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ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/peptides_GLFQ.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/UbPTMs_PTMs_Summary.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/Peptides_UbPTMs.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/proteins_GLFQ.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/Proteins_UbPTMs.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/MAEA_KO_GLFQ_2.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/MAEA_KO_UbPTMs_1.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/SC_UbPTMs_1.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/GID8_KO_GLFQ_1.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/SC_GLFQ_2.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/GID8_KO_GLFQ_2.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/SC_GLFQ_1.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/MAEA_KO_GLFQ_3.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/MAEA_KO_UbPTMs_2.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/MAEA_KO_GLFQ_1.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/GID8_KO_UbPTMs_3.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/GID8_KO_GLFQ_3.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/SC_GLFQ_3.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/MAEA_KO_UbPTMs_3.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/SC_UbPTMs_3.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/GID8_KO_UbPTMs_2.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/GID8_KO_UbPTMs_1.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075792/SC_UbPTMs_2.d.zipprimary200OKdgr8@cornell.eduNelson SimwelaMass SpectrometryBottom-up proteomicsTuberculosisTuberculosisUbiquitylationGid/ctlh complexInnate immunityMetabolismMacrophageshttps://www.ebi.ac.uk/pride/archive/projects/PXD075792Cell CultureMacrophageMacrophage infection and protein lysate preparation Approximately 1 × 10⁸ BMDMhs per biological replicate (in triplicate: scramble control, GID8-/-, and MAEA-/-) were infected with Mtb Erdman at an MOI of 1.5 for 48 hours. After 48 hours, cells were harvested by scraping in ice-cold 1× PBS. Infected cells were sterilized to completely inactivate Mtb by overnight incubation in 90% methanol. The following day, methanol-fixed cells were removed from the BSL3 facility, washed twice with 1× PBS, and resuspended in lysis buffer (8 M urea, 150 mM NaCl, 50 mM TEAB, 1× Halt protease and phosphatase inhibitors). Resuspended cell lysates were sonicated on ice using a large-tip probe at 40% amplitude for three 10-second cycles, with 30-second intervals between cycles (5 seconds on, 5 seconds off). Sonicated lysates were clarified by centrifugation at 14,000 rpm for 30 minutes at 4 °C. Supernatants were transferred to new tubes and protein concentration was measured using the Pierce™ Rapid Gold BCA Protein Assay Kit with a 2 mg/mL albumin standard dilution series. Lysates were stored at -80 °C until shipment to Creative Proteomics (Shirley, New York) where protein analysis was performed. Approximately 5 mg of total protein was used as input for each replicate. Sample preparation for proteomics Cell lysates were subjected to both global LFQ proteomic analysis and diGly profiling. Samples stored at −80 °C were thawed on ice prior to processing. Protease and deubiquitinase inhibitors were added (1 mM PMSF and 1% PR-619; Sigma-Aldrich), followed by vortexing and centrifugation at 4,500 × g for 10 min at 4 °C. Supernatants were collected, and protein concentrations were re-measured using a BCA assay. Trypsin digestion Equal amounts of protein were adjusted to 200 μL in 8 M urea. Samples were reduced with 5 mM dithiothreitol (DTT) at 37 °C for 45 min and alkylated with 11 mM iodoacetamide in the dark at room temperature for 15 min. Proteins were precipitated with four volumes of cold acetone at −20 °C for 2 hours, pelleted by centrifugation, air-dried, and resuspended in 25 mM ammonium bicarbonate. Resuspended protein samples were digested overnight at 37 °C with sequencing-grade trypsin (Promega). Digested peptides were desalted using C18 solid-phase extraction columns (Millipore), quantified using the Pierce™ Quantitative Peptide Assay kit (Thermo Fisher Scientific), concentrated, and vacuum-dried prior to LC-MS/MS analysis. An aliquot of the peptides was used for LFQ proteomics, while the rest were subjected to diGly immunoaffinity enrichment. Enrichment of diGly modified peptides For ubiquitin remnant profiling, digested peptides were subjected to immunoaffinity enrichment of di-glycine (K-ε-GG)-modified peptides using anti-diglycine-lysine antibody-conjugated agarose beads (PTM Biolabs). Peptides were dissolved in enrichment buffer (80% acetonitrile/6% trifluoroacetic acid saturated with glycine) and incubated with pre-washed antibody-conjugated beads on a rotating platform