scholarly journals Coupled protein quality control during nonsense mediated mRNA decay

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.

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

2015 ◽  
Vol 60 (3) ◽  
pp. 1438-1449 ◽  
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.

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

Science ◽  
2015 ◽  
Vol 349 (6243) ◽  
pp. 91-95 ◽  
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.

scholarly journals ER-associated degradation: Protein quality control and beyond

2014 ◽  
Vol 204 (6) ◽  
pp. 869-879 ◽  
Author(s):  
Annamaria Ruggiano ◽  
Ombretta Foresti ◽  
Pedro Carvalho
Keyword(s):  
Quality Control ◽  
Endoplasmic Reticulum ◽  
Protein Degradation ◽  
Control Systems ◽  
Protein Quality ◽  
Protein Quality Control ◽  
Secretory Proteins ◽  
Toxic Species ◽  
Cellular Factors

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.

scholarly journals Characterization of Rapidly Degraded Polypeptides in Mammalian Cells Reveals a Novel Layer of Nascent Protein Quality Control

2005 ◽  
Vol 281 (1) ◽  
pp. 392-400 ◽  
Author(s):  
Shu-Bing Qian ◽  
Michael F. Princiotta ◽  
Jack R. Bennink ◽  
Jonathan W. Yewdell
Keyword(s):  
Quality Control ◽  
Mammalian Cells ◽  
Protein Quality ◽  
Protein Quality Control

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

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.

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

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.

scholarly journals Loss of protein quality control gene UBR1 sensitizes Saccharomyces cerevisiae to the aminoglycoside hygromycin B

Fine Focus ◽  
2020 ◽  
Vol 6 (1) ◽  
pp. 76-83
Author(s):  
Avery M. Runnebohm ◽  
Melissa D. Evans ◽  
Adam E. Richardson ◽  
Samantha M. Turk ◽  
James B. Olesen ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Quality Control ◽  
Ubiquitin Ligase ◽  
Protein Quality ◽  
Protein Quality Control ◽  
Eukaryotic Cells ◽  
Hygromycin B ◽  
Eukaryotic Microorganism ◽  
Human Enzyme ◽  
A Site

Ubr1 is a conserved ubiquitin ligase involved in the degradation of aberrant proteins in eukaryotic cells. The human enzyme is found mutated in patients with Johanson-Blizzard syndrome. We hypothesized that Ubr1 is necessary for optimal cellular fitness in conditions associated with elevated abundance of aberrant and misfolded proteins. Indeed, we found that loss of Ubr1 in the model eukaryotic microorganism Saccharomyces cerevisiae strongly sensitizes cells to hygromycin B, which reduces translational fidelity by causing ribosome A site distortion. Our results are consistent with a prominent role for Ubr1 in protein quality control. We speculate that disease manifestations in patients with Johanson-Blizzard syndrome are linked, at least in part, to defects in protein quality control caused by loss of Ubr1 function.

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