scholarly journals Branching and Mixing: New Signals of the Ubiquitin Signaling System

2020 ◽  
Author(s):  
Daniel Perez-Hernandez ◽  
Marta L. Mendes ◽  
Gunnar Dittmar
Keyword(s):  
Protein Degradation ◽  
Posttranslational Modifications ◽  
Protein Targeting ◽  
Ubiquitin Chain ◽  
Multiple Signals ◽  
Additional Layer ◽  
Ubiquitin System ◽  
Ubiquitin Molecule ◽  
A Chain ◽  
Cellular Compartments

Posttranslational modifications allow cells and organisms to adapt to their environment without the need to synthesize new proteins. The ubiquitin system is one of the most versatile modification systems as it does not only allow a simple on–off modification but, by forming a chain of ubiquitin molecules, allows conveying multiple signals. The structure of the chains is dependent on the linkage to the previous ubiquitin molecule as every lysine can serve as an acceptor point for this modification. Different chain types code for specific signals ranging from protein degradation to protein targeting different cellular compartments. Recently the code of ubiquitin signals has been further expanded as branching and mixing of different chain types has been detected. As an additional layer of complexity, modifications of the ubiquitin chain by ubiquitin-like modifiers, like NEDD8, SUMO, or ISG15, have been found. Here we will discuss the different chain types and the technical challenges which are associated with analyzing ubiquitin topology-based signaling.

scholarly journals UBL domain of Usp14 and other proteins stimulates proteasome activities and protein degradation in cells

2018 ◽  
Vol 115 (50) ◽  
pp. E11642-E11650 ◽  
Author(s):  
Hyoung Tae Kim ◽  
Alfred L. Goldberg
Keyword(s):  
Protein Degradation ◽  
Atp Hydrolysis ◽  
Deubiquitinating Enzyme ◽  
Wild Type ◽  
Peptide Hydrolysis ◽  
Ubiquitin Chain ◽  
Important Regulator ◽  
General Response ◽  
Ubiquitin Conjugate ◽  
Stimulation Of

The best-known function of ubiquitin-like (UBL) domains in proteins is to enable their binding to 26S proteasomes. The proteasome-associated deubiquitinating enzyme Usp14/UBP6 contains an N-terminal UBL domain and is an important regulator of proteasomal activity. Usp14 by itself represses multiple proteasomal activities but, upon binding a ubiquitin chain, Usp14 stimulates these activities and promotes ubiquitin-conjugate degradation. Here, we demonstrate that Usp14’s UBL domain alone mimics this activation of proteasomes by ubiquitin chains. Addition of this UBL domain to purified 26S proteasomes stimulated the same activities inhibited by Usp14: peptide entry and hydrolysis, protein-dependent ATP hydrolysis, deubiquitination by Rpn11, and the degradation of ubiquitinated and nonubiquitinated proteins. Thus, the binding of Usp14’s UBL (apparently to Rpn1’s T2 site) seems to mediate the activation of proteasomes by ubiquitinated substrates. However, the stimulation of these various activities was greater in proteasomes lacking Usp14 than in wild-type particles and thus is a general response that does not involve some displacement of Usp14. Furthermore, the UBL domains from hHR23 and hPLIC1/UBQLN1 also stimulated peptide hydrolysis, and the expression of hHR23A’s UBL domain in HeLa cells stimulated overall protein degradation. Therefore, many UBL-containing proteins that bind to proteasomes may also enhance allosterically its proteolytic activity.

scholarly journals Arginine Methylation Controls the Subcellular Localization and Functions of the Oncoprotein Splicing Factor SF2/ASF

2010 ◽  
Vol 30 (11) ◽  
pp. 2762-2774 ◽  
Author(s):  
Rahul Sinha ◽  
Eric Allemand ◽  
Zuo Zhang ◽  
Rotem Karni ◽  
Michael P. Myers ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Subcellular Localization ◽  
Posttranslational Modifications ◽  
Target Genes ◽  
Positive Charge ◽  
Arginine Methylation ◽  
Sr Protein ◽  
Functional Studies ◽  
Eukaryotic Proteomes ◽  
Cellular Compartments

