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9 protocols using smurf1

1

Immunoprecipitation and Ubiquitination Analysis

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Immunoprecipitation was performed as previously described.48 (link) MC3T3-E1 cells or primary osteoblasts were treated with 5 μmol·L1 MG132 (Sigma) for 6 h. Cells were lysed in buffer (150 mmol·L1 NaCl, 50 mmol·L1 Tris, pH 7.8, 10% glycerol, 1 mmol·L1 EGTA, 0.5% NP-40, 1 mmol·L1 EDTA, 1 mmol·L1 PMSF, 1× cocktail) on ice with vigorous shaking for 30 min. The lysates were centrifuged at 4 °C at 12 000 r·min1 for 15 min. Twenty microliters of lysate was saved as the total protein sample. The rest of the supernatant was incubated with 20 μL of protein A/G (Santa Cruz) for 40 min to exclude nonspecific binding. After 10 min of centrifugation at 12 000 r·min1, the supernatant was subjected to IP with Runx2 antibody (Cell Signaling Technology, 12556S) and protein A/G at 4 °C for 4 h. The antibody and protein A/G were incubated for 2 h in advance. Finally, the protein A/G beads were collected and washed with cell lysis buffer twice. The lysates were subjected to western blotting with the indicated antibody. The following antibodies were used in the study: ubiquitin (1:2 000, Cell Signaling Technology, 3936S), GAPDH (1:5 000, Abways Technology, AB0036), Runx2 antibody (1:1 000, CST, 12556S), NONO (1:1 000, Abways Technology, CY8525), SFPQ (1:1 000, Abways Technology, CY8089), Smurf1 (1:1 000, Santa Cruz, sc-100616), and HA-tag (1:2 000, Cell Signaling Technology, #3724S).
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2

Immunofluorescence Microscopy of Smurf1, Cytoskeleton, and Odontogenic Proteins

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Tissue sections and HAT‐7 (Osaka Dental University) cells were fixed, washed, blocked and incubated with antibodies as follows: Smurf1 (1:50, Santa Cruz, USA), F‐actin (Phalloidin‐iFluor 488, 1:1000, Abcam, USA), F‐actin (Phalloidin‐iFluor 594, 1:1000, Abcam, USA), RhoA (1:50, Proteintech, China), AMBN (1:50, Santa Cruz, USA), AMGN (1:50, Santa Cruz, USA), Alexa Fluor 594 goat anti rabbit (1:1000, Invitrogen, USA), Alexa Fluor 594 goat anti mouse (1:1000, Invitrogen, USA) and Alexa Fluor 488 goat anti mouse (1:1000, Invitrogen, USA). The images were observed and taken under fluorescence microscope (Olympus, Japan).
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3

Immunoprecipitation and Immunoblotting Assay

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Immunoprecipitation and immunoblotting were carried out as described previously [46 (link)]. The following antibodies were used: IRF3 (1:1000, Santa Cruz, sc-9082), p-IRF3 (1:1000, Cell Signaling, 4947S), OTUD1 (1:1000, Abcam, ab182511), Flag (1:5000, Sigma, F7425), β-actin (1:5000, Proteintech, 66009-1-Ig), Myc (1:5000, Abmart, m2002), MAVS (1:1000, Santa Cruz, sc-166583), TRAF3 (1:1000, Cell Signaling, 4729S), TRAF6 (1:1000, Abcam, ab94720), TBK1 (1:1000, Cell Signaling, 3013S), RIG-I (1:1000, Cell Signaling, 4200S), Smurf1 (1:1000, Santa Cruz, sc-100616), Smurf2 (1:1000, Santa Cruz, sc-25511), Ub (1:1000, Santa Cruz, sc-8017), HA (1:5000, Abcam, ab9110), K48-Ub (1:1000, Cell Signaling, 4289S), and VSVG (1:5,000, Santa Cruz, sc-66180).
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4

SMURF1-p27 Interaction Protocols

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For the His-p27 pulldown: FLAG-SMURF1 (BPS Bioscience) was rocked at 4°C with (His)6-p27 (purified in house) and Ni-NTA beads (Qiagen) (blocked with BSA for 1 h) for 2 h in 1× ubiquitination buffer (40 mM Tris pH 7.6, 5 mM MgCl2, 2 mM DTT). Beads were pelleted in a microfuge and washed 5×. Flowthrough and bead-bound proteins fractions were run on 10.5% SDS-PAGE gels. Antibodies used were SMURF1 (sc-100616 Santa Cruz Biotechnology) and p27 (AF2256 R&D Systems).
For the Myc-SMURF1 -HECT pulldown: Myc-SMURF1 -HECT (Addgene 13677) was transfected into HELA cells using Lipofectamine 3000 as per the manufacturer’s instructions. Cells were lysed in RIPA buffer (Thermo Scientific) and SMURF1 was immunoprecipitated using an anti-Myc antibody (9E10 Santa Cruz Biotechnology) and protein G agarose (Roche). Beads were then rotated with (His)6-p27 (purified in house) in 1× ubiquitination buffer (40 mM Tris pH 7.6, 5 mM MgCl2, 2 mM DTT) at 4 °C for 2 h. Beads were pelleted in a microfuge and washed 5×. Flowthrough and bead-bound proteins fractions were run on 10.5% SDS-PAGE gels. Antibodies used were SMURF1 (sc-100616 Santa Cruz Biotechnology) and p27 (AF2256 R&D Systems).
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5

