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Cysteine

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Cysteine is an amino acid that plays a crucial role in the structure and function of proteins. It contains a sulfhydryl group (-SH) that allows it to form disulfide bridges, which are important for the stabilization of protein structures. Cysteine is commonly used in various laboratory applications and can be found in a variety of Thermo Fisher Scientific's product offerings.

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21 protocols using cysteine

1

Folding and Purification of MVIIA Variants

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Crude peptides were all purchased from Beijing SciLight Biotechnology Ltd. Co.; glutathione (GSH), oxidized glutathione (GSSG), DTT, and cysteine were obtained from Gibco (Carlsbad, CA). All other reagents were analytically pure. All peptides were folded and purified as described previously [24 (link),25 (link)]. The amino acid sequences of MVIIA and its variants are listed in Scheme 1.
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2

Anaerobic Growth of ASF Bacteria

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ASF bacteria were grown under anaerobic conditions in supplemented BHI medium as previously described (Biggs et al., 2017 (link)). Frozen stocks of individual ASF strains were streaked on supplemented BHI agar plates [250mL of deionized water, 250mL of tap water, 18.5g of BBL™ BHI (BD Biosciences, 299070), 6.5g of Bacto™ agar (BD Biosciences, 214010), 2.5g of Bacto™ Yeast extract (BD Biosciences, 288620), 0.1 mL of vitamin K1 (Millipore Sigma, 95271) stock solution (1% vitamin K1 in absolute ethanol, stored at −80°C), 0.25mL of hemin (Millipore Sigma, 51280) stock solution (10mg/mL), 0.25g cysteine (Gibco, 810–1033IM), 25mL of FBS (ThermoFisher, 35010CV), 25mL of horse serum (ThermoFisher, 26050088) and 25mL sheep serum (Millipore Sigma, S2263)] and incubated in the anaerobic chamber at 37°C until growth was visible. Plates were kept moist by daily addition of 100uL of sterile reduced PBS to support the growth of fastidious strains.
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3

Isolation and Culture of Murine Chondrocytes

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Fresh cartilage tissues were isolated from the knee joints of newborn mice and digested for 6 h at 37 °C in DMEM F12 medium (Hyclone, Logan, UT, USA), which contained 10% FBS (Gibco, New York, NY, USA), P/S (meilunbio, Dalian, China), cysteine and collagenase P (Sigma, St. Louis, MO, USA), and the digestion was terminated by adding the complete medium to the basal digest. The digest was then collected and centrifuged at 200 g for 15 min. The supernatant was removed, the precipitate was resuspended in 10 mL DMEM F12 + P/S + FBS, and the suspension was filtered through a 100 mm Falcon filter in a fresh 50 mL test tube. Next, the pellet was resuspended in DMEMF12 + P/S + FBS by centrifuging the tube at 200 g for 5 min, and the suspension was filtered through a 40 mm Falcon filter into the used 50 mL tube. The filter was flushed with 10 mL DMEMF12 + P/S + FBS, and the suspension was again filtered through the used filter. The centrifugation and suspension cycles were performed twice. Finally, chondrocytes were obtained and inoculated in 6‐well plates at 5 × 105 cells·mL−1. Chondrocytes were cultured in a humidified environment supplemented with 10% FBS, 0.1% P/S, 50 mg·mL−1l‐ascorbic acid (Gibco, New York, NY, USA), and cysteine solution (35.1 mg·mL−1) containing 5% carbon dioxide at 37 °C. The culture medium was changed every 2 days.
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4

