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Non-infected cells were used as controls. For affinity purification of NS5, 10 million cells were lysed in 1 ml of IP lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, Complete protease inhibitor tablet (EDTA-free) and 0.5% IGEPAL CA-630) for 30 min at 4°C. Lysates were clarified by centrifugation at 5,000g for 20 min at 4°C. Clarified lysates were incubated with 10 µg of anti-TBEV NS5 antibody overnight at 4°C. Following incubation, 40 µl of Pierce Protein A/G magnetic beads (#88802, Thermo Fisher Scientific) were added to lysates – antibody mixture, and incubated for 2 hours at 4°C. Beads were washed four times with IP washing buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% IGEPAL CA-630). 3 µL of beads were eluted with 1X Protein Sample Loading Buffer (Li-Cor Bioscience) and 1X NuPAGE reducing agent (Thermo Fisher Scientific). The eluate was analyzed by SDS PAGE and silver staining (Pierce). For MS, immunoprecipitates were directly digested on beads. Beads were washed once and resuspended with 40 µl of 2M urea, 50 mM Tris pH 8.0 and 1 mM DTT, and incubated for 30 min at 37°C with shaking at 700 rpm. Iodoacetamide (Sigma-Aldrich) was added to 3 mM final concentration and incubated at room temperature for 45 min in the dark with shaking. Digestion was performed by adding 3 mM DTT and 750 ng of sequencing grade modified trypsin (Promega) and incubating at 37°C with shaking overnight. Finally, supernatants were collected to fresh tubes and an additional 500 ng of sequencing grade modified trypsin was added and incubated for 2 hours at 37°C with shaking. Digested samples were desalted using C18 solid phase extraction columns (C18 BioPurSPN, Nest Group) according to the manufacturer’s instructions. Desalted samples were vacuum centrifuged to dryness and resuspended in 0.1% formic acid for mass spectrometry analysis.PrideNot availableTo build a spectral library, samples from each set of biological replicates were pooled and acquired in data-dependent manner. Data-dependent acquisition (DDA) was performed by acquiring a full scan over a m/z range of 375-1025 in the Orbitrap at 120,000 resolving power (@ 200 m/z) with a normalized AGC target of 100%, an RF lens setting of 30%, and an instrument-controlled ion injection time. Dynamic exclusion was set to 30 seconds, with a 10 p.p.m. exclusion width setting. Peptides with charge states 2-6 were selected for MS/MS interrogation using higher energy collisional dissociation (HCD) with a normalized HCD collision energy of 28%, with 3 seconds of MS/MS scans per cycle. Data-independent analysis (DIA) was performed on all individual samples. A full scan was collected at 60,000 resolving power over a scan range of 390-1010 m/z, an instrument controlled AGC target, an RF lens setting of 30%, and an instrument controlled maximum injection time, followed by DIA scans using 8 m/z isolation windows over 400-1000 m/z at a normalized HCD collision energy of 28%. The Spectronaut algorithm was used to build spectral libraries from DDA data, identify peptides/proteins, and extract intensity information from DIA data [56]. DDA data were searched against the Homo sapiens UniProt reference proteome (downloaded on August 23, 2023) and TBEV protein sequences. False discovery rates were estimated using a decoy database strategy. All data were filtered to achieve a false discovery rate of 0.01 for peptide-spectrum matches, peptide identifications, and protein identifications. Search parameters included a fixed modification for carbamidomethyl cysteine and variable modifications for N-terminal protein acetylation, and methionine oxidation. All other search parameters were Biognosys