scholarly journals A novel polyubiquitin chain linkage formed by viral Ubiquitin prevents cleavage by deubiquitinating enzymes

2019 ◽  
Author(s):  
Hitendra Negi ◽  
Pothula Puroshotham Reddy ◽  
Chhaya Patole ◽  
Ranabir Das
Keyword(s):  
Biochemical Properties ◽  
Autographa Californica ◽  
Polyubiquitin Chain ◽  
Deubiquitinating Enzymes ◽  
Polyubiquitin Chains ◽  
Antiviral Responses ◽  
Binding Domains ◽  
Central Helix ◽  
Ubiquitin Binding ◽  
The Stability

ABSTRACTThe Baculoviridae family of viruses encode a viral Ubiquitin gene. Although the viral Ubiquitin is homologous to eukaryotic Ubiquitin (Ub), preservation of this gene in the viral genome indicates a unique function that is absent in the host eukaryotic Ub. We report the structural, biophysical, and biochemical properties of the viral Ubiquitin from Autographa Californica Multiple Nucleo-Polyhedrosis Virus (AcMNPV). The structure of viral Ubiquitin (vUb) differs from Ub in the packing of the central helix α1 to the beta-sheet of the β-grasp fold. Consequently, the stability of the fold is lower in vUb compared to Ub. However, the surface properties, ubiquitination activity, and the interaction with Ubiquitin binding domains are similar between vUb and Ub. Interestingly, vUb forms atypical polyubiquitin chain linked by lysine at the 54th position (K54). The K54-linked polyubiquitin chains are neither effectively cleaved by deubiquitinating enzymes, nor are they targeted by proteasomal degradation. We propose that modification of proteins with the viral Ubiquitin is a mechanism to counter the host antiviral responses.

scholarly journals A novel polyubiquitin chain linkage formed by viral Ubiquitin is resistant to host deubiquitinating enzymes

2020 ◽  
Vol 477 (12) ◽  
pp. 2193-2219
Author(s):  
Hitendra Negi ◽  
Pothula Purushotham Reddy ◽  
Vineeth Vengayil ◽  
Chhaya Patole ◽  
Sunil Laxman ◽  
...  
Keyword(s):  
Viral Genome ◽  
Viral Proteins ◽  
Biochemical Properties ◽  
Autographa Californica ◽  
Polyubiquitin Chain ◽  
Deubiquitinating Enzymes ◽  
Polyubiquitin Chains ◽  
Binding Domains ◽  
Central Helix ◽  
Ubiquitin Binding

The Baculoviridae family of viruses encode a viral Ubiquitin (vUb) gene. Though the vUb is homologous to the host eukaryotic Ubiquitin (Ub), its preservation in the viral genome indicates unique functions that are not compensated by the host Ub. We report the structural, biophysical, and biochemical properties of the vUb from Autographa californica multiple nucleo-polyhedrosis virus (AcMNPV). The packing of central helix α1 to the beta-sheet β1–β5 is different between vUb and Ub. Consequently, its stability is lower compared with Ub. However, the surface properties, ubiquitination activity, and the interaction with Ubiquitin-binding domains are similar between vUb and Ub. Interestingly, vUb forms atypical polyubiquitin chain linked by lysine at the 54th position (K54), and the deubiquitinating enzymes are ineffective against the K54-linked polyubiquitin chains. We propose that the modification of host/viral proteins with the K54-linked chains is an effective way selected by the virus to protect the vUb signal from host DeUbiquitinases.

scholarly journals Function of the p97–Ufd1–Npl4 complex in retrotranslocation from the ER to the cytosol

2003 ◽  
Vol 162 (1) ◽  
pp. 71-84 ◽  
Author(s):  
Yihong Ye ◽  
Hemmo H. Meyer ◽  
Tom A. Rapoport
Keyword(s):  
Atp Hydrolysis ◽  
Bound State ◽  
Polyubiquitin Chain ◽  
Polyubiquitin Chains ◽  
Evolutionarily Conserved ◽  
The Family ◽  
Complex Functions ◽  
Ubiquitin Binding ◽  
Subsequent Degradation ◽  
Er Membrane

