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44 protocols using coenzyme a

1

Enzymatic Loading of Acyl Carrier Proteins

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In vitro loading reactions were performed on 500 μM apo ACP9 samples by incubation with 5 μM recombinant Sfp [28 (link)], 2 mM coenzyme A or its derivatives malonyl, butyryl, 2-butenoyl, β-hydroxybutyryl, acetoacetyl, hexanoyl or octanoyl CoA (all Sigma) in pH 7.5 phosphate buffer with 10 mM magnesium chloride at 20°C for 1 h. 10 mM DTT was added when handling coenzyme A and holo mACP9 to prevent disulfide bond formation between exposed thiol groups. Samples were subjected to size exclusion chromatography as described above prior to further analysis. In each case, the identity and extent of modification was monitored by ESI MS (Supplementary Figures S3–S9).
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2

Cinnamate and Coumarin Synthesis Protocols

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The following acids were used: ferulic (Aldrich), coumaric (Sigma), cinnamic (Sigma), and caffeic (Fluka). coumarins used were: coumarin (Sigma), daphnetin (Sigma), esculetin (Sigma), esculin (Sigma), fraxetin (Extrasynthèse), fraxin (Extrasynthèse), isoscopoletin (Extrasynthèse), limetin (Herboreal), scoparon (Herboreal), 6-methoxycoumarin (Apin Chemicals), 7-methoxycoumarin (Herboreal), scopoletin (Herboreal), scopolin (Aktin Chemicals Inc.), umbelliferone (Extrasynthèse), skimmin (Aktin Chemicals Inc.), and 4-methylumbelliferon (Sigma). The CoA thiol esters of the cinnamates (cinnamoyl-CoA, p-coumaroyl-CoA, caffeoyl-CoA, and feruloyl-CoA) were enzymatically synthesized as described by Vialart et al. (2012) (link). P-coumarate and coenzyme A (CoA) were purchased from Sigma-Aldrich. Kanamycin, chloramphenicol, and isopropyl-β-d-thio-galactopyrannoside (IPTG) were purchased from Duchefa.
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3

Yeast Hexokinase Enzymatic Assay

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All buffers, reagents and cofactors (for example, bis-tris propane, glucose, limonene, pinene, sabinene, FBP, ATP, NAD(P)+, coenzyme A and so on) were purchased from Sigma-Aldrich. Yeast Hex (H6380) was from Sigma. Hexanes, isopropyl myristate and nonane were from ARCOS and were the highest grade available. Liquid and solid media for growth of E. coli was from Fisher Scientific (BD Difco).
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4

Metabolomic Standards for SAM and SAH

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S-(5′-Adenosyl)-l-methionine chloride dihydrochloride (A7007), crystalline S-(5′-Adenosyl)-l-homocysteine (A9384), Nicotinamide Adenine Dinucleotide Phosphate (N5755), Acetyl-Coenzyme A (A2056), Coenzyme A (C4812) and Flavine Adenine Dinucleotide (F6625) were obtained from Sigma-Aldrich. Nicotinamide Adenine Dinucleotide (10127964001) was from Roche Basel, Switzerland. The metabolomics standard SAMd3 (D-4093) was bought from CDN Isotopes Pointe-Claire, Canada, SAHd4 was from Cayman Chemical (9000372); tritiated SAM-[methyl-2H] at 250 μCi (NET155V250UC) was from PerkinElmer Waltham, US. Pierce™ Trypsin, MS-grade (90059) was from ThermoFisher Scientific Waltham, US.
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5

Metabolic Modulation in Cancer Cells

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DCA, 3-bromopyruvate, sodium pyruvate, coenzyme A, glutamine, uridine and daunomycin were purchased from Sigma. Dulbecco’s Modified Eagle’s Medium (DMEM) and fetal bovine serum (FBS) were purchased from GIBCO. 14C-6-glucose was purchased from Moravek Biochemicals. Mouse monoclonal anti-P-glycoprotein was purchased from Santa Cruz Biotechnology and rabbit polyclonal anti-PDK2 was purchased from Protein Tech. 99mTc-MIBI (methoxyisobutylisonitrile) was purchased from Shanghai Hinko and 18 F-fluorodeoxyglucose was produced in our laboratory.
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6

Enzymatic Assay for IpfF Activity

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To detect the CoA activity of IpfF with different substrates, IpfF was purified in the same manner as described by Aguilar-Romero et al. [3 (link)]. The assays were performed with 1 mg purified IpfF in 50 mM Tris-HCl pH 7.5, with 0.5 mM substrate, 0.5 mM Coenzyme A (Sigma-Aldrich, Steinheim, Germany), 1 mM ATP (Sigma-Aldrich, Steinheim, Germany), 2 mM MgCl2, and 0.2 mM DTT. The enzymatic reactions were performed at room temperature (25–27 °C) for 35–58 min and the depletion of substrates and the formation of products were analyzed by HPLC (see Section 2.7).
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7

