Email updates

Keep up to date with the latest news and content from Genome Biology and BioMed Central.

Protein family review

Adenosine deaminases acting on RNA (ADARs): RNA-editing enzymes

Liam P Keegan*, Anne Leroy, Duncan Sproul and Mary A O'Connell

Author Affiliations

Medical Research Council Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK

For all author emails, please log on.

Genome Biology 2004, 5:209  doi:

The electronic version of this article is the complete one and can be found online at: http://genomebiology.com/2004/5/2/209


Published:2 February 2004

© 2004 BioMed Central Ltd

Summary

Adenosine deaminases acting on RNA (ADARs) were discovered as a result of their ability extensively to deaminate adenosines in any long double-stranded RNA, converting them to inosines. Subsequently, ADARs were found to deaminate adenosines site-specifically within the coding sequences of transcripts encoding ion-channel subunits, increasing the diversity of these proteins in the central nervous system. ADAR1 is now known to be involved in defending the genome against viruses, and it may affect RNA interference. ADARs are found in animals but are not known in other organisms. It appears that ADARs evolved from a member of another family, adenosine deaminases acting on tRNAs (ADATs), by steps including fusion of two or more double-stranded-RNA binding domains to a common type of zinc-containing adenosine-deaminase domain.

Gene organization and evolutionary history

ADAR genes in chordate and invertebrate genomes

The role of ADARs is to deaminate adenosine to inosine non-specifically in long double-stranded RNA (dsRNA) or site-specifically in transcripts. Non-specific adenosine deamination has a role in defence against viruses that have dsRNA stages in their life-cycle [1], as hypermutation of the viral genome by adenosine-to-inosine conversion disrupts viral open reading frames. The second role of ADARs, site-specific deamination of individual adenosines in pre-mRNAs, can change individual codons in open reading frames, including start or stop codons, or it may affect splicing or untranslated regions [2].

The first ADAR gene to be identified was the vertebrate ADAR1. The protein was purified from Xenopus, bovine liver and calf thymus using non-specific deamination of dsRNA as an assay [3-5], and peptide-sequence information was used to design PCR primers to clone the gene [6,7]. The ADAR1 gene was found to encode three double-stranded-RNA binding domains (dsRBDs) and a deaminase domain with zinc-binding motifs (Figure 1), similar to those of zinc-dependent cytosine deaminases and to the cytosine-to-uracil RNA-editing enzyme APOBEC1. The first example of site-specific editing, in a pre-mRNA encoding the vertebrate glutamate-receptor subunit GluR-B, was found at the same time; editing converts a glutamine codon to an arginine codon (Q to R in the single-letter amino-acid code) [8]. ADAR1 was unable to catalyze site-specific editing of the Q/R editing site in the GluR-B transcript in vitro, however. This observation led to the idsentification of ADAR2, which edits the GluR-B Q/R site specifically [9,10]. ADAR2 contains two dsRBDs and an adenosine-deaminase domain (Figure 1). Other ADAR genes in vertebrates and ADAR genes in other organisms were identified either by PCR using primers derived from the deaminase motifs or by sequence homology.

thumbnailFigure 1. Primary structures of ADARs and ADATs (adenosine deaminases acting on tRNAs), showing arrangements of dsRNA-binding domains and deaminase domains. The deaminase motifs (I-III) consist of four or five highly conserved amino acids surrounding each of the cytosines and histidines that bind zinc. Proteins have been drawn to scale and are aligned at the catalytic glutamate residue (E) in the active site in adenosine deaminase motif I. The deaminase domains of ADAR and ADAT1 proteins are larger than the core deaminase domain (which we define as the region of homology between Tad2/ADAT2 and Tad3/ADAT3) because of the insertion of sequence between the second and third zinc-chelating residues, separating deaminase motifs II and III, and probably also because of fusion with a carboxy-terminal subdomain of unknown origin. Abbreviation: aa, amino acids.

There are two ADAR-like genes in vertebrate genomes, encoding enzymes with unknown function. The ADAR3 gene, also called Red2, is very similar to ADAR2 (Figure 2) [11]. It has all the key conserved residues that are known to be required for catalysis, but it has been shown to lack non-specific and site-specific dsRNA adenosine-deaminase activity [12]. ADAR3 may have arisen from ADAR2 by gene duplication within the chordate lineage. ADAR3 is very well conserved in fish genomes, even though no function has been ascribed to it, suggesting that it is active on an unknown substrate. A fourth ADAR-like gene in vertebrates, TENR, is expressed in the male germline and has only one dsRBD [13]. TENR lacks a key catalytic glutamate residue in the deaminase domain and also lacks zinc-chelating residues; the protein has not been characterized. We have been able to identify TENR genes only in mammalian and not in fish genomes.

thumbnailFigure 2. A phylogenetic tree of core deaminase sequences. Protein sequences that are predicted from genomic sequences rather than from full cDNA sequences are indicated by asterisks. The vertebrate genes listed include one from the crab-eating monkey Macacus fascicularis. The fish genomes examined are from the zebrafish Danio rerio and pufferfish, Takifugu rubripes and Tetraodon fluviatilis. Two tunicate genomes have been examined, from Ciona intestinalis and Ciona savigni. One squid (Loligo pealeii) is included (J. Rosenthal, personal communication). The insect genomes are of the two Drosophila species, Drosophila melanogaster and Drosophila pseudoobscura, and the malaria mosquito Anopheles gambiae. Alignments were made using T-COFFEE, the boundaries of the core deaminase domain were specified and a tree based on the alignment was generated using MEGA. Bootstrap values are given on all branches.

The presence of four ADAR genes in vertebrates represents a degree of gene-family expansion in the chordate lineage similar to that found in many other gene families, notably including the cytosine deaminases acting on RNA (CDARs) [14]. The vertebrate ADAR genes are unlinked in the genome, but some chordate genomes contain multiple copies of particular ADAR genes: for example, the Xenopus genome, which is large and not completely sequenced, contains two ADAR1 genes, and Takifugu rubripes has two ADAR2 genes.

