L isoleucine

A pure standard solution of n‐alkanes (from n‐C7 to n‐C30) for linear retention indices (I^T) calibration and system quality control was from Merck (Milan, Italy) and prepared in toluene at the concentration of 100 mg L⁻¹.
The internal standard (IS) 1,4-dibromobenzene (from Merck, Milan, Italy) solution was prepared in toluene at a concentration of 10 g L⁻¹.
Pure reference standards used for identity confirmation of pyruvic acid, lactic acid, malonic acid, succinic acid, malic acid, 2-ketoglutaric acid, 3-hydroxybutyric acid, fumaric acid, 2-keto-3-metilvaleric acid, aspartic acid, hippuric acid, citric acid, uric acid, l-alanine, l-valine, l-leucine, l-proline, glycine, l-threonine, l-tyrosine, l-phenylalanine, l-isoleucine, l-methionine, l-cysteine, l-ornithine, l-tryptophan, xylitol, ribitol, fructose, galactose, glucose, mannitol, myo-inositol, glycerol, palmitic acid, stearic acid, and creatinine were from Merck (Milan, Italy).
Derivatizing agents O-methyl hydroxylamine hydrochloride (MOX), N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA), and LC-grade pyridine, n-hexane, dichloromethane, and toluene used as solvents were all from Merck (Milan, Italy).

Sucrose (the sugar), the bitter caffeine, the amino acids L-Aspartic acid, L-Glutamic acid, L-Glutamine, L-Lysine, L-Asparagine, L-Arginine, L-Methionine, L-Glycine, L-Threonine, L-Valine, L-Proline, L-Leucine, L-Phenylalanine, L-Histidine, L-Isoleucine, L-Serine, L-Glutamic acid monosodium salt (MSG), the ribonucleotides Inosine 5′-monophosphate (IMP) and Guanosine 5′-monophosphate (GMP) were purchased from Sigma Aldrich (Milwaukee,USA). All the chemicals are of analytical grade (>99.5%).

Catechin (C, ≥98%), galloCatechin (GC, ≥98%), galloCatechin-3-gallate (GCG, ≥98%), epiCatechin (EC, ≥98%), epiCatechin-3-gallate (ECG, ≥98%), epigalloCatechin (EGC, ≥98%), epigalloCatechin-3-gallate (EGCG, ≥98%), caffeine (CAF, ≥98%), theaflavins (TF, ≥95%), theaflavins-3-gallate (TF3G, ≥98%), theaflavin-3′-gallate (TF3′G, ≥98%), theaflavine-3,3′-digallate (TFDG, ≥98%), quercetin-3-O-galactoside (≥98%), myricetin-3-O-galactoside (≥98%), kaempferol-3-O-rutinoside (≥98%), vitexin (≥98%), astragaloside (≥98%), quercetin (≥98%), and kaempferol (≥98%) were purchased from Shanghai yuanye Bio-Technology Co., Ltd. (Shanghai, China). l-alanine, l-arginine, l-aspartic acid, l-cystine, l-glutamic acid, glycine, l-histidine, l-isoleucine, l-leucine, l-lysine, l-methionine, l-phenylalanine, l-proline, l-serine, l-threonine, l-tyrosine, l-valine, l-asparagine, l-glutamine, theanine, γ-aminobutyric acid, and l-tryptophan were purchased from Sigma (Sigma-Aldrich Co., St. Louis, MO, USA). Anthrone reagent and ninhydrin/formic acid reducing agent were purchased from BeiJing DingGuochangSheng Biotech. Co., Ltd. (Bejing, China). Ethyl caprate (≥99%) was purchased from Shanghai Macklin Biochemical Technology Co., Ltd. (Shanghai, China), and n-alkane mixed standard C7-C40 was purchased from o2si (o2si smart solutions—an LGC Standards Company, Charleston, SC, USA).

