Quantitative proteomic analysis of Shigella flexneri and Shigella sonnei Generalized Modules for Membrane Antigens (GMMA) reveals highly pure preparations.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26746581", "kind": "science-record", "revision": 6, "content_hash": "sha256:f0fdf44563bdd992ae66cac8c447e9c7b0e35a4e0b34624946ac760a82ffee8a", "created_at": "2026-11-01T15:40:15Z", "updated_at": "2026-11-01T21:20:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Quantitative proteomic analysis of Shigella flexneri and Shigella sonnei Generalized Modules for Membrane Antigens (GMMA) reveals highly pure preparations.", "doi": "10.1016/j.ijmm.2015.12.003", "pmid": "26746581", "authors": ["Luana Maggiore", "Lu Yu", "Ulrich Omasits", "Omar Rossi", "Gordon Dougan", "Nicholas R Thomson", "Allan Saul", "Jyoti S Choudhary", "Christiane Gerke"], "journal": "International journal of medical microbiology : IJMM", "year": 2016, "abstract": "Outer membrane blebs are naturally shed by Gram-negative bacteria and are candidates of interest for vaccines development. Genetic modification of bacteria to induce hyperblebbing greatly increases the yield of blebs, called Generalized Modules for Membrane Antigens (GMMA). The composition of the GMMA from hyperblebbing mutants of Shigella flexneri 2a and Shigella sonnei were quantitatively analyzed using high-sensitivity mass spectrometry with the label-free iBAQ procedure and compared to the composition of the solubilized cells of the GMMA-producing strains. There were 2306 proteins identified, 659 in GMMA and 2239 in bacteria, of which 290 (GMMA) and 1696 (bacteria) were common to both S. flexneri 2a and S. sonnei. Predicted outer membrane and periplasmic proteins constituted 95.7% and 98.7% of the protein mass of S. flexneri 2a and S. sonnei GMMA, respectively. Among the remaining proteins, small quantities of ribosomal proteins collectively accounted for more than half of the predicted cytoplasmic protein impurities in the GMMA. In GMMA, the outer membrane and periplasmic proteins were enriched 13.3-fold (S. flexneri 2a) and 8.3-fold (S. sonnei) compared to their abundance in the parent bacteria. Both periplasmic and outer membrane proteins were enriched similarly, suggesting that GMMA have a similar surface to volume ratio as the surface to periplasmic volume ratio in these mutant bacteria. Results in S. flexneri 2a and S. sonnei showed high reproducibility indicating a robust GMMA-producing process and the low contamination by cytoplasmic proteins support the use of GMMA for vaccines. Data are available via ProteomeXchange with identifier PXD002517.", "claims": [{"id": "claim-method", "statement": "There was no statistically significant difference in the enrichment of membrane proteins compared to periplasmic proteins in either the Sf2a or Ss preparations (p = 0.94 and 0.85 by t test, for Sf2a and Ss, respectively).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26746581", "locator": "sections[12] \"Composition of predicted outer membrane and periplasmic proteins in GMMA\" paragraph 9", "quote": "There was no statistically significant difference in the enrichment of membrane proteins compared to periplasmic proteins in either the Sf2a or Ss preparations (p = 0.94 and 0.85 by t test, for Sf2a and Ss, respectively)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Vizcaino et al., 2014) via the PRIDE partner repository with the dataset identifier PXD002517.