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Kliuchnikova AA, Goncharov AO, Levitsky LI, Pyatnitskiy MA, Novikova SE, Kuznetsova KG, Ivanov MV, Ilina IY, Farafonova TE, Zgoda VG, Gorshkov MV, Moshkovskii SA. Proteome-Wide Analysis of ADAR-Mediated Messenger RNA Editing during Fruit Fly Ontogeny. J Proteome Res 2020; 19:4046-4060. [PMID: 32866021 DOI: 10.1021/acs.jproteome.0c00347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Adenosine-to-inosine RNA editing is an enzymatic post-transcriptional modification which modulates immunity and neural transmission in multicellular organisms. In particular, it involves editing of mRNA codons with the resulting amino acid substitutions. We identified such sites for developmental proteomes of Drosophila melanogaster at the protein level using available data for 15 stages of fruit fly development from egg to imago and 14 time points of embryogenesis. In total, 40 sites were obtained, each belonging to a unique protein, including four sites related to embryogenesis. The interactome analysis has revealed that the majority of the editing-recoded proteins were associated with synaptic vesicle trafficking and actomyosin organization. Quantitation data analysis suggested the existence of a phase-specific RNA editing regulation with yet unknown mechanisms. These findings supported the transcriptome analysis results, which showed that a burst in the RNA editing occurs during insect metamorphosis from pupa to imago. Finally, targeted proteomic analysis was performed to quantify editing-recoded and genomically encoded versions of five proteins in brains of larvae, pupae, and imago insects, which showed a clear tendency toward an increase in the editing rate for each of them. These results will allow a better understanding of the protein role in physiological effects of RNA editing.
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Affiliation(s)
- Anna A Kliuchnikova
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a, Malaya Pirogovskaya, Moscow 119435, Russia.,Pirogov Russian National Research Medical University, 1, Ostrovityanova, Moscow 117997, Russia
| | - Anton O Goncharov
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a, Malaya Pirogovskaya, Moscow 119435, Russia.,Institute of Biomedical Chemistry, 10, Pogodinskaya, Moscow 119121, Russia
| | - Lev I Levitsky
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38, bld. 1, Leninsky Prospect, Moscow 119334, Russia
| | - Mikhail A Pyatnitskiy
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a, Malaya Pirogovskaya, Moscow 119435, Russia.,Institute of Biomedical Chemistry, 10, Pogodinskaya, Moscow 119121, Russia
| | | | - Ksenia G Kuznetsova
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a, Malaya Pirogovskaya, Moscow 119435, Russia
| | - Mark V Ivanov
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38, bld. 1, Leninsky Prospect, Moscow 119334, Russia
| | - Irina Y Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a, Malaya Pirogovskaya, Moscow 119435, Russia
| | | | - Victor G Zgoda
- Institute of Biomedical Chemistry, 10, Pogodinskaya, Moscow 119121, Russia.,Skolkovo Institute of Science and Technology, 30, bld. 1, Bolshoy Boulevard, Moscow 121205, Russia
| | - Mikhail V Gorshkov
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38, bld. 1, Leninsky Prospect, Moscow 119334, Russia
| | - Sergei A Moshkovskii
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a, Malaya Pirogovskaya, Moscow 119435, Russia.,Pirogov Russian National Research Medical University, 1, Ostrovityanova, Moscow 117997, Russia
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Abstract
Adenosine-to-inosine RNA editing is a conserved process, which is performed by ADAR enzymes. By changing nucleotides in coding regions of genes and altering codons, ADARs expand the cell's protein repertoire. This function of the ADAR enzymes is essential for human brain development. However, most of the known editing sites are in non-coding repetitive regions in the transcriptome and the purpose of editing in these regions is unclear. Recent studies, which have shown that editing levels of transcripts vary between tissues and developmental stages in many organisms, suggest that the targeted RNA and ADAR editing are both regulated. We discuss the implications of these findings, and the possible role of RNA editing in innate immunity.
