Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAP stalling-derived genome instability underlies ribosomal antibiotics efficacy and resistance evolution (ChIP-seq data)

ABSTRACT: Bacteria often evolve antibiotic resistance through mutagenesis. However, the processes causing the mutagenesis have not been fully resolved. Here we found that a broad range of ribosome-targeting antibiotics caused mutations through an underexplored pathway. Focusing on the clinically important aminoglycoside gentamicin, we found that the translation inhibitor caused genome-wide premature stalling of RNA polymerase (RNAP) in a loci-dependent manner. Further analysis showed that the stalling was caused by disruption of transcription-translation coupling. Anti-intuitively, the stalled RNAPs subsequently induced lesions to the DNA via transcription-coupled repair. While most of the bacteria were killed by genotoxicity, a small subpopulation acquired mutations via SOS-induced mutagenesis. Given that these processes were triggered shortly after antibiotic addition, resistance rapidly emerged in the population. Our work revealed a new mechanism of action of ribosomal antibiotics, illustrates the importance of dissecting the complex interplay between multiple molecular processes in understanding antibiotic efficacy, and suggests new strategies for countering the development of resistance.

ORGANISM(S): Escherichia coli

PROVIDER: GSE267245 | GEO | 2024/05/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

RNAP stalling-derived genome instability underlies ribosomal antibiotics efficacy and resistance evolution

Project description:Bacteria often evolve antibiotic resistance through mutagenesis. However, the processes causing the mutagenesis have not been fully resolved. Here we found that a broad range of ribosome-targeting antibiotics caused mutations through an underexplored pathway. Focusing on the clinically important aminoglycoside gentamicin, we found that the translation inhibitor caused genome-wide premature stalling of RNA polymerase (RNAP) in a loci-dependent manner. Further analysis showed that the stalling was caused by disruption of transcription-translation coupling. Anti-intuitively, the stalled RNAPs subsequently induced lesions to the DNA via transcription-coupled repair. While most of the bacteria were killed by genotoxicity, a small subpopulation acquired mutations via SOS-induced mutagenesis. Given that these processes were triggered shortly after antibiotic addition, resistance rapidly emerged in the population. Our work revealed a new mechanism of action of ribosomal antibiotics, illustrates the importance of dissecting the complex interplay between multiple molecular processes in understanding antibiotic efficacy, and suggests new strategies for countering the development of resistance.

2024-06-24 | GSE240474 | GEO

Aminoglycoside heteroresistance in Enterobacter cloacae is driven by the cell envelope stress response.

Project description:Enterobacter cloacae is a Gram-negative nosocomial pathogen of the ESKAPE priority group with increasing multi-drug resistance via the acquisition of resistance plasmids. However, E. cloacae can also display phenotypic antimicrobial resistance, such as heteroresistance or persistence. Here we report that E. cloacae ATCC 13047 and six strains isolated from patients with blood infections display heteroresistance or persistence to aminoglycosides. E. cloacae heteroresistance is transient, accompanied with formation of "petite" colonies and increased MIC against gentamicin and other aminoglycosides used in the clinic, but not other antibiotic classes. To explore the underlying mechanisms, we performed RNA sequencing of heteroresistant bacteria, which revealed global gene-expression changes and a signature of the CpxRA cell envelope stress response. Deletion of the cpxRA two-component system abrogated aminoglycoside heteroresistance and petite colony formation, pointing to its indispensable role in phenotypic resistance. The introduction of a constitutively active allele of cpxA led to high aminoglycoside MICs, consistent with cell envelope stress driving these behaviours in E. cloacae. Cell envelope stress can be caused by environmental cues, including heavy metals. Indeed, bacterial exposure to copper increased gentamicin MIC in the wild type, but not the ΔcpxRA mutant. Moreover, copper exposure also elevated the gentamicin MICs of bloodstream isolates, suggesting that CpxRA- and copper-dependent aminoglycoside resistance is broadly conserved in E. cloacae strains. Altogether, we establish that E. cloacae relies on transcriptional reprogramming via the envelope stress response pathway for transient resistance to a major class of frontline antibiotic.

