title: HMP33
organism: Escherichia coli BW25113
description: Protocols: The E. coli BW25113 strain and derivatives were used throughout this study. Genome engineering of E. coli was facilitated by λ-red recombination, P1 transduction and/or site-specific Tn-7 transposon. All ALE experiments were performed at 37C using M9. When passing manually, cells were grown in 250 ml glass flasks containing 25 ml fresh medium and required supplements in an orbital 311DS shaker (Labnet) at 250 rpm. Cells were passed daily and cell density was maintained at an OD600 value of 0.2-0.4 after 24 h of growth. Experiments were stopped when growth rate of the cells reached 0.6-0.7 h-1 and evolved cells were obtained by serial plating. At least three lineages of the initial strain were maintained during manual passages. When passages were automated, experiments were performed according to [PMID: 25304508] and six lineages of the initial strain were usually maintained. When cells were evolved under tBPt-dependent selection conditions, phenylalanine at 100 mg/l was supplemented. The melatonin pathway was evolved in the presence of 100 mg/l of methionine and 5HTP. Antibiotics were not supplied during ALE. Unless stated otherwise on the publication, all strains were maintained at 37℃ in LB (Lennox) (Sigma Aldrich), 2xYT or M9 media containing 1xM9 minimal salts (BD Difco™), 2 mM MgSO4, 100 μM CaCl2, 500-fold diluted trace minerals (10 g/l FeCl3·6H2O, 2 g/l ZnSO4·7H2O, 0.4 g/l CuCl2·2H2O, 1 g/l MnSO4·H2O, 0.6 g/l CoCl2·6H2O, and 1.6 mM EDTA, pH 8.0), 1x ATCC® Vitamin Supplement (ATCC MD-VS™), and 0.2% glucose (w/v). Unless stated otherwise, ampicillin and spectinomycin were used at 50 mg/l; chloramphenicol and kanamycin were used at 25 mg/l. Total DNA was extracted using a PureLink Genomic DNA Kit (Invitrogen). DNA libraries were prepared using a Kapa Hyper Prep Library Prep Kit (Roche Molecular Systems).
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2018-06-01T17:03:06Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2018-05-11T15:18:15Z
attributes.tag: External Id
attributes.value: SAMEA4659674
attributes.tag: INSDC center name
attributes.value: Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark
attributes.tag: INSDC first public
attributes.value: 2018-06-01T17:03:06Z
attributes.tag: INSDC last update
attributes.value: 2018-05-11T15:18:15Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-6779:HMP33
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: growth condition
attributes.value: tBPt selection 2nd ALE
attributes.tag: sample name
attributes.value: E-MTAB-6779:HMP33
attributes.tag: scientific_name
attributes.value: Escherichia coli BW25113
attributes.tag: strain
attributes.value: HMP33