Amember of the family of ATPases associated with diverse cellular activities, called p97 in mammals and Cdc48 in yeast, associates with the cofactor Ufd1–Npl4 to move polyubiquitinated polypeptides from the endoplasmic reticulum (ER) membrane into the cytosol for their subsequent degradation by the proteasome. Here, we have studied the mechanism by which the p97–Ufd1–Npl4 complex functions in this retrotranslocation pathway. Substrate binding occurs when the first ATPase domain of p97 (D1 domain) is in its nucleotide-bound state, an interaction that also requires an association of p97 with the membrane through its NH2-terminal domain. The two ATPase domains (D1 and D2) of p97 appear to alternate in ATP hydrolysis, which is essential for the movement of polypeptides from the ER membrane into the cytosol. The ATPase itself can interact with nonmodified polypeptide substrates as they emerge from the ER membrane. Polyubiquitin chains linked by lysine 48 are recognized in a synergistic manner by both p97 and an evolutionarily conserved ubiquitin-binding site at the NH2 terminus of Ufd1. We propose a dual recognition model in which the ATPase complex binds both a nonmodified segment of the substrate and the attached polyubiquitin chain; polyubiquitin binding may activate the ATPase p97 to pull the polypeptide substrate out of the membrane.

Orchestra for assembly and fate of polyubiquitin chains

2005 ◽  
Vol 41 ◽  
pp. 1-14 ◽  
Author(s):  
Kuhlbrodt Kirsten ◽  
Mouysset Julien ◽  
Hoppe Thorsten
Keyword(s):  
Protein Degradation ◽  
Ubiquitin Ligase ◽  
Chain Elongation ◽  
Polyubiquitin Chain ◽  
Ubiquitin Chain ◽  
Polyubiquitin Chains ◽  
Intracellular Signals ◽  
Ubiquitin Binding ◽  
Ubiquitin Ligase E3 ◽  
Ubiquitin Conjugating Enzyme

Selective protein degradation by the 26 S proteasome usually requires a polyubiquitin chain attached to the protein substrate by three classes of enzymes: a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2), and a ubiquitin ligase (E3). This reaction can produce different polyubiquitin chains that, depending on size and linkage type, can provide distinct intracellular signals. Interestingly, polyubiquitination is sometimes regulated by additional conjugation factors, called E4s (polyubiquitin chain conjugation factors). Yeast UFD2 (ubiquitin fusion degradation protein-2), the first E4 to be described, binds to the ubiquitin moieties of preformed conjugates and catalyses ubiquitin-chain elongation together with E1, E2, and E3. Recent studies have illustrated that the E4 enzyme UFD2 co-operates with an orchestra of ubiquitin-binding factors in an escort pathway to transfer and deliver polyubiquitinated substrates to the 26 S proteasome. Here we propose a model in which E4-dependent polyubiquitination pathways are modulated by different ubiquitin-binding proteins, using ataxin-3 as an example.

Ubiquitylation within signaling pathways in- and outside of inflammation

2007 ◽  
Vol 97 (03) ◽  
pp. 370-377 ◽  
Author(s):  
Karin Hochrainer ◽  
Joachim Lipp
Keyword(s):  
Signaling Pathways ◽  
26S Proteasome ◽  
Virus Budding ◽  
Polyubiquitin Chains ◽  
Amino Acid Peptide ◽  
Binding Domains ◽  
Ubiquitin Binding ◽  
Different Types ◽  
Lysine Residues ◽  
Ubiquitin Molecule

SummaryUbiquitin is a highly conserved 76-amino-acid peptide that becomes covalently attached to lysine residues of target proteins. Since ubiquitin itself contains seven lysine residues, ubiquitin molecules can generate different types of polyubiquitin chains. Lys48-linked polyubiquitylation is well-known as posttrans-lational tag for targeting proteins for degradation by the 26S proteasome. Recent studies have revealed several new functions of ubiquitin, e.g. activation of protein kinases, control of gene transcription, DNA repair and replication, intracellular trafficking and virus budding. These functions are mainly mediated by Lys63 polyubiquitin chains or attachment of a single ubiquitin molecule to one or several lysine residues within the target protein. Importantly, protein ubiquitylation exhibits inducibility, reversibilty and recognition by specialized ubiquitin-binding domains, features similar to protein phosphorylation. In this review we comprehensively describe regulations of protein ubiquitylation and their impact on distinct signaling pathways.