The Drosophila genome encodes one ADAR, which has two dsRBDs and a deaminase domain and is more similar to vertebrate ADAR2 than to ADAR1 [15]. We searched for ADAR genes in the complete genome sequences of the primitive chordates Ciona intestinalis and Ciona savigni (our unpublished work); predicted deaminase domains were found that seem to correspond to ADAR1 and ADAR2 as well as a separate ADAT1 gene (see below; Figure 2) [16]. We have not proven that these are full ADAR1 genes, because there is no cDNA sequence available for them and because the full genes with dsRBDs are difficult to predict from the genome sequence. ADAR1-like deaminase domains are clearly present in basal chordates, however. This is a little surprising and argues against the idea that ADAR1 and ADAR2 diverged from a parental gene during the period of widespread gene duplications in early vertebrate evolution; it suggests, instead, that the ADAR duplication occurred earlier (our unpublished work). An ADAR2 gene has been cloned from the squid Loligo pealeii, but it is not clear whether squid also have an ADAR1 gene.

The genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae contain two ADAR genes, adr1 and adr2 [17]. The deaminase domains of ADR1 and ADR2 are not closely related to each other, and their names do not reflect a direct correspondence with vertebrate ADAR1 and ADAR2 proteins; the sequences differ so much from vertebrate ADARs that it is impossible to make such links (Figure 2). Both adr1 and adr2 are required for editing activity in vivo, and the proteins may form heterodimers. ADR1 has two dsRBDs; ADR2 has only one and lacks the active-site glutamate. The C. elegans adr1 gene structure shows some resemblance to the Drosophila Adar gene, however. In addition to encoding an ADAR with two dsRBDs, C. elegans adr1, like Drosophila Adar, produces several isoforms by alternative 3' splice-site usage affecting the sequence between the dsRBDs.

Human ADAR1 has two transcription start sites and two promoters, leading to production of a shorter isoform that lacks the first 296 residues of the long form (Figure 1). The first 530 amino acids of human ADAR1, up to the middle of the first dsRBD, is encoded by a single exon. Interestingly, each of the regions encoding the three dsRBDs in ADAR1 is interrupted in the middle by an intron in a conserved position, suggesting that they could have arisen by duplication of a pair of exons. The deaminase motifs are encoded on separate exons. Human ADAR2 has both dsRBDs on one exon, as does ADAR3. As in human ADAR1 the deaminase motifs are encoded on separate exons but intron positions in the deaminase domain are not well conserved between human ADAR1 and ADAR2. Human ADAR2 produces two isoforms one of which (ADAR-2L) has an exonized Alu sequence that inserts an additional 40 amino acids between the second and third deaminase motifs (the ADAR2-S form lacking the Alu sequence is shown in Figures 1 and 3). These splice variants should not be confused with the two distinct ADAR2a and ADAR2b genes found in the genome of T. rubripes. Alternative splice forms of ADAR3 or TENR have not been described.

thumbnailFigure 3. An alignment of core deaminase domains from vertebrate ADAR1 and ADAR2 proteins, showing residues characteristic for each. Asterisks indicate cysteines and histidines that chelate zinc, as in Figure 1, and the three active-site motifs are bracketed.

Evolution of ADAR genes from ADAT genes

So far, ADARs have been found only in multicellular animals; they are clearly absent from yeast and have not been reported in protozoa. Searches in the yeast and Drosophila genomes for proteins with ADAR-type deaminase motifs led to the identification of an adenosine deaminase acting on tRNA (Tad1/ADAT) that deaminates adenosine to inosine in tRNAAla at position 37, adjacent to the anticodon [16]. ADAT1 has an adenosine-deaminase domain but lacks dsRBDs. Our present view of ADAR evolution is that the first ADAR evolved in protozoans or lower multicellular animals from an ADAT1-like protein by acquisition of dsRBDs and residue changes in the adenosine-deaminase domain.

Editing also occurs at position 34 within the anticodons of several vertebrate tRNAs. Searches for adenosine-deaminase domain sequences in the yeast genome led to the identification of Tad2/ADAT2, which, as a heterodimer with Tad3/ADAT3, deaminates position 34 of tRNAs. This is the wobble base-pairing position in the anticodons of seven tRNAs in yeast [18]. Unlike ADAT1, the ADAT2 and ADAT3 proteins are essential in yeast. The loop between deaminase motifs II and III of the ADARs and ADAT1 is absent from ADAT2 and ADAT3 (Figure 1). A deaminase domain with motifs II and III closer together is characteristic of the free-nucleotide cytosine deaminases and CDARs such as APOBEC1 and its relatives. The presence of such a domain in CDARs and ADATs further supports the idea that ADARs, ADATs and CDARs had a common ancestor [19]. Only ADAT2, and not ADAT3, has the conserved glutamate residue associated with adenosine deaminase motif I, so the heterodimer has only one active site.

ADAT1, ADAT2 and ADAT3 are present in all eukaryotes examined, although we have not found any sequence encoding an ADAT1 in the nematode genomes. ADAT2 and ADAT3 are homologous to each other over a stretch of 120 amino acids containing the deaminase motifs, but the remaining parts of the proteins are not clearly homologous to one another or to the larger deaminase domains of ADAT1s or ADARs. The carboxy-terminal region in vertebrate ADAT2 proteins is even shorter than in the yeast ADAT2 proteins. We have taken the region of homology between ADAT2 and ADAT3 to define a core deaminase domain and used protein sequence alignments of this region to construct the evolutionary tree shown in Figure 2.

