Protein Quality Control in Chloroplasts: A Current Model of D1 Protein Degradation in the Photosystem II Repair Cycle

Even with the assistance of many cellular factors, a significant fraction of newly synthesized proteins ends up misfolded. Cells evolved protein quality control systems to ensure that these potentially toxic species are detected and eliminated. The best characterized of these pathways, the ER-associated protein degradation (ERAD), monitors the folding of membrane and secretory proteins whose biogenesis takes place in the endoplasmic reticulum (ER). There is also increasing evidence that ERAD controls other ER-related functions through regulated degradation of certain folded ER proteins, further highlighting the role of ERAD in cellular homeostasis.

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The Toxicity of a Novel Antifungal Compound Is Modulated by Endoplasmic Reticulum-Associated Protein Degradation Components

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02239-15 ◽

2015 ◽

Vol 60 (3) ◽

pp. 1438-1449 ◽

Cited By ~ 8

Author(s):

Shriya Raj ◽

Karthik Krishnan ◽

David S. Askew ◽

Olivier Helynck ◽

Peggy Suzanne ◽

...

Keyword(s):

Quality Control ◽

Endoplasmic Reticulum ◽

Protein Degradation ◽

Mammalian Cells ◽

Protein Quality ◽

Protein Quality Control ◽

Antifungal Compound ◽

Content Type ◽

Enhanced Sensitivity ◽

Fungal Organisms

In a search for new antifungal compounds, we screened a library of 4,454 chemicals for toxicity against the human fungal pathogenAspergillus fumigatus. We identified sr7575, a molecule that inhibits growth of the evolutionary distant fungiA. fumigatus,Cryptococcus neoformans,Candida albicans, andSaccharomyces cerevisiaebut lacks acute toxicity for mammalian cells. To gain insight into the mode of inhibition, sr7575 was screened against 4,885S. cerevisiaemutants from the systematic collection of haploid deletion strains and 977 barcoded haploid DAmP (decreased abundance by mRNA perturbation) strains in which the function of essential genes was perturbed by the introduction of a drug resistance cassette downstream of the coding sequence region. Comparisons with previously published chemogenomic screens revealed that the set of mutants conferring sensitivity to sr7575 was strikingly narrow, affecting components of the endoplasmic reticulum-associated protein degradation (ERAD) stress response and the ER membrane protein complex (EMC). ERAD-deficient mutants were hypersensitive to sr7575 in bothS. cerevisiaeandA. fumigatus, indicating a conserved mechanism of growth inhibition between yeast and filamentous fungi. Although the unfolded protein response (UPR) is linked to ERAD regulation, sr7575 did not trigger the UPR inA. fumigatusand UPR mutants showed no enhanced sensitivity to the compound. The data from this chemogenomic analysis demonstrate that sr7575 exerts its antifungal activity by disrupting ER protein quality control in a manner that requires ERAD intervention but bypasses the need for the canonical UPR. ER protein quality control is thus a specific vulnerability of fungal organisms that might be exploited for antifungal drug development.

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Coupled protein quality control during nonsense mediated mRNA decay

10.1101/2021.12.22.473893 ◽

2021 ◽

Author(s):

Alison J Inglis ◽

Alina Guna ◽

Angel Galvez Merchan ◽

Akshaye Pal ◽

Theodore K Esantsi ◽

...

Keyword(s):

Quality Control ◽

Protein Degradation ◽

Ubiquitin Ligase ◽

Mammalian Cells ◽

Molecular Mechanisms ◽

Protein Quality ◽

Protein Quality Control ◽

Mrna Degradation ◽

Protein Product ◽

Reporter System

Translation of mRNAs containing premature termination codons (PTCs) can result in truncated protein products with deleterious effects. Nonsense-mediated decay (NMD) is a surveillance path-way responsible for detecting and degrading PTC containing transcripts. While the molecular mechanisms governing mRNA degradation have been extensively studied, the fate of the nascent protein product remains largely uncharacterized. Here, we use a fluorescent reporter system in mammalian cells to reveal a selective degradation pathway specifically targeting the protein product of an NMD mRNA. We show that this process is post-translational, and dependent on an intact ubiquitin proteasome system. To systematically uncover factors involved in NMD-linked protein quality control, we conducted genome-wide flow cytometry-based screens. Our screens recovered known NMD factors, and suggested a lack of dependence on the canonical ribosome-quality control (RQC) pathway. Finally, one of the strongest hits in our screens was the E3 ubiquitin ligase CNOT4, a member of the CCR4-NOT complex, which is involved in initiating mRNA degradation. We show that CNOT4 is involved in NMD coupled protein degradation, and its role depends on a functional RING ubiquitin ligase domain. Our results demonstrate the existence of a targeted pathway for nascent protein degradation from PTC containing mRNAs, and provide a framework for identifying and characterizing factors involved in this process.

