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5 protocols using rlysozyme

1

BRCA1 Fusion Protein Synthesis and Purification

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GST-BRCA1 fusion proteins were synthesized in Escherichia coli and purified on glutathione–sepharose beads (GE healthcare). NETN 250 (250 mM NaCl) precleared HeLa whole-cell extracts (XRN2 binding) or HeLa chromatin fractions (TERRA binding) were incubated with 2 μg of bead-bound GST fusion proteins or GST beads only. The immune complexes were then analyzed by SDS gel electrophoresis and immunoblotting.
Truncated GST-BRCA1-F3 fusion proteins or BRCA1 GST-F2-ΔNLS1 and GST-F2-R506S fusion proteins were generated in BL21(DE3) E. coli (Life Technologies) for 16 h at 30 °C using the Overnight Express Autoinduction system (Novagen). Bacterial pellets were incubated in BugBuster Master Mix (Millipore) supplemented with 1 KU/ml rLysozyme (Millipore), benzonase 25 U/ml (Millipore), and protease inhibitors for 30 min at room temperature (RT) at constant rotation and subsequently cleared by centrifugation. GST-tagged proteins were purified from bacterial lysates using Novagen BugBuster GSTBind Purification kit (Millipore) and used for TERRA pulldown assays.
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2

E. coli Strain Characterization and Enzymatic Assays

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Escherichia coli MET1158 strain, E. coli LW7 pLW11 and E. coli pBAC-LacZ were donated by Prof Karina Xavier (Instituto Gulbenkian de Ciência, Portugal), Prof. William Bentley (University of Meriland, USA) and Keith Joung (Addgene plasmid # 13422), respectively.
All chemicals were purchased from Sigma (USA) if not otherwise stated. DPD was acquired from Carbosynth (Compton, Berkshire, UK). PD-10 desalting columns and Protino® Ni-NTA columns (1 mL) for protein purification were purchased from GE Healthcare Lifescience (Chicago, IL, USA) and Macherey-Nagel (Düren, Germany), respectively. Pierce Coomassie Plus Assay Kit was obtained from Thermo Fisher Scientific (Waltham, MA, USA). ATP Bioluminescence CLS II kit was purchased from Roche Diagnostics GmbH (Basel, Switzerland), Kinase-Glo Max Luminescent kinase assay kit from Promega Corp. (Madison, WI, USA) and ADP-Quest kit from DiscoveRx Corp. (Fremont, CA, USA). PopCulture™reagent and rLysozyme™ were purchased from Millipore (Burlington, MA, USA). Plates were purchased from Greiner Bio One (KremsMünster, Austria), for assay development and screening campaign, and from Thermo Fisher Scientific (Waltham, MA, USA) for AI-2 QS interference assay.
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3

Enzymatic Analysis of Carbohydrates

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Monosaccharide
standards (xylose, glucuronic acid, arabinose, glucose, galactose,
and fucose), carboxymethyl-cellulose, Avicel PH-101, NAD+, NADP+, ATP, MgCl2, cellobiose, and 1-methoxy-5-methylphenazinium
methyl sulfate (mPMS, ref M8640) were purchased from Sigma-Aldrich.
Xylobiose (O-XBI), cellohexaose (O-CHE), aldouronic acids mixture
(O-AMXR), beechwood xylan (P-XYLNBE), wheat arabinoxylan (P-WAXYL),
endo-β-1,4-glucanase (E-CELBA), β-glucosidase (E-BGLUC),
a mixture of galactose dehydrogenase and galactose mutarotase (E-GALMUT),
uronate dehydrogenase (K-URONIC), α-glucuronidase (E-AGUBS),
xylose dehydrogenase (K-xylose), β-xylosidase (E-BXEBP), and
endo-β-1,4-xylanase (E-XYLNP) were purchased from Megazyme,
Ireland. Water-soluble tetrazolium salt (WST-1, ref W201-10) was purchased
from NBS Biologicals, Huntingdon, UK, while rLysozyme was sourced
from Merck and 1-bromo-3,5-bis(trifluoromethyl)benzene was from Alfa
Aesar. Glucokinase (AE00171), glucose-6-phosphate dehydrogenase (AE00111)
and arabinofuranosidase 51B from Cellvibrio japonicus (CZ0707) were purchased from NZYtech, Lisboa, Portugal.
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4

Disulfide Bond Formation in E. coli Cytoplasm

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To promote the formation of disulfide bonds in the cytoplasm of E. coli, the expression host Rosetta-gami 2 (DE3) was used, which carries the glutathione reductase (gor) and thioredoxin reductase (trxB) mutations (Novagen, 2011 ). The E. coli Rosetta-gami 2 (DE3) was transformed with the following pETDUET-1-cloned plasmids: HisPDI9-StrepIRE1ALD, HisPDI9-StrepIRE1BLD, HisPDI9, StrepIRE1ALD, and StrepIRE1BLD, including all aforementioned mutant constructs containing the specific cysteine to alanine substitution. Transformed cells were grown to approximately OD600nm = 0.5–0.6 and induced with 0.2 mM IPTG for 3 h at 30°C. After induction, cells were harvested for extraction of soluble proteins under nonreducing conditions using the BugBuster Protein Extraction Reagent (EMD Millipore, Burlington, MA, USA) supplemented with phenylmethylsulfonyl fluoride (PMSF), benzonase nuclease, and rLysozyme (EMD Millipore, Burlington, MA, USA).
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5

Microfluidic Generation of Monodisperse Droplets

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Monodisperse water-in-oil droplets were generated on flow-focusing chips with three inlets connected via PTFE tubing (0.38 mm ID, 1.09 mm OD, Portex) to glass syringes (SGE). These contained (a) 1.75% (v/v) 008-FluoroSurfactant (RAN Biotechnologies) in fluorinated oil HFE-7500, (b) 100 mM Tris-HCl pH 8.0, 100 mM NaCl, 50 μg/mL kanamycin supplemented with 0.8x CelLytic B and 30 kU/ml rLysozyme (Merck) as lysis agents, the fluorogenic substrate fluorescein-di-β-D-glucuronide (FD-β-GlcA, 10 μM), 100 nM fluorescein (as offset) and (c) the bacterial suspension. Flow control was achieved by low-pressure syringe pumps (neMESYS). The flow rates were set to 500 μL/h for oil and to 50 μL/h for the aqueous solutions, resulting in the generation of droplets with a volume of 4 pL at a rate of 6.6 kHz. The process was visually monitored under a microscope (Navitar) equipped with a camera (ALLIED Vision Technologies) and a high-speed Phantom camera (v7.2, Vision Research). A series of stills is shown in Supplementary Figure 4 to illustrate droplet formation.
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