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Affiliation(s)
- Nabeel S Ganem
- a Faculty of Biology , Technion- Israel Institute of Technology , Technion City , Haifa , Israel
| | - Ayelet T Lamm
- a Faculty of Biology , Technion- Israel Institute of Technology , Technion City , Haifa , Israel
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Abstract
Adenosine deaminases acting on RNA (ADARs) are zinc-containing enzymes that deaminate adenosine bases to inosines within dsRNA regions in transcripts. In short, structured dsRNA hairpins individual adenosine bases may be targeted specifically and edited with up to one hundred percent efficiency, leading to the production of alternative protein variants. However, the majority of editing events occur within longer stretches of dsRNA formed by pairing of repetitive sequences. Here, many different adenosine bases are potential targets but editing efficiency is usually much lower. Recent work shows that ADAR-mediated RNA editing is also required to prevent aberrant activation of antiviral innate immune sensors that detect viral dsRNA in the cytoplasm. Missense mutations in the ADAR1 RNA editing enzyme cause a fatal auto-inflammatory disease, Aicardi–Goutières syndrome (AGS) in affected children. In addition RNA editing by ADARs has been observed to increase in many cancers and also can contribute to vascular disease. Thus the role of RNA editing in the progression of various diseases can no longer be ignored. The ability of ADARs to alter the sequence of RNAs has also been used to artificially target model RNAs in vitro and in cells for RNA editing. Potentially this approach may be used to repair genetic defects and to alter genetic information at the RNA level. In this review we focus on the role of ADARs in disease development and progression and on their potential use to artificially modify RNAs in a targeted manner.
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Affiliation(s)
- Prajakta Bajad
- a Medical University of Vienna, Center of Anatomy and Cell Biology , Department of Cell- and Developmental Biology , Schwarzspanierstrasse, Vienna , Austria
| | - Michael F Jantsch
- a Medical University of Vienna, Center of Anatomy and Cell Biology , Department of Cell- and Developmental Biology , Schwarzspanierstrasse, Vienna , Austria
| | - Liam Keegan
- b CEITEC at Masaryk University , Kamenice, Czech Republic
| | - Mary O'Connell
- b CEITEC at Masaryk University , Kamenice, Czech Republic
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Mazloomian A, Meyer IM. Genome-wide identification and characterization of tissue-specific RNA editing events in D. melanogaster and their potential role in regulating alternative splicing. RNA Biol 2016; 12:1391-401. [PMID: 26512413 PMCID: PMC4829317 DOI: 10.1080/15476286.2015.1107703] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
RNA editing is a widespread mechanism that plays a crucial role in diversifying gene products. Its abundance and importance in regulating cellular processes were revealed using new sequencing technologies. The majority of these editing events, however, cannot be associated with regulatory mechanisms. We use tissue-specific high-throughput libraries of D. melanogaster to study RNA editing. We introduce an analysis pipeline that utilises large input data and explicitly captures ADAR's requirement for double-stranded regions. It combines probabilistic and deterministic filters and can identify RNA editing events with a low estimated false positive rate. Analyzing ten different tissue types, we predict 2879 editing sites and provide their detailed characterization. Our analysis pipeline accurately distinguishes genuine editing sites from SNPs and sequencing and mapping artifacts. Our editing sites are 3 times more likely to occur in exons with multiple splicing acceptor/donor sites than in exons with unique splice sites (p-value < 2.10−15). Furthermore, we identify 244 edited regions where RNA editing and alternative splicing are likely to influence each other. For 96 out of these 244 regions, we find evolutionary evidence for conserved RNA secondary-structures near splice sites suggesting a potential regulatory mechanism where RNA editing may alter splicing patterns via changes in local RNA structure.
