Transfection With Plasmid Causing Stable Expression of a Foreign Gene Affects General Proteome Pattern in Giardia lamblia Trophozoites.

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Basic research is usually performed with the strain WBC6 and includes genetic manipulations such as transfections. Here, we investigate how transfection with a plasmid causing stable expression of a foreign gene affects the whole proteome pattern. Using shotgun mass spectrometry, we compare the proteomes of untransfected trophozoites to trophozoites transfected with Escherichia coli glucuronidase A (GusA). Besides GusA, which is detected in the transfected trophozoites only, the proteomes of untransfected and transfected trophozoites differ by 132 differentially expressed proteins. In particular, transfection induces antigenic variation. Since transfection causing stable expression affects the proteome pattern, transfection experiments should take into account this effect. Due to a unique peptide panel, GusA is an example for a suitable internal standard for experiments involving transfected cells. Data are available via ProteomeXchange with identifier PXD022565.", "claims": [{"id": "claim-method", "statement": "Differential expression tests were performed by applying the (Welch-) Student’s t-test (unequal variance).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33392107", "locator": "sections[7] \"Statistics\" paragraph 4", "quote": "Differential expression tests were performed by applying the (Welch-) Student’s t-test (unequal variance)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2019) partner repository with the dataset identifier PXD022565.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33392107", "locator": "sections[6] \"Proteomics\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2019) partner repository with the dataset identifier PXD022565."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33392107"], "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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2019) partner repository with the dataset identifier PXD022565.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2019) partner repository with the dataset identifier PXD022565.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Transfection with Glucuronidase A affects general proteome pattern in Giardia lamblia trophozoites", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33392107:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3a4faa7a28100b14013133d1e570a7dbe0775ababf9f218d179b033eb4f84aac", "bytes": 884, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#T1", "version": null, "note": "Major housekeeping proteins and transgenes in untransfected Giardia lamblia WBC6 wildtype (WT) and Escherichia coli glucuronidase A (GusA)-transfected trophozoites.", "structure": {"pmcid": "PMC7775365", "section_index": 9, "section_title": "Proteome Parameters of Giardia lamblia Trophozoites", "row_count": 8, "column_count": 6}, "table": {"label": "Table 1", "caption": "Major housekeeping proteins and transgenes in untransfected Giardia lamblia WBC6 wildtype (WT) and Escherichia coli glucuronidase A (GusA)-transfected trophozoites.", "rows": [["Protein", "Accession No.", "LFQ", "iTop3"], ["", "", "WT", "GusA", "WT", "GusA"], ["Pyruvate ferredoxin oxidoreductase", "17063", "10,464 ± 407", "8,096 ± 70", "249 ± 36", "196 ± 17"], ["Arginine deiminase", "112103", "31,263 ± 450", "39,025 ± 1,129", "1,110 ± 431", "1,550 ± 289"], ["Thioredoxin-reductase", "9827", "1,725 ± 556", "1,804 ± 458", "108 ± 42", "144 ± 33"], ["Glutamate dehydrogenase", "21942", "10,315 ± 1015", "7,159 ± 826", "309 ± 39", "216 ± 39"], ["Glucuronidase A", "P05804", "nd", "128 ± 7", "nd", "13 ± 2"], ["Puromycin-N acetyltransferase", "P13249", "nd", "nd", "nd", "Nd"]], "row_count": 8, "column_count": 6, "numeric_cells": 24, "header_rows": 2, "locator": "section[9]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:33392107:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:45167246ac244b597560756806bb492e748a5cd33c88e50b2d6b871dba12291e", "bytes": 818, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T2", "version": null, "note": "Overview of differentially expressed proteins in untransfected G. lamblia wildtype (WT) and E. coli glucuronidase A-transfected trophozoites (GusA).", "structure": {"pmcid": "PMC7775365", "section_index": 11, "section_title": "Differentially Expressed Proteins", "row_count": 11, "column_count": 3}, "table": {"label": "Table 2", "caption": "Overview of differentially expressed proteins in untransfected G. lamblia wildtype (WT) and E. coli glucuronidase A-transfected trophozoites (GusA).", "rows": [["(Hypothetical) function", "Higher in WT", "Higher in GusA"], ["Surface antigens: (a) Variant-specific surface proteins", "1", "14"], ["(b) High cysteine membrane proteins", "2", "0"], ["21.1 proteins (ankyrin repeat proteins without kinase domain)", "1", "3"], ["Gene expression, cell cycle, development", "3", "11"], ["Intermediary metabolism", "5", "12"], ["Transport of micromolecules", "0", "1"], ["Cytoskeleton, flagella, adhesion and organelle transport", "2", "5"], ["Chaperones", "0", "2"], ["Hypothetical", "25", "45"], ["Total", "39", "93"]], "row_count": 11, "column_count": 3, "numeric_cells": 21, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:33392107:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2e70471e9c587cae9103eb38bc8dde5dc715e870e9a159228816c8332ed14d4e", "bytes": 1152, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T3", "version": null, "note": "Major surface antigens without significant differences in expression levels between untransfected G. lamblia WBC6 wildtype (WT) and E. coli glucuronidase A (GusA)-transfected trophozoites.", "structure": {"pmcid": "PMC7775365", "section_index": 12, "section_title": "Antigenic Variation", "row_count": 11, "column_count": 6}, "table": {"label": "Table 3", "caption": "Major surface antigens without significant differences in expression levels between untransfected G. lamblia WBC6 wildtype (WT) and E. coli glucuronidase A (GusA)-transfected trophozoites.", "rows": [["Accession N°", "Annotation", "LFQ", "iTop3"], ["", "", "WT", "GusA", "WT", "GusA"], ["GL50803_101074", "VSP with INR; VSP-88", "1,315 ± 172", "1,740 ± 148", "746 ± 162", "975 ± 185"], ["GL50803_112207", "VSP", "102 ± 44", "35 ± 2", "168 ± 88", "24 ± 2"], ["GL50803_137612", "VSP", "195 ± 28", "352 ± 27", "119 ± 10", "218 ± 24"], ["GL50803_137613", "VSP with INR; VSP-188", "3,368 ± 217", "3,170 ± 96", "3,104 ± 96", "2,728 ± 237"], ["GL50803_137617", "VSP", "102 ± 3", "123 ± 4", "66 ± 3", "79 ± 3"], ["GL50803_137618", "VSP with INR; VSP-8", "979 ± 173", "637 ± 54", "619 ± 157", "386 ± 37"], ["GL50803_15317", "HCMP group 1", "835 ± 110", "401 ± 23", "495 ± 102", "330 ± 29"], ["GL50803_221693", "(hypothetical), VSPA6", "124 ± 60", "48 ± 4", "179 ± 75", "42 ± 3"], ["GL50803_33279", "VSP", "181 ± 12", "118 ± 9", "276 ± 6", "150 ± 4"]], "row_count": 11, "column_count": 6, "numeric_cells": 49, "header_rows": 2, 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Here, we investigate how transfection with a plasmid causing stable expression of", "f untransfected trophozoites to trophozoites transfected with Escherichia coli glucuronidase A (GusA)", "usA). Besides GusA, which is detected in the transfected trophozoites only, the proteomes of untransf"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ts the whole proteome pattern. 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