Cargo competition for a dimerization interface restricts and stabilizes a bacterial protease adaptor

Abstract

Bacterial protein degradation is a regulated process aided by protease adaptors that alter specificity of energy-dependent proteases. In Caulobacter crescentus, cell cycle–dependent protein degradation depends on a hierarchy of adaptors, such as the dimeric RcdA adaptor, which binds multiple cargo and delivers substrates to the ClpXP protease. RcdA itself is degraded in the absence of cargo, and how RcdA recognizes its targets is unknown. Here, we show that RcdA dimerization and cargo binding compete for a common interface. Cargo binding separates RcdA dimers, and a monomeric variant of RcdA fails to be degraded, suggesting that RcdA degradation is a result of self-delivery. Based on HDX-MS studies showing that different cargo rely on different regions of the dimerization interface, we generate RcdA variants that are selective for specific cargo and show cellular defects consistent with changes in selectivity. Finally, we show that masking of cargo binding by dimerization also limits substrate delivery to restrain overly prolific degradation. Using the same interface for dimerization and cargo binding offers an ability to limit excess protease adaptors by self-degradation while providing a capacity for binding a range of substrates.

The midnolin-proteasome pathway catches proteins for ubiquitination-independent degradation

“…Our results suggest the midnolin-proteasome pathway may represent a general mechanism by which the proteasome bypasses the traditional ubiquitination system to achieve selective degradation of many nuclear proteins. It has been reported that in bacteria, which do not contain the ubiquitin-proteasome system, a hierarchy of adaptors mediate selective degradation of diverse proteins by the proteasome-equivalent ClpXP protease complex ( 54 , 55 ). Thus, it will be of interest to determine whether, in the course of evolution, additional proteins have evolved to recruit proteins directly to the proteosome for degradation.…”

Proteomics, phylogenetics, and coexpression analyses indicate novel interactions in the plastid CLP chaperone-protease system

“…It took several laboratories and many publications to begin to establish these regulatory functions. It is also important to note that several of these adaptors are themselves substrate for degradation by the Clp system ( 71 ). Because elucidation of Clp adaptor functions and even substrates can be so daunting, we carried out a comprehensive analysis of these 22 candidate adaptors and substrates through computational analysis (summarized in Fig.…”

Structure of Phosphorylated-like ClpXP Adaptor RssB Reveals an Interface Switch for Activation

“…RcdA dimers can readily be detected in solution, and critically RcdA and cargo both compete for the same RcdA interface. This competition determines the fate of RcdA itself since RcdA homodimers are degraded by ClpXP, while bound cargo stabilizes RcdA against proteolysis 52,53 .…”