Metabolite Standards for Biochemical Analysis

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Metabolite standards were obtained at high purity. If not otherwise indicated, the product number refers to Sigma-Aldrich: sodium citrate (71635), sodium isocitrate (I1252), cis-aconitic acid (A3412), sodium α-ketoglutarate (K2010), sodium succinate (14160), succinic semialdehyde (Santa Cruz Biotechnology, F1114), sodium fumarate (F1506), L-malic acid (M6413), sodium pyruvate (P2256), oxaloacetic acid (O4126), iron acetate (FeAc, 339199), FeCl2 (372870), FeCl3 (157740), Fe(ClO4)2 (334081), Fe(ClO4)3 (309281), ferrocene (F408), FeS(268704), H3PO4 (P5811), 2-mercaptoethanol (Merck Millipore, 805740), cysteine (30095), DL-ethionine (E5139), dimethylsulfoxid (D8418), homocysteic acid (69453), NaHSO3 (Acros Organics, 41944), methionine (M9375), ammonium peroxydisulfate (Fischer Scientific, 10219790), sodium sulfite Na2SO3 (Fischer Scientific, 10070400), sodium sulfate Na2SO4 (Fischer Scientific, 10493372). All water was obtained commercially at UPLC-MS purity (Biosolve Chemicals, Cat no. 23214102).
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5

Metabolite Standards for Biochemical Analysis

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Metabolite standards were obtained at high purity. If not otherwise indicated, the product number refers to Sigma-Aldrich: sodium citrate (71635), sodium isocitrate (I1252), cis-aconitic acid (A3412), sodium α-ketoglutarate (K2010), sodium succinate (14160), succinic semialdehyde (Santa Cruz Biotechnology, F1114), sodium fumarate (F1506), L-malic acid (M6413), sodium pyruvate (P2256), oxaloacetic acid (O4126), iron acetate (FeAc, 339199), FeCl2 (372870), FeCl3 (157740), Fe(ClO4)2 (334081), Fe(ClO4)3 (309281), ferrocene (F408), FeS(268704), H3PO4 (P5811), 2-mercaptoethanol (Merck Millipore, 805740), cysteine (30095), DL-ethionine (E5139), dimethylsulfoxid (D8418), homocysteic acid (69453), NaHSO3 (Acros Organics, 41944), methionine (M9375), ammonium peroxydisulfate (Fischer Scientific, 10219790), sodium sulfite Na2SO3 (Fischer Scientific, 10070400), sodium sulfate Na2SO4 (Fischer Scientific, 10493372). All water was obtained commercially at UPLC-MS purity (Biosolve Chemicals, Cat no. 23214102).
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6

Glutathione and Cysteine Derivatives Analysis

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Glutathione was purchased from Alfa Aesar (Ward Hill, MA USA). Cysteine, ammonium formate, and 2,3-dimethoxy-5-methyl-1,4-benzoquinone (BQ) were obtained from Acros Organic (Geel, Belgium). HomoCysteine, penicillamine, cys-gly, γ-glu-cys, N-cyclohexylmaleimide and N-tert-butylmaleimide were purchased from Sigma Aldrich (Saint Louis, MO USA). Formic acid and ammonium hydroxide were obtained from Fisher Scientific (Pittsburgh, PA USA). LC-MS grade water and acetonitrile were from Honeywell Burdick and Jackson (Muskegon, MI USA).
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7

Culturing and Maintaining Legionella

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Strains, plasmids, and primers used in this study are listed in Table S4 in the supplemental material. L. pneumophila Philadelphia-1 laboratory-derived strain Lp02, a thymidine auxotroph, was cultured at 37°C in AYE broth and on ACES-buffered charcoal (Fisher)-yeast extract (Becton, Dickinson) (CYE) agar supplemented with 100 µg/ml thymidine (Sigma), 400 µg/ml cysteine (Fisher), and 135 µg/ml ferric nitrate (J. T. Baker) (51 (link)). thymidine was omitted when culturing thymidine prototroph strains. When necessary for antibiotic selection of mutants or plasmids, media were supplemented with kanamycin (Sigma) (10 µg/ml); chloramphenicol (Fisher) (5 µg/ml); or gentamicin (Gibco) (10 µg/ml). Where indicated, gene expression was induced by adding IPTG (Gold Biotechnology) to reach a final concentration of 200 µM. For all experiments, colonies were first inoculated into broth, incubated overnight, and diluted to an optical density at 600 nm (OD600) of 0.05 to 0.2 and then cultured to the E phase (OD600 of 1.0 to 2.0) or PE phase (OD600 of 3.7 to 4.0), as indicated.
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8

