ArticleMolecular biology of the cell2016
A robust platform for chemical genomics in bacterial systems.
Article in Molecular biology of the cell, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
36 citing papers in PubMed.
- Article
- Genome-wide network of antibiotic susceptibility in Pseudomonas aeruginosa.The Journal of antimicrobial chemotherapy · 2026Article
- Mixing Is Dispensable for Optical Density-Based High-Throughput Growth Screening Assay in Fission Yeast.International journal of molecular sciences · 2026Article
- ChemGenXplore: an interactive tool for exploring and analysing chemical genomic data.Bioinformatics (Oxford, England) · 2026Article
- Identifying Modulators of the Post-Antibiotic Effect.ACS infectious diseases · 2025Article
- Perturbation ofmBio · 2025Article
- Exploiting the fitness cost of metallo-β-lactamase expression can overcome antibiotic resistance in bacterial pathogens.Nature microbiology · 2025Article
- A screen for cell envelope stress uncovers an inhibitor of prolipoprotein diacylglyceryl transferase, Lgt, iniScience · 2024Article
- Integrating bacterial molecular genetics with chemical biology for renewed antibacterial drug discovery.The Biochemical journal · 2024Review
- Fluorescent riboswitch-controlled biosensors for the genome scale analysis of metabolic pathways.Scientific reports · 2024Article
- A mobile CRISPRi collection enables genetic interaction studies for the essential genes of Escherichia coli.Cell reports methods · 2024Article
- Systematic investigation of recipient cell genetic requirements reveals important surface receptors for conjugative transfer of IncI2 plasmids.Communications biology · 2023Article
- Central metabolism is a key player in E. coli biofilm stimulation by sub-MIC antibiotics.PLoS genetics · 2023Article
- A Normalization Protocol Reduces Edge Effect in High-Throughput Analyses of Hydroxyurea Hypersensitivity in Fission Yeast.Biomedicines · 2023Article
- Complete genomes and comparative analyses of Streptomyces phages that influence secondary metabolism and sporulation.Scientific reports · 2023Article
- Group B Streptococcus Cas9 variants provide insight into programmable gene repression and CRISPR-Cas transcriptional effects.Communications biology · 2023Article
- ChemGAPP: a tool for chemical genomics analysis and phenotypic profiling.Bioinformatics (Oxford, England) · 2023Article
- Article
- Analysis of a Library ofAntibiotics (Basel, Switzerland) · 2022Article
- Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
While genetic perturbation has been the conventional route to probing bacterial systems, small molecules are showing great promise as probes for cellular complexity. Indeed, systematic investigations of chemical-genetic interactions can provide new insights into cell networks and are often starting points for understanding the mechanism of action of novel chemical probes. We have developed a robust and sensitive platform for chemical-genomic investigations in bacteria. The approach monitors colony volume kinetically using transmissive scanning measurements, enabling acquisition of growth rates and conventional endpoint measurements. We found that chemical-genomic profiles were highly sensitive to concentration, necessitating careful selection of compound concentrations. Roughly 20,000,000 data points were collected for 15 different antibiotics. While 1052 chemical-genetic interactions were identified using the conventional endpoint biomass approach, adding interactions in growth rate resulted in 1564 interactions, a 50-200% increase depending on the drug, with many genes uncharacterized or poorly annotated. The chemical-genetic interaction maps generated from these data reveal common genes likely involved in multidrug resistance. Additionally, the maps identified deletion backgrounds exhibiting class-specific potentiation, revealing conceivable targets for combination approaches to drug discovery. This open platform is highly amenable to kinetic screening of any arrayable strain collection, be it prokaryotic or eukaryotic.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.