An Escherichia coli homolog of ADAT2, tadA, forms homodimers and is able to edit position 34 in tRNAArg2, which is the only known target in E. coli [20]. The evolution of a heterodimeric ADAT2/ADAT3 in eukaryotes, presumably from a tadA-like precursor, coincided with an increase in the number of tRNAs that have inosine at the wobble position. In higher eukaryotes, eight tRNA classes are edited, and these are encoded by multi-copy genes, so the total number of tRNA gene transcripts edited is 111 in C. elegans and 56 in D. melanogaster [21].

The tadA protein edits a minisubstrate consisting of the anticodon stem-loop of E. coli tRNAArg2 [20]. ADAT1 from yeast, however, clearly requires other parts of the tRNA in addition to the anticodon stem and loop, and it evidently recognizes a longer portion of the tRNA substrate [16]. The definition of ADARs and ADATs on the basis of whether their substrate is tRNA or mRNA does not coincide with classification based on the structures of their deaminase domains and their interactions with RNA. ADAT2 and ADAT3 are different in size, structure and mode of interaction with tRNA from ADAT1, which has a clearly ADAR-like deaminase domain. The ADAT1-type deaminase could have evolved from an ADAT2-like protein in one of two ways: either a loop was inserted between the second and third zinc-chelating residues to give ADAR deaminase motif III, or ADARs have a hybrid active site created by fusion of another protein at what is now the loop, with ADAR motif III and the carboxy-terminal part of the deaminase domain deriving from another protein.

Inosine has been found in archaeal tRNA [21,22], so the core adenosine-deaminase domain may be very ancient. Inosine could have been produced easily from adenosine even earlier, by RNA-mediated catalysis, and inosine may have been excluded rather than unavailable when the canonical base set for Watson-Crick base-pairing evolved to give unambiguous rules for RNA replication. The wobble base-pairing of tRNAs now appears to be a means to economize on tRNAs rather than a relic of some ancient type of translation apparatus, as the inosine in archaeal tRNA is not in the anticodon. In eukaryotes, there have been two rounds of evolutionary expansion in targets of the inosine-producing RNA-editing apparatus, first to increase the number of tRNAs edited at the anticodon wobble position by Tad2/ADAT2 and Tad3/ADAT3 and second (in animals) to include pre-mRNAs and dsRNA as targets of ADARs.

Characteristic structural features

The adenosine deaminase domain

Experimental exchanges of the deaminase domains of ADAR1 and ADAR2 have shown that the deaminase domain determines the difference in specificity between the two proteins [23]. With the availability of more genomic sequences, we have aligned 14 different sequences of ADAR1 and ADAR2 deaminase domains and found a high degree of conservation in a region of 179 amino acids (Figure 3). The amino acids that are downstream of the second deaminase motif appear to specify the enzyme that is encoded. The sequence differences between ADAR1 and ADAR2 that are highlighted (Figure 3) make it possible to assign newly sequenced vertebrate ADAR genes as ADAR1 or ADAR2 orthologs, even in cases in which there in no full-length cDNA sequence and the number of dsRNA-binding domains is not known. With this obvious difference close to the catalytic site, it is not surprising that ADAR1 and ADAR2 show very little overlap in the specific sites they edit in transcripts, despite the fact that they both perform the same enzymatic activity. The three active site sequence motifs are particularly characteristic of ADARs. Each motif contains a cysteine or histidine that is thought to chelate zinc at the active site (asterisks in Figure 3); the first deaminase motif (CHAE) includes a glutamate (E) that is required for catalysis.

Structural information is available for one E. coli free-nucleotide cytosine deaminase [24]. This protein has deaminase-domain motifs similar to ADAT2 and tadA and dimerizes so that each monomer contributes to form the active site; it has very little homology to ADARs apart from the zinc-binding motifs, and it is not clear whether the ADARs dimerize in an equivalent way around the active site. The additional sequence between motif II and motif III in ADARs may be incompatible with this mechanism of dimerization. Structural information from this cytosine deaminase cannot be used reliably to model ADAR deaminase domains but may be more useful for modeling the deaminase domains of ADAT2 and ADAT3.

We do not know how the deaminase domain interacts with RNA. The ADAR2 deaminase domain without dsRBDs is capable of site-specific editing in vivo [25], and the same is true of the Drosophila ADAR deaminase domain (G. Ring and M.O'C., unpublished observations). The ADAR deaminase domain was therefore a dsRNA-binding domain even before it acquired dsRBDs. It clearly evolved from ADAT1 [19], but the residues responsible for binding to tRNA in ADAT1 and in the heterodimer ADAT2/ADAT3 are as yet unknown. Considering the sequence homology between the ADARs and ADAT1, the intriguing possibility arises that recognition of pre-mRNA and tRNA substrates by these proteins follows a common structural model. Both ADARs and ADAT1 probably flip the target adenosine out of the DNA and into the enzyme's active site; studies with a fluorescent adenine analog at a second GluR-B DNA-editing site (the R/G site) are consistent with base-flipping by ADAR2 [26,27]. (The R/G site is separated from the Q/R site and is more experimentally accessible.) Consistent with this idea, some similarity to DNA methyltransferases that flip out the target base has been found in the deaminase domain of ADARs [13].

Double-stranded RNA-binding domains

DsRBDs are not diagnostic of ADARs, as they occur in a very wide variety of proteins [28]. The number of dsRBDs and the sequence conservation within them and in the linkers connecting them help to distinguish ADAR1 and ADAR2 homologs in vertebrate genomes, however. X-ray crystal-structure determination and nuclear magnetic resonance (NMR) analysis of dsRBD-RNA complexes have revealed that the dsRBDs of other proteins bind non-sequence-specifically to the sugar phosphate backbone of dsRNA [29,30]. It was therefore surprising when it was demonstrated in vitro that the two dsRBDs of ADAR2 recognize the R/G site in GluR-B with some specificity, even in the absence of the deaminase domain [27]. Binding of the dsRBDs alters the conformation of the substrate around the edited position; this is thought to aid base-flipping.

