Pull-down of polyP chains and associated proteins with PPBD as a bait

CobB interacts polyP in E. coli stressed cells. The goal of the performed experiment was to identify proteins interacting polyP in E. coli cells encountering amino acid starvation. We used Co-NTA resin with immobilized PPBD for capturing and isolation of polyP, together with bound proteins. The MS analysis followed by a Mascot search against the E. coli database revealed 98 proteins identified (based on ≥ 3 peptides) in the extract prepared from wild-type E. coli MG1655 grown for 3 hours in MOPS. It must be pointed out that we obtained high background in the control lysate prepared from Δppk mutant, however in a comparative analysis, 21 proteins were qualified as interesting candidates that bind polyP in the tested conditions. Among them, CobB deacetylase was identified.