Protein ubiquitination is an important post-translational modification involved in several essential signalling pathways. It has different effects on the target protein substrate, i.e., it can trigger the degradation of the protein in the proteasome, change the interactions of the modified protein with its partners, or affect its localization and activity. In order to understand the molecular mechanisms underlying the consequences of protein ubiquitination, scientists have to face the challenging task of producing ubiquitinated proteins for structural characterization with X-ray crystallography and/or nuclear magnetic resonance (NMR) spectroscopy. These techniques require milligrams of homogeneous samples of high purity. The strategies proposed so far for the production of ubiquitinated proteins can be divided into two groups, i.e., chemical (or non-enzymatic) and enzymatic methodologies. In this review, we summarize the still very sparse examples available in the literature that describe successful

Author Summary Autophagy is an evolutionarily conserved process that sequestrates and delivers cytoplasmic macromolecules and organelles to the vacuoles or lysosomes for degradation. In plants, autophagy is involved in supplying internal nutrients during starvation and in promoting cell survival during senescence and during biotic and abiotic stresses. Arabidopsis NBR1 is a homolog of mammalian autophagy cargo adaptors P62 and NBR1. Disruption of Arabidopsis NBR1 caused increased sensitivity to a spectrum of abiotic stresses but had no significant effect on plant senescence, responses to carbon starvation, or resistance to a necrotrophic pathogen. NBR1 contains an ubiquitin-binding domain, and the compromised stress tolerance of autophagy mutants was associated with increased accumulation of NBR1 and ubiquitin-positive cellular protein aggregates in the insoluble protein fraction under stress conditions. Based on these results, we propose that NBR1 targets ubiquitinated protein aggregates most likely

We tested the effect of proteasome inhibition on keratins in cultured HT29 cells (Fig. 1 A). ALLN increased the level of detectable ubiquitinated proteins (lane 4), and generated K8 (lane 6) and K18 (lane 8) ladders. However, the extent of ladder formation was minimal and required significant over-exposure for visualization, and several anti-Ub Abs did not bind K8/18 immunoprecipitates likely due to inability to precipitate the ubiquitinated keratins (not shown). This led us to test keratin ubiquitination in a cell transfection system that included cotransfection of His-tagged Ub with K8 and/or K18 to allow isolation of the ubiquitinated proteins. Proteasome inhibition of keratin-transfected BHK cells markedly increased the ability to detect ubiquitinated proteins as determined by blotting of total cell lysates or cell fractions that are collected with a Ni column in order to isolate His-tagged ubiquitinated proteins (Fig. 1 B). Confirmation of K8/18 ubiquitination was obtained by immunoblotting ...

The cytoplasmic signal adaptor protein designated sequestosome1 (SQSTM1) (A170 in mouse, ZIP in rat or p62 in human) plays a key role in modulating signal transduction via membrane receptors. SQSTM1 has a UBA ubiquitin-binding domain in the C-terminus and participates in the assembly of ubiquitinated protein aggregates termed sequestosome and modulation of ubiquitination pathways involved in NF-κB activity and receptor trafficking. We have found that deficiency of SQSTM1 in mice exhibits mature-onset obesity accompanied by insulin and leptin resistance. We previously established that redox sensitive transcription factor Nrf2 upregulates SQSTM1 expression in response to atherogenic stimuli or laminar shear stress in vascular cells, and here examine role of SQSTM1 in neointimal hyperplasia and vascular remodeling in vivo following carotid artery ligation. Neointimal hyperplasia was markedly enhanced at proximal sites of ligation after 3 weeks in SQSTM1−/− (n=10) compared with wild type mice ...

Protein ubiquitination is a key regulatory process essential to life at a cellular level; significant efforts have been made to identify ubiquitinated proteins through proteomics studies but the level of success has not reached that of heavily studied post-translational modifications such as phosphorylation. of more than 400 ubiquitinated Phentolamine HCl proteins a fraction of which were found to be sensitive to HRD1 and were therefore deemed candidate substrates. In a second approach ubiquitinated peptides were enriched after tryptic digestion by peptide immunoprecipitation using an antibody specific for the diglycine-labeled internal lysine residue indicative of protein ubiquitination with peptides and ubiquitination sites identified by LC-MS/MS. Peptide immunoprecipitation resulted in identification of over 1800 ubiquitinated peptides on over 900 proteins in each study with several proteins emerging as sensitive to HRD1 levels. Notably significant overlap exists between the HRD1 substrates ...

