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81 protocols using mono q

1

Purification of Ctf4 Protein Complexes

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Cleared lysate containing His-tagged full-length Ctf4 or Ctf4CTD was incubated with 1 ml Ni-NTA resin (QIAGEN), washed with 20 ml Buffer A (50 mM NaH2PO4 pH 8.0, 300 mM NaCl, 20 mM imidazole) and eluted five times each with 1 ml Buffer A containing 250 mM imidazole. The resulting elution was dialysed in 2 L 100 mM NaCl, 20 mM Tris pH 8.0, 1 mM DTT for 2 hours with fresh buffer exchanged after the first hour. The dialysed elution was further purified by Mono Q (GE Healthcare) ion exchange through a 0.1-1 M NaCl gradient in 20 mM Tris pH 8.0, 1 mM DTT over 40 ml with 0.5 ml elutions. Peak fractions from the Mono Q were concentrated and polished via Superdex 200 16/600 HiLoad or 10/300 GL (GE Healthcare) size exclusion chromatography in Buffer B (150 mM NaCl, 20 mM Tris pH 8.0). Peak elutions were pooled and concentrated to 5 mg/ml and stored at −80°C in 2 nmol aliquots.
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2

Purification of Mutant RNAP Holoenzymes

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For experiments in Fig. 1B, [531Ser→Leu]β-RNAP σ70 holoenzyme was prepared from E. coli strain XE54 (Tang et al., 1994 (link)) transformed with plasmid pRL706-531L [constructed from plasmid pRL706 (Severinov et al., 1997 (link)) by use of site-directed mutagenesis (QuikChange Site-Directed Mutagenesis Kit; Agilent)], using culture and induction procedures, polyethylenimine precipitation, ammonium sulfate precipitation, immobilized-metal-ion affinity chromatography on Ni-NTA agarose (Qiagen), and anion-exchange chromatography on Mono Q (GE Healthcare), as in Niu et al., 1996 (link).
For experiments in Fig. S3C, E. coli RNAP σ70 holoenzyme and [565Glu→Asp]β-RNAP σ70 holoenzyme were prepared from E. coli strain XE54 (Tang et al., 1994 (link)) transformed with plasmid pRL706 (Severinov et al., 1997 (link)) or pRL706-565D (Zhang et al., 2014 (link)), using the same procedures.
For experiments in Fig. 3D, E. coli RNAP σ70 holoenzyme was prepared from E. coli strain XE54 (Tang et al., 1994 (link)) transformed with plasmid pREII-NHα (Niu et al., 1996 (link)), using culture and induction procedures, polyethylenimine precipitation, ammonium sulfate precipitation, immobilized-metal-ion affinity chromatography on Ni-NTA agarose (Qiagen), and anion-exchange chromatography on Mono Q (GE Healthcare), as in Degen et al., 2014 (link).
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3

Purification of T. thermophilus RNAP

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T. thermophilus RNAP core enzyme was prepared was prepared from T. thermophilus strain H8 (DSM 579; DSMZ), using polyethylenimine precipitation, ammonium sulfate precipitation, cation-exchange chromatography on SP Sepharose FF (GE Healthcare), anion-excahnge chromatography on Mono Q (GE Healthcare), and cation-exchange chromatography on Mono S (GE Healthcare); T. thermophilus σA was prepared from E. coli strain BL21(DE3) transformed with pET28a-Tt-σA, using immobilized-metal-ion affinity chromatography on Ni-NTA agarose (Qiagen) and anion-exchange chromatography on Mono Q (GE Healthcare); T. thermophilus RNAP core enzyme and T. thermophilus σA were combined to yield T. thermophilus RNAP σA holoenzyme; and T. thermophilus RNAP σA holoenzyme was further purified using size-exclusion chromatography on Superdex 200 (GE Healthcare), as in Zhang et al., 2014 (link).
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4

