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11 protocols using anti sumo1

1

Antibodies and Reagents for Proteomics

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The following antibodies were used for western blot analysis: anti-PD-L1 (cat.no. NBP1-76769; NOVUS), anti-β-actin (cat.no. ab8224; Abcam), anti-NOX4 (cat.no. ab109225; Abcam), anti-ZNF24 (cat.no. NBP1-82866; NOVUS), anti-UBE2I (cat.no. ab75854; Abcam), and anti-SUMO-1 (cat.no. ab32058; Abcam). Antibodies used for immunohistochemistry analysis were the following: anti-PD-L1 (cat.no. NBP1-76769; NOVUS), anti-NOX4 (cat.no. ab109225; Abcam), anti-ZNF24 (cat.no. NBP1-82866; NOVUS), and anti-CD8 (cat.no. ab237709; Abcam). Anti-UBE2I (cat.no. ab75854; Abcam), anti-SUMO-1 (cat.no. ab32058; Abcam), and anti-ZNF24 (cat.no. A303-091A; Thermo Fisher Scientific) were used for Immunoprecipitation (IP). Oleic acid, palmitic acid, Oil Red O, and MitoTEMPO were purchased from Sigma-Aldrich (St. Louis, MO). Reactive oxygen species (ROS) assay, Nacetyl-cysteine (NAC), JC-1-Mitochondrial Membrane Potential Assay Kit, and LDH Cytotoxicity Assay Kit were obtained from Beyotime Institute of Biotechnology (Jiangsu, China). Alanine aminotransferase (ALT) and aspartate transaminase (AST) assay kit were acquired from Nanjing Jiancheng Bioengineering Institute (Jiangsu, China).
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2

In vitro and in vivo SUMOylation assays

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For in vitro SUMOylation assays, proteins were incubated in 20 µL of reaction buffer (50 mM Tris-HCl, 100 mM NaCl, 15% glycerol, 5 mM ATP, 10 mM MgCl2, pH 7.8) with or without 1 µg of SUMO1 protein (Abcam, Cambridge, UK), E1 (0.5 µg of human SAE1 full and 0.5 µg of SAE2/UBA2 peptide), E2 (2 µg of MdSCE1 customized by Abmart), and 8 µg of GST-MdSIZ1 or His-MdMYB30 protein for 3 h at 37°C. Next, 10% SDSpolyacrylamide gel immunoblot analysis was performed with anti-His and anti-SUMO1 antibodies (Abcam). For in vivo SUMOylation assays, three 3-week-old transgenic apple calli were extracted with IP lysis/wash buffer, and soluble extracts were IPed with anti-Flag antibody using a Pierce Crosslink IP kit following the manufacturer's instructions. Lastly, 8% SDS-polyacrylamide gel immunoblot analysis was performed with anti-Myc (Abmart), anti-GFP(Abmart), and anti-SUMO1(Abcam) antibodies. For the SUMO conjugate assay, total proteins of plant tissue were extracted with 50 mM Tris-HCl (pH 8), 150 mM NaCl, 0.2% Triton X-100, 1 mM PMSF, and 5 mM EDTA. Next, 10% SDS-polyacrylamide gel immunoblot analysis was performed with anti-SUMO1 and anti-actin antibodies (Abcam). Anti-actin antibody was used to ensure equivalent protein loading.
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3

Immunoprecipitation and Western Blot Analysis

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Cells were lysed in a buffer containing 1% Triton X-100, 0,1% SDS, 50 mmol/L Tris-HCl pH 7.4, 150 mmol/L NaCl, 0,5% sodium deoxycholate, 1 mmol/L EGTA, 1 mmol/L EDTA, 5 mmol/L MgCl2, 1 mmol/L PMSF, 1 mmol/L Na3VO4, 5 mmol/L NaF pH 8, 20 mmol/L N-ethyl-malemide, 10 μg/mL of aprotinin and 5 μg/mL leupeptin, incubated 30 min on ice and then centrifugated at 13000 X g for 30 minutes at 4 °C and the supernatant was collected as whole-cell extract. Bio-Rad Protein Assay was used to determine protein concentration.
Immunoprecipitations was performed as previously described57 (link) using anti-PVR (SKII.4) or control mouse IgG (Santa Cruz Biotechnology). Immunoprecipitates or total cell lysates were resolved by SDS-polyacrylamide gel (PAGE), proteins were then electro-blotted onto nitrocellulose membranes (Schleicher & Schuell, GEH10600002), and western blotting was performed as previously described57 (link) with the following Abs: anti-PVR (S-18, Santa Cruz Biotechnology), anti-SUMO1 (Abcam, Y299), anti-UBC9 (BD Biosciences, 50/ubc9), anti-β actin (Sigma-Aldrich, AC-74). Fiji Image J software was used to perform densitometric analysis.
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4

SUMO1 Regulation of STAT1 Phosphorylation

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COS-7 and U3C or U3A cells were transiently transfected with WT or mutant STAT1 constructs, and SUMO1 construct. Cells were lysed in lysis buffer supplemented with N-ethylmaleimide (NEM, 20mM; Sigma) and protease inhibitors. For immunoprecipitation, whole cell lysates were incubated with anti-STAT1 antibody (or isotype control antibody; Santa Cruz Biotechnology) and protein G-Sepharose (Amersham Biosciences) overnight at 4°C. The beads were washed, heated, and the proteins resolved by immunoblotting for SUMO-STAT1 proteins. For analysis of the cell lysates, equal amounts of proteins were transferred to PVDF membranes and were incubated with the primary antibodies, anti-pSTAT1 Tyr701, anti-STAT1, anti-SENP1 (Cell Signaling), and anti-SUMO-1 (Abcam). Blots were stripped and re-probed with anti-STAT1 and anti-tubulin (Millipore) antibodies to assess protein loading.
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5

