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ubxd2 (Proteintech)

Name: ubxd2
Brand: Proteintech
Rating: 93 (8 reviews)

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Proteintech ubxd2
Ubxd2, supplied by Proteintech, used in various techniques. Bioz Stars score: 93/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/ubxd2/product/Proteintech
Average 93 stars, based on 8 article reviews

ubxd2 - by Bioz Stars, 2026-02

93/100 stars

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A. Volcano plot of the (−log10-transformed P value versus the log2-transformed ratio of wildtype/ UBXD8 KO) proteins identified from HeLa cells. n = 3 biologically independent samples for each genotype. P values were determined by empirical Bayesian statistical methods (two-tailed t test adjusted for multiple comparisons using Benjamini-Hochberg’s correction method) using the LIMMA R package; for parameters, individual P values and q values, see Supplementary Dataset. Peroxisomal proteins important for biogenesis (dark blue) and metabolism (red) are highlighted. This dataset has been previously published in and is reanalyzed here. B. Schematic of tandem mass tag (TMT) proteomic hits in distinct peroxisomal pathways. C. Peroxisomal proteins identifies in (A) show reduced expression in UBXD8 KO compared to wildtype HeLa and Hek293T cells. D. Quantification of (C). **** : P<0.0001, N=3, Unpaired T-test.

Journal: bioRxiv

Article Title: The p97-UBXD8 complex maintains peroxisome abundance by suppressing pexophagy

doi: 10.1101/2024.09.24.614749

Figure Lengend Snippet: A. Volcano plot of the (−log10-transformed P value versus the log2-transformed ratio of wildtype/ UBXD8 KO) proteins identified from HeLa cells. n = 3 biologically independent samples for each genotype. P values were determined by empirical Bayesian statistical methods (two-tailed t test adjusted for multiple comparisons using Benjamini-Hochberg’s correction method) using the LIMMA R package; for parameters, individual P values and q values, see Supplementary Dataset. Peroxisomal proteins important for biogenesis (dark blue) and metabolism (red) are highlighted. This dataset has been previously published in and is reanalyzed here. B. Schematic of tandem mass tag (TMT) proteomic hits in distinct peroxisomal pathways. C. Peroxisomal proteins identifies in (A) show reduced expression in UBXD8 KO compared to wildtype HeLa and Hek293T cells. D. Quantification of (C). **** : P<0.0001, N=3, Unpaired T-test.

Article Snippet: The p97 (10736-1-AP; WB: 1:2000), UBXD8 (16251-1-AP; WB: 1:2000), UBXD2 (21052-1-AP; WB: 1:2000), HRD1 (13473-1-AP; WB: 1:2000), AMFR/GP78 (16675-1-AP; WB: 1:2000), VAPB (14477-1-AP; WB: 1:2000), PEX5 ( ) (12545-1-AP; WB 1:500), PEX19 (14713-1-AP; WB 1:1000), MLYCD (15265-1-AP; WB 1:2000), PECR (14901-1-AP; WB 1:1000), DECR (25855-1-AP; WB 1:1000), PMP70/ABCD3 (66697-1-Ig; WB 1:1000; IF 1:400), PEX3 (10946-1-AP; WB 1:1000), ACBD5 (21080-1-AP; WB 1:1000), GFP(66002-1-AP; WB: 1:2000) and ATG5 (10181-2-AP; WB 1:1000) antibodies were from Proteintech Inc.