scholarly journals DNA methylation modifier LSH inhibits p53 ubiquitination and transactivates p53 to promote lipid metabolism

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Ling Chen ◽  
Ying Shi ◽  
Na Liu ◽  
Zuli Wang ◽  
Rui Yang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Lipid Metabolism ◽  
Cancer Progression ◽  
Coiled Coil ◽  
Alternative Mechanism ◽  
Polyubiquitin Chains ◽  
Lipid Catabolism ◽  
Binding Domains ◽  
The Stability ◽  
In Cis

Abstract Background The stability of p53 is mainly controlled by ubiquitin-dependent degradation, which is triggered by the E3 ubiquitin ligase MDM2. The chromatin modifier lymphoid-specific helicase (LSH) is essential for DNA methylation and cancer progression as a transcriptional repressor. The potential interplay between chromatin modifiers and transcription factors remains largely unknown. Results Here, we present data suggesting that LSH regulates p53 in cis through two pathways: prevention proteasomal degradation through its deubiquitination, which is achieved by reducing the lysine 11-linked, lysine 48-linked polyubiquitin chains (K11 and K48) on p53; and revival of the transcriptional activity of p53 by forming a complex with PKM2 (pyruvate kinase 2). Furthermore, we confirmed that the LSH–PKM2 interaction occurred at the intersubunit interface region of the PKM2 C-terminal region and the coiled-coil domains (CC) and ATP-binding domains of LSH, and this interaction regulated p53-mediated transactivation in cis in lipid metabolism, especially lipid catabolism. Conclusion These findings suggest that LSH is a novel regulator of p53 through the proteasomal pathway, thereby providing an alternative mechanism of p53 involvement in lipid metabolism in cancer.

Properties of natural and artificial proteins displaying multiple ubiquitin-binding domains

2010 ◽  
Vol 38 (1) ◽  
pp. 40-45 ◽  
Author(s):  
Fernando Lopitz-Otsoa ◽  
Manuel S. Rodríguez ◽  
Fabienne Aillet
Keyword(s):  
Effector Proteins ◽  
Target Protein ◽  
Polyubiquitin Chains ◽  
Artificial Proteins ◽  
Binding Domains ◽  
Cellular Factors ◽  
Evolutionary Advantage ◽  
Ubiquitin Binding ◽  
Tandem Ubiquitin Binding Entities

Ubiquitylation provides a rapid alternative to control the activity of crucial cellular factors through the remodelling of a target protein. Diverse ubiquitin chains are recognized by domains with affinity for UBDs (ubiquitin-binding domains) present in receptor/effector proteins. Interestingly, some proteins contain more than one UBD and the preservation of this structure in many species suggests an evolutionary advantage for this topology. Here, we review some typical proteins that naturally contain more than one UBD and emphasize how such structures contribute to the mechanism they mediate. Characteristics such as higher affinities for polyubiquitin chains and chain-linkage preferences can be replicated by the TUBEs (tandem ubiquitin-binding entities). Furthermore, TUBEs show two additional properties: protection of ubiquitylated substrates from deubiquitylating enzymes and interference with the action of the proteasome. Consequently, TUBEs behave as ‘ubiquitin traps’ that efficiently capture endogenous ubiquitylated proteins. Interpretations and hypothetical models proposed by different groups to understand the synchronous action of multiple UBDs are discussed herein.

The ‘dark matter’ of ubiquitin-mediated processes: opportunities and challenges in the identification of ubiquitin-binding domains

2019 ◽  
Vol 47 (6) ◽  
pp. 1949-1962 ◽  
Author(s):  
EH Radley ◽  
J Long ◽  
KC Gough ◽  
R Layfield
Keyword(s):  
Dark Matter ◽  
Current Knowledge ◽  
Polyubiquitin Chain ◽  
Web Based ◽  
Diverse Range ◽  
Cellular Processes ◽  
Binding Domains ◽  
Ubiquitin System ◽  
Ubiquitin Binding ◽  
Experimental Approaches