ABSTRACT Alternative splicing and posttranslational modifications (PTMs) are major sources of protein diversity in eukaryotic proteomes. The SR protein SF2/ASF is an oncoprotein that functions in pre-mRNA splicing, with additional roles in other posttranscriptional and translational events. Functional studies of SR protein PTMs have focused exclusively on the reversible phosphorylation of Ser residues in the C-terminal RS domain. We confirmed that human SF2/ASF is methylated at residues R93, R97, and R109, which were identified in a global proteomic analysis of Arg methylation, and further investigated whether these methylated residues regulate the properties of SF2/ASF. We show that the three arginines additively control the subcellular localization of SF2/ASF and that both the positive charge and the methylation state are important. Mutations that block methylation and remove the positive charge result in the cytoplasmic accumulation of SF2/ASF. The consequent decrease in nuclear SF2/ASF levels prevents it from modulating the alternative splicing of target genes, results in higher translation stimulation, and abrogates the enhancement of nonsense-mediated mRNA decay. This study addresses the mechanisms by which Arg methylation and the associated positive charge regulate the activities of SF2/ASF and emphasizes the significance of localization control for an oncoprotein with multiple functions in different cellular compartments.

scholarly journals Going in GTP cycles in the nucleolus

2005 ◽  
Vol 168 (2) ◽  
pp. 177-178 ◽  
Author(s):  
Tom Misteli
Keyword(s):  
Signaling Pathways ◽  
Protein Targeting ◽  
Nucleolar Localization ◽  
Specific Localization ◽  
Extracellular Stimuli ◽  
Cellular Compartments ◽  
Increased Retention

Proteins are directed to cellular compartments by specific localization signals. A GTP-driven cycle has now been identified as a mechanism for protein targeting to the nucleolus. The involvement of a GTP switch suggests that nucleolar localization can be regulated and may be responsive to extracellular stimuli via signaling pathways. The uncovered mechanism also implies that localization is determined by increased retention rather than directed targeting.

Stress-induced alterations in autophagic pathway: relationship to ubiquitin system

1992 ◽  
Vol 262 (4) ◽  
pp. C1031-C1038 ◽  
Author(s):  
A. L. Schwartz ◽  
R. A. Brandt ◽  
H. Geuze ◽  
A. Ciechanover
Keyword(s):  
Heat Stress ◽  
Protein Degradation ◽  
Cell Lines ◽  
Mutant Cell ◽  
Buoyant Density ◽  
Nutrient Deprivation ◽  
Temperature Sensitive ◽  
Lysosomal Hydrolases ◽  
Ubiquitin Pathway ◽  
Ubiquitin System

The autophagic response of the cell to nutrient deprivation or heat stress is characterized by an increase in the rate of cellular protein degradation. Using temperature-sensitive mutant cell lines that harbor a mutation in the ubiquitin pathway, we have recently shown that this response is dependent on a functional ubiquitin-activating enzyme E1. The ubiquitin pathway is involved in a multitude of cellular events including protein degradation, the best understood of these. Herein the activation of the ubiquitin molecule via E1 is followed by its covalent conjugation to acceptor proteins followed by proteolysis. It is therefore important to study the linkage between the autophagic response and E1. Using these same cell lines, CHO E36 and CHO ts20, we demonstrate that after heat stress or nutrient deprivation there is a rapid and reversible decrease in the buoyant density of subcellular vesicles containing lysosomal hydrolases, a characteristic found to accompany autophagy. This stress-induced change is found in all cell lines examined, independent of the activity of the E1. The light-density vesicles, which comigrate with endosomes on colloidal silica gradients, are not accessible to the endocytic marker transferrin-horseradish peroxidase (HRP) after cellular uptake and subsequent HRP-mediated density shift analysis. Furthermore, morphology of the isolated fractions from control and stress-induced cells was similar. These results thus demonstrate the changes in hydrolase-containing intracellular vesicles that accompany nutritional deprivation or heat stress and support the notion that the linkage of the autophagic response to the ubiquitin system is at a step in autophagy which does not affect the formation of autophagic vesicles.

scholarly journals The Png1–Rad23 complex regulates glycoprotein turnover

2006 ◽  
Vol 172 (2) ◽  
pp. 211-219 ◽  
Author(s):  
Ikjin Kim ◽  
Jungmi Ahn ◽  
Chang Liu ◽  
Kaori Tanabe ◽  
Jennifer Apodaca ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Substrate Specificity ◽  
Protein Degradation ◽  
Binding Proteins ◽  
Degradation Pathways ◽  
Ricin A Chain ◽  
Substrate Degradation ◽  
A Chain ◽  
Specific Degradation ◽  
Ricin A