Techniques: Transformation Assay, Two Tailed Test, Expressing

A. HeLa wildtype and UBXD8 KO cells stained for peroxisomes using peroxisomal matrix marker catalase B. Quantification of average peroxisome per cell and average peroxisome size from (A). At least 100 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals **** : P<0.0001, N=3, Unpaired T-test. C. Peroxisome abundance in wildtype and UBXD8 KO cells that have either no peroxisomes or less then 10 peroxisomes per cell. D. Rescue of peroxisome number in UBXD8 KO cells transfected with either UBXD8-HA, UBXD8-UBA*-HA, UBXD8-ΛUAS-HA or UBXD8-UBX*-HA. Cells were stained for peroxisomes using peroxisomal matrix marker catalase. E. Quantification of average peroxisome per cell from HeLa wildtype and UBXD8 KO cells as well as UBXD8 KO cells transfected with either UBXD8-HA, UBXD8-UBA*-HA, UBXD8-ΛUAS-HA or UBXD8-UBX*-HA (D). Peroxisome numbers were quantified in cells expressing HA-tagged UBXD8 constructs only. At least 100 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals **, **** : P<0.05, 0.0001. Two-way ANOVA with Tukey’s multiple comparisons test. F. Immunoblots of constructs transfected. Scale bar is 10μM.

Journal: bioRxiv

Article Title: The p97-UBXD8 complex maintains peroxisome abundance by suppressing pexophagy

doi: 10.1101/2024.09.24.614749

Figure Lengend Snippet: A. HeLa wildtype and UBXD8 KO cells stained for peroxisomes using peroxisomal matrix marker catalase B. Quantification of average peroxisome per cell and average peroxisome size from (A). At least 100 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals **** : P<0.0001, N=3, Unpaired T-test. C. Peroxisome abundance in wildtype and UBXD8 KO cells that have either no peroxisomes or less then 10 peroxisomes per cell. D. Rescue of peroxisome number in UBXD8 KO cells transfected with either UBXD8-HA, UBXD8-UBA*-HA, UBXD8-ΛUAS-HA or UBXD8-UBX*-HA. Cells were stained for peroxisomes using peroxisomal matrix marker catalase. E. Quantification of average peroxisome per cell from HeLa wildtype and UBXD8 KO cells as well as UBXD8 KO cells transfected with either UBXD8-HA, UBXD8-UBA*-HA, UBXD8-ΛUAS-HA or UBXD8-UBX*-HA (D). Peroxisome numbers were quantified in cells expressing HA-tagged UBXD8 constructs only. At least 100 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals **, **** : P<0.05, 0.0001. Two-way ANOVA with Tukey’s multiple comparisons test. F. Immunoblots of constructs transfected. Scale bar is 10μM.

Techniques: Staining, Marker, Transfection, Expressing, Construct, Western Blot

A. Hela cells were transfected with siRNAs to HRD1, and cells were stained for catalase (see also Supplementary Figure 3). Quantification of number of peroxisomes per cell, at least 100 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals. ns: not significant, **** : P<0.0001. One-way ANOVA with Dunnett’s multiple comparisons test. B. Quantification of peroxisome per cell in HEK293T wildtype and GP78 KO cells. At least 100 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals. **** : P<0.0001. Unpaired T-test. C. HeLa wildtype and UBXD2 KO cells stained for peroxisomes using catalase. D. Quantification of peroxisome per cell from (C). At least 100 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals. NS: not significant. Unpaired T-test. E. Immunoblots of Hela wildtype (untreated or treated with DTT) and UBXD8 KO for ER stress markers BiP and ATF4. N=3, F. rt-qPCR of xbp1 total and xbp1 spliced (xbp1s) mRNA transcripts in wildtype and UBXD8 KO cells treated with 1.5 mM DTT for 4 hours. N=3. NS: Not significant, *, **** : P < 0.01, 0.0001. Two-way ANOVA with Dunnett’s post-hoc analysis. Scale bar is 10μM.

Journal: bioRxiv

Article Title: The p97-UBXD8 complex maintains peroxisome abundance by suppressing pexophagy

