title: Identification of antibiotic stress-inducible promoters: a systematic approach to novel pathway-specific reporter assays for antibacterial drug discovery.
abstract: As present antibiotics therapy becomes increasingly ineffectual, new technologies are required to identify and develop novel classes of antibacterial agents. An attractive alternative to the classical target-based approach is the use of promoter-inducible reporter assays for high-throughput screening. The wide usage of these assays is, however, limited by the small number of specifically responding promoters that are known at present. This work describes a novel approach for identifying genetic regulators that are suitable for the design of pathway-specific assays. The basis for the proposed strategy is a large set of antibiotics-triggered expression profiles ("Reference Compendium"). Pattern recognition algorithms applied to the expression data pinpoint the relevant transcription-factor-binding sites in whole-genome sequences. Using this technique, we constructed a fatty-acid-pathway-specific reporter assay that is based on a novel stress-inducible promoter. In a proof-of-principle experiment, this assay was shown to enable screening for new small-molecule inhibitors of bacterial growth.
authors.affiliation: Genedata AG, Postfach 254, CH-4016, Basel, Switzerland. Hans-Peter.Fischer@genedata.com
authors.forename: Hans Peter
authors.initials: HP
authors.lastname: Fischer
authors.forename: Nina A
authors.initials: NA
authors.lastname: Brunner
authors.forename: Bernd
authors.initials: B
authors.lastname: Wieland
authors.forename: Jesse
authors.initials: J
authors.lastname: Paquette
authors.forename: Ludwig
authors.initials: L
authors.lastname: Macko
authors.forename: Karl
authors.initials: K
authors.lastname: Ziegelbauer
authors.forename: Christoph
authors.initials: C
authors.lastname: Freiberg
mesh_terms: D024506:5' Flanking Region / Q000187:drug effects / Q000235:genetics; D000595:Amino Acid Sequence; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001407:Bacillus / Q000187:drug effects / Q000235:genetics; D001665:Binding Sites / Q000235:genetics; D002457:Cell Extracts / Q000737:chemistry; D002874:Chromosome Mapping; D016384:Consensus Sequence; D017124:Conserved Sequence; D015195:Drug Design; D004353:Drug Evaluation, Preclinical / Q000379:methods; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D005227:Fatty Acids / Q000096:biosynthesis; D020869:Gene Expression Profiling / Q000379:methods; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects / Q000235:genetics; D005809:Genes, Regulator / Q000187:drug effects / Q000235:genetics; D017930:Genes, Reporter / Q000187:drug effects* / Q000235:genetics; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D009876:Operon / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000187:drug effects*; D014157:Transcription Factors / Q000235:genetics
chemical_list: D000900:Anti-Bacterial Agents; D002457:Cell Extracts; D005227:Fatty Acids; D014157:Transcription Factors