The heat shock response in Escherichia coli is governed by the concentration of the highly unstable sigma factor sigma(32). The essential protein HflB (FtsH), known to control proteolysis of the phage lambda cII protein, also governs sigma(32) degradation: an HflB-depleted strain accumulated sigma(32) and induced the heat shock response, and the half-life of sigma(32) increased by a factor up to 12 in mutants with reduced HflB function and decreased by a factor of 1.8 in a strain overexpressing HflB. The hflB gene is in the ftsJ-hflB operon, one promoter of which is positively regulated by heat shock and sigma(32). The lambda cIII protein, which stabilizes sigma(32) and lambda cII, appears to inhibit the HflB-governed protease. The E. coli HflB protein controls the stability of two master regulators, lambda cII and sigma(32), responsible for the lysis-lysogeny decision of phage lambda and the heat shock response of the host.