doi: 10.1101/2024.09.24.614749

Figure Lengend Snippet: A. Hela cells were transfected with siRNAs to HRD1, and cells were stained for catalase (see also Supplementary Figure 3). Quantification of number of peroxisomes per cell, at least 100 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals. ns: not significant, **** : P<0.0001. One-way ANOVA with Dunnett’s multiple comparisons test. B. Quantification of peroxisome per cell in HEK293T wildtype and GP78 KO cells. At least 100 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals. **** : P<0.0001. Unpaired T-test. C. HeLa wildtype and UBXD2 KO cells stained for peroxisomes using catalase. D. Quantification of peroxisome per cell from (C). At least 100 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals. NS: not significant. Unpaired T-test. E. Immunoblots of Hela wildtype (untreated or treated with DTT) and UBXD8 KO for ER stress markers BiP and ATF4. N=3, F. rt-qPCR of xbp1 total and xbp1 spliced (xbp1s) mRNA transcripts in wildtype and UBXD8 KO cells treated with 1.5 mM DTT for 4 hours. N=3. NS: Not significant, *, **** : P < 0.01, 0.0001. Two-way ANOVA with Dunnett’s post-hoc analysis. Scale bar is 10μM.

Techniques: Transfection, Staining, Western Blot, Quantitative RT-PCR

A. Volcano plot of the total cholesterol esters and triacylglycerol species identified using lipidomics of whole cell extracts of HEK-293T cells (−log10-transformed P value versus the log2-transformed ratio of UBXD8 KO: wildtype). VLCFA species indicated for CE (orange) and TG (dark blue). This dataset has been previously published in and is reanalyzed here. B. VLCFA species indicated for phosphatidylserine (PS) (green), phosphatidylethanolamine (PE) (red) and phosphatidylcholine (PC) (violet). Lipids were measured by LC-MS/MS following normalization by total protein amount. (n ≥ 3 biologically independent experiments were performed, each with duplicate samples). This dataset has been previously published in and is reanalyzed here. C. Immunoblots of catalase levels in whole cell lysates of HeLa wildtype and UBXD8 KO cells. D. Quantification of catalase levels in (C). N=3 independent experiments. NS: not significant. Unpaired T-test. E. Catalase activity was quantified using a commercial kit. N=3 independent experiments. ** : P<0.0001, Unpaired T-Test.

Journal: bioRxiv

Article Title: The p97-UBXD8 complex maintains peroxisome abundance by suppressing pexophagy

doi: 10.1101/2024.09.24.614749

Figure Lengend Snippet: A. Volcano plot of the total cholesterol esters and triacylglycerol species identified using lipidomics of whole cell extracts of HEK-293T cells (−log10-transformed P value versus the log2-transformed ratio of UBXD8 KO: wildtype). VLCFA species indicated for CE (orange) and TG (dark blue). This dataset has been previously published in and is reanalyzed here. B. VLCFA species indicated for phosphatidylserine (PS) (green), phosphatidylethanolamine (PE) (red) and phosphatidylcholine (PC) (violet). Lipids were measured by LC-MS/MS following normalization by total protein amount. (n ≥ 3 biologically independent experiments were performed, each with duplicate samples). This dataset has been previously published in and is reanalyzed here. C. Immunoblots of catalase levels in whole cell lysates of HeLa wildtype and UBXD8 KO cells. D. Quantification of catalase levels in (C). N=3 independent experiments. NS: not significant. Unpaired T-test. E. Catalase activity was quantified using a commercial kit. N=3 independent experiments. ** : P<0.0001, Unpaired T-Test.

Techniques: Transformation Assay, Liquid Chromatography with Mass Spectroscopy, Western Blot, Activity Assay

A. GFP-UBXD8 and RFP-SKL were transiently transfected into COS-7 or HeLa cells and stained with BODIPY (665/676) to label lipid droplets. B. HeLa cells were transfected with FLAG-tagged wildtype UBXD8 or UBXD8 domain deletions (UBA, UAS and UBX) (in green) and RFP-SKL (in red). C . Quantification of (B) showing number of peroxisomes with UBXD8 localization. 15-20 cells were analyzed in N=3 independent experiments. Scatter plot shows mean and std.dev. ns: not significant, ** : P<0.001. One-way ANOVA with Dunnett’s multiple comparisons test. Scale bar is 5μM.

