scholarly journals ER-Associated Degradation of Membrane Proteins in Yeast

2006 ◽  
Vol 6 ◽  
pp. 967-983 ◽  
Author(s):  
Cédric Pety de Thozée ◽  
Michel Ghislain
Keyword(s):  
Quality Control ◽  
Membrane Proteins ◽  
Control Systems ◽  
Protein Unfolding ◽  
Secretory Pathway ◽  
Retrograde Transport ◽  
26S Proteasome ◽  
Post Translational Modifications ◽  
Final Destination ◽  
Polypeptide Folding

Proteins destined for the secretory pathway are translocated into the endoplasmic reticulum (ER), where they are subjected to a variety of post-translational modifications before they reach their final destination. Newly synthesized proteins that have defect in polypeptide folding or subunit assembly are recognized by quality control systems and eliminated by the 26S proteasome, a cytosolic ATP-dependent proteolytic machinery. Delivery of non-native ER proteins to the proteasome requires retrograde transport across the ER membrane and depends on a protein-unfolding machine consisting of Cdc48p, Ufd1p, and Npl4p. Recent studies in yeast have highlighted the possible function of the Sar1p/COPII machinery in ER-associated degradation of some lumenal and membrane proteins.

scholarly journals Distinct retrieval and retention mechanisms are required for the quality control of endoplasmic reticulum protein folding

2001 ◽  
Vol 155 (3) ◽  
pp. 355-368 ◽  
Author(s):  
Shilpa Vashist ◽  
Woong Kim ◽  
William J. Belden ◽  
Eric D. Spear ◽  
Charles Barlowe ◽  
...  
Keyword(s):  
Quality Control ◽  
Endoplasmic Reticulum ◽  
Secretory Pathway ◽  
Protein Translocation ◽  
Retrograde Transport ◽  
26S Proteasome ◽  
Misfolded Proteins ◽  
Mutant Proteins ◽  
Endoplasmic Reticulum Protein ◽  
Quality Control Mechanism

Proteins destined for the secretory pathway must first fold and assemble in the lumen of endoplasmic reticulum (ER). The pathway maintains a quality control mechanism to assure that aberrantly processed proteins are not delivered to their sites of function. As part of this mechanism, misfolded proteins are returned to the cytosol via the ER protein translocation pore where they are ubiquitinated and degraded by the 26S proteasome. Previously, little was known regarding the recognition and targeting of proteins before degradation. By tracking the fate of several mutant proteins subject to quality control, we demonstrate the existence of two distinct sorting mechanisms. In the ER, substrates are either sorted for retention in the ER or are transported to the Golgi apparatus via COPII–coated vesicles. Proteins transported to the Golgi are retrieved to the ER via the retrograde transport system. Ultimately, both retained and retrieved proteins converge at a common machinery at the ER for degradation. Furthermore, we report the identification of a gene playing a novel role specific to the retrieval pathway. The gene, BST1, is required for the transport of misfolded proteins to the Golgi, although dispensable for the transport of many normal cargo proteins.

scholarly journals A Novel Mechanism for Localizing Membrane Proteins to YeastTrans-Golgi Network Requires Function of Synaptojanin-like Protein

2001 ◽  
Vol 12 (10) ◽  
pp. 3175-3190 ◽  
Author(s):  
Seon-Ah Ha ◽  
Jeremy T. Bunch ◽  
Hiroko Hama ◽  
Daryll B. DeWald ◽  
Steven F. Nothwehr
Keyword(s):  
Membrane Proteins ◽  
Secretory Pathway ◽  
Protein A ◽  
Retrograde Transport ◽  
Cell Fractionation ◽  
Gene Encoding ◽  
Phosphoinositide Phosphatase ◽  
Endosomal Membranes ◽  
Delivery Mechanism ◽  
Golgi Network

Localization of resident membrane proteins to the yeasttrans-Golgi network (TGN) involves both their retrieval from a prevacuolar/endosomal compartment (PVC) and a “slow delivery” mechanism that inhibits their TGN-to-PVC transport. A screen for genes required for the slow delivery mechanism uncoveredINP53, a gene encoding a phosphoinositide phosphatase. A retrieval-defective model TGN protein, A(F→A)-ALP, was transported to the vacuole in inp53 mutants approximately threefold faster than in wild type. Inp53p appears to function in a process distinct from PVC retrieval because combining inp53 with mutations that block retrieval resulted in a much stronger phenotype than either mutation alone. In vps27 strains defective for both anterograde and retrograde transport out of the PVC, a loss of Inp53p function markedly accelerated the rate of transport of TGN residents A-ALP and Kex2p into the PVC. Inp53p function is cargo specific because a loss of Inp53p function had no effect on the rate of Vps10p transport to the PVC in vps27 cells. The rate of early secretory pathway transport appeared to be unaffected ininp53 mutants. Cell fractionation experiments suggested that Inp53p associates with Golgi or endosomal membranes. Taken together, these results suggest that a phosphoinositide signaling event regulates TGN-to-PVC transport of select cargo proteins.

