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An I for an A: Dynamic Regulation of Adenosine Deamination-Mediated RNA Editing

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An I for an A: Dynamic Regulation of Adenosine Deamination-Mediated RNA Editing G C A T T A C G G C A T genes Review An I for an A: Dynamic Regulation of Adenosine Deamination-Mediated RNA Editing Cornelia Vesely and Michael F. Jantsch * Division of Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria; [email protected] * Correspondence: [email protected] Abstract: RNA-editing by adenosine deaminases acting on RNA (ADARs) converts adenosines to inosines in structured RNAs. Inosines are read as guanosines by most cellular machineries. A to I editing has two major functions: first, marking endogenous RNAs as “self”, therefore helping the innate immune system to distinguish repeat- and endogenous retrovirus-derived RNAs from invading pathogenic RNAs; and second, recoding the information of the coding RNAs, leading to the translation of proteins that differ from their genomically encoded versions. It is obvious that these two important biological functions of ADARs will differ during development, in different tissues, Citation: Vesely, C.; Jantsch, M.F. An upon altered physiological conditions or after exposure to pathogens. Indeed, different levels of I for an A: Dynamic Regulation of ADAR-mediated editing have been observed in different tissues, as a response to altered physiology Adenosine Deamination-Mediated or upon pathogen exposure. In this review, we describe the dynamics of A to I editing and summarize RNA Editing. Genes 2021, 12, 1026. the known and likely mechanisms that will lead to global but also substrate-specific regulation of A https://doi.org/10.3390/genes12071026 to I editing. Academic Editors: Pierre Barraud, Keywords: RNA modification; ADAR; regulation; RNA processing; adenosine deamination Carine Tisne and Stefanie Kellner Received: 12 June 2021 Accepted: 30 June 2021 1. Background ADARs Published: 1 July 2021 Adenosine deaminases acting on RNA (ADARs) convert adenosines to inosines in structured and double-stranded RNAs (Figure1). ADAR activity has been detected in all Publisher’s Note: MDPI stays neutral metazoa tested so far and genomic sequencing has revealed ADAR-like enzymes in all with regard to jurisdictional claims in published maps and institutional affil- tested metazoan species [1]. iations. Evolutionary, ADARs are related to Adenosine Deaminases Acting on tRNAs (ADATs), which are tRNA deaminating enzymes that are responsible for the introduction of inosines at the wobble position of certain tRNAs [2]. ADARs acquired double-stranded RNA- binding domains that allow them to bind to their substrate RNAs [3]. Depending on the organismic group, different types of ADARs exist that all harbor the deaminase domain at Copyright: © 2021 by the authors. their C-terminal ends but contain a variable number of RNA-binding motifs (Figure1). Licensee MDPI, Basel, Switzerland. In mammals, three ADAR family members can be found. The most obvious differences This article is an open access article between these three family members are seen in the number of double-stranded RNA- distributed under the terms and conditions of the Creative Commons binding domains and in the amino-terminal extensions of the ADAR enzymes. While Attribution (CC BY) license (https:// ADAR1 harbors three dsRBDs, ADAR2 and ADAR3 contain only two dsRBDs. In the amino- creativecommons.org/licenses/by/ terminal regions of the ADARs, additional nucleic acid-binding domains but also regions 4.0/). controlling intracellular localization of the harboring enzymes can be found (Figure1). Genes 2021, 12, 1026. https://doi.org/10.3390/genes12071026 https://www.mdpi.com/journal/genes Genes 2021, 12, 1026 2 of 12 Genes 2021, 12, x FOR PEER REVIEW 2 of 12 Figure 1. Activity and architecture of mammalian ADARs. (A) Adenosine deaminases acting on RNAFigure convert 1. Activity adenosines and architecture via hydrolytic of mammalian deamination ADARs. to inosines. (A) Adenosine (B) Three deaminases ADAR genes acting can beon foundRNA convert in mammals, adenosines ADAR1, via ADAR2 hydrolytic and deamination ADAR3. ADAR1 to inosines. is expressed (B) Three in two ADAR isoforms, genes ADAR1 can be p150found of in 150 mammals, kDa, which ADAR1, is expressed ADAR2 from and an ADAR3. interferon-inducible ADAR1 is expressed promoter, andin two ADAR1 isoforms, p110, ADAR1 which isp150 constitutively of 150 kDa, expressed. which is Allexpressed ADARs from contain an ainterferon-inducible deaminase domain atpromoter, their C-terminus. and ADAR1 However, p110, thewhich catalytic is constitutively domain of ADAR3expressed. is enzymatically All ADARs contain inactive. a Substratedeaminase engagement domain at their of the C-terminus. ADARs is mediatedHowever, via the a