Harris IS, Endress JE, Coloff JL, Selfors LM, McBrayer SK, Rosenbluth JM, Takahashi N, Dhakal S, Koduri V, Oser MG, Schauer NJ, Doherty LM, Hong AL, Kang YP, Younger ST, Doench JG, Hahn WC, Buhrlage SJ, DeNicola GM, Kaelin WG, Brugge JS. Deubiquitinases Maintain Protein Homeostasis and Survival of Cancer Cells upon Glutathione Depletion. Cell Metab. 2019 05 07; 29(5):1166-1181.e6 ...

Akimov V, et al. (2018) UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites. Nat Struct Mol Biol 25, 631-640 ...

Akimov V, et al. (2018) UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites. Nat Struct Mol Biol 25, 631-640 ...

The p62/SQSTM1 (sequestosome 1) protein which acts as a cargo receptor for autophagic degradation of ubiquitinated targets is up-regulated by various stressors. vesicle called an autophagosome. In turn autophagosomes fuse with lysosomes and their contents are degraded by lysosomal hydrolases (29). Because p62 binds to ubiquitin and to LC3 it is both a selective autophagy substrate and a cargo receptor for autophagic degradation of ubiquitinated targets (30 -34). p62 forms cytosolic inclusion bodies distinct from aggresomes which contain ubiquitinated protein aggregates that subsequently can be degraded by autophagy (30 34 Using conditional Atg7 knock-out mice it has been reported that when autophagy is usually abolished in the liver p62 accumulates in aggregates phase II drug-metabolizing enzymes and antioxidant proteins are strongly induced and the liver becomes grossly enlarged and suffers loss of function. Hepatic dysfunction in such mice is usually relieved when p62 is also knocked out (32). ...

The ternary complex containing UFD1, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope (By similarity). Acts as a negative regulator of type I interferon production via the complex formed with VCP and UFD1, which binds to DDX58/RIG-I and recruits RNF125 to promote ubiquitination and degradation of DDX58/RIG-I (PubMed:26471729).

Endosomal protein that forms a complex with Hse1p; required for recycling Golgi proteins, forming lumenal membranes and sorting ubiquitinated proteins destined for degradation; has Ubiquitin Interaction Motifs which bind ubiquitin (Ubi4p ...

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Essential component of the ubiquitin-dependent proteolytic pathway which degrades ubiquitin fusion proteins. The ternary complex containing UFD1, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope. It may be involved in the development of some ectoderm-derived structures (By similarity). Acts as a negative regulator of type I interferon production via the complex formed with VCP and NPLOC4, which binds to DDX58/RIG-I and recruits RNF125 to promote ubiquitination and degradation of DDX58/RIG-I (PubMed:26471729). The protein encoded by this gene forms a complex with two other proteins, nuclear protein localization-4 and valosin-containing protein, and this complex is necessary for the degradation of ubiquitinated proteins. In addition, this

Protein ubiquitination regulates protein stability and modulates the composition of signaling complexes. A20 is a negative regulator of inflammatory signaling, but the molecular mechanisms involved are ill understood. Here, we generated Tnfaip3 gene-targeted A20 mutant mice bearing inactivating mutations in the zinc finger 7 (ZnF7) and ZnF4 ubiquitin-binding domains, revealing that binding to polyubiquitin is essential for A20 to suppress inflammatory disease. We demonstrate that a functional ZnF7 domain was required for recruiting A20 to the tumor necrosis factor receptor 1 (TNFR1) signaling complex and to suppress inflammatory signaling and cell death. The combined inactivation of ZnF4 and ZnF7 phenocopied the postnatal lethality and severe multiorgan inflammation of A20-deficient mice. Conditional tissue-specific expression of mutant A20 further revealed the key role of ubiquitin-binding in myeloid and intestinal epithelial cells. Collectively, these results demonstrate that the anti-inflammatory and