scholarly journals A Nucleus-based Quality Control Mechanism for Cytosolic Proteins

2010 ◽  
Vol 21 (13) ◽  
pp. 2117-2127 ◽  
Author(s):  
Rupali Prasad ◽  
Shinichi Kawaguchi ◽  
Davis T.W. Ng
Keyword(s):  
Quality Control ◽  
Control Systems ◽  
Ubiquitin Ligase ◽  
Nuclear Import ◽  
Control Mechanism ◽  
E3 Ubiquitin Ligase ◽  
26S Proteasome ◽  
Cytosolic Proteins ◽  
Hsp70 Chaperone ◽  
Quality Control Mechanism

Intracellular quality control systems monitor protein conformational states. Irreversibly misfolded proteins are cleared through specialized degradation pathways. Their importance is underscored by numerous pathologies caused by aberrant proteins. In the cytosol, where most proteins are synthesized, quality control remains poorly understood. Stress-inducible chaperones and the 26S proteasome are known mediators but how their activities are linked is unclear. To better understand these mechanisms, a panel of model misfolded substrates was analyzed in detail. Surprisingly, their degradation occurs not in the cytosol but in the nucleus. Degradation is dependent on the E3 ubiquitin ligase San1p, known previously to direct the turnover of damaged nuclear proteins. A second E3 enzyme, Ubr1p, augments this activity but is insufficient by itself. San1p and Ubr1p are not required for nuclear import of substrates. Instead, the Hsp70 chaperone system is needed for efficient import and degradation. These data reveal a new function of the nucleus as a compartment central to the quality control of cytosolic proteins.

scholarly journals A Striking Quality Control Subcompartment in Saccharomyces cerevisiae: The Endoplasmic Reticulum-associated Compartment

2004 ◽  
Vol 15 (2) ◽  
pp. 908-921 ◽  
Author(s):  
Gregory Huyer ◽  
Gaby L. Longsworth ◽  
Deborah L. Mason ◽  
Monica P. Mallampalli ◽  
J. Michael McCaffery ◽  
...  
Keyword(s):  
Quality Control ◽  
Endoplasmic Reticulum ◽  
Membrane Proteins ◽  
Secretory Pathway ◽  
Secretory Protein ◽  
Cellular Functions ◽  
Er Quality Control ◽  
Fluorescence And Electron Microscopy ◽  
The Unfolded Protein Response ◽  
Mutant Forms

The folding of nascent secretory and membrane proteins is monitored by the endoplasmic reticulum (ER) quality control system. Misfolded proteins are retained in the ER and can be removed by ER-associated degradation. As a model for the ER quality control of multispanning membrane proteins in yeast, we have been studying mutant forms of Ste6p. Here, we identify mislocalized mutant forms of Ste6p that induce the formation of, and localize to, prominent structures that are absent in normal cells. We have named these structures ER-associated compartments (ERACs), based on their juxtaposition to and connection with the ER, as observed by fluorescence and electron microscopy. ERACs comprise a network of tubulo-vesicular structures that seem to represent proliferated ER membranes. Resident ER lumenal and membrane proteins are present in ERACs in addition to their normal ER localization, suggesting there is no barrier for their entry into ERACs. However, the forms of Ste6p in ERACs are excluded from the ER and do not enter the secretory pathway; instead, they are ultimately targeted for ER-associated degradation. The presence of ERACs does not adversely affect secretory protein traffic through the ER and does not lead to induction of the unfolded protein response. We propose that ERACs may be holding sites to which misfolded membrane proteins are specifically diverted so as not to interfere with normal cellular functions. We discuss the likelihood that related ER membrane proliferations that form in response to certain other mutant or unassembled membrane proteins may be substantially similar to ERACs.

scholarly journals The evolving role of ubiquitin modification in endoplasmic reticulum-associated degradation

2017 ◽  
Vol 474 (4) ◽  
pp. 445-469 ◽  
Author(s):  
G. Michael Preston ◽  
Jeffrey L. Brodsky
Keyword(s):  
Endoplasmic Reticulum ◽  
Secretory Pathway ◽  
Integral Membrane Proteins ◽  
26S Proteasome ◽  
Polyubiquitin Chain ◽  
Post Translational Modifications ◽  
Cytoplasmic Face ◽  
And Control ◽  
Ubiquitination Machinery