for 1-2 hours at 4°C. After incubation, beads were washed sequentially with 50% acetonitrile/6% trifluoroacetic acid/200 mM NaCl and 30% acetonitrile/0.1% trifluoroacetic acid. Bound peptides were eluted with 10% ammonia solution, vacuum-dried, desalted using C18 ZipTips, and quantified prior to LC-MS/MS analysis.PrideNot availableDatabase search and quantification Raw data were processed using FragPipe (v21.1). Spectra were searched against a combined FASTA database (58,907 sequences) supplemented with decoy and contaminant sequences to control false discovery rates (FDR). Precursor and fragment mass tolerances were set to 20 ppm. For global proteomics, trypsin was specified as the digestion enzyme with up to two missed cleavages permitted. Carbamidomethylation of cysteine was set as a fixed modification, and oxidation of methionine and protein N-terminal acetylation were included as variable modifications. For ubiquitylomics, trypsin and Lys-C were specified as proteases with up to two missed cleavages allowed. Carbamidomethylation (C) was set as a fixed modification, and oxidation (M), protein N-terminal acetylation, and ubiquitylation (diGly modification on K) were included as variable modifications, with a maximum of three variable modifications per peptide. The minimum site localization probability for ubiquitylation sites was set to 0.75. Peptide- and protein-level FDRs were controlled at 1%, and decoy and contaminant hits were excluded from downstream analyses. LFQ was performed using IonQuant with match-between-runs (MBR) and MaxLFQ enabled. Differential abundance and ubiquitylation analysis For LFQ global proteomics, 6,239 proteins matching the mouse protein database were identified. For ubiquitin remnant profiling, 31,749 ubiquitylation sites were detected. After filtering for proteins and peptides identified in all replicates of at least one condition (scramble control, GID8-/- and MAEA-/-), a total of 5,087 proteins were retained in the LFQ global proteomics dataset. After similar filtering, 23,841 ubiquitylation sites across 4,268 proteins were retained in the ubiquitylation profiling dataset. Differentially abundant proteins and ubiquitylated peptides were defined as those with absolute fold change (FC) > 1.3 (Up) or < 1.3 (Down) and p < 0.05. Statistical comparison and downstream data analysis was carried out using the proteomic data analysis package DEP in R (64).ProteomicsDavid G RussellDepartment of Microbiology & Immunology, Cornell University College of Veterinary MedicinePARTIALMus Musculus (mouse)nvs23@cornell.edu42094500 Simwela NV, Johnston L, Sassetti CM, Russell DG. Ubiquitylation by the GID/CTLH complex regulates the metabolic and innate immune response of macrophages to infection by Mycobacterium tuberculosis. bioRxiv. 2026:2026.04.24.720540 10.64898/2026.04.24.720540Cornell UniversityUnited StatesThe GID/CTLH E3 ligase complex is implicated in several biological processes, yet its full substrate repertoire remains poorly defined. We recently identified the complex as a broad modulator of macrophage responses to Mycobacterium tuberculosis (Mtb) infection. Here, we use label-free proteomics and diGly capture analysis of Mtb-infected macrophages to define the GID/CTLH-dependent ubiquitylome. We identify thousands of dynamically altered ubiquitylation sites, with strong enrichment among proteins involved in cellular metabolism and innate immune signaling. Concurrent proteome analysis revealed extensive rewiring in GID/CTLH-deficient macrophages, with >90% of enriched pathways among increased proteins consisting of metabolic targets. Notably, inhibitory phosphatases (PTEN, INPP5D) also emerged as candidate substrates. Functional studies revealed proteasome-dependent stabilization of PTEN and INPP5D in GID/CTLH-deficient macrophages with each phosphatase individually exerting an influence on Mtb intracellular survival. Together, our study defines a GID/CTLH-dependent ubiquitylome in macrophages and identifies the complex as a central regulator of metabolism and antimicrobial immunity.Ubiquitylation by the GID/CTLH complex regulates the metabolic and innate immune response of macrophages to infection by Mycobacterium tuberculosis.Simwela Nelson V NV, Johnston Luana L, Sassetti Christopher M CM, Russell David G DGfalseUbiquitylation by the GID/CTLH complex regulates the metabolic and innate immune response of macrophages to infection by Mycobacterium tuberculosisThe GID/CTLH E3 ligase complex is implicated in several biological processes, yet its full substrate repertoire remains poorly defined. We recently identified the complex as a broad modulator of macrophage responses to Mycobacterium tuberculosis (Mtb) infection. Here, we use label-free proteomics and diGly capture analysis of Mtb-infected macrophages to define the GID/CTLH-dependent ubiquitylome. We identify thousands of