Protein profile of different cellular fractions from Mycobacterium tuberculosis strains after exposure to isoniazid.

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Here, we present a detailed analysis, looking at the protein variation in the Mtb cell due to exposure of sub-inhibitory concentrations of INH, evaluating three different variables: cellular fraction, genetic lineage, and INH phenotypic profile. Mass spectrometry analysis demonstrated that the most significantly affected cellular fraction was the membrane and the INH resistant strains showed the highest number of proteins altered when they were exposed to INH. Raw data are available via ProteomeXchange with identifier PXD007588.", "claims": [{"id": "claim-method", "statement": "Differences between protein abundances, expressed as normalized spectra abundance factors (NSAF values) among the two different conditions (exposed versus non-exposed to INH) in each pair were tested by two tailed Student's t-test, resulting in four pair comparisons. 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The resulting samples were standardized to the same amount of total purified protein for digestion with trypsin followed by nanoLC-MS/MS analysis as previously described[1]. Using the platforms Sorcerer2™ and SEQUEST, the resulting spectra were analyzed using the identification criteria previously defined by Nieto et al. and the Mtb strain H37Rv Tuberculist database[1]. Finally, western blot analysis was conducted for five Mtb proteins to confirm mass spectrometry findings."], ["Data source location", "Fort Collins, Colorado."], ["Data accessibility", "Raw data of this article are available via ProteomeXchange with identifier PXD007588"], ["Related research article", "Nieto R LM, Mehaffy C, Islam MN, Fitzgerald B, Belisle J, Prenni J et al. Biochemical characterization of isoniazid resistant. Mol Cell Proteomics.2018. Epub 2018/05/29.https://doi.org/10.1074/mcp.RA118.000821. PubMed PMID: 29,844,232[1]."]], "row_count": 10, "column_count": 2, "numeric_cells": 3, "header_rows": 0, "locator": "section[1]/table-wrap[1]#undtbl1"}}, {"id": "asset:table:pmid:31193076:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:75c3e692f48f0606afbaf23adf01d74b81e0694ddd005b2bc1c253682a806340", "bytes": 1528, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[2]#undtbl2", "version": null, "note": null, "structure": {"pmcid": "PMC6517567", "section_index": 1, "section_title": "p", "row_count": 1, "column_count": 1}, "table": {"label": null, "caption": null, "rows": [["Value of the data•This data shows the first characterization of changes at the proteome level after the exposure of Mycobacterium tuberculosis (Mtb) to isoniazid (INH), looking at different subcellular levels (cytosol, cell wall, membrane and secreted proteins) and using a very sensitive methodology: label-free quantitative proteomics (by LC-MS/MS), complemented [1] with western blot (WB).•This data brings upfront the importance of studying the bacterial proteome of laboratory and clinically relevant genotypes and phenotypes (drug-susceptible and drug-resistant to INH), when Mtb is in contact with one of its more potent drugs.•Common protein variations commonly found in both INH-related phenotypes of Mtb (INH susceptible and resistant), were associated with lipid biosynthesis, central carbon metabolism, lipoproteins, and the INH activator (KatG).•Reduced levels of some proteins presented here were also revealed in our previous study that compared clonal strains of Mtb after acquisition of INH resistance [1], which could be reflecting the steps towards bacterial adaptation to tolerate INH.•The metabolic routes and the specifically identified proteins could serve as potentially complementary drug targets, in the design of more rationalized anti-TB therapy using INH, which is still one of the best treatment options for patients suffering from TB."]], "row_count": 1, "column_count": 1, "numeric_cells": 1, "header_rows": 0, "locator": "section[1]/table-wrap[2]#undtbl2"}}, {"id": "asset:table:pmid:31193076:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fee34448ed2567645e16be3a7759359f71251c11c70e2a17dc6397b3a0adbcec", "bytes": 476, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[2]/table-wrap[1]#tbl1", "version": null, "note": "Significantly altered proteins in Mtb strains after exposure to INH classified according their susceptibility profile to INH and genetic background pair comparisons tested with t-test, corrected with Benjamini-Hochberg (BH)a with different false discovery rates (Q) values. 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Log2foldchangeNSAFexposedtoINHNSAFnon−exposedtoINH.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[2]/table-wrap[1]#tbl1"}}], "gaps": ["asset:data:geo:PXD007588 not downloaded", "asset:data:geo:PXD007588 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differences between protein abundances, expressed as normalized spectra abundance factors (NSAF values) among the two different conditions (exposed versus non-exposed to INH) in each pair were tested by two tailed Student's t-test, resulting in four pair comparisons. 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