factory defaults.ProteomicsJeffrey JohnsonIcahn School of Medicine at Mount SinaiPARTIALHomo Sapiens (human)jeffrey.johnson@mssm.eduNot availableIcahn School of Medicine at Mount SinaiUnited StatesfalseNuclear activities and interactome of the NS5 protein of Tick-Borne Encephalitis VirusOrthoflaviviruses are RNA viruses responsible for significant diseases in humans, domesticated animals and wildlife. Their NS5 protein is central in viral replication, functioning both as an RNA-dependent RNA polymerase and a methyltransferase, while also modulating cellular processes, including the interferon response. Although viral replication is cytoplasmic, the NS5 protein of several mosquito-borne orthoflaviviruses cycles between the cytoplasm and the nucleus of infected human cells. However, the nuclear localization and function of NS5 of tick-borne orthoflaviviruses, such as tick-borne encephalitis virus (TBEV), remained poorly understood. Microscopy analysis and cell fractionation revealed that the NS5 protein of TBEV localized to both the cytoplasm and nucleoplasm of infected cells. Mutagenesis studies identified critical residues required for its nuclear targeting. Mutating these residues in a TBEV replicon abolished viral replication. Immunoprecipitation-mass spectrometry analyses performed in two human cell lines infected with TBEV recovered 352 NS5 partners. Among them, 187 were nuclear or partially nuclear. By integrating our interactome data with that of Powassan virus (POWV), another tick-borne orthoflavivirus, we refined a list of 20 high-confidence NS5 partners, including splicing factors and chromatin modulators. Functional analysis revealed that seven of these nuclear partners significantly modulated viral replication, further underscoring the importance of nuclear NS5 in the viral life cycle. Our work advances our understanding of the nuclear function of the NS5 proteins of tick-borne orthoflaviviruses.2026-07-282026-07-09PXD080823NEWT:3555NEWT:71647NEWT:330879NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:10245NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:43186NEWT:428146NEWT:498257NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:661410NEWT:638632NEWT:263737NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:383379NEWT:1401257NEWT:418106NEWT:10029NEWT:913645NEWT:44491NEWT:641809NEWT:27933NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:79329NEWT:4442NEWT:192875NEWT:1214915NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:160621NEWT:212790NEWT:931281NEWT:4432NEWT:5762NEWT:5763NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NEWT:2246NEWT:2652724NEWT:1912919NEWT:5757NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:752555NEWT:498211NEWT:5759NEWT:1736231NEWT:5518NEWT:398007NEWT:1392NEWT:498217NEWT:498216NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:1367269NEWT:145458NEWT:633149NEWT:1149786NEWT:10239NEWT:68895NEWT:44685NEWT:161934NEWT:4897NEWT:1148NEWT:5744NEWT:5508NEWT:3329NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1235816NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1287689NEWT:1390NEWT:11557NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:3711NEWT:935293NEWT:375146NEWT:2065263NEWT:1772NEWT:118698NEWT:1616117NEWT:263NEWT:118696NEWT:52283NEWT:11988NEWT:284812NEWT:8175NEWT:400667NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:459758NEWT:3702NEWT:243277NEWT:1246791NEWT:7067NEWT:118694NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:7070NCBITaxon:287NEWT:408172NEWT:408170NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:1436733NEWT:460519NEWT:1247411NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:9483NEWT:333760NEWT:56636NEWT:1513458NEWT:1233681NCBITaxon:40559