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4 protocols using yeast extract

1

Culturing C. difficile and E. coli Strains

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C. difficile strains ATCC BAA-1804, ATCC BAA-1870, ATCC BAA-1803, ATCC BAA-1801, ATCC BAA-1875, ATCC BAA-1812, ATCC BAA-1814, ATCC 43598, and ATCC BAA-1382 were obtained from ATCC while C. difficile strain ATCC 9689 was acquired from Microbiologics. All strain stocks were stored at −80°C. Strains of C. difficile were grown anaerobically at 37°C in BHIS medium (37 g/liter brain heart infusion [BHI] [BD Biosciences], 5 g/liter yeast extract [Research Products International], 435 mg/liter L-cysteine hydrochloride monohydrate [RPI], 1g/liter sodium taurocholate [GoldBio]) and were maintained in cooked meat broth with iron, hemin, and vitamin K (Hardy Diagnostics). In cases where agar plating of C. difficile was necessary BHI agar with horse blood and taurocholate (Anaerobe Systems) were used. Escherichia coli strains were grown shaking (250 RPM) at 37C in Luria broth (RPI).
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2

Protein Expression and Purification Protocol

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All organic solvents (methanol, ethanol, acetone, dimethyl formamide (DMF) and, N,N-diisopropylethylamine (DIPEA)) were HPLC grade (Fisher Scientific) and used without further purification. E. coli cells (BL21 and NEB 5-alpha) were purchased from New England Biolabs. Lysozyme and Sephadex LH-20 were purchased from Sigma-Aldrich. BLUEStain protein ladder and ampicillin were purchased from Gold Biotechnology. Yeast extract, L-proline, tryptone, glycerol, and other bacterial culture media components were purchased from Research Products International. All materials for SDS-PAGE were obtained from Bio-Rad. PE/Cyanine7 anti-human EGFR antibody was purchased from BioLegend. Cy5.5 NHS ester was obtained from Lumi Probe. DMEM/F12, DMEM, fetal bovine serum (FBS), PenStrep, and other cell culture reagents were obtained from Corning Life Sciences.
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3

Yeast Strain Manipulation Techniques

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All yeast strains and plasmids (Supplementary file 1) were manipulated using standard techniques (Amberg et al., 2005 ). Yeast cells were cultivated in liquid or on solid agar plates of rich or synthetic media, as appropriate to maintain plasmid selection. Rich growth medium was YPD (1% yeast extract (#Y20020, Research Products International Corp., Mount Prospect, IL), 2% peptone (#P20241, RPI Corp.), 2% dextrose (#G32045, RPI Corp.)). Synthetic growth medium was based on YC (0.1 g/L Arg, Leu, Lys, Thr, Trp, and uracil; 0.05 g/L Asp, His, Ile, Met, Phe, Pro, Ser, Tyr, and Val; 0.01 g/L adenine; 1.7 g/L Yeast Nitrogen Base (YNB) without amino acids or ammonium sulfate; 5 g/L ammonium sulfate; 2% dextrose) with individual components (from Sigma Aldrich, St. Louis, MO, or RPI Corp.) eliminated as appropriate for plasmid selection. For solid media, agar (#A20030, RPI Corp.) was added to 2%. G418 sulfate (Geneticin, #G1000, US Biological) was added to YPD at 200 µg/mL for selection of kanMX. Mycophenolic acid (MPA) was added to YPD to a final concentration of 100 µg/mL of the active drug. Sporulation was induced in 1% potassium acetate, 0.05% glucose, 20 mg/L leucine, 40 mg/L uracil. Bacterial strain DH5alpha was used to propagate plasmids. Yeast transformation was performed using the Frozen-EZ Yeast Transformation Kit II (Zymo Research).
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4

Purification and Characterization of StsA

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Materials and reagents were purchased from
Gold Biotechnology, Fisher Scientific, or Sigma-Aldrich unless otherwise
noted. Yeast extract and tryptone were purchased from Research Products
International. Molecular biology reagents for cloning (e.g., restriction
enzymes, Q5 polymerase, T4 DNA ligase, and deoxynucleotides) were
purchased from New England Biolabs. Oligonucleotide primers and gene
blocks were obtained from Integrated DNA Technologies. DNA spin columns
were purchased from Epoch Life Sciences. Sanger sequencing was performed
by the Roy J. Carver Biotechnology Center (University of Illinois
at Urbana-Champaign). Polymerase chain reactions were performed using
a Bio-Rad S1000 thermal cycler. Escherichia coli DH5α and BL21(DE3) strains were used for plasmid maintenance
and protein overexpression, respectively. Expressed StsA was purified
using an Agilent 1200 series HPLC fitted with a 10 × 250 mm C18
column (Macherey Nagel). Mass spectroscopy was performed using a Bruker
Daltonics UltrafleXtreme MALDI-TOF mass spectrometer and a ThermoFisher
Scientific Orbitrap Fusion ESI-MS using an Advion TriVersa Nanomate
100.
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