TABLE 2.

Overall performance of functional reporter strains

TypeClassGeneReference compoundaMaximal induction (min)Induction factorb (fold)RLUcConcn (μg/ml)Z′d
ArrayeReporterArrayReporterBasalInducedMICInductionf
Generic pathwaysFatty acid biosynthesisfabHBCeruleninAll20028.33.74191,62881-640.36
glpDgCeruleninAll18012.62.07421881-8<0
Protein biosynthesisyrzIhClindamycin80360104.12.519561020.25-8<0
Cell wall biosynthesisypbGiVancomycin40, 808011.42.02168820.250.125-0.25<0
Compound classesQuinolonesjdinBkCiprofloxacin8024014.815.41,27216,9280.50.06-40.43
yneAlCiprofloxacin8024019.016.12184,4870.50.125-40.54
yorBlCiprofloxacin8020014.128.161618,1810.50.06-40.51
GlycopeptidesytrAVancomycin104042.93.42281,5500.250.125-20.26
ywoBVancomycin106062.11.9451010.250.125-2<0
Individual compoundsCycloserineydeKCycloserine4016056.22.292382328-640.02
RifampicinyvgSRifampicin808046.23.7863220.1250.008-0.125<0
ClindamycinexpZClindamycinAll30076.35.111664420.25-20.03
  • a Compound for which the highest level of upregulation was observed in expression profiling experiments. This compound was also used to determine Z′.

  • b Induction factors for the reporter strains were calculated from a set of experiments designed to evaluate the reporter strains in a high-throughput mode.

  • c RLU, mean relative light units, as measured in a set of experiments designed to evaluate the functionality of the reporter strains (see Results). Indicated are the values measured without compound treatment (basal) and after treatment with the reference compounds (induced) at the optimal time points and concentrations.

  • d The Z′ factor is a measure of assay robustness in high-throughput applications (35).

  • e Gene expression profiles were collected after 10, 40, and 80 min of compound treatment.

  • f Concentration window in which significant upregulation was observed.

  • g glpD was selected as a specific marker gene for triclosan, but the reporter strain was responsive to cerulenin as well.

  • h Two false-negative (puromycin and actinonin) and three compounds that elicited unexpected positive responses (5-fluoruracil, nitrofurantoin, and nalidixic acid) were detected with the yrzI reporter strain.

  • i One false-negative (ristocetin) and one compound that elicited an unexpected positive response (polymyxin B) were detected with the ypbG reporter strain.

  • j Genes were selected as marker genes for topoisomerases, but not all strains elicited a signal with the coumarins.

  • k Two compounds that elicited unexpected positive responses were detected with the dinB reporter strain, azaserine and 5 fluoruracil.

  • l One compound that elicited an unexpected positive response was detected with the yneA and the yorB reporter strains, azaserine.