scholarly journals Parallel genome-wide CRISPR analysis identifies a role for heterotypic ubiquitin chains in ER-associated degradation

2018 ◽  
Author(s):  
Dara E. Leto ◽  
David W. Morgens ◽  
Lichao Zhang ◽  
Christopher P. Walczak ◽  
Joshua E. Elias ◽  
...  
Keyword(s):  
Protein Degradation ◽  
Ubiquitin Proteasome System ◽  
Human Cells ◽  
Secretory Proteins ◽  
Substrate Selectivity ◽  
Substrate Degradation ◽  
Genome Wide ◽  
Ubiquitin Proteasome ◽  
Ubiquitin Conjugation ◽  
Secretory System

SummaryThe ubiquitin proteasome system (UPS) maintains the integrity of the proteome and controls the abundance of key regulators of cellular function by selective protein degradation, but how foldingdefective proteins in the secretory system are selected from the large and diverse constellation of membrane and secretory proteins and efficiently delivered to proteasomes in the cytosol is not well understood. To determine the basis of substrate selectivity in human cells, we developed a transcriptional shut off approach to conduct parallel, unbiased, genome-wide CRISPR analysis of structurally and topologically diverse ER-associated degradation (ERAD) clients. Highly quantitative screen metrics allowed precise dissection of entire pathways, enabling identification of unique substrate-specific combinations of recognition and ubiquitin conjugation modules. Our analysis identified cytosolic ubiquitin conjugating machinery that has not been previously linked to ERAD but collaborates with membrane-integrated ubiquitin ligases to conjugate branched or mixed ubiquitin chains to promote efficient and processive substrate degradation.

scholarly journals Ccr4 is a novel shuttle factor required for ubiquitin-dependent proteolysis by the 26S proteasome

2020 ◽  
Author(s):  
Ganapathi Kandasamy ◽  
Ashis Kumar Pradhan ◽  
R Palanimurugan
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Degradation ◽  
Ubiquitin Proteasome System ◽  
Proteasomal Degradation ◽  
Rna Degradation ◽  
26S Proteasome ◽  
Cellular Proteins ◽  
Cellular Homeostasis ◽  
Substrate Degradation ◽  
Ubiquitin Proteasome

AbstractDegradation of short-lived and abnormal proteins are essential for normal cellular homeostasis. In eukaryotes, such unstable cellular proteins are selectively degraded by the ubiquitin proteasome system (UPS). Furthermore, abnormalities in protein degradation by the UPS have been linked to several human diseases. Ccr4 protein is a known component of the Ccr4-Not complex, which has established roles in transcription, mRNA de-adenylation and RNA degradation etc. Excitingly in this study, we show that Ccr4 protein has a novel function as a shuttle factor that promotes ubiquitin-dependent degradation of short-lived proteins by the 26S proteasome. Using a substrate of the well-studied ubiquitin fusion degradation (UFD) pathway, we found that its UPS-mediated degradation was severely impaired upon deletion of CCR4 in Saccharomyces cerevisiae. Additionally, we show that Ccr4 binds to cellular ubiquitin conjugates and the proteasome. In contrast to Ccr4, most other subunits of the Ccr4-Not complex proteins are dispensable for UFD substrate degradation. From our findings we conclude that Ccr4 functions in the UPS as a shuttle factor targeting ubiquitylated substrates for proteasomal degradation.

scholarly journals Adaptability of the ubiquitin-proteasome system to proteolytic and folding stressors

2020 ◽  
Vol 220 (3) ◽  
Author(s):  
Jeremy J. Work ◽  
Onn Brandman
Keyword(s):  
Ubiquitin Proteasome System ◽  
Environmental Stressors ◽  
Quantitative Measurements ◽  
Substrate Degradation ◽  
Degradation Rates ◽  
Ubiquitin Proteasome ◽  
Substrate Stability ◽  
Quantitative Understanding ◽  
Proteolytic Stress ◽  
Stress Dependent

Aging, disease, and environmental stressors are associated with failures in the ubiquitin-proteasome system (UPS), yet a quantitative understanding of how stressors affect the proteome and how the UPS responds is lacking. Here we assessed UPS performance and adaptability in yeast under stressors using quantitative measurements of misfolded substrate stability and stress-dependent UPS regulation by the transcription factor Rpn4. We found that impairing degradation rates (proteolytic stress) and generating misfolded proteins (folding stress) elicited distinct effects on the proteome and on UPS adaptation. Folding stressors stabilized proteins via aggregation rather than overburdening the proteasome, as occurred under proteolytic stress. Still, the UPS productively adapted to both stressors using separate mechanisms: proteolytic stressors caused Rpn4 stabilization while folding stressors increased RPN4 transcription. In some cases, adaptation completely prevented loss of UPS substrate degradation. Our work reveals the distinct effects of proteotoxic stressors and the versatility of cells in adapting the UPS.

scholarly journals E2A protein degradation by the ubiquitin-proteasome system is stage-dependent during muscle differentiation

Oncogene ◽  
2006 ◽  
Vol 26 (3) ◽  
pp. 441-448 ◽  
Author(s):  
L Sun ◽  
J S Trausch-Azar ◽  
A Ciechanover ◽  
A L Schwartz
Keyword(s):  
Protein Degradation ◽  
Ubiquitin Proteasome System ◽  
Muscle Differentiation ◽  
Ubiquitin Proteasome