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26746581", "locator": "sections[10] \"Bioinformatics\" paragraph 4", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Vizcaino et al., 2014) via the PRIDE partner repository with the dataset identifier PXD002517."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used label-free iBAQ quantitative proteomics to compare GMMA with solubilized bacterial cells, and its source data are available through ProteomeXchange under identifier PXD002517.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26746581", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The composition of the GMMA from hyperblebbing mutants of Shigella flexneri 2a and Shigella sonnei were quantitatively analyzed using high-sensitivity mass spectrometry with the label-free iBAQ procedure and compared to the composition of the solubilized cells of the GMMA-producing strains."}, {"asset": "source:pmid:26746581", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Data are available via ProteomeXchange with identifier PXD002517."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used label-free iBAQ quantitative proteomics to compare GMMA with solubilized bacterial cells, and its source data are available through ProteomeXchange under identifier PXD002517.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:26746581"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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["Outer membrane lipoprotein (OM lipo)", "28.00", "32.34", "66", "75", "2.72", "4.05", "52", "59"], ["Periplasmic", "19.86", "18.25", "105", "133", "2.2", "2.28", "90", "127"], ["Total predicted outer membrane/periplasmic", "95.70", "98.71", "204", "247", "8.29", "11.37", "164", "219"], ["Cytoplasmic"], ["Ribosomal", "0.86", "0.28", "43", "35", "15.03", "15.08", "53", "53"], ["Other cytoplasmic", "0.63", "0.20", "177", "93", "65.08", "61.30", "1137", "1198"], ["Cytoplasmic membrane"], ["Tail-specific protease", "1.15", "0.21", "1", "1", "0.03", "0.02", "1", "1"], ["Other cytoplasmic membrane", "0.24", "0.13", "53", "29", "7.00", "6.44", "291", "346"], ["Extracellular", "0.00", "–", "1", "0", "0.02", "0.01", "5", "4"], ["Unknown"], ["YajG", "1.28", "0.34", "1", "1", "0.04", "0.05", "1", "1"], ["Other unknown", "0.13", "0.13", "35", "28", "4.51", "5.72", "216", "245"], ["Total predicted non-OM/periplasmic", "4.30", "1.29", "311", "187", "91.71", "88.63", "1704", "1848"]], "row_count": 19, "column_count": 9, "numeric_cells": 95, "header_rows": 3, "locator": "section[12]/table-wrap[1]#tbl0005"}}, {"id": "asset:table:pmid:26746581:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7895e552d6c23c3a597d9b9f879832c7a20f6bd18ca63c7f48d398c9ca9dffc7", "bytes": 4032, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#tbl0010", "version": null, "note": "40 most abundant proteins found in GMMA (by average % mass in Sf2a and Ss GMMA).", "structure": {"pmcid": "PMC4820968", "section_index": 12, "section_title": "Composition of predicted outer membrane and periplasmic proteins in GMMA", "row_count": 41, "column_count": 7}, "table": {"label": "Table 