TY - JOUR T1 - Proteogenomics of adenosine-to-inosine RNA editing in fruit fly JF - bioRxiv DO - 10.1101/101949 SP - 101949 AU - Ksenia G. Kuznetsova AU - Irina Y. Ilina AU - Alexey L. Chernobrovkin AU - Svetlana E. Novikova AU - Tatyana E. Farafonova AU - Dmitry S. Karpov AU - Mark V. Ivanov AU - Olga E. Voronko AU - Ekaterina V. Ilgisonis AU - Anna A. Kliuchnikova AU - Victor G. Zgoda V AU - Roman A. Zubarev AU - Mikhail V. Gorshkov AU - Sergei A. Moshkovskii Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/01/30/101949.abstract N2 - Adenosine-to-inosine RNA editing is one of the most common types of RNA editing, a posttranscriptional modification made by special enzymes. We present a proteomic study on this phenomenon for Drosophila melanogaster. Tree deep proteome data sets for Canton-S fruit fly line were used in the study: two taken from public repository and the third one obtained here for the isolated brains. A customized protein sequence database was generated using results of genome-wide adenosine-to-inosine RNA studies in fruit fly and applied for identifying the edited proteins. The total number of 56 edited proteins was found in all data sets, 7 of them being shared between the whole insect, head and brain proteomes. Two edited sites in syntaxin 1A (Syx1a) and complexin (cpx) belonging to a presynaptic vesicle fusion complex were selected for validation by targeted analysis. The results obtained for two selected peptides using Multiple Reaction Monitoring have shown remarkably constant ratios of unedited-to-edited protein variants in flies raised under different ambient temperatures of 10, 20 and 30°C. Specifically, these ratios were 34.5:1 and 2.1:1 for Syx1a and cpx, respectively. The work demonstrates the feasibility to identify the RNA editing event at the proteome level using shotgun proteomics and customized edited protein database.BCAbicinchoninic acidTEABCtriethylammonium bicarbonateIAMiodoacetamiderpmrounds per minuteHCDhigher-energy collisional dissociationVAIVariant Annotation IntegratorRADARrigorously annotated database of A-to-I RNA editingADARadenosine deaminase, RNA specific.FDRfalse discovery ratePSMpeptide spectrum matchFmoc9-fluorenyl methyloxy carbonylOtButert-butylDMFdimethylformamideHCTUO-(1H-6-Chloro-benzotriazole-1-yl)-1,1,3,3-tetramethylaminium hexafluorophosphateTMP2,4,6-TrimethylpyridineTISTriisopropylsilaneQqQtriple quadruploleCVcoefficient of varianceSNPsingle nucleotide polymorphismSNARESNAP (Soluble NSF Attachment Protein) REceptorGOgene ontologyMRMmultiple reaction monitoringCEcollision energy ER -