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5 protocols using yeast synthetic drop out medium

1

Cultivation and Transformation of S. boulardii

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For transformations S. boulardii was cultured in yeast-peptone-dextrose (YPD) medium (10 g/L yeast extract, 20 g/L casein peptone and 20 g/L glucose (Sigma Aldrich)). Transformations were streaked on synthetic complete medium without uracil plates (SC U-; 6.7 g/L yeast nitrogen base without amino acids, 1.92 g/L Yeast Synthetic Drop-out Medium without uracil, 10 g/L agar and 20 g/L glucose (Sigma Aldrich)) or SC U- supplemented with geneticin (1.7 g/L yeast nitrogen base without amino acids and ammonium sulphate, 1 g/L monosodium glutamate, 1.92 g/L Yeast Synthetic Drop-out Medium without uracil, 200 mg/L geneticin (G418), 10 g/L agar and 20 g/L glucose (Sigma Aldrich)). In vitro characterisations were cultured in synthetic complete (6.7 g/L yeast nitrogen base without amino acids, 1.6 g/L Yeast Synthetic Drop-out Medium without leucine and 76 mg/L leucine) with one of the following carbon sources as appropriate 20 g/L glucose, 20 g/L fructose, 19 g/L sucrose, 16 g/L inulin or 32.4 g/L sodium acetate (Sigma Aldrich). E. coli was cultured in LB supplemented with 100 mg/L ampicillin sodium salt (Sigma Aldrich). All cultures were incubated at 37 °C and 250 rpm.
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2

Yeast Choline Uptake via HNM1

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S. cerevisiae acquires choline via HNM1. The S. cerevisiae Hnm1 mutants were acquired from Dharmacons. WT and Hnm1 mutant yeasts were grown in Yeast extract-Peptone-Dextrose (YPD) medium at 30 °C overnight before transformation. The pESC-HIS-hMfsd7c plasmid was transformed into WT and Hnm1 mutant yeasts following the previously described protocol.43 (link) After heat shock at 42 °C for 30 min and recovery in YPD for 2 h, the yeasts were spread on 2% agar plates prepared in yeast nitrogen base (YNB) medium (Sigma-Aldrich) supplemented with 2% glucose and yeast synthetic drop-out medium supplements without histidine (Sigma-Aldrich). Positive colonies were picked up randomly and further confirmed by transport assay and western blot.
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3

Glutathione Redox State and Mitochondrial Morphology

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The glutathione redox state has been tested on 105 cells·mL −1 grown in SC (0.67% w/v yeast nitrogen base with aminoacids, 2% w/v dextrose; Sigma-Aldrich, St. Louis, MO, USA) medium, treated for 24 h with 50 mg·L−1 of CdS QDs; the cellular extract and glutathione levels were determined as described in Pasquali et al. (2017) [20 (link)]. To determine the mitochondrial morphotype wild type strain, tolerant and sensitive mutants were transformed with the plasmid pYX-142 mtRFP as described by Pasquali et al. (2017) [20 (link)]. Each strain was grown in the selective SC-LEU medium (0.67% w/v yeast nitrogen base w/o aminoacids, 0.16% w/v yeast synthetic drop-out medium supplement w/o leucine, 2% w/v dextrose; Sigma-Aldrich, St. Louis, MO, USA) containing 50 mg·L−1 of CdS QDs, for a 24 h treatment. Microscope images were taken using an Axio Imager 2 (Zeiss, Oberkochen, Germany). The experiments were performed in triplicate. Additional methods related to the growth characteristics data of the wild type strain, and the tolerant and sensitive mutants are reported in the Supplementary Materials.
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4

Propagation and Culture of E. coli and S. cerevisiae

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E. coli DH5ɑ was used for propagating all plasmids and grown at 37 °C in Luria Broth (LB) medium containing the appropriate antibiotics for plasmid selection (ampicillin 100 μg/mL, chloramphenicol 34 μg/mL, or kanamycin 50 μg/mL). S. cerevisiae strain BY474139 (link) (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0) was used for all yeast experiments. For succinic acid experiments, fully complemented yeast strains were created by restoring the missing auxotrophic markers on a single-copy plasmid37 (link). Yeast extract peptone dextrose (YPD) was used for culturing cells in preparation for transformation: 1% (w/v) Bacto Yeast Extract (Merck), 2% (w/v) Bacto Peptone (Merck), 2% glucose (VWR). Fluorescent reporter assay experiments were performed in synthetic complete (SC) medium: 2% (w/v) glucose (VWR), 0.67% (w/v) Yeast Nitrogen Base without amino acids (Sigma), 0.14% (w/v) Yeast Synthetic Drop-out Medium Supplements without histidine, leucine, tryptophan, and uracil (Sigma), 20 mg/L uracil (Sigma), 100 mg/L leucine (Sigma), 20 mg/L histidine (Sigma), and 20 mg/mL tryptophan (Sigma). Succinic acid production experiments were performed in synthetic minimal (SD) medium: 2% (w/v) glucose (VWR), and 0.67% (w/v) Yeast Nitrogen Base without amino acids (Sigma).
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5

Bacterial and Yeast Culture Conditions

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The chemically competent Escherichia coli DH5α strain was used for plasmid
propagation and cloning. E. coli strains
were grown in 2xYT media supplemented with 100 μg/mL ampicillin
at 37 °C and 250 rpm. Yeast was grown in a synthetic complete-dropout
medium, made with 6.7 g/L yeast nitrogen base without amino acids
(Sigma), 1.4 g/L yeast synthetic dropout medium supplements (Sigma)
lacking uracil, histidine, leucine, and tryptophan, supplemented with
2% w/v glucose. Histidine, uracil, leucine, and tryptophan were added
as needed for auxotrophic selection. Yeast in preculture tubes was
grown at 30 °C and 250 rpm, while incubation in 96-well deep
plates took place at 30 °C and 300 rpm.
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