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Affiliation(s)
- Alborz Mazloomian
- a Centre for High-Throughput Biology; Department of Computer Science and Department of Medical Genetics ; University of British Columbia ; Vancouver ; BC , Canada
| | - Irmtraud M Meyer
- a Centre for High-Throughput Biology; Department of Computer Science and Department of Medical Genetics ; University of British Columbia ; Vancouver ; BC , Canada
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Mannion N, Arieti F, Gallo A, Keegan LP, O'Connell MA. New Insights into the Biological Role of Mammalian ADARs; the RNA Editing Proteins. Biomolecules 2015; 5:2338-62. [PMID: 26437436 PMCID: PMC4693238 DOI: 10.3390/biom5042338] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/09/2015] [Accepted: 09/11/2015] [Indexed: 12/20/2022] Open
Abstract
The ADAR proteins deaminate adenosine to inosine in double-stranded RNA which is one of the most abundant modifications present in mammalian RNA. Inosine can have a profound effect on the RNAs that are edited, not only changing the base-pairing properties, but can also result in recoding, as inosine behaves as if it were guanosine. In mammals there are three ADAR proteins and two ADAR-related proteins (ADAD) expressed. All have a very similar modular structure; however, both their expression and biological function differ significantly. Only two of the ADAR proteins have enzymatic activity. However, both ADAR and ADAD proteins possess the ability to bind double-strand RNA. Mutations in ADARs have been associated with many diseases ranging from cancer, innate immunity to neurological disorders. Here, we will discuss in detail the domain structure of mammalian ADARs, the effects of RNA editing, and the role of ADARs in human diseases.
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Affiliation(s)
- Niamh Mannion
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, 21 Shelley Road, Glasgow G12 0ZD, UK.
| | - Fabiana Arieti
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.
| | - Angela Gallo
- Oncohaematoogy Department, Ospedale Pediatrico Bambino Gesù (IRCCS) Viale di San Paolo, Roma 15-00146, Italy.
| | - Liam P Keegan
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.
| | - Mary A O'Connell
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.
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Li X, Overton IM, Baines RA, Keegan LP, O'Connell MA. The ADAR RNA editing enzyme controls neuronal excitability in Drosophila melanogaster. Nucleic Acids Res 2013; 42:1139-51. [PMID: 24137011 PMCID: PMC3902911 DOI: 10.1093/nar/gkt909] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
RNA editing by deamination of specific adenosine bases to inosines during pre-mRNA processing generates edited isoforms of proteins. Recoding RNA editing is more widespread in Drosophila than in vertebrates. Editing levels rise strongly at metamorphosis, and Adar5G1 null mutant flies lack editing events in hundreds of CNS transcripts; mutant flies have reduced viability, severely defective locomotion and age-dependent neurodegeneration. On the other hand, overexpressing an adult dADAR isoform with high enzymatic activity ubiquitously during larval and pupal stages is lethal. Advantage was taken of this to screen for genetic modifiers; Adar overexpression lethality is rescued by reduced dosage of the Rdl (Resistant to dieldrin), gene encoding a subunit of inhibitory GABA receptors. Reduced dosage of the Gad1 gene encoding the GABA synthetase also rescues Adar overexpression lethality. Drosophila Adar5G1 mutant phenotypes are ameliorated by feeding GABA modulators. We demonstrate that neuronal excitability is linked to dADAR expression levels in individual neurons; Adar-overexpressing larval motor neurons show reduced excitability whereas Adar5G1 null mutant or targeted Adar knockdown motor neurons exhibit increased excitability. GABA inhibitory signalling is impaired in human epileptic and autistic conditions, and vertebrate ADARs may have a relevant evolutionarily conserved control over neuronal excitability.
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Affiliation(s)
- Xianghua Li
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, Scotland, UK, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK and Department of Molecular Biosciences, The Wenner Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden
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Singh M. Dysregulated A to I RNA editing and non-coding RNAs in neurodegeneration. Front Genet 2013; 3:326. [PMID: 23346095 PMCID: PMC3551214 DOI: 10.3389/fgene.2012.00326] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 12/28/2012] [Indexed: 12/14/2022] Open
Abstract
RNA editing is an alteration in the primary nucleotide sequences resulting from a chemical change in the base. RNA editing is observed in eukaryotic mRNA, transfer RNA, ribosomal RNA, and non-coding RNAs (ncRNA). The most common RNA editing in the mammalian central nervous system is a base modification, where the adenosine residue is base-modified to inosine (A to I). Studies from ADAR (adenosine deaminase that act on RNA) mutants in Caenorhabditis elegans, Drosophila, and mice clearly show that the RNA editing process is an absolute requirement for nervous system homeostasis and normal physiology of the animal. Understanding the mechanisms of editing and findings of edited substrates has provided a better knowledge of the phenotype due to defective and hyperactive RNA editing. A to I RNA editing is catalyzed by a family of enzymes knows as ADARs. ADARs modify duplex RNAs and editing of duplex RNAs formed by ncRNAs can impact RNA functions, leading to an altered regulatory gene network. Such altered functions by A to I editing is observed in mRNAs, microRNAs (miRNA) but other editing of small and long ncRNAs (lncRNAs) has yet to be identified. Thus, ncRNA and RNA editing may provide key links between neural development, nervous system function, and neurological diseases. This review includes a summary of seminal findings regarding the impact of ncRNAs on biological and pathological processes, which may be further modified by RNA editing. NcRNAs are non-translated RNAs classified by size and function. Known ncRNAs like miRNAs, smallRNAs (smRNAs), PIWI-interacting RNAs (piRNAs), and lncRNAs play important roles in splicing, DNA methylation, imprinting, and RNA interference. Of note, miRNAs are involved in development and function of the nervous system that is heavily dependent on both RNA editing and the intricate spatiotemporal expression of ncRNAs. This review focuses on the impact of dysregulated A to I editing and ncRNAs in neurodegeneration.
