In the proteasome holoenzyme, the hexameric ATPases (Rpt1-Rpt6) enable degradation of ubiquitinated proteins by unfolding and translocating them into the proteolytic core particle. During early-stage proteasome assembly, individual Rpt proteins assemble into the hexameric “Rpt ring” through binding to their cognate chaperones: Nas2, Hsm3, Nas6, and Rpn14. Here, we show that Rpt ring assembly employs a specific ubiquitination-mediated control. An E3 ligase, Not4, selectively ubiquitinates Rpt5 during Rpt ring assembly. To access Rpt5, Not4 competes with Nas2 until the penultimate step and then with Hsm3 at the final step of Rpt ring completion. Using the known Rpt–chaperone cocrystal structures, we show that Not4-mediated ubiquitination sites in Rpt5 are obstructed by Nas2 and Hsm3. Thus, Not4 can distinguish a Rpt ring that matures without these chaperones, based on its accessibility to Rpt5. Rpt5 ubiquitination does not destabilize the ring but hinders incorporation of incoming subunits—Rpn1 ubiquitin receptor and Ubp6 deubiquitinase—thereby blocking progression of proteasome assembly and ubiquitin regeneration from proteasome substrates. Our findings reveal an assembly checkpoint where Not4 monitors chaperone actions during hexameric ATPase ring assembly, thereby ensuring the accuracy of proteasome holoenzyme maturation.

The proteasome holoenzyme is a molecular machine that degrades most proteins in eukaryotes. In the holoenzyme, its heterohexameric ATPase injects protein substrates into the proteolytic core particle, where degradation occurs. The heterohexameric ATPase, referred to as 'Rpt ring', assembles through six ATPase subunits (Rpt1-Rpt6) individually binding to specific chaperones (Rpn14, Nas6, Nas2, and Hsm3). Here, our findings suggest that the onset of Rpt ring assembly can be regulated by two alternative mechanisms. Excess Rpt subunits relative to their chaperones are sequestered into multiple puncta specifically during early-stage Rpt ring assembly. Sequestration occurs during stressed conditions, for example heat, which transcriptionally induce Rpt subunits. When the free Rpt pool is limited experimentally, Rpt subunits are competent for proteasome assembly even without their cognate chaperones. These data suggest that sequestration may regulate amounts of individual Rpt subunits relative to their chaperones, allowing for proper onset of Rpt ring assembly. Indeed, Rpt subunits in the puncta can later resume their assembly into the proteasome. Intriguingly, when proteasome assembly resumes in stressed cells or is ongoing in unstressed cells, excess Rpt subunits are recognized by an alternative mechanism-degradation by the proteasome holoenzyme itself. Rpt subunits undergo proteasome assembly until the holoenzyme complex is generated at a sufficient level. The fully-formed holoenzyme can then degrade any remaining excess Rpt subunits, thereby regulating its own Rpt ring assembly. These two alternative mechanisms, degradation and sequestration of Rpt subunits, may help control the onset of chaperone-mediated Rpt ring assembly, thereby promoting proper proteasome holoenzyme formation. by guest on July 10, 2020 http://www.jbc.org/ Downloaded from Figure 1. Proteasome holoenzyme formation requires chaperone-mediated Rpt ring assembly during heat stress. A and B, upon heat stress, early-stage Rpt ring assembly requires the chaperones. Yeast strains were grown at 30°C (lanes 1 -4), and then exposed to heat stress at 37°C for 4 h (lanes 5-8). Proteasome activities were assessed by subjecting whole-cell lysates (60 g) to native PAGE and in-gel peptidase assays using the fluorogenic peptide substrate, LLVY-AMC (panel i). After imaging the native gels in panel i, 0.02% SDS was added to activate free CP in panel ii; SDS denatures the substrate entry gate of the CP (25). Native gels were then subjected to immunoblotting (IB) to detect levels of the Rpt5-Rpt4 modules (t5-t4 module) and proteasome holoenzymes (panel iii). Pgk1 is a loading control. B, Pgk1 blot in lanes 1-4 and 5-8 derives from two different gels, which were processed the same in parallel during immunoblotting and signal detection. C and D, ubiquitinated protein degradation requires chaperone-mediated proteasome assembly during heat stress. Whole-cell lysates (20 g) from samples as in A and B were subjected to 10% BisTris SDS-PAGE and immunoblotting for ubiquitin....

In the proteasome holoenzyme, the hexameric ATPases (Rpt1‐Rpt6) enable degradation of ubiquitinated proteins by unfolding and translocating them into the proteolytic core particle. During early‐stage proteasome assembly, individual Rpt proteins assemble into the hexameric ‘Rpt ring’ through binding to their cognate chaperones: Nas2, Hsm3, Nas6 and Rpn14. Here, we show that Rpt ring assembly employs a specific ubiquitination‐mediated control. An E3 ligase, Not4, selectively ubiquitinates Rpt5 during Rpt ring assembly. To access Rpt5, Not4 competes with Nas2 until the penultimate step, and then with Hsm3 at the final step of Rpt ring completion. Using the known Rpt‐chaperone co‐crystal structures, we show that Not4‐mediated ubiquitination sites in Rpt5 are obstructed by Nas2 and Hsm3. Thus, Not4 can distinguish a Rpt ring that matures without these chaperones, based on its accessibility to Rpt5. Rpt5 ubiquitination does not destabilize the ring, but hinders incorporation of incoming subunits—Rpn1 ubiquitin receptor and Ubp6 deubiquitinase, thereby blocking progression of proteasome assembly and ubiquitin regeneration from proteasome substrates. Our findings reveal an assembly checkpoint where Not4 monitors chaperone actions during hexameric ATPase ring assembly, thereby ensuring the accuracy of proteasome holoenzyme maturation.Support or Funding InformationBoettcher Webb‐Waring Biomedical Research Award and 1R01GM127688‐01A1 from NIH (S.P.)This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.