Identification of antibiotic stress-inducible promoters: a systematic approach to novel pathway-specific reporter assays for antibacterial drug discovery.
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.
Fischer
Hans Peter
HP
Genedata AG, Postfach 254, CH-4016, Basel, Switzerland. Hans-Peter.Fischer@genedata.com
Brunner
Nina A
NA
Wieland
Bernd
B
Paquette
Jesse
J
Macko
Ludwig
L
Ziegelbauer
Karl
K
Freiberg
Christoph
C
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
D000900:Anti-Bacterial Agents; D002457:Cell Extracts; D005227:Fatty Acids; D014157:Transcription Factors