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Regulation of Endoplasmic Reticulum-Associated Protein Degradation (ERAD) by Ubiquitin.

Lemus L, Goder V - Cells (2014)

Bottom Line: Quality control of protein folding inside the endoplasmic reticulum (ER) includes chaperone-mediated assistance in folding and the selective targeting of terminally misfolded species to a pathway called ER-associated protein degradation, or simply ERAD.Recently it became evident, however, that the poly-ubiquitin chains (PUCs) on ERAD substrates are often subject to extensive remodeling, or processing, at several stages during ERAD.This review recapitulates the current knowledge and recent findings about PUC processing on ERAD substrates and ubiquitination of ERAD machinery components and discusses their functional consequences.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Seville, Av. Reina Mercedes 6, 41012 Seville, Spain.

ABSTRACT
Quality control of protein folding inside the endoplasmic reticulum (ER) includes chaperone-mediated assistance in folding and the selective targeting of terminally misfolded species to a pathway called ER-associated protein degradation, or simply ERAD. Once selected for ERAD, substrates will be transported (back) into the cytosol, a step called retrotranslocation. Although still ill defined, retrotranslocation likely involves a protein conducting channel that is in part formed by specific membrane-embedded E3 ubiquitin ligases. Early during retrotranslocation, reversible self-ubiquitination of these ligases is thought to aid in initiation of substrate transfer across the membrane. Once being at least partially exposed to the cytosol, substrates will become ubiquitinated on the cytosolic side of the ER membrane by the same E3 ubiquitin ligases. Ubiquitin on substrates was originally thought to be a permanent modification that (1) promotes late steps of retrotranslocation by recruiting the energy-providing ATPase Cdc48p/p97 via binding to its associated adaptor proteins and that (2) serves to target substrates to the proteasome. Recently it became evident, however, that the poly-ubiquitin chains (PUCs) on ERAD substrates are often subject to extensive remodeling, or processing, at several stages during ERAD. This review recapitulates the current knowledge and recent findings about PUC processing on ERAD substrates and ubiquitination of ERAD machinery components and discusses their functional consequences.

No MeSH data available.


Models for PUC processing as a mechanism for protein retrotranslocation. (A) Ubiquitination of the substrate on the cytosolic side of the ER membrane by an E3 ligase promotes binding to the hexameric Cdc48p, via its ubiquitin-binding cofactors Npl4p and Ufd1p. ATP hydrolysis by Cdc48p is thought to promote the complete retrotranslocation and substrate extraction from the ER membrane. See text for details. (B) In the mammalian system, the p97-associated DUB Ataxin-3 acts downstream of protein retrotranslocation and might promote the removal of ubiquitins from longer PUCs. This is thought to be required for the generation of PUCs with optimal binding affinities to proteasomal shuttle factors or to the proteasome itself. See text for details. (C) The p97-associated DUB YOD1 is thought to act upstream of protein retrotranslocation. Its activity was suggested to be needed for the complete removal of PUCs to allow passage of the substrate through the pore of p97. ATP hydrolysis would then couple protein retrotranslocation with protein unfolding. Subsequently, reubiquitination by an E3 ligase would allow substrate targeting to the proteasome. See text for details.
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cells-03-00824-f003: Models for PUC processing as a mechanism for protein retrotranslocation. (A) Ubiquitination of the substrate on the cytosolic side of the ER membrane by an E3 ligase promotes binding to the hexameric Cdc48p, via its ubiquitin-binding cofactors Npl4p and Ufd1p. ATP hydrolysis by Cdc48p is thought to promote the complete retrotranslocation and substrate extraction from the ER membrane. See text for details. (B) In the mammalian system, the p97-associated DUB Ataxin-3 acts downstream of protein retrotranslocation and might promote the removal of ubiquitins from longer PUCs. This is thought to be required for the generation of PUCs with optimal binding affinities to proteasomal shuttle factors or to the proteasome itself. See text for details. (C) The p97-associated DUB YOD1 is thought to act upstream of protein retrotranslocation. Its activity was suggested to be needed for the complete removal of PUCs to allow passage of the substrate through the pore of p97. ATP hydrolysis would then couple protein retrotranslocation with protein unfolding. Subsequently, reubiquitination by an E3 ligase would allow substrate targeting to the proteasome. See text for details.