Enzymatic Assay for Acetylation Activity

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ATP, Coenzyme A, NAD+, L-malic acid, citrate synthase (CS), and malate dehydrogenase (MDH) were purchased from Sigma. The acetic acid detection kit was purchased from R-biopharm. Fluor de Lys peptide and the developing reagent were purchased from Enzo Life Sciences. The unlabeled peptides (Ac-KGGAKac-COO, Ac-KGGAKac-NH2, and Ac-KGGAKacW-NH2) were purchased from Peptide2.0 (>85 % purity). Cobalt and magnesium were purchased as ICP standards from GFS Chemicals and the acetic acid standard was purchased from the Ricca Chemical Company. Chelex 100 resin was purchased from Bio-Rad. HDAC3/NCOR1 was purchased from Enzo Life Sciences. Ethylenediaminetetraacetic acid (EDTA) was purchased from Sigma-Aldrich at >99 % purity. All other materials were purchased from Fisher and were of a purity >95 % unless otherwise noted.
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8

Synthesis and Characterization of Carboxylic Acid Derivatives

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3-pyridinemethanol, potassium tert-butoxide, toluene, dichloromethane, ethylmalonic acid, 2,2-dimethylmalonic acid, methylsuccinic acid, glutaric acid, n-adipic acid, n-suberic acid, n-sebacic acid, n-octanoylglycine, n-decanoylglycine, glycine methylester hydrochloride, 2-ethylhexanoic acid, 2-ethyloctanoic acid, 4-ethyloctanoic acid, tetrahydrofurane, carbonyldiimidazole, 2-mercapto-ethanol, 2-(N-morpholino) ethanesulfonic acid (MES) monohydrate, and coenzyme A were from Sigma-Aldrich (now Merck). ethylmalonic acid (methyl-d3) was from Cambridge Isotope Laboratories. Methanol, acetonitrile, isopropanol (MS-grade), formic acid, and ammonium formate (all MS-grade) were from Biosolve. n-Hexane was from VWR chemicals. Ethylmalonyl-CoA was from CoALA Biosciences. Hydrochloric acid (37%) was from Merck. 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDAC) was from Thermo Fisher Scientific.
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9

NMT1 Inhibitor Screening Assay

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For screening of NMT1 inhibitors or the measurement of IC50, the 1× reaction buffer (50 mM HEPES and 0.5 mM EDTA), 140 nM of NMT1 purified enzyme (See the NMT1 purification Section, the enzyme stock was preserved in the buffer containing 1mM EDTA, 250 mM NaCl, and 20 mM Tris pH 8.5), 5 µM of peptide Gly-Ser-Asn-Lys-Ser-Lys-Pro-Lys (derived from the N-terminus of human pp60Src tyrosine kinase), and the inhibitor at 0, 10, 20, 40, 80, 120, 160, or 200 µM respectively were mixed in a 96-well plate. After incubation at 30 °C for 10 min, the reaction was started by adding 1 µM myristoyl coenzyme A (Avanti Polar Lipids). The total volume of the above mixture was set 80 µL/well. After incubation at 30 °C for 60 min, the released coenzyme A was detected by adding 80 µL of 30 µM of 7-diethylamino-3-(4’-maleimidylphenyl)-4-methylcoumarin (CPM) stock solution (Sigma Aldrich) to each well and incubated in the dark for 12 min. The fluorescence intensity was measured by a Flex Station 3, microplate reader (excitation at 390 nm; emission at 479 nm).
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10

Purification of Pyruvate Dehydrogenase Complex

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Sodium pyruvate, thiamine pyrophosphate (TPP), dichloromethane, coenzyme A (CoASH), CAPS (3-(cyclohexylamino)-propanesulfonic acid), EPPS (N-(2-hydroxyethyl)-piperazine-N′-3-propanesulfonic acid), lysozyme, porcine pyruvate dehydrogenase (PDH), and methyl viologen (MV) were purchased from Sigma-Aldrich Canada Ltd. (ON, Canada). Desulfocoenzyme A was synthesized [33 (link)]. DNase I for the cell lysis buffer preparation was obtained from Roche (Roche Applied Science, QC, Canada). The chemicals used in the growth media were all commercially available. Yeast extract was acquired from EMD (EMD Chemicals, Inc., NJ, USA) and Trypticase soy broth (TSB) was purchased from Becton-Dickinson (BD Bioscience, Mississauga, ON, Canada). All of the FPLC columns and chromatographic media were purchased from GE Healthcare (QC, Canada). The Hydroxyapatite chromatography material, Bradford reagent, acrylamide, and molecular weight standards were purchased from Bio-Rad Laboratories (ON, Canada).
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