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Lahiri"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Chemical cross-linking coupled with mass spectrometry proteomics","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Chromosome replication","Cross-link ms","Phosphoproteomics","Ino80","Yeast ddk"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD053426"],"sample_protocol":["For LC-MS purposes, desalted peptides were injected in an Ultimate 3000 RSLCnano system and separated in a 25-cm analytical column (75µm ID, 1.6µm C18, IonOpticks) with a 50 min gradient from 2 to 35% or 60-min gradient from 2 to 32% ACN in 0.1% formic acid for proteome and phosphoproteome analysis, respectively.Phospho proteome: The effluent from the HPLC was directly electrosprayed into an Orbitrap Exploris-480 operated in data dependent mode to automatically switch between full scan MS and MS/MS acquisition. Survey full scan MS spectra (from m/z 350–1400) were acquired with resolution R=60,000 at 400 m/z (AGC target of 3×106). The 15 most intense peptide ions with charge states between 2 and 5 were sequentially isolated to a target value of 2×105, fragmented at 30% normalized collision energy and acquired with resolution R=15,000. Typical mass spectrometric conditions were: spray voltage, 1.5 kV; no sheath and auxiliary gas flow; heated capillary temperature, 275° C; ion selection threshold, 5×103 counts. For phosphopeptides, MS2 resolution was increased to R=30,000 and ion selection threshold to 3×104 counts.nWhole proteome: Eluting peptides were ionized in a nanoESI source and on-line detected on a QExactive HF mass spectrometer. The mass spectrometer was operated in a TOP10 method in positive ionization mode, detecting eluting peptide ions in the m/z range from 375 to 1,600 and performing MS/MS analysis of up to 10 precursor ions. Peptide ion masses were acquired at a resolution of 60,000 (at 200 m/z). High-energy collision induced dissociation (HCD) MS/MS spectra were acquired at a resolution of 15,000 (at 200 m/z). All mass spectra were internally calibrated to lock masses from ambient siloxanes. Precursors were selected based on their intensity from all signals with a charge state from 2+ to 5+, isolated in a 2 m/z window and fragmented using a normalized collision energy of 27%. To prevent repeated fragmentation of the same peptide ion, dynamic exclusion was set to 20 s.  Cross-linking mass spectrometry The INO80 complex (1 µg in total of INO80 or INO80-AA) was cross-linked for 20 min at 30° C on a thermomixer at 1200 rpm. Cross-linked product was separated on SDS-PAGE followed by silver staining. The optimal INO80 concentration was determined be 25 µg and 15 µg at 1200 rpm, 20 min, 30° C. The optimal DSBU cross-linker concentration for INO80 was 58 µM and for the INO80-AA was 100 µM. The reaction with optimal protein and cross-liner concentration was performed at 1200 rpm, 20 min, 30° C. The reaction was quenched by adding ammonium bicarbonate to a final concentration of 100 mM and incubated for 10 min at 30°C subsequently followed by protein denaturation, alkylation, and tryptic digest. Cross-linked samples were denatured by adding two sample volumes of 8 M urea, reduced with 5 mM Tris (2-carboxyethyl) phosphine (TCEP) and alkylated by the addition of 10 mM iodoacetamide (IAM) for 40 min at RT in the dark. Proteins were digested with 0.5 μg Lys-C at 35°C for 2 hr, diluted with 50 mM ammonium bicarbonate, and digested with trypsin 0.5 μg overnight. Peptides were acidified with 1% trifluoroacetic acid (TFA) and purified by reversed phase chromatography using C18 material (Empore) on C18 stage tips. Further, cross-linked peptides were enriched on a Superdex Peptide PC 3.2/30 column using water/acetonitrile/TFA (75/25/0.1) as mobile phase at a flow rate of 50 μl/min. Fractions containing cross-linked peptides were analysed by liquid chromatography (Dionex 3000, Thermo Fisher Scientific) coupled to tandem mass spectrometry (LC-MS/MS) using a TimsTOF Pro instrument (Bruker Daltonics). LC-MS Analysis of enriched cross-linked peptides Cross-linked peptides were injected and separated on a PepSep column (25 cm, inner diameter 150 µm, Bruker Daltonics) by an online reversed-phase chromatography with a 50 min gradient from 3 to 43 % of Buffer B containing 100% ACN, 0.1% formic acid) at a flow rate of 300 nl/min. Eluting peptides were directly sprayed through the CSI source into the TimsTOF Pro. Each sample was measured in three independent technical replicates. The mass spectrometric measurement was performed in data-dependent acquisition mode with a top 10 method. The same settings were applied as described. As template the standard DDA-PASEF MS Method provided by Bruker Daltonics was used. Only precursor ions of +3 to +8 charge (in case for DSBU +2 to +8 charge) were selected for fragmentation scan. Raw data files were searched with MaxQuant software package (version 2.0.2.0) with following parameters: Enzyme specificity set to trypsin with a maximum number of missed cleavages 3; DSBU specificity linking (K,S,T,Y); fixed modifications carbamidomethyl (C); variable modifications, oxidation (M). PSM FDR crosslink set to 5%. Inter- and Intra-Crosslinks were filtered by applying an MS1 tolerance window of -3 to 3 ppm and a score ≥ 60. Cross-links were visualized as network plots using the webserver xiNET."