NEWT:506599NEWT:2853422NEWT:81077NEWT:84588NEWT:1679718NEWT:480NEWT:65349NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NCBITaxon:4932NEWT:109760NEWT:943274NEWT:644223NEWT:235443NEWT:108458NEWT:5936NEWT:272623NEWT:272624NEWT:320637NEWT:983964NEWT:118499NEWT:11706NEWT:32644NEWT:527796NEWT:1130798NEWT:55529NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1116234NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:3983NEWT:352472NEWT:1071661NEWT:1202532NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:1218097NCBITaxon:50557NEWT:39251NEWT:39491NCBITaxon:5811NEWT:29491NEWT:101841NEWT:2014887NEWT:33952NEWT:153009NEWT:261756NEWT:571256NEWT:40483NEWT:63366NEWT:63367NEWT:688333NEWT:215402NCBITaxon:548681NEWT:318586NEWT:272634NEWT:198107NEWT:9031NEWT:1872122NEWT:1308NEWT:7091NEWT:1034015NEWT:760568NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:97477NEWT:7111NEWT:347515NEWT:172269NEWT:9534NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:8694NEWT:4093NEWT:4096NEWT:8692NEWT:2903NEWT:185579NEWT:941442NEWT:536088NEWT:13076NEWT:1226408NEWT:7108NEWT:40479NEWT:43989NEWT:4076NEWT:142615NEWT:317NEWT:1006581NEWT:885318NEWT:39488NEWT:550NEWT:4081NEWT:273068NEWT:554NEWT:98334NEWT:451516NEWT:552NEWT:4084NEWT:63577NEWT:36185NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:114155NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:8654NEWT:8658NEWT:1268063NEWT:8655NEWT:5147NEWT:98351NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:207559NEWT:407821NCBITaxon:2NEWT:85057NEWT:985076NEWT:568708NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:267671NEWT:28532NEWT:353152NEWT:8496NEWT:7165NEWT:27448NEWT:40674NEWT:1194669NEWT:51329NEWT:243230NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:1328388NEWT:104395NEWT:9557NEWT:6289NEWT:377586NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:9554NEWT:118562NEWT:725NEWT:7137NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:214053NEWT:80863NEWT:90675NEWT:105231NEWT:104385NEWT:74649NEWT:52638NEWT:57075NEWT:206672NEWT:4097NEWT:8697NEWT:8695NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:9545NEWT:7370NEWT:9793NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:255470NEWT:27457NEWT:38783NEWT:4006NEWT:6426NCBITaxon:5476NEWT:6669NEWT:9935NEWT:89453NEWT:287889NEWT:1114301NEWT:51515NEWT:588596NEWT:51511NEWT:8845NEWT:92867NEWT:92866NEWT:419610NEWT:5334NEWT:51750NEWT:202950NEWT:382352NEWT:413071NCBITaxon:10239NCBITaxon:714NEWT:295027NCBITaxon:11320NEWT:632957NEWT:11051NEWT:9925NEWT:89462NCBITaxon:9606NEWT:452680NEWT:8839NEWT:90690NEWT:1436183NEWT:4232NEWT:2758385NEWT:416348NEWT:11298NEWT:171101NEWT:714NEWT:5322NEWT:421932NEWT:312017NEWT:196627NEWT:200308NEWT:553470NEWT:200302NEWT:870435NEWT:284593NEWT:100392NEWT:5315NEWT:9913NEWT:265872NEWT:105841NEWT:337330NEWT:2666255NEWT:2285NEWT:999810NCBITaxon:5693NEWT:28995NEWT:1392998NEWT:380394NEWT:981087NEWT:180066NEWT:226900NEWT:1266738NEWT:231490NEWT:244704NEWT:7725NEWT:430615NEWT:563041NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1416333NEWT:35024NEWT:135461NEWT:1678078NEWT:7962NEWT:749906NEWT:418985NEWT:1817808NEWT:749907NEWT:145262NEWT:145263NEWT:69014NEWT:142809NEWT:694569NEWT:27606NEWT:9739NEWT:59202NEWT:9975NEWT:8643NEWT:51953NEWT:3197NEWT:860688NEWT:13443NEWT:8644NEWT:36329NEWT:62615NEWT:5141NEWT:46360NCBITaxon:3044782NEWT:1333550NEWT:160235NEWT:72407NEWT:8639NEWT:1928434NEWT:8637NEWT:349741NEWT:409859NEWT:157295NEWT:2096NEWT:509169NEWT:3051137NEWT:192222NEWT:9721NEWT:137221NEWT:9963NEWT:1617910NEWT:565050NEWT:409860NEWT:2785785NEWT:411901NEWT:8626NEWT:105884NCBITaxon:9615NEWT:8621NEWT:58334NEWT:452659NEWT:1193501NEWT:58331NEWT:6689NEWT:8624NEWT:5116NEWT:8623NEWT:5597NCBITaxon:3077NEWT:298315NEWT:8618NEWT:70448NEWT:9704NEWT:698