Dataset Information

Proteomic Profiling of Mycobacterium tuberculosis in Response to ILE Treatment

ABSTRACT: This study aims to elucidate the global proteomic changes in Mycobacterium tuberculosis upon treatment with the novel compound ilamycin E(ILE), which targets the Clp protease system. Label-free quantitative proteomics was employed to assess differential protein expression after ILE exposure. The results reveal that ILE induces significant alterations in the expression of proteins involved in proteolysis, stress response, redox homeostasis, and energy metabolism, providing valuable insights into the adaptive response and potential mechanism of action of ILE in M. tuberculosis. These data support further development of ILE as a candidate anti-mycobacterial agent targeting intracellular proteostasis.

INSTRUMENT(S):

ORGANISM(S): Mycobacterium Tuberculosis H37ra

SUBMITTER: Cuiting Fang

LAB HEAD: Tianyu Zhang

PROVIDER: PXD066355 | Pride | 2026-02-09

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	ILE-1-SampleInfo.xml	Xml
	ILE-1-analysis.0.result_c	Other
	ILE-1-analysis.tdf	Other
	ILE-1-analysis.tdf_bin	Other
	ILE-1_S6-C4_1_21912_5.3.236.mgf	Mgf

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Publications

Mutations in ClpC1 or ClpX subunit of caseinolytic protease confer resistance to ilamycins in mycobacteria.

Gao Yamin Y Fang Cuiting C Zhou Biao B Hameed H M Adnan HMA Sun Changli C Tian Xirong X He Jing J Han Xingli X Zhang Han H Li Jun J Ju Jianhua J Chen Xinwen X Zhong Nanshan N Ma Junying J Xiong Xiaoli X Zhang Tianyu T

Communications biology 20250813 1

The mycobacterial caseinolytic protease (Clp) system has been recognized as a promising therapeutic target. In this study, we identify two novel ilamycin analogs, ilamycin E (ILE) and ilamycin F (ILF), both targeting the ClpC1 component of the ClpC1P1P2 proteasome. ILE potently disrupts ClpC1P1P2-mediated proteolysis, leading to delayed bactericidal activity, while ILF also binds ClpC1, albeit with lower affinity. Notably, we discover and validate a unique mutation in clpX and a novel insertion ...[more]

PMID: 40804467

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Project description:Transcription profiling of wild type, relA-, and relA-spoT-, crp-, dksA-, rpoS-, lrp- mutant strains of E. coli starved for isoleucine Bacteria comprehensively reorganize their global gene expression when faced with nutrient exhaustion. In Escherichia coli and other free-living bacteria, the alarmone ppGpp facilitates this massive response by directly or indirectly coordinating the down-regulation of genes of the translation apparatus, and the induction of biosynthetic genes and the general stress response. Such a large reorientation likely requires the cooperative activities of many different genetic regulators, yet the structure of the transcription network below the level of ppGpp remains poorly defined. Using isoleucine starvation as an experimental model system for amino acid starvation, we identified genes that required ppGpp, Lrp, and RpoS for their induction. Surprisingly, despite the fact that the overwhelming majority of genes controlled by Lrp and RpoS required ppGpp for their activation, we found that these two regulons were not induced simultaneously. The data reported here suggest that metabolic genes, such as those of the Lrp regulon, require only a low basal level of ppGpp for their efficient induction. In contrast, the RpoS-dependent general stress response is not robustly induced until relatively high levels of ppGpp accumulate. Here we describe a data-driven conceptual model that explains how bacterial cells allocate transcriptional resources between metabolic and stress survival processes by discretely tuning regulatory activities to a central indicator of cellular physiology. The regulatory structure that emerges is consistent with a rheostatic model of the stringent response that allows cells to efficiently adapt to a wide range of nutritional environments. Keywords: genetic modification design; stress response; isoleucine starvation Two experiments were run. First experiment: WT and several mutant strains were starved for isoleucine (exhaustion of 60 uM ile). 40 minutes after starvation, RNA was extracted. All samples were compared to RNA from rapidly growing WT cells in identical medium replete with isoleucine (400 uM). 16 samples were hybridized: duplicates of 8 strains/conditions. Wildtype in log phase (OD = 0.4) with replete ile was control for ile starved samples. Second experiment: WT strain was starved for isoleucine (exhaustion of 60 uM ile). RNA was extracted at 12 timepoints as the cells entered stationary phase. All samples were compared to RNA from rapidly growing WT cells in identical medium replete with isoleucine (400 uM). 14 samples were hybridized: duplicates of the control condition and single timepoints during starvation. Wildtype in log phase (OD = 0.4) with replete ile was control for ile starved samples.