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Proteins were precipitated by phenol/chloroform-method, shortly dried and then reconstituted and incubated in alkylation buffer (100 mM ABC, 0.1% SDC, 12 mM CAA, 5 mM TCEP) for 30 min. Trypsin was added in an enzyme to protein ratio of 1:50. Tryptic digestion was performed for 16 h at 37 °C. Samples were acidified to pH 2.1 using 10 % formic acid and centrifuged at 14.000 g for 10 min to remove the SDC. Supernatants were collected to a new tube and dried under vacuum. Samples were desalted using Oasis HLB µElution plates. In the final step of the elution, 60 % acetonitrile in 0.1 % formic acid was used. Samples for the spectral library generation were separated by high-pH offline fractionation (ThermoFisher) to achieve higher resolved spectral information. All samples were dried and dissolved in loading buffer (2% acetonitrile, 0.1% formic acid in ultra-pure water). For HPLC quality control an indexed retention time calibration, Biognosys retention peptides were spiked in all samples. Generated peptides for both spectral library generation and time-resolved analysis were subjected to an LC-MS system consisting of an Orbitrap Fusion Lumos mass spectrometer coupled to an Ultimate 3000 RSLC nanoflow system (both Thermo Fisher Scientific). Peptides were loaded on an Acclaim Pepmap C18 trap (Thermo Fisher Scientific) and separation was performed by a 50 cm µPACTM analytical column (PharmaFluidics) at a flow rate of 500 nL/min using a 120 min acetonitrile gradient. The gradient was ramping from 3.4% acetonitrile to 21% for the first 65 min, then reaching 42% after 97 min, approaching the maximum of 75.6% within the next 2 min, stagnating there for 3 more minutes, followed by a fast decrease to 3.6% acetonitrile again within 2 min and then stagnating at low acetonitrile for the last 16 min.PrideNot availableFor the spectral library generation containing high quality spectra, the MS instrument was operated in a data-dependent acquisition (DDA) mode automatically switching from MS and MS2 scans based on the abundance of peptides. However, for analysis of the time-resolved samples, the instrumentation was operating in a data-independent acquisition (DIA) mode. Key features include MS full scans at 60.000 resolution, an AGC target set to 3e6 at a maximum injection time of 60 ms and a precursor mass range from 396 m/z to 1071 m/z resulting in 85 DIA scan events on a MS2 level with the size of 9 m/z. The looping DIA MS2 scans were performed with the Orbitrap analyzer at 15.000 resolution covering most of the m/z peptide precursor space. Staggered windows were utilized to capture high quality spectral information at overlapping windows. HCD collision energy was set to 33% at both DDA and DIA mode. Using the database of P. aeruginosa strain PA14 from pseudomonas.com with 5983 entries, fragmentation spectra resulting from eluting peptides for spectral library generation were analyzed by MaxQuant (version 1.6.3.3) implementing the probabilistic scoring model of the search engine rbamidomethylation of cysteines was set as fixed modification and oxidation of methionines, deamidation of asparagins/ glutamins and N-terminal acetylation as variable modifications. Raw files from spectral library generation were processed using a FDR of 1 %. MaxQuant output tables were loaded into Spectronaut (Biognosys) for spectral library construction. Default settings were used for the generation of the proteome spectral library. The time-resolved DIA raw files were analyzed utilizing Spectronaut's search engine Pulsar (15.1.210713.50606). The samples of four replicates for each of the ten timepoints were analyzed in DIA-NN (v1.8) in default settings.ProteomicsSusanne HäußlerInstitute of Molecular Bacteriology, TWINCORE – Centre for Experimental and Clinical Infection Research GmbH, 30625 Hanover, Germany; Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124 Braunschweig, GermanyPARTIALBacteriaPseudomonas Aeruginosa42826134 Frommeyer YN,Sun J,Wu J,Kennepohl B,Witte J,Gomez NO,Battermann J,Becker L,Cetraro P,Verstraten R,Tomasch J,Pich A,Depledge DP,Dedon PC,Häussler S Dynamic tRNA modification programs align codon usage with growth-phase-specific gene expression in Pseudomonas aeruginosa. Proc Natl Acad Sci U S A. 2026 Oct 6 123(40):e2615985123 10.1073/pnas.2615985123benedikt.kennepohl@helmholtz-hzi.deTwincore HannoverGermanyPost-transcriptional transfer RNA (tRNA) modifications dynamically regulate translational capacity, yet whether the tRNA epitranscriptome is temporally coordinated with gene expression programs during bacterial growth remains unknown. Here, we combine time-resolved nanopore tRNA sequencing, liquid chromatography-tandem mass spectrometry modification profiling, transcriptomics, and proteomics across the Pseudomonas aeruginosa PA14 growth cycle to show that tRNA-modifying enzymes, the corresponding tRNA modifications, and modification-dependent genes are expressed in a coordinated temporal cascade. GidA-dependent 5-methylaminomethyl-2-thiouridine (mnm5s2U) modifications exemplify this program: GidA expression peaks during early growth, followed by rising mnm5s2U levels coinciding with maximal expression of genes enriched in rare AGA and UUA codons, with a concomitant enrichment of virulence-associated functions. This