One feature of dsRBDs is that they are multi-functional and are not equivalent to each other. Some have evolved to become protein-protein-interaction domains [28]. The amino terminus and the first dsRBD of Drosophila ADAR are required for dimerization in a similar way to the dimerization of dsRNA-dependent protein kinase (PKR) via its dsRBDs [31,32]. The third dsRBD of ADAR1 contains a novel nuclear localization sequence [33].

Localization and function

ADARs are primarily nuclear proteins, but ADAR1 is expressed in two forms and the longer isoform (which is inducible by interferon) is found predominantly in the cytoplasm [34]. The shorter form is a shuttling protein that cycles in and out of the nucleus; blocking its export causes accumulation in the nucleus [35,36]. ADAR1 (both forms) and ADAR2 can accumulate in the nucleolus [36,37]; this accumulation is dependent on binding to RNA, probably non-specifically in the nucleolus. Transfection of HeLa cells with transcripts that are known to be edited causes both ADAR proteins to relocate from the nucleolus to the nucleoplasm, suggesting that the nucleolus could be a site of accumulation or storage of the proteins when substrate is limiting [36].

The known function of the vertebrate ADARs is to edit transcripts expressed in the central nervous system. The paradigmatic example of site-specific RNA editing is the editing of the GluR-B Q/R site by ADAR2 [8]. Glutamate is the major excitatory neurotransmitter in the vertebrate brain, and GluR-B encodes a subunit of the α-amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA) class of glutamate receptors, which are heterotetramers formed from subunits encoded by several genes. The Q/R editing event changes a key residue within the ion pore of the channel; the unedited Q form of the GluR-B subunit renders AMPA receptors more permeable to calcium ions. The Q/R editing site in the GluR-B transcript in vertebrates is the only known site that is edited more than 99.9% of the time. Studies on knockout mice show that the GluR-B transcript must be edited when it is present [38], but mice with deletions of the GluR-B gene are viable because of redundancy with other subunit genes [39].

Gene-targeting studies in mice show that ADAR2 is required primarily for site-specific editing at the GluR-B Q/R site [38]. Mice with mutations in ADAR2 die as pups, suffering from epilepsy-like seizures and localized neurodegeneration in the hippocampus [38]. These phenotypes are consistent with calcium influx through AMPA receptors. The defects in ADAR2 mutant mice are rescued by expression GluR-B(R). More recently, studies in which mutated forms of GluR-B were expressed in hippocampal-cell cultures have shown that the unedited GluR-B(Q) isoform completes the tetramer formation required to move from the endoplasmic reticulum to the synapse much more quickly than edited GluR-B(R) isoform. RNA editing thereby restricts trafficking of AMPA receptors to the cell membrane [40,41], affecting an important aspect of plasticity at glutamatergic synapses.

The transcript encoding the metabotropic serotonin receptor 5-HT2C is also edited site-specifically by both ADAR1 and ADAR2, in a region involved in coupling to G-proteins [42]. This target has generated considerable recent interest because levels of editing may be influenced by factors that alter levels of serotonin in the brain, such as depression [43]. Very recent gene-targeting experiments on mouse ADAR1 show that ADAR1 does contribute to site-specific editing and that the gene is essential [44,45]. Mutant embryos die at embryonic day 12.5 with hematopoiesis defects and liver degeneration. Cultured cells from a variety of different tissues in ADAR1 mutant mice undergo stress-induced apoptosis in response to serum starvation. It is not known whether this phenotype arises from failure to edit some unknown site-specific anti-apoptotic RNA-editing target or from failure of a more generalized non-specific RNA-editing activity. The reasons to think ADAR1 might have a wider role than ADAR2 include, in addition to the more severe knockout phenotype [44,45], more widespread expression, an additional promoter for interferon-inducible transcripts and additional Z-DNA binding domains in ADAR1 [46].

From the search for homologs of ADARs in other species (Figure 2), it becomes apparent that ADAR3 and TENR are probably functional. Both are thought not to have any enzymatic activity on dsRNA, but ADAR3 is conserved between fish and mammals, and TENR is found in mammals and is testis-specific. Considering the importance of APOPEC-3G [47], which was regarded for many years as a non-functional editing enzyme but now appears to be a DNA-editing enzyme active against human immunodeficiency virus (HIV), these ADAR orphans may yet surprise us.

Mechanism

The ADAR enzymes probably bind to many transcripts non-productively, as binding and catalysis are independent events [48,49]. Until recently, it was thought that ADARs bind to editing sites as monomers, because ADARs are purified as monomers and because the pre-mRNAs that are edited do not contain any obviously symmetrical RNA sequence that would suggest binding by a dimer. Recent work from many groups has demonstrated, however, that the catalytic ADAR is a dimer [50-52]. Yeast two-hybrid studies with Drosophila ADAR show that ADAR dimerizes using the first dsRBD and sequences amino-terminal to it [52]. Studies in vitro indicate that dimerization requires RNA binding and that ADAR must be a dimer on RNA to be enzymatically active. It is not known whether the minimal dimerization region of one monomer contacts the equivalent part of another monomer or a different part of the protein, such as the deaminase domain.

The dimerization of ADARs is probably what controls the specificity of editing, as two monomers must bind for catalysis to occur. This dimerization model predicts that if another adenosine was placed approximately 17 base-pairs away from a known edited site, this adenosine would also be edited. Evidence consistent with this model comes from an experiment by Herbert and Rich [25], in which multiple base changes in the GluR-B R/G substrate 16-19 base-pairs away from the R/G site created new editing sites at these positions and also affected editing at the R/G site itself so that an adjacent adenosine was now also edited.

