Discovery and Characterization of ZUFSP/ZUP1, a Distinct Deubiquitinase Class Important for Genome Stability

Abstract

Deubiquitinating enzymes (DUBs) are important regulators of ubiquitin signaling. Here, we report the discovery of deubiquitinating activity in ZUFSP/C6orf113. High-resolution crystal structures of ZUFSP in complex with ubiquitin reveal several distinctive features of ubiquitin recognition and catalysis. Our analyses reveal that ZUFSP is a novel DUB with no homology to any known DUBs, leading us to classify ZUFSP as the seventh DUB family. Intriguingly, the minimal catalytic domain does not cleave polyubiquitin. We identify two ubiquitin binding domains in ZUFSP: a ZHA (ZUFSP helical arm) that binds to the distal ubiquitin and an atypical UBZ domain in ZUFSP that binds to polyubiquitin. Importantly, both domains are essential for ZUFSP to selectively cleave K63-linked polyubiquitin. We show that ZUFSP localizes to DNA lesions, where it plays an important role in genome stability pathways, functioning to prevent spontaneous DNA damage and also promote cellular survival in response to exogenous DNA damage.

Keywords: DNA damage response; DNA repair; DUB; Lys63 chains; deubiquitinating enzyme; polyubiquitin; ubiquitin signaling; uniquitin binding domain.

Graphical abstract

Figure 1

Identification of ZUFSP as a DUB (A) Schematic representation of DUB profiling pipeline. (B) Halo-tagged Ub or propargylated Ub (Ub-Prg) coupled to HaloLink resin was incubated with cell extracts. Captured material was separated by SDS-PAGE and silver stained. (C) Summary of DUBs identified by mass spectrometry using the Halo-C3-Ub-Prg probe with lysates of HEK293 and Jurkat cells. The last column shows the total number of annotated DUBs in each family (metalloproteases are not included). (D) The ZUFSP minimal catalytic domain (294–578) was reacted with the HA-Ub-Prg or HA-UFM1-Prg probes for indicated times. Reaction products were separated by SDS-PAGE gel stained using Coomassie blue. (E) Schematic domain structure of ZUFSP. Zinc finger (ZNF) domains (pink), motif interacting with Ub (MIU) domain (orange), and minimal catalytic domain (blue) are depicted. (F) Sequence alignment of human ZUFSP with mouse (Mm) Ufsp1 and Ufsp2. Secondary structure elements are shown for Ufsp2. Conserved catalytic residues are highlighted with blue asterisks; missing His is highlighted with a blue triangle. Fully conserved residues are shaded in red. See also Figure S1.

Figure 2

ZUFSP Is a Distinct Class of Deubiquitinating Enzymes (A) Overall structure of the ZUFSP catalytic core domain. The secondary structural elements, α helix, β strand, and 3–10 helix, are highlighted in actinium blue, light purple, and light orange, respectively, with covalently bound Ub (yellow). The vinylthioether linkage connecting Ub with the catalytic cysteine of ZUFSP is shown in stick format. The catalytic core domain is connected to the helical arm indicated as ZHA (light blue) via a helix-loop-helix motif (salmon red, α2 and α3). The N terminus highlighted in orange is part of the MIU motif. Below: schematic representation of the ZUFSP 232–578 construct. Colors depicting the domains correspond to colors of the structure. (B) Topology diagram showing ZUFSP architecture in 2D representation. The catalytic triad residues are indicated (asterisk). (C) Representative electron density. 2F_o-F_c map of the residues corresponding to ZHA and the preceding loop contoured at 1σ. (D) Close-up view highlighting catalytic triad residues C360, H491, and D512 and the oxyanion hole forming residue Q487. (E–H) Close-up view of structure based alignments of ZUFSP with top matches based on the DALI server: Atg4b (PDB:2CY7) (E), UFSP1 (PDB: 2Z84) (F), UFSP2 (PDB: 3OQC) (G), and Staphopain (PDB:1CV8) (H). (I) Structural alignment of Ub with UFM1. The secondary structure elements for both Ub and UFM1 are shown. The Ub residues interacting with ZHA are indicated in asterisks. Fully conserved residues are shaded in red. (J) Steric clash of UFM1 β1-β2 loop with ZHA as seen from the structural alignment of UFM1 onto Ub (K) Electrostatic surface potential based representation shows the hydrophobic pocket formed by the aliphatic portions of Q487, Q489, Q547, and Q549. (L) The C terminus of Ub (yellow) in the narrow ZUFSP catalytic groove (M) Structural superposition of UFM1 (light blue). Bulky V82 of UFM1 clashes with the β6-β7 loop in ZUFSP. See also Figure S2.

Figure 3

ZUFSP Helical Arm Is a UBD (A) ZHA-Ub interaction is predominantly hydrophobic. The interface shows the I44 patch (purple) on Ub (yellow) surface engaging with F260, L263, and Y267 residues of ZHA (cartoon representation, light blue). (B) The network of interactions between ZHA and Ub, which include hydrophobic interactions, a salt bridge between K6 and E256 of ZHA and cation-π pair (K6-F260) is depicted. (C) ZUFSP ZHA is conserved in evolution. Sequence alignment of ZHA from different organisms is shown. Secondary structure assignment is based on human ZUFSP. The ZHA residues interacting with Ub are highlighted with asterisks. Some species like N. vectensis and S. pombe altogether lack ZHA. (D) Surface representation showing conserved residues on the surface of ZUFSP based on the sequence alignment in Figure S3 generated with the Consurf server (http://consurf.tau.ac.il). The residues around the catalytic center and Ub interacting ZHA patch are conserved through evolution. (E) Interactions of distal Ub with ZUFSP. The Ub C-terminal residues R72 and R74 are involved in a network of ionic interactions with D406 and E428 of the catalytic domain. (F) Structure of the MIU of RABEX5 (pink) in complex with Ub (yellow) (PDB: 2FIF) shown in cartoon representation. (G) Structure of the ZHA of ZUFSP (blue) in complex with Ub (yellow) shown in cartoon representation. (H) Comparison of MIU and ZHA interactions with Ub. Superposition of structures shown in (F) and (G) aligned on Ub. See also Figure S3.