936NEWT:8855NEWT:9940NEWT:3168NEWT:1247190NEWT:521001NEWT:192011NEWT:1813887NEWT:118702NEWT:118700NEWT:2126719NEWT:224911NEWT:118705NCBITaxon:11552NEWT:334249NEWT:6945NEWT:184922NEWT:6703NEWT:2104NEWT:6943NEWT:2NEWT:157546NEWT:870726NEWT:474186NEWT:38942NEWT:1493NEWT:307972NEWT:1496NEWT:2102NEWT:3674NEWT:660469NEWT:1365186NEWT:38949NEWT:45474NEWT:1299114NEWT:1590841NEWT:2282334NEWT:4513NEWT:1247NEWT:70667NEWT:869728NEWT:5843NEWT:6938NEWT:376741NCBITaxon:39054NCBITaxon:10407NEWT:1736309NEWT:4751NEWT:10360NEWT:47664NEWT:317548NEWT:15819NEWT:3654NEWT:237561NEWT:1085956NEWT:5833NEWT:3659NEWT:6928NEWT:1239NEWT:36745NEWT:499229NEWT:400727NEWT:272563NEWT:11009NEWT:82688NEWT:5823NEWT:3885NEWT:3888NEWT:5821NEWT:44139NEWT:649408NCBITaxon:4895NCBITaxon:4896NEWT:6915NEWT:3649NEWT:101510NEWT:28903NEWT:3880NEWT:272559NEWT:28909NEWT:515849NEWT:3641NEWT:466585NEWT:1000589NEWT:85963NEWT:85962NEWT:42197NEWT:143361NEWT:12993NEWT:398580NEWT:4565NEWT:1264690NEWT:515619NEWT:1299NEWT:316407NEWT:34305NCBITaxon:183674NEWT:167387NEWT:84645NEWT:44586NEWT:1123294NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:5888NEWT:211586NEWT:747078NEWT:1282NEWT:1283NEWT:431241NEWT:4550NEWT:1000561NEWT:2133NEWT:4555NEWT:294381NEWT:197NEWT:1390363NEWT:35889NEWT:288705NEWT:29176NEWT:4787NEWT:3217NEWT:4547NEWT:3218NEWT:556182NEWT:1270NEWT:374990NEWT:1432059NEWT:154293NEWT:156471NEWT:4784NEWT:3694NEWT:360106NEWT:156476NEWT:4543NEWT:4785NEWT:360104NEWT:1857017NEWT:10117NEWT:10359NEWT:10116NEWT:1280NEWT:10358NEWT:1735272NEWT:83334NEWT:83332NEWT:317513NEWT:580240NEWT:294128NEWT:11676NEWT:100226NEWT:718308NEWT:4530NEWT:54126NEWT:75058NEWT:13616NEWT:172NEWT:296543NEWT:173NEWT:316435NEWT:42157NEWT:1895NEWT:1034304NEWT:105023NEWT:866628NEWT:215358NEWT:64152NEWT:4924NEWT:749200NEWT:2748NEWT:8049NEWT:9378NEWT:990346NEWT:145953NEWT:257309NEWT:100816NEWT:203124NEWT:192952NEWT:230741NEWT:8296NEWT:117008NCBITaxon:1313NEWT:167748NEWT:44544NEWT:529818NEWT:400540NEWT:4911NEWT:645463NEWT:152480NEWT:129249NEWT:1077286NEWT:943129NEWT:1221594NEWT:990119NEWT:77216NEWT:1111708NEWT:227321NEWT:493760NEWT:281677NEWT:106590NEWT:260710NEWT:257313NEWT:3827NEWT:400772NEWT:128161NEWT:930945NEWT:1162296NEWT:106592NEWT:46704NEWT:482428NEWT:1187947NEWT:269796NEWT:10312NCBITaxon:1773NEWT:54571NEWT:9598NEWT:8030NEWT:1423772NEWT:53232NEWT:1639NEWT:188229NEWT:246437NEWT:3818NEWT:4909NEWT:759272NEWT:432359NEWT:1182263NEWT:943146NEWT:2711NEWT:537457NEWT:9103NEWT:715877NEWT:862238NEWT:29159NEWT:10306NEWT:9595NEWT:8022NEWT:145943NEWT:595536NEWT:240906NEWT:593117NEWT:89920NEWT:29158NEWT:3633NEWT:3635NEWT:5811NEWT:3879NEWT:180923NEWT:1328881NEWT:411483NEWT:76336NEWT:3870NEWT:884019NEWT:198215NEWT:411490NEWT:200298NEWT:169963NEWT:587NEWT:588NEWT:585NEWT:343NEWT:225117NEWT:746128NEWT:5801NEWT:43665NEWT:212035NCBITaxon:1653394NEWT:1266464NEWT:1205NEWT:367830NEWT:178616NEWT:375451NEWT:357NEWT:9172NEWT:2770979NEWT:2010198NEWT:1277351NEWT:457428NEWT:106178NEWT:411469NEWT:84023NEWT:1679NEWT:559292NEWT:569NEWT:411464NEWT:411460NEWT:2762NEWT:1174673NEWT:1328426NEWT:562NEWT:28035NEWT:411470NEWT:2094720NCBITaxon:2697049NCBITaxon:138NEWT:28038NEWT:1663NEWT:62141NEWT:1423NEWT:4932NEWT:3603NEWT:2756NEWT:2759NEWT:3848NEWT:3847NEWT:38293NEWT:1428NEWT:339NEWT:327159NEWT:178876NEWT:1660NEWT:2751NEWT:327160NEWT:573NEWT:571NEWT:12922NEWT:241368NEWT:518766NEWT:42528NEWT:2664373NEWT:190802NEWT:9417NEWT:1216979NEWT:7237NEWT:509924NEWT:115104NEWT:1121114NEWT:663NEWT:8570NEWT:1081927NEWT:1238993NEWT:67825NEWT:187878NEWT:220668NEWT:1821314NEWT:1249668NEWT:426430NEWT:9407NEWT:9646NEWT:5286NEWT:7227NEWT:7469NEWT:9402NEWT:9644NEWT:415540NEWT:675060NEWT:334542NEWT:313625NEWT:27592NEWT:426428NEWT:227289NEWT:63459NEWT:127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