Proteomic Characterization of Aggregating Proteins after the Inhibition of the Ubiquitin Proteasome System

Wilde, Inga; Brack, Maria; Winget, Jason M.; Mayor, Thibault

doi:10.1021/pr1008543

Cited by 55 publications

(53 citation statements)

References 77 publications

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“…Indeed, any alteration of PQC processes usually results in accumulation of misfolded and aggregated proteins (Hamano et al, 2008;Korolchuk et al, 2009;Latonen et al, 2011;Welch, 2004;Wilde et al, 2011). We observed that NF-kB-deficient cells possess a higher content of multiubiquitylated and aggregated proteins than control cells.…”

Section: Discussionmentioning

confidence: 66%

NF-κB regulates protein quality control after heat stress through modulation of the BAG3–HspB8 complex

Nivon

Abou‐Samra

Richet³

et al. 2012

Journal of Cell Science

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SummaryWe previously found that the NF-kB transcription factor is activated during the recovery period after heat shock; moreover, we demonstrated that NF-kB is essential for cell survival after heat shock by activating autophagy, a mechanism that probably helps the cell to cope with hyperthermic stress through clearance of damaged proteins. In this study, we analyze the involvement of NF-kB in basal and heat-stress-induced protein quality control, by comparing the level of multiubiquitylated and/or aggregated proteins, and proteasome and autophagic activity in NF-kB-competent and NF-kB-incompetent cells. We show that NF-kB has only a minor role in basal protein quality control, where it modulates autophagosome maturation. By contrast, NF-kB is shown to be a key player in protein quality control after hyperthermia. Indeed, NF-kB-incompetent cells show highly increased levels of multiubiquitylated and/or aggregated proteins and aggresome clearance defects; a phenotype that disappears when NF-kB activity is restored to normal. We demonstrate that during heat shock recovery NF-kB activates selective removal of misfolded or aggregated proteins -a process also called 'aggrephagy' -by controlling the expression of BAG3 and HSPB8 and by modulating the level of the BAG3-HspB8 complex. Thus NF-kB-mediated increase in the level of the BAG3-HspB8 complex leads to upregulation of aggrephagy and clearance of irreversibly damaged proteins and might increase cell survival in conditions of hyperthermia.

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Section: Discussionmentioning

confidence: 66%

NF-κB regulates protein quality control after heat stress through modulation of the BAG3–HspB8 complex

Nivon

Abou‐Samra

Richet³

et al. 2012

Journal of Cell Science

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“…This process requires autophagosomal membrane receptors like multi-domain scaffold/adaptor protein p62/SQSTM-1, or a neighbour of BRCA1 gene 1 (NBR1) protein [66]. It has been reported that p62 binds non-covalently to the ubiquitin of polyubiquitinated proteins and then polymerises into cytosolic, nuclear and lysosomal aggregates.…”

Section: Crosstalk Between Proteasomal System Degradation and Autophamentioning

confidence: 99%

“…Aggresomes are predominantly present in perinuclear compartments, and they are considered to be a place of selective autophagy of damaged proteins that are isolated from other cytoplasmic components [129]. The clearance of polyubiquitinated proteins present in aggresome is mediated by ubiquitin-binding proteins like p62/SQSTM1 (Figure 2 to be a connecting link between autophagy and proteasome-mediated proteolysis, and its level strongly increases during exposure to various oxidative agents and proteasomal inhibitors, such as MG-132, lactacystin, epoxomicin and PSI [66,[130][131][132]. Furthermore, proteasomal inhibition caused by MG-132 leads to accumulation of p62/SQSTM1 bound irreversibly to perinuclear protein aggregates [132].…”

Section: Formation Of Aggresomesmentioning

confidence: 99%

Crosstalk between autophagy and proteasome protein degradation systems: possible implications for cancer therapy

Wójcik

2014

Folia Histochem Cytobiol.

