RNA editing by adenosine deaminases generates RNA and protein diversity
Introduction
RNA editing has been defined as a co- or post-transcriptional RNA processing reaction other than capping, splicing or 3′-end formation that changes the nucleotide sequence of the RNA substrate. RNA editing reactions occur in many organisms and operate by different molecular mechanisms, either by insertion or deletion of nucleotides or by base modification. The first case of RNA editing discovered was the insertion and deletion of uridine nucleotides in trypanosome mitochondrial mRNAs, which is required to generate functional proteins 〚1〛, 〚2〛. Base conversion appears to be the major type of RNA editing in the nucleus of higher eukaryotes 〚3〛 and the best-characterized reactions are hydrolytic deaminations 〚4〛, 〚5〛, 〚6〛 where a genomically encoded cytidine (C) or adenosine (A) is converted to uridine (U) and inosine (I), respectively 〚7〛, 〚8〛, 〚9〛 (see Fig. 1 for the A to I reaction mechanism).
The nucleoside inosine was first detected in cytoplasmic tRNA 〚10〛, 〚11〛 and later in messenger RNA precursors (pre-mRNAs) and in viral transcripts 〚8〛, 〚9〛, 〚12〛. Only a few pre-mRNA substrates have been identified. Nevertheless, it has been estimated that IMP is present at high amounts in rat poly(A)+ RNAs, particularly in brain, where one IMP is present for every 17,000 nucleotides, suggesting an important role for adenosine deamination 〚13〛. Indeed, it is clear that the impact of such a conversion in a tRNA or a pre-mRNA can be significant. Inosine in tRNA anticodons is believed to play a crucial role in translation by enlarging the codon recognition capacity, increasing the decoding efficiency and preventing frameshifts 〚14〛, 〚15〛, 〚16〛. A to I conversions in pre-mRNA coding or non-coding sequences (introns, UTRs) can alter the specificity of a codon or can affect splicing, generating protein isoforms with different functions not expected from the corresponding genomic sequence 〚8〛, 〚9〛, 〚12〛, 〚17〛. Thus, the consequences of RNA editing challenged the idea that the gene number is the major determinant to generate RNA and protein diversity in an organism.
In this review, we focus on the A to I conversion reactions and provide an overview of the superfamily of RNA-dependent adenosine deaminases which catalyse the reaction and their known substrates, the mechanism of action of these enzymes and also the effects of this widespread modification on the function of the target transcripts.
Section snippets
The enzymes
The enzymes catalysing A to I conversion in pre-mRNAs are known as adenosine deaminases that act on RNA (ADARs) 〚18〛. These enzymes form a protein family with members throughout the metazoan kingdom. In humans, three ADARs and their corresponding genes were identified, ADAR1, ADAR2 and ADAR3 〚8〛, 〚9〛, 〚17〛, whereas in lower metazoan organisms, such as Drosophila melanogaster 〚19〛 or Caenorhabditis elegans 〚20〛, only one ADAR gene has been found. ADAR1 and ADAR2 are expressed in almost all cell
The substrates
Studies to identify modified nucleosides in tRNAs led to the detection for the first time in yeast tRNAAla of inosine at position 34 (the first anticodon position or wobble position) and N1-methylinosine (m1I) at position 37 (3′ adjacent to the anticodon) 〚10〛, 〚11〛 (Table 1, Fig. 4b). m1I formation at position 37 occurs in two steps, adenosine deamination followed by methylation 〚11〛, 〚100〛. Further investigations revealed that inosine was present either in all eukaryotic tRNAAla at these two
Evolution
The catalytic domain of ADARs and ADATs, even though these enzymes are specific for adenosine, shows the sequence signatures of cytidine deaminases acting on mononucleotides (CDAs) or on RNA (CDARs) and not those of adenosine deaminases acting on mononucleotides (ADAs) 〚8〛, 〚110〛 (Fig. 3). However, ADAR and ADAT1 deaminase domain sequences appeared to be more related to each other than to those of CDAs, CDARs and other ADATs (Fig. 3). In contrast, the deaminase domains of ADAT2 and ADAT3 show a
Conclusions
RNA editing is now recognized as an important mechanism to generate RNA and protein diversity. Different means are used by ADARs to modify the genomically encoded information. ADAR-mediated A to I editing can selectively alter codon specificity when taking place within mRNA coding regions and seemingly subtle changes in amino acid sequences can affect the functional properties of the corresponding proteins. Considering the fact that in vivo editing ranges from a few percent to almost 100% and
Acknowledgments
We thank Mary O'Connell for critically reading the manuscript. Work in the authors' laboratory is supported by the University of Basel, the Swiss National Science Foundation and the Louis-Jeantet-Foundation for Medicine. Myriam Schaub is the recipient of a fellowship from the Association pour la Recherche sur le Cancer (ARC) and the Human Frontier Science Program (HFSP) Organization.
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