Purification of Ctf4 Protein Complexes

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Cleared lysate containing His-tagged full-length Ctf4 or Ctf4CTD was incubated with 1 ml Ni-NTA resin (QIAGEN), washed with 20 ml Buffer A (50 mM NaH2PO4 pH 8.0, 300 mM NaCl, 20 mM imidazole) and eluted five times each with 1 ml Buffer A containing 250 mM imidazole. The resulting elution was dialysed in 2 L 100 mM NaCl, 20 mM Tris pH 8.0, 1 mM DTT for 2 hours with fresh buffer exchanged after the first hour. The dialysed elution was further purified by Mono Q (GE Healthcare) ion exchange through a 0.1-1 M NaCl gradient in 20 mM Tris pH 8.0, 1 mM DTT over 40 ml with 0.5 ml elutions. Peak fractions from the Mono Q were concentrated and polished via Superdex 200 16/600 HiLoad or 10/300 GL (GE Healthcare) size exclusion chromatography in Buffer B (150 mM NaCl, 20 mM Tris pH 8.0). Peak elutions were pooled and concentrated to 5 mg/ml and stored at −80°C in 2 nmol aliquots.
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5

Fluorescent Labeling of A24C PepQ

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A24C PepQ was labelled using either 5-iodoacetamidofluorescein (fluorescein, F), 5-(2-acetamidoethyl) aminonaphthalene 1-sulfonate (EDANS, ED), tetramethylrhodamine-5-iodoacetamide dihydroiodide (tetramethylrhoadmine, TMR), or Oregon Green 488 iodoacetamide (Oregon Green, OG). All dyes were obtained from Invitrogen (Molecular Probes). PepQ (∼10 mg ml−1 in 50 mM Tris, pH 8, 100 mM KCl, 1 mM MgCl2) was reduced with 0.5 mM tris(2-carboxyethyl)phosphine (TCEP) TCEP and labelled with a 10-fold excess of reactive dye, added in 1 addition for 3 h at 23°C. The reaction was quenched by adding glutathione (5 mM), and the labelled PepQ was first separated from unbound dye by gel filtration (PD-10 column, Pharmacia), followed by re-purification of the labelled protein with high-resolution ion exchange chromatography (MonoQ, GE). The extent of labelling was determined by protein quantification by the Bradford assay (Bio-Rad) and dye quantification under denaturing conditions using known dye molar extinction coefficients37 (link)63 (link). Unique labelling of a single cysteine was verified by both denaturing anion exchange chromatography (MonoQ, GE) in 8 M urea buffer and by detection of a single major and fluorescent tryptic peptide upon separation by C8 reverse-phase chromatography63 (link).
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6

Purification of Thermus thermophilus RNAP

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T. thermophilus RNAP core enzyme was prepared from T. thermophilus strain H8 (DSM 579; DSMZ), using cell lysis, polyethylenimine precipitation, ammonium sulfate precipitation, cation-exchange chromatography on SP Sepharose FF (GE Healthcare), anion-exchange chromatography on Mono Q 10/100 GL (GE Healthcare), and cation-exchange chromatography on Mono S HR (GE Healthcare), as in Zhang et al., 2012 (link) and Maffioli et al., 2017 (link).
T. thermophilus σA was prepared by co-expression of a gene for N-terminally hexahistidine-tagged T. thermophilus σA in E. coli, followed by cell lysis, immobilized-metal-ion affinity chromatography on Ni-NTA agarose (Qiagen) and anion-exchange chromatography on Mono Q (GE Healthcare), as in Zhang et al., 2012 (link).
T. thermophilus RNAP σA holoenzyme was prepared by combining T. thermophilus RNAP core enzyme and T. thermophilus σA, followed by size-exclusion chromatography on Superdex 200 (GE Healthcare), as in Zhang et al., 2014 (link).
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7