Chemical Synthesis of Ubiquitinated Peptides with Varying Lengths and Types of Ubiquitin Chains to Explore the Activity of Deubiquitinases | Dr. Sudhir N. Bavikar; Liat Spasser; Mahmood Haj-Yahya; Dr. Subramanian Vedhanarayanan Karthikeyan; Tal Moyal; Dr. K. S. Ajish Kumar; Prof. Ashraf Brik | download | BookSC. Download books for free. Find books

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Component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. This complex plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins, which could impair cellular functions, and by removing proteins whose functions are no longer required. Therefore, the proteasome participates in numerous cellular processes, including cell cycle progression, apoptosis, or DNA damage repair.

Regulatory particle non-ATPase 12A; Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. May help to control the degradation of one or more factors that repress cytokinin signaling. Plays an important role for balancing cell expansion with cell proliferation rates during shoot development (267 aa ...

Quantitative profiling of ubiquitylated proteins reveals proteasome substrates and the substrate repertoire influenced by the Rpn10 receptor pathway. Mol Cell Proteomics. 6(11):1885-95 (2007 ...

Scott, Daniel and Garner, Tom P. and Long, Jed and Strachan, Jo and Mistry, Sharad C. and Bottrill, Andrew R. and Tooth, David J. and Searle, Mark S. and Oldham, Neil J. and Layfield, Rob (2016) Mass spectrometry insights into a tandem ubiquitin-binding domain hybrid engineered for the selective recognition of unanchored polyubiquitin. Proteomics, 16 (14). pp. 1961-1969. ISSN 1615-9861 ...

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TY - JOUR. T1 - Ubiquilin interacts with ubiquitylated proteins and proteasome through its ubiquitin-associated and ubiquitin-like domains. AU - Ko, Han Seok. AU - Uehara, Takashi. AU - Tsuruma, Kazuhiro. AU - Nomura, Yasuyuki. N1 - Funding Information: We thank Dr. Keiji Tanaka (Tokyo Metropolitan Institute of Medical Science), Dr. Hiroyuki Kawahara, and Prof. Hideyoshi Yokosawa (Hokkaido University) for the provision of plasmids and their helpful discussions. This work was supported by a Grant-in-Aid from the Ministry of Education, Science, and Sports of Japan.. PY - 2004/5/21. Y1 - 2004/5/21. N2 - Mammalian cells acquire tolerance against multiple stressors through the high-level expression of stress-responsible genes. We have previously demonstrated that protein-disulfide isomerase (PDI) together with ubiquilin are up-regulated in response to hypoxia/brain ischemia, and play critical roles in resistance to these damages. We show here that ubiquilin interacts preferentially with ...

Acyl-CoA:1,2-diacylglycerol acyltransferase (DGAT)-2 is one of the two DGAT enzymes that catalyzes the synthesis of triacylglycerol, which is an important form of stored energy for eukaryotic organisms. There is currently limited information available regarding how DGAT2 and triacylglycerol synthesis are regulated. Recent studies have indicated that DGAT2 can be regulated by changes in gene expression. How DGAT2 is regulated post-transcriptionally remains less clear. In this study, we demonstrated that DGAT2 is a very unstable protein and is rapidly degraded in an ubiquitin-dependent manner via the proteasome. Many of the 25 lysines present in DGAT2 appeared to be involved in promoting its degradation. However, the six C-terminal lysines were the most important in regulating stability. We also demonstrated that acyl-CoA:monoacylglycerol acyltransferase (MGAT)-2, an enzyme with extensive sequence homology to DGAT2 that catalyzes the synthesis of diacylglycerol, was also ubiquitinated. However, ...

