Insight into the RssB-Mediated Recognition and Delivery of σs to the AAA+ Protease, ClpXP

In Escherichia coli, SigmaS (sigma(S)) is the master regulator of the general stress response. The cellular levels of sigma(S) are controlled by transcription, translation and protein stability. The turnover of sigma(S), by the AAA+ protease (ClpXP), is tightly regulated by a dedicated adaptor protein, termed RssB (Regulator of Sigma S protein B)-which is an atypical member of the response regulator (RR) family. Currently however, the molecular mechanism of sigma(S) recognition and delivery by RssB is only poorly understood. Here we describe the crystal structures of both RssB domains (RssBN and RssBC) and the SAXS analysis of full-length RssB (both free and in complex with sigma(S)). Together with our biochemical analysis we propose a model for the recognition and delivery of sigma(S) by this essential adaptor protein. Similar to most bacterial RRs, the N-terminal domain of RssB (RssB(N)) comprises a typical mixed (beta alpha)(5)-fold. Although phosphorylation of RssBN (at Asp58) is essential for high affinity binding of sigma(S), much of the direct binding to sigma(S) occurs via the C-terminal effector domain of RssB (RssBC). In contrast to most RRs the effector domain of RssB forms a beta-sandwich fold composed of two sheets surrounded by alpha-helical protrusions and as such, shares structural homology with serine/threonine phosphatases that exhibit a PPM/PP2C fold. Our biochemical data demonstrate that this domain plays a key role in both substrate interaction and docking to the zinc binding domain (ZBD) of ClpX. We propose that RssB docking to the ZBD of ClpX overlaps with the docking site of another regulator of RssB, the anti-adaptor IraD. Hence, we speculate that docking to ClpX may trigger release of its substrate through activation of a closed state (as seen in the RssB-IraD complex), thereby coupling adaptor docking (to ClpX) with substrate release. This competitive docking to RssB would prevent futile interaction of ClpX with the IraD-RssB complex (which lacks a substrate). Finally, substrate recognition by RssB appears to be regulated by a key residue (Arg117) within the alpha 5 helix of the N-terminal domain. Importantly, this residue is not directly involved in sigma(S) interaction, as sigma(S) binding to the R117A mutant can be restored by phosphorylation. Likewise, R117A retains the ability to interact with and activate ClpX for degradation of sigma(S), both in the presence and absence of acetyl phosphate. Therefore, we propose that this region of RssB (the alpha 5 helix) plays a critical role in driving interaction with sigma(S) at a distal site.