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Toxin-mediated ribosome stalling as a complementary tool to annotate bacterial ORFs

ABSTRACT: The goal of this project is to identify proteins upon the expression of VapC4 (Rv0595c).

INSTRUMENT(S):

ORGANISM(S): Bacteria Mycobacterium Tuberculosis H37rv

DISEASE(S): Tuberculosis

SUBMITTER: Safreen Sain

LAB HEAD: Nancy A Woychik

PROVIDER: PXD071737 | Pride | 2026-04-27

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	ECL00141.mgf	Mgf
	ECL00141.mzid	Mzid
	ECL00141.raw	Raw
	ECL00142.mgf	Mgf
	ECL00142.mzid	Mzid

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1 - 5 of 20

Publications

Harnessing toxin-mediated ribosome stalling as a complementary tool to annotate bacterial ORFs.

Troian Eduardo A EA Barth Valdir C VC Chauhan Unnati U Zheng Haiyan H Zhao Caifeng C Zeng Jumei J Husson Robert N RN Woychik Nancy A NA

Nucleic acids research 20260401 7

The Mycobacterium tuberculosis (Mtb) VapC4 endoribonuclease toxin exclusively cleaves and inactivates tRNACys, which leads to extensive ribosome stalling at Cys codons. Serendipitously, the precise position of stalled ribosomes is revealed within our 5' RNA-seq datasets used to identify and validate the tRNA target of the toxin, precluding the need for Ribo-seq. Here we show how mapping of stalled ribosomes can be harnessed as an innovative tool for reliable detection of new Cys-containing Mtb o ...[more]

PMID: 42011780

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Toxin-mediated ribosome stalling as a complementary tool to annotate bacterial ORFs

Project description:The goal of this project is to identify newly synthesized proteins upon expression of VapC4 (Rv0595c) in M. tuberculosis mc2 6202 or ∆vapBC4 strains.

2026-04-27 | PXD071729 | Pride

Phosphorylation of CFP10 modulates Mycobacterium tuberculosis virulence

Project description:Virulence effectors secreted by Mycobacterium tuberculosis (Mtb) help subvert host immune mechanisms and, therefore, are critical for establishing infection and pathogenesis. However, knowledge in terms of signaling mechanisms that modulate the secretion of virulence factors is sparse. We performed high-throughput secretome, phosphoproteome, and phospho-secretome analysis of Mtb. We combined the analysis with empirical validations to show regulation of mycobacterial secretion through protein phosphorylation. System level PPI network analysis superimposed with the secretome, phosphoproteome, and phospho-secretome profile revealed an intricate relationship between phosphorylation and secretion. At the core of the network was a key virulence factor CFP10. We identified PknA to be the kinase responsible for phosphorylating CFP10. Using genetic tools, we show that phosphomimetic mutation of CFP10 negatively regulates the secretion of virulence mediator ESAT6. Significantly, the dynamics of CFP10 phosphorylation strongly influenced bacterial virulence and survival within macrophages and mice. Together, the results show that the dynamic phosphorylation status of the secretory protein CFP10 regulates the secretion of virulence factors and impacts virulence.

2023-09-22 | PXD045586 | Pride

Mycobacterium tuberculosis VapC4 toxin engages small ORFs to initiate an integrated oxidative and copper stress response

Project description:Analyzing newly synthesized protein after VapC4 induction in mycobacterium tuberculosis mc26206

2022-02-17 | PXD025774 | Pride

Hydrogen sulfide stimulates Mycobacterium tuberculosis respiration and growth to exacerbate TB disease

Project description:The aim of this experiment was to determine how exposure of Hydrogen sulfide impacts gene expression in Mycobacterium tuberculosis. RNA was isolated from actively growing mycobacterial cells (0.6-0.8 OD600) using Trizol according to established protocols (27). Briefly, cells were exposed to 25 µM GYY4137 for 1 hr under carefully controlled conditions (n=3/group) and RNA isolated. Unexposed cells received spent GYY4137 (without any capacity to produce Hydrogen sulfide).

2020-01-04 | E-MTAB-7421 | biostudies-arrayexpress

Global Gene expression data from Mycobacterium tuberculosis treated with new TB drug named Bedaquiline

Project description:Sirturo or Bedaquiline has been shown to inhibit the ATP synthase of Mycobacterium tuberculosis. We used microarrays to investigate compound-induced gene expression changes in general as well as effects on the transcription of the different ATP synthase genes and other metabolic pathways. Log phase Mycobacterium tuberculosis were cultivated in Middlebrook 7H9 broth and treated with 1 M-BM-5M Bedaquiline. We have extracted RNA from five different time-points after treatment: 0 min (T0), 30 min (T30), 60 min (T60), 180 min (T180) and 360 min (T360).

2014-03-03 | E-GEOD-43749 | biostudies-arrayexpress

Changes in the Membrane-Associated Proteins of Exosomes Released from Human Macrophages after Mycobacterium tuberculosis Infection - Biotinylated

Project description:Tuberculosis (TB) is the deadliest infectious disease worldwide. One obstacle hindering the elimination of TB is our lack of understanding of host-pathogen interactions. Exosomes, naturally loaded with microbial molecules, are circulating markers of TB. Changes in the host protein composition of exosomes from Mycobacterium tuberculosis (Mtb)-infected cells have not been described, can contribute to our understanding of the disease process, and serve as a direct source of biomarkers or as capture targets to enrich for exosomes containing microbial molecules. Here, the protein composition of exosomes from Mtb-infected and uninfected THP-1-derived macrophages was evaluated by tandem-mass-spectrometry and differences in protein abundances were assessed. Our results show that infection with Mtb leads to significant changes in the protein composition of exosomes. Specifically, 41 proteins were significantly more abundant in exosomes from Mtb-infected cells; 63% of these were predicted to be membrane associated. Thus, we used a novel biotinylation strategy to verify protein localization, and confirmed the localization of some of these proteins in the exosomal membrane. Our findings reveal another important scenario where Mtb could be influencing changes in host cells that unveil new features of the host-pathogen interaction and may also be exploited as a source of biomarkers for TB.

