sister clade to all other land plants (embryophytes) and hornworts as the sister group to vascular plants. A most parsimonious explanation for the evolution of the C-to-U type of plant organelle RNA editing postulates a single gain in the ancestor of all embryophytes (filled circle) and a secondary loss in the marchantiid liverworts (open circle). The reverse type of U-to-C editing arises in the common ancestor of hornworts and tracheophytes (upward triangle) and is strongly decreased in frequency in the seed plant lineage (downward triangle)

Fig. 4

Several plant-specific pentatricopeptide repeat (PPR) proteins of the PLS subgroup with variable repeat motif lengths including short (S) and long (L) variants of the classic 35-amino-acid-long PPR motif (P) and carboxy-terminal protein domain extensions E, E+, and DYW have been shown to be involved in plant organelle RNA editing (bottom). The DYW domain has been proposed to carry the editing (cytidine deaminase) activity, but some PLS proteins without the DYW domain (top) have also been identified as RNA editing site recognition factors. The PPR motifs are assumed to recognize RNA primary sequences, presumably on a one-PPR-repeat-per-nucleotide basis, although the exact binding code is currently unclear. Perhaps more than one PLS protein and/or additional, currently uncharacterized, factors (“X?”) are involved to provide sequence specificity and/or enzymatic activities

Fig. 5

In the different domains of life, several different types of RNA editing act on tRNA molecules, here shown in the general tRNA consensus structure featuring the acceptor stem (top), the dihydrouridine (D) arm (left), the anticodon arm (bottom), the pseudouridine (Ψ) arm (right), and the size-variable arm between the latter two. Pseudouridine and dihydrouridine are only two examples of the more than 100 different types of nucleotide modifications, besides frequent base methylations, described for tRNAs (and rRNAs); many of these also occur in the tRNA acceptor stems [264]. The deamination type of C-to-U and A-to-I nucleotide conversions obscures the boundary in the definition of modification versus editing. Anticodon positions in the tRNA consensus are 34, 35, and 36; the 3′ terminal (discriminator) nucleotide is number 73 to which the CCA (italics) end for subsequent aminoacylation is normally added after tRNA 3′-processing. Main size variations are introduced by the size-variable arm and occasional additional nucleotides in the dihydrouridine arm. The nucleotide replacement type of editing in the 5′ half of the acceptor stem has been identified in the protist Acanthamoeba castellanii and in chytridiomycete fungi. RNA editing of the A-to-I deamination type in the anticodon (bold) altering codon recognition appears common; the C-to-U deamination type of editing was initially observed in marsupials. Cytidine-to-uridine base exchanges of the deamination type may affect many different tRNA positions in plant organelles, the most prominent example being 18 C-to-U exchanges in the mitochondrial tRNA-Pro in the lycophyte Isoetes engelmannii [88]. Similarly, the cytidine or uridine insertion type of editing in myxomycetes can affect all regions of a tRNA molecule. Correction of acceptor stem base pairing in the 3′ half of the stem seems to involve different biochemical activities in different organisms, including oligo-adenyl-transferase, terminal CCA-transferase, or RNA-directed RNA polymerase. Editing of cytidine to the universally conserved uridine nucleotide in position 8 (bold underlined) has recently been shown for the majority of tRNAs in the archaeon Methanopyrus kandleri