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CAND1 inhibits Cullin-2-RING ubiquitin ligases for enhanced substrate specificity

Abstract

Through targeting essential cellular regulators for ubiquitination and serving as a major platform for discovering proteolysis-targeting chimera (PROTAC) drugs, Cullin-2 (CUL2)-RING ubiquitin ligases (CRL2s) comprise an important family of CRLs. The founding members of CRLs, the CUL1-based CRL1s, are known to be activated by CAND1, which exchanges the variable substrate receptors associated with the common CUL1 core and promotes the dynamic assembly of CRL1s. Here we find that CAND1 inhibits CRL2-mediated protein degradation in human cells. This effect arises due to altered binding kinetics, involving CAND1 and CRL2VHL, as we illustrate that CAND1 dramatically increases the dissociation rate of CRL2s but barely accelerates the assembly of stable CRL2s. Using PROTACs that differently recruit neo-substrates to CRL2VHL, we demonstrate that the inhibitory effect of CAND1 helps distinguish target proteins with different affinities for CRL2s, presenting a mechanism for selective protein degradation with proper pacing in the changing cellular environment.

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Fig. 1: CAND1 binds unneddylated CUL2 and inhibits the degradation of CRL2 target proteins.
Fig. 2: Eliminating neddylation, but not deneddylation, inhibits ARV-771 induced degradation of BRD2.
Fig. 3: Dynamic assembly and disassembly of CRL2s in human cell lysate.
Fig. 4: Characterization of CUL2–VBC and CUL2–CAND1 interactions.
Fig. 5: Effects of CAND1 on the kon and koff of the CUL2–VBC interaction.
Fig. 6: Substrate receptor module alone does not accelerate the dissociation of CUL2–CAND1.
Fig. 7: The accelerated disassembly of CRL2 by CAND1 has a stronger impact on the degradation of substrates that bind CRL2s with lower affinity.

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Data availability

All data supporting the findings of this study are available within the paper. The proteomics data have been deposited to the PRIDE with the dataset identifier PXD045609. The UniProt Homo sapiens protein database is accessible through the link https://www.uniprot.org/proteomes/. Source data are provided with this paper.

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Acknowledgements

We thank S.-O. Shan (California Institute of Technology) for helpful discussion on kinetics data. We thank S.J. Elledge (Harvard Medical School) and D.C. Scott (St. Jude Children’s Research Hospital) for reagents. Mass spectrometry was provided by the Indiana University School of Medicine Center for Proteome Analysis. The Octet RED384 system for BLI assays was provided by the Chemical Genomics Facility at Purdue Institute for Drug Discovery. This work was supported by National Institutes of Health grant no. R35GM138016 (to X.L.) and an American Heart Association Career Development Award no. 20CDA35270030 (to X.L.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

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Contributions

K.W. and X.L. designed the experiments and prepared the manuscript. K.W. performed all experiments unless stated otherwise. S.D. performed the assay in Fig. 1b. L.L. generated baculovirus stock for protein expression and aided experiments in Extended Data Fig. 6b,c. J.R.L. synthesized GGGGKAMCA peptides, aided data interpretation and manuscript writing. X.L conceived the study and supervised the project.

Corresponding author

Correspondence to Xing Liu.

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Nature Structural & Molecular Biology thanks Alessio Ciulli and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available. Dimitris Typas was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. Peer reviewer reports are available.

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Extended data

Extended Data Fig. 1 ARV-771 induced degradation of BRD2 in the presence of elevated levels of VHL.

a-c, WT and DKO cells expressing the same level of VHL show no difference in BRD2 degradation. a, WT cells contained a lower level of VHL than the DKO cells. WTVHL (WT cells containing transgenic VHL) and DKO cells expressed equal levels of VHL. b, Cells in a were treated with 50 nM ARV-771 for the indicated time and immunoblotted with anti-BRD2 antibody. Quantitative analyses of BRD2 degradation were shown in c. Error bars represent SEM; n = 3 independent experiments.

Source data

Extended Data Fig. 2 Effects of CSN5i-3 on the degradation of CODD in the WT and DKO cells.

a, b, WT cells expressing FLAGCODD were pretreated with 200 µM desferrioxamine. DMSO or 1 µM CSN5i-3 was added to the medium 1 h before washing off the inhibitors. Cells were then treated with 60 μg/ml cycloheximide (CHX) for the indicated time and were immunoblotted with anti-FLAG antibody. Quantitative analyses of FLAGCODD degradation in a were shown in b. Error bars represent SEM; n = 3 independent experiments. c, d, Same as in a, b except that DKO cells were used. Error bars represent SEM; n = 3 independent experiments.