Journal: bioRxiv

Article Title: The p97-UBXD8 complex maintains peroxisome abundance by suppressing pexophagy

doi: 10.1101/2024.09.24.614749

Figure Lengend Snippet: A. GFP-UBXD8 and RFP-SKL were transiently transfected into COS-7 or HeLa cells and stained with BODIPY (665/676) to label lipid droplets. B. HeLa cells were transfected with FLAG-tagged wildtype UBXD8 or UBXD8 domain deletions (UBA, UAS and UBX) (in green) and RFP-SKL (in red). C . Quantification of (B) showing number of peroxisomes with UBXD8 localization. 15-20 cells were analyzed in N=3 independent experiments. Scatter plot shows mean and std.dev. ns: not significant, ** : P<0.001. One-way ANOVA with Dunnett’s multiple comparisons test. Scale bar is 5μM.

Techniques: Transfection, Staining

A. Schematic for pexophagy flux reporter. B. Representative images of wildtype and UBXD8 KO cells transfected with GFP-Cherry-PEX26. C. Wildtype and UBXD8 KO cells were transfected with the flux reporter and treated with 150 nM Torin1 for 18 hours. Quantification showing the ratio of GFP: (GFP + mCherry + ) in Hela wildtype and UBXD8 KO cells. 50-100 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals. **, ***, **** : P<0.01, 0.001, 0.0001. Two-way ANOVA with Šidáks multiple comparisons test. D. Representative images of HeLa control or p97 siRNAs and GFP-Cherry-PEX26. E. Quantification showing the ratio of GFP: (GFP + mCherry + ) in Hela control, or p97 depleted cells. 50-100 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals. *, **, **** : P<0.05, 0.001, 0.0001. Two-way ANOVA with Tukey’s multiple comparisons test. F. Immunoblot showing p97. Scale bar is 10 μM.

Journal: bioRxiv

Article Title: The p97-UBXD8 complex maintains peroxisome abundance by suppressing pexophagy

doi: 10.1101/2024.09.24.614749

Figure Lengend Snippet: A. Schematic for pexophagy flux reporter. B. Representative images of wildtype and UBXD8 KO cells transfected with GFP-Cherry-PEX26. C. Wildtype and UBXD8 KO cells were transfected with the flux reporter and treated with 150 nM Torin1 for 18 hours. Quantification showing the ratio of GFP: (GFP + mCherry + ) in Hela wildtype and UBXD8 KO cells. 50-100 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals. **, ***, **** : P<0.01, 0.001, 0.0001. Two-way ANOVA with Šidáks multiple comparisons test. D. Representative images of HeLa control or p97 siRNAs and GFP-Cherry-PEX26. E. Quantification showing the ratio of GFP: (GFP + mCherry + ) in Hela control, or p97 depleted cells. 50-100 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals. *, **, **** : P<0.05, 0.001, 0.0001. Two-way ANOVA with Tukey’s multiple comparisons test. F. Immunoblot showing p97. Scale bar is 10 μM.

Techniques: Transfection, Control, Western Blot

A. Representative images of HeLa cells transfected with control and UBXD8 or ATG5 siRNAs and stained for catalase. B. Quantification of peroxisomes per cell from (A). 50-100 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals. **** = P<0.0001. Two-way ANOVA with Dunnett’s multiple comparisons test. C. Immunoblot of UBXD8 and ATG5. D. Representative images of HeLa cells (wildtype and UBXD8 KO) transfected with GFP-USP30. Cells were stained for catalase. E. Quantification of peroxisomes per cell in GFP-USP30 transfected cells. 50-100 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals. ***, **** = P< 0.001, 0.0001. Two-way ANOVA with Dunnett’s multiple comparisons test N=3, 2-way ANOVA. F. Immunoblot of GFP-USP30 expression. G. Wildtype and UBXD8 KO HeLa cells were stained with NBR1 and catalase. H. Mander’s colocalization of images in (G). 100-120 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals. **** :P< 0.0001. Students unpaired T-test. F. Immunoblot of GFP-USP30 expression. Scale bar is 10 μM (A and D) and 5 μM (G).

