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20 protocols using pet28a

1

Purification and Storage of LbCas12a and AsCas12

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LbCas12a was expressed and purified as previously described.[11] In brief, the coding sequences of LbCas12a were codon‐optimized and synthesized by Genscript (Nanjing, China) and then cloned into pET28a (Novagen) with a C‐terminal 10× His tag. The coding sequence of AsCas12 was synthesized by Genscript (Nanjing, China) as previously described.[26] The pET28a–Cas12a plasmid was transformed into Escherichia coli BL21 (DE3) and induced with 0.2 × 10−3m Isopropyl ß‐D‐1‐thiogalactopyranoside (IPTG) for 16 h at 18 °C before the cell harvesting. After cell pellets lysis, the Cas12a protein was purified using a Ni–NTA (Nickel‐nitrilotracetic acid) resin column and heparin sepharose column according to the manufacturer's instructions (G.E. Healthcare). Then the purified Cas12a protein was concentrated into storage buffer (50 × 10−3m Tris‐HCl, pH 7.5, 500 × 10−3m NaCl, 10% (v/v) glycerol, 2 × 10−3m dithiothreitol), quantitated using the BCA Protein Assay Kit (Thermo Fisher Scientific, MA, USA), and frozen at −80 °C until use.
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2

Recombinant Protein Expression for BRD Family

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The pET-28a(+) plasmid containing the BRD3 D1 and BRD3 D2 were purchased from GenScript. The Escherichia coli strain BL21 star(DE3) was transformed with the BRD3 D1 and BRD3 D2 plasmids and plated onto an agar plates containing kanamycin (100 mg/L) and chloramphenicol (35 mg/L). The plates were incubated overnight at 37 °C. A 5 mL LB culture with kanamycin(100 mg/L) and chloramphenicol (35 mg/L) was inoculated using a single colony from each plate and grown overnight at 37 °C and shaking at 220 rpm. Four primary cultures were used to inoculate 1 L of LB media containing chloramphenicol (35 mg/L) and kanamycin (100 mg/L) until the optical density at 600 nm had reached 0.6–0.8. At this point, an equilibration time of 30 min at 20 °C and 220 rpm was followed by the addition of 1 mM IPTG to induce protein expression. The culture was shaken for 16 h at 20 °C and 220 rpm. Cells were pelleted by centrifugation at 8000g and stored at −20 °C until purification. BRD4 D1, BRD2 D1, and BRDT D1 were expressed and purified as previous reported.33 (link)
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3

Recombinant Expression of Mif2 Proteins

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Expression of core histones was described previously (Mizuguchi et al. 2007 (link); Xiao et al. 2011 (link)). Plasmids expressing full-length Mif2 and truncated forms, residues 256–530 of the Mif2c dimer, residues 345–549, and residues 365–530, were a generous gift from S.C. Harrison (Cohen et al. 2008 (link)). Plasmids expressing Mif2 256–365 and 256–356 and the Mif2cath dimer with the AT-hook motif (residues 357–364) GRPRGRPK changed to AAADADAA were synthesized and cloned into the expression vector pET28a (Celtek Genes). Additional DHBD and human CENP-C motif constructs were also synthesized and cloned into pET28a (GenScript USA, Inc.). For more efficient removal of the His tag, the thrombin cleavage site of the original Mif2(256–530) plasmid was replaced with a precision proteinase cleavage site. Details are available on request.
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4

Recombinant PD-L1 and PD-1 Constructs

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Constructs encoding the extracellular regions of human PD-L1 D1D2 (18–237), PD-L D1 (18–134), and PD-1 (33–150) with a C-terminal avitag (GGLNDIFEAQKIEWHE) were synthesized and cloned into pET28a by GenScript. A C-terminal avitag construct of PD-L1 D1D2 (18–237) was produced by mutagenesis (https://openwetware.org/wiki/%27Round-the-horn_site-directed_mutagenesis, accessed February 2, 2022) (58 (link)). PD-L1 D2 (130–239) was cloned into the pLEICS-05 vector by PROTEX (University of Leicester). PD-L1 and PD-1 constructs were expressed and refolded as previously reported (6 (link)). Proteins were purified using a Superdex 75 26/600 gel filtration column (GE Healthcare) equilibrated in 25 mM KH2PO4, pH 7.4, 25 mM NaCl, and 10 μM EDTA. Isotopically labeled PD-L1 D1 was expressed in modified Spizizen’s minimal media (59 (link), 60 (link)), incorporating 15N-NH4Cl and 13C-glucose, and was refolded and purified as aforementioned.
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5