sequential pattern is consistent with a feedforward architecture in which the modification machinery acts in advance of translational demands. This mechanism is especially relevant for a set of horizontally acquired genes, suggesting that temporally programmed tRNA epitranscriptomic remodeling may help bridge local codon usage deviations between horizontally acquired genes and the core translational context.Dynamic tRNA modification programs align codon usage with growth-phase-specific gene expression in Pseudomonas aeruginosa.Frommeyer Yannick Noah YN, Sun Jingjing J, Wu Junzhou J, Kennepohl Benedikt B, Witte Julius J, Gomez Nicolas Oswaldo NO, Battermann Jana J, Becker Leon L, Cetraro Pierina P, Verstraten Ruth R, Tomasch Jürgen J, Pich Andreas A, Depledge Daniel P DP, Dedon Peter C PC, Häussler Susanne SfalseDynamic tRNA modification programs align codon usage with growth-phase-specific gene expression in Pseudomonas aeruginosaPost-transcriptional tRNA modifications dynamically regulate translational capacity, yet whether the tRNA epitranscriptome is temporally coordinated with gene expression programs during bacterial growth remains unknown. Here, we combine time-resolved nanopore tRNA sequencing, LC-MS/MS modification profiling, transcriptomics, and proteomics across the Pseudomonas aeruginosa PA14 growth cycle to show that tRNA-modifying enzymes, the corresponding tRNA modifications, and modification-dependent genes are expressed in a coordinated temporal cascade. GidA-dependent mnm⁵s²U modifications exemplify this program: GidA expression peaks during early growth, followed by rising mnm⁵s²U levels coinciding with maximal expression of genes enriched in rare AGA and UUA codons, with a concomitant enrichment of virulence-associated functions. This sequential pattern is consistent with a feedforward architecture in which the modification machinery anticipates translational demand. This mechanism is especially relevant for a set of horizontally acquired genes, suggesting that temporally programmed tRNA modifications bridge local codon usage deviations between horizontally acquired genes and the core translational context.2026-10-032026-04-14PXD077153NEWT:3555NEWT:71647NEWT:330879NEWT:35554NCBITaxon:12939NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:10245NEWT:55153NEWT:10244NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:351581NEWT:43186NEWT:428146NEWT:498257NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:661410NEWT:638632NEWT:263737NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:67352NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:383379NEWT:1401257NEWT:418106NEWT:10029NEWT:913645NEWT:44491NEWT:641809NEWT:27933NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7719NEWT:7959NEWT:2261NEWT:868565NEWT:31156NEWT:3112NEWT:79329NEWT:4442NEWT:31155NEWT: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:347256NEWT:1736231NEWT:5518NEWT:398007NEWT:1527468NEWT: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:980415NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:459758NEWT:3702NEWT:1245466NEWT:243277NEWT:1246791NEWT:7067NEWT:118694NEWT:586722NEWT: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:1348799NEWT:9483NEWT:333760NEWT:56636NEWT:1513458NEWT:1233681NCBITaxon:40559NEWT:506599NEWT:2853422NEWT:81077NEWT:84588NEWT:1679718NEWT:480NEWT:65349NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:128017NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NEWT:34613NCBITaxon:4932NEWT:109760NEWT:943274NEWT:644223NEWT:235443NEWT:108458NEWT:5936NEWT:272623NEWT:272624NEWT:320637NEWT:2719099NEWT:886559NEWT:55521NEWT:983964NEWT:118499NEWT:11706NEWT:32644NEWT:527796NEWT:1130798NEWT:55529NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1116234NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:3983NEWT:203696NEWT:352472NEWT:1071661NEWT:1202532NEWT:360094NEWT:470NEWT:41364NEWT:5911NEWT:1313NEWT:1218097NCBITaxon:50557NEWT:39251NEWT:39491NEWT:212142NCBITaxon:5811NEWT:29491NEWT:101841NEWT:2014887NEWT:33952NEWT:153009NEWT:261756NEWT:571256NEWT:40483NEWT:63366NEWT:63367NEWT:688333NEWT:215402NCBITaxon:548681NEWT:318586NCBITaxon:5820NEWT:1547NEWT:272634NEWT:198107NEWT:9031NEWT:1872122NEWT:1308NEWT:7091NEWT:1034015NEWT:760568NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:97477NEWT:7111NEWT:347515NEWT:172269NEWT:9534NEWT:6269NEWT: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:634955NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:13095NEWT:162425NEWT:216257NEWT:102169NEWT:208893NEWT:9986NEWT:4054NEWT:8654NEWT:8658NEWT:1268063NEWT:8657NEWT:8655NEWT:5147NEWT:98351NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:207559NEWT:407821NCBITaxon:2NEWT:85057NEWT:985076NEWT:568708NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:267671NEWT:28532NEWT:198618NEWT:353152NEWT:8496NEWT:7165NEWT:1257118NEWT:27448NEWT:40674NEWT:1194669NEWT:51329NEWT:243230NEWT:443906NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:1328388NEWT:104395NEWT:9557NEWT:9315NEWT:6289NEWT:377586NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:9554NEWT:118562NEWT:725NEWT:7137NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:2925NEWT:214053NCBITaxon:10298NEWT:80863NEWT:90675NEWT:105231NEWT:104385NEWT:74649NEWT:52638NEWT:57075NEWT:206672NEWT:4097NEWT:8697NEWT:8695NEWT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