Journal: bioRxiv

Article Title: The p97-UBXD8 complex maintains peroxisome abundance by suppressing pexophagy

doi: 10.1101/2024.09.24.614749

Figure Lengend Snippet: A. Representative images of HeLa cells transfected with control and UBXD8 or ATG5 siRNAs and stained for catalase. B. Quantification of peroxisomes per cell from (A). 50-100 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals. **** = P<0.0001. Two-way ANOVA with Dunnett’s multiple comparisons test. C. Immunoblot of UBXD8 and ATG5. D. Representative images of HeLa cells (wildtype and UBXD8 KO) transfected with GFP-USP30. Cells were stained for catalase. E. Quantification of peroxisomes per cell in GFP-USP30 transfected cells. 50-100 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals. ***, **** = P< 0.001, 0.0001. Two-way ANOVA with Dunnett’s multiple comparisons test N=3, 2-way ANOVA. F. Immunoblot of GFP-USP30 expression. G. Wildtype and UBXD8 KO HeLa cells were stained with NBR1 and catalase. H. Mander’s colocalization of images in (G). 100-120 cells were analyzed in N=3 independent experiments. Violin plot shows median and 95% confidence intervals. **** :P< 0.0001. Students unpaired T-test. F. Immunoblot of GFP-USP30 expression. Scale bar is 10 μM (A and D) and 5 μM (G).

Techniques: Transfection, Control, Staining, Western Blot, Expressing

A. HEK293T cells were treated with 150 nM Torin or 50 nM bafilomycin A (BafA) for 24 hours and then with 100 μg/ ml cycloheximide for the indicated time points to stop translation. Immunoblots showing PMP70 half-life. B. Quantification of PMP70 levels normalized to GAPDH from (A). N=3 independent experiments. **, *** : P< 0.01, 0.001. Two-way ANOVA with Tukey’s multiple comparisons test. C. HEK293T cells were transfected with HA-ubiquitin and treated with 150 nM Torin-1 in the presence or absence of 5 μM Bortezomib (Btz) or 50 nM BafA for 24 hours. Cells were lysed in SDS, and denaturing HA immunoprecipitations were performed. Immunoblots of indicated proteins showing increased ubiquitylation of PMP70 in cells treated with Btz or BafA. N=3 independent experiments. D. HEK293T cells were transfected with HA-ubiquitin and siRNAs to control, UBXD8 or p97. Cells were treated with 150 nM Torin-1 for 24 hours. Cells were lysed in SDS, and denaturing HA immunoprecipitations were performed. Immunoblots of indicated proteins showing increased ubiquitylation of PMP70 in cells depleted of UBXD8 and p97. N=3 independent experiments. E. Model showing p97-UBXD8 suppression of pexophagy.

Journal: bioRxiv

Article Title: The p97-UBXD8 complex maintains peroxisome abundance by suppressing pexophagy

doi: 10.1101/2024.09.24.614749

Figure Lengend Snippet: A. HEK293T cells were treated with 150 nM Torin or 50 nM bafilomycin A (BafA) for 24 hours and then with 100 μg/ ml cycloheximide for the indicated time points to stop translation. Immunoblots showing PMP70 half-life. B. Quantification of PMP70 levels normalized to GAPDH from (A). N=3 independent experiments. **, *** : P< 0.01, 0.001. Two-way ANOVA with Tukey’s multiple comparisons test. C. HEK293T cells were transfected with HA-ubiquitin and treated with 150 nM Torin-1 in the presence or absence of 5 μM Bortezomib (Btz) or 50 nM BafA for 24 hours. Cells were lysed in SDS, and denaturing HA immunoprecipitations were performed. Immunoblots of indicated proteins showing increased ubiquitylation of PMP70 in cells treated with Btz or BafA. N=3 independent experiments. D. HEK293T cells were transfected with HA-ubiquitin and siRNAs to control, UBXD8 or p97. Cells were treated with 150 nM Torin-1 for 24 hours. Cells were lysed in SDS, and denaturing HA immunoprecipitations were performed. Immunoblots of indicated proteins showing increased ubiquitylation of PMP70 in cells depleted of UBXD8 and p97. N=3 independent experiments. E. Model showing p97-UBXD8 suppression of pexophagy.

Techniques: Western Blot, Transfection, Ubiquitin Proteomics, Control

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