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Acyl coa

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Acyl-CoAs are a class of organic compounds that serve as important intermediates in various metabolic pathways, including fatty acid metabolism and energy production. These molecules are composed of a fatty acid chain attached to the coenzyme A (CoA) group. Acyl-CoAs play a crucial role in the process of beta-oxidation, where they are used as substrates for the breakdown of fatty acids to generate energy for the cell.

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12 protocols using acyl coa

1

Malonyl-CoA and Radiolabeled Acetate Protocol

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Malonyl coenzyme A (malonyl-CoA), acyl-CoAs, fatty acids, NADH, NADPH, and antibiotics were purchased from Sigma-Aldrich (St. Louis, MO, USA); Takara Biotechnology Co., Ltd. (Dalian, China) provided molecular biology reagents; the Ni2+-agarose columns were purchased from Invitrogen (Shanghai, China); American Radiolabeled Chemicals, Inc. (St. Louis, MO, USA) provided sodium [1-14C] acetate (specific activity, 50 mCi/mM); and Bio-Rad (Hercules, CA, USA) provided the Quick Start Bradford dye reagent. All other reagents were of the highest available quality.
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2

Acyl-CoA Chloramphenicol Acetyltransferase Assay

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Acyl-CoAs were purchased from Sigma, and E. coli CAT was purchased from Promega (part # E1051). The reaction contained 1.25 unit of CAT (one unit is defined as the amount of enzyme required to transfer 1 nmol of acetate to chloramphenicol in one minute at 37 °C), 250 μM acyl-CoA, 280 μM chloramphenicol, in 100 μl of 100 mM Tris buffer, pH 7.8. A reaction without CAT was served as control. The reaction was incubated at 37 °C for 2 h, and ethyl acetate (100 μL) was added to stop the reaction. The mixture was centrifuged (10,000 × g) for 10 min, and the ethyl acetate phase was collected and dried under a N2 flow. Methanol (100 μL) was added to dissolve the residues, and a fraction (20 μL) of the methanol solution was injected into HPLC for analysis (Agilent 1200 with a ZORBAX SB-C18 column, 4.6 mm × 150 mm, 5 μ). Acetonitrile (solvent B) and water (solvent A) were used as the mobile phases with a flow rate of 1.0 mL/min. The program was as follow: 10% B for 5 min, 10–90% B in A over 20 min, 90–100% B in A over 1 min, 100% B for 4 min, 100–10% B in A over 4 min, 10% B for 4 min. The detection wavelength was 220 nm. The peak integration area of the acylated chloramphenicol products on HPLC was used to calculate the conversion rate of each of the reactions with a different acyl-CoA substrate.
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3

Recombinant Protein Purification Protocol

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Malonyl-CoA, acetyl-CoA, acyl-CoAs, fatty acids, NADH, NADPH, and antibiotics were purchased from Sigma-Aldrich. Takara Biotechnology Co. provided molecular biology reagents. Novagen provided the pET vectors. Ni-agarose columns were obtained from Invitrogen. GE healthcare provided the HiTrap Q strong anion-exchange column and Bio-Rad provided the Quick Start Bradford dye reagent. All other reagents were of the highest available quality. Takara Biotechnology Co. synthesized the oligonucleotide primers.
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4

Bacterial Growth, Reagents, and Enzymes

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Escherichia coli (DH5α, Invitrogen Life Technology, Carlsbad, CA; BLR (DE3), EMD Biosciences, Madison, WI) were grown in Luria Broth (Invitrogen Life Technology) media. Organic acids, acyl-CoAs, antibiotics, and oligonucleotide primers were purchased from Sigma-Aldrich (St. Louis, MO). Restriction enzymes were bought from New England Biolabs (Ipswich, MA).
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5

DNase I Footprinting Assay Protocol

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All acyl-CoAs were purchased from Sigma–Aldrich. Oligonucleotides used in this study were synthesized by Invitrogen and are listed in Table S1. Double-stranded Omft, and mutants thereof, were prepared from single-stranded oligonucleotides by mixing two oligos in equal molar amounts, heating the mixed oligos for 5 min at 95 °C and then gradually cooling the oligos to the room temperature. DNase I footprinting assays were contracted to Profacgen.
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6

