## 5 Mechanisms for Triggering \(\sigma\) Factor Release from Anti-\(\sigma\) Factors
### Regulated Proteolysis  
Regulated intramembrane proteolysis (RIP) is a mechanism for signal transduction across membranes that is found in all kingdoms [68] and is commonly used to control ECF \(\sigma\) factors in response to extracytoplasmic stimuli. It usually involves the sequential cleavage of a membrane-traversing anti-\(\sigma\) by an external \"site-1\" protease followed by cleavage in the plane of the membrane by a \"site-2\" protease, resulting in the release of the cytoplasmic domain. In _E. coli_, RIP controls the release of \(\sigma^{\mathrm{E}}\) from RseA in response to outer membrane dysfunction (Figure 4a). Site-1 proteolysis of the C-terminal extracytoplasmic domain of RseA is catalyzed by the periplasmic protease DegS, following the accumulation of C-terminal peptides from unfolded outer membrane proteins (OMPs) that activate DegS by binding to its PDZ domain [69, 70]. This initial cleavage generates a substrate for the site-2 protease RseP (YaeL) that cleaves RseA on the cytoplasmic side of the membrane, thereby releasing a \(\sigma^{\mathrm{E}}\)/RseA-ASD complex into the cytoplasm [71, 72]. Although \(\sigma^{\mathrm{E}}\) is still unable bind to RNAP at this point, the site-2 cleavage of RseA leaves a C-terminal sequence that directs its rapid degradation by the ClpXP system, thereby releasing \(\sigma^{\mathrm{E}}\)[73]. However, to fully induce \(\sigma^{\mathrm{E}}\) another regulator needs to be inactivated. RseB is a periplasmic protein that binds to RseA to inhibit DegS-dependent cleavage [74] (Figure 4a). Recently it was shown that inhibition by RseB is prevented by lipopolysaccharide schemadide intermediates that bind directly to RseB. Therefore the activation of \(\sigma^{\mathrm{E}}\) requires two distinct stress signals (OMPs and LPS assembly components) with \"AND\" logic, which ensures that \(\sigma^{\mathrm{E}}\) is not switched on inadvertently [75].  
An analogous system occurs in _B. subtilis_ where \(\sigma^{\mathrm{W}}\) is sequestered by the trans-membrane ZASD anti-\(\sigma\) factor RsiW. In response to a signal that is generated by antimicrobial peptides or other agents that damage the cell envelope, RsiW is sequentially cleaved by the site-1 protease PrsW and the site-2 protease RasP [76, 77]. Unlike DegS, PrsW is an integral membrane protease, consistent with the absence of a periplasm in this Gram-positive organism. Another difference is that the extracytoplasmic portion of the site-1 cleavage product needs to be trimmed before it becomes a substrate for RasP [78]. As is the case in _E. coli_, site-2 cleavage reveals a C-terminus that targets the protein for degradation by the ClpXP system, thereby fully releasing the \(\sigma\)[79].  
Finally, RIP is involved in the activation of \(\sigma\) factors involved in iron-uptake in _P. aeruginosa_ by cell surface signalling. In _P. aeruginosa_\(\sigma^{\mathrm{FpvI}}\) and \(\sigma^{\mathrm{PsvAs}}\) direct expression of the ferrippyoverdine siderophore outer membrane receptor (FpvA) and pyoverdine synthesis, respectively, and unusually are controlled by the same anti-\(\sigma\) factor, FrvR [80]. When pyoverdine binds to FpvA, a signal is transferred via the periplasmic domain of FpvA to FrvR, resulting in the degradation of FrvR by the RseP orthologue MucP [81]. As with _E. coli_\(\sigma^{\mathrm{E}}\) and _B. subtilis_\(\sigma^{\mathrm{W}}\), the remaining \(\sigma\)-bound portion of FrvR is thought to be degraded by the Clp protease system [81, 82].