2018-08-06 | PXD010659 | Pride

HLA-E Presents Glycopeptides from the Mtb Protein MPT32 to Human CD8 T Cells

Project description:Infection with Mycobacterium tuberculosis (Mtb), the bacterium that causes Tuberculosis, remains a global health concern. Both classically and non-classically restricted cytotoxic CD8+ T cells are important to the control of Mtb infection. We and others have demonstrated that the non-classical MHC I molecule HLA-E can present pathogen-derived peptides to CD8+ T cells. In this manuscript, we identified the antigen recognized by an HLA-E-restricted CD8+ T cell clone isolated from an Mtb latently infected individual as a peptide from the Mtb protein, MPT32. Recognition by the CD8+ T cell clone required N-terminal O-linked mannosylation of MPT32 by a mannosyltransferase encoded by the Rv1002c gene. This is the first description of a post-translationally modified Mtb-derived protein antigen presented in the context of an HLA-E specific CD8+ T cell immune response. The identification of an immune response that targets a unique mycobacterial modification is novel and has practical impact in the development of vaccines and diagnostics.

2018-10-26 | PXD005765 | Pride

Mycobacterium tuberculosis H37Rv (WT) versus Mut1 and Comp1

Project description:Transcriptional profiling of H37Rv (WT), Mut1 and Comp1 bacteria under aerobic (Aer/0 day, i.e 0 D) and hypoxic conditions (Hyp/5 days standing culture, i.e 5 D). Mut1: H37Rv carrying devR gene disruption by in frame insertion of kanamycin resistance cassette and expressing DevRN-Kan fusion protein. Comp1: Mut1 complemented with low copy number plasmid carrying devR gene expressed from its native constitutive upstream promoter. (Reference: Majumdar et al., 2010, PLoS One 5:e9448). Goal is to compare transcriptional patterns of WT, Mut1 and Comp1 strains under aerobic (0 D) and hypoxic (5 D) conditions in vitro. Two color and One-color experiments,Organism: Mycobacterium tuberculosis, Genotypic Technology designed Custom Mycobacterium tuberculosis H37Rv Whole Genome 8x15k GE Microarray (AMADID-020181)

2011-09-30 | E-GEOD-30264 | biostudies-arrayexpress

Pain-killer carprofen elicits pleiotropic modes of bactericidal action with potential to reverse antimicrobial resistance in tuberculosis.

Project description:The alarming rise of antimicrobial resistance in Mycobacterium tuberculosis coupled with the shortage of new antibiotics has made tuberculosis (TB) control a global health priority. Non-steroidal anti-inflammatory drugs (NSAIDs) inhibit the growth of multi-drug resistant isolates of M. tuberculosis. Repurposing NSAIDs, with known clinical properties and safety records, offers a direct route to clinical trials. Therefore we investigated the novel mechanisms of anti-mycobacterial action of the NSAID, carprofen. Integrative molecular and microbiological approaches revealed that carprofen, a bactericidal drug, inhibited bacterial drug efflux mechanisms. In addition, carprofen restricted mycobacterial biofilm-like growth, highlighting the requirement of efflux-mediated communicative systems for the formation of biofilms. Transcriptome profiling revealed that carprofen likely acts by inhibiting respiration through the disruption of membrane potential, which may explain why spontaneous drug-resistant mutants could not be raised due to the pleiotropic nature of carprofen’s anti-tubercular action. This immunomodulatory drug has the potential to reverse TB antimicrobial resistance by inhibiting drug efflux pumps and biofilm formation, and paves a new chemotherapeutic path for tackling tuberculosis.

2020-08-15 | E-MTAB-6191 | biostudies-arrayexpress

Immunopeptidomics reveals determinants of Mycobacterium tuberculosis antigen presentation on MHC class I (DDA data)

Project description:Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is a leading cause of infectious disease mortality worldwide for which no sufficiently protective vaccine exists. CD8+ T cells contribute to protective immunity to TB, but the antigenic targets presented on MHC-I by macrophages infected with virulent Mtb for recognition by CD8+ T cells have not been conclusively defined. Here, we use mass spectrometry to directly identify Mtb-derived peptides presented on MHC class I (MHC-I) by infected primary human monocyte-derived macrophages. We identified 16 MHC-I peptides derived from 12 Mtb proteins, and validated these identifications using internal standard parallel reaction monitoring (SureQuant). Our results show that this set of antigens is highly enriched for substrates of type VII secretion systems (T7SS) relative to the Mtb proteome. Our results identify specific Mtb proteins that may be suitable targets for subunit vaccines designed to elicit protective CD8+ T cell-mediated immunity and suggest that T7SS substrates may be a fruitful class of antigens to prioritize for further vaccine target discovery efforts. Note: donors labeled A, C, D, E, H, and I in file names here are renamed sequentially (A, B, C, D, E, and F) in the manuscript describing this study to avoid confusion.

2023-04-24 | PXD037837 | Pride

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