2023-10-18 | GSE236124 | GEO

Transcription profiling of Pseudomonas aeruginosa representational genomic libraries to identify aminoglycoside resistance genes

Project description:For this study, we created three highly representational different sized genomic libraries of P. aeruginosa PAO1 within the vector pBTB-1. Vector pBTB-1 is a low copy number broad host range plasmid containing a Ã-lactamase resistance marker, a pBAD promoter upstream of the cloning site, as well as transcriptional terminators flanking the cloning site to aid in insert stability. These libraries were transformed into the recombination-deficient P. aeruginosa PAO1 mutant, PAO2003, pooled, and parallel selections performed to identify via traditional sequencing or SCALEs the genomic regions capable of conferring increased tolerance to amikacin, gentamicin, or tobramycin. These antibiotics are all structurally related but have differing substitution patterns on their aminoglycoside backbones. These differences in structure and substitution patterns impact the activity of each antibiotic. We chose to study three different aminoglycosides in attempts to identify genomic regions capable of conferring resistance to not only a specific aminoglycoside, but also to the more general class of aminoglycosides.

2009-12-19 | E-MEXP-2396 | biostudies-arrayexpress

RNA polymerase stalling-derived genome instability underlies ribosomal antibiotic efficacy and resistance evolution

Project description:In bacteria, the precise coordination of DNA replication, transcription and translation is mediated by dynamic interactions among the corresponding macromolecular machineries, playing a pivotal role in maintaining cellular homeostasis. Here we showed that such coordination could be hijacked by ribosome antibiotics to trigger secondary damage predominantly contributing to their efficacy, via a yet overlooked reverse-central-dogma pathway. Through the utilization of a self-establishing transcription dynamics profiling method, complemented by genetic and biochemical approaches, we unveil that the disruption of transcription-translation coupling leads to premature stalling of RNA polymerase (RNAP) at genome scale, subsequently triggering extensive genomic instability. Moreover, a distinct subpopulation exhibits hyperactivation of the SOS response, facilitating an inducible evolutionary path towards genetic resistance characterized by a unique mutation spectrum. Our findings reveal the emergence of secondary drug damage resulting from network disorder, and establish a framework to understand antibiotic efficacy and induced mutagenesis from a systems biology perspective.

2023-12-24 | GSE234254 | GEO

Collateral sensitivity of antibiotic resistant bacteria to antimicrobial peptides

Project description:Cationic antimicrobial peptides (CAPs) are promising novel alternatives to conventional antibacterial agents, but the overlap in resistance mechanisms between small-molecule antibiotics and CAPs is unknown. Does evolution of antibiotic resistance decrease (cross-resistance) or increase (collateral sensitivity) susceptibility to CAPs? We systematically addressed this issue by studying the susceptibilities of a comprehensive set of antibiotic resistant Escherichia coli strains towards 24 antimicrobial peptides. Strikingly, antibiotic resistant bacteria frequently showed collateral sensitivity to CAPs, while cross-resistance was relatively rare. We identified clinically relevant multidrug resistance mutations that simultaneously elevate susceptibility to certain CAPs. Transcriptome and chemogenomic analysis revealed that such mutations frequently alter the lipopolysaccharide composition of the outer cell membrane and thereby increase the killing efficiency of membrane-interacting antimicrobial peptides. Furthermore, we identified CAP-antibiotic combinations that rescue the activity of existing antibiotics and slow down the evolution of resistance to antibiotics. Our work provides a proof of principle for the development of peptide based antibiotic adjuvants that enhance antibiotic action and block evolution of resistance.

2018-03-29 | GSE96706 | GEO

Overlap in antibiotic stress responses leads to cross-resistance between ribosomal acting drugs in Mycobacterium abscessus.

Project description:Mycobacterium abscessus is an opportunistic pathogen notorious for its resistance to most classes of antibiotics and low cure rates. In addition to the highly impermeable mycomembrane, M. abscessus carries an array of shared and species-specific defence mechanisms. However, it remains unknown whether M. abscessus’ antibiotic stress response is fine-tuned or an all-or-nothing response. A deeper understanding of underlying resistance and tolerance mechanisms is pivotal in development of targeted therapeutic regimens. We elucidate the transcriptomic response of M. abscessus to antibiotics recommended in treatment guidelines. The M. abscessus ATCC 19977 strain was used. Bacteria were subjected to sub-inhibitory concentrations of drugs for 4- and 24-hours, followed by RNA sequencing. In addition, time-kill kinetic analysis was performed using bacteria after pre-exposure to clarithromycin, amikacin or tigecycline for 24-hours. Lastly, Pan-genome analysis of 35 strains from all three subspecies was performed. Mycobacterium abscessus shows both drug-specific and communal transcriptomic responses to antibiotic exposure. Key features of its tolerance to antibiotics are drug-specific converting enzymes, target protection and shifts in its respiratory chain and metabolic state. The observed transcriptomic responses are likely not strain-specific, as genes involved in tolerance are found in all included strains, with the exception of erm(41) in M. abscessus subspecies massiliense. Due to the communal response elicited by ribosomal-targeting antibiotics, exposure to any of these drugs rapidly induces tolerance mechanisms that decrease susceptibility to ribosome-targeting drugs from multiple classes. Screening high-risk patients (e.g. those with bronchiectasis) for M. abscessus infection prior to starting macrolide or aminoglycoside maintenance therapy is warranted.