2", "caption": "40 most abundant proteins found in GMMA (by average % mass in Sf2a and Ss GMMA).", "rows": [["Gene name", "Location", "Protein name", "Uniprot name", "Average % mass in GMMA", "% mass in Sf2a GMMA", "% mass in Ss GMMA"], ["SF2457T_0298", "OM", "Outer membrane protein C", "E3XX60_SHIFL", "13.411", "14.619", "12.203"], ["SF2457T_0799", "OM", "Outer membrane protein A", "E3XYK2_SHIFL", "11.943", "10.615", "13.271"], ["SS53G_3941", "OM", "Outer membrane protein X", "E9UMG3_SHISO", "8.506", "11.829", "5.183"], ["SS53G_0415", "OM lipo", "Repeated sequence found in lipoLPP family prot.", "E7JU63_SHISO", "7.261", "9.955", "4.566"], ["SF2457T_4977", "PP", "Protease Do (HtrA)", "E3YA49_SHIFL", "4.604", "7.366", "1.842"], ["SS53G_2965", "OM lipo", "Entericidin B", "E7K193_SHISO", "4.257", "0.101", "8.413"], ["SS53G_0370", "OM lipo", "Outer membrane lipoprotein pcp", "E7JU20_SHISO", "3.528", "4.570", "2.485"], ["tolB", "PP", "Protein tolB", "TOLB_SHISS", "2.859", "2.637", "3.080"], ["SS53G_0760", "OM", "Outer membrane porin protein LC", "E7JV54_SHISO", "2.419", "0.479", "4.358"], ["SF2457T_3748", "OM", "Outer membrane protein", "E3Y6Q5_SHIFL", "2.145", "2.654", "1.636"], ["yaeT", "OM", "Outer membrane protein assembly factor yaeT", "YAET_SHISS", "1.646", "2.258", "1.035"], ["lpoA", "OM lipo", "Penicillin-binding protein activator LpoA", "LPOA_SHIF8", "1.595", "1.679", "1.510"], ["SF2457T_0832", "OM", "Outer membrane protein F", "E3XYN5_SHIFL", "1.471", "1.036", "1.905"], ["SGF_01778", "OM lipo", "Glycoprotein-polysaccharide metabolism", "E7TB57_SHIFL", "1.465", "0.280", "2.650"], ["SS53G_1454", "OM lipo", "Osmotically inducible lipoprotein B", "E7JX36_SHISO", "1.256", "1.692", "0.820"], ["lamB", "OM", "Maltoporin", "LAMB_SHISS", "1.156", "0", "2.312"], ["slp", "OM lipo", "OM protein induced after carbon starvation", "Q3YWI0_SHISS", "1.151", "0.014", "2.288"], ["SGF_00427", "OM", "Aerobactin siderophore receptor IutA", "E7T7F9_SHIFL", "0.977", "1.486", "0.468"], ["SF2457T_4357", "PP", "Peptidyl-prolyl cis-trans isomerase", "E3Y8E7_SHIFL", "0.932", "0.968", "0.896"], ["pal", "OM lipo", "Peptidoglycan-associated lipoprotein", "E7K8X6_SHISO", "0.873", "0.930", "0.816"], ["SS53G_1748", "PP", "Putative uncharacterized protein", "E7JXX8_SHISO", "0.869", "1.080", "0.658"], ["SS53G_0544", "OM lipo", "SmpA/OmlA family protein", "E7JUJ2_SHISO", "0.829", "0.170", "1.489"], ["yajG", "Unknown", "Putative polymerase/proteinase", "Q3Z4W9_SHISS", "0.808", "1.276", "0.340"], ["SF2457T_2094", "PP", "Periplasmic oligopeptide-binding protein", "E3Y260_SHIFL", "0.769", "1.065", "0.473"], ["SF2457T_2279", "CytoM", "Tail-specific protease", "E3Y2N8_SHIFL", "0.679", "1.152", "0.206"], ["surA", "PP", "Chaperone surA", "SURA_SHISS", "0.623", "0.787", "0.458"], ["SF2457T_0435", "OM", "Long-chain fatty acid outer membrane transporter", "E3XXF4_SHIFL", "0.622", "0.062", "1.181"], ["SS53G_1935", "OM lipo", "SmpA/OmlA family protein", "E7JYG3_SHISO", "0.611", "0.858", "0.364"], ["degQ", "PP", "Serine endoprotease", "Q3YX14_SHISS", "0.592", "0.053", "1.132"], ["SS53G_3947", "PP", "Putative uncharacterized protein", "E9UMG9_SHISO", "0.540", "0.816", "0.265"], ["SF2457T_3200", "OM lipo", "Pectinesterase B", "E3Y553_SHIFL", "0.532", "0.651", "0.414"], ["SF2457T_3582", "OM