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9 protocols using histidinol

1

Cell Culture Conditions and Treatments

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HCT116 cells were maintained in McCoy’s 5A media (Cytiva, SH30200FS), and T98G, Hela, mouse embryonic fibroblasts and 293T cells were maintained in Dulbecco’s Modified Eagle’s medium (Sigma-Aldrich, D5796) at 37°C with 5% CO2. All media were supplemented with 10% fetal bovine serum and 1X penicillin/streptomycin (Gibco, 15070063). For experiments involving thapsigargin (Sigma, T9033), tunicamycin (Sigma, T7765) and histidinol (Sigma, H6647), media were supplemented with 1X GlutaMAX (Gibco, 35050079) and 1X MEM Non-Essential Amino Acids (Gibco, 11140050).
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2

Generation of Immortalized Fibroblasts

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Sept7 floxed mouse embryonic fibroblasts were generated from E15 day embryos and maintained under standard conditions. Sept7 floxed adult tail fibroblasts (TFs) were isolated from 6–8 weeks old mice tail tips. Minced tail tips were sequentially digested with collagenase and trypsin at 37°C and plated on collagen coated dishes in DMEM supplemented with 20% serum, non-essential amino acids and antibiotics. The cells were splitted 1∶4 and maintained in the same growth medium without coated dishes. To immortalize primary TFs, cells were co-transfected with pSV40Tag encoding simian virus 40 large T antigen and pREP8 plasmid (Invitrogen) in a 10∶1 mixture; colonies were selected with 2 mM histidinol (Sigma). Jurkat cells were maintained in RPMI-1640 medium supplemented with 15% serum, 1 mM pyruvate and antibiotics. Post electroporation cells were additionally supported by 2 ng/ml IL2.
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3

Immortalization of Primary Mouse Embryonic Fibroblasts

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All cell lines were maintained in standard growth medium -DMEM/high glucose, 1 mM glutamine, 10% FCS (20% for MEFs), 1x Penicillin/Streptomycin. Transient transfections were performed using polyethyleneimine (PEI) reagent as described previously24 (link). Sept7 floxed mouse (Sept7tm1Mgl)14 (link) embryonic fibroblasts were generated from E14 day embryos. Aseptically minced embryos after removing head and red organs were further disaggregated by mincing in a solution of Trypsin-EDTA/DNAseI and incubation with 5 mm glass beads with vigorous shaking at RT for 15 min. The isolated cells were transferred to a fresh tube and resuspended in standard growth medium with 50 μg/ml gentamycin, plated in T25 flasks and propagated at 37 °C with 5% CO2. The cells were splitted 1:4 and maintained in the same growth medium. To immortalize primary MEFs, cells were co-transfected with pSV40Tag encoding simian virus 40 large T-antigen and pREP8 plasmid (Invitrogen) in a 10:1 mixture; colonies were selected with 2 mM histidinol (Sigma). For proliferation assays, MEF clones were seeded in 96 well plates and on alternate days viable cell population were quantified by WST-1 assay (Roche).
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4

Investigating Nutrient Sensing Pathways in MEFs

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Antibodies against S6K1 (#9202), S6K phosphorylated at Thr-389 (#9205), eIF2α (#9722) were from Cell Signaling Technology, antibody against eIF2α phosphorylated at Ser-51 (ab32157) was from Abcam. Dulbecco’s Modified Eagle’s Medium (DMEM) and Dulbecco’s Modified Eagle’s Medium/Nutrient F-12 Ham’s DMEM/F12 used for leucine deprived medium were from Sigma. DMEM without amino acids was from Genaxxon. DMEM used for arginine deprived medium was from ThermoFisher Scientific. Fetal bovine serum (FBS) was from Gibco and had been dialysed (using a membrane with a cut-off of 3500 Da) against phosphate-buffered saline (PBS) (pH: 7.4) at 4 °C. MEFs deficient in GCN221 (link) and ATF438 (link) were kindly donated by Prof. D. Ron (Institute of Metabolic Science, Cambridge, UK), eIF2αS51A/S51A 39 (link) MEFs were kindly provided by Dr R. J. Kaufman (La Jolla, California, University of Michigan, USA). Actinomycin D, tunicamycin and histidinol were from Sigma.
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5