Construction and Expression of DHFR Variants

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Human DHFR cDNA fragments were inserted into the pTR1412 vector (Geffen et al., 2016) in frame after the URA3-HA-GFP fusion (Genscript). Full-length DHFR was expressed in yeast from pTR1412 lacking the URA3-HA-GFP fusion (Genscript). Point mutations were generated by Genscript. For expression of the Trx1 fusion proteins, the fragments were inserted in frame after myc-tagged TRX1 in the pESC vector (Genscript). For production of DHFR and DHFR variants in E. coli, codon optimized human DHFR was produced as a 6His-SUMO1 fusion from pET28a (Genscript).
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6

Engineered α-Glucanotransferase from T. uzoniensis

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4-α-Glucanotransferase from Thermoproteus uzoniensis (TuαGT, GenBank Accession WP_013679179.1) was produced recombinantly essentially as described [13 (link)]. Genes codon-optimised for Escherichia coli encoding full-length TuαGT connected N-terminally to the indicated SBD (SBDSt1, Uniprot Accession Q6R608_2 residues 3–112; SBDSt2, Uniprot Accession Q6R608_2 residues 147–259; SBDGA, Uniprot Accession P69328.1, residues 538–639) via an 18-residues linker (TTGESRFVVLSDGLMREM), that naturally connects the SBDSt1-SBDSt2 tandem with the CD in StDPE2 [14 (link)], were purchased and cloned into the expression vector pET-28a (+) using the restriction sites NheI and XhoI (GenScript, Leiden, The Netherlands) in frame with the N-terminal His-tag.
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7

Recombinant TDP1 Protein Production

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Synthetic DNA encoding human TDP1 (residues 149–608) [14 (link)] was cloned into pET-28a(+) (GenScript), which was then transformed into Escherichia coli BL21(DE3) for recombinant protein production. Protein production was induced with 1 mM isopropyl ß-D-1-thiogalactopyranoside (IPTG) at 28 °C with overnight incubation. TDP1 was purified using affinity and size exclusion chromatography. The purified protein was aliquoted and stored at −80 °C until use.
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8

Heterologous Expression of 3-epi-DON Genes

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Six potential candidates responsible for the transformation of 3-keto DON to 3-epi-DON activity were selected from Supplementary Table S1, their subcellular localization was predicted using PSORTb 3.0 (Yu et al., 2010 (link)) and SignalP 4.0 (Petersen et al., 2011 (link)); all proteins were predicted to be cytosolic. The genes were then codon optimized for synthesis in E. coli, synthesized and cloned into pET28A by Genscript (Piscataway, NJ, United States). The genes were inserted to pET28A using NdeI and BamHI restriction sites to produce proteins with N-terminal polyhistidine tags. Their protein sequences can be found in Supplementary Table S2. Each construct was transformed separately into E. coli BL21; a single colony was selected for protein expression.
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9

Membrane Scaffold Protein Variants for Nanodiscs

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Two variants of the membrane scaffold protein (MSP), needed for nanodisc assembly, were expressed and purified as described previously: MSP1E3D1, which contains three additional helices (repeats of helices 4, 5 and 6) compared to the MSP1D1 sequence (Denisov et al. 2007 (link)), and MSP1D1-Δh5, which lacks helix 5 of MSP1D1 (Hagn et al. 2013 (link)). The pET-28a MSP1E3D1 plasmid was obtained from Addgene (Addgene plasmid 20066). The nucleotide encoding MSP1D1Δh5 was obtained from GenScript and cloned into plasmid pET-28a (EMD) as described (Ding et al. 2015 (link)). The MSPs were purified by Ni-affinity chromatography and the C-terminal His tags were removed by proteolysis with tobacco etch virus.
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10

Codon-optimized TfNCS Expression in E. coli

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The codon-optimised gene encoding TfNCS (lacking 19 amino acids from the N-terminus) was integrated into the expression vector pET-28a(+) (GenScript, Nanjing, China) and introduced into Escherichia coli BL21 (DE3) cells (Novagen, Germany) for protein expression. The mutants mentioned above were obtained using site-directed mutagenesis of the WT gene. For protein expression, a single colony was cultured in Luria–Bertani (LB) medium at 37 °C for 12 h, and then 1 mL fresh culture was transferred into 100 mL Terrific-Broth (TB) medium. A 100 mL volume of TB medium contained with 12 g L−1 peptone, 24 g L−1 yeast extract, 5 g L−1 glycerol, 2.31 g L−1 KH2PO4 and 12.54 g L−1 K2HPO4. The working concentration of kanamycin in TB was 50 µg mL−1, and cultures were grown at 37 °C. When the OD600 of TB medium reached 0.6–0.8, 0.2 mM isopropyl β-d-thiogalactoside (IPTG) was added and culturing was continued at 16 °C for 20–24 h, cells were collected by centrifugation for subsequent experiments.
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