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6 protocols using dm 17

1

Western Blot Antibody Validation Protocol

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The following primary antibodies were used at the stated dilutions: anti-human TRAK1 at 1:2,000 (HPA005853; Sigma-Aldrich), anti-Myc at 1:5,000 (05-724; EMD Millipore), anti-OGT at 1:2,000 (DM-17; Sigma-Aldrich), anti-HA at 1:5,000 (ab9110; Abcam), anti-FLAG 1:5,000 (F7425; Sigma-Aldrich), anti-FHL2 1:1,000 (HPA006028; Sigma-Aldrich), anti-GAPDH 1:5,000 (6C5; EMD Millipore), and anti–6X-HIS at 1:1,000 (MA1-21315; Thermo Fisher Scientific). For chemiluminescence detection of proteins on Western blots, HRP-conjugated secondary antibodies to mouse, rabbit, and rat (Jackson ImmunoResearch Laboratories, Inc.) were used at 1:5,000 along with Pierce SuperSignal West Dura (Thermo Fisher Scientific). For fluorescence detection (used for all quantitative blots), 800CW donkey anti-rabbit, 680RD donkey anti-rabbit, 680RD donkey anti-mouse, 800CW donkey anti-mouse, and 800CW goat anti-rat were used at 1:5,000 (LI-COR Biosciences), and all blots were scanned by the Odyssey CLx Imaging System.
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2

Cellular Protein Quantification and O-GlcNAc Detection

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Total cellular protein was harvested and quantified from NRCMs using established protocols [20 (link),36 (link),37 (link),39 (link)–42 (link),45 (link)–48 (link),50 (link),53 (link),58 (link)]. Standard Western blotting procedures were used to probe for O-GlcNAc (anti-O-GlcNAc, CTD110.6; Biolegend), OGT (DM-17; Sigma) and OGA (anti-NCOAT; Sigma). Antibodies for α-tubulin (Sigma) and ATP5A (Abcam) were used as loading controls for whole-cell and mitochondrial protein respectively. Protein expression levels were quantified by densitometric analysis. For O-GlcNAc Western blots, the entire lane was quantified to determine overall protein O-GlcNAcylation [20 (link),36 (link),37 (link),39 (link)–42 (link),44 (link),45 (link),48 (link)].
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3

Immunoblotting for O-GlcNAc Signaling Proteins

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Whole cell protein extracts were lysed by probe sonication in buffer consisting of 50 mM Tris-HCl at pH 8.0, 150 mM NaCl, 1% Triton X-100 or Tween, and 2 mM EDTA (including protease and phosphatase inhibitors (Roche) and 1 μM Thiamet-G). Samples were separated by SDS-PAGE (4–12% Bio-Rad), transferred to nitrocellulose membranes, and blocked with 5% milk (LabScientific, inc.) or BSA (Sigma) in PBS with Tween 20 (Sigma). The following primary antibodies were used to detect the indicated proteins: anti-OGT (DM-17, Sigma and sc-32921, Santa Cruz Biotech), anti-OCT4 (MAB4401, Millipore), anti-O-GlcNAc (RL2, Thermo Scientific), anti-OGA (SAB4200267, Sigma), anti-PAX6 (PRB-278P, Covance), antitubulin (T5168, Sigma), anti-GFAT1 (3818, Cell Signaling), anti-GNPNAT1 (SAB2701548, Sigma), anti-PGM3 (sc-100410, Santa Cruz Biotech), anti-UAP1 (GTX103592, GeneTex), anti-NAGK (N6788, Sigma), and anti-GALE (ab155997, abcam). The following horseradish peroxidase-linked secondary antibodies were used for detection at a dilution ratio of 1:5000 goat antirabbit-HRP-conjugated secondary antibody (4010–05, Southern Biotech) and goat antimouse-HRP-conjugated secondary antibody (1010–05, Southern Biotech).
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4

Immunoblotting and Affinity Purification of Post-Translationally Modified Proteins in CD8+ T Cells