lipo", "Peptidase family M48 family protein", "E3Y5Y2_SHIFL", "0.530", "0.555", "0.504"], ["livJ", "PP", "High-affinity amino acid transport system", "Q3YW68_SHISS", "0.521", "0.264", "0.777"], ["yeaF", "OM", "Putative uncharacterized protein yeaF", "Q3Z2C1_SHISS", "0.507", "0.479", "0.535"], ["SS53G_4569", "OM lipo", "Putative phospholipid-binding domain protein", "E7K576_SHISO", "0.468", "0.535", "0.401"], ["SF2457T_4988", "OM", "Ferrichrome-iron receptor", "E3YA60_SHIFL", "0.435", "0.816", "0.053"], ["SF2457T_4129", "PP", "PP dipeptide transport protein", "E3Y7S0_SHIFL", "0.434", "0.401", "0.467"], ["ybjP", "OM lipo", "Putative enzyme", "Q0T8Q3_SHIF8", "0.414", "0.429", "0.400"], ["SF2457T_3629", "OM", "Serine protease eatA", "E3Y628_SHIFL", "0.410", "0.115", "0.705"], ["yfgL", "OM-Lipo", "Outer membrane assembly lipoprotein YfgL", "E7JUN3_SHISO", "0.409", "0.571", "0.246"]], "row_count": 41, "column_count": 7, "numeric_cells": 163, "header_rows": 1, "locator": "section[12]/table-wrap[2]#tbl0010"}}, {"id": "asset:table:pmid:26746581:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6b55adce4c45496c243278380b9ba8c4f96ab09ac8fdee5b5e1bee7a705c2d7d", "bytes": 3633, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#tbl0015", "version": null, "note": "Proteins preferentially found in Ss GMMA.", "structure": {"pmcid": "PMC4820968", "section_index": 13, "section_title": "Comparative analysis of Sf2a and Ss GMMA and lysates", "row_count": 38, "column_count": 7}, "table": {"label": "Table 3", "caption": "Proteins preferentially found in Ss GMMA.", "rows": [["Gene name", "Location", "Protein name", "Uniprot name", "% mass in Ss GMMA", "Ratio", "Theoretically present in Sf2a*"], ["Predicted outer membrane and periplasmic localized proteins with at least 0.01% mass in Ss GMMA not found in Sf2a GMMA"], ["SS53G_2461", "PP", "Maltose-binding periplasmic protein", "E7JZV4_SHISO", "0.799", "−**", "+"], ["SS53G_0290", "OM lipo", "TonB-dependent Receptor Plug domain protein", "E7JTU0_SHISO", "0.732", "−", "−"], ["SS53G_3463", "OM", "Iron(III) dicitrate transport protein fecA", "E7K2N5_SHISO", "0.589", "−", "−"], ["cirA", "OM", "OM receptor for iron-regulated colicin I receptor", "Q3Z051_SHISS", "0.430", "−", "−"], ["exc", "OM lipo", "Entry exclusion protein 2", "A4SH43_SHISS", "0.423", "−", "−"], ["SS53G_3761", "OM", "Ferrichrome-iron receptor", "E7K3K6_SHISO", "0.396", "−", "−"], ["SS53G_2464", "PP", "Maltose operon periplasmic protein", "E7JZV7_SHISO", "0.337", "−", "+"], ["ycdO", "PP", "UPF0409 protein ycdO", "YCDO_SHISS", "0.276", "−", "+"], ["SS53G_0127", "OM", "Putative tonB-dependent receptor yncD", "E7JTC8_SHISO", "0.159", "−", "−"], ["hdeA", "PP", "Putative uncharacterized protein hdeA", "Q3YWI4_SHISS", "0.140", "−", "+"], ["mdoG", "PP", "Glucans biosynthesis protein G", "OPGG_SHISS", "0.106", "−", "+"], ["SS53G_2146", "PP", "Putative uncharacterized protein", "E7JZ10_SHISO", "0.064", "−", "−"], ["SS53G_0128", "PP", "PQQ enzyme repeat family protein", "E7JTC9_SHISO", "0.058", "−", "−"], ["SS53G_5268", "OM", "TonB-dependent Receptor Plug domain protein", "E7K7A5_SHISO", "0.053", "−", "+"], ["SS53G_2796", "OM lipo", "Inner membrane lipoprotein yiaD", "E7K0S5_SHISO", "0.051", "−", "+"], ["SSON_1625", "PP", "Putative