catalytic variable numberdomain of double-strandedADAR3 is enzymatically RNA-binding inactive. domains Substrate (dsRBDs) engagement that interact of the ADARs is mediated via a variable number of double-stranded RNA-binding domains (dsRBDs) that with structured and double-stranded RNAs. The amino termini of the ADAR proteins are quite interact with structured and double-stranded RNAs. The amino termini of the ADAR proteins are divergent. While the N-terminus of ADAR1 harbors a Z-DNA binding domain (ZBD) that is able quite divergent. While the N-terminus of ADAR1 harbors a Z-DNA binding domain (ZBD) that is toable interact to interact with with Z-DNA Z-DNA and and ZRNA, ZRNA, the the long long N terminusN terminus of of ADAR1 ADAR1 p150 p150 also also harbors harbors a a nuclear nuclear exportexport signalsignal (NES),(NES), resultingresulting inin mostlymostly cytoplasmiccytoplasmic localizationlocalization ofof thisthis interferon-inducedinterferon-induced isoform.isoform. AA nuclearnuclear localizationlocalization signal signal (NLS)(NLS) thatthat overlapsoverlaps thethe thirdthird dsRBDdsRBD ofof ADAR1ADAR1 isis negativelynegatively regulatedregulated byby RNARNA binding.binding. AsAs aa consequence,consequence, thethe p150p150 isoformisoform ofof ADAR1ADAR1 cancan shuttleshuttle betweenbetween thethe nucleus nucleus andand cytoplasm.cytoplasm. The The N-terminus N-terminus of of ADAR2 ADAR2 harbors harbors its its classical classical nuclear nuclear localization localization signal. signal. The The cat- catalyticallyalytically inactive inactive ADAR3 ADAR3 protein protein contains contains an an N-terminally N-terminally located located RNA-binding RNA-binding domain domain (RBD). (RBD). 2.2. FunctionFunction ofof ADARsADARs InIn mammals,mammals, catalytic catalytic activity activity for ADAR1for ADAR1 and ADAR2and ADAR2 can be can detected, be detected, while ADAR3 while isADAR3 seemingly is seemingly inactive [ 4inactive]. Consequently, [4]. Consequently, it has been it proposed has been that proposed the biological that the function biological of ADAR3function lies of ADAR3 in its ability lies in to its compete ability withto compete other ADARs with other for RNAADARs binding. for RNA Consistent binding. withCon- asistent function with in modulatinga function in the modulating extent of the the RNA extent editing, of the loss RNA of ADAR3editing, isloss associated of ADAR3 with is minorassociated learning with alterations minor learning in mice alterations [5]. in mice [5]. LossLoss ofof ADAR1ADAR1 oror ADAR2,ADAR2, inin contrast,contrast, leadsleads toto dramaticdramatic phenotypes.phenotypes. LossLoss ofof ADAR1ADAR1 leadsleads toto embryonic lethality lethality in in mice mice that that is isaccompanied accompanied by byliver liver disintegration disintegration and and a dra- a dramaticmatic increase increase in interferon in interferon signaling signaling [6,7]. [This6,7]. phenotype This phenotype can be canrescued be rescued by the deletion by the deletionof cytoplasmic of cytoplasmic RNA sensors RNA Mda5 sensors or MAVS, Mda5 or strongly MAVS, suggesting strongly suggesting that in the that absence in the of absenceADAR1-mediated of ADAR1-mediated RNA editing, RNA endogenous editing, endogenous RNAs are RNAs interpreted are interpreted as foreign as or foreign viral orby viral by the innate antiviral immune system [8–10]. Interestingly, ADAR1 can also prevent Genes 2021, 12, 1026 3 of 12 inadvertent activation of PKR-mediated shut-down of translation, suggesting that ADAR1 is a general modulator of RNA-sensing pattern recognition receptors [11]. Interestingly, ADAR1 is expressed in two versions. A constitutively expressed isoform gives rise to a 110 kDa protein that is mostly localized to the nucleus [12]. In contrast, an interferon- induced isoform of 150 kDa is primarily localized to the cytoplasm due to the presence of an amino terminal nuclear export signal that is missing in the shorter isoform [13,14]. The extended amino terminus of the ADAR1 p150 isoform also harbors two Z-DNA binding domains (ZBDs) that can bind left-handed Z-DNA but also Z-RNA [15]. The ZBDs have also been implicated in recognizing viral RNAs. The precise function of the constitutively expressed ADAR1 p110 isoform that is predominantly localized to the nucleus is not well understood. Seemingly, ADAR1 p110 cannot compensate for loss of the ADAR1 p150 as the selective deletion of the ADAR1 p150 isoform still leads to embryonic lethality [10,16]. ADAR2 is most strongly expressed in the nervous system but also in some organs such as the intestine and the vasculature [17,18]. Loss of ADAR2 in mice leads to lethality around three weeks post-partum, which is accompanied by epileptic seizures [19]. Interestingly, a knock-in of a pre-edited version of the glutamate receptor subunit
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