Adar RNA editing-dependent and -independent effects are required for brain and innate immune functions in Drosophila

. 2020 Mar 27 ; 11 (1) : 1580. [epub] 20200327

Jazyk angličtina Země Velká Británie, Anglie Médium electronic

Typ dokumentu časopisecké články, Research Support, N.I.H., Extramural, práce podpořená grantem, Research Support, U.S. Gov't, Non-P.H.S.

Perzistentní odkaz   https://www.medvik.cz/link/pmid32221286

Grantová podpora
R01 GM124215 NIGMS NIH HHS - United States
U.1275.01.005.00001.01 Medical Research Council - United Kingdom
K22 HG000044 NHGRI NIH HHS - United States
T32 GM007276 NIGMS NIH HHS - United States
R01 MH115080 NIMH NIH HHS - United States
T32 HG000044 NHGRI NIH HHS - United States
R01 GM102484 NIGMS NIH HHS - United States

Odkazy

PubMed 32221286
PubMed Central PMC7101428
DOI 10.1038/s41467-020-15435-1
PII: 10.1038/s41467-020-15435-1
Knihovny.cz E-zdroje

ADAR RNA editing enzymes are high-affinity dsRNA-binding proteins that deaminate adenosines to inosines in pre-mRNA hairpins and also exert editing-independent effects. We generated a Drosophila AdarE374A mutant strain encoding a catalytically inactive Adar with CRISPR/Cas9. We demonstrate that Adar adenosine deamination activity is necessary for normal locomotion and prevents age-dependent neurodegeneration. The catalytically inactive protein, when expressed at a higher than physiological level, can rescue neurodegeneration in Adar mutants, suggesting also editing-independent effects. Furthermore, loss of Adar RNA editing activity leads to innate immune induction, indicating that Drosophila Adar, despite being the homolog of mammalian ADAR2, also has functions similar to mammalian ADAR1. The innate immune induction in fly Adar mutants is suppressed by silencing of Dicer-2, which has a RNA helicase domain similar to MDA5 that senses unedited dsRNAs in mammalian Adar1 mutants. Our work demonstrates that the single Adar enzyme in Drosophila unexpectedly has dual functions.

Zobrazit více v PubMed

Sinigaglia K, et al. ADAR RNA editing in innate immune response phasing, in circadian clocks and in sleep. Biochim Biophys. Acta Gene Regul. Mech. 2019;1862:356–369. doi: 10.1016/j.bbagrm.2018.10.011. PubMed DOI

Nishikura K. Functions and regulation of RNA editing by ADAR deaminases. Annu. Rev. Biochem. 2010;79:321–349. doi: 10.1146/annurev-biochem-060208-105251. PubMed DOI PMC

Bazak L, et al. A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes. Genome Res. 2014;24:365–376. doi: 10.1101/gr.164749.113. PubMed DOI PMC

Ramaswami G, et al. Identifying RNA editing sites using RNA sequencing data alone. Nat. Methods. 2013;10:128–132. doi: 10.1038/nmeth.2330. PubMed DOI PMC

Tan MH, et al. Dynamic landscape and regulation of RNA editing in mammals. Nature. 2017;550:249–254. doi: 10.1038/nature24041. PubMed DOI PMC

Graveley BR, et al. The developmental transcriptome of Drosophila melanogaster. Nature. 2011;471:473–479. doi: 10.1038/nature09715. PubMed DOI PMC

Sapiro AL, et al. Illuminating spatial A-to-I RNA editing signatures within the Drosophila brain. Proc. Natl Acad. Sci. 2019;116:2318–2327. doi: 10.1073/pnas.1811768116. PubMed DOI PMC

St Laurent G, et al. Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila. Nat. Struct. Mol. Biol. 2013;20:1333–1339. doi: 10.1038/nsmb.2675. PubMed DOI

Heale BS, et al. Editing independent effects of ADARs on the miRNA/siRNA pathways. Embo J. 2009;28:3145–3156. doi: 10.1038/emboj.2009.244. PubMed DOI PMC

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. doi: 10.1093/nar/gkg681. PubMed DOI PMC

Nishikura K, Sakurai M, Ariyoshi K, Ota H. Antagonistic and stimulative roles of ADAR1 in RNA silencing. RNA Biol. 2013;10:1240–1247. doi: 10.4161/rna.25947. PubMed DOI PMC

Vesely C, Tauber S, Sedlazeck FJ, von Haeseler A, Jantsch MF. Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs. Genome Res. 2012;22:1468–1476. doi: 10.1101/gr.133025.111. PubMed DOI PMC

Vesely C, et al. ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain. Nucleic Acids Res. 2014;42:12155–12168. doi: 10.1093/nar/gku844. PubMed DOI PMC

Ota H, et al. ADAR1 forms a complex with Dicer to promote microRNA processing and RNA-induced gene silencing. Cell. 2013;153:575–589. doi: 10.1016/j.cell.2013.03.024. PubMed DOI PMC

