A robust platform for chemical genomics in bacterial systems

French, Shawn; Mangat, Chand S.; Bharat, Amrita; Côté, Jean-Philippe; Mori, Hirotada; Brown, Eric D.

doi:10.1091/mbc.e15-08-0573

Cited by 65 publications

(98 citation statements)

References 52 publications

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“…S1). Finally, we monitored the growth of every double deletion mutant over 18 h using the method of French et al (27). …”

Section: Resultsmentioning

confidence: 99%

“…Following incubation, the colonies were transferred to LB agar plates containing both apramycin and kanamycin to select for the double deletion mutants. Plates were incubated at 37°C for 18 h, and images were acquired every 20 min using high-quality scanners as previously described (27). The antibiotic selection did not have differential fitness effects on the different mutants (Fig.…”

Section: Methodsmentioning

confidence: 99%

“…Mating plates were imaged by the method of French et al (27), using the normalization process described therein. Briefly, plates are scanned using Epson Perfection V750 transmissive scanners.…”

Section: Methodsmentioning

confidence: 99%

“…Images were analyzed using ImageJ (59), and the amount of light absorbed by colonies during the transmissive scanning was quantified as integrated density, a value that tracks with cell number in a linear manner. Full details of the image acquisition and analysis are available in the article by French et al (27). We further normalized our data to account for the expected growth of the double deletion mutant, which corresponds to the product of the growth of each single mutant compared to the growth of the WT.…”

Section: Methodsmentioning

confidence: 99%

“…S3 in the supplemental material). Genetic interaction networks were prepared using the R statistical computing language (60) and BioLayout Express 3D (61) by the method of French et al (27). …”

Section: Methodsmentioning

confidence: 99%

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The Genome-Wide Interaction Network of Nutrient Stress Genes in Escherichia coli

Côté

French

Gehrke

et al. 2016

mBio

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Conventional efforts to describe essential genes in bacteria have typically emphasized nutrient-rich growth conditions. Of note, however, are the set of genes that become essential when bacteria are grown under nutrient stress. For example, more than 100 genes become indispensable when the model bacterium Escherichia coli is grown on nutrient-limited media, and many of these nutrient stress genes have also been shown to be important for the growth of various bacterial pathogens in vivo. To better understand the genetic network that underpins nutrient stress in E. coli, we performed a genome-scale cross of strains harboring deletions in some 82 nutrient stress genes with the entire E. coli gene deletion collection (Keio) to create 315,400 double deletion mutants. An analysis of the growth of the resulting strains on rich microbiological media revealed an average of 23 synthetic sick or lethal genetic interactions for each nutrient stress gene, suggesting that the network defining nutrient stress is surprisingly complex. A vast majority of these interactions involved genes of unknown function or genes of unrelated pathways. The most profound synthetic lethal interactions were between nutrient acquisition and biosynthesis. Further, the interaction map reveals remarkable metabolic robustness in E. coli through pathway redundancies. In all, the genetic interaction network provides a powerful tool to mine and identify missing links in nutrient synthesis and to further characterize genes of unknown function in E. coli. Moreover, understanding of bacterial growth under nutrient stress could aid in the development of novel antibiotic discovery platforms.

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“…S1). Finally, we monitored the growth of every double deletion mutant over 18 h using the method of French et al (27). …”

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

The Genome-Wide Interaction Network of Nutrient Stress Genes in Escherichia coli

Côté

French

Gehrke

et al. 2016

mBio

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Perspectives on the antibiotic contamination, resistance, metabolomics, and systemic remediation

et al. 2021

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Antibiotics have been regarded as the emerging contaminants because of their massive use in humans and veterinary medicines and their persistence in the environment. The global concern of antibiotic contamination to different environmental matrices and the emergence of antibiotic resistance has posed a severe impact on the environment. Different mass-spectrometry-based techniques confirm their presence in the environment. Antibiotics are released into the environment through the wastewater steams and runoff from land application of manure. The microorganisms get exposed to the antibiotics resulting in the development of antimicrobial resistance. Consistent release of the antibiotics, even in trace amount into the soil and water ecosystem, is the major concern because the antibiotics can lead to multi-resistance in bacteria which can cause hazardous effects on agriculture, aquaculture, human, and livestock. A better understanding of the correlation between the antibiotic use and occurrence of antibiotic resistance can help in the development of policies to promote the judicious use of antibiotics. The present review puts a light on the remediation, transportation, uptake, and antibiotic resistance in the environment along with a novel approach of creating a database for systemic remediation, and metabolomics for the cleaner and safer environment.

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A cell-based approach to characterize antimicrobial compounds through kinetic dose response

MacNair

Stokes

French

et al. 2016

Bioorganic & Medicinal Chemistry

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A robust platform for chemical genomics in bacterial systems

Cited by 65 publications

References 52 publications

The Genome-Wide Interaction Network of Nutrient Stress Genes in Escherichia coli

The Genome-Wide Interaction Network of Nutrient Stress Genes in Escherichia coli

Perspectives on the antibiotic contamination, resistance, metabolomics, and systemic remediation

A cell-based approach to characterize antimicrobial compounds through kinetic dose response

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