Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065397/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065397/RPS4B_combined_psm.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065397/RPS5_combined_psm.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065397/20250617_009_S961322_RPS4B_WT_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065397/20250530_009_S950061_RPS5_WT_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065397/20250617_004_S961318_RPS4B_KD_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065397/20250617_002_S961316_RPS4B_KD_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065397/20250617_003_S961317_RPS4B_KD_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065397/20250530_013_S950065_RPS5_KD_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065397/20250530_014_S950066_RPS5_KD_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065397/20250530_012_S950064_RPS5_KD_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065397/20250617_010_S961323_RPS4B_WT_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065397/20250530_011_S950063_RPS5_WT_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065397/20250530_010_S950062_RPS5_WT_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD065397/20250617_011_S961324_RPS4B_WT_3.rawprimaryOK200cyril.zipfel@botinst.uzh.chKyle W. BenderData-dependent acquisitionMass SpectrometryBottom-up proteomicsBik1PhosphorylationIn vitrohttps://www.ebi.ac.uk/pride/archive/projects/PXD0653971 ug of kinase and substrate were combined in a 25 ul volume and reactions were initiated by the addition of ATP to a final concentration of 100 uM. Reactions were stopped by the addition of 25 ul of 7.4 M urea, 10 mM TCEP, and 30 mM CAA and heating at 60 degrees C for 60 minutes. Reactions were diluted to 250 ul with 50 mM ammonium bicarbonate and digested with either Asp-N (RPS4B) or trypsin+Asp-N (sequentially, RPS5). Peptides were cleaned up using the StageTip method and analyzed on an Exploris 480 Orbitrap mass spectrometer downstream of a Waters M-Class LC system.PrideNot availableRaw files were processed using MSFragger (version 4.2) implemented in fragpipe (version 23) using default closed-search settings. MS/MS spectra were searched against an E. coli database (Uniprot ID UP000000625, downloaded June 4, 2024) with sequences for HisMBP-RPS4B, HisMBP-RPS5, and His-BIK1 added. Protease was set as Asp-N (for RSP4B) or trypsing+Asp-N (for RPS5), allowing for up to 2 missed cleavages. Carbamidomethylation of cysteines was set as a fixed modification with methionine oxidation, N-terminal acetylation, and phosphorylation of serine, threonine and tyrosine set as variable modifications. Label-free quantification was performed IonQuant (version 1.11.19) using default settings implemented in fragpipe with the match between runs feature enabled.ProteomicsProf. Dr.Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, SwitzerlandPARTIALEscherichia Colikyle.bender@botinst.uzh.ch41663532 Toth R, Choi S, Le Naour-Vernet M, Schwanke F, Johnson JL, Tee EE, Yaron-Barir TM, Khochaba E, Derbyshire P, Colo A, Köster P, Huntsman EM, Herold L, Lee Y, Fernández-Fernández ÁD, Ahn HK, Dindas J, Bjornson M, Rhodes J, Song B, Wang W, Smokvarska M, Bayer EM, Zhou JM, Cantley LC, Jones JDG, Bender KW, Menke FLH, Faulkner C, Zipfel C, DeFalco TA. Motif-based substrate mapping of the receptor-like cytoplasmic kinase BIK1 reveals novel components and regulatory nodes of plant immunity. Nat Plants. 2026 12(2):465-480 10.1038/s41477-025-02218-zInstitute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, SwitzerlandSwitzerlandPlant cell surface pattern recognition receptors (PRRs) perceive non- or altered-self elicitors to induce immune responses. PRRs relay information across the plasma membrane and trigger downstream signalling via receptor-like cytoplasmic kinases such as BOTRYTIS-INDUCED KINASE 1 (BIK1). BIK1 associates with several PRRs and acts as a key executor of immune responses through the phosphorylation of substrate proteins. However, a comprehensive understanding of how BIK1 targets specific substrates and a full repertoire of these substrates are lacking. Here we defined the substrate specificity of BIK1 and used these data to predict candidate substrates in Arabidopsis. Using high-throughput biochemical and genetic screening of these candidates, we confirmed many as direct BIK1 substrates in vitro and novel regulators of plant immunity. Among the BIK1 substrates identified are MULTIPLE C2 DOMAIN AND TRANSMEMBRANE REGION PROTEIN 3, which we reveal regulates flagellin 22 (flg22)-induced plasmodesmata closure and immunity, and members of the largely uncharacterized CYCLIN-DEPENDENT KINASE-LIKE family, which we uncover as novel negative regulators of immunity. In parallel, we interrogated intracellular NUCLEOTIDE-BINDING LEUCINE-RICH REPEAT (NLR) immune receptors for potential BIK1 phosphorylation motifs and identified multiple NLRs as direct BIK1 substrates. We reveal that BIK1 phosphorylation regulates NLR oligomerization, thus controlling a key activation step for