PMID:21185072

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Citation

Nichols, RJ, Sen, S, Choo, YJ, Beltrao, P, Zietek, M, Chaba, R, Lee, S, Kazmierczak, KM, Lee, KJ, Wong, A, Shales, M, Lovett, S, Winkler, ME, Krogan, NJ, Typas, A and Gross, CA (2011) Phenotypic landscape of a bacterial cell.Cell 144:143-56

Abstract

The explosion of sequence information in bacteria makes developing high-throughput, cost-effective approaches to matching genes with phenotypes imperative. Using E. coli as proof of principle, we show that combining large-scale chemical genomics with quantitative fitness measurements provides a high-quality data set rich in discovery. Probing growth profiles of a mutant library in hundreds of conditions in parallel yielded > 10,000 phenotypes that allowed us to study gene essentiality, discover leads for gene function and drug action, and understand higher-order organization of the bacterial chromosome. We highlight new information derived from the study, including insights into a gene involved in multiple antibiotic resistance and the synergy between a broadly used combinatory antibiotic therapy, trimethoprim and sulfonamides. This data set, publicly available at http://ecoliwiki.net/tools/chemgen/, is a valuable resource for both the microbiological and bioinformatic communities, as it provides high-confidence associations between hundreds of annotated and uncharacterized genes as well as inferences about the mode of action of several poorly understood drugs.

Links
Keywords

phenotype; phenomic profiling; phenotypic signature; hierarchical clustering; responsive genome; high-throughput; chemical genomics; stress; essential; function; antibiotic resistance; synergy

Main Points of the Paper

  • Key Motivation- provide phenotypes for mutants of genes without functional annotation
  • Central Goal- systematically evaluate the impact of every gene deletion on E.coli fitness in diverse environments
  • Phenomic Profiling- quantitative description of the response of all single-gene deletions to physiologically relevant stresses and drug challenges
    • profiled ~4,000 genes in 324 conditions covering 114 unique stresses (more than half were antimicrobial/antibiotic stress)
    • identified thousands of phenotypes
    • identified a diverse set of conditionally essential genes
      • Identified 116 rich-media conditionally essential (CE) genes
    • facilitates high-confidence association of genes of unknown function to those of known function
    • generates numerous leads concerning drug function
  • Hierarchical clustering
  • Phenotypic Signature- response of each mutant strain across all conditions
    • high correlation b/t two phenotypic signatures implies a functional connection b/t genes

Materials and Methods Used

Strain Details

  • Keio single-gene deletion library
  • essential gene hypomorphs
  • RNA/small protein knockout library

Equipment and Reagents

Procedure

Phenomic Profiling

Data Analysis

Hierarchical clustering

Phenotype Annotations

See Help:AnnotationTable for details on how to edit this table.

Species Taxon ID Strain Gene (if known) OMP Phenotype Details Evidence Notes

Escherichia coli

K-12 BW25113

ECK3620-RFAP

sensitivity to 0.1% bile salts

Growth

slow growth

Growth Curve

rfaP phosphorylates core heptose of lipopolysaccharide

Escherichia coli

K-12 BW25113

ECK0223-LPCA

sensitivity to 1.2 mM DIBUCAINE

Growth

slow growth

Growth Curve

the target of DIBUCAINE is the membrane (pmf)

Escherichia coli

K-12 BW25113

ECK3610-RFAF

sensitivity to 0.1% bile salts

Growth

slow growth

Growth Curve

rfaF = ADP-heptose:LPS heptosyltransferase II

target of bile salts: membrane

Escherichia coli

K-12 BW25113

ECK3042-RFAE

sensitivity to 30 µg/ml NOVOBIOCIN

Growth

slow growth

Growth Curve

ECK3042-RFAE = heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase

the target of NOVOBIOCIN is DNA gyrase

Escherichia coli

K-12 BW25113

ECK3610-RFAE

sensitivity to 0.1% bile salts

Growth

slow growth

Growth Curve

ECK3042-RFAE = heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase

target of bile salts: membrane


Notes

References

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