Site-2 proteases (S2Ps) are intramembrane metalloproteases that cleave transmembrane substrates in all domains of life. Many S2Ps, including human S2P and Mycobacterium tuberculosis Rip1, have multiple substrates in vivo, which are often transcriptional regulators. However, S2Ps will also cleave transmembrane sequences of nonsubstrate proteins, suggesting additional specificity determinants. Many S2Ps also contain a PDZ domain, the function of which is poorly understood. Here, we identify an M. tuberculosis protein, PDZ-interacting protease regulator 1 (Ppr1), which bridges between the Rip1 PDZ domain and anti-sigma factor M (Anti-SigM), a Rip1 substrate, but not Anti-SigK or Anti-SigL, also Rip1 substrates. In vivo analyses of Ppr1 function indicate that it prevents nonspecific activation of the Rip1 pathway while coupling Rip1 cleavage of Anti-SigM, but not Anti-SigL, to site-1 proteolysis. Our results support a model of S2P substrate specificity in which a substratespecific adapter protein tethers the S2P to its substrate while holding the protease inactive through its PDZ domain.intramembrane proteolysis | signal transduction | Tuberculosis | Sigma factor R egulated intramembrane proteolysis (RIP) is a widely distributed mechanism of signal transduction across membranes in which specialized intramembrane cleaving proteases (iCLIPs) cleave the transmembrane segments of substrate proteins (1, 2). The site-2 (S2) proteases (S2Ps) are one class of iCLIP that is widely distributed from bacteria to human cells and participate in such diverse pathways as lipid biosynthesis (1, 3, 4), sporulation (5), membrane stress (6, 7), alginate production (8), and polar morphogenesis (9). In bacteria, PDZ domain containing S2Ps often control the release of extracytoplasmic function sigma factors from the membrane through proteolysis of their cognate membrane-bound anti-sigma factors (10, 11). S2Ps are so named because the intramembrane cleavage event follows cleavage by a site-1 (S1) protease (S1P). The S1P first cleaves the periplasmic domain of the anti-sigma factor in response to an extracellular signal. Only after S1 cleavage does the S2P cleave near the cytoplasmic side of the transmembrane domain of the anti-sigma factor, liberating the anti-sigma/sigma factor complex from the membrane into the cytoplasm where the sigma factor can associate with RNA polymerase. A specific extracytoplasmic stimulus can thus be coupled to a transcriptional response through a coordinated proteolytic cascade.One of the major unanswered questions in S2P-mediated RIP is how these proteases achieve specificity in signaling. In many cases, S2Ps have multiple substrates, including human S2P, which cleaves SREBPs, ATF6, and CREB-H (12, 13); Bacillus subtilis RasP, which cleaves both RsiW as well as FtsL (14, 15); and Mycobacterium tuberculosis regulated intramembrane protease 1 (Rip1), which cleaves three anti-sigma factors, Anti-SigK (RskA), Anti-SigL (RslA), and Anti-SigM (RsmA) (3), as well as PBP3 (16). However, there is substantial evidence t...