Mentions: Shortly after the discovery of ERAD it became clear that ubiquitination of substrates has an important role not only for their ultimate degradation by also for their retrotranslocation [39,40,41]. Major insights into the mechanism that links ubiquitination with retrotanslocation came from the discovery that Cdc48p (p97 in mammals), a well-conserved hexameric AAA-ATPase, is involved in ERAD [42,43]. Cdc48p is a very abundant protein found in the cytosol and nucleus, and it has multiple cellular functions beyond ERAD. They involve control of the cell cycle, membrane fusion, autophagy and DNA repair, reviewed in [44]. The distinct cellular roles of Cdc48p are determined through binding to different co-factors. This is particularly relevant for the recruitment of Cdc48p to ubiquitin. Although it has been shown that Cdc48p itself can bind to ubiquitin via its N-domain, its ERAD-specific co-factors Npl4p and Ufd1p (Npl4 and Ufd1) provide additional binding sites to ubiquitin [45]. For instance, mammalian Npl4 possesses a ubiquitin-binding zinc finger motif (which is not present in the yeast orthologue) whereas Ufd1p has a conserved so-called UT3 motif. This UT3 motif makes Ufd1p to prefer the binding to poly-ubiquitin over mono-ubiquitin, suggesting that some PUCs have formed on substrates at the stage when it connects to Cdc48p [46]. Important for the proposed role of Cdc48p in substrate retrotranslocation is also the finding that it is recruited to the ER membrane via direct binding to E3 ligases such as Hrd1p (and gp78) or, independently, via binding to one of its co-factors and integral membrane protein Ubx2p (UbxD8), which is part of both the Hrd1- and Doa10-complexes [47,48,49,50]. Thus, by binding to ubiquinated substrates on the one hand and to the ER membrane on the other hand, Cdc48p might pull substrates out of or across the membrane like a molecular ratchet, fueled by repeating cycles of ATP hydrolysis and the accompanying conformational changes (Figure 3A) [51,52]. Whether substrate ubiquitination generally precedes binding to Cdc48p and its co-factors or whether initial binding of non-ubiquitinated substrates to Cdc48p would facilitate their subsequent ubiquitination by E3 ligases, especially with respect to the build-up of PUCs on substrates, is still not clear. However, several recent reports place Cdc48p in the center of the processing of PUCs. This has important implications for mechanistic aspects of ERAD and provides new models for how substrates are retrotranslocated and how they are targeted to the proteasome after retrotranslocation.


Regulation of Endoplasmic Reticulum-Associated Protein Degradation (ERAD) by Ubiquitin.

Lemus L, Goder V - Cells (2014)

Models for PUC processing as a mechanism for protein retrotranslocation. (A) Ubiquitination of the substrate on the cytosolic side of the ER membrane by an E3 ligase promotes binding to the hexameric Cdc48p, via its ubiquitin-binding cofactors Npl4p and Ufd1p. ATP hydrolysis by Cdc48p is thought to promote the complete retrotranslocation and substrate extraction from the ER membrane. See text for details. (B) In the mammalian system, the p97-associated DUB Ataxin-3 acts downstream of protein retrotranslocation and might promote the removal of ubiquitins from longer PUCs. This is thought to be required for the generation of PUCs with optimal binding affinities to proteasomal shuttle factors or to the proteasome itself. See text for details. (C) The p97-associated DUB YOD1 is thought to act upstream of protein retrotranslocation. Its activity was suggested to be needed for the complete removal of PUCs to allow passage of the substrate through the pore of p97. ATP hydrolysis would then couple protein retrotranslocation with protein unfolding. Subsequently, reubiquitination by an E3 ligase would allow substrate targeting to the proteasome. See text for details.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4197631&req=5

