Multiple assembly chaperones govern biogenesis of the proteasome regulatory particle base

Abstract

The central protease of eukaryotes, the 26S proteasome, has a 20S proteolytic core particle (CP) and an attached 19S regulatory particle (RP). The RP is further subdivided into lid and base subcomplexes. Little is known about RP assembly. Here, we show that four conserved assembly factors govern biogenesis of the yeast RP base. Nas2 forms a complex with the Rpt4 and Rpt5 ATPases and enhances 26S proteasome formation in vivo and in vitro. Other RP subcomplexes contain Hsm3, which is related to mammalian proteasome subunit S5b. Hsm3 also contributes to base assembly. Larger Hsm3-containing complexes include two additional proteins, Nas6 and Rpn14, which function as assembly chaperones as well. Specific deletion combinations affecting these four factors cause severe perturbations to RP assembly. Our results demonstrate that proteasomal RP biogenesis requires multiple, functionally overlapping chaperones and suggest a model in which subunits form specific subcomplexes that then assemble into the base.

Fig. 1

NAS2 is a dosage suppressor of the rpt4-G106D ATPase mutant. A. Illustration of the doubly capped form of the 26S proteasome. The composition of the yeast 20S proteasome core particle (CP) and the 19S regulatory particle (RP) is given. B. The des5 mutation (rpt4-G106D) suppresses the lethality caused by galactose-dependent overexpression of the Dsk2 polyubiquitin-binding protein (bottom panel) but causes temperature-sensitive growth. C. Domain organization of the Nas2 and Rpt4 proteins and the position of the rpt4-G106D mutation (and two other tested mutations). CC, putative coiled coil. Rpt4-G106 is at the end of the CC. D. Low-copy (YCp-NAS2) and high-copy (YEp-NAS2) plasmids expressing NAS2 suppress the temperature-sensitive growth of the rpt4-G106D mutant.

Fig. 2

Nas2 affects proteasome function but is not part of the 26S proteasome. A. Anti-ubiquitin immunoblots showing polyubiquitin conjugate accumulation in rpt4-G106D cells. Left, effect of low-copy (YCp) and high-copy (YEp) expression of NAS2 on rpt4-G106D. Right, effect of nas2Δ on ubiquitin-conjugate profiles. Levels of proteasome components in the strains are shown below. Pgk1 serves as a loading control. B. Anti-Nas2 immunoblot analysis of yeast proteins separated by SDS-PAGE (left) or by nondenaturing PAGE (right). C. Gel filtration analysis of Nas2 and proteasomal proteins from WT and rpt4-G106D cells. Equivalent amounts of protein were loaded from each extract onto a Superose-6 column, and fractions were subjected to immunoblotting with antibodies to the indicated proteins.

Fig. 3

The rpt4-G106D and nas2Δ mutants have proteasome assembly defects. A. Immunoblot analysis of nondenaturing PAGE-separated proteins from yeast whole-cell extracts. The faint central band in the anti-Rpt5 blot is of unknown composition. B. Nondenaturing gel separation of proteins from yeast extracts followed by gel overlay with the fluorogenic substrate Suc-LLVY-AMC to assay proteasomal activity. Left panel, effect of low-copy (YCp) and high-copy (YEp) expression of NAS2 on functional proteasome formation. Right panel, effect of nas2Δ on assembly. Addition of SDS to the reaction buffer activates the otherwise latent CP and Blm10-CP (unlabeled band above free CP). C. A C-terminal Flag tag on Rpn5 does not disrupt the Rpn5-containing RP subcomplex in rpt4-G106D cells (arrowhead). D. Nondenaturing gel separation of Flag-affinity purified proteins from rpt4-G106D RPN5-FLAG cells. MS/MS analysis of the indicated band from the GelCode Blue-stained gel demonstrated that it was the 9-subunit RP lid. Asterisk, a band that is likely the free RP but was not analyzed. Unlike panel C, gel separation included a stacking gel and was run longer. E. A triplicated Flag tag on Rpt4 does not disrupt the Rpt4-containing RP subcomplex in rpt4-G106D cells (arrowhead). F. Nondenaturing gel separation of Flag-affinity purified proteins from rpt4-G106D RPT4-3xFLAG cells. MS/MS analysis of the indicated band from the GelCode Blue-stained gel yielded Rpt4 and Rpt5 from the RP base. Asterisk, as in panel D. PAGE was done with a 5.5% PA separating gel instead of the 4% used in other panels, and a stacking gel was used.