Source data

Extended Data Fig. 3 Assessing dynamic assembly and disassembly of CRL2s in human cell lysates.

a, Trial of bait protein immobilization for the BLI experiments. GSTVBC at various concentrations were incubated with anti-GST antibody coated biosensors, and the sensor response levels were recorded over time. For all BLI experiments in this study, 100 nM GSTVBC was used for loading, and a minimal response level of 1 nm was achieved before the kinetic binding assay was initiated. b, Representative results of GSTVBC loading for the BLI assay shown in Fig. 3a. c, Schematic illustration of CRISPR/Cas9-mediated epitope tagging on the endogenous CUL2 locus in DKO cells. Single-stranded oligodeoxynucleotide (ssODN) carrying the coding sequence for the StrepII tag was used as the homology-directed repair (HDR) template. Red arrows indicate primers (1 F, 2 F, 3 F, 1 R, 2 R) used for screening the correctly tagged cells. d, The guide RNA (gRNA) targeting CUL2 as illustrated in c is efficient in inducing double strain breaks at the target site. Cell populations electroporated with the plasmid expressing gRNA and Cas9 were harvested for genomic DNA extraction and PCR with the 3 F and 1 R primer set as illustrated in c. Sequencing chromatograms of PCR products spanning the target sites were shown. e, Successful gene editing in the knock-in clonal cell line was identified using the primer sets ‘1 F + 1 R’ and ‘2 F + 2 R’ as illustrated in c. f, Sequencing chromatograms confirming the correct genomic sequences at the 5’ and 3’ junctions of the HDR region in the knock-in cell line. g, Immunoblots validating the successful preparation of SILAC samples illustrated in Fig. 3d. h, Estimation of the VHL concentration in HEK293 cells. Total cell extract from WT cells and recombinant VHL standards were immunoblotted with anti-VHL antibody. Levels of VHL in the WT cells were calculated based on the standard curve generated from the known amounts of recombinant VHL standards.

Source data

Extended Data Fig. 4 Quantitative analyses of interactions between CUL2 and VBC, and between CUL2 and CAND1.

a, Sequence alignment of ELOC1-40 from different species. b, Representative results of GSTVBC loading for the BLI assay shown in Fig. 4a. c, d, BLI analyses revealing kon (c) and koff (d) for CUL2 binding to VBC that contains different ELOC isoforms. n = 3. See the ‘Methods’ section for more details. e, Measurements of kobs for VBC binding to CUL2. Real-time CFP fluorescence upon mixing increasing concentrations of VBCFlAsH to 10 nM CFPCUL2 in a stopped-flow fluorimeter. Signal changes with background (determined by the ‘buffer’ group) subtraction were fit to two-phase exponential curves. The fast-phase and slow-phase rates (kobs) were plotted to give kon,fast and kon,slow, respectively. f, g, Estimation of the CUL2•CAND1 dissociation rate in human cell lysate. f, Schematic workflow of the assay. Relative levels of co-precipitated CAND1HA were calculated from CAND1HA/StrepIICUL2 intensity ratios followed by normalizing these ratios to that obtained from the 0-min sample. The normalized data were fit to a single exponential curve to obtain t1/2 and koff (g). n = 2. h, i, CAND1 produced from insect cells, but not bacterial cells, forms CUL2•CAND1 as stable as the CUL2•CAND1 in human cell lysate (f,g,). h, GST pulldown analyses of recombinant CUL2 bound to GSTCAND1 produced from E. coli or insect cells in the presence of CUL2split chase for indicated time. Samples were fractionated on SDS-PAGE gels and immunoblotted with indicated antibodies. Intensity ratios of the CUL2 and GSTCAND1 bands were fit to single exponential curves to obtain t1/2 (i). n = 3. j, Measurement of kobs for CAND1 binding to CUL2. Real-time AMCA fluorescence upon addition of increasing concentrations of FlAsHCAND1 to CUL2AMCA. Signal changes were fit to one phase exponential curves. CAND1 was purified from insect cells. Error bars represent SEM (d) or SD (i). ‘n’ indicates number of independent experiments. P values were determined by two-sided t-tests with no adjustments.