Gallo A, Vukic D, Michalik D, O’Connell MA, Keegan LP. ADAR RNA editing in human disease; more to it than meets the I. Hum. Genet. 2017;136:1265–1278. doi: 10.1007/s00439-017-1837-0. PubMed DOI

Walkley CR, Li JB. Rewriting the transcriptome: adenosine-to-inosine RNA editing by ADARs. Genome Biol. 2017;18:205. doi: 10.1186/s13059-017-1347-3. PubMed DOI PMC

Liddicoat BJ, et al. RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself. Science. 2015;349:1115–1120. doi: 10.1126/science.aac7049. PubMed DOI PMC

Mannion NM, et al. The RNA-editing enzyme ADAR1 controls innate immune responses to RNA. Cell Rep. 2014;9:1482–1494. doi: 10.1016/j.celrep.2014.10.041. PubMed DOI PMC

Pestal K, et al. Isoforms of RNA-editing enzyme ADAR1 independently control nucleic acid sensor MDA5-driven autoimmunity and multi-organ development. Immunity. 2015;43:933–944. doi: 10.1016/j.immuni.2015.11.001. PubMed DOI PMC

Higuchi M, et al. Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2. Nature. 2000;406:78–81. doi: 10.1038/35017558. PubMed DOI

Krestel HE, et al. A genetic switch for epilepsy in adult mice. J. Neurosci. 2004;24:10568–10578. doi: 10.1523/JNEUROSCI.4579-03.2004. PubMed DOI PMC

Keegan LP, et al. Functional conservation in human and Drosophila of Metazoan ADAR2 involved in RNA editing: loss of ADAR1 in insects. Nucleic Acids Res. 2011;39:7249–7262. doi: 10.1093/nar/gkr423. PubMed DOI PMC

Keegan L, Khan A, Vukic D, O’Connell M. ADAR RNA editing below the backbone. Rna. 2017;23:1317–1328. doi: 10.1261/rna.060921.117. PubMed DOI PMC

Palladino MJ, Keegan LP, O’Connell MA, Reenan RA. A-to-I pre-mRNA editing in Drosophila is primarily involved in adult nervous system function and integrity. Cell. 2000;102:437–449. doi: 10.1016/S0092-8674(00)00049-0. PubMed DOI

Robinson, J., Paluch, J., Dickman, D. & Joiner, W. ADAR-mediated RNA editing suppresses sleep by acting as a brake on glutamatergic synaptic plasticity. Nat. Commun.7, 10512 (2016). PubMed PMC

Luo D, Kohlway A, Pyle AM. Duplex RNA activated ATPases (DRAs) platforms for RNA sensing, signaling and processing. RNA Biol. 2013;10:111–120. doi: 10.4161/rna.22706. PubMed DOI PMC

Jepson JE, et al. Engineered alterations in RNA editing modulate complex behavior in Drosophila: regulatory diversity of adenosine deaminase acting on RNA (ADAR) targets. J. Biol. Chem. 2011;286:8325–8337. doi: 10.1074/jbc.M110.186817. PubMed DOI PMC

Zhang R, Deng P, Jacobson D, Li JB. Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing. PLoS Genet. 2017;13:e1006563. doi: 10.1371/journal.pgen.1006563. PubMed DOI PMC

Benzer S. Behavioral mutants of Drosophila isolated by countercurrent distribution. Proc. Natl Acad. Sci. USA. 1967;58:1112–1119. doi: 10.1073/pnas.58.3.1112. PubMed DOI PMC

Keegan LP, et al. Tuning of RNA editing by ADAR is required in Drosophila. Embo J. 2005;24:2183–2193. doi: 10.1038/sj.emboj.7600691. PubMed DOI PMC

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. doi: 10.1017/S1355838200000248. PubMed DOI PMC

Matthews MM, et al. Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity. Nat. Struct. Mol. Biol. 2016;23:426–433. doi: 10.1038/nsmb.3203. PubMed DOI PMC

Savva, Y. A. et al. Auto-regulatory RNA editing fine-tunes mRNA re-coding and complex behaviour in Drosophila. Nat. Commun.3, 10.1038/ncomms1789 (2012). PubMed PMC

Cho DS, et al. Requirement of dimerization for RNA editing activity of adenosine deaminases acting on RNA. J. Biol. Chem. 2003;278:17093–17102. doi: 10.1074/jbc.M213127200. PubMed DOI

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. doi: 10.1093/emboj/cdg327. PubMed DOI PMC

Deddouche S, et al. The DExD/H-box helicase Dicer-2 mediates the induction of antiviral activity in drosophila. Nat. Immunol. 2008;9:1425–1432. doi: 10.1038/ni.1664. PubMed DOI