Figure 4

Dissecting PolyUb Binding of ZUFSP (A) DUB assays of ZUFSP^cat and ZUFSP^MIU-cat with the indicated polyUbs. Reaction products were separated by SDS-PAGE and silver stained. (B) Alignment of the MIU from ZUFSP with the consensus MIU motif (Penengo et al., 2006). (C) Ub pull-down assay where HALO-MIU-ZHA immobilized on HaloLink resin was incubated with tetra-Ub (UB4) of different linkages. Bound material was separated by SDS-PAGE and silver stained. Asterisks denote unspecific bands. (D) Indicated HALO-fusion proteins were incubated with UB4 and processed as in (B). Captured chain types are highlighted in the Binding Summary section. (E) ESPRIPT sequence alignment of ZNF4 from ZUFSP with UBZ of DNA polymerase η (POLH) and FAAP20. Residues highlighted within blue frames are important for ZUFSP ZNF4 polyUb binding. (F) Recombinant HALO-ZNF4 wild-type (WT) and various point mutants were analyzed for binding to tetra-K48 linked chains. Bound material was separated by SDS-PAGE and stained by Coomassie blue. See also Figure S4.

Figure 5

ZUFSP Catalytic Activity Requires the UBZ Domain (A) DUB assay of ZUFSP^ZNF4-MIU-cat. Purified protein was incubated with each Ub4 chain type for the indicated time points, and reaction products were separated by SDS-PAGE and silver stained. (B) DUB assay as in (A) comparing DUB activity of the indicated ZUFSP constructs. (C) DUB assay monitoring K63-pentaUb cleavage by ZUFSP^ZNF4-MIU-Cat, with reaction products visualized as in (A). (D) DUB assay comparing activity of the indicated ZUFSP mutants at cleaving K63-tetraUb (E) Comparison of DUB activities of ZUFSPZNF4-MIU-Cat with UBZ mutant that cannot bind ubiquitin. Percentage of cleaved tetraUb was quantified from Sypro Ruby-stained gels. Data from three independent experiments were fitted using nonlinear regression, one phase exponential decay. SD error bars are shown. (F) DUB assay as in (D) monitoring cleavage of K63-linked tetraUb. (G) Model depicting substrate binding and catalysis in ZUFSP. The distal Ub is stabilized by contacts with the ZHA domain (violet) and the catalytic core (blue). The polyUb binding UBZ domain (ZNF4) (pink) is required for catalytic activity and we suggest that it may form the proximal Ub binding S1’ site. See also Figure S5.

Figure 6

ZUFSP Is a Putative DNA Replication and Repair Factor (A) Immunoprecipitation of endogenous ZUFSP reveals distinct biological functions. DAVID analysis for Gene Ontology Biological Processes (GOBP) showing enrichment for the top hits. (B) Subset of ZUFSP interaction map showing proteins involved in DNA repair, DNA replication, and negative regulation of DNA recombination. (C) HeLa cells were transfected with YFP-ZUFSP, subjected to laser micro-irradiation, and imaged at the indicated time. Scale bar, 10 μm. (D) HeLa cells were transfected with YFP-ZUFSP, pre-treated with DMSO or MG132 (3 hr), subjected to laser micro-irradiation, and imaged at the indicated time and then fixed and processed for immunostaining with the indicated antibodies. Scale bar, 10 μm. (E) HeLa wild-type (WT) of ΔUBC13 cells were transfected with YFP-ZUFSP, subjected to laser micro-irradiation, and imaged at the indicated time and then fixed and processed for immunostaining with the indicated antibodies. Scale bar, 10 μm. See also Figure S6.

Figure 7

ZUFSP Prevents Spontaneous DNA Damage and Promotes Cellular Survival in Response Exogenous DNA Damage (A) U2-OS cells were transfected with control (siCTRL) or ZUFSP (siZUFSP) siRNAs for 72 hr and then lysed and analyzed by immunoblotting with the indicated antibodies. (B) U2-OS cells were transfected with the indicated siRNAs for 72 hr and then subjected to pre-extraction and fixation and processed for immunostaining with the indicated antibodies. Scale bar, 10 μm. (C) QIBC analysis of chromatin-bound γH2AX and 53BP1 from (B). A representative experiment is shown from at least n = 3 independent biological experiments. (D) U2-OS cells were transfected with the indicated siRNAs for 72 hr and then fixed and processed for immunostaining with the indicated antibodies. Scale bar, 10 μm. (E) QIBC analysis from the samples shown in (D) using the combination of cyclin A and DAPI signals to differentiate cell-cycle phases, with coloring indicating the total 53BP1 foci intensity per nucleus. (F) U2OS cells were treated with siCTRL or siZUFSP (#2) siRNAs and with or without doxycycline (DOX) to induce expression of siRNA-resistant (^∗siR#2) GFP-ZUFSP wild-type (WT) or C360S alleles. Cells were processed for immunostaining and enumerated for 53BP1 positivity. Data represent mean ± SEM from two biologically independent experiments using technical duplicates per data point. (G) Clonogenic survival of U2-OS cells transfected with the indicated siRNA and then treated with various doses of ionizing radiation (IR). Data represent mean ± SEM from two biologically independent experiments using technical triplicates per data point. (H) As for (F), but with camptothecin (CPT). See also Figure S7.