2022-01-25 | GSE163621 | GEO

Gene expression in Escherichia coli treated with human PGRP, gentamicin, and CCCP

Project description:Human Peptidoglycan Recognition Proteins (PGRPs) kill bacteria, likely by over-activating stress responses in bacteria. To gain insight into the mechanism of PGRP killing of Escherichia coli and bacterial defense against PGRP killing, gene expression in E. coli treated with a control protein (bovine serum albumin, BSA), human recombinant PGRP (PGLYRP4), gentamicin (aminoglycoside antibiotic), and CCCP (membrane potential decoupler) were compared. Each treatment induced unique and somewhat overlapping pattern of gene expression. PGRP highly increased expression of genes for oxidative and disulfide stress, detoxification and efflux of Cu, As, and Zn, repair of damaged proteins and DNA, methionine and histidine synthesis, energy generation, and Fe-S clusters repair. PGRP also caused marked decrease in the expression of genes for Fe uptake and motility. Gene expression microarray in E. coli exposed to a human bactericidal innate immunity protein, PGRP, showed induction of oxidative stress response and defense genes, with different expression pattern than E. coli exposed to an aminoglycoside antibiotic and a membrane potential decoupler.

2014-07-25 | GSE44211 | GEO

Dual Function of Tropodithietic Acid as Antibiotic and Signaling Molecule in Quorum Sensing

Project description:The marine bacterium Phaeobacter inhibens produces tropodithietic acid (TDA), a broad-spectrum antibiotic and anticancer agent. TDA allows P. inhibens to antagonize other bacteria, including several pathogens, and eukaryotes. Since recently antibiotics are also discussed to function as intermicrobial signals. Here we show that ~10% of the genes of P. inhibens are strongly influenced by N-acyl-homoserine lactone (AHL) mediated quorum sensing (QS), switching the bacteriumâs life style from attached to free-living. In an AHL negative mutant of P. inhibens subinhibitory concentrations of TDA caused the same regulatory effect as the AHL. This demonstrates that bacteria can produce antibiotic compounds not only as weapons, but also to substitute their endogenous AHL molecule in QS. The dual function of TDA probably supports the QS system to accelerate regulatory processes and points to a so far neglected role of antibiotics at subinhibitory concentrations in the environment and in microbial interactions. Comparison of whole transcriptomes of wildytype, quorum sensing mutants (pgaI and pgaR) and pgaI grown supplemented with subinhibitory concentration of the antibiotic TDA. RNA isolated in the late exponential growth phase. 4 biological replicates investigated for each strain.

2016-03-15 | E-GEOD-79173 | biostudies-arrayexpress

Dual Function of Tropodithietic Acid as Antibiotic and Signaling Molecule in Quorum Sensing

Project description:The marine bacterium Phaeobacter inhibens produces tropodithietic acid (TDA), a broad-spectrum antibiotic and anticancer agent. TDA allows P. inhibens to antagonize other bacteria, including several pathogens, and eukaryotes. Since recently antibiotics are also discussed to function as intermicrobial signals. Here we show that ~10% of the genes of P. inhibens are strongly influenced by N-acyl-homoserine lactone (AHL) mediated quorum sensing (QS), switching the bacterium’s life style from attached to free-living. In an AHL negative mutant of P. inhibens subinhibitory concentrations of TDA caused the same regulatory effect as the AHL. This demonstrates that bacteria can produce antibiotic compounds not only as weapons, but also to substitute their endogenous AHL molecule in QS. The dual function of TDA probably supports the QS system to accelerate regulatory processes and points to a so far neglected role of antibiotics at subinhibitory concentrations in the environment and in microbial interactions.

2016-03-15 | GSE79173 | GEO

Gene expression in Escherichia coli treated with human PGRP, gentamicin, and CCCP

2014-07-25 | E-GEOD-44211 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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