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Abstract:The Ubiquitin-Proteasomes System (UPS) and autophagy, two main intracellular protein degradation pathways within the eukaryotic cells which were originally regarded as rather independent, seem to be very closely related. Proteasome inhibitors, including the multipathway inhibitor bortezomib, are drawing increased attention for their therapeutic potential in the treatment of chronic inflammation and cancer, especially tumours with a high degree of malignancy. The over-activation of autophagy induces cell death and may act as a powerful tumour-suppressing mechanism. However, autophagy, serving as an important mechanism to generate nutrients in time of cellular stresses, may directly contribute to the survival of cells treated with proteasome inhibitors, and in consequence, may decrease the effectiveness of therapy. Results of studies performed on several cancer cell lines demonstrated synergy between proteasome inhibitors and autophagy inhibitors. Those results became the base for ongoing clinical trials investigating autophagy inhibition in combination with anti-cancer therapies, including bortezomib. This review provides summary of the latest data on the functioning of the UPS and the mechanisms of autophagy. The new insights describing the main pathways of autophagy activation in response to UPS inhibition related to: (i) Unfolded Protein Response, (ii) PI3K/Akt/mTOR pathway, and (iii) formation of aggresomes, are discussed. It is concluded that concomitant inhibition of the two main cellular protein degradation systems may provide new therapeutic modalities for cancer treatment.

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“…15 N/ 14 N peak intensities were quantified by MSQuant (v1.5b7) using proteins with at least two peptides with an ion score of at least 15 (the averaged false discovery rate (FDR) of peptides based on Decoy analysis was Ͻ0.85%). We established the cut-off based on the 15 N/ 14 N ratio distribution in the control lysate sample, so that less than 5% of the quantified proteins were considered enriched in the control lysate (22).…”

Section: Methodsmentioning

confidence: 99%

System-wide Analysis Reveals Intrinsically Disordered Proteins Are Prone to Ubiquitylation after Misfolding Stress

Fang

Comyn

et al. 2013

Molecular & Cellular Proteomics

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Damaged and misfolded proteins that are no longer functional in the cell need to be eliminated. Failure to do so might lead to their accumulation and aggregation, a hallmark of many neurodegenerative diseases. Protein quality control pathways play a major role in the degradation of these proteins, which is mediated mainly by the ubiquitin proteasome system. Despite significant focus on identifying ubiquitin ligases involved in these pathways, along with their substrates, a systems-level understanding of these pathways has been lacking. For instance, as misfolded proteins are rapidly ubiquitylated, unconjugated ubiquitin is rapidly depleted from the cell upon misfolding stress; yet it is unknown whether certain targets compete more efficiently to be ubiquitylated. Using a system-wide approach, we applied statistical and computational methods to identify characteristics enriched among proteins that are further ubiquitylated after heat shock. We discovered that distinct populations of structured and, surprisingly, intrinsically disordered proteins are prone to ubiquitylation. Proteomic analysis revealed that abundant and highly structured proteins constitute the bulk of proteins in the low-solubility fraction after heat shock, but only a portion is ubiquitylated. In contrast, ubiquitylated, intrinsically disordered proteins are enriched in the low-solubility fraction after heat shock. These proteins have a very low abundance in the cell, are rarely encoded by essential genes, and are enriched in binding motifs. In additional experiments, we confirmed that several of the identified intrinsically disordered proteins were ubiquitylated after heat shock and demonstrated for two of them that their disordered regions are important for ubiquitylation after heat shock. We propose that intrinsically disordered regions may be recognized by the protein quality control machinery and thereby facilitate the ubiquitylation of proteins after heat shock. Molecular & Cellular

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Proteomic Characterization of Aggregating Proteins after the Inhibition of the Ubiquitin Proteasome System

Cited by 55 publications

References 77 publications

NF-κB regulates protein quality control after heat stress through modulation of the BAG3–HspB8 complex

NF-κB regulates protein quality control after heat stress through modulation of the BAG3–HspB8 complex

Crosstalk between autophagy and proteasome protein degradation systems: possible implications for cancer therapy

System-wide Analysis Reveals Intrinsically Disordered Proteins Are Prone to Ubiquitylation after Misfolding Stress

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