Characterization of the Burkholderia thailandensis SOS Response by Using Whole-Transcriptome Shotgun Sequencing

Abstract

ABSTRACTThe bacterial SOS response is a well-characterized regulatory network encoded by most prokaryotic bacterial species and is involved in DNA repair. In addition to nucleic acid repair, the SOS response is involved in pathogenicity, stress-induced mutagenesis, and the emergence and dissemination of antibiotic resistance. Using high-throughput sequencing technology (SOLiD RNA-Seq), we analyzed theBurkholderia thailandensisglobal SOS response to the fluoroquinolone antibiotic, ciprofloxacin (CIP), and the DNA-damaging chemical, mitomycin C (MMC). We demonstrate that aB. thailandensis recAmutant (RU0643) is ∼4-fold more sensitive to CIP in contrast to the parental strainB. thailandensisDW503. Our RNA-Seq results show that CIP and MMC treatment (P< 0.01) resulted in the differential expression of 344 genes inB. thailandensisand 210 genes in RU0643. Several genes associated with the SOS response were induced and includelexA,uvrA,dnaE,dinB,recX, andrecA. At the genome-wide level, we found an overall decrease in gene expression, especially for genes involved in amino acid and carbohydrate transport and metabolism, following both CIP and MMC exposure. Interestingly, we observed the upregulation of several genes involved in bacterial motility and enhanced transcription of aB. thailandensisgenomic island encoding aSiphoviridaebacteriophage designated ϕE264. UsingB. thailandensisplaque assays and PCR withB. malleiATCC 23344 as the host, we demonstrate that CIP and MMC exposure inB. thailandensisDW503 induces the transcription and translation of viable bacteriophage in a RecA-dependent manner. This is the first report of the SOS response inBurkholderiaspp. to DNA-damaging agents. We have identified both common and unique adaptive responses ofB. thailandensisto chemical stress and DNA damage.