Paradkar PN, Trinidad L, Voysey R, Duchemin J-B, Walker PJ. Secreted Vago restricts West Nile virus infection in Culex mosquito cells by activating the Jak-STAT pathway. Proc. Natl Acad. Sci. 2012;109:18915–18920. doi: 10.1073/pnas.1205231109. PubMed DOI PMC

Galiana-Arnoux D, Dostert C, Schneemann A, Hoffmann JA, Imler JL. Essential function in vivo for Dicer-2 in host defense against RNA viruses in drosophila. Nat. Immunol. 2006;7:590–597. doi: 10.1038/ni1335. PubMed DOI

Lee YS, et al. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell. 2004;117:69–81. doi: 10.1016/S0092-8674(04)00261-2. PubMed DOI

Paradkar PN, Duchemin J-B, Voysey R, Walker PJ. Dicer-2-dependent activation of Culex Vago occurs via the TRAF-Rel2 signaling pathway. PLoS Neglected Tropical Dis. 2014;8:e2823. doi: 10.1371/journal.pntd.0002823. PubMed DOI PMC

Maldonado C, Alicea D, Gonzalez M, Bykhovskaia M, Marie B. Adar is essential for optimal presynaptic function. Mol. Cell. Neurosci. 2013;52:173–180. doi: 10.1016/j.mcn.2012.10.009. PubMed DOI PMC

Rice GI, et al. Mutations in ADAR1 cause Aicardi-Goutieres syndrome associated with a type I interferon signature. Nat. Genet. 2012;44:1243–1248. doi: 10.1038/ng.2414. PubMed DOI PMC

Livingston JH, et al. A type I interferon signature identifies bilateral striatal necrosis due to mutations in ADAR1. J. Med Genet. 2014;51:76–82. doi: 10.1136/jmedgenet-2013-102038. PubMed DOI

Vitali P, Scadden AD. Double-stranded RNAs containing multiple IU pairs are sufficient to suppress interferon induction and apoptosis. Nat. Struct. Mol. Biol. 2010;17:1043–1050. doi: 10.1038/nsmb.1864. PubMed DOI PMC

Scadden AD, Smith CW. Specific cleavage of hyper-edited dsRNAs. Embo J. 2001;20:4243–4252. doi: 10.1093/emboj/20.15.4243. PubMed DOI PMC

Louber J, Brunel J, Uchikawa E, Cusack S, Gerlier D. Kinetic discrimination of self/non-self RNA by the ATPase activity of RIG-I and MDA5. BMC Biol. 2015;13:54. doi: 10.1186/s12915-015-0166-9. PubMed DOI PMC

Rawling DC, Fitzgerald ME, Pyle AM. Establishing the role of ATP for the function of the RIG-I innate immune sensor. Elife. 2015;4:e09391. doi: 10.7554/eLife.09391. PubMed DOI PMC

Anchisi S, Guerra J, Garcin D. RIG-I ATPase activity and discrimination of self-RNA versus non-self-RNA. MBio. 2015;6:e02349–02314. doi: 10.1128/mBio.02349-14. PubMed DOI PMC

Lawlor KT, et al. Double-stranded RNA is pathogenic in Drosophila models of expanded repeat neurodegenerative diseases. Hum. Mol. Genet. 2011;20:3757–3768. doi: 10.1093/hmg/ddr292. PubMed DOI

Khan A, et al. Membrane and synaptic defects leading to neurodegeneration in Adar mutant Drosophila are rescued by increased autophagy. BMC Biol. 2020;18:15. doi: 10.1186/s12915-020-0747-0. PubMed DOI PMC

Kehl, S. R. et al. TAK1 converts Sequestosome 1/p62 from an autophagy receptor to a signaling platform. EMBO reports20 (2019). PubMed PMC

Gurung, S., Evans, A. J., Wilkinson, K. A. & Henley, J. ADAR2 mediated Q/R editing of GluK2 regulates homeostatic plasticity of kainate receptors. bioRxiv, 10.1101/308650 (2018). PubMed

Penn AC, Balik A, Greger IH. Reciprocal regulation of A-to-I RNA editing and the vertebrate nervous system. Front Neurosci. 2013;7:61. doi: 10.3389/fnins.2013.00061. PubMed DOI PMC

Ren X, et al. Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9. Proc. Natl Acad. Sci. USA. 2013;110:19012–19017. doi: 10.1073/pnas.1318481110. PubMed DOI PMC

Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. doi: 10.1186/s13059-014-0550-8. PubMed DOI PMC

Anders S, Reyes A, Huber W. Detecting differential usage of exons from RNA-seq data. Genome Res. 2012;22:2008–2017. doi: 10.1101/gr.133744.111. PubMed DOI PMC

Reyes A, et al. Drift and conservation of differential exon usage across tissues in primate species. Proc. Natl Acad. Sci. USA. 2013;110:15377–15382. doi: 10.1073/pnas.1307202110. PubMed DOI PMC

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...