Super-SILAC reveals intricate crosstalk between lipopolysaccharide, phospholipid and fatty acid metabolism in Escherichia coli

The only membrane-anchored and essential ATP-dependent protease in Escherichia coli is FtsH. It controls the intracellular concentration of the deacetylase LpxC, which catalyses the first committed step in lipopolysaccharide biosynthesis. LpxC stability is strictly regulated in a growth rate-dependent manner to ascertain a vital equilibrium of lipopolysaccharide (LPS) and phospholipid biosynthesis. Previous studies suggested the involvement of yet unknown factors in LpxC degradation. Aiming at the identification of such factors that are predicted to be associated with LpxC and/or FtsH at high and low growth rates, we established a quantitative super-SILAC LC-MS/MS-based approach. The identification of known LpxC and FtsH interactors validated our approach. Several enzymes involved in fatty acid biosynthesis and degradation, including the central regulator FadR, interacted with LpxC and/or FtsH and showed a significant impact on LpxC stability. The newly identified LpxC and FtsH interactor WaaH, a LPS-modifying enzyme, stimulates LpxC degradation. Our results go beyond the previously established link between LPS and phospholipid biosynthesis and uncover a far-reaching network that controls LPS biosynthesis by involving multiple enzymes in fatty acid metabolism and phospholipid biosynthesis and modification.