Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of the effect of ClpC1 directed antibiotics on ClpC1, ClpC2 and ClpC3 protein levels.

ABSTRACT: Ecumicin and Cyclomarin A (CymA) are known antimicrobial compounds that target the NTD of ClpC1. In proteomics analysis of compound treated M. smegmatis, two novel protein, ClpC2 and ClpC3, have been identified as strong interactors of those compounds in addition to ClpC1. In this study we used PRM to monitor the levels of ClpC1, ClpC2 and ClpC3 over time after treatment with CymA or ecumicin or CymA-based BacPROTACs.

ORGANISM(S): Mycolicibacterium Smegmatis

SUBMITTER: David Hoi

PROVIDER: PXD037198 | panorama | Wed Jun 07 00:00:00 BST 2023

REPOSITORIES: PanoramaPublic

ACCESS DATA

Json Xml

Publications

Clp-targeting BacPROTACs impair mycobacterial proteostasis and survival.

Hoi David M DM Junker Sabryna S Junk Lukas L Schwechel Kristin K Fischel Katharina K Podlesainski David D Hawkins Paige M E PME van Geelen Lasse L Kaschani Farnusch F Leodolter Julia J Morreale Francesca Ester FE Kleine Stefan S Guha Somraj S Rumpel Klaus K Schmiedel Volker M VM Weinstabl Harald H Meinhart Anton A Payne Richard J RJ Kaiser Markus M Hartl Markus M Boehmelt Guido G Kazmaier Uli U Kalscheuer Rainer R Clausen Tim T

Cell 20230502 10

The ClpC1:ClpP1P2 protease is a core component of the proteostasis system in mycobacteria. To improve the efficacy of antitubercular agents targeting the Clp protease, we characterized the mechanism of the antibiotics cyclomarin A and ecumicin. Quantitative proteomics revealed that the antibiotics cause massive proteome imbalances, including upregulation of two unannotated yet conserved stress response factors, ClpC2 and ClpC3. These proteins likely protect the Clp protease from excessive amount ...[more]

PMID: 37137307

Similar Datasets

Effects of androgen treatment on genital fibroblasts

Project description:e tested the responses of normal and AIS genital fibroblasts to dihydrotestosterone (DHT), under culture conditions similar to those that were reported to produce aromatase induction in these cells [8]. Cells were treated with DHT (100-1,000 nM) both at confluency (G0) and during exponential growth, and transcript levels were assessed using DNA microarrays. A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed. Keywords: compound_treatment_design

2005-12-21 | GSE3871 | GEO

Human scrotum and labia majora samples treated with DHT and/or AZA

Project description:Human scrotum and labia majora samples treated with DHT and/or AZA A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed. Compound Based Treatment: dihydrotestosterone (DHT), 5-aza-deoxy-cytidine (AZA), none or both Cell Line: normal scrotum or labia majora derived from complete androgen insensitivity syndrome due to inactivating mutation of the androgen receptor gene

2009-05-20 | GSE11847 | GEO

LFQ proteomics analysis of M. smegmatis treated with BacPROTACs.

Project description:To monitor selective degradation of ClpC1 and ClpC2 using BacPROTAC compounds in M. smegmatis we performed a LFQ proteomics analysis treating the cells at bactericidal compound concentration. We detected degradation of both proteins and additional dysregulation of the mycobacterial PQC system.

2023-06-07 | PXD037235 | Pride

Transcriptomic analysis of Human Umbilical Vein Endothelial Cells (HUVEC) in response to compound treatment

Project description:Human Umbilical Vein Endothelial Cells were treated with three newly synthesized compounds and DMSO as vehicle. Total RNA was isolated 6 and 24h after treatment and gene expression analysis was performed. Three independent experiments were performed, corresponding to rep1, rep2 and rep3. Experiment 1 (rep1) contained all substances at both time points tested. Experiment 2 (rep2) contained two of the compounds and control DMSO at both time points. Experiment 3 (rep3) contained the third compound and control DMSO at both time points.