sulfatase", "Q3Z1P2_SHISS", "0.047", "−", "−"], ["SS53G_0368", "OM lipo", "Putative uncharacterized protein", "E7JU18_SHISO", "0.036", "−", "−"], ["SS53G_4157", "PP", "Putative uncharacterized protein", "E7K461_SHISO", "0.032", "−", "+"], ["yehZ", "PP", "Putative transport system permease protein", "Q3Z073_SHISS", "0.026", "−", "+"], ["SS53G_4973", "PP", "Acid-resistance protein", "E7K6I7_SHISO", "0.025", "−", "+"], ["SS53G_0106", "PP", "Bacterial extracellular solute-binding family protein", "E7JTA7_SHISO", "0.024", "−", "−"], ["SSON_1637", "PP", "Putative hemin-binding lipoprotein", "Q3Z1N0_SHISS", "0.022", "−", "−"], ["tauA", "PP", "Taurine transport system periplasmic protein", "Q3Z543_SHISS", "0.019", "−", "−"], ["SS53G_3203", "OM lipo", "Putative uncharacterized protein", "E7K1X5_SHISO", "0.015", "−", "+"], [""], ["Predicted outer membrane and periplasmic localized proteins highly enriched in Ss GMMA compared to Sf2a GMMA***"], ["lamB", "OM", "Maltoporin", "LAMB_SHISS", "2.312", "6017", ""], ["slp", "OM lipo", "Outer membrane protein induced after carbon starvation", "Q3YWI0_SHISS", "2.288", "163", ""], ["glpQ", "PP", "Glycerophosphodiester phosphodiesterase, periplasmic", "Q3YZW7_SHISS", "0.609", "193", ""], ["SS53G_4155", "OM lipo", "Putative polysaccharide export protein gfcE", "E7K459_SHISO", "0.313", "170", ""], ["SS53G_3546", "PP", "Putative phospholipid-binding domain protein", "E7K2W6_SHISO", "0.249", "321", ""], ["SS53G_4156", "OM", "Putative uncharacterized protein", "E7K460_SHISO", "0.216", "239", ""], ["SS53G_5756", "PP", "Glutamate/aspartate periplasmic-binding protein", "E7K8P1_SHISO", "0.105", "230", ""], ["ycdB", "PP", "Peroxidase ycdB (Deferrochelatase/peroxidase EfeB)", "YCDB_SHISS", "0.091", "246", ""], ["ymcC", "OM lipo", "Putative regulator", "Q3Z3D5_SHISS", "0.052", "376", ""], ["blc", "OM lipo", "Outer membrane lipoprotein", "Q3YUI9_SHISS", "0.051", "329", ""]], "row_count": 38, "column_count": 7, "numeric_cells": 77, "header_rows": 1, "locator": "section[13]/table-wrap[1]#tbl0015"}}, {"id": "asset:table:pmid:26746581:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0b6e1f4bde4a1308209d55f86e7328021af1ec2dbedabff52a2f11c3dc36634b", "bytes": 718, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[2]#tbl0020", "version": null, "note": "Proteins preferentially found in Sf2a GMMA.", "structure": {"pmcid": "PMC4820968", "section_index": 13, "section_title": "Comparative analysis of Sf2a and Ss GMMA and lysates", "row_count": 6, "column_count": 6}, "table": {"label": "Table 4", "caption": "Proteins preferentially found in Sf2a GMMA.", "rows": [["Gene name", "Location", "Protein name", "Uniprot name", "% mass in Sf2a GMMA", "Theoretically present in Ss*"], ["Predicted outer membrane and periplasmic localized proteins with at least 0.01% mass in Sf2a GMMA not found in Ss GMMA"], ["SF2457T_1008", "OM lipo", "Uncharacterized lipoprotein ydcL", "E3XZ64_SHIFL", "0.035", "−"], ["SF2457T_0155", "OM lipo", "Lipoprotein", "E3XWR9_SHIFL", "0.035", "−"], ["sitA", "PP", "Iron transport protein", "Q3Z1C5_SHISS", "0.024", "+"], ["SF2457T_3658", "OM", "Antigen 43", "E3Y656_SHIFL", "0.014", "−"]], "row_count": 6, "column_count": 6, "numeric_cells": 11, "header_rows": 1, 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