Fig. 4

Nas2 forms a complex with Rpt4 and Rpt5, which stimulates 26S proteasome formation in vitro. A. Co-purification of endogenous Rpt4 and Rpt5 with chromosomally expressed Nas2-Flag. Eluted proteins were tested for the indicated proteasomal subunits by immunoblotting. Pre1-Flag (CP β4 subunit) served as a positive purification control. B. Affinity-purified Nas2-Flag-Rpt4-Rpt5 complexes resolved on an SDS gel and stained with Coommassie Blue. Control, purification from a strain without Flag-tagged Nas2. C. Nas2-Rpt4-Rpt5 complexes stimulate 26S proteasome formation in vitro. Control eluate is derived from cells lacking the Flag tag on Nas2. Assembly reactions were done at 24°C. Diagram of the experimental scheme is shown. D. Stimulation of assembly of 26S proteasomes by purified Nas2-Rpt4-Rpt5 requires proteasome components from the target yeast extract. 26S proteasomes and RP-derived components were pre-cleared from RPN2-GST cell extracts by binding to glutathione-Sepharose.

Fig. 5

Hsm3 enhances RP assembly in vivo. A. Two novel complexes that include the Rpt1 ATPase accumulate in rpt4-G106D cells (labeled I and II in the immunoblot). B. Flag affinity-purified complexes from rpt4-G106D RPT1-FLAG-His6 ated by native gel PAGE, stained with GelCode Blue, excised, and analyzed by MS/MS. The proteins identified in each band are listed. C. Domain organization of Hsm3, Nas6, and Rpn14 proteins. D. RP assembly defects in hsm3Δ and base subunit mutants. Analysis was done as in Fig. 3A. Arrowheads, two Rpt5-containing complexes that accumulate in rpt1ts (cim5-1). E. Two slow-migrating complexes from cim5-1 (and at a lower level, WT) cells contain Hsm3 (arrowheads labeled I and II). F. Purification of complexes I and II from cim5-1 HSM3-FLAG cells with analysis as in panel B. The protein complexes identified by MS/MS from each band are listed.

Fig. 6

Nas6 and Rpn14 are also important for RP base assembly. A. Serial dilutions of the indicated double mutants were spotted onto YPD plates and incubated at the indicated temperatures for 2 d. B. Immunoblot analysis of nondenaturing gel-separated proteins from the indicated mutants. The 4xΔ strain is a nas2Δ nas6Δ hsm3Δ rpn14Δ quadruple mutant. C. Comparison of strains by nondenaturing gel/anti-Rpt5 immunoblotting. The free RP and free base are labeled by the upper two arrowheads based on the MS/MS analysis done in Fig. 5F and immunoblot analyses. Lower arrowhead, likely Rpt4-Rpt5 complex (based on co-migration on native gels with species observed in rpt4-G106D). D. High-copy RPN14 stimulates RP base formation whereas NAS6 stimulates full RP assembly in rpt4-G106D cells. Native gel immunoblotting was done as in panel B. E. Growth of the strains combining mutations in Nas6 or Rpn14 and base subunit Rpt6 (cim3-1) was evaluated as in panel A.

Fig. 7

Model for the assembly of the proteasome regulatory particle and the role of RP base assembly chaperones. The inferred point of each chaperone’s release is shown at the step after the latest complex in which it was detected. See text for details.