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["MaxQuant search parameters: For phospho proteome identification, MaxQuant 2.0.3.0 software package was used. Parent ion and fragment mass tolerances were 8 ppm and 0.5 Da, respectively, and allowance for two missed cleavages was made. Yeast canonical protein database from UniProt (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)), filtered to retain only the reviewed entries were used for the searches. Regular MaxQuant conditions were the following: site FDR, 0.01; protein FDR, 0.05; minimum peptide length, 6; variable modifications, oxidation (M); phospho (STY); fixed modifications, carbamidomethyl (C); peptides for protein quantitation, razor and unique; minimum peptides, 2; minimum ratio count, 2. Proteins were validated on the basis of at least one unique peptide detected in the proteome of all the three replicates or in at least two of the three replicates. For whole proteome identification, MaxQuant search parameters were identical except for the variable modifications, which were oxidation (M); acetyl (protein N-term); acetyl (K); dimethyl (KR); methyl (KR). Data analysis: The phospho-proteomics data was analysed using an R-script developed in-house. Differential and quantitative analysis was performed using phospho-sites with a 75% or higher probability of occurrence (according to MaxQuant output). Phospho-sites and proteins that were present in at least 75% of the replicates were considered for the downstream analysis. Intensity based absolute quantification (iBAQ) values were used to quantify the abundance of phospho-sites and compare it in different conditions. Differential expression analysis at the whole and phospho proteome level was carried out using the DEP package. Briefly, after filtering for all the experimental and analytical contaminants missing values were imputed by the Bayesian principal component analysis (BPCA) method followed by limma statistical analysis (Zhang et al., 2018) using a p-value cut-off of 0.05. The phospho-site abundances were normalised to the total protein abundance of the respective proteins.  GO term analysis: GO term analysis for the corresponding proteins of the overlapping phosphosites within the DDK active fractions of sc7-4 and Hydroxyurea screens were performed in ImShot (Aftab et al., 2022) Pusing the following parameters: p-value cutoff – 0.05, p-value adjustment – Benjamini-Hochberg (BH), Database: org.Sc.sgd.db, Redundancy removed, Minimal and maximal size of genes – 1 and 500 respectively."],"omics_type":["Proteomics"],"labhead":["Axel Imhof"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Histone Modifications Group Zentrallabor für Proteinanalytik BioMedical Center Faculty of Medicine Ludwig-Maximilians-University of Munich Germany"],"species":["Saccharomyces Cerevisiae (baker's Yeast)"],"publication":["41904138 Bansal P, Lahiri S, Kumar CN, Furtmeier J, Spechtenhauser L, Galanti L, Barba Tena JD, Chacin E, Linder G, Ortíz-Bazán MÁ, Müller M, Vizjak P, Straub T, Mueller-Planitz F, Stigler J, Aguilera A, Gómez-González B, Pfander B, Korber P, Imhof A, Kurat CF. Dbf4-dependent kinase finetunes Ino80 function at chromosome replication origins. Nat Commun. 2026 17(1):3029 10.1038/s41467-026-70698-4"],"submitter_mail":["shibojyoti.lahiri@med.uni-muenchen.de"],"submitter_affiliation":["Ludwig-Maximilians-University of Munich"],"submitter_country":["Germany"],"additional_accession":[]},"is_claimable":false,"name":"Dbf4-Dependent Kinase Finetunes INO80 Function at Chromosome Replication Origins","description":"The highly conserved Dbf4-Dependent Kinase (DDK) plays a pivotal role in the nucleus during S phase, where it directly phosphorylates the replicative helicase, the minichromosome maintenance (MCM) complex. This leads to the initiation of chromosome replication. However, aside from the MCM complex, few other targets have been identified to date, leaving DDK an understudied kinase.  