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8 protocols using anti gst

1

Western Blot Analysis of Mitochondrial Proteins

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NuPAGE™ 4-12% Bis-Tris Protein Gels and NuPAGE® MOPS SDS running buffer was applied for SDS-PAGEs and immunoblot analyses. The following antibodies were used for western blot analyses: Anti-RpL3 (Santa Cruz, sc-86828), anti-RpL7a (Cell Signaling, 2415S), anti-RpS19 (Santa Cruz, sc-100836), anti-RpS6 (Cell Signaling, 2317S), anti-C-IV s.1 (Abcam, ab14705), anti-C-I 30 (Abcam, ab14711), anti-C-I 75 (GeneTex, GTX105270), anti-CORE2 (Abcam, ab14745), anti-TOM20 (Santa Cruz, sc-17764, sc-11415), anti-TOM40 (Santa Cruz, sc-11414), anti-PINK1 (Abcam, ab23707), anti-GST (Sigma, G7781; for mRNP immunoblot), anti-GST (GenScript, A00865; for PLA), anti-myc (Cell Signaling, 2272S), anti-HA (Sigma, 11867423001), anti-GFP (Abcam, ab13970), anti-puromycin (Millipore, MABE343), anti-ABCE1 (a gift from Dr. R Hegde), anti-Pelo (Abcam, ab140615), anti-NOT4 (Abcam, ab72049), anti-dNOT4 (a gift from Dr. E Wahle), anti-dPelo (a gift from Dr. J Han), anti-Ub (Santa Cruz, sc-8017), anti-p-S65-Ub (Millipore, ABS1513-I), anti-K48-Ub (Abcam, ab140601), anti-K63-Ub (Millipore, 05-1308), anti-OPTN (Abcam, ab23666), anti-NDP52 (Abcam, ab68588), anti-P62 (PROGEN, GP62-C), anti-dP62/Ref2P (Abcam, ab-178440), anti-p-TBK1 (Cell Signaling, 5843S), anti-TBK1 (Cell Signaling, 3013S), anti-LC3B (Cell signaling, 2775S).
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2

GST Pull-Down Assay for Protein Interactions

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The GST pull-down assay was performed as described previously (51 (link)). Briefly, approximately 10 μg of purified GST-NC2β or GST-GFP fusion proteins were incubated with His-ARP8 in 500 μl incubated buffer (50 mM Tris–HCl, pH 6.8, 250 mM NaCl, 1.5% glycerol, 0.6% Triton X-100, and 0.1% Tween) for 4 h at 4°C. The beads were washed three times with incubation buffer. The washed beads were boiled in 1× SDS loading buffer, and the precipitates were separated by SDS-PAGE, followed by western blot analysis with anti-GST (GenScript, catalog no. A00866) and anti-His (Abmart, catalog no. M30111) antibodies.
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3

Protein Interaction Assays with Tagged Proteins

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TYLCV V2, SlGRXC6, and SlNTRC80 ORFs were cloned into pET32a, pGEX4T-1, or pHMTC to make constructs expressing His6-, GST-, or MBP-tagged proteins. All constructs were transformed into E. coli BL21 (DE3) cells and cultured at 37°C. After the OD600 had reached ∼0.6, β-D-thiogalactoside (IPTG) was added to the cultures and incubated for 4 hours. Bacterial cells were pelleted, resuspended with phosphate-buffered saline (PBS) buffer, and sonicated to break cells. The His6-, GST-, and MBP-fused proteins were individually purified using a nickel-nitrilotriacetic acid (Ni-NTA) resin binding column (Qiagen, Germany), GST binding column (Qiagen, Germany), and MBP binding column (Novagen, Germany), respectively, according to manufacturer’s instructions. Competitive pulldown assays were performed as described previously [20 (link)] with minor modifications. Briefly, the indicated amounts of His6-V2 or His6 were mixed with 2 μg of GST-SlGRXC6 for 1 h before being incubated with 2 μg of MBP-SlNTRC80 for pulldown assays. The column-bound proteins were eluted and detected by immunoblotting with anti-His6 (Abcam, UK), anti-MBP (Sigma, USA), or anti-GST (GenScript, USA) antibody.
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4

Protein Interaction Analysis via GST Pulldown

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Purified MBP-PAB2 or MBP-PAB4 protein (100 pmol) was incubated with 25 μl of pierce glutathione magnetic agarose beads to be pre-cleared in 200 µL IPP buffer (150 mM NaCl, 0.1% NP-40, 10 mM Tris, pH 7.4, 0.5 mM DTT) for 1 h with gentle rotation at 4 °C. Then, the pre-cleared MBP-PAB2 or MBP-PAB4 protein was mixed with 100 pmol GST or GST-ECT2 fragments for 2 h at 4 °C with gentle rocking and equal amount of pierce glutathione magnetic agarose beads. The beads were then washed five times with 0.5 ml binding buffer and proteins were eluted by boiling the beads with 40 μl SDS loading buffer at 95 °C for 10 min. Proteins were analyzed by 12% SDS–PAGE followed by western blotting analysis with anti-MBP (Mei5bio) and anti-GST (Genscript).
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5

