Protein degradation is a central component of the protein quality control system. Here we show that efficient proteolysis in Escherichia coli requires the active acetyl phosphate pathway. Deletion of this pathway, leading to depletion of acetyl phosphate, results in temperature sensitivity and reduced rate of ATP-dependent proteolysis. The effect on proteolysis is general, as can be seen from the slowing down of the degradation of unstable proteins, including puromycin-derived peptides. In addition, reduced intracellular concentrations of acetyl phosphate brings about an increase in the levels of protein aggregates, which contain a wide range of proteins, as expected if a broad spectrum of substrates are involved. Additional outcomes of acetyl phosphate deficiency are elevation in the transcript levels of heat shock genes and increased thermotolerance. In E. coli the acetyl phosphate pathway is the only source of acetyl phosphate, which is a key metabolic compound involved in major cellular processes. In this communication we present evidence for the general role of the acetyl phosphate pathway in protein degradation.