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PAQR9 Modulates BAG6-mediated protein quality control of mislocalized membrane proteins

Biochemical Journal ◽

10.1042/bcj20190620 ◽

2020 ◽

Vol 477 (2) ◽

pp. 477-489

Author(s):

Xue You ◽

Yijun Lin ◽

Yongfan Hou ◽

Lijiao Xu ◽

Qianqian Cao ◽

...

Keyword(s):

Mass Spectrometry ◽

Quality Control ◽

Membrane Proteins ◽

Protein Degradation ◽

Degradation Rate ◽

Protein Quality ◽

Protein Quality Control ◽

Dependent Manner ◽

Cellular Homeostasis ◽

Protein Degradation Rate

Protein quality control is crucial for maintaining cellular homeostasis and its dysfunction is closely linked to human diseases. The post-translational protein quality control machinery mainly composed of BCL-2-associated athanogene 6 (BAG6) is responsible for triage of mislocalized membrane proteins (MLPs). However, it is unknown how the BAG6-mediated degradation of MLPs is regulated. We report here that PAQR9, a member of the Progesterone and AdipoQ receptor (PAQR) family, is able to modulate BAG6-mediated triage of MLPs. Analysis with mass spectrometry identified that BAG6 is one of the major proteins interacting with PAQR9 and such interaction is confirmed by co-immunoprecipitation and co-localization assays. The protein degradation rate of representative MLPs is accelerated by PAQR9 knockdown. Consistently, the polyubiquitination of MLPs is enhanced by PAQR9 knockdown. PAQR9 binds to the DUF3538 domain within the proline-rich stretch of BAG6. PAQR9 reduces the binding of MLPs to BAG6 in a DUF3538 domain-dependent manner. Taken together, our results indicate that PAQR9 plays a role in the regulation of protein quality control of MLPs via affecting the interaction of BAG6 with membrane proteins.

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Recent advances in measuring and understanding the regulation of exercise-mediated protein degradation in skeletal muscle

AJP Cell Physiology ◽

10.1152/ajpcell.00115.2021 ◽

2021 ◽

Author(s):

Yusuke Nishimura ◽

Ibrahim Musa ◽

Lars Holm ◽

Yu-Chiang Lai

Keyword(s):

Skeletal Muscle ◽

Quality Control ◽

Protein Degradation ◽

Protein Turnover ◽

Degradation Rate ◽

Protein Quality ◽

Muscle Protein ◽

Protein Quality Control ◽

Muscle Protein Degradation ◽

Protein Degradation Rate

Skeletal muscle protein turnover plays a crucial role in controlling muscle mass and protein quality control, including sarcomeric (structural and contractile) proteins. Protein turnover is a dynamic and continual process of protein synthesis and degradation. The ubiquitin proteasome system (UPS) is a key degradative system for protein degradation and protein quality control in skeletal muscle. UPS-mediated protein quality control is known to be impaired in ageing and diseases. Exercise is a well-recognized non-pharmacological approach to promote muscle protein turnover rates. Over the past decades, we have acquired substantial knowledge of molecular mechanisms of muscle protein synthesis after exercise. However, there has been considerable gaps in the mechanisms of how muscle protein degradation is regulated at the molecular level. The main challenge to understand muscle protein degradation is due in part to the lack of solid stable isotope tracer methodology to measure muscle protein degradation rate. Understanding the mechanisms of UPS with the concomitant measurement of protein degradation rate in skeletal muscle will help identify novel therapeutic strategies to ameliorate impaired protein turnover and protein quality control in ageing and diseases. Thus, the goal of this present review is to highlight how recent advances in the field may help improve our understanding of exercise-mediated protein degradation. We discuss 1) the emerging roles of protein phosphorylation and ubiquitylation modifications in regulating proteasome-mediated protein degradation after exercise and 2) methodological advances to measure in vivo myofibrillar protein degradation rate using stable isotope tracer methods.

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CRL2 aids elimination of truncated selenoproteins produced by failed UGA/Sec decoding

Science ◽

10.1126/science.aab0515 ◽

2015 ◽

Vol 349 (6243) ◽

pp. 91-95 ◽

Cited By ~ 34

Author(s):

Hsiu-Chuan Lin ◽

Szu-Chi Ho ◽

Yi-Yun Chen ◽

Kay-Hooi Khoo ◽

Pang-Hung Hsu ◽

...

