Defining the Pseudomonas aeruginosa SOS Response and its Role in the Global Response to the Antibiotic Ciprofloxacin

Pseudomonas aeruginosa infections can be virtually impossible to eradicate and the evolution of resistance during antibiotic therapy is a significant concern. In this study, we use DNA microarrays to characterize the global transcriptional response of P. aeruginosa to clinical-like doses of the antibiotic ciprofloxacin and also to determine the component that is regulated by LexA cleavage and the SOS response. We find that genes involved in virtually every facet of metabolism are down-regulated in response to ciprofloxacin. The LexA-controlled SOS regulon identified by microarray analysis includes only fifteen genes, but does include several genes that encode proteins involved in recombination and replication, including two inducible polymerases known to play a role in mutation and the evolution of antibiotic resistance in other organisms. The data suggests that the inhibition of LexA cleavage during therapy might help combat this pathogen by decreasing its ability to adapt and evolve resistance. Keywords: Time course of response of P. aeruginosa to the antibiotic ciprofloxacin Sample preparation and data analysis. For each strain (PAO1 and the lexA uninducible mutant), 5 clones were inoculated in LB and grown 18 h. Cultures were diluted 1:500 and grown to mid-log phase (OD600 ~0.4-0.5) at which point ciprofloxacin was added to a final concentration of 1 μg/ml. At 0, 30 and 120 minutes following ciprofloxacin addition, appropriate volumes from each of the 5 cultures per strain were pooled and added to 2 volumes of RNAprotect reagent (Qiagen); cell pellets were stored at 4 ºC until RNA extraction. Total RNA was extracted using the RNeasy Mini kit (Qiagen) at the end of the sample collection period. This procedure was repeated three independent times to generate three samples each just prior to and 120 minutes post ciprofloxacin addition.