cells-03-00824-f003: Models for PUC processing as a mechanism for protein retrotranslocation. (A) Ubiquitination of the substrate on the cytosolic side of the ER membrane by an E3 ligase promotes binding to the hexameric Cdc48p, via its ubiquitin-binding cofactors Npl4p and Ufd1p. ATP hydrolysis by Cdc48p is thought to promote the complete retrotranslocation and substrate extraction from the ER membrane. See text for details. (B) In the mammalian system, the p97-associated DUB Ataxin-3 acts downstream of protein retrotranslocation and might promote the removal of ubiquitins from longer PUCs. This is thought to be required for the generation of PUCs with optimal binding affinities to proteasomal shuttle factors or to the proteasome itself. See text for details. (C) The p97-associated DUB YOD1 is thought to act upstream of protein retrotranslocation. Its activity was suggested to be needed for the complete removal of PUCs to allow passage of the substrate through the pore of p97. ATP hydrolysis would then couple protein retrotranslocation with protein unfolding. Subsequently, reubiquitination by an E3 ligase would allow substrate targeting to the proteasome. See text for details.
Mentions: Shortly after the discovery of ERAD it became clear that ubiquitination of substrates has an important role not only for their ultimate degradation by also for their retrotranslocation [39,40,41]. Major insights into the mechanism that links ubiquitination with retrotanslocation came from the discovery that Cdc48p (p97 in mammals), a well-conserved hexameric AAA-ATPase, is involved in ERAD [42,43]. Cdc48p is a very abundant protein found in the cytosol and nucleus, and it has multiple cellular functions beyond ERAD. They involve control of the cell cycle, membrane fusion, autophagy and DNA repair, reviewed in [44]. The distinct cellular roles of Cdc48p are determined through binding to different co-factors. This is particularly relevant for the recruitment of Cdc48p to ubiquitin. Although it has been shown that Cdc48p itself can bind to ubiquitin via its N-domain, its ERAD-specific co-factors Npl4p and Ufd1p (Npl4 and Ufd1) provide additional binding sites to ubiquitin [45]. For instance, mammalian Npl4 possesses a ubiquitin-binding zinc finger motif (which is not present in the yeast orthologue) whereas Ufd1p has a conserved so-called UT3 motif. This UT3 motif makes Ufd1p to prefer the binding to poly-ubiquitin over mono-ubiquitin, suggesting that some PUCs have formed on substrates at the stage when it connects to Cdc48p [46]. Important for the proposed role of Cdc48p in substrate retrotranslocation is also the finding that it is recruited to the ER membrane via direct binding to E3 ligases such as Hrd1p (and gp78) or, independently, via binding to one of its co-factors and integral membrane protein Ubx2p (UbxD8), which is part of both the Hrd1- and Doa10-complexes [47,48,49,50]. Thus, by binding to ubiquinated substrates on the one hand and to the ER membrane on the other hand, Cdc48p might pull substrates out of or across the membrane like a molecular ratchet, fueled by repeating cycles of ATP hydrolysis and the accompanying conformational changes (Figure 3A) [51,52]. Whether substrate ubiquitination generally precedes binding to Cdc48p and its co-factors or whether initial binding of non-ubiquitinated substrates to Cdc48p would facilitate their subsequent ubiquitination by E3 ligases, especially with respect to the build-up of PUCs on substrates, is still not clear. However, several recent reports place Cdc48p in the center of the processing of PUCs. This has important implications for mechanistic aspects of ERAD and provides new models for how substrates are retrotranslocated and how they are targeted to the proteasome after retrotranslocation.

Bottom Line: Quality control of protein folding inside the endoplasmic reticulum (ER) includes chaperone-mediated assistance in folding and the selective targeting of terminally misfolded species to a pathway called ER-associated protein degradation, or simply ERAD.Recently it became evident, however, that the poly-ubiquitin chains (PUCs) on ERAD substrates are often subject to extensive remodeling, or processing, at several stages during ERAD.This review recapitulates the current knowledge and recent findings about PUC processing on ERAD substrates and ubiquitination of ERAD machinery components and discusses their functional consequences.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Seville, Av. Reina Mercedes 6, 41012 Seville, Spain.

ABSTRACT
Quality control of protein folding inside the endoplasmic reticulum (ER) includes chaperone-mediated assistance in folding and the selective targeting of terminally misfolded species to a pathway called ER-associated protein degradation, or simply ERAD. Once selected for ERAD, substrates will be transported (back) into the cytosol, a step called retrotranslocation. Although still ill defined, retrotranslocation likely involves a protein conducting channel that is in part formed by specific membrane-embedded E3 ubiquitin ligases. Early during retrotranslocation, reversible self-ubiquitination of these ligases is thought to aid in initiation of substrate transfer across the membrane. Once being at least partially exposed to the cytosol, substrates will become ubiquitinated on the cytosolic side of the ER membrane by the same E3 ubiquitin ligases. Ubiquitin on substrates was originally thought to be a permanent modification that (1) promotes late steps of retrotranslocation by recruiting the energy-providing ATPase Cdc48p/p97 via binding to its associated adaptor proteins and that (2) serves to target substrates to the proteasome. Recently it became evident, however, that the poly-ubiquitin chains (PUCs) on ERAD substrates are often subject to extensive remodeling, or processing, at several stages during ERAD. This review recapitulates the current knowledge and recent findings about PUC processing on ERAD substrates and ubiquitination of ERAD machinery components and discusses their functional consequences.

No MeSH data available.