The 26S Proteasome Switches Between ATP‐Dependent and Independent Mechanisms in Response to Substrate Ubiquitination

Abstract

The Ubiquitin‐Proteasome System is responsible for the bulk of protein degradation in eukaryotic cells. Proteins are generally targeted to the 26S proteasome by the attachment of polyubiquitin chains. A number of proteins also contain ubiquitin‐independent degrons (UbID) that allow for proteasomal targeting without the need for ubiquitination. UbID substrates are degraded less processively than ubiquitinated substrates, but the mechanism underlying this difference remains unclear. We therefore designed two model substrates containing both a ubiquitination site and a UbID for a more direct comparison. We found UbID degradation to be overall less robust with complete degradation only occurring with relatively unstable substrates (those that were at least transiently unfolded as determined by protease sensitivity). Surprisingly, UbID degradation was unaffected by the non‐hydrolyzable ATP analog ATPγS, which halts ATP‐dependent engagement and translocation of substrates. Furthermore, ubiquitin‐dependent degradation proceeded in a strikingly similar fashion to UbID degradation in the presence of ATPγS, suggesting the 26S proteasome may have a “default” ATP‐ and ubiquitin‐independent mechanism that is capable of unfolding and degrading less‐stable proteins.