DT40 Cell Transfections and Culture

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DT40 cell transfections and culture were described previously25 (link)46 (link)47 (link). Antibiotics used were Puromycin (0.5 μg/ml); Hygromycin (2 mg/ml, Roche 10843555001); Blasticidin (20 μg/ml, Melford B1105); Histidinol (1 mg/ml, SIGMA H6647-3G), G418 (2 mg/ml, Calbiochem 345812) in RPMI-1640 (Gibco/Invitrogen 3187-025)
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6

Mutagenic Fibrinogen Expression in CHO Cells

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The fibrinogen γ chain expression vector pMLP-γ [51 (link)] was altered with six mutagenic primer pairs (Supplementary Material, Table S1), and the resultant expression vectors γL276P, γT277R, γT277P, γY278H, γA279D, and γY280C and the wild-type were co-transfected with the histidinol selection plasmid (pMSVhis) into CHO cells that expressed normal human fibrinogen Aα and Bβ chains. Colonies were selected on histidinol (Sigma-Aldrich, St. Louis, MO, USA) and 10–12 cell lines per variant were established as described previously [35 (link)]. The highest expressing γT277R or γY278H fibrinogen-producing CHO cell lines were cultured using a roller bottle system. Fibrinogens were purified from the harvested culture medium using ammonium sulfate precipitation followed by immunoaffinity chromatography utilizing a calcium-dependent monoclonal antibody (IF-1, LSI Medience, Tokyo, Japan), as described previously [44 (link)]. After elution, fibrinogen was dialyzed, and the purity and characterization of the proteins were determined using SDS-PAGE. Wild-type and γY275C recombinant fibrinogens were used as prepared previously [15 (link)].
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7

Inhibitors of Cellular Processes

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Halofuginone (#32481), Tunicamycin (#T7765), Histidinol (#6647), Borrelidin (#B3061), and Cycloheximide (#C7698) were purchased from Sigma‐Aldrich, MLN4924 (#S7109‐SEL) was purchased from Stratech and MG‐132 (#1748) was purchased from Tocris Bioscience.
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8

Analysis of ER Stress Responses

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2-Deoxyglucose (Sigma, St Louis, MO), histidinol (Sigma) and DTT (Nacalai Tesque, Kyoto, Japan) was dissolved in distilled, sterilized water. Tunicamycin (Nacalai Tesque) and thapsigargin (Wako Pure Chemical Industries, Osaka, Japan) were dissolved in dimethyl sulfoxide. Hydrogen peroxide was purchased from WAKO. These compounds were added to culture medium, with the solvent being less than 0.5% of the medium’s volume. The following commercially available antibodies were used: rabbit anti-TBL2 and anti-ATF4 (ProteinTech, Chicago, IL), anti-PERK, anti-eIF2 alpha (abcam, Cambridge, MA), anti-phospho-PERK (BioLegend, San Diego, CA), anti-phospho-eIF2 alpha (Ser51), anti-calnexin (Cell Signaling Technology, Danvers, MA), anti-KDEL for GRP78 (StressGen, Victoria, BC, Canada) anti-FLAG M2 (Sigma), and HRP- or FITC-conjugated anti-V5 (Invitrogen), HRP-conjugated anti-rabbit or mouse IgG (GE Healthcare Bio-Sciences Corp, Piscataway, NJ).
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9

Alanine Scanning of PDGFR Epitope

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Five different sets of Alanine mutations were introduced into the epitope of VH PAM -V16F4. The template for mutagenesis (GenScript) was the full-length human PDGFR cDNA inserted into the retroviral vector pLHDCX2 (22) . The PDGFR mutants were termed Ala-scans and numbered from the N-to the C-terminus (according to the corresponding peptides): Ala-scan1: 109 EDDD 112 to 109 AAAA 112 , Ala-scan2: 149 TFT 151 to 149 AAA 151 , Ala-scan3: 262 QATR 265 to 262 AAAA 265 . Two longer Ala-scans were generated combining Ala-scan1 and 2 (Ala-scan4) or Ala-scan1, 2 and 3 (Ala-scan5). The five Ala-scans were individually transfected into PA317 cells (ATCC) with
Lipofectamine to produce retroviral virions (23) . Virus-containing medium was collected, concentrated (25,000 g, 90 minutes, 4°C) and used to infect F-/-cells ( 12) grown in DMEM with 8 µg/ml polybrene (hexadimethrine bromide; Sigma-Aldrich) for 24 hours. Successfully infected cells were selected in histidine-free DMEM containing 5 mM histidinol (Sigma-Aldrich) (24) . Mutated PDGFR expression was assessed by FACS using VH PAM -V16F4 and mab 1264 antibodies.
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