Dss1 is a 26S proteasome ubiquitin receptor

Abstract

The ubiquitin-proteasome system is the major pathway for protein degradation in eukaryotic cells. Proteins to be degraded are conjugated to ubiquitin chains that act as recognition signals for the 26S proteasome. The proteasome subunits Rpn10 and Rpn13 are known to bind ubiquitin, but genetic and biochemical data suggest the existence of at least one other substrate receptor. Here, we show that the phylogenetically conserved proteasome subunit Dss1 (Sem1) binds ubiquitin chains linked by K63 and K48. Atomic resolution data show that Dss1 is disordered and binds ubiquitin by binding sites characterized by acidic and hydrophobic residues. The complementary binding region in ubiquitin is composed of a hydrophobic patch formed by I13, I44, and L69 flanked by two basic regions. Mutations in the ubiquitin-binding site of Dss1 cause growth defects and accumulation of ubiquitylated proteins.

Graphical abstract

Figure 1

The Rpn10 UIM Is Not Responsible for the rhp23Δrpn10Δ Synthetic Lethality (A) Substrate recognition by the 26S proteasome is mediated via intrinsic receptors that are subunits (Rpn10 and Rpn13) and extrinsic receptors that are UBL-UBA domain cofactors (Rhp23/Rad23 and Dph1/Dsk2). The substrate is depicted as a black thread, and ubiquitin is depicted as a gray sphere. (B) The domain organization of full-length (FL) Rpn10, Rpn10ΔUIM (deleted of the UIM domain to abolish ubiquitin binding), and Rpn10ΔN82 (82-residue N-terminal deletion to abolish proteasome binding) (Seeger et al., 2003). (C) In vivo assay of rpn10Δ and rhp23Δ deletion strains transformed to express the indicated constructs. The two strains were crossed to generate a double deletion. Following crossing, 10,000 spores were plated on media that selected for both deletion mutants and the expression vector. See also Figure S1.

Figure 2

Dss1 Interacts Directly with Ubiquitin (A) K48- and K63-linked ubiquitin chains (3 μg per assay) (input) were coprecipitated with GST-Dss1. GST and GST-Rhp23 proteins were included as negative and positive controls, respectively. The precipitated material was analyzed by SDS-PAGE and western blotting using antibodies to ubiquitin. Equal loading was checked by staining with Coomassie brilliant blue (CBB). (B) I44A and wild-type (wt) monoubiquitin (10 μg) (input) were coprecipitated with GST-Dss1. GST and GST-Rhp23 proteins were included as negative and positive controls, respectively. The precipitated material was analyzed by SDS-PAGE and western blotting using antibodies to ubiquitin. Equal loading was checked by staining with CBB. (C) PONDR (blue) and IUPred (red) sequence analysis predicted Dss1 to be largely unstructured at physiological pH. PONDR predicted a short C-terminal stretch to be structured. (D) C^α secondary chemical shifts of Dss1 confirm the predominantly disordered structure. Positive C^α secondary chemical shifts identify α-helical structure in the C terminus from F55 through K66 indicated by a blue bar. (E) ¹H-¹⁵N HSQC spectrum of Dss1 in the absence (red) and presence (blue) of a 50-fold molar excess of ubiquitin. Residues marked with an asterisk disappeared from the HSQC spectrum on addition of ubiquitin. (F) Plot of the per-residue calculated chemical shift perturbation (CSP) (see Supplemental Information) comparing identical samples of Dss1 in the absence and presence of a 50-fold molar excess of ubiquitin, revealing two UBSs, UBS-I and UBS-II, indicated by red bars. The horizontal dashed lines illustrate the average CSP and the average CSP plus 1 SD. Residues marked with an asterisk disappeared from the HSQC spectrum on addition of ubiquitin. See also Figure S2.

Figure 3

Dss1 Exploits a Tripartite Binding Site on Ubiquitin (A) Changes in peak intensities of ubiquitin in response to Dss1 binding. The red dashed line marks residues where the intensity decreased to less than 35%, and the black solid line marks those residues where the intensities are less than 10% of the unbound. The red dots mark proline residues not visible in the spectra. (B and C) Changes in peak intensities of ubiquitin by Dss1 addition mapped onto the 3D structure of ubiquitin (Protein Data Bank ID 1D3Z) (Cornilescu et al., 1998). The protein structure is shown in green. Light blue indicate residues with peak intensities decreased to less than 35%, and dark blue decreased to less than 10%. (B) is oriented as in (D) with the β sheet facing the viewer, and in (C), the opposite side is shown with the α helix facing the viewer. (D) Ribbon representation of ubiquitin with the same color coding as in (B) and with specific residues labeled. Three lysine residues, K11, K48, and K63 of ubiquitin are shown in magenta sticks. (E and F) Electrostatic surface representation of ubiquitin, calculated using PyMOL. Negative potentials are shown in red, positive potentials are shown in blue, and uncharged regions are shown in white. The tripartite Dss1 binding area is circled. (E) has the same orientation as in (B), and (F) has the same as in (C). See also Figure S3.

Figure 4

UBSs in Dss1 Are Required for Proteasome Function (A) K48-linked (left panel) and K63-linked (right panel) ubiquitin chains (input) (3 μg per assay) were coprecipitated with GST-Dss1, GST-Dss1 UBS-I mutant (L40A/W41A/W45A), GST-Dss1 UBS-II mutant (F18A/F21A/W26A), and GST-Dss1 UBS-I and UBS-II mutant (F18A/F21A/W26A/L40A/W41A/W45A). GST and GST-Rhp23 proteins were included as negative and positive controls, respectively. The precipitated material was analyzed by SDS-PAGE and western blotting using antibodies to ubiquitin. Equal loading was checked by staining with Ponceau S. (B) The dss1Δ strains transformed with the indicated expression constructs were analyzed for growth on solid media at 30°C and 37°C. The pictures were taken after 72 hr. (C) The dss1Δ strains transformed with the indicated expression constructs were analyzed for the presence of ubiquitin-protein conjugates by blotting. Expression of the various Dss1 proteins was confirmed by blotting for the GFP tag. Tubulin served as a loading control. wt, wild-type. (D) A dss1Δ strain was transformed with the indicated expression vectors for Dss1-GFP fusion proteins and used for immunoprecipitations with antibodies to GFP. The precipitated material was analyzed by SDS-PAGE and western blotting using antibodies to the proteasome subunit Mts4/Rpn1 and GFP on Dss1. Dss1 expression was not visible in whole cell lysates but was clearly enriched in the precipitated material. FL, full-length. (E) Plating assay of the dss1Δrhp23Δrpn10Δ strain with the indicated expression constructs. The dss1Δrpn10Δ strain transformed with the indicated constructs was crossed to dss1Δrhp23Δ cells to generate a triple deletion. Following crossing, 10,000 spores were plated under selection for the deleted genes and the expression vector. (F) Plating assays of the dss1Δrhp23Δrpn10Δ and dss1Δrhp23Δrpn10ΔUIM strains with the indicated Rpn10 and Dss1 expression constructs, as shown in Figure 4E were quantified. Following crossing, 10,000 spores were plated under selection for the deleted genes and the expression vectors. Viable spores were counted and normalized to the controls (Rpn10 FL and Dss1 wild-type). Data are presented as mean ± SEM (n = 6). See also Figure S4.