scholarly journals Post-translational regulation of ubiquitin signaling

2019 ◽  
Vol 218 (6) ◽  
pp. 1776-1786 ◽  
Author(s):  
Lei Song ◽  
Zhao-Qing Luo
Keyword(s):  
Translational Regulation ◽  
Covalent Attachment ◽  
Immune Disorders ◽  
Post Translational Modification ◽  
Polyubiquitin Chains ◽  
Cellular Processes ◽  
Lysine Residues ◽  
Substrate Proteins ◽  
Ubiquitination Machinery ◽  
Integrate Development

Ubiquitination regulates many essential cellular processes in eukaryotes. This post-translational modification (PTM) is typically achieved by E1, E2, and E3 enzymes that sequentially catalyze activation, conjugation, and ligation reactions, respectively, leading to covalent attachment of ubiquitin, usually to lysine residues of substrate proteins. Ubiquitin can also be successively linked to one of the seven lysine residues on ubiquitin to form distinctive forms of polyubiquitin chains, which, depending upon the lysine used and the length of the chains, dictate the fate of substrate proteins. Recent discoveries revealed that this ubiquitin code is further expanded by PTMs such as phosphorylation, acetylation, deamidation, and ADP-ribosylation, on ubiquitin, components of the ubiquitination machinery, or both. These PTMs provide additional regulatory nodes to integrate development or insulting signals with cellular homeostasis. Understanding the precise roles of these PTMs in the regulation of ubiquitin signaling will provide new insights into the mechanisms and treatment of various human diseases linked to ubiquitination, including neurodegenerative diseases, cancer, infection, and immune disorders.

scholarly journals Mechanisms, regulation and consequences of protein SUMOylation

2010 ◽  
Vol 428 (2) ◽  
pp. 133-145 ◽  
Author(s):  
Kevin A. Wilkinson ◽  
Jeremy M. Henley
Keyword(s):  
Protein Function ◽  
Covalent Attachment ◽  
Post Translational Modification ◽  
Cellular Processes ◽  
Wide Range ◽  
Lysine Residues ◽  
Ubiquitination Pathway ◽  
Regulate Protein ◽  
Substrate Proteins ◽  
Protein Sumoylation

The post-translational modification SUMOylation is a major regulator of protein function that plays an important role in a wide range of cellular processes. SUMOylation involves the covalent attachment of a member of the SUMO (small ubiquitin-like modifier) family of proteins to lysine residues in specific target proteins via an enzymatic cascade analogous to, but distinct from, the ubiquitination pathway. There are four SUMO paralogues and an increasing number of proteins are being identified as SUMO substrates. However, in many cases little is known about how SUMOylation of these targets is regulated. Compared with the ubiquitination pathway, relatively few components of the conjugation machinery have been described and the processes that specify individual SUMO paralogue conjugation to defined substrate proteins are an active area of research. In the present review, we briefly describe the SUMOylation pathway and present an overview of the recent findings that are beginning to identify some of the mechanisms that regulate protein SUMOylation.

scholarly journals Development of a yeast model to study the contribution of vacuolar polyphosphate metabolism to lysine polyphosphorylation

2019 ◽  
Vol 295 (6) ◽  
pp. 1439-1451 ◽  
Author(s):  
Cristina Azevedo ◽  
Yann Desfougères ◽  
Yannasittha Jiramongkol ◽  
Hamish Partington ◽  
Sasanan Trakansuebkul ◽  
...  
Keyword(s):  
Cell Lysis ◽  
Covalent Attachment ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
Target Domain ◽  
Inorganic Polyphosphate ◽  
Topoisomerase 1 ◽  
Lysine Residues ◽  
Polyphosphate Metabolism ◽  
Nuclear Targets

