Applicability of chromatographic co-elution for antibiotic research

Identification of the molecular target is crucial for evaluating novel antibiotics. To support target identification, a label-free method based on chromatographic co-elution (TICC) has been developed previously. In TICC, an alteration in the elution profile of the target-bound drug compared to free drug in ion exchange chromatography is used to identify potential target proteins from elution fractions. We investigated the applicability of TICC for antibiotic research by evaluating which proteins, i.e. putative targets, can be monitored in Bacillus subtilis. Coelution of components of known protein complexes was used as a read-out for nativity of the chromatography. We identified 920 proteins covering 66% of known essential proteins, including most clinically exploited target proteins. Using correlation profiling, protein complex integrity was demonstrated for known cytosolic complexes like RNA polymerase and the cytosolic components of ATP synthase. Raw data and ProteinLynxGlobalServer (PLGS) output files for protein identification in a fractionated cytosolic protein extracts are uploaded to support main text and supplementary file data of a submitted manuscript entitled “Combining chromatographic co-elution and proteomic profiling for antibiotic target identification”.