Cultivation and Genetic Manipulation of E. coli and C. difficile

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Escherichia coli strains were grown at 37°C in LB (Luria Broth, Difco Laboratories) [22 ]. E. coli TG1 was used as the host for plasmid constructions. E. coli HB101 (pRK24) was used for mating experiments. The following antibiotics (Eurobio) were added to the culture medium: kanamycin (40 mg L-1), ampicillin (100 mg L-1), chloramphenicol (12.5 or 25 mg L-1). C. difficile strains, 630Δerm [23 (link)],NF2184 (the cwp84 mutant strain, [ErR]) [9 (link)] and the NF2184 containing the pMTL960Ωcwp84 or the pVP75 plasmids, were grown at 37°C in Brain Heart Infusion (BHI) or BHIS+ glucose (BHI supplemented with Yeast Extract (5mg.ml-1, Difco), cysteine (0.1%; Fisher) and glucose (0.1 M; Sigma)). The following antibiotics were added to the culture medium: thiamphenicol (15 mg L-1, MP Biomedical), supplement (composed of 250 mg L-1 of D-cycloserine and of 8 mg mL-1 of cefoxitin, Oxoid), and erythromycin (5 mg L-1, sigma-aldrich). C. difficile strains were grown in anaerobic condition (90% N2, 5% CO2 and 5% H2; Messer) in anaerobic chamber. The CD1064, P30, 4684/08, 3457, 95–1078, R20291, VPI11186, CD196, 79685, CD4, IT1106 and 95–1578 come from our lab collection [19 (link)]. Ribotype analysis was performed by “CNR Bactéries anaérobies et botulisme (Clostridium difficile)—Laboratoire Associé” (Hopital Saint-Antoine, Paris) using the method described by Stubbs et al. [24 (link)].
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9

Cultivation and Diversity Analysis of Gut Microbiota

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B. bifidum LMG11041 was grown on selective media MRSc [De Man, Rogosa and Sharpe agar (VWR chemicals, USA)] supplemented with 0.25% (w/v) cysteine (VWR chemicals) and F. prausnitzii M21/2 in modified Brain Hearth Infusion (mBHI; Oxoid, UK). BHI medium was prepared following manufacturer instructions plus 5 g/L yeast extract (Oxoid), 0.05% (w/v) cysteine, 0.1% maltose (w/v) (Sigma-Aldrich, Germany), and 0.1% cellobiose (w/v) (Sigma-Aldrich).
For fecal microbiota viability and diversity assays 4 different media were used: GAMc, Gifu Anaerobic Medium (HyServe GmbH, Germany), plus 0.25% (w/v) cysteine; modified BHI supplemented (mBHIb) or not (mBHI) with 10% (v/v) defibrinated horse blood (Fisher scientific, USA) and Anaerobe Basal Medium (Oxoid) supplemented with 10% (v/v) defibrinated horse blood (ABMb). Differential colonies were selected attending to characteristics related mainly to their size, shape, elevation, margin, appearance, consistency, color and opacity.
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10

Cell Proliferation Assay under Amino Acid Deprivation

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Cells were plated at the density of 3000 cells/cm2 in standard medium and incubated overnight at 37°C and 5% CO2. After 18 h, cells were washed twice with phosphate-buffered saline (PBS) and, to verify the response to the cysteine or methionine deprivation, cells were incubated in medium without cysteine and methionine (Invitrogen Inc., Carlsbad, CA, USA), possibly supplemented with limiting concentration of cysteine (0.025, 0.05, 0.1 mM) or methionine (0.025, 0.1 mM) (Sigma Aldrich Inc.) or with antioxidants glutathione (0.08, 0.2, 0.8, 2, 4, 16 mM) or MitoTEMPO (10 μM) (Sigma Aldrich Inc.). To measure cell proliferation, cells were treated with trypsin at 0, 3, 6, 24, 30, 48, 54, 72 hours after medium change. Viable (i.e., unstained) cells were counted in a Bürker chamber after staining with 0.5% trypan blue. In amino acid re-feeding and foci formation experiments, qualitative evaluation of cell proliferation was obtained by staining with 0.2% Crystal violet (diluted in water from Giemsa Stain 0.4%, Sigma Aldrich Inc.). After 45 minutes of incubation in the dark at RT, cells were washed twice with water, photographed, and counted.
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