A recently-discovered protein post-translational modification, lysine polyphosphorylation (K-PPn), consists of the covalent attachment of inorganic polyphosphate (polyP) to lysine residues. The nonenzymatic nature of K-PPn means that the degree of this modification depends on both polyP abundance and the amino acids surrounding the modified lysine. K-PPn was originally discovered in budding yeast (Saccharomyces cerevisiae), in which polyP anabolism and catabolism are well-characterized. However, yeast vacuoles accumulate large amounts of polyP, and upon cell lysis, the release of the vacuolar polyP could nonphysiologically cause K-PPn of nuclear and cytosolic targets. Moreover, yeast vacuoles possess two very active endopolyphosphatases, Ppn1 and Ppn2, that could have opposing effects on the extent of K-PPn. Here, we characterized the contribution of vacuolar polyP metabolism to K-PPn of two yeast proteins, Top1 (DNA topoisomerase 1) and Nsr1 (nuclear signal recognition 1). We discovered that whereas Top1-targeting K-PPn is only marginally affected by vacuolar polyP metabolism, Nsr1-targeting K-PPn is highly sensitive to the release of polyP and of endopolyphosphatases from the vacuole. Therefore, to better study K-PPn of cytosolic and nuclear targets, we constructed a yeast strain devoid of vacuolar polyP by targeting the exopolyphosphatase Ppx1 to the vacuole and concomitantly depleting the two endopolyphosphatases (ppn1Δppn2Δ, vt-Ppx1). This strain enabled us to study K-PPn of cytosolic and nuclear targets without the interfering effects of cell lysis on vacuole polyP and of endopolyphosphatases. Furthermore, we also define the fundamental nature of the acidic amino acid residues to the K-PPn target domain.

Structural basis for CARM1 inhibition by indole and pyrazole inhibitors

2011 ◽  
Vol 436 (2) ◽  
pp. 331-339 ◽  
Author(s):  
John S. Sack ◽  
Sandrine Thieffine ◽  
Tiziano Bandiera ◽  
Marina Fasolini ◽  
Gerald J. Duke ◽  
...  
Keyword(s):  
Hormone Receptors ◽  
Catalytic Domain ◽  
Multiple Roles ◽  
Structural Basis ◽  
Titration Calorimetry ◽  
Post Translational Modification ◽  
Cellular Processes ◽  
Binding Cavity ◽  
Arginine Residues ◽  
Substrate Proteins

CARM1 (co-activator-associated arginine methyltransferase 1) is a PRMT (protein arginine N-methyltransferase) family member that catalyses the transfer of methyl groups from SAM (S-adenosylmethionine) to the side chain of specific arginine residues of substrate proteins. This post-translational modification of proteins regulates a variety of transcriptional events and other cellular processes. Moreover, CARM1 is a potential oncological target due to its multiple roles in transcription activation by nuclear hormone receptors and other transcription factors such as p53. Here, we present crystal structures of the CARM1 catalytic domain in complex with cofactors [SAH (S-adenosyl-L-homocysteine) or SNF (sinefungin)] and indole or pyazole inhibitors. Analysis of the structures reveals that the inhibitors bind in the arginine-binding cavity and the surrounding pocket that exists at the interface between the N- and C-terminal domains. In addition, we show using ITC (isothermal titration calorimetry) that the inhibitors bind to the CARM1 catalytic domain only in the presence of the cofactor SAH. Furthermore, sequence differences for select residues that interact with the inhibitors may be responsible for the CARM1 selectivity against PRMT1 and PRMT3. Together, the structural and biophysical information should aid in the design of both potent and specific inhibitors of CARM1.

scholarly journals Systematic approaches to identify E3 ligase substrates

2016 ◽  
Vol 473 (22) ◽  
pp. 4083-4101 ◽  
Author(s):  
Mary Iconomou ◽  
Darren N. Saunders
Keyword(s):  
Cell Cycle Progression ◽  
Target Identification ◽  
Ubiquitin Proteasome System ◽  
Model Systems ◽  
Covalent Attachment ◽  
Post Translational Modification ◽  
Diverse Range ◽  
E3 Ligases ◽  
Ubiquitin Proteasome ◽  
Substrate Proteins

Protein ubiquitylation is a widespread post-translational modification, regulating cellular signalling with many outcomes, such as protein degradation, endocytosis, cell cycle progression, DNA repair and transcription. E3 ligases are a critical component of the ubiquitin proteasome system (UPS), determining the substrate specificity of the cascade by the covalent attachment of ubiquitin to substrate proteins. Currently, there are over 600 putative E3 ligases, but many are poorly characterized, particularly with respect to individual protein substrates. Here, we highlight systematic approaches to identify and validate UPS targets and discuss how they are underpinning rapid advances in our understanding of the biochemistry and biology of the UPS