dynamically altered ubiquitylation sites, with strong enrichment among proteins involved in cellular metabolism and innate immune signaling. Concurrent proteome analysis revealed extensive rewiring in GID/CTLH-deficient macrophages, with >90% of enriched pathways among increased proteins consisting of metabolic targets. Notably, inhibitory phosphatases (PTEN, INPP5D) also emerged as candidate substrates. Functional studies revealed proteasome-dependent stabilization of PTEN and INPP5D in GID/CTLH-deficient macrophages with each phosphatase individually exerting an influence on Mtb intracellular survival. Together, our study defines a GID/CTLH-dependent ubiquitylome in macrophages and identifies the complex as a central regulator of metabolism and antimicrobial immunity.2026-06-242026-03-18PXD075792NEWT:3555NEWT:71647NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:96731NEWT:383379NEWT:10029NEWT:913645NEWT:44491NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:4442NEWT:192875NEWT:12637NEWT:59729NEWT:2164133NEWT:108061NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:931281NEWT:658457NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:5759NEWT:1736231NEWT:1392NEWT:498217NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:633149NEWT:10239NEWT:44685NEWT:161934NEWT:1148NEWT:5508NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1390NEWT:11557NEWT:1094343NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:935293NEWT:375146NEWT:118698NEWT:263NEWT:118696NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:3702NEWT:243277NEWT:7067NEWT:118694NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:408172NEWT:408170NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:1436733NEWT:460519NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:9483NEWT:1513458NCBITaxon:40559NEWT:84588NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NCBITaxon:4932NEWT:644223NEWT:235443NEWT:108458NEWT:272623NEWT:272624NEWT:320637NEWT:983964NEWT:118499NEWT:32644NEWT:527796NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:352472NEWT:1071661NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:39491NCBITaxon:5811NEWT:29491NEWT:2014887NEWT:33952NEWT:261756NEWT:571256NEWT:40483NEWT:272634NEWT:9031NEWT:1872122NEWT:7091NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:7111NEWT:347515NEWT:9534NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:4093NEWT:4096NEWT:185579NEWT:941442NEWT:13076NEWT:7108NEWT:40479NEWT:4076NEWT:317NEWT:1006581NEWT:885318NEWT:39488NEWT:550NEWT:4081NEWT:273068NEWT:554NEWT:98334NEWT:451516NEWT:36185NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:114155NEWT:6494NEWT:6491NEWT:507601NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:1268063NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:407821NCBITaxon:2NEWT:985076NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:28532NEWT:353152NEWT:8496NEWT:27448NEWT:1194669NEWT:51329NEWT:243230NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:104395NEWT:6289NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:80863NEWT:105231NEWT:52638NEWT:57075NEWT:4097NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:7370NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:38783NEWT:4006NEWT:6426NCBITaxon:5476NEWT:6669NEWT:9935NEWT:89453NEWT:287889NEWT:51515NEWT:588596NEWT:51511NEWT:8845NEWT:92867NEWT:92866NEWT:5334NEWT:51750NEWT:202950NEWT:382352NEWT:413071NEWT:632957NEWT:9925NEWT:89462NEWT:8839NEWT:90690NEWT:4232NEWT:2758385NEWT:11298NEWT:171101NEWT:714NEWT:421932NEWT:312017NEWT:196627NEWT:200308NEWT:200302NEWT:870435NEWT:284593NEWT:100392NEWT:5315NEWT:9913NEWT:265872NEWT:105841NEWT:337330NEWT:2666255NEWT:2285NEWT:999810NCBITaxon:5693NEWT:1392998NEWT:380394NEWT:981087NEWT:180066NEWT:226900NEWT:430615NEWT:563041NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1416333NEWT:1678078NEWT:749906NEWT:418985NEWT:1817808NEWT:749907NEWT:145263NEWT:694569NEWT:27606NEWT:9739NEWT:59202NEWT:9975NEWT:51953NEWT:3197NEWT:860688NEWT:13443NEWT:36329NEWT:62615NCBITaxon:3044782NEWT:160235NEWT:72407NEWT:349741NEWT:157295NEWT:2096NEWT:192222NEWT:9721NEWT:137221NEWT:9963NEWT:1617910NEWT:565050NEWT:2785785NEWT:411901NEWT:105884NCBITaxon:9615NEWT:58334NEWT:1193501NEWT:58331NEWT:6689NEWT:298315NEWT:70448NEWT:698936NEWT:9940NEWT:3168NEWT:521001NEWT:192011NEWT:1813887NEWT:118702NEWT:118700NEWT:224911NEWT:118705NCBITaxon:11552NEWT:6945NEWT:184922NEWT:6703NEWT:2104NEWT:2NEWT:157546NEWT:474186NEWT:38942NEWT:307972NEWT:1496NEWT:2102NEWT:45474NEWT:1590841NEWT:4513NEWT:1247NEWT:6938NEWT:376741NCBITaxon:10407NEWT:1736309NEWT:4751NEWT:10360NEWT:47664NEWT:317548NEWT:15819NEWT:3654NEWT:237561NEWT:5833NEWT:6928NEWT:1239NEWT:36745NEWT:272563NEWT:82688NEWT:3885NEWT:3888NEWT:5821NEWT:44139NCBITaxon:4896NEWT:6915NEWT:3649NEWT:101510NEWT:28903NEWT:3880NEWT:272559NEWT:28909NEWT:515849NEWT:3641NEWT:466585NEWT:1000589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