Source data

Extended Data Fig. 5 Interactions between CUL2 and VBC in the presence of CAND1.

a, Measurements of kobs for VBC binding to CUL2 preassembled with CAND1. Same as in Extended Data Fig. 4e except that 20 nM CAND1 was preincubated with 10 nM CFPCUL2. Signal changes with background subtraction (background determined by the ‘buffer’ group) were fit to one-phase exponential curves to give kobs. CAND1 was produced from insect cells. b,c, CAND1 accelerates the disassembly of CRL2VHL in human cell lysate. The schematic workflow of the experiment is depicted in b. Samples were immunoblotted with anti-VHL, anti-StrepII, and anti-CAND1 antibodies (c). Both short (S.E.) and long (L.E.) exposure for anti-VHL signals are shown. d, CAND1 accelerates the disassembly of CUL2•VBC in vitro. Same as in Fig. 5c except with 100 nM of different CAND1 proteins added in the presence of VBC chase. Both CAND1 and CAND1β++ were generated from bacterial cells. CAND1β++ showed no notable effect on the CFPCUL2-VBCFlAsH FRET signal. e, Structural alignment of CUL1•CAND1 complex (PDB ID: 1U6G) and CUL2•VBC complex (PDB ID: 5N4W) based on the N-terminal amino acid sequences (1-300) of cullins. f, Measurements of kobs for CUL2•VBC dissociation by CAND1. Real-time detection of CFP fluorescence in a stopped-flow apparatus upon addition of increasing concentrations of CAND1 together with 100 nM VBC chase to 10 nM CFPCUL2 preincubated with 10 nM VBCFlAsH. Final concentrations after mixing the two solutions in the stopped-flow fluorimeter were shown. Signal changes were fit to single exponential curves to obtain the kobs. CAND1 was produced from insect cells.

Source data

Extended Data Fig. 6 CUL2•CAND1 dissociation and its effect on CUL2 neddylation.

a, Measurements of kobs for FlAsHCAND1 binding to CUL2AMCA preassembled with VBC. Same as in Extended Data Fig. 4j except that 20 nM VBC was preincubated with 5 nM CUL2AMCA. Signal changes were fit to one phase exponential curves. CAND1 was purified from insect cells. b,c, kon for CAND1 binding to CUL2 preassembled with VBC. b, Measurement of kobs for FlAsHCAND1 binding to CUL2AMCA preassembled with VBC. Same as in Extended Data Fig. 6a except that 1 μM VBC was preincubated with 5 nM CUL2AMCA. Signal changes were fit to one-phase exponential curves to obtain kobs, which were plotted against FlAsHCAND1 concentrations in (c). Linear slope in (c) gave the kon. Error bars represent SEM; n = 4 independent experiments. CAND1 was purified from insect cells. d, HEK293 cells were treated with 1 µM CSN5i-3 for indicated time, and the rate of CUL2 neddylation was monitored using immunoblot with anti-CUL2 antibody. The proportion of unneddylated CUL2 in the whole CUL2 population (CUL2Total) versus time was plotted and fit to a single exponential curve to obtain the kobs. Error bars represent SEM; n = 3 independent experiments. CUL2N8: neddylated CUL2.

Source data

Extended Data Fig. 7 ZBC hardly accelerates the disassembly of CUL2•CAND1.

a, StrepII-tag affinity pulldown assay confirming the binding between recombinant StrepIICUL2 and ZBC. b, c, Similar to Fig. 6h, i except that VBC was replaced by ZBC. Samples were immunoblotted with anti-CAND1, anti-StrepII, and anti-ELOB antibodies.

Source data

Extended Data Fig. 8 PROTAC induced degradation of BRD2 and BRD3 in WT and DKO cells.

a, Schematic illustration for the MZ-1 and SIM1 mediated interactions between VHL and bromodomain proteins. b, As in Fig. 7a except that 0.3 µM MZ-1 was used in place of 1 µM MZ-1. Error bars represent SEM; n = 3 independent experiments.

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Wang, K., Diaz, S., Li, L. et al. CAND1 inhibits Cullin-2-RING ubiquitin ligases for enhanced substrate specificity. Nat Struct Mol Biol 31, 323–335 (2024). https://doi.org/10.1038/s41594-023-01167-5

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