Analysis of Staphylococcus aureus transcriptome changes in response to inhibition of Rho activity by bicyclomycin

The transcriptomes of Δrho mutant cells and of wild-type cells grown in RPMI medium with or without 40 or 80 µg/ml of BCM were analyzed using Agilent microarrays in order to analyze the effects of the Rho inhibitor bicyclomycin (BCM) treatment on antisense transcription and changes in the expression of protein coding genes. All antisense RNAs exhibiting higher levels in the rho mutant compared to the wild-type showed similar levels in BCM-treated wild-type cells (80 µg/ml BCM). In addition, microarray data revealed activation of the SaeR regulon in the presence of BCM as observed in the rho mutant. S. aureus HG001 and its isogenic Δrho mutant were grown in RPMI medium. At OD600 of 0.2 (early exponential phase), controls were taken and the wild-type culture was split in pre-warmed flasks for BCM treatment. After 70 min (exponential phase), rho mutant and wild-type samples (untreated and with 40 or 80 µg/ml BCM) were collected. Microarray hybridizations were performed with RNA from two biological replicates. The individual samples were labeled with Cy5; a reference pool containing equal amounts of RNA from all 10 samples was labeled with Cy3.