Characterization of DNA Damage Response Pathways

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Hydroxyurea (HU, a final concentration of 2 mM was used throughout this study), cycloheximide (CHX, a final concentration of 50 μg/ml was used) and the ATR inhibitor NU6027 (a final concentration of 10 μM was used), were purchased from Sigma. BrdU (a final concentration of 20 μM was used) was from BD Biosciences.
Rabbit polyclonal antibodies used for immunoblotting and/or immunoprecipitaion including anti-MYC (A190–205A), anti-HA (A190–208A), anti-USP20 (A301–189A), anti-CLASPIN (A300–267A), anti-HERC2 (A301–905A), anti-ATR (A300–138A) were from the Bethyl Laboratories; Chk1 antibody (sc-8408) was from the Santa Cruz Biotechnology. Rabbit monoclonal antibody anti-GST (A00865) was from the GenScript. Mouse monoclonal antibody anti-FLAG M2 (F1804) was from Sigma. Phospho-Chk1 (Ser345) (Rabbit mAb #2348) and Phospho-(Ser/Thr) ATM/ATR substrate antibody (#2851) were from Cell Signaling. Anti-BrdU fluorescein isothiocyanate (FITC) (347583) used for immunofluorescence was from BD Biosciences.
The detailed information of all the expression constructs is available upon request.
All cell lines were cultured in high-glucose Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum at 37°C.
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6

Comprehensive Mitochondrial Protein Analysis

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S. pombe whole cell extracts were prepared by alkaline extraction (58 (link)) or by breaking cells with glass beads using a FastPre-24 bead beater (MP Biomedicals) (59 (link)). Mitochondrial protein extracts were prepared as described above. Proteins were resolved by electrophoresis on SDS-PAGE, and the separated protein bands were transferred electrophoretically to a Hybond ECL transfer membrane (GE healthcare). Blots were probed with anti-Cox1 (1:1000), anti-Cox2 (1:1000), anti-Cox3 (1:400), anti-Cox4 (1:1000) and anti-Cob1 (1:500), anti-Trz2 (1:1000), anti-Sla1 (1:5000), anti-HSP60 (1:1000; Sangon Biotech), anti-FLAG (1:000; Sigma), anti-CBP (1:1000; GenScript), anti-HA (1:2000; Sigma-Aldrich), anti-c-Myc (1:2000; Affinity Biotech), anti-His (1:2000; GenScript) and anti-GST (1:2000; GenScript) Abs. Secondary Abs used were IRDye 800CW conjugated goat anti-rabbit or anti-mouse Abs (LI-COR Biosciences). Bands were detected using an Odyssey near-infrared fluorescence scanner (LI-COR Biosciences).
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7

Western Blot Antibody Optimization

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Primary antibodies used were anti-FLAG (MilliporeSigma; catalog no.: F1804, 1:8000 dilution), anti-GFP (Santa Cruz; catalog no.: SC-9996, 1:1000 dilution), anti-GST (GenScript; catalog no.: A00865, 1:2000 dilution), anti-ORC2 (BD Biosciences; catalog no.: 551178, 1:1000 dilution), anti-PCNA (PC10; Santa Cruz; catalog no.: SC-56, 1:4000 dilution), anti-SDE2 (Sigma Atlas; catalog no.: HPA031255, 1:4000 dilution), anti-TIM (Bethyl; catalog no.: A300-961A, 1:2000 dilution), and antivinculin (H-300; Santa Cruz; catalog no.: SC-5573, 1:1000 dilution). Secondary antibodies used were antimouse immunoglobulin HRP (Cell Signaling Technology; catalog no.: 7076, 1:4000 dilution) and anti-rabbit immunoglobulin (Cell Signaling Technology; catalog no.: 7074, 1:4000 dilution). Chemical and reagent information are provided in Table S2.
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8

Purification and Analysis of GST and MBP Fusion Proteins

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Pull-down analysis was performed according to Friedrich et al. (2021) . Recombinant GST and MBP fusion proteins were produced in the BL21 strain of E. coli and then were purified using Mag-Beads GST (Sangon, China) or Amylose Resin (New England Biolabs). The purified proteins were immunoblotted with anti-GST (GenScript, 1:2,000) or anti-MBP (New England Biolabs, 1:5,000) antibodies. The relevant primer sequences are listed in Supplemental Data Set 1.
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