Insights into the role and mechanism of the AAA+ adaptor ClpS

Protein degradation is a vital process in cells for quality control and participation in regulatory pathways. Intracellular ATP-dependent proteases are responsible for regulated degradation and are highly controlled in their function, especially with respect to substrate selectivity. Adaptor proteins that can associate with the proteases add an additional layer of control to substrate selection. Thus, understanding the mechanism and role of adaptor proteins is a critical component to understanding how proteases choose their substrates. In this thesis, I examine the role of the intracellular protease ClpAP and its adaptor ClpS in Escherichia coli. ClpS binds to the N-terminal domain of ClpA and plays dual roles in ClpAP substrate selectivity: ClpS inhibits the degradation of some substrates such as ssrA-tagged proteins and enhances the degradation of other substrates such as N-end-rule proteins. We wished to elucidate how ClpS influences ClpAP substrate selection, and found that the stoichiometry of ClpS binding to ClpA is one level of regulation. Furthermore, we demonstrated that the N-terminal extension of ClpS is vital for the adaptor’s role in delivering N-end-rule substrates to ClpAP for degradation, but this extension is not required for inhibition of ssrA-tagged proteins. Truncation studies of the ClpS N-terminal extension showed a dramatic length-dependence on Nend-rule protein delivery, and the chemical composition of this portion of ClpS also affected the ability to degrade N-degron-bearing substrates. Evidence suggests that ClpS allosterically affects the ClpA enzyme, causing a modulation in substrate specificity, and preliminary studies localized the point of contact by the ClpS N-terminal extension to the ClpA pore region. ClpS therefore represents a new type of adaptor protein that modulates substrate selection allosterically, rather than simply recruiting and tethering substrates to the protease. To further understand the role of ClpS and ClpAP in the cell, we conducted a proteomic-based search for ClpS-dependent ClpAP substrates. A list of putative substrates was generated from these experiments, and we believe that ClpAP plays a key role in quality control, perhaps through the degradation of N-end-rule substrates. Combined with mechanistic studies, these physiological studies aid in the understanding of how ClpS influences substrate recognition by ClpAP. Thesis Supervisor: Tania A. Baker Title: E. C. Whitehead Professor of Biology