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13 protocols using anti gfp hrp

1

Quantification of Plant Membrane Proteins

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Roots were sampled and frozen in liquid nitrogen. Total proteins were obtained using the Plant Total Protein Extraction Kit (Sigma) and quantified with the PerceTM660nm Protein Assay using a BSA standard curve. Membrane proteins were obtained by disrupting roots in a buffer containing a plant anti-protease cocktail (Sigma-Aldrich) and anti-phosphatases (30 mM glycerophosphate, 5 mM molybdate, and 10 mM NaF). The whole membrane fraction was then isolated by centrifugation (100000g, 4h) on a 55% sucrose cushion. Immunoblot analysis was performed on 40-50 μg of proteins using anti-GFPHRP 1:2500 (Miltenyi Biotec, 130-091-833), anti-NRT1.1 1:5000 (AS12 2611, Agrisera) and anti-PIP2.1 1:5000 61 (link). Coomassie Brilliant Blue staining of blots was used to control protein levels after electro-transfer. Un-cropped versions of the blots are provided in Supplementary Fig. 7 and 8. Band intensity quantification was performed using a chemioluminiescent image analyzer LAS3000 (Fujifilm) and ImageGauge (Fujifilm) software.
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2

Immunoaffinity Purification of LecRK Proteins

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Leaves collected from 6-week-old T0 transgenic N. benthamiana plants were ground in liquid nitrogen and subsequently incubated for 30 min in an extraction buffer containing 150 mM NaCl, 50 mM Tris–HCl pH 8.0, 1.0 % IGEPAL® CA-630 (Sigma) and one protease inhibitor cocktail tablet per 50 mL (Roche). The homogenate was centrifuged at 18,000 rpm for 20 min and the supernatant was incubated with GFP-trap_A® beads (Chromotek) at 4 °C for 1–2 h. After incubation, GFP-beads were spinned down and washed six times with extraction buffer. Proteins were eluted from GFP-trap_A® beads by boiling for 5 min, separated on an 8 % SDS-PAGE gel and electroblotted onto PVDF membrane (Bio-Rad). Accumulation of eGFP-tagged LecRK-I.9 and LecRK-IX.1 was detected by immunoblotting using anti-GFP-HRP (Miltenyi Biotec). Supersignal West Femto Chemiluminescent Substrate (Thermo Scientific) was used for signal development. Coomassie brilliant blue staining was used to indicate the amount of loading.
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3

Immunoblotting analysis of EV-A71 proteins

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Proteins from purified EV-A71 virions and protein lysates were mixed with Laemmli buffer and separated by 10% SDS-PAGE. The proteins were transferred onto nitrocellulose membranes, which were blocked with 5% skimmed milk in 0.05% Tween-20 phosphate buffered saline (0.05% PBST) for 1 hour at room temperature. The pooled human serum samples were pre-treated additionally with RIDA RF-Absorbens (R-Biopharm AG, Germany) or DTT (Invitrogen, USA) for IgM- and IgG-specific antibody detection, respectively. The membrane was then incubated with 1:5000 diluted anti-GFP-HRP (Miltenyi Biotec, Germany), 1:300 diluted pooled human serum, 1:100 diluted Light Diagnostics EV-A71 monoclonal antibody 3323 (mAb 3323; Millipore, USA) or 1:1000 diluted EV-A71-specific mAb 979 (Millipore, USA) for 1 hour at room temperature, followed by secondary antibody incubation with the 1:5000 diluted HRP-conjugated polyclonal rabbit anti-human IgM (KPL, USA), 1:3000 diluted Amersham ECL human IgG, HRP-linked whole Ab from sheep (GE Healthcare, USA) or 1:5000 diluted HRP-conjugated goat anti-mouse (Gene Tex, USA) antibody. The immunoblot was developed with Clarity Western ECL Substrate (Bio-Rad, USA) and detected by chemiluminescence. The sizes of the protein bands were determined using the Precision Plus Protein WesternC Standard (Bio-Rad, USA).
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4

Protein Separation and Detection

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Crude cell lysates were separated in 4–12% Bis-Tris NuPAGE gels (Life), and electro-blotted onto PVDF membranes (Pierce). Proteins were revealed using the following primary antibodies: mouse monoclonals anti-A2 (Abcam) and anti-GFP-HRP (Miltenyi Biotec), mouse monoclonal anti-tubulin (Sigma), and anti-rabbit or anti-mouse HRP-conjugated secondary antibodies (Pierce).
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5

Co-immunoprecipitation of AtNHR2A-GFP and His-AtENGD-1

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To validate the interaction between AtNHR2A-GFP and His-AtENGD-1, AtNHR2A-GFP and GFP were transiently expressed in N. benthamiana, and proteins extracted as described above. His-AtENGD-1 was expressed and purified in E. coli. Thereafter, 5 μg of the purified His-AtENGD-1 were mixed with 100 μg of total protein extracted from N. benthamiana plants transiently expressing AtNHR2A-GFP or GFP, and subjected to co-immunoprecipitation with GFP Trap-A beads (Chromotek, Germany), as described above. The co-immunoprecipitated samples were washed, eluted in 2 × SDS protein loading buffer, resolved by SDS-PAGE, and transferred to a nitrocellulose membrane for Western blotting using anti-His (1:500 dilution; Cell Signaling Technology) or anti-GFP-HRP (1:1000 dilution; Miltenyi Biotec, Bergisch Gladbach, Germany) antibodies.
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6

