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4 protocols using α his

1

Protein Extraction and Analysis Protocols

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Protein extracts were prepared from TCA-fixed cells. TCA pellets were resuspended in 2× urea buffer (62.5 mM Tris, pH 6.8, 10% glycerol, 4% SDS, 5% β-mercaptoethanol, 8 M urea, and bromophenol blue) and vortexed 3 min at 4°C with 0.5-mm glass beads. After boiling, samples were analyzed using standard SDS-PAGE and Western blotting procedures. Antibodies used included α-GFP (11 814 460 001; Roche), α-PGK1 (A6457; Invitrogen), α-GST (G1160; Sigma), α-His (H1029; Sigma), α-me3K9H3 (NBP1-30141; Novus), GαR-HRP (170-6515; Biorad), and GαM-HRP HRP (170-6516; Biorad). The signal was visualized using SuperSignal West Pico PLUS (1863096; Thermo Fisher Scientific) and film (SuperRX, 47410 19236; Fuji). Protein extracts for in vitro kinase assays were prepared as follows: exponentially growing yeast cells were lysed by freezer milling (Kraft et al., 2012 (link)) and the powder was resuspended in PBS buffer with 3 mM EDTA, Roche Inhibitor Tablet, Sigma Inhibitors of yeast proteases, 0.5% Triton X-100, and 2 mM DTT. The extract was cleared by centrifugation at 235,000 ×g, and equal amounts of the supernatant were used for the in vitro kinase assays.
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2

Western Blot Analysis of Trypanosome Cytoskeleton

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Whole cells or detergent-extracted cytoskeleton (CSK) samples were prepared as previously described [9 (link)] with a concentration of 1 × 107 or 2 × 107 (BSF or PCF) cells/well, as mentioned according to the experiments. Whole cell (T), CSK-enriched pellets (P), and soluble proteins (S) were prepared as described before [21 (link)], with the addition of 1% NP-40 and 150 mM NaCl. Proteins were separated on SDS-PAGE and transferred onto 0.2 μm PVDF membrane. The following primary antibodies were used in the indicated cases: α-BILBO1 (pAb 1:200), α-TbKINX1B (rabbit polyclonal 1:2000 or mouse monoclonal 1:1000), α-Tubulin (TAT1, 1:1000, [34 (link)]), anti-enolase (1:10,000), and α-His (Sigma H-1029, 1:3000). Incubations with secondary antibodies goat α-rabbit HRP (Jackson 115-055-068) and goat α-mouse HRP (Jackson 115-035-044) were also performed as cited above. Labelling was revealed with Clarity ECL Substrate (Bio-Rad) and revealed using ImageQuant LAS400. Quantifications were performed using ImageJ. Errors bars in graphs represent the standard error (n = 3).
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3

Immunoprecipitation and Immunoblotting of Lem27

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HEK293T cells were resuspended with 1 ml NP40 lysis buffer for 10 min on ice, and the lysates were then centrifugated at 12,000xg at 4°C for 10 min. Beads coated with Flag- or HA-specific antibody were added to cleared lysates and incubated on a rotatory shaker for 8 hr at 4°C. After washed three times with the NP40 lysis buffer, aliquots of beads were mixed with the purified Lem27 or Lem27C24A in 20 μL DUB buffer at 37°C. At the indicated time points, reactions were stopped by adding 5 μL 5 × SDS loading buffer and were heated at 95°C for 5 min. After SDS-PAGE, proteins were transferred onto nitrocellulose membranes (Pall Life Sciences) for immunoblotting after being blocked in 5% nonfat milk in PBST buffer for 1 hr. Primary antibodies used in this study and their dilutions are as follows: α-Flag(Sigma, Cat# F1804, 1: 3000), α-GFP(Sigma, cat# G7781, 1:5000), α-His(Sigma, cat# H1029, 1: 10,000), α-HA (Santa Cruz, cat# sc-7392, 1: 1000), α-ICDH (1: 20,000) (Xu et al., 2010 (link)), α-tubulin (DSHB, E7, 1: 10,000). Antibodies specific for Lem27 were generated by immunization of rabbits with purified His6-Lem27 using a standard procedure (AbMax Biotechnology Co., LTD, Beijing, China) and were used at 1:500. Washed membranes were incubated with appropriate IRDye secondary antibodies and signals were detected and analyzed by an Odyssey CLx system (LI-COR).
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4

Lem27 DUB Activity Assay

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HEK293T cells were resuspended with 1 ml NP40 lysis buffer for 10 min on ice, and the lysates were then centrifugated at 12,000xg at 4°C for 10 min. Beads coated with Flagor HA-specific antibody were added to cleared lysates and incubated on a rotatory shaker for 8 h at 4°C. After washed three times with the NP40 lysis buffer, aliquots of beads were mixed with the purified Lem27 or Lem27C24A in 20 μL DUB buffer at 37°C. At the indicated time points, reactions were stopped by adding 5 μL 5×SDS loading buffer and were heated at 95°C for 5 min. After SDS-PAGE, proteins were transferred onto nitrocellulose membranes (Pall Life Sciences) for immunoblotting after being blocked in 5% nonfat milk in PBST buffer for 1h. Primary antibodies used in this study and their dilutions are as follows:
α-Flag(Sigma, Cat# F1804, 1: 3000), α-GFP(Sigma, cat# G7781, 1:5000), α-His(Sigma, cat# H1029, 1: 10,000), α-HA (Santa Cruz, cat# sc-7392, 1: 1000), α-ICDH (1: 20,000) 64 (link) , α-tubulin (DSHB, E7, 1: 10,000). Antibodies specific for Lem27 were generated by immunization of rabbits with purified His6-Lem27 using a standard procedure (AbMax Biotechnology Co., LTD, Beijing, China) and were used at 1:500. Washed membranes were incubated with appropriate IRDye secondary antibodies and signals were detected and analyzed by an Odyssey CLx system (LI-COR).
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