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Affiliation(s)
- Minati Singh
- Department of Internal Medicine, University of Iowa Iowa City, IA, USA
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Ghosh S, Wang Y, Cook JA, Chhiba L, Vaughn JC. A molecular, phylogenetic and functional study of the dADAR mRNA truncated isoform during Drosophila embryonic development reveals an editing-independent function. ACTA ACUST UNITED AC 2013; 3:20-30. [PMID: 25414802 PMCID: PMC4235677 DOI: 10.4236/ojas.2013.34a2003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Adenosine Deaminases Acting on RNA (ADARs) have been studied in many animal phyla, where they have been shown to deaminate specific adenosines into inosines in duplex mRNA regions. In Drosophila, two isoform classes are encoded, designated full-length (contains the editase domain) and truncated (lacks this domain). Much is known about the full-length isoform, which plays a major role in regulating functions of voltage-gated ion channel proteins in the adult brain. In contrast, almost nothing is known about the functional significance of the truncated isoform. In situ hybridization shows that both isoform mRNA classes are maternally derived and transcripts for both localize primarily to the developing central nervous system. Quantitative RT-PCR shows that about 35% of all dADAR mRNA transcripts belong to the truncated class in embryos. 3′-RACE results show that abundance of the truncated isoform class is developmentally regulated, with a longer transcript appearing after the mid-blastula transition. 3′-UTR sequences for the truncated isoform have been determined from diverse Drosophila species and important regulatory regions including stop codons have been mapped. Western analysis shows that both mRNA isoform classes are translated into protein during embryonic development, as full-length variant levels gradually diminish. The truncated protein isoform is present in every Drosophila species studied, extending over a period spanning about 40 × 106 years, implying a conserved function. Previous work has shown that a dADAR protein isoform binds to the evolutionarily conserved rnp-4f pre-mRNA stem-loop located in the 5′-UTR to regulate splicing, while no RNA editing was observed, suggesting the hypothesis that it is the non-catalytic truncated isoform which regulates splicing. To test this hypothesis, we have utilized RNAi technology, the results of which support the hypothesis. These results demonstrate a novel, non-catalytic function for the truncated dADAR protein isoform in Drosophila embryonic development, which is very likely evolutionarily conserved.
