The origin of the ADAR gene family and animal RNA editing

Abstract

Background: ADAR (adenosine deaminase acting on RNA) proteins convert adenosine into inosine in double-stranded RNAs and have been shown to increase gene product diversity in a number of bilaterians, particularly mammals and flies. This enzyme family appears to have evolved from an ADAT (adenosine deaminase acting on tRNA) ancestor, via the addition of a double-stranded RNA binding domain. The modern vertebrate ADAR family is comprised of ADAD, ADAR2 and ADAR1, each of which has a conserved domain architecture. To reconstruct the origin of this protein family, we identified and categorised ADAR family members encoded in the genomes and/or transcriptomes of early-branching metazoan and closely related non-metazoan taxa, including thirteen sponge and ten ctenophore species.

Results: We demonstrate that the ADAR protein family is a metazoan innovation, with the three ADAR subtypes being present in representatives of the earliest phyletic lineages of animals - sponges and ctenophores - but not in other closely related choanoflagellate and filasterean holozoans. ADAR1 is missing from all ctenophore genomes and transcriptomes surveyed. Depending on the relationship of sponges and ctenophores to the rest of the Metazoa, this is consistent with either ADAR1 being lost in ctenophores, as it has been in multiple metazoan lineages, or being an innovation that evolved after ctenophores diverged from the rest of the animal kingdom. The presence of Z-DNA binding domains in some sponge ADARs indicates an ancestral ADAR included this domain and it has been lost in multiple animal lineages.

Conclusions: The ADAR family appears to be a metazoan innovation, with all family members in place in the earliest phyletic branches of the crown Metazoa. The presence of ADARs in sponges and ctenophores is consistent with A-to-I editing being a post-transcriptional regulatory mechanism that was used by the last common ancestor to all living animals and subsequently has been preserved in most modern lineages.

Figure 1

Reconstruction of ADAR gene and domain evolution. The table (right) lists the number of ADAR family members identified in each species. ADARs are classified based on their domain architecture, as shown by the ‘ball-and-stick’ protein models above each ADAR name. The Z-DNA/RNA binding (ZB) and double-stranded RNA binding (dsRB) domains of the ADAR1 model are marked with an ‘n’ to indicate that multiple copies of these domains may be present in different species. The domain architectures of all ADAR1-like proteins are depicted on the far right. The ADAR gene counts were used to reconstruct ADAT/ADAR evolution, as mapped to the phylogenetic tree as coloured squares (left). Searches for adenosine deaminase (AD), dsRB and ZB domains were performed to determine the phylogenetic positions of whole-genome domain origin and loss events, regardless of ADAT/ADAR complement; these events are also mapped to the tree as coloured shapes. Green boxes separate the tree into the main phylogenetic groupings: Bilateria (B), Eumetazoa (E), Metazoa (M), Holozoa (H) and Opisthokonta (O). For clarity, we present the sponge and ctenophore lineages on equal footing, and depict all three ADARs as present in the metazoan stem. The loss and gain of the ADAR1-like gene is marked with a question mark to illustrate the uncertainty in reconstructing these evolutionary events, which are elaborated upon further in Figure 3 and Additional file 2.

Figure 2

ADAR family member distribution in sponges and ctenophores. As in Figure 1, the number of candidate ADAR family members identified in each sponge and ctenophore genome (indicated by an asterisk) or transcriptome is shown. The domain architectures of ADAR1-like sequences are given on the far right. The phylogenetic relationships within the ctenophore (C, top) and sponge (S, bottom) lineages are depicted to the left. ADAR2 sequences indicated by a ^ are predicted to encode three dsRB domains. Amphimedon queenslandica and Pseudospongosorites suberitoides are abbreviated to conserve space.

Figure 3

Possible scenarios for ADAR evolution in the metazoan ancestor. Five different scenarios of gene gain and loss events could explain the ADAR family distribution observed in sponges, ctenophores and eumetazoans, depending on whether sponges or ctenophores are the earliest-branching metazoan lineage. Filled and blank shapes represent gene (coloured squares) or ZB domain (triangles) gain and loss events, respectively. In panel v, the arrow represents the possible conversion of an ADAR1-like sequence to an ADAD-like architecture via domain loss.