Enzymatic Synthesis and Purification of Acyl-CoA Thioesters

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Acyl-CoAs (C4:0, C6:0, C8:0, C10:0, C12:0), coenzyme A sodium salt, malonyl-CoA, succinyl-CoA, succinate, malonate, Percoll, streptozotocin (STZ), 5,5-dithio-bis(2-nitrobenzoic acid) (DTNB), PEG 1500, and defatted bovine serum albumin (BSA) were purchased from Sigma. 10,12-tricosadiynoic acid (TDYA) and dodecanedioic acid (DCA12) were from Tokyo Chemical Industry. The mono-CoA thioesters of dodecanedioic acid (DC12-CoA), sebacic acid (DC10-CoA), suberic acid (DC8-CoA), and adipic acid (DC6-CoA) were enzymatically prepared by a microsomal acyl-CoA synthetase and purified by high-performance liquid chromatography as previously described (30 (link)). All other chemical reagents used were of analytical grade or better.
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7

Codon-Optimized AgmNAT Protein Expression

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The AgmNAT gene was codon optimized and synthesized by Genscript. Ambion RETROscript® Kit, ProBond™ nickel-chelating resin, and MicroPoly(A) PuristTM was purchased from Invitrogen. Oligonucleotides were purchased from Eurofins MWG Operon. PfuUltra High-Fidelity DNA polymerase was purchased from Agilent. BL21 (DE3) E.coli cells and pET-28a(+) vector were purchased from Novagen. NdeI, XhoI, Antarctic Phosphatase, and T4 DNA ligase were purchased from New England Biolabs. Kanamycin monosulfate and IPTG were purchased from Gold Biotechnology. Acyl-CoAs were purchased from Sigma-Aldrich. Cayman Chemical commercially synthesized N1-acetylspermidine. All other reagents were of the highest quality and purchased from either Sigma-Aldrich or Fisher Scientific.
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8

Radioactive Fatty Acid Synthesis Assay

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Malonyl-CoA, acetyl-CoA, acyl-CoAs, fatty acids, NADH, NADPH, and antibiotics were purchased from Sigma-Aldrich. Sodium [1-14C]acetate (57.0 mCi/mmol), [1-14C]acetyl-CoA (55.0 mCi/mmol), [1-14C]octanoyl-CoA (57.0 mCi/mmol), [1-14C]lauric acid (55.0 mCi/mmol), and [2-14C]Malonyl-CoA (55.0 mCi/mmol) were purchased from Amersham-Pharmacia Biotechnology. Restriction endonucleases and T4 ligase got from NEB Inc. Ni-agarose columns were obtained from Invitrogen. Oligonucleotides were synthesized by IDT and were listed in Table S4. The ACGT Inc provides the sequencing service.
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9

Metabolic Profiling with HPLC-MS

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DMEM (Cat#11965) was purchased from ThermoFisher (Waltham, MA, USA). Oasis HLB SPE columns were purchased from Waters (Milford, MA, USA). 5-sulfosalicylic acid, etomoxir, pantothenate, dephospho-CoA, and acyl CoA standards were purchased from Sigma-Aldrich (St. Louis, MO, USA). (E)-but-2-enoyl Coenzyme A (crotonoyl CoA) was purchased from Avanti Polar Lipids (Alabaster, Alabama, USA).
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10

Acylsugar Biosynthesis Assay Protocol

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Assays were run in 100 mM sodium phosphate buffer at a total volume of 60 mL with pH 6 as the default unless otherwise stated. Acyl-CoA (or CoA) was added to a final concentration of 100 mM and obtained from Sigma-Aldrich. Acylsugar acceptors, such as I3:22, were dried down using a SpeedVac and dissolved in an ethanol:water mixture (1:1) with 1 mL added to the reaction. Six microliters of enzyme was added to each reaction (or water). The assays were incubated at 30°C for 30 min unless otherwise stated. After the incubation, 2 volumes of stop solution, composed of a 1:1 mixture of acetonitrile and isopropanol with 0.1% (v/v) formic acid and 1 mM telmisartan as internal standard (Sigma-Aldrich), was added to the assays and mixed by pipetting. Reactions were stored in the 220°C freezer for 20 min and centrifuged at 17,000g for 5 min. The supernatant was transferred to LC-MS autosampler vials and stored at 220°C. For negative control assays in Supplemental Figures S7 andS8, an aliquot of the enzyme was incubated at 95°C for 10 min to inactivate it.
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