The endoplasmic reticulum (ER) serves as a warehouse for factors that augment and control the biogenesis of nascent proteins entering the secretory pathway. In turn, this compartment also harbors the machinery that responds to the presence of misfolded proteins by targeting them for proteolysis via a process known as ER-associated degradation (ERAD). During ERAD, substrates are selected, modified with ubiquitin, removed from the ER, and then degraded by the cytoplasmic 26S proteasome. While integral membrane proteins can directly access the ubiquitination machinery that resides in the cytoplasm or on the cytoplasmic face of the ER membrane, soluble ERAD substrates within the lumen must be retrotranslocated from this compartment. In either case, nearly all ERAD substrates are tagged with a polyubiquitin chain, a modification that represents a commitment step to degrade aberrant proteins. However, increasing evidence indicates that the polyubiquitin chain on ERAD substrates can be further modified, serves to recruit ERAD-requiring factors, and may regulate the ERAD machinery. Amino acid side chains other than lysine on ERAD substrates can also be modified with ubiquitin, and post-translational modifications that affect substrate ubiquitination have been observed. Here, we summarize these data and provide an overview of questions driving this field of research.

scholarly journals Vps52p, Vps53p, and Vps54p Form a Novel Multisubunit Complex Required for Protein Sorting at the Yeast Late Golgi

2000 ◽  
Vol 11 (1) ◽  
pp. 305-323 ◽  
Author(s):  
Elizabeth Conibear ◽  
Tom H. Stevens
Keyword(s):  
Membrane Proteins ◽  
Membrane Trafficking ◽  
Secretory Pathway ◽  
Protein Sorting ◽  
Retrograde Transport ◽  
Carboxypeptidase Y ◽  
Golgi Membrane ◽  
Triple Mutant ◽  
Protein Traffic ◽  
Golgi Compartment

The late Golgi of the yeast Saccharomyces cerevisiaereceives membrane traffic from the secretory pathway as well as retrograde traffic from post-Golgi compartments, but the machinery that regulates these vesicle-docking and fusion events has not been characterized. We have identified three components of a novel protein complex that is required for protein sorting at the yeast late Golgi compartment. Mutation of VPS52, VPS53, orVPS54 results in the missorting of 70% of the vacuolar hydrolase carboxypeptidase Y as well as the mislocalization of late Golgi membrane proteins to the vacuole, whereas protein traffic through the early part of the Golgi complex is unaffected. Avps52/53/54 triple mutant strain is phenotypically indistinguishable from each of the single mutants, consistent with the model that all three are required for a common step in membrane transport. Native coimmunoprecipitation experiments indicate that Vps52p, Vps53p, and Vps54p are associated in a 1:1:1 complex that sediments as a single peak on sucrose velocity gradients. This complex, which exists both in a soluble pool and as a peripheral component of a membrane fraction, colocalizes with markers of the yeast late Golgi by immunofluorescence microscopy. Together, the phenotypic and biochemical data suggest that VPS52, VPS53, andVPS54 are required for the retrograde transport of Golgi membrane proteins from an endosomal/prevacuolar compartment. The Vps52/53/54 complex joins a growing list of distinct multisubunit complexes that regulate membrane-trafficking events.

scholarly journals Protein folding state-dependent sorting at the Golgi apparatus

2019 ◽  
Vol 30 (17) ◽  
pp. 2296-2308 ◽  
Author(s):  
Doris Hellerschmied ◽  
Yevgeniy V. Serebrenik ◽  
Lin Shao ◽  
George M. Burslem ◽  
Craig M. Crews
Keyword(s):  
Quality Control ◽  
Golgi Apparatus ◽  
Protein Unfolding ◽  
Secretory Pathway ◽  
Protein Quality ◽  
Specific Protein ◽  
Major Protein ◽  
Unfolded Proteins ◽  
Lysosomal Degradation ◽  
Folded Proteins

In eukaryotic cells, organelle-specific protein quality control (PQC) is critical for maintaining cellular homeostasis. Despite the Golgi apparatus being the major protein processing and sorting site within the secretory pathway, how it contributes to PQC has remained largely unknown. Using different chemical biology-based protein unfolding systems, we reveal the segregation of unfolded proteins from folded proteins in the Golgi. Quality control (QC) substrates are subsequently exported in distinct carriers, which likely contain unfolded proteins as well as highly oligomerized cargo that mimic protein aggregates. At an additional sorting step, oligomerized proteins are committed to lysosomal degradation, while unfolded proteins localize to the endoplasmic reticulum (ER) and associate with chaperones. These results highlight the existence of checkpoints at which QC substrates are selected for Golgi export and lysosomal degradation. Our data also suggest that the steady-state ER localization of misfolded proteins, observed for several disease-causing mutants, may have different origins.