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Affiliation(s)
- Sushmita Ghosh
- Department of Biology, Cell Molecular and Structural Biology Program, Miami University, Oxford, USA
| | - Yaqi Wang
- Department of Biology, Cell Molecular and Structural Biology Program, Miami University, Oxford, USA
| | - John A Cook
- Department of Biology, Cell Molecular and Structural Biology Program, Miami University, Oxford, USA
| | - Lea Chhiba
- Department of Biology, Cell Molecular and Structural Biology Program, Miami University, Oxford, USA
| | - Jack C Vaughn
- Department of Biology, Cell Molecular and Structural Biology Program, Miami University, Oxford, USA
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Masliah G, Barraud P, Allain FHT. RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence. Cell Mol Life Sci 2012; 70:1875-95. [PMID: 22918483 DOI: 10.1007/s00018-012-1119-x] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 08/01/2012] [Accepted: 08/06/2012] [Indexed: 10/28/2022]
Abstract
The double-stranded RNA binding domain (dsRBD) is a small protein domain of 65-70 amino acids adopting an αβββα fold, whose central property is to bind to double-stranded RNA (dsRNA). This domain is present in proteins implicated in many aspects of cellular life, including antiviral response, RNA editing, RNA processing, RNA transport and, last but not least, RNA silencing. Even though proteins containing dsRBDs can bind to very specific dsRNA targets in vivo, the binding of dsRBDs to dsRNA is commonly believed to be shape-dependent rather than sequence-specific. Interestingly, recent structural information on dsRNA recognition by dsRBDs opens the possibility that this domain performs a direct readout of RNA sequence in the minor groove, allowing a global reconsideration of the principles describing dsRNA recognition by dsRBDs. We review in this article the current structural and molecular knowledge on dsRBDs, emphasizing the intricate relationship between the amino acid sequence, the structure of the domain and its RNA recognition capacity. We especially focus on the molecular determinants of dsRNA recognition and describe how sequence discrimination can be achieved by this type of domain.
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Affiliation(s)
- Grégoire Masliah
- Institute of Molecular Biology and Biophysics, ETH Zurich, Schafmattstrasse 20, 8093 Zürich, Switzerland
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Abstract
Double-stranded RNA (dsRNA) functions both as a substrate of ADARs and also as a molecular trigger of innate immune responses. ADARs, adenosine deaminases that act on RNA, catalyze the deamination of adenosine (A) to produce inosine (I) in dsRNA. ADARs thereby can destablize RNA structures, because the generated I:U mismatch pairs are less stable than A:U base pairs. Additionally, I is read as G instead of A by ribosomes during translation and by viral RNA-dependent RNA polymerases during RNA replication. Members of several virus families have the capacity to produce dsRNA during viral genome transcription and replication. Sequence changes (A-G, and U-C) characteristic of A-I editing can occur during virus growth and persistence. Foreign viral dsRNA also mediates both the induction and the action of interferons. In this chapter our current understanding of the role and significance of ADARs in the context of innate immunity, and as determinants of the outcome of viral infection, will be considered.
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Affiliation(s)
- Charles E Samuel
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA.
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Barraud P, Heale BSE, O'Connell MA, Allain FHT. Solution structure of the N-terminal dsRBD of Drosophila ADAR and interaction studies with RNA. Biochimie 2011; 94:1499-509. [PMID: 22210494 DOI: 10.1016/j.biochi.2011.12.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 12/18/2011] [Indexed: 10/14/2022]
Abstract
Adenosine deaminases that act on RNA (ADAR) catalyze adenosine to inosine (A-to-I) editing in double-stranded RNA (dsRNA) substrates. Inosine is read as guanosine by the translation machinery; therefore A-to-I editing events in coding sequences may result in recoding genetic information. Whereas vertebrates have two catalytically active enzymes, namely ADAR1 and ADAR2, Drosophila has a single ADAR protein (dADAR) related to ADAR2. The structural determinants controlling substrate recognition and editing of a specific adenosine within dsRNA substrates are only partially understood. Here, we report the solution structure of the N-terminal dsRNA binding domain (dsRBD) of dADAR and use NMR chemical shift perturbations to identify the protein surface involved in RNA binding. Additionally, we show that Drosophila ADAR edits the R/G site in the mammalian GluR-2 pre-mRNA which is naturally modified by both ADAR1 and ADAR2. We then constructed a model showing how dADAR dsRBD1 binds to the GluR-2 R/G stem-loop. This model revealed that most side chains interacting with the RNA sugar-phosphate backbone need only small displacement to adapt for dsRNA binding and are thus ready to bind to their dsRNA target. It also predicts that dADAR dsRBD1 would bind to dsRNA with less sequence specificity than dsRBDs of ADAR2. Altogether, this study gives new insights into dsRNA substrate recognition by Drosophila ADAR.
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Affiliation(s)
- Pierre Barraud
- Institute of Molecular Biology and Biophysics, ETH Zurich, Schafmattstrasse 20, CH-8093 Zürich, Switzerland
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