Keyword(s):

Quality Control ◽

Control System ◽

Protein Degradation ◽

Genetic Code ◽

Ubiquitin Ligase ◽

Protein Quality ◽

Translation Termination ◽

Protein Quality Control ◽

Selenium Intake ◽

Protein Quality Control System

Selenocysteine (Sec) is translated from the codon UGA, typically a termination signal. Codon duality extends the genetic code; however, the coexistence of two competing UGA-decoding mechanisms immediately compromises proteome fidelity. Selenium availability tunes the reassignment of UGA to Sec. We report a CRL2 ubiquitin ligase–mediated protein quality-control system that specifically eliminates truncated proteins that result from reassignment failures. Exposing the peptide immediately N-terminal to Sec, a CRL2 recognition degron, promotes protein degradation. Sec incorporation destroys the degron, protecting read-through proteins from detection by CRL2. Our findings reveal a coupling between directed translation termination and proteolysis-assisted protein quality control, as well as a cellular strategy to cope with fluctuations in organismal selenium intake.

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ER protein quality control and proteasome-mediated protein degradation

Seminars in Cell and Developmental Biology ◽

10.1006/scdb.1999.0321 ◽

1999 ◽

Vol 10 (5) ◽

pp. 507-513 ◽

Cited By ~ 248

Author(s):

Jeffrey L. Brodsky ◽

Ardythe A. McCracken

Keyword(s):

Quality Control ◽

Protein Degradation ◽

Protein Quality ◽

Protein Quality Control

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Bacterial Proteasomes: Mechanistic and Functional Insights

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.00036-16 ◽

2016 ◽

Vol 81 (1) ◽

Cited By ~ 13

Author(s):

Samuel H. Becker ◽

K. Heran Darwin

Keyword(s):

Quality Control ◽

Protein Degradation ◽

Protein Quality ◽

Protein Quality Control ◽

Cellular Physiology ◽

Recent Developments ◽

Accessory Factors

SUMMARY Regulated proteolysis is essential for the normal physiology of all organisms. While all eukaryotes and archaea use proteasomes for protein degradation, only certain orders of bacteria have proteasomes, whose functions are likely as diverse as the species that use them. In this review, we discuss the most recent developments in the understanding of how proteins are targeted to proteasomes for degradation, including ATP-dependent and -independent mechanisms, and the roles of proteasome-dependent degradation in protein quality control and the regulation of cellular physiology. Furthermore, we explore newly established functions of proteasome system accessory factors that function independently of proteolysis.

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Abstract 30: Nub1l Suppresses Neddylation And Enhances Misfolded Protein Clearance In Cardiomyocytes

Circulation Research ◽

10.1161/res.115.suppl_1.30 ◽

2014 ◽

Vol 115 (suppl_1) ◽

Author(s):

Huabo Su ◽

Jie Li ◽

Wenxia Ma ◽

Ning Hou ◽

Faqian Li

Keyword(s):

Quality Control ◽

Protein Degradation ◽

Cardiac Disease ◽

Protein Modification ◽

Protein Quality ◽

Ischemia Reperfusion ◽

Protein Quality Control ◽

Misfolded Protein ◽

Dependent Manner

Protein modification by ubiquitin (Ub) or Ub-like proteins such as NEDD8 (neddylation) constitutes a fundamental regulatory mechanism of protein function. In contrast to well-recognized role of Ub in protein degradation, little is known about the role of NEDD8 in protein quality control. We have previously revealed that CM-restricted inactivation of deneddylation, a process that removes NEDD8 from modified proteins, accumulates neddylated proteins and impairs proteasomal and autophagic proteolysis. Here we report that proteasome inhibitors, simulated ischemia/reperfusion and H2O2 significantly increase NEDD8 conjugates in cardiomyocytes (CMs). Immunoprecipitation analysis reveals mixed modification of these proteins by Ub and NEDD8. Expression of NEDD8 but not the conjugation-deficient mutant increases neddylated proteins and accumulates a proteasome surrogate substrate GFPu in a dose-dependent manner, suggesting that excessive neddylation disrupts proteasomal proteolysis. We further targets to NUB1L, a UBL (Ub-like domain)-UBA (Ub associating domain) family protein that was shown to negatively regulate neddylation. NUB1L expression markedly reduces free NEDD8 by promoting its degradation, and abrogates proteasome inhibition-induced neddylation in CMs. Suppression of neddylation by NUB1L expression enhances GFPu degradation at baseline, and attenuates GFPu accumulation upon sI/R and H2O2 treatment. Furthermore, NUB1L expression promotes, while down-regulation of NUB1L impairs, the clearance of a bona fide misfolded protein in CMs. NUB1L expression also ameliorates proteotoxic stress- and sI/R-induced CM injury. Finally, increased NEDD8 conjugates are evident in the mouse hearts of a number of cardiac disease models as well as in human failing hearts. Together, our findings suggest that excessive neddylation disrupts protein quality control and that antagonizing neddylation by NUB1L promotes misfolded protein degradation. Targeting neddylation/NUB1L could be a novel therapeutic strategy for prevention and treatment of insufficient protein quality control-associated cardiac disease.

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