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TCR stimulated CD8+ T cells were purified by magnetic separation (Stemcell Technologies) prior to protein extraction. Standard immunoblotting protocols were used19 (link). Blots were probed with antibodies recognizing, dilutions and clone/catalog numbers in brackets: c-Myc (1:1000, #9402), pY694 STAT5 (1:2000, #9351), pan STAT5 (1:1000, #9363), pT389 S6K (1:1000, #9239), S6K (1:1000, #5610) (Cell Signalling Technology), SMC1 (1:5000, A300-055A, Bethyl), β–tubulin (1:5000, H-235) (Santa Cruz), OGT (1:1000, DM17, Sigma) and O-GlcNAc (1:3000, RL2, Abcam). Lysate made from 2 × 108 day 6 CTLs were used for the succinylated wheat germ agglutinin (sWGA) affinity purifications. One half of the lysate was treated with CpOGA and other half was left untreated. Before sWGA affinity purifications, the lysates were precleared with agarose beads for 30 min at 4 °C. 50 µl sWGA beads (L-1020S, Vector Laboratories) were incubated for 16 h with the lysates and beads were washed 4 times with PBS before adding the LDS-loading buffer. For GFP-myc immune-purification, 2 × 108 GFP-MycKI CTLs were lysed and half the lysate was treated with CpOGA or left untreated before the immune-purification. The lysates were incubated with GFP-binder agarose beads (ChromoTek) for 90 min at 4 °C. Beads were washed three times with NP40 buffer before adding the LDS-loading buffer for immunoblotting.
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5

Immunoblotting and Affinity Purification of Post-Translationally Modified Proteins in CD8+ T Cells

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TCR stimulated CD8+ T cells were purified by magnetic separation (Stemcell Technologies) prior to protein extraction. Standard immunoblotting protocols were used19 (link). Blots were probed with antibodies recognizing, dilutions and clone/catalog numbers in brackets: c-Myc (1:1000, #9402), pY694 STAT5 (1:2000, #9351), pan STAT5 (1:1000, #9363), pT389 S6K (1:1000, #9239), S6K (1:1000, #5610) (Cell Signalling Technology), SMC1 (1:5000, A300-055A, Bethyl), β–tubulin (1:5000, H-235) (Santa Cruz), OGT (1:1000, DM17, Sigma) and O-GlcNAc (1:3000, RL2, Abcam). Lysate made from 2 × 108 day 6 CTLs were used for the succinylated wheat germ agglutinin (sWGA) affinity purifications. One half of the lysate was treated with CpOGA and other half was left untreated. Before sWGA affinity purifications, the lysates were precleared with agarose beads for 30 min at 4 °C. 50 µl sWGA beads (L-1020S, Vector Laboratories) were incubated for 16 h with the lysates and beads were washed 4 times with PBS before adding the LDS-loading buffer. For GFP-myc immune-purification, 2 × 108 GFP-MycKI CTLs were lysed and half the lysate was treated with CpOGA or left untreated before the immune-purification. The lysates were incubated with GFP-binder agarose beads (ChromoTek) for 90 min at 4 °C. Beads were washed three times with NP40 buffer before adding the LDS-loading buffer for immunoblotting.
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6

Quantifying Protein Modifications by Western Blot

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For Western blot analysis, protein samples were separated by SDS/PAGE and transferred on to nitrocellulose membrane (Whatman). The membranes were blocked for 1 h in 5% non-fat milk powder or 5% BSA in TBS-0.2% Tween20 (TBS-T) buffer for 1 h at room temperature with gentle shaking. Then, the following primary antibodies, diluted in blocking buffer, were added to the membranes overnight at 4°C: anti-OGT (DM-17, Sigma–Aldrich), anti-OGT (Abcam ab177941), anti-O-GlcNAc (RL2, Abcam), anti-O-GlcNAc [C-terminal domain (CTD) 110.6, Cell Signaling], anti-TOM20 (F-10, Santa Cruz Biotechnology), anti-ATP synthase β subunit (ATPB, 3D5, Abcam), anti-Timm13 (A01, Abnova), anti-HSP60 (D307, Cell Signaling), anti-α-tubulin (12G10, Developmental Studies Hybridoma Bank, University of Iowa) and anti-α-tubulin (11H10, Cell Signaling). The following fluorescent secondary antibodies, diluted in 1% milk in TBS-T, were added to the membranes for 1 h at room temperature: donkey anti-rabbit 800, donkey anti-mouse 680, goat anti-rabbit 800 and goat anti-mouse 680 (LI-COR). Images were acquired and analysed using the LI-COR Odyssey Image System.
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