Proteome-wide identification of in vitro substrates for P. aeruginosa ClpXP

we treated the cell lysates of ΔclpX mutant with or without P. aeruginosa ClpXP protease and used Label-free quantitative techniques (LFQ) to identify and quantify the proteolytic targets of ClpXP (p.aeruginosa PAO1). As a result, 3338 proteins were identified and 2493 proteins were quantified. The abundance (LFQ intensity) of 44 proteins were decreased (≥1.5-fold, p < 0.05) by the treatment with ClpXP. Moreover, we observed that there are 31 proteins which have valid LFQ intensity values in all the three biological replicates of the control group but not in the experimental group (i.e., ClpXP-treated). These results suggest that exogenously added ClpXP has a profound effect on the abundance of proteins in our in vitro assays and that those 75 proteins may serve as potential substrates for the P. aeruginosa ClpXP.