P3-147: Axonal transport of the ubiquitin-proteasome system and it relevance for protein degradation

2011 ◽  
Vol 7 ◽  
pp. S562-S564
Author(s):  
Maria Gabriela Otero ◽  
Lucas Cromberg ◽  
Tomas Falzone
Keyword(s):  
Protein Degradation ◽  
Axonal Transport ◽  
Ubiquitin Proteasome System ◽  
Ubiquitin Proteasome

scholarly journals Multiubiquitin Chain Receptors Define a Layer of Substrate Selectivity in the Ubiquitin-Proteasome System

Cell ◽  
2004 ◽  
Vol 118 (1) ◽  
pp. 99-110 ◽  
Author(s):  
Rati Verma ◽  
Robert Oania ◽  
Johannes Graumann ◽  
Raymond J Deshaies
Keyword(s):  
Ubiquitin Proteasome System ◽  
Substrate Selectivity ◽  
Ubiquitin Proteasome

scholarly journals Efficient APC/C substrate degradation in cells undergoing mitotic exit depends on K11 ubiquitin linkages

2015 ◽  
Vol 26 (24) ◽  
pp. 4325-4332 ◽  
Author(s):  
Mingwei Min ◽  
Tycho E. T. Mevissen ◽  
Maria De Luca ◽  
David Komander ◽  
Catherine Lindon
Keyword(s):  
Cell Cycle Progression ◽  
Degradation Kinetics ◽  
Ubiquitin Proteasome System ◽  
Mitotic Exit ◽  
Anaphase Promoting Complex ◽  
Polyubiquitin Chains ◽  
Substrate Degradation ◽  
Ubiquitin Proteasome ◽  
In Cells

The ubiquitin proteasome system (UPS) directs programmed destruction of key cellular regulators via posttranslational modification of its targets with polyubiquitin chains. These commonly contain Lys-48 (K48)–directed ubiquitin linkages, but chains containing atypical Lys-11 (K11) linkages also target substrates to the proteasome—for example, to regulate cell cycle progression. The ubiquitin ligase called the anaphase-promoting complex/cyclosome (APC/C) controls mitotic exit. In higher eukaryotes, the APC/C works with the E2 enzyme UBE2S to assemble K11 linkages in cells released from mitotic arrest, and these are proposed to constitute an improved proteolytic signal during exit from mitosis. We tested this idea by correlating quantitative measures of in vivo K11-specific ubiquitination of individual substrates, including Aurora kinases, with their degradation kinetics tracked at the single-cell level. All anaphase substrates tested by this methodology are stabilized by depletion of K11 linkages via UBE2S knockdown, even if the same substrates are significantly modified with K48-linked polyubiquitin. Specific examination of substrates depending on the APC/C coactivator Cdh1 for their degradation revealed Cdh1-dependent enrichment of K11 chains on these substrates, whereas other ubiquitin linkages on the same substrates added during mitotic exit were Cdh1-independent. Therefore we show that K11 linkages provide the APC/C with a means to regulate the rate of substrate degradation in a coactivator-specified manner.

scholarly journals Involvement of the Ubiquitin-Proteasome System in the Formation of Experimental Postsurgical Peritoneal Adhesions

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Clara Di Filippo ◽  
Pasquale Petronella ◽  
Fulvio Freda ◽  
Marco Scorzelli ◽  
Marco Ferretti ◽  
...  
Keyword(s):  
Protein Degradation ◽  
Ubiquitin Proteasome System ◽  
20S Proteasome ◽  
Intracellular Protein ◽  
Peritoneal Adhesions ◽  
Proteasome Subunit ◽  
Peritoneal Tissue ◽  
Intracellular Protein Degradation ◽  
Ubiquitin Proteasome

We investigated the Ubiquitin-Proteasome System (UPS), major nonlysosomal intracellular protein degradation system, in the genesis of experimental postsurgical peritoneal adhesions. We assayed the levels of UPS within the adhered tissue along with the development of peritoneal adhesions and used the specific UPS inhibitor bortezomib in order to assess the effect of the UPS blockade on the peritoneal adhesions. We found a number of severe postsurgical peritoneal adhesions at day 5 after surgery increasing until day 10. In the adhered tissue an increased values of ubiquitin and the 20S proteasome subunit, NFkB, IL-6, TNF-αand decreased values of IkB-beta were found. In contrast, bortezomib-treated rats showed a decreased number of peritoneal adhesions, decreased values of ubiquitin and the 20S proteasome, NFkB, IL-6, TNF-α, and increased levels of IkB-beta in the adhered peritoneal tissue. The UPS system, therefore, is primarily involved in the formation of post-surgical peritoneal adhesions in rats.

Regulation of ubiquitin-proteasome system-mediated Tip110 protein degradation by USP15

2014 ◽  
Vol 54 ◽  
pp. 10-19 ◽  
Author(s):  
Khalid Amine Timani ◽  
Ying Liu ◽  
Attaya Suvannasankha ◽  
Johnny J. He
Keyword(s):  
Protein Degradation ◽  
Ubiquitin Proteasome System ◽  
Ubiquitin Proteasome
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