The AAA plus FtsH Protease Degrades an ssrA-Tagged Model Protein in the Inner Membrane of Escherichia coli

In eubacteria, the tmRNA system frees ribosomes that stall during protein synthesis and adds an ssrA tag to the incompletely translated polypeptide to target it for degradation. The AAA+ ClpXP protease degrades most ssrA-tagged proteins in the Escherichia coli cytoplasm and was recently shown to degrade an ssrA-tagged protein in the inner membrane. However,, we find that tmRNA-mediated tagging of E. coli ProW(1-182), a different inner-membrane protein, results in degradation by the membrane-tethered AAA+ FtsH protease. ClpXP played no role in the degradation of ProW(1-182) in vivo. These studies suggest that a complex distribution of proteolytic labor maintains protein quality control in the inner membrane.