Frontiers

There are important questions that remain to be answered regarding the structures, substrates and regulation of ADARs and on the links between RNA editing and RNA interference. The structure of an adenosine-deaminase domain from an ADAR or ADAT1 protein remains to be elucidated. The details of how the multiple domains in ADARs interact with substrate RNA must be resolved either with ADAR-RNA cocrystals or structure-function studies guided by the structures of the individual domains. Structural information on a CDAR will also be necessary to resolve finally the relationship between ADARs and the other members of the cytosine deaminase superfamily.

There are likely to be many more transcripts in humans that are edited than have been found so far. Comparison of the human genome with another suitably distant chordate genome sequence is likely to identify them, as indicated by the recent success in using comparison of Drosophila genome sequences to identify 24 novel transcripts with editing at 53 individual sites [53]. Exons encoding editing sites have reduced levels of synonymous codon substitution and are more highly conserved than exons in general, because of the requirement for an RNA duplex. When genomic sequences of D. melanogaster and D. pseudoobscura genes encoding ion-channel subunits and synaptic-vesicle fusion proteins were compared [53], edited exons were identified by their higher conservation. Using this method on the human genome requires identifying a vertebrate genome with sufficient sequence divergence from ours.

Discovering regulatory mechanisms for RNA-editing activity is a key issue in explaining why RNA editing occurs. Editing is certainly tissue-specific - as shown by the expression patterns of ADARs and their substrates - and the expression of the interferon-inducible form of ADAR1 is increased by interferon, viral infection, or dsRNA, but there may be further levels of regulation, particularly in neurons. Understanding regulation may also relate A-to-I RNA editing to other types of editing in mitochondria and chloroplasts that are mechanistically very different but might have some parallel evolutionary rationale.

Work on the C. elegans ADARs implicates RNA editing in the antagonizing of RNA interference [54,55]. ADAR RNA editing is part of a wider biology of dsRNA that has gained renewed attention since the discovery of RNA interference. Double-stranded RNA genomes are now found only in some viruses, and higher eukaryotic cells recognize dsRNA as a hallmark of infection, but dsRNA genomes may have been more widespread in the very distant past. Proteins that recognize the A-form structure of dsRNA are very different from, and some of them may be much more ancient than, the large number of proteins that recognize the B-form helix of DNA. The core deaminase domain of ADARs and ADATs seems to be an ancient protein domain that, like RNA-dependent RNA polymerase and other dsRNA-binding proteins of the RNA interference system, has acquired new roles in recognizing dsRNA genomes as foreign. The conjunction of RNA editing and RNA interference is a lively area for further research. Thus, the study of RNA editing continues to raise fascinating questions about the evolution of genomes, and is likely to give insights into a range of other areas in the near future.

References

  1. Kumar M, Carmichael GC: Nuclear antisense RNA induces extensive adenosine modifications and nuclear retention of target transcripts.

    Proc Natl Acad Sci USA 1997, 94:3542-3547.

    Polyoma virus dsRNA is retained in the nucleus when extensively edited.

    PubMed Abstract | Publisher Full Text OpenURL

  2. Keegan LP, Gallo A, O'Connell MA: The many roles of an RNA editor.

    Nat Rev Genet 2001, 2:869-878.

    A review on A-to-I and to U RNA editing, emphasizing the similarities; it predates most of the recent work on DNA C-to-U editing.

    PubMed Abstract | Publisher Full Text OpenURL

  3. Hough RF, Bass BL: Purification of the Xenopus laevis dsRNA adenosine deaminase.

    J Biol Chem 1994, 269:9933-9939.

    This article and [4,5] describe the purification of ADAR1.

    PubMed Abstract | Publisher Full Text OpenURL

  4. Kim U, Garner TL, Sanford T, Speicher D, Murray JM, Nishikura K: Purification and characterization of double-stranded RNA adenosine deaminase from bovine nuclear extracts.

    J Biol Chem 1994, 269:13480-13489.

    See [3].

    PubMed Abstract | Publisher Full Text OpenURL

  5. O'Connell MA, Keller W: Purification and properties of double-stranded RNA-specific adenosine deaminase from calf thymus.

    Proc Natl Acad Sci USA 1994, 91:10596-10600.

    See [3].

    PubMed Abstract | Publisher Full Text OpenURL

  6. Kim U, Wang Y, Sanford T, Zeng Y, Nishikura K: Molecular cloning of cDNAs for double-stranded RNA adenosine deaminase, a candidate enzyme for nuclear RNA editing.

    Proc Natl Acad Sci USA 1994, 91:11457-11461.

    This article and [7] describe the cloning of ADAR1.

    PubMed Abstract | Publisher Full Text OpenURL

  7. O'Connell MA, Krause S, Higuchi M, Hsuan JJ, Totty NF, Jenny A, Keller W: Cloning of cDNAs encoding mammalian double-stranded RNA-specific adenosine deaminase.

    Mol Cell Biol 1995, 15:1389-1397.

    See [6].

    PubMed Abstract | Publisher Full Text OpenURL

  8. Higuchi M, Single FN, Köhler M, Sommer B, Sprengel R, Seeburg PH: RNA editing of AMPA receptor subunit GluR-B: a base-paired intron-exon structure determines position and efficiency.

    Cell 1993, 75:1361-1370.

    This article describes the structure required for editing at the GluR-B Q/R site.

    PubMed Abstract OpenURL

  9. Melcher T, Maas S, Herb A, Sprengel R, Seeburg PH, Higuchi M: A mammalian RNA editing enzyme.

    Nature 1996, 379:460-464.

    The cloning of ADAR2 using ESTs.

    PubMed Abstract | Publisher Full Text OpenURL

  10. O'Connell MA, Gerber A, Keller W: Purification of human double-stranded RNA-specific editase1 (hRed1), involved in editing of brain glutamate receptor B pre-mRNA.

    J Biol Chem 1997, 272:473-478.

