VPS34 K29/K48 branched ubiquitination governed by UBE3C and TRABID regulates autophagy, proteostasis and liver metabolism

Chen, Yu-Hsuan; Huang, Tzu-Yu; Lin, Yu-Tung; Lin, Shu‐Yu; Li, Wen-Hsin; Hsiao, Hsiang-Jung; Yan, Ruei-Liang; Tang, Hong-Wen; Shen, Zhao-Qing; Chen, Guang-Chao; Wu, Kuen‐Phon; Tsai, Ting‐Fen; Chen, Ruey‐Hwa

doi:10.1038/s41467-021-21715-1

Cited by 52 publications

(33 citation statements)

References 63 publications

(58 reference statements)

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“…Thus, the current model of aggrephagy indicates that p62 governs a sequential recruitment of upstream ATG proteins, such as ULK1 complex, VPS34 complex and ATG16L1, followed by a replacement of the ULK1 complex with the ATG8 family proteins for autophagosome expansion. Accordingly, blockage of VPS34 activity impairs aggrephagy to impede the clearance of ubiquitinated protein aggregates [ 20 , 21 ].…”

Section: Introductionmentioning

confidence: 99%

Long noncoding RNA BCRP3 stimulates VPS34 and autophagy activities to promote protein homeostasis and cell survival

et al. 2022

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Background Autophagy plays important roles in cell homeostasis and protein quality control. Long non-coding RNAs (lncRNAs) have been revealed as an emerging class of autophagy regulators, but the majority of them function in regulating the expression of autophagy-related genes. LncRNAs that directly act on the core autophagic proteins remain to be explored. Methods Immunofluorescence staining and Western blotting were used to evaluate the function of BCRP3 in autophagy and aggrephagy. RNA immunoprecipitation and in vitro RNA–protein binding assay were used to evaluate the interaction of BCRP3 with its target proteins. Phosphatidylinositol 3-phosphate ELISA assay was used to quantify the enzymatic activity of VPS34 complex. qRT-PCR analysis was used to determine BCRP3 expression under stresses, whereas mass spectrometry and Gene Ontology analyses were employed to evaluate the effect of BCRP3 deficiency on proteome changes. Results We identified lncRNA BCRP3 as a positive regulator of autophagy. BCRP3 was mainly localized in the cytoplasm and bound VPS34 complex to increase its enzymatic activity. In response to proteotoxicity induced by proteasome inhibition or oxidative stress, BCRP3 was upregulated to promote aggrephagy, thereby facilitating the clearance of ubiquitinated protein aggregates. Proteomics analysis revealed that BCRP3 deficiency under proteotoxicity resulted in a preferential accumulation of proteins acting in growth inhibition, cell death, apoptosis, and Smad signaling. Accordingly, BCRP3 deficiency in proteotoxic cells compromised cell proliferation and survival, which was mediated in part through the upregulation of TGF-β/Smad2 pathway. Conclusions Our study identifies BCRP3 as an RNA activator of the VPS34 complex and a key role of BCRP3-mediated aggrephagy in protein quality control and selective degradation of growth and survival inhibitors to maintain cell fitness.

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Section: Introductionmentioning

confidence: 99%

Long noncoding RNA BCRP3 stimulates VPS34 and autophagy activities to promote protein homeostasis and cell survival

et al. 2022

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“…Cells were lysed with RIPA buffer containing 50 mM Tris pH 7.5, 150 mM NaCl, 1% NP-40, 0.5% deoxycholic acid, 0.1% SDS, 1 mM DTT, 1 mM phenylmethylsulphonyl fluoride (PMSF), 1 μg/ml aprotinin, 1 μg/ml leupeptin, 1 mM sodium vanadate, 4 mM sodium pyrophosphate and 20 mM NaF. Immunoprecipitation and Western blot using cell lysates with equal amounts of proteins were performed as described [ 36 ].…”

Section: Methodsmentioning

confidence: 99%

Long noncoding RNA Smyca coactivates TGF-β/Smad and Myc pathways to drive tumor progression

et al. 2022

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Background Metastasis and chemoresistance are major culprits of cancer mortality, but factors contributing to these processes are incompletely understood. Methods Bioinformatics methods were used to identify the relations of Smyca expression to clinicopathological features of human cancers. RNA-sequencing analysis was used to reveal Smyca-regulated transcriptome. RNA pull-down and RNA immunoprecipitation were used to examine the binding of Smyca to Smad3/4 and c-Myc/Max. Chromatin immunoprecipitation and chromatin isolation by RNA purification were used to determine the binding of transcription factors and Smyca to various gene loci, respectively. Real-time RT-PCR and luciferase assay were used to examine gene expression levels and promoter activities, respectively. Xenograft mouse models were performed to evaluate the effects of Smyca on metastasis and chemoresistance. Nanoparticle-assisted gapmer antisense oligonucleotides delivery was used to target Smyca in vivo. Results We identify lncRNA Smyca for its association with poor prognosis of many cancer types. Smyca potentiates metabolic reprogramming, migration, invasion, cancer stemness, metastasis and chemoresistance. Mechanistically, Smyca enhances TGF-β/Smad signaling by acting as a scaffold for promoting Smad3/Smad4 association and further serves as a Smad target to amplify/prolong TGF-β signaling. Additionally, Smyca potentiates c-Myc-mediated transcription by enhancing the recruitment of c-Myc/Max complex to a set of target promoters and c-Myc binding to TRRAP. Through potentiating TGF-β and c-Myc pathways, Smyca synergizes the Warburg effect elicited by both pathways but evades the anti-proliferative effect of TGF-β. Targeting Smyca prevents metastasis and overcomes chemoresistance. Conclusions This study uncovers a lncRNA that coordinates tumor-relevant pathways to orchestra a pro-tumor program and establishes the clinical values of Smyca in cancer prognosis and therapy.

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“…Having noted that most K29 linkages are part of conjugates that contain K48 connections [39], polymers with K29/K48 branches were found to trigger the elimination of long-studied model substrates of the ubiquitin proteasome system [76,97]. Similar chain topologies also allow for proteasomal recognition of the VPS34 kinase [101], a crucial regulator of proteotoxic stress, and they elicit the efficient removal of PROTAC-dependent substrates of CUL2 VHL and CUL4 CRBN [82]. The K29-specific branching E3 ligase TRIP12 also helps degrade the FBW7 substrate adaptor of SCF E3 ligases [88].…”

Section: Proteolytic Functionsmentioning

confidence: 99%

Assembly and function of branched ubiquitin chains

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et al. 2022

Trends in Biochemical Sciences

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VPS34 K29/K48 branched ubiquitination governed by UBE3C and TRABID regulates autophagy, proteostasis and liver metabolism

Cited by 52 publications

References 63 publications

Long noncoding RNA BCRP3 stimulates VPS34 and autophagy activities to promote protein homeostasis and cell survival

Long noncoding RNA BCRP3 stimulates VPS34 and autophagy activities to promote protein homeostasis and cell survival

Long noncoding RNA Smyca coactivates TGF-β/Smad and Myc pathways to drive tumor progression

Assembly and function of branched ubiquitin chains

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