these immune receptors. Together, our unbiased biochemical screens shed light on the central role of BIK1 as a key kinase shaping multiple layers of plant immune signalling.Motif-based substrate mapping of the receptor-like cytoplasmic kinase BIK1 reveals novel components and regulatory nodes of plant immunity.Toth Ryan R, Choi Sera S, Le Naour-Vernet Marie M, Schwanke Florian F, Johnson Jared L JL, Tee Estee E EE, Yaron-Barir Tomer M TM, Khochaba Eleanor E, Derbyshire Paul P, Colo Anka A, Köster Philipp P, Huntsman Emily M EM, Herold Laura L, Lee Yoonyoung Y, Fernández-Fernández Álvaro D ÁD, Ahn Hee-Kyung HK, Dindas Julian J, Bjornson Marta M, Rhodes Jack J, Song Beibei B, Wang Weibing W, Smokvarska Marija M, Bayer Emmanuelle M EM, Zhou Jian-Min JM, Cantley Lewis C LC, Jones Jonathan D G JDG, Bender Kyle W KW, Menke Frank L H FLH, Faulkner Christine C, Zipfel Cyril C, DeFalco Thomas A TAfalseIdentification of BIK1-targeted phosphorylation sites on NLRsBIK1 is a central regulator of signaling downstream of the activation of patter recognition receptors and may represent a functional link between pattern- and effector- triggered immunity in plants. Among myriad BIK1 substrates are several intracellular immune receptors. This project aims to map BIK1-targeted phosphorylation sites on two such receptors.2026-03-022025-06-24PXD065397NEWT:3555NEWT:71647NEWT:330879NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:43186NEWT:498257NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:638632NEWT:263737NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:96731NEWT:383379NEWT:10029NEWT:913645NEWT:44491NEWT:641809NEWT:27933NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:79329NEWT:4442NEWT:192875NEWT:12637NEWT:59729NEWT:2164133NEWT:108061NEWT:60711NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:160621NEWT:212790NEWT:931281NEWT:4432NEWT:5762NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NEWT:2246NEWT:2652724NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:752555NEWT:498211NEWT:5759NEWT:1736231NEWT:5518NEWT:398007NEWT:1392NEWT:498217NEWT:498216NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:633149NEWT:10239NEWT:44685NEWT:161934NEWT:4897NEWT:1148NEWT:5744NEWT:5508NEWT:3329NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1287689NEWT:1390NEWT:11557NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:3711NEWT:935293NEWT:375146NEWT:2065263NEWT:118698NEWT:1616117NEWT:263NEWT:118696NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:3702NEWT:243277NEWT:1246791NEWT:7067NEWT:118694NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:7070NEWT:408172NEWT:408170NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1436733NEWT:460519NEWT:1247411NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:333760NEWT:1513458NEWT:1233681NCBITaxon:40559NEWT:506599NEWT:2853422NEWT: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:55529NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1116234NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:3983NEWT:352472NEWT:1071661NEWT:1202532NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:1218097NEWT:39491NCBITaxon:5811NEWT:29491NEWT:2014887NEWT:33952NEWT:153009NEWT:261756NEWT:571256NEWT:40483NEWT:63366NEWT:63367NEWT:688333NEWT:215402NCBITaxon:548681NEWT:272634NEWT:9031NEWT:1872122NEWT:7091NEWT:1034015NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:7111NEWT:347515NEWT:9534NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:8694NEWT:4093NEWT:4096NEWT:8692NEWT:2903NEWT:185579NEWT:941442NEWT:536088NEWT:13076NEWT:1226408NEWT:40479NEWT:43989NEWT:4076NEWT:142615NEWT:317NEWT:1006581NEWT:885318NEWT:39488NEWT:550NEWT:4081NEWT:273068NEWT:554NEWT:98334NEWT:451516NEWT:4084NEWT:63577NEWT:36185NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:114155NEWT:6494NEWT:6491NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:8654NEWT:8658NEWT:1268063NEWT:8655NEWT:98351NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:207559NEWT:407821NCBITaxon:2NEWT:85057NEWT:985076NEWT:568708NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:267671NEWT:28532NEWT:353152NEWT:8496NEWT:7165NEWT:27448NEWT:40674NEWT:1194669NEWT:243230NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:1328388NEWT:9557NEWT:6289NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:9554NEWT:725NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:214053NEWT:80863NEWT:90675NEWT:105231NEWT:74649NEWT:52638NEWT:57075NEWT:4097NEWT:8697NEWT:8695NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:9545NEWT:7370NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:255470NEWT:38783NEWT:4006NEWT:6426NCBITaxon:5476NEWT:6669NEWT:9935NEWT:89453NEWT:287889NEWT:1114301NEWT:51515NEWT:588596NEWT:51511NEWT:8845NEWT:92867NEWT:92866NEWT:5334NEWT:51750NEWT:202950NEWT:382352NEWT:413071NCBITaxon:10239NCBITaxon:714NEWT:295027NCBITaxon:11320NEWT:632957NEWT:11051NEWT:9925NEWT:89462NCBITaxon:9606NEWT:8839NEWT:90690NEWT:1436183NEWT:4232NEWT:2758385NEWT: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:326423NEWT:452467NEWT:198822NEWT:36111NEWT:32642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