    The purification of ADAR2 from HeLa nuclear extracts.

    PubMed Abstract | Publisher Full Text OpenURL

  11. Melcher T, Maas S, Herb A, Sprengel R, Higuchi M, Seeburg PH: RED2, a brain specific member of the RNA-specific adenosine deaminase family.

    J Biol Chem 1996, 271:31795-31798.

    This article and [12] describe the cloning of ADAR3.

    PubMed Abstract | Publisher Full Text OpenURL

  12. Chen CX, Cho DS, Wang Q, Lai F, Carter KC, Nishikura K: A third member of the RNA-specific adenosine deaminase gene family, ADAR3, contains both single- and double-stranded RNA binding domains.

    RNA 2000, 6:755-767.

    See [11].

    PubMed Abstract | Publisher Full Text OpenURL

  13. Hough RF, Bass BL: Analysis of Xenopus dsRNA adenosine deaminase cDNAs reveals similarities to DNA methlytransferases.

    RNA 1997, 3:356-370.

    A proposal that the carboxy-terminal part of ADAR deaminase domains resembles proteins that flip out and methylate bases in DNA.

    PubMed Abstract | Publisher Full Text OpenURL

  14. Jarmuz A, Chester A, Bayliss J, Gisbourne J, Dunham I, Scott J, Navaratnam N: An anthropoid-specific locus of orphan C to U RNA-editing enzymes on chromosome 22.

    Genomics 2002, 79:285-296.

    The identification of multiple genes homologous to APOBEC.

    PubMed Abstract | Publisher Full Text OpenURL

  15. Palladino MJ, Keegan LP, O'Connell MA, Reenan RA: dADAR, a Drosophila double-stranded RNA-specific adenosine deaminase is highly developmentally regulated and is itself a target for RNA editing.

    RNA 2000, 6:1004-1018.

    The cloning of Drosophila Adar.

    PubMed Abstract | Publisher Full Text OpenURL

  16. Gerber A, Grosjean H, Melcher T, Keller W: Tad1p, a yeast tRNA-specific adenosine deaminase, is related to the mammalian pre-mRNA editing enzymes ADAR1 and ADAR2.

    EMBO J 1998, 17:4780-4789.

    Tad1p, identified from genomic sequences, shows a clear evolutionary relationship to ADARs. This paper also includes RNA-interaction studies.

    PubMed Abstract | Publisher Full Text OpenURL

  17. Tonkin LA, Saccomanno L, Morse DP, Brodigan T, Krause M, Bass BL: RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans.

    EMBO J 2002, 21:6025-6035.

    The identification of C. elegans adr1 and adr2 genes and a description of the behavioral phenotypes associated with mutants.

    PubMed Abstract | Publisher Full Text OpenURL

  18. Gerber AP, Keller W: An adenosine deaminase that generates inosine at the wobble position of tRNAs.

    Science 1999, 286:1146-1149.

    The cloning of Tad2 from genomic sequence and of Tad3 after purification of the protein complex.

    PubMed Abstract | Publisher Full Text OpenURL

  19. Gerber AP, Keller W: RNA editing by base deamination: more enzymes, more targets, new mysteries.

    Trends Biochem Sci 2001, 26:376-384.

    A review of ADARs and ADATs, discussing the evolutionary relationships.

    PubMed Abstract | Publisher Full Text OpenURL

  20. Wolf J, Gerber AP, Keller W: tadA, an essential tRNA-specific adenosine deaminase from Escherichia coli.

    EMBO J 2002, 21:3841-3851.

    The cloning of E. coli tadA and RNA-interaction studies.

    PubMed Abstract | Publisher Full Text OpenURL

  21. Marck C, Grosjean H: tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anti-codon-sparing strategies and domain-specific features.

    RNA 2002, 8:1189-1232.

    Analysis of tRNA genes in 50 genome sequences shows that wobble base-pairing and inosine in the anticodon allow eukaryotes to read the 61 sense codons using smaller sets of tRNAs.

    PubMed Abstract | Publisher Full Text OpenURL

  22. Grosjean H, Auxilien S, Constantinesco F, Simon C, Corda Y, Becker HF, Foiret D, Morin A, Jin YX, Fournier M, Fourrey JL: Enzymatic conversion of adenosine to inosine and to N1-methylinosine in transfer RNAs: a review.

    Biochimie 1996, 78:488-501.

    A review of the inosines in eukaryotic, prokaryotic and archaeal tRNAs.

    PubMed Abstract | Publisher Full Text OpenURL

  23. Wong SK, Sato S, Lazinski DW: Substrate recognition by ADAR1 and ADAR2.

    RNA 2001, 7:846-858.

    The authors found that the deaminase domain determines specificity in domain-swap constructs.

    PubMed Abstract | Publisher Full Text OpenURL

  24. Betts L, Xiang S, Short SA, Wolfenden R, Carter CW Jr: Cytidine deaminase. The 2.3 Å crystal structure of an enzyme: transition-state analog complex.

    J Mol Biol 1994, 235:635-656.

    The determination of the structure of E. coli free-nucleotide cytosine deaminase (ECCDA).

    PubMed Abstract | Publisher Full Text OpenURL

  25. Herbert A, Rich A: The role of binding domains for dsRNA and Z-DNA in the in vivo editing of minimal substrates by ADAR1.

    Proc Natl Acad Sci USA 2001, 98:12132-12137.

    The deaminase domain of ADAR1 edits without dsRBDs.

    PubMed Abstract | Publisher Full Text OpenURL

  26. Stephens OM, Yi-Brunozzi HY, Beal PA: Analysis of the RNA-editing reaction of ADAR2 with structural and fluorescent analogues of the GluR-B R/G editing site.

    Biochemistry 2000, 39:12243-12251.

    Evidence that the target adenosine is flipped out of dsRNA for deamination.