This review focuses on recent insights into the mechanisms and the biological functions of the proteasome. This large ATP-dependent proteolytic complex is the main site for protein degradation in mammalian cells and catalyses the rapid degradation of ubiquitinated proteins, and is the source of most antigenic peptides used by the immune system to screen for viruses and cancer. ATP is required to unfold globular proteins to open the gated channel into the 20S proteasome and to facilitate protein translation into it. Inhibitors of its proteolytic activity are widely used as research tools and have proven effective in cancer therapy. ...

The levels and distribution of ubiquitinated histone H2A (uH2A) have been studied in normal and transformed human cells using a monoclonal antibody (mAb E6C5) that reacts specifically with this ubiquitin conjugate as determined by two-dimensional gel

Reactome is pathway database which provides intuitive bioinformatics tools for the visualisation, interpretation and analysis of pathway knowledge.

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(G) Ubiquitinated kinds of AIB1 in cells grown on different rigidity substrates with Period or CCTf overexpression or knockdown ended up detected employing

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Any process that activates or increases the frequency, rate or extent of protein ubiquitination involved in ubiquitin-dependent protein catabolic process.

Most proteins in cells undergo post-translational modifications giving them structural and functional diversity for diverse roles in biological processes. Experimental identification and validation of posttranslational modifications (PTMs) is labor-intensive task and can be expensive in the absence of prior knowledge concerning PTMs. Analyzing the ubiquitome is one of the most exciting and challenging tasks in current proteomics research. A lack of curated datasets of ubiquitinated proteins presents the ultimate limiting factor in studying substrate selection mechanism in ubiquitination making it difficult to evaluate, and compare target sites. As more and more ligases are identified there exists an urgent need to rapidly and precisely identify enzyme-specific substrates to decode their selectivity and specificity [8]. Computational prediction of PTM sites has provided researchers with information on the high probability PTM sites for further experimental characterizations like PHOSIDA and ...

Ubiquitination-the covalent conjugation of ubiquitin (Ub) to other cellular proteins-regulates a wide range of cellular processes. Often, multiple Ub molecules are added to the substrate to form a Ub chain. Distinct outcomes have been observed for substrates modified with multi-Ub chains linked through particular lysine residues. However, recent studies suggest that Ub chain linkages may not be the key determinant for substrate fate. Here, we review evidence suggesting that Ub-binding proteins play a pivotal role in determining the outcome of substrate ubiquitination. In fulfilling their functions in proteasome-mediated proteolysis or signaling, Ub receptors link ubiquitinated proteins to downstream molecules through protein-protein interactions. Studies of Ub-binding factors may therefore hold the key to understanding the diverse functions of the Ub molecule.. ...

Regulatory particle AAA-ATPase 2A; The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex. Is required for the maintenance of postembryonic root and shoot meristems. Has a specific role in the regulation of organs size (443 aa ...

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In mammalian cells, the 26S proteasomes vary in composition. In addition to the standard 28 subunits in the 20S core particle and 19 subunits in each 19S regulatory particle, a small fraction (abo ...

Ubiquitin-dependent regulation of endocytosis plays an important part in the control of signal transduction, and a critical issue in the understanding of signal transduction therefore relates to regulation of ubiquitination in the endocytic pathway. We discuss here what is known of the mechanisms by which signaling controls the activity of the ubiquitin ligases that specifically recognize the targets of ubiquitination on the endocytic pathway, and suggest alternative mechanisms that deserve experimental investigation.

Ubiquitin regulates a myriad of important cellular processes through covalent attachment to its substrates. A classic role for ubiquitin is to flag proteins for destruction by the proteasome. Recent studies indicate that ubiquitin-binding proteins (e.g. Rad23, Dsk2, Rpn10) play a pivotal role in transferring ubiquitylated proteins to the proteasome. However, the specific role of these ubiquitin receptors remains poorly defined. A key to unraveling the functions of these ubiquitin receptors is to identify their cellular substrates and biological circuits they are involved in. Although many strategies have been developed for substrate isolation, the identification of physiological targets of proteolytic pathways has proven to be quite challenging. Using a genome-wide functional screen, we have identified 11 yeast genes that cause slower growth upon their overexpression in cells lacking two ubiquitin-binding proteins Rad23 and Dsk2. Our results suggest that proper functioning of Rad23 and Dsk2 is required

