Control of the sigmaE-dependent extracytoplasmic stress response by regulated proteolysis

The Escherichia coli σE stress-response pathway controls the expression of genes encoding periplasmic folding catalysts, proteases, biosynthesis enzymes for lipid A (a component of lipopolysaccharide or LPS) and a number of other genes, most of which encode proteins that are known or predicted to either function in the envelope or affect envelope functions. RseA, the major negative regulator of σE activity, is a membrane-spanning protein whose cytoplasmic face functions as an antisigma factor. When E. coli is subjected to heat or other stresses that generate unfolded envelope proteins, especially unfolded outer membrane porins (OMPs), RseA is degraded and σE activity is induced. In this thesis, I have dissected the proteolytic pathway that degrades RseA and the signals that induce this pathway. I present evidence that RseA is degraded by a proteolytic cascade initiated by the inner membrane protease DegS, a member of the HtrA/DegP protease family, and continued by YaeL, an ortholog of S2 protease, which carries out regulated intramembrane proteolysis in mammalian cells. I also show that DegS and YaeL are essential for E. coli viability because of their roles in activating σ E, which is itself essential for E. coli viability. Finally, I have dissected one mechanism for inducing σE activity. I present evidence that the PDZ domain of DegS inhibits DegS protease activity. Additionally, I show that PDZ domain-binding peptides homologous to the C-termini of OMPs induce σE in a PDZ domain-dependent manner. The simplest explanation of these results is that such peptides, and by extension overexpressed and unfolded OmpC, promote DegS-mediated cleavage of RseA and subsequent σE activation by antagonizing the autoinhibitory PDZ domain of DegS. These findings significantly advance our understanding of how σE-inducing signals are detected and how they are transduced within the σE pathway. Moreover, they constitute the first evidence that binding of a ligand to the PDZ domain of a protease promotes degradation of a specific substrate of that protease.