Sulfuric acid, sodium hydroxide, acetonitrile (Ultra high performance liquid chromatography (UHPLC) grade), ethylenediaminetetraacetic acid (EDTA), sodium borate, and hydrochloric acid were obtained from Panreac (Castelar del Vallés, Barcelona, Spain). Sodium acetate (anhydrous), trimethylamine (TEA), phosphoric acid, ammonium molybdate, and methyl cellulose were purchased from Sigma-Aldrich (Darmstadt, Germany). Standard of amino acids (L-arginine (Arg), L-alanine (Ala), L-asparagine (Asn), L-aspartic acid (Asp), glycine (Gly), L-glutamic acid (Glu), L-glutamine (Gln), L-histidine (His), L-isoLeucine (Ileu), Leucine (Leu), L-Lysine (Lys), L-norvaline (Nor), L-phenylalanine (Phe), L-proline (Pro), L-serine (Ser), L-threonine (Thr), L-tryptophan (Trp), L-tyrosine (Tyr), and L-valine (Val)) were purchased from Sigma-Aldrich (Steinheim, Germany). All the other chemicals and reagents used were of analytical grade.

The strain S. haloaromaticamans used in the current study was isolated from soil of a wastewater disposal site and it was able to degrade the fungicide OPP only when supplemented with CA (Perruchon et al., 2016 (link)). The bacterium was routinely cultivated in minimal salts media supplemented with nitrogen (MSMN), OPP (30–50 mg L^–1) and CA in a shaking incubator at 27°C in the dark. MSMN preparation and OPP chromatographic analysis was as described by Perruchon et al. (2016) (link), while bacterial growth was determined by measurement of the optical density at 600 nm (OD₆₀₀). Inoculation of flasks was performed by fresh bacterial cells grown at the mid-log phase, pelleted by centrifugation, washed three times with sterile ddH₂O and resuspended with MSMN to an OD₆₀₀ of 0.1.
L-methionine, L-isoleucine, L-tyrosine, L-phenylalanine, L-homoserine, O-succinyl-L-homoserine, L-cystathionine, L-homocysteine and cyanocobalamin (synonym to vitamin B12 in the manuscript), were purchased by Sigma-Aldrich (Taufkirchen, Germany) and they were used for the preparation of aqueous solutions (0.05 mM). These were filter sterilized and used for the preparation of MSMN containing amino acids, B12 and intermediates of methionine biosynthesis at the desired concentrations.

The parental wild-type yeast strain used in this study was BY4741. All gene deletions, genomic integrations, and plasmid transformations were done in this background using standard methods. For a complete list of strains used, see S1 Table.
Yeast cultures were grown at 30°C in YPD or synthetic defined (SD) media with appropriate nutrient dropouts. SD media used for growth of yeast cultures contained: 2% w/v dextrose (Thermo Fisher Scientific, Waltham, MA), 13.4 g/L Yeast Nitrogen Base without Amino Acids (BD Biosciences, San Jose, CA), 0.03 g/L L-isoleucine (Sigma-Aldrich, St. Louis, MO), 0.15 g/L L-valine (Sigma-Aldrich), 0.04 g/L adenine hemisulfate (Sigma-Aldrich), 0.02 g/L L-arginine (Sigma-Aldrich), 0.03 g/L L-lysine (Sigma-Aldrich), 0.05 g/L L-phenylalanine (Sigma-Aldrich), 0.2 g/L L-Threonine (Sigma-Aldrich), 0.03 g/L L-tyrosine (Sigma-Aldrich), 0.018 g/L L-histidine (Sigma-Aldrich), 0.09 g/L L-leucine (Sigma-Aldrich), 0.018 g/L L-methionine (Sigma-Aldrich), 0.036 g/L L-tryptophan (Sigma-Aldrich), and 0.018 g/L uracil (Sigma-Aldrich). Media additionally contained 5 mM or 10 mM guanidinium hydrochloride (Sigma-Aldrich) where indicated and bortezomib (LC Laboratories, Woburn, MA) treatment lasted 4 hours.