Bortezomib and SUMO Signaling Pathway

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Bortezomib was purchased from Janssen-Cilag (Buckinghamshire, UK) and was dissolved in dimethyl sulfoxide (DMSO). Anti-hnRNP K antibody was purchased from Cell Signaling Technology (New England Biolabs, Schwalbach, Germany) and Santa Cruz Biotechnology (Santa Cruz, Dallas, TX), anti-pan-SUMO, anti-SUMO-1, anti-SENP1, and anti-SENP2 antibodies were purchased from Abcam (Cambridge, MA), anti-c-Myc and anti-HA antibodies were purchased from Cell Signaling Technology, and anti-GAPDH antibody was purchased from GeneTex (Irvine, CA).
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6

Investigating SUMO Regulation in Metabolic Pathways

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Recombinant human TNF-α, IL-1β, and IL-17α were purchased from R&D Systems (Bio-Techne), and LPS was obtained from MilliporeSigma. DMEM, FBS, antibiotics, trypsin EDTA, PBS, and other products for cell culture were purchased from Invitrogen, Thermo Fisher Scientific. The primary antibodies used were as follows: anti-SAE1 (ab38434, Abcam), anti-UBA2 (ab189289, Abcam), anti–SUMO-1 (ab11672, Abcam), and anti-STAT5A (ab32043, Abcam) were purchased from Abcam. Anti-HK2 (2867, Cell Signaling Technology), anti-PFKP (8164, Cell Signaling Technology), anti-PKM2 (4053, Cell Signaling Technology), and anti–p-PKM2 (3827, Cell Signaling Technology) were purchased from Cell Signaling Technology. Anti–β-actin (A5441) was purchased from MilliporeSigma. GA (15:1) was purchased from MilliporeSigma. SKN was purchased from Selleckchem.
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7

Quantifying SUMO Conjugation Levels

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Whole cell lysates were prepared and subjected to SDS-PAGE as described
previously.9 (link) The antibodies used in this study were: anti-SUMO-1
(rabbit polyclonal, in house), ant-SUMO-2,3 (rabbit polyclonal, in house),
anti-Ubc9 (rabbit monoclonal, Abcam (Cambridge, UK)) and anti-β-actin
(mouse monoclonal, Sigma (St. Louis, MO, USA)). Intensities of bands were
analysed using Image-J (NIH (Bethesda, MD, USA)). In order to measure SUMO
conjugation levels, the region corresponding to molecular weights above
100 kDa in each lane was cropped and the total intensity was analysed.
The densities were normalized with corresponding actin levels and expressed as
the ratio to control (DMSO alone).
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8

Immunofluorescence Analysis of SUMO1, SMAD4, and Vimentin

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Treated A549 cells were fixed with 4% paraformaldehyde for 30 min and permeabilized with 0.3% Triton X-100 for 10 min at room temperature. After blocking with 1% BSA for 30 min at room temperature, the primary antibodies anti-SUMO1 (ab11672, Abcam, Cambridge, UK), anti-SMAD4 (#38454S, Cell Signaling Technology, Danvers, MA, USA), and anti-Vimentin (#5741S, Cell Signaling Technology) were diluted with PBS, and incubated overnight at 4 °C. Then, the cells were washed three times with PBS and incubated with the secondary antibodies goat anti-rabbit IgG H&L (Alexa FluorR488) (ab150077, green) and goat anti-mouse IgG H&L(Alexa FluorR594) (ab150116, red). Finally, an anti-fluorescence quenching sealing solution (including 4′,6-diamidino-2-phenylindole (DAPI)) was used to stain nuclei (blue) and seal the slides. Stained slides were observed under confocal microscopy. Finally, all steps after the inclusion of secondary antibody were performed in the dark.
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9

Insulin Signaling Pathway Analysis

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All chemicals were purchased from Sigma-Aldrich unless otherwise stated. All tissue culture reagents were purchased from ThermoFisher. Mercodia Rat Insulin ELISA kits were purchased from Diagenics Ltd (Milton Keynes, UK). Anti SUMO1 (used 1:500), Ubc9 (used 1:1000) and syntaxin1A (used 1:250) antibodies were all purchased from Abcam Plc (Cambridge, UK). Anti beta-tubulin antibody (used 1:5000) was purchased from Sigma-Aldrich. Secondary antibodies were all purchased from Li-Cor Biosystems (used 1:10,000) (Cambridge, UK). INS-1E cells were a kind gift from Claes Wollheim (Lund, Sweden). HEK293T cells were a kind gift from Jeremy Henley (Bristol, UK), as were pXLG transfers vectors for lentivirus construction.
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10

Detecting Protein SUMOylation in Plants

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Total proteins were extracted from 10-day-old seedlings. Equal quantities of each sample were separated on a 12% (w/v) sodium dodecyl sulfate polyacrylamide gel electrophoresis gel and transferred to polyvinylidene fluoride membranes. Proteins were probed by immunoblot analysis with anti-AOX (Agrisera, https:// www.agrisera.com), anti-Flag (Sigma-Aldrich) or anti-SUMO1 (Abcam, https://www.abcam.com) antibodies. For SUMOylation determination in planta, Flag-MYB30 protein was first immunoprecipitated with anti-Flag conjugated agarose (Sigma-Aldrich) in 10day-old Pro35S::MYB30-Flag/Col-0, Pro35S::Flag-MYB30/siz-2 and Pro35S::Flag-MYB30 K283R /Col-0 as well as Pro35S::Flag-CRCK3/Col-0 transgenic plants, respectively, treated with 100 mM NaCl for the indicated periods of time. The resulting proteins were probed by immunoblot analysis with anti-Flag and anti-SUMO1 antibodies.
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