Peptidic degron for IMiD-induced degradation of heterologous proteins

Koduri, Vidyasagar; McBrayer, Samuel K.; Liberzon, Ella; Wang, Adam C.; Briggs, Kimberly J.; Cho, Hyejin; Kaelin, William G.

doi:10.1073/pnas.1818109116

Cited by 48 publications

(50 citation statements)

References 26 publications

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“…2b). It was reported that an N-terminal IKZF3 degron (I3D) tag did not induce degradation 11 . Therefore, to examine whether the position of the S4D tag affected the degradation of the tagged proteins, expression vectors encoding S4D-Venus or Venus-S4D were constructed, which S4D tag was fused to N-or C-terminus of Venus protein, respectively ( Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Indeed, in 2019, a peptide degron tag using the second zinc finger domain (ZNF2) of IKZF3 was reported. The tagged proteins were degraded by IMiD treatment in cultured cells and in xenograft models of kidney, breast, and brain cancer 11 . However, its use was still limited to the C-terminus of the protein of interest and overexpressed tagged proteins, not endogenous proteins 11 .…”

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confidence: 99%

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An IMiD-induced SALL4 degron system for selective degradation of target proteins

et al. 2020

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Regulating the amount of proteins in living cells is a powerful approach for understanding the functions of the proteins. Immunomodulatory drugs (IMiDs) induce the degradation of neosubstrates by interacting with celebron (CRBN) in the cullin E3 ubiquitin ligase complex (CRL4CRBN). Here, we developed the IMiD-dependent Sal-like protein 4 (SALL4) degron (S4D) system for chemical protein knockdown. In transient assays, an N- or C-terminal S4D tag induced the degradation of proteins localized to various subcellular compartments, including the plasma membrane. The activity of luciferase-S4D was reduced by 90% within 3 h of IMiD treatment. IMiD treatment reduced the expression of endogenous S4D-fused RelA and IκBα in knock-in (KI) experiments. Interestingly, the IκBα knockdown suggested that there may be another, unknown mechanism for RelA translocation to the nucleus. Furthermore, 5-hydroxythalidomide as a thalidomide metabolite specifically degradated S4D-tagged protein. These results indicate that the S4D system is a useful tool for cellular biology.

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

An IMiD-induced SALL4 degron system for selective degradation of target proteins

et al. 2020

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“…The previously described Y130L mutant version of UBE2M was employed to modify CUL1-RBX1 with the I44A mutant version of NEDD8 39 . IKZF1 ZF2 (residues 141–169, with two point mutations K157R K165R and with a lysine added at position 140 to create a single target lysine at the N-terminus 57 was cloned with an N-terminal GST with a 3C-Prescission cleavage site and a non-cleavable C-terminal Strep-tag. IKZF1 ZF2 was purified by GST affinity chromatography, 3C-Prescission cleavage overnight, and size exclusion chromatography.…”

Section: Methodsmentioning

confidence: 99%

NEDD8 nucleates a multivalent cullin–RING–UBE2D ubiquitin ligation assembly

Baek

Krist

Prabu

et al. 2020

Nature

199

264

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Virtually all eukaryotic processes are regulated by cullin-RING E3 ligase (CRL)-catalyzed protein ubiquitylation 1 , which is exquisitely controlled by cullin modification with the ubiquitin (UB)-like protein NEDD8 2 – 6 . However, how CRLs catalyze ubiquitylation, and the basis for NEDD8 activation, remain unknown. We report the cryo EM structure of a chemically-trapped complex representing the ubiquitylation intermediate whereby neddylated CRL1 β-TRCP promotes UB transfer from the E2 UBE2D to its recruited substrate phosphorylated IκBα. The structure shows that NEDD8 acts as a nexus binding disparate cullin elements and the RING-activated UB-linked UBE2D. Concomitant local structural remodeling and large-scale CRL domain movements converge to juxtapose the substrate and ubiquitylation active site. The results explain how a distinctive UB-like protein alters the functions of its targets, and show how numerous NEDD8-dependent interprotein interactions and conformational changes synergistically configure a catalytic CRL architecture that is both robust for rapid substrate ubiquitylation and fragile to enable ensuing cullin-RING functions.

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“…However, degrader development is hindered by a reliance on target-specific chemical matter, which is unavailable for the majority of the proteome. To address this challenge, several strategies aimed at the direct control of cellular protein levels have been recently developed, including methods that use small molecules [3][4][5][6][7][8][9] , nanobodies 10 , or antibodies 11 .…”

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confidence: 99%

Rapid and direct control of target protein levels with VHL-recruiting dTAG molecules

et al. 2020

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Chemical biology strategies for directly perturbing protein homeostasis including the degradation tag (dTAG) system provide temporal advantages over genetic approaches and improved selectivity over small molecule inhibitors. We describe dTAGV-1, an exclusively selective VHL-recruiting dTAG molecule, to rapidly degrade FKBP12F36V-tagged proteins. dTAGV-1 overcomes a limitation of previously reported CRBN-recruiting dTAG molecules to degrade recalcitrant oncogenes, supports combination degrader studies and facilitates investigations of protein function in cells and mice.

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Peptidic degron for IMiD-induced degradation of heterologous proteins

Cited by 48 publications

References 26 publications

An IMiD-induced SALL4 degron system for selective degradation of target proteins

An IMiD-induced SALL4 degron system for selective degradation of target proteins

NEDD8 nucleates a multivalent cullin–RING–UBE2D ubiquitin ligation assembly

Rapid and direct control of target protein levels with VHL-recruiting dTAG molecules

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