Relative and Quantitative Phosphoproteome Analysis of Macrophages in Response to Infection by Virulent and Avirulent Mycobacteria Reveals a Distinct Role of the Cytosolic RNA Sensor RIG-I in Mycobacterium tuberculosis Pathogenesis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32407090", "kind": "science-record", "revision": 3, "content_hash": "sha256:433e34fad5558a24c2ac939ac9fb71d619922382823425eff60b9e0d16569dae", "created_at": "2026-11-01T17:33:39Z", "updated_at": "2026-11-01T21:23:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Relative and Quantitative Phosphoproteome Analysis of Macrophages in Response to Infection by Virulent and Avirulent Mycobacteria Reveals a Distinct Role of the Cytosolic RNA Sensor RIG-I in Mycobacterium tuberculosis Pathogenesis.", "doi": "10.1021/acs.jproteome.9b00895", "pmid": "32407090", "authors": ["Eira Choudhary", "C Korin Bullen", "Renu Goel", "Alok Kumar Singh", "Monali Praharaj", "Preeti Thakur", "Rohan Dhiman", "William R Bishai", "Nisheeth Agarwal"], "journal": "Journal of proteome research", "year": 2020, "abstract": "Comparative phosphoproteomics of Mycobacterium tuberculosis (Mtb)- and Mycobacterium bovis BCG (BCG)-infected macrophages could be instrumental in understanding the characteristic post-translational modifications of host proteins and their subsequent involvement in determining Mtb pathogenesis. To identify proteins acquiring a distinct phosphorylation status, herein, we compared the phosphorylation profile of macrophages upon exposure to Mtb and BCG. We observed a significant dephosphorylation of proteins following Mtb infection relative to those with uninfected or BCG-infected cells. A comprehensive tandem mass tag mass spectrometry (MS) approach detected ∼10% phosphosites on a variety of host proteins that are modulated in response to infection. Interestingly, the innate immune-enhancing interferon (IFN)-stimulated genes were identified as a class of proteins differentially phosphorylated during infection, including the cytosolic RNA sensor RIG-I, which has been implicated in the immune response to bacterial infection. We show that Mtb infection results in the activation of RIG-I in primary human macrophages. Studies using RIG-I knockout macrophages reveal that the Mtb-mediated activation of RIG-I promotes IFN-β, IL-1α, and IL-1β levels, dampens autophagy, and facilitates intracellular Mtb survival. To our knowledge, this is the first study providing exhaustive information on relative and quantitative changes in the global phosphoproteome profile of host macrophages that can be further explored in designing novel anti-TB drug targets. The peptide identification and MS/MS spectra have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD013171.", "claims": [{"id": "claim-method", "statement": "Quantified mass spectrometry data from 2 biological replicates were statistically analysed using a two-tailed student’s t-test by the Prism 7.0 software.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32407090", "locator": "sections[16] \"Statistical analysis\" paragraph 2", "quote": "Quantified mass spectrometry data from 2 biological replicates were statistically analysed using a two-tailed student’s t-test by the Prism 7.0 software."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data obtained from this study were submitted to public data repositories. The peptide identifications and MS/MS spectra have been deposited to the ProteomeXchange Consortium (55) via the PRIDE partner repository with the dataset identifier PXD013171. We have also submitted the data to Massive database that can be accessed through ftp://MSV000083308@massive.ucsd.edu.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32407090", "locator": "sections[29] \"Data availability\" paragraph 2", "quote": "The raw data obtained from this study were submitted to public data repositories. The peptide identifications and MS/MS spectra have been deposited to the ProteomeXchange Consortium (55) via the PRIDE partner repository with the dataset identifier PXD013171. We have also submitted the data to Massive database that can be accessed through ftp://MSV000083308@massive.ucsd.edu."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Phosphopeptides with p values of <0.05 and fold change in expression by >1.2 or <0.8 were considered for further analysis by Ingenuity Pathway Analysis (IPA) software.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:32407090", "locator": "sections[16] \"Statistical analysis\" paragraph 2", "quote": "Phosphopeptides with p values of <0.05 and fold change in expression by >1.2 or <0.8 were considered for further analysis by Ingenuity Pathway Analysis (IPA) software."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Phosphopeptides with p values of <0.05 and fold change in expression by >1.2 or <0.8 were considered for further analysis by Ingenuity Pathway Analysis (IPA) software.", "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:32407090"], "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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