Identification of novel oxygen sensors using a combined approach in Xanthomonas campestris pv. campestris

Per-ARNT-Sim (PAS) domains are important signaling modules that monitor changes in various stimuli, such as oxygen, light, voltage and small ligands, etc. In bacteria, despite the abundance of putative PAS domain containing proteins (PAS proteins), little is known regarding their sensory specificity. Several PAS domains in Xanthomonas campestris pv. campestris (Xcc) and 16 known PAS domains were subjected to clustering analysis on the basis of secondary structure topology (SST), and a putative oxygen-signaling cluster was revealed, which contained three known oxygen-signaling PAS domains and four Xcc PAS domains. Genetics assays under variable oxygen conditions confirmed the four Xcc PAS domains involving oxygen signaling. Therefore, the proposal of clustering on the basis of SST combining molecular genetics assays was verified as a feasible and effective method of identifying novel oxygen sensors, and four potential oxygen-signaling components (i.e., four PAS domain-containing proteins) in Xcc, including a GGDEF characterized protein and three hybrid HK (HK/RR hybrid) proteins were revealed using this methodology.