    PubMed Abstract | Publisher Full Text OpenURL

  27. Yi-Brunozzi HY, Stephens OM, Beal PA: Conformational changes that occur during an RNA editing adenosine deamination reaction.

    J Biol Chem 2001, 276:37827-37833.

    A truncated ADAR2 with only dsRBD1, dsRBD2 and the linker between them binds a minisubstrate with some specificity and alters the conformation of bases near the target adenosine.

    PubMed Abstract | Publisher Full Text OpenURL

  28. Saunders LR, Barber GN: The dsRNA binding protein family: critical roles, diverse cellular functions.

    FASEB J 2003, 17:961-983.

    A recent review on dsRNA-binding domains.

    PubMed Abstract | Publisher Full Text OpenURL

  29. Ryter JM, Schultz SC: Molecular basis of double-stranded RNA-protein interactions: structure of a dsRNA-binding domain complexed with dsRNA.

    EMBO J 1998, 17:7505-7513.

    A cocrystal of a dsRBD with dsRNA shows an absence of amino-acid side-chain contacts with bases for this particular dsRBD.

    PubMed Abstract | Publisher Full Text OpenURL

  30. Castrignano T, Chillemi G, Varani G, Desideri A: Molecular dynamics simulation of the RNA complex of a double-stranded RNA-binding domain reveals dynamic features of the intermolecular interface and its hydration.

    Biophys J 2002, 83:3542-3552.

    Modeling the dynamics of the interaction between dsRBDs and RNA, based on the NMR structure of a complex.

    PubMed Abstract | Publisher Full Text OpenURL

  31. Patel RC, Sen GC: Requirement of PKR dimerization mediated by specific hydrophobic residues for its activation by double-stranded RNA and its antigrowth effects in yeast.

    Mol Cell Biol 1998, 18:7009-7019.

    This article and [32] describe the dimerization of PKR via its dsRBDs.

    PubMed Abstract | Publisher Full Text OpenURL

  32. Zhang F, Romano PR, Nagamura-Inoue T, Tian B, Dever TE, Mathews MB, Ozato K, Hinnebusch AG: Binding of double-stranded RNA to protein kinase PKR is required for dimerization and promotes critical autophosphorylation events in the activation loop.

    J Biol Chem 2001, 276:24946-24958.

    See [31].

    PubMed Abstract | Publisher Full Text OpenURL

  33. Eckmann CR, Neunteufl A, Pfaffstetter L, Jantsch MF: The human but not the Xenopus RNA-editing enzyme ADAR1 has an atypical nuclear localization signal and displays the characteristics of a shuttling protein.

    Mol Biol Cell 2001, 12:1911-1924.

    This paper describes the nuclear localization sequence of ADAR1 in its third dsRBD.

    PubMed Abstract | Publisher Full Text OpenURL

  34. Patterson JB, Samuel CE: Expression and regulation by interferon of a doubled-stranded-RNA-specific adenosine deaminase from human cells: evidence for two forms of the deaminase.

    Mol Cell Biol 1995, 15:5376-5388.

    The cloning and gene structure of human ADAR1. The long form of ADAR1 shuttles between the nucleus and the cytoplasm and is induced by interferon.

    PubMed Abstract | Publisher Full Text OpenURL

  35. Poulsen H, Nilsson J, Damgaard CK, Egebjerg J, Kjems J: CRM1 mediates the export of ADAR1 through a nuclear export signal within the Z-DNA binding domain.

    Mol Cell Biol 2001, 21:7862-7871.

    A nuclear export signal is present in the amino terminus of hADAR1.

    PubMed Abstract | Publisher Full Text OpenURL

  36. Desterro JM, Keegan LP, Lafarga M, Berciano MT, O'Connell M, Carmo-Fonseca M: Dynamic association of RNA-editing enzymes with the nucleolus.

    J Cell Sci 2003, 116:1805-1818.

    ADAR1 and ADAR2 are sequestered in the nucleolus, and mobilize to the nucleoplasm when a target RNA is overexpressed.

    PubMed Abstract | Publisher Full Text OpenURL

  37. Sansam CL, Wells KS, Emeson RB: Modulation of RNA editing by functional nucleolar sequestration of ADAR2.

    Proc Natl Acad Sci USA 2003, 100:14018-14023.

    Human ADAR2 is sequestered in the nucleolus, probably by binding to rRNA because inhibition of ribosomal RNA synthesis or the introduction of mutations in the dsRBDs within ADAR2 results in translocation of the protein to the nucleoplasm.

    PubMed Abstract | Publisher Full Text OpenURL

  38. Higuchi M, Maas S, Single FN, Hartner J, Rozov A, Burnashev N, Feldmeyer D, Sprengel R, Seeburg PH: Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2.

    Nature 2000, 406:78-81.

    Vertebrate ADAR2 has one key target. Expression of the edited GluR-B(R) isoform rescues the mutant phenotype of a mouse ADAR2 knockout.

    PubMed Abstract | Publisher Full Text OpenURL

  39. Jia Z, Agopyan N, Miu P, Xiong Z, Henderson J, Gerlai R, Taverna FA, Velumian A, McDonald J, Carlen P, et al.: Enhanced LTP in mice deficient in the AMPA receptor GluR2.

    Neuron 1996, 17:945-956.

    Failure to edit GluR-B is very toxic, but deletion of GluR-B is less toxic.

    PubMed Abstract | Publisher Full Text OpenURL

  40. Greger IH, Khatri L, Ziff EB: RNA editing at arg607 controls AMPA receptor exit from the endoplasmic reticulum.

    Neuron 2002, 34:759-772.

    The retention of the GluR-B subunit in the endoplasmic reticulum is controlled by the presence of arginine at the Q/R editing site.

    PubMed Abstract | Publisher Full Text OpenURL

  41. Greger IH, Khatri L, Kong X, Ziff EB: AMPA receptor tetramerization is mediated by q/r editing.

    Neuron 2003, 40:763-774.

