ArticleNucleic acids research2022
Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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Who cites it
20 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis Driven Strain Design for Mitigating Oxidative Stresses Important in Biomanufacturing.ACS synthetic biology · 2024Pooled it
- Convergent methodologies in prosthetic joint infection research: integrating transdisciplinary approaches to understand and prevent biofilm-driven failure of orthopaedic prostheses.Journal of medical microbiology · 2026Review
- Bacterial co-detection is associated with higher multidrug-resistantJAC-antimicrobial resistance · 2026Article
- The transcriptional regulatory network of the Escherichia coli MG1655 reference strain.Nucleic acids research · 2026Article
- Minimal gene signatures enable high-accuracy prediction of antibiotic resistance in Pseudomonas aeruginosa.NPJ systems biology and applications · 2025Article
- Transcriptome and interactome-based analyses to unravel crucial proteins and pathways involved in Acinetobacter baumannii pathogenesis.Molecular diversity · 2025Article
- A transcriptional plasticity-aware framework for RNA-seq differential expression analysis.Briefings in bioinformatics · 2025Article
- Targeting Acinetobacter baumannii resistance-nodulation-division efflux pump transcriptional regulators to combat antimicrobial resistance.npj antimicrobials and resistance · 2025Review
- iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets.Nucleic acids research · 2025Article
- Multi-omic analysis tools for microbial metabolites prediction.Briefings in bioinformatics · 2024Review
- Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment.Nature communications · 2024Article
- Siderophores promote cooperative interspecies and intraspecies cross-protection against antibiotics in vitro.Nature microbiology · 2024Article
- Article
- Molecular Insights Into the Role of Gut Microbiota in Antibiotic Therapy Selection and Resistance Mitigation.Cureus · 2023Review
- Machine learning uncovers themSystems · 2023Article
- Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance.Cell reports · 2023Article
- Independent Component Analysis Reveals the Transcriptional Regulatory Modules inInternational journal of molecular sciences · 2023Article
- Robust ParB Binding to Half-International journal of molecular sciences · 2023Article
- Field ponding water exacerbates the dissemination of manure-derived antibiotic resistance genes from paddy soil to surrounding waterbodies.Frontiers in microbiology · 2023Article
- Responses of carbapenemase-producing and non-producing carbapenem-resistantFrontiers in microbiology · 2022Article
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Abstract
Pseudomonas aeruginosa is an opportunistic pathogen and major cause of hospital-acquired infections. The virulence of P. aeruginosa is largely determined by its transcriptional regulatory network (TRN). We used 411 transcription profiles of P. aeruginosa from diverse growth conditions to construct a quantitative TRN by identifying independently modulated sets of genes (called iModulons) and their condition-specific activity levels. The current study focused on the use of iModulons to analyze the biofilm production and antibiotic resistance of P. aeruginosa. Our analysis revealed: (i) 116 iModulons, 81 of which show strong association with known regulators; (ii) novel roles of regulators in modulating antibiotics efflux pumps; (iii) substrate-efflux pump associations; (iv) differential iModulon activity in response to beta-lactam antibiotics in bacteriological and physiological media; (v) differential activation of 'Cell Division' iModulon resulting from exposure to different beta-lactam antibiotics and (vi) a role of the PprB iModulon in the stress-induced transition from planktonic to biofilm lifestyle. In light of these results, the construction of an iModulon-based TRN provides a transcriptional regulatory basis for key aspects of P. aeruginosa infection, such as antibiotic stress responses and biofilm formation. Taken together, our results offer a novel mechanistic understanding of P. aeruginosa virulence.
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