Transcriptomic analysis of ArlRS two-component signaling regulon, a global regulator, in Staphylococcus aureus

The two-component signal transduction system plays an important role for bacteria to adapt to diverse niches by sensing the environmental stimuli and modulating gene expression. In Staphylococcus aureus, at least 16 pairs of two-component systems have been discovered and some of them coordinate with different regulators to modulate the expression of virulence factors. The availability of complete genome sequences, and transcriptome and proteome, enables us to identify the genes mediated by different regulators. The RT-PCR-based method and microarray technology have made it feasible for high throughput screening of genomewide transcription profiles. These techniques have been used to investigate different TCS in S. aureus and to identify the regulons of regulators in different bacterial systems. Therefore, combined with the inactivation of gene expression, microarray technology should be more useful to identify genes transcriptionally controlled by the TCS system. We propose that similar approaches can be used to understand the regulon of ArlRS two-component signaling by the comparison of gene expression profiles between wild type and arlR mutant. This chapter provides detailed protocols for identification of arlRS regulon using Affymetrix S. aureus chips and describes general considerations of microarray assay.