2016-06-30 | GSE75588 | GEO

Real-time quantitative PCR miRNA analysis of human hepatocytes

Project description:Primary human hepatocytes were treated with compounds modulating steatosis: palmitic acid, compound C and metformin qPCR miRNA expression profiling. Hepatocytes were treated as indicated in the summary. Equal amount total RNA was pooled prior to miRNA expression analysis

2020-02-11 | GSE145039 | GEO

Transcriptomic analysis of Human Umbilical Vein Endothelial Cells (HUVEC) in response to compound treatment

2016-06-30 | E-GEOD-75588 | biostudies-arrayexpress

Small molecule inhibitors suppress expression of both type III secretion and amylovoran biosynthesis genes in Erwinia amylovora

Project description:Microarray analysis of E. amylovora treated with compounds no. 3 and no. 9 identified a total of 588 significantly differentially expressed genes. Among them, 95 and 78 genes were, respectively, induced and suppressed by both compounds as compared to DMSO control. Majority of T3SS genes in E. amylovora including hrpL and avrRpt2 effector gene were suppressed by both compounds. Compound no. 3 also suppressed the transcription of amylovoran precursor and biosynthesis genes. On the other hand, both compounds significantly induced expression of glycogen biosynthesis genes and siderophore biosynthesis, regulatory and transport genes. Furthermore, many membrane, lipoprotein and exported protein encoding genes were also activated by both compounds. Erwinia amylovora WT strain treated with compound No. 3 and No. 9 and compared to DMSO control. Four biological replicates for each chemical treatment (two samples were combined) were hybridized to three arrays. Four biological replicates (two each combined) for DMSO treatment were hybridized to two arrays.

2013-12-24 | E-GEOD-45602 | biostudies-arrayexpress

Human scrotum and labia majora samples treated with DHT and/or AZA

2009-05-20 | E-GEOD-11847 | biostudies-arrayexpress

Antitumor efficacy of RAF inhibitor GDC-0879 involving BRAFV600E mutational status and ERK/MAPK pathway suppression

Project description:Unsupervised hierarchical clustering revealed a strong similarity in gene modulation resulting from either compound treatment or BRAF ablation mediated by RNA interference relative to DMSO-treated control samples . Keywords: Expression Array

2009-10-01 | GSE13487 | GEO

Investigating the multi-mechanistic anticancer effects of 4-bisarylurea thiouracil derivatives in breast cancer cells

Project description:The study reports the synthesis of a series of 4-bisarylureathiouracil derivatives (6a-e) for potential use in breast cancer treatment. In vitro cytotoxicity was assessed in MCF-7 and MDA-MB-231 human breast cancer cell lines, revealing significant anti-cancer activity. Compound 6e exhibited the highest cytotoxicity, with IC50 values of 7.94 μM for MCF-7 and 6.67 μM for MDA-MB-231, although it was also the most toxic to RAW 264.7 macrophage cells. In contrast, compound 6c demonstrated strong efficacy against both cancer cell lines (IC50 = 9.23 ± 0.6 μM for MCF-7 and 7.72 ± 0.6 μM for MDA-MB-231) while maintaining selectivity (SI values >10.8 and > 12.9, respectively). Flow cytometry and caspase-3 assays indicated that compounds 6a-c induced apoptosis in MCF-7 cells. In anti-inflammatory assays, compounds 6a and 6d showed significant effects, while 6c demonstrated the weakest, suggesting its cytotoxicity is not linked to anti-inflammatory properties. Compound 6c was prioritised for further investigation because of its preferential targeting of cancer cells. Proteomic analysis of 6c-treated cells revealed significant dysregulation of apoptosis, angiogenesis and VEGF signalling, Rho signal transduction, and pi3k-akt signalling pathways. These findings highlighted the potential of compounds 6a-e as effective anticancer agents, warranting further investigation and optimization for therapeutic applications.

2025-07-19 | PXD065576 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data