This thesis deals with an important post-translational modification, ubiquitination. An important part of ubiquitin, regulatory protein, is the N-terminus and seven lysine residues, through which originates mutual binding of ubiquitin molecules in the polyubiquitin chain. The various possibilities of binding provide diversity in the creation of polyubiquitin chains, and thus their significance. Since ubiquitinated proteins in the analyzed protein mixtures exist mostly as a minor component, the first important and difficult step is their correct separation and identification. Experimental part of this work deals with precisely this part of the research and thus contains optimization methods for isolating and identifying of ubiquitin proteins by antibodies on the peptide and protein level. It has been shown that the optimization takes more time and work, thus future progressin this area is expected. …víceméně ...

The proteasome is a protein-destroying apparatus involved in many essential cellular functions, such as regulation of cell cycle, cell differentiation, signal transduction pathways, antigen processing for appropriate immune responses, stress signaling, inflammatory responses, and apoptosis. It is capable of degrading a variety of cellular proteins in a rapid and timely fashion and most substrate proteins are modified by ubiquitin before their degradation by the proteasome. The proteasome is a large protein complex consisting of a proteolytic core called the 20S particle and ancillary factors that regulate its activity in various ways. The most common form is the 26S proteasome containing one 20S core particle and two 19S regulatory particles that enable the proteasome to degrade ubiquitinated proteins by an ATP-dependent mechanism. Another form is the immunoproteasome containing two 11S regulatory particles, PA28 alpha and PA28 beta, which are induced by interferon gamma under the conditions of ...

The proteasome is a protein-destroying apparatus involved in many essential cellular functions, such as regulation of cell cycle, cell differentiation, signal transduction pathways, antigen processing for appropriate immune responses, stress signaling, inflammatory responses, and apoptosis. It is capable of degrading a variety of cellular proteins in a rapid and timely fashion and most substrate proteins are modified by ubiquitin before their degradation by the proteasome. The proteasome is a large protein complex consisting of a proteolytic core called the 20S particle and ancillary factors that regulate its activity in various ways. The most common form is the 26S proteasome containing one 20S core particle and two 19S regulatory particles that enable the proteasome to degrade ubiquitinated proteins by an ATP-dependent mechanism. Another form is the immunoproteasome containing two 11S regulatory particles, PA28 alpha and PA28 beta, which are induced by interferon gamma under the conditions of ...

Uniprot: Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process. The ternary complex containing UFD1, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope. Regulates E3 ubiquitin-protein ligase activity of RNF19A. Component of the VCP/p97-AMFR/gp78 complex that participates in the final step of the sterol-mediated ubiquitination and endoplasmic ...

Injury and loss of podocytes are leading factors of glomerular disease and renal failure. The postmitotic podocyte is the primary glomerular target for toxic, immune, metabolic, and oxidant stress, but little is known about how this cell type copes with stress. Recently, autophagy has been identified as a major pathway that delivers damaged proteins and organelles to lysosomes in order to maintain cellular homeostasis. Here we report that podocytes exhibit an unusually high level of constitutive autophagy. Podocyte-specific deletion of autophagy-related 5 (Atg5) led to a glomerulopathy in aging mice that was accompanied by an accumulation of oxidized and ubiquitinated proteins, ER stress, and proteinuria. These changes resulted ultimately in podocyte loss and late-onset glomerulosclerosis. Analysis of pathophysiological conditions indicated that autophagy was substantially increased in glomeruli from mice with induced proteinuria and in glomeruli from patients with acquired proteinuric diseases. ...

Background: Ubiquitination is a vital posttranslational protein modification involved in the regulation of many eukaryotic signalling pathways. Aberrant ubiquitin signalling is known to be a molecular causality of certain cancer, neurodegenerative, immune system or cardiovascular diseases. The recent development of mass spectrometry methods enables qualitative and quantitative ubiquitination...

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VCP (valosin containing protein), Authors: Yalcin Erzurumlu, Recep Ilhan, Oguz Gozen, Petek Ballar. Published in: Atlas Genet Cytogenet Oncol Haematol.