Immunoprecipitation of AtNHR2A-GFP and AtNHR2B-GFP

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Four-week-old complementation lines expressing AtNHR2A-GFP and AtNHR2B-GFP in the Atnhr2a and Atnhr2b mutant backgrounds, respectively (Singh et al., 2018 (link)), and one line expressing GFP were flood-inoculated (Ishiga et al., 2011 (link)) with P. syringae pv. tabaci at 1 × 106CFU/mL to induce expression of AtNHR2A-GFP and AtNHR2B-GFP. Inoculated leaves were collected at 6 hpi and flash frozen in liquid nitrogen. Approximately 1 g of tissue (from 20 plants/genotype/treatment) was manually ground and homogenized in 6 mL of Co-IP extraction buffer [100 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM EDTA, 10 mM MgCl2, 10% Glycerol, 0.2% Nonidet P-40, 1 mM phenylmethylsulfonyl fluoride (PMSF), 5 mM dithiothreitol (DTT), and 1X Proteinase inhibitor cocktail (Sigma Aldrich, St. Louis, MO, United States)]. Extracts were incubated in ice for 30 min and centrifuged twice at 13,000 rpm for 30 min at 4°C. Clear supernatants were transferred to new pre-chilled 50-mL falcon tubes and total protein concentrations were measured using Bradford Assay (BioRad, Hercules, CA, United States). Protein expression was confirmed by Western blot using anti-GFP-HRP (1:1000 dilution; Miltenyi Biotec, Auburn, CA, United States) and detected by luminol solution (ImmunoCruz, SantaCruz Biotechnology Inc., Dallas, TX, United States) (Supplementary Figure S1A).
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7

Western Blot Analysis of Ubiquitinated H2B

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Anti‐GFP‐HRP and anti‐FLAG‐HRP antibodies were obtained from Miltenyi Biotec, USA. Ubiquitinated H2B monoclonal antibody (NRO3) was obtained from Medimabs, Canada. Western blots were performed using the Bio‐Rad trans‐blot turbo system using polyvinylidene difluoride (PVDF) membranes. The blots were blocked using TBS/2% BSA/0.3% Tween‐20 and 1 h shaking at room temperature. Here, 1 : 5000 dilutions of the antibodies were used for detection using chemiluminescence and the Clarity Western ECL substrate (Bio‐Rad). For detection of H2Bub, a secondary anti‐rabbit‐HRP antibody was used (1 : 5000 dilution).
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8

Analysis of Protein Expression in Arabidopsis

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Total protein was extracted from 5-day-old seedlings that had been exposed to white light for 3 h, transferred to darkness for 21 h, and exposed to continuous red light for 4 days. Protein concentrations were determined by the Bradford assay (Bio-Rad). Thirty micrograms of protein extract were separated by SDS-PAGE, transferred onto polyvinylidene fluoride (PVDF) membranes, and treated with horseradish peroxidase (HRP)-conjugated antibodies against GFP (anti-GFP-HRP, 1:10 000, Miltenyi Biotec) or anti-tubulin (mouse monoclonal, 1:10 000, Sigma-Aldrich) and HRP-conjugated anti-mouse antibodies (rabbit polyclonal, 1:10 000, Abcam). The blots were visualized using the Western Lightning Plus Enhanced Chemiluminescence kit (PerkinElmer) and the X-Doc System (Bio-Rad). Precision Plus Protein Dual Color Standards (Bio-Rad) were used as protein size markers.
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9

Analyzing Glycosylation of Recombinant Proteins

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For co-expression with different constructs, agrobacteria were mixed, infiltrated into leaves and harvested at the indicated time points. For the block of α-mannosidases, 50 μM kifunensine (Santa Cruz Biotechnology) was co-infiltrated with the agrobacteria suspension and for the block of α-glucosidases 200 μM castanospermine (Sigma-Aldrich) was co-infiltrated. Crude protein extracts or purified protein were subjected to SDS-PAGE under reducing or non-reducing (no reducing agent, no boiling of samples) conditions and after blotting the proteins were detected using anti-His (Thermo Fisher Scientific), anti-RBD (Sino Biological) anti-GFP-HRP (Miltenyi Biotec), anti-RFP (Chromotek) and anti-HA (Roche) antibodies. For deglycosylation, proteins were denatured and incubated with or without Endo H or PNGase F (both from NEB) according to the manufacturer’s instructions.
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10

Immunoblot and ChIP-seq Antibody Protocol

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Antibodies used for immunoblot experiments: anti-GFP-HRP (Milteny Biotec #130-091-833); monoclonal anti-FLAG M2 (Sigma-Aldrich #F3165); anti-HA-HRP (Roche #3F10), anti-H2B (Millipore #07–371) or kindly provided by Prof. Spiker, anti-H2Bub (Medimabs #MM-0029); anti-H3K4me2 (Millipore #07–030); anti-H3K4me3 (Millipore #05–745); anti-H3K9me1 (Millipore #07–450); anti-H3K27me3 (Millipore #07–449); anti-H3K36me3 (Millipore #07–353); anti-H3ac (Millipore #06–599); anti-H3K9ac (Millipore #06–942); anti-H3K27ac (Millipore #07–360); anti-H4ac (Millipore #06–598); anti-H3 (Millipore #05–499); anti-RPT5 (Enzo Life Sciences# BML-PW8245). Antibodies used in cytological analyses: Anti-MYC (Millipore #05–724) or anti-GFP (ThermoFisher Scientific #A11122) primary antibodies, Alexa-488 coupled anti-mouse (ThermoFisher Scientific #A11001) or anti-rabbit (ThermoFisher Scientific #A11008) secondary antibodies. Antibodies used in ChIP-seq analyses: anti-H2Bub (Medimabs #MM-0029-P).
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