Ubiquitin modifications of target proteins act to localise, direct and specify a diverse range of cellular processes, many of which are biomedically relevant. To allow this diversity, ubiquitin modifications exhibit remarkable complexity, determined by a combination of polyubiquitin chain length, linkage type, numbers of ubiquitin chains per target, and decoration of ubiquitin with other small modifiers. However, many questions remain about how different ubiquitin signals are specifically recognised and transduced by the decoding ubiquitin-binding domains (UBDs) within ubiquitin-binding proteins. This review briefly outlines our current knowledge surrounding the diversity of UBDs, identifies key challenges in their discovery and considers recent structural studies with implications for the increasing complexity of UBD function and identification. Given the comparatively low numbers of functionally characterised polyubiquitin-selective UBDs relative to the ever-expanding variety of polyubiquitin modifications, it is possible that many UBDs have been overlooked, in part due to limitations of current approaches used to predict their presence within the proteome. Potential experimental approaches for UBD discovery are considered; web-based informatic analyses, Next-Generation Phage Display, deubiquitinase-resistant diubiquitin, proximity-dependent biotinylation and Ubiquitin-Phototrap, including possible advantages and limitations. The concepts discussed here work towards identifying new UBDs which may represent the ‘dark matter’ of the ubiquitin system.

Probing Affinity and Ubiquitin Linkage Selectivity of Ubiquitin-Binding Domains Using Mass Spectrometry

2012 ◽  
Vol 134 (14) ◽  
pp. 6416-6424 ◽  
Author(s):  
Kleitos Sokratous ◽  
Lucy V. Roach ◽  
Debora Channing ◽  
Joanna Strachan ◽  
Jed Long ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Binding Domains ◽  
Ubiquitin Binding

scholarly journals Biochemical and Structural Characterization of Cross-Linked Enzyme Aggregates (CLEAs) of Organic Solvent Tolerant Protease

Catalysts ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 55 ◽  
Author(s):  
Muhammad Syafiq Mohd Razib ◽  
Raja Noor Zaliha Raja Abd Rahman ◽  
Fairolniza Mohd Shariff ◽  
Mohd Shukuri Mohamad Ali
Keyword(s):  
Structural Analysis ◽  
Organic Solvent ◽  
Average Diameter ◽  
Relative Activity ◽  
Biochemical Properties ◽  
Biochemical Interaction ◽  
Organic Solvent Tolerant ◽  
Random Aggregate ◽  
Solvent Tolerant ◽  
The Stability

Cross-linked enzyme aggregates (CLEAs) is an immobilization technique that can be used to customize enzymes under an optimized condition. Structural analysis on any enzyme treated with a CLEA remains elusive and has been less explored. In the present work, a method for preparing an organic solvent tolerant protease using a CLEA is disclosed and optimized for better biochemical properties, followed by an analysis of the structure of this CLEA-treated protease. The said organic solvent tolerant protease is a metalloprotease known as elastase strain K in which activity of the metalloprotease is measured by a biochemical interaction with azocasein. Results showed that when a glutaraldehyde of 0.02% (v/v) was used under a 2 h treatment, the amount of recovered activity in CLEA-elastase was highest. The recovered activity of CLEA-elastase and CLEA-elastase-SB (which was a CLEA co-aggregated with starch and bovine serum albumin (BSA)) were at an approximate 60% and 80%, respectively. The CLEA immobilization of elastase strain K allowed the stability of the enzyme to be enhanced at high temperature and at a broader pH. Both CLEA-elastase and CLEA-elastase-SB end-products were able to maintain up to 67% enzyme activity at 60 °C and exhibiting an enhanced stability within pH 5–9 with up to 90% recovering activity. By implementing a CLEA on the organic solvent tolerant protease, the characteristics of the organic solvent tolerant were preserved and enhanced with the presence of 25% (v/v) acetonitrile, ethanol, and benzene at 165%, 173%, and 153% relative activity. Structural analysis through SEM and dynamic light scattering (DLS) showed that CLEA-elastase had a random aggregate morphology with an average diameter of 1497 nm.

scholarly journals Poly‐ubiquitin chains paradox: development of novel and selective poly‐ubiquitin binding domains (LB184)

2014 ◽  
Vol 28 (S1) ◽  
Author(s):  
Valerie Brubaker ◽  
Christian Loch ◽  
Kathryn Longenecker ◽  
James Strickler
Keyword(s):  
Binding Domains ◽  
Ubiquitin Binding
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