    Shows how the arginine introduced in the pore of GluR-B by RNA editing leads to a pool of the subunit in the endoplasmic reticulum, facilitating incorporation of GluR-B in most AMPA receptors and ensuring impermeability to calcium.

    PubMed Abstract | Publisher Full Text OpenURL

  42. Burns CM, Chu H, Rueter SM, Hutchinson LK, Canton H, Sanders-Bush E, Emeson RB: Regulation of serotonin-2C receptor G-protein coupling by RNA editing.

    Nature 1997, 387:303-308.

    The identification of serotonin 5-HT2C receptor pre-mRNA as an interesting new target of RNA editing.

    PubMed Abstract | Publisher Full Text OpenURL

  43. Niswender CM, Herrick-Davis K, Dilley GE, Meltzer HY, Overholser JC, Stockmeier CA, Emeson RB, Sanders-Bush E: RNA editing of the human serotonin 5-HT2C receptor. Alterations in suicide and implications for serotonergic pharmacotherapy.

    Neuropsychopharmacology 2001, 24:478-491.

    One of several studies examining the effect of psychiatric conditions and the drugs used to treat them on the pattern of serotonin receptor isoforms generated by RNA editing.

    PubMed Abstract | Publisher Full Text OpenURL

  44. Hartner JC, Schmittwolf C, Kispert A, Mueller AM, Higuchi M, Seeburg PH: Liver disintegration in the mouse embryo by deficiency in RNA editing enzyme ADAR1.

    J Biol Chem 2004, 279:4894-4902.

    The knockout of ADAR1 in mice has an embryonic-lethal phenotype that includes defects in liver hematopoiesis. The target causing these defects is unknown.

    Publisher Full Text OpenURL

  45. Wang Q, Miyakoda M, Yang W, Khillan J, Stachura DL, Weiss MJ, Nishikura K: Stress-induced apoptosis associated with Null mutation of ADAR1 RNA editing deaminase gene.

    J Biol Chem 2004, 279:4952-4961.

    The knockout of ADAR1 in mice is embryonic lethal and cells from many tissues show stress-induced apoptosis. The target causing these defects is unknown.

    Publisher Full Text OpenURL

  46. Herbert A, Alfken J, Kim YG, Mian IS, Nishikura K, Rich A: A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase.

    Proc Natl Acad Sci USA 1997, 94:8421-8426.

    The amino terminus of ADAR1 has two copies of a small domain that binds Z-DNA.

    PubMed Abstract | Publisher Full Text OpenURL

  47. Vartanian JP, Sommer P, Wain-Hobson S: Death and the retrovirus.

    Trends Mol Med 2003, 9:409-413.

    A recent review on the role of DNA editing by APOBEC-3G in inhibiting HIV replication. The activation-induced deaminase (AID) is another APOBEC relative that deaminates DNA.

    PubMed Abstract | Publisher Full Text OpenURL

  48. Kallman AM, Sahlin M, Ohman M: ADAR2 A-I editing: site selectivity and editing efficiency are separate events.

    Nucleic Acids Res 2003, 31:4874-4881.

    The structures of RNA substrates determine the affinity of binding and efficiency of editing.

    PubMed Abstract | Publisher Full Text OpenURL

  49. Klaue Y, Kallman AM, Bonin M, Nellen W, Ohman M: Biochemical analysis and scanning force microscopy reveal productive and nonproductive ADAR2 binding to RNA substrates.

    RNA 2003, 9:839-846.

    The structures of RNA substrates mean that some binding sites may not be well edited.

    PubMed Abstract | Publisher Full Text OpenURL

  50. Jaikaran DC, Collins CH, MacMillan AM: Adenosine to inosine editing by ADAR2 requires formation of a ternary complex on the GluR-B R/G site.

    J Biol Chem 2002, 277:37624-37629.

    The first evidence from kinetic studies that ADAR2 dimerizes.

    PubMed Abstract | Publisher Full Text OpenURL

  51. Cho DS, Yang W, Lee JT, Shiekhattar R, Murray JM, Nishikura K: Requirement of dimerization for RNA editing activity of adenosine deaminases acting on RNA.

    J Biol Chem 2003, 278:17093-17102.

    ADAR1 and ADAR2 extracted from insect cells are dimers, and dimerization is required for activity.

    PubMed Abstract | Publisher Full Text OpenURL

  52. Gallo A, Keegan LP, Ring GM, O'Connell MA: An ADAR that edits transcripts encoding ion channel subunits functions as a dimer.

    EMBO J 2003, 22:3421-3430.

    Yeast two-hybrid studies define an amino-terminal dimerization function in Drosophila ADAR that is required for activity.

    PubMed Abstract | Publisher Full Text OpenURL

  53. Hoopengardner B, Bhalla T, Staber C, Reenan R: Nervous system targets of RNA editing identified by comparative genomics.

    Science 2003, 301:832-836.

    The identification by a novel genomic technique of many new editing targets in Drosophila, including one that is conserved in humans.

    PubMed Abstract | Publisher Full Text OpenURL

  54. Knight SW, Bass BL: The role of RNA editing by ADARs in RNAi.

    Mol Cell 2002, 10:809-817.

    C. elegans mutations in Adr genes enhance transgene silencing. The authors propose that ADARs and RNA interference compete for a dsRNA substrate.

    PubMed Abstract | Publisher Full Text OpenURL

  55. Tonkin LA, Bass BL: Mutations in RNAi rescue aberrant chemotaxis of ADAR mutants.

    Science 2003, 302:1725.

    This paper extends the work in [53] to show that the entire phenotype of adr mutants in C. elegans can be attributed to their role in antagonizing RNA interference.

    PubMed Abstract | Publisher Full Text OpenURL