Misfolded proteins in the endoplasmic reticulum (ER) are destroyed by a pathway termed ER-associated protein degradation (ERAD). Glycans are often removed from glycosylated ERAD substrates in the cytosol before substrate degradation, which maintains the efficiency of the proteasome. Png1, a deglycosylating enzyme, has long been suspected, but not proven, to be crucial in this process. We demonstrate that the efficient degradation of glycosylated ricin A chain requires the Png1–Rad23 complex, suggesting that this complex couples protein deglycosylation and degradation. Rad23 is a ubiquitin (Ub) binding protein involved in the transfer of ubiquitylated substrates to the proteasome. How Rad23 achieves its substrate specificity is unknown. We show that Rad23 binds various regulators of proteolysis to facilitate the degradation of distinct substrates. We propose that the substrate specificity of Rad23 and other Ub binding proteins is determined by their interactions with various cofactors involved in specific degradation pathways.

scholarly journals RING domains act as both substrate and enzyme in a catalytic arrangement to drive self-anchored ubiquitination

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Leo Kiss ◽  
Dean Clift ◽  
Nadine Renner ◽  
David Neuhaus ◽  
Leo C. James
Keyword(s):  
Posttranslational Modifications ◽  
Substrate Binding ◽  
Cellular Level ◽  
Chemical Mechanism ◽  
Chain Elongation ◽  
Ubiquitin Chain ◽  
E3 Ligases ◽  
Physiological Processes ◽  
Ubiquitin Conjugation ◽  
Ring E3 Ligases

AbstractAttachment of ubiquitin (Ub) to proteins is one of the most abundant and versatile of all posttranslational modifications and affects outcomes in essentially all physiological processes. RING E3 ligases target E2 Ub-conjugating enzymes to the substrate, resulting in its ubiquitination. However, the mechanism by which a ubiquitin chain is formed on the substrate remains elusive. Here we demonstrate how substrate binding can induce a specific RING topology that enables self-ubiquitination. By analyzing a catalytically trapped structure showing the initiation of TRIM21 RING-anchored ubiquitin chain elongation, and in combination with a kinetic study, we illuminate the chemical mechanism of ubiquitin conjugation. Moreover, biochemical and cellular experiments show that the topology found in the structure can be induced by substrate binding. Our results provide insights into ubiquitin chain formation on a structural, biochemical and cellular level with broad implications for targeted protein degradation.

scholarly journals Intracellular Dynamics of the Ubiquitin-Proteasome-System

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 367 ◽  
Author(s):  
Maisha Chowdhury ◽  
Cordula Enenkel
Keyword(s):  
Cell Cycle ◽  
Protein Degradation ◽  
Mammalian Cells ◽  
Cell Cycle Progression ◽  
Current Knowledge ◽  
Ubiquitin Proteasome System ◽  
Yeast Cells ◽  
Ubiquitin Chain ◽  
Dividing Cells ◽  
Ubiquitin Proteasome

The ubiquitin-proteasome system is the major degradation pathway for short-lived proteins in eukaryotic cells. Targets of the ubiquitin-proteasome-system are proteins regulating a broad range of cellular processes including cell cycle progression, gene expression, the quality control of proteostasis and the response to geno- and proteotoxic stress. Prior to degradation, the proteasomal substrate is marked with a poly-ubiquitin chain. The key protease of the ubiquitin system is the proteasome. In dividing cells, proteasomes exist as holo-enzymes composed of regulatory and core particles. The regulatory complex confers ubiquitin-recognition and ATP dependence on proteasomal protein degradation. The catalytic sites are located in the proteasome core particle. Proteasome holo-enzymes are predominantly nuclear suggesting a major requirement for proteasomal proteolysis in the nucleus. In cell cycle arrested mammalian or quiescent yeast cells, proteasomes deplete from the nucleus and accumulate in granules at the nuclear envelope (NE) / endoplasmic reticulum ( ER) membranes. In prolonged quiescence, proteasome granules drop off the nuclear envelopeNE / ER membranes and migrate as droplet-like entitiesstable organelles  throughout the cytoplasm, as thoroughly investigated in yeast. When quiescence yeast cells are allowed to resume growth, proteasome granules clear and proteasomes are rapidly imported into the nucleus.Here, we summarize our knowledge about the enigmatic structure of proteasome storage granules and the trafficking of proteasomes and their substrates between the cyto- and nucleoplasm.Most of our current knowledge is based on studies in yeast. Their translation to mammalian cells promises to provide keen insight into protein degradation in non-dividing cells, which comprise the majority of our body’s cells.

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