scholarly journals Ubr1 and Ubr2 Function in a Quality Control Pathway for Degradation of Unfolded Cytosolic Proteins

2010 ◽  
Vol 21 (13) ◽  
pp. 2102-2116 ◽  
Author(s):  
Nadinath B. Nillegoda ◽  
Maria A. Theodoraki ◽  
Atin K. Mandal ◽  
Katie J. Mayo ◽  
Hong Yu Ren ◽  
...  
Keyword(s):  
Quality Control ◽  
Control Systems ◽  
Molecular Chaperones ◽  
Direct Interaction ◽  
Ubiquitin Proteasome System ◽  
Growth Potential ◽  
Protein Homeostasis ◽  
Potential Toxicity ◽  
Polypeptide Folding ◽  
Ubiquitin Proteasome

Quality control systems facilitate polypeptide folding and degradation to maintain protein homeostasis. Molecular chaperones promote folding, whereas the ubiquitin/proteasome system mediates degradation. We show here that Saccharomyces cerevisiae Ubr1 and Ubr2 ubiquitin ligases promote degradation of unfolded or misfolded cytosolic polypeptides. Ubr1 also catalyzes ubiquitinylation of denatured but not native luciferase in a purified system. This activity is based on the direct interaction of denatured luciferase with Ubr1, although Hsp70 stimulates polyubiquitinylation of the denatured substrate. We also report that loss of Ubr1 and Ubr2 function suppressed the growth arrest phenotype resulting from chaperone mutation. This correlates with increased protein kinase maturation and indicates partitioning of foldable conformers toward the proteasome. Our findings, based on the efficiency of this quality control system, suggest that the cell trades growth potential to avert the potential toxicity associated with accumulation of unfolded or misfolded proteins. Ubr1 and Ubr2 therefore represent E3 components of a novel quality control pathway for proteins synthesized on cytosolic ribosomes.

scholarly journals Ribosome-associated quality control of membrane proteins at the endoplasmic reticulum

2020 ◽  
Vol 133 (22) ◽  
pp. jcs251983
Author(s):  
Ben P. Phillips ◽  
Elizabeth A. Miller
Keyword(s):  
Quality Control ◽  
Endoplasmic Reticulum ◽  
Membrane Proteins ◽  
Control Systems ◽  
Protein Misfolding ◽  
Substrate Recognition ◽  
Protein Homeostasis ◽  
Cellular Toxicity ◽  
Future Studies ◽  
Protein Biogenesis

ABSTRACTProtein synthesis is an energetically costly, complex and risky process. Aberrant protein biogenesis can result in cellular toxicity and disease, with membrane-embedded proteins being particularly challenging for the cell. In order to protect the cell from consequences of defects in membrane proteins, quality control systems act to maintain protein homeostasis. The majority of these pathways act post-translationally; however, recent evidence reveals that membrane proteins are also subject to co-translational quality control during their synthesis in the endoplasmic reticulum (ER). This newly identified quality control pathway employs components of the cytosolic ribosome-associated quality control (RQC) machinery but differs from canonical RQC in that it responds to biogenesis state of the substrate rather than mRNA aberrations. This ER-associated RQC (ER-RQC) is sensitive to membrane protein misfolding and malfunctions in the ER insertion machinery. In this Review, we discuss the advantages of co-translational quality control of membrane proteins, as well as potential mechanisms of substrate recognition and degradation. Finally, we discuss some outstanding questions concerning future studies of ER-RQC of membrane proteins.

Unrestrictive protein modification localization and quality control for open search of mass spectra

2018 ◽  
Author(s):  
Zhiwu An ◽  
Fuzhou Gong ◽  
Yan Fu
Keyword(s):  
Mass Spectrometry ◽  
Quality Control ◽  
Tandem Mass Spectrometry ◽  
Mass Spectra ◽  
Protein Modification ◽  
Software Tool ◽  
Tandem Mass ◽  
Simulation Data ◽  
Post Translational Modifications

We have developed PTMiner, a first software tool for automated, confident filtering, localization and annotation of protein post-translational modifications identified by open (mass-tolerant) search of large tandem mass spectrometry datasets. The performance of the software was validated on carefully designed simulation data. <br>

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