Recombinant Protein Purification and Activation

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InpA was produced as a recombinant protein in Escherichia coli and purified as previously described [12 (link), 13 (link)] by affinity chromatography on Fast Flow Ni-NTA (Ni2+-nitrilotriacetate)–Sepharose (Qiagen) followed by anion exchange chromatography (MonoQ, GE Healthcare). The active concentration of InpA was determined by active-site titration using an appropriate dilution of a standardized 1 mM aqueous solution of the protease inhibitor N-(trans-epoxysuccinyl)-L-leucine 4-guanidinobutylamide (E-64) (Sigma-Aldrich; product E3132) needed for total inactivation of the proteinase. Residual enzyme activity was determined by measurement of fluorescence (λex = 380 nm and λem = 460 nm) of AMC (7-amino-4-methylcoumarin) released from t-butoxycarbonyl-Val-Leu-Lys-AMC as described previously [13 (link)]. Immediately before use, InpA was activated by incubation for 15 min with 3 mM DTT in 0.1 M Tris–HCl, 0.14 M NaCl, pH 7.5 [50 ]. When used for protein breakdown assays under non-reducing conditions, the above buffer was exchanged for that without reducing agent by ultrafiltration using 10 kDa cut-off Microcons (Amicon).
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8

Purification and Application of Trypanosomal Substrate

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TS was expressed in Escherichia coli BL21 and purified to homogeneity by immobilized metal affinity chromatography through Ni2-charged Hi-Trap chelating columns (GE Healthcare) and ion-exchange chromatography (Mono Q; GE Healthcare) as described previously, followed by passage through a polymyxin column (Pierce) for endotoxin depletion (Leguizamon et al., 1999 (link)). As described above (Section Timeline of HIV/Trypanosoma cruzi Co-infection Assays), astrocytes were exposed to 1 μg/ml of TS (active, or inactive isoform) according the Tc/HIV timeline (Figure 2A) replacing trypomastigotes.
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9

Recombinant XPA Protein Purification

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Human XPA was cloned into pET32a vector (Novagen) with a cleavable TRX-6XHis-S tag at the N terminus and expressed in Rosetta2 cells (Invitrogen). Protein expression was induced by the addition of 0.5 mM IPTG and 50 μM ZnCl2 at 15°C for 16 hr. The cells were lysed by EmulsiFlex-C5. XPA was purified using HisTrap columns (GE Healthcare) before and after removing the affinity tag by PreScission Protease. The tag-free XPA was further purified with Mono Q and Superdex 200 columns (GE Healthcare). XPA peak fractions in 20 mM Tris (pH 7.4), 150 mM NaCl, 25 μM ZnCl2, 1mM DTT were pooled and concentrated to 10 mg/ml for storage at −80°C. For activity assays, XPA was thawed and purified over a Superdex 75 column (GE Healthcare) in 25 mM Tris (pH 7.5), 150 mM NaCl, 2 mM DTT, and 5% glycerol.
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10

Purification and Biotinylation of FmlH Lectin

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FmlH protein used in crystallographic studies was expressed and purified as previously described. Briefly, protein was expressed in the periplasm of E. coli C600 cells containing pTRC99a encoding the first 182 amino acids of the CFT073 FmlH protein (corresponding to the signal sequence and lectin domain) and a C-terminal 6x-his tag. Periplasmic isolates were prepared as previously described and were washed over a cobalt affinity column (GoldBio) and eluted in 20 mM Tris 8.0 + 250 mM imidazole. Fractions containing protein of the expected molecular weight were then diluted 5-fold in 20 mM Tris 8.0 to a final concentration of 50 mM Imidazole, washed over an anion exchange column (GE Healthcare Mono Q) with 20 mM Tris 8.0, and eluted in 20 mM Tris 8.0 + 250 mM NaCl. Resulting fractions were pooled and dialyzed in 1 mM HEPES pH 7.5 + 50 mM NaCl and concentrated as needed for further study. Protein used in ELISA assays was biotinylated using anNHS-PEG4-Biotin and Biotinylation Kits (ThermoFisher).
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