SMURF1 Expression in BMP2-Treated hMSCs

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100,000 HMSCs were cultured in 6 well plates and treated with BMP2 FEEs (20x106 particles). Untreated cells served as control. Each experiment was performed in triplicate. 48 hours post treatment, the total protein from the cells was isolated and 20μg of protein from each group (estimated using BCA assay kit from Thermo Scientific) was resolved by SDS PAGE followed by western blotting for SMURF1 (Santa Cruz 1/500) and tubulin (loading control, 1/2000 Sigma) with the corresponding secondary antibodies and imaged using a Licor Odyssey CLX imager.
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6

Comprehensive Immunoblotting Antibody Panel

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Primary antibodies used against proteins were as follow: SMURF1 (Santa Cruz, sc-100616), SMURF1 (Abcam, ab57573), BiP/GRP78 (ABclonal, A0241); Actin (Sigma, A1978), p62 (MBL, PM045); LC3B (Sigma, L7543); Phospho-IRE1(S724) (ABclonal, AP0878); IRE1(ABclonal, A17940); Phospho-JNK1/2/3 (T183+T183+T221) (Abmart, T55541); JNK (ABclonal, A4867); Phospho-eIF2α (Ser51) (ABclonal, AP0692); eIF2α (ABclonal, A0764); XBP1 (ABclonal, A1731); ATF4 (Santa Cruz, sc-390063); CHOP (ABclonal, A6504); BCL-2 (ABmart, T40056); Flag M2 (Sigma, F3165); GFP-tag (Proteintech, 66002-1-lg); HA-tag (MBL, M180-3); Myc-Tag (Proteintech, 16286-1-AP); NRF2 (Proteintech, 16396-1-AP); KEAP1 (Proteintech, 10503-2-AP); Ubiquitin (MBL, D058-3); alpha Tubulin (Abcam, ab7291), Histone H2B (Santa Cruz, sc-515808); Caspase3 (Santa Cruz, sc-7272); Ki67 (Abcam, ab16667).
Secondary antibodies used were as follow: goat anti-mouse IgG secondary antibody (BOSTER, BA1050); goat anti-rabbit IgG secondary antibody (BOSTER, BA1054); Alexa Fluor® 555 goat anti-mouse IgG (Life Technologies, A21425); ImmPRESSTM HRP anti-Rabbit IgG (VECTOR, MP-7401); ImmPRESSTM HRP anti-Mouse IgG (VECTOR, MP-7402); Rabbit anti-mouse IgG (CST, 58802) and Mouse anti-Rabbit IgG (CST, 93702) were used to avoid interference of the IgG heavy chain.
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7

Chondrocyte Signaling Pathway Analysis

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Transfected cells or limbs of knock-in mice were lysed in ice-cold radio immunoprecipitation assay (RIPA) buffer containing 0.01% protease (Sigma-Aldrich, USA) for 30 min at 4°C. Cell lysis was centrifuged at 12000 rpm for 15 min at 4°C and the protein concentrations were quantified using the Bicinchoninic Acid (BCA) kit (Sigma-Aldrich, USA). SDS-PAGE and western blotting were performed using standard techniques. The primary antibodies of GDF5, SOX9, COL2A1, SMURF1, ID1 and phosphorylated SMAD1/5/8 (Santa Cruz, USA) were used at a dilution of 1:1000, and β-tubulin (Abcam, USA) was used at a dilution of 1:10000 in PBS-Tween 20.
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8

Protein Expression Analysis in Odontogenesis

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Cells were lysed with RIPA buffer (Millipore, USA). Extracted proteins were quantified using the BCA Protein Assay (Bio‐Rad, USA). 20 μg of protein lysates from each group were separated by SDS‐polyacrylamide gel electrophoresis (SDS‐PAGE) then transferred onto polyvinylidene fluoride (PVDF) membranes. After being blocked with 5% skim milk, the PVDF membranes were incubated with antibodies. The primary ones were as follows: Smurf1 (1:200, Santa Cruz, USA), AMBN (1:500, Santa Cruz, USA), AMGN (1:500, Santa Cruz, USA), MMP20 (1:1000, Proteintech, China), KLK4 (1:500, Absin, China), RhoA (1:1000, Proteintech, China) and GAPDH (1:1000, Servicebio, China).
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9

Western Blot Analysis of Protein Expressions

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Cells were lysed in RIPA buffer (150mM NaCl, 1% Nonidet P-40, 0.5% sodium deoxycholate, 0.1% sodium dodecyl sulfate, 50mM Tris pH 8.0), supplemented with protease inhibitors and phosphatase inhibitors, 50mM sodium fluoride, 100mM b-glycerophosphate and 1mM sodium orthovanadate. Protein estimation was performed on the lysates and equal amounts of protein lysates were boiled in 2X sample buffer. Thereafter, samples were loaded onto 10% SDS-PAGE gels and transferred onto 0.45µM PVDF membranes (Millipore). The membranes were blocked in 5% milk and probed with specific antibodies overnight at 4˚C. For visualization of protein signals, blots were incubated with secondary antibodies which were HRP-linked and detected using chemiluminescence. The following antibodies were used: TRAF4 1:2000 (D1N3A, CST), E-cadherin 1:1000 (Cat no. 610181, BD), N-cadherin 1:1000 (Cat no. 610920, BD), Vimentin 1:5000 (CST), SLUG 1:1000 (C19G7, CST), SNAIL 1:1000 (C15D3, CST), Flag 1:5000 (M2, Sigma Aldrich), phospho-Serine 1:1000 (612546, BD), SMURF1 1:1000 (45-K, Santa Cruz), Myc 1:5000 (9E10, Santa Cruz), HA 1:5000 (Y11, Santa Cruz), GFP 1:5000 (FL, Santa Cruz) and GAPDH 1:10,000 (MAB374, Millipore).
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