Here, we describe a two-pronged mass spectrometry-based approach and define the nuclear DDK-dependent phosphoproteome, which consists of approximately 400 phosphorylation events. Within this network, we found that DDK directly phosphorylates the Arp8 subunit of the multi-subunit chromatin remodeler complex INO80. Arp8 phosphorylation stabilises INO80’s intramolecular complex integrity, which finetunes its nucleosome spacing activity at replication origins. This adjustment of origin chromatin architecture stimulates replication and is important for the response to replication stress. Our results represent a significant advance in our understanding of the molecular mechanisms underlying the regulation of replication origins.","dates":{"publication":"2026-04-06","submission":"2024-06-26"},"accession":"PXD053426","cross_references":{"TAXONOMY":["NEWT:3555","NEWT:71647","NEWT:330879","NEWT:35554","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:32049","NEWT:1392696","NEWT:259447","NEWT:295546","NEWT:45351","NEWT:445974","NEWT:43179","NEWT:180454","NEWT:5722","NCBITaxon:1280","NEWT:1129","NEWT:309807","NEWT:55153","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:10036","NEWT:1590","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:1147161","NEWT:638632","NEWT:263737","NEWT:224326","NEWT:1333499","NCBITaxon:79857","NEWT:1096976","NEWT:5702","NEWT:95648","NEWT:1589","NEWT:135622","NEWT:1349","NEWT:96731","NEWT:383379","NEWT:10029","NEWT:913645","NEWT:44491","NEWT:556484","NEWT:317447","NEWT:4688","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:3112","NEWT:4442","NEWT:192875","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:108061","NEWT:1316931","NEWT:224308","NEWT:3347","NEWT:511145","NEWT:931281","NEWT:4432","NEWT:658457","NEWT:1310161","NEWT:77133","NEWT:295358","NEWT:145481","NCBITaxon:79824","NEWT:2246","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:44447","NEWT:752555","NEWT:498211","NEWT:5759","NEWT:1736231","NEWT:5518","NEWT:398007","NEWT:1392","NEWT:498217","NEWT:498216","NEWT:2242","NEWT:11320","NEWT:286","NEWT:391619","NEWT:246196","NEWT:287","NEWT:246197","NEWT:633149","NEWT:10239","NEWT:44685","NEWT:161934","NEWT:4897","NEWT:1148","NEWT:5508","NEWT:5507","NEWT:410661","NEWT:55571","NEWT:35500","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:4896","NEWT:1287689","NEWT:1390","NEWT:11557","NEWT:1094343","NEWT:1336795","NEWT:644042","NEWT:294","NEWT:1773","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:3711","NEWT:935293","NEWT:375146","NEWT:2065263","NEWT:118698","NEWT:1616117","NEWT:263","NEWT:118696","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44664","NEWT:47946","NEWT:3702","NEWT:243277","NEWT:7067","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:33548","NEWT:274","NEWT:408172","NEWT:408170","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:1436733","NEWT:460519","NEWT:1247411","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:333760","NEWT:1513458","NEWT:1233681","NCBITaxon:40559","NEWT:506599","NEWT:84588","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:508771","NEWT:1883446","NEWT:253","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:93062","NCBITaxon:4932","NEWT:644223","NEWT:235443","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:320637","NEWT:983964","NEWT:118499","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:3988","NEWT:1255228","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:3983","NEWT:352472","NEWT:1071661","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:39491","NCBITaxon:5811","NEWT:29491","NEWT:2014887","NEWT:33952","NEWT:261756","NEWT:571256","NEWT:40483","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:272634","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:141262","NEWT:108931","NEWT:1055524","NEWT:4087","NEWT:9778","NEWT:306","NEWT:150475","NEWT:303","NEWT:267872","NEWT:7111","NEWT:347515","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:4090","NEWT:4092","NEWT:9541","NEWT:8694","NEWT:4093","NEWT:4096","NEWT:8692","NEWT:185579","NEWT:941442","NEWT:13076","NEWT:1226408","NEWT:40479","NEWT:43989","NEWT:4076","NEWT:317","NEWT:1006581","NEWT:885318","NEWT:39488","NEWT:550","NEWT:4081","NEWT:273068","NEWT:554","NEWT:98334","NEWT:451516","NEWT:4084","NEWT:63577","NEWT:36185","NEWT:1225786","NEWT:7574","NEWT:1715256","NEWT:30640","NEWT:575412","NEWT:929793","NEWT:29204","NEWT:28112","NEWT:114155","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:6239","NEWT:162425","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8655","NEWT:1263854","NEWT:118503","NEWT:2059687","NEWT:160488","NEWT:28104","NEWT:207559","NEWT:407821","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:986","NEWT:52641","NEWT:7159","NEWT:28532","NEWT:353152","NEWT:8496","NEWT:27448","NEWT:40674","NEWT:1194669","NEWT:243230","NEWT:1080772","NEWT:519","NEWT:8479","NEWT:8485","NEWT:6063","NEWT:49240","NEWT:6289","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:469008","NEWT:256318","NEWT:9321","NEWT:206411","NCBITaxon:6191","NEWT:596153","NEWT:229533","NEWT:1836","NEWT:214053","NEWT:80863","NEWT:105231","NEWT:74649","NEWT:52638","NEWT:57075","NEWT:4097","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:9785","NEWT:6279","NEWT:1123869","NEWT:9544","NEWT:7370","NEWT:83906","NCBITaxon:780","NCBITaxon:1502","NEWT:6282","NEWT:1134506","NEWT:38783","NEWT:4006","NEWT:6426","NCBITaxon:5476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