Journal: Cell reports
Article Title: TRIM21-dependent target protein ubiquitination mediates cell-free Trim-Away.
doi: 10.1016/j.celrep.2023.112125
Figure Lengend Snippet: Figure 1. Cell-free Trim-Away in Xenopus egg extracts (A) Domain architectures of full-length (FL) TRIM21 and a minimal TRIM21 construct (TRIM21R-R-PS). R, RING domain; B, B-box domain; CC, coiled-coil domain; PS, PRYSPRY domain; Fc, antibody fragment. (B) Simplified schematic of the current Trim-Away model. The target protein of interest (red) is bound by an antibody (yellow), which in turn is recognized by TRIM21 (shades of blue). Subsequent TRIM21 activation results in sequential mono- and polyubiquitination of its N terminus with K63-linked polyubiquitin, which requires the E2 ubiquitin-conjugating enzymes UBE2W and UBE2N/UBE2V2, respectively. The polyubiquitin chain on TRIM21 has been proposed to promote the proteasomal degradation of all three components. (C) Trim-Away of endogenous TFIIS in Xenopus egg extract (high-speed supernatant [HSS]) comparing recombinant human TRIM21FL and TRIM21R-R-PS (final concentrations of 1 mM). (D) Trim-Away of TFIIS in HSS using TRIM21R-R-PS in the presence of inhibitors targeting E1 enzyme (MLN7243), the proteasome (MG-262), p97 (NMS-873), or the NEDD8-activating enzyme to inhibit Cullin-RING E3 ligases (MLN4924). (E) Endogenous TFIIS was targeted by TRIM21R-R-PS in three types of Xenopus egg extract: low-speed supernatant (LSS), HSS, and nucleoplasmic extract (NPE). Note that TFIIS is more abundant in NPE than in LSS and HSS. (F) Egg extracts were supplemented with 250 nM recombinant HpaII, a bacterial DNA methyltransferase, to compare Trim-Away efficiencies using TRIM21R-R-PS
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal anti-TRIM21 Cell Signaling Technology Cat# 92043; RRID:AB_2800177 Rabbit polyclonal anti-TFIIS Antigen: xlTFIIS full-length This paper; Pocono Rabbit Farm and Laboratory Custom Project 35585 Rabbit polyclonal anti-M.HpaII Larsen et al.34 N/A Rabbit polyclonal anti-PEX5 Romano et al.35 N/A Rabbit polyclonal anti-PNKP Stinson et al.17 N/A Rabbit polyclonal anti-FAF1 Kochenova et al.36 N/A Rabbit polyclonal anti-FAF1 Abcam Cat# ab202298 Rabbit polyclonal anti-UBXN7 Kochenova et al.36 N/A Rabbit polyclonal anti-NPL4 Kochenova et al.36 N/A Rabbit polyclonal anti-NPL4 Heubes et al.37 N/A Rabbit polyclonal anti-UFD1 Heubes et al.37 N/A Rabbit polyclonal anti-AND1 Antigen: xlAND1 846-1127 This paper; Pocono Rabbit Farm and Laboratory Custom Projects 35808 and 35809 Rabbit polyclonal anti-TRAIP-C Dewar et al.38 N/A Rabbit polyclonal anti-TRAIP-I Antigen: xlTRAIP 336-351 This paper; Vivitide Custom Project 4961 Rabbit polyclonal anti-LacI Antigen: LacI-Bio This paper; BioGenes GmbH Custom Projects 28548 and 28549 Rabbit polyclonal anti-p97 Heubes et al.37 N/A Rabbit polyclonal anti-H3 Cell Signaling Technology Cat# 9715; RRID: AB_331563 Mouse monoclonal anti-Ub Santa Cruz Biotechnology Cat# sc-8017; RRID: AB_628423 Rabbit monoclonal anti-K48 polyubiquitin Cell Signaling Technology Cat# 8081; RRID: AB_10859893 Rabbit monoclonal anti-K63 polyubiquitin Abcam Cat# ab179434; RRID:AB_2895239 Goat Anti-Rabbit IgG (H+L), HRPconjugated Jackson ImmunoResearch Cat# 111-035-003; RRID: AB_2313567 Mouse Anti-Rabbit IgG (L), HRPconjugated Jackson ImmunoResearch Cat# 211-032-171; RRID: AB_2339149 Rabbit Anti-Mouse IgG (H+L), HRPconjugated Jackson ImmunoResearch Cat# 315-035-003; RRID: AB_2340061 Mouse Anti-Rabbit IgG (H+L), unconjugated Jackson ImmunoResearch Cat# 211-005-109; RRID: AB_2339147 Streptavidin (HRP) Abcam Cat# ab7403 Bacterial and virus strains E. coli OverExpressTM C41(DE3) Chemically Competent Cells Sigma Cat# CMC0017 Chemicals, peptides, and recombinant proteins NEBuilder HiFi DNA Assembly Master Mix New England Biolabs Cat# E2621L IPTG Sigma Cat# I5502 DTT Bio-Rad Cat# 1610611 cOmpleteTM EDTA-free Protease Inhibitor Cocktail Roche Cat# 11873580001 (Continued on next page) Cell Reports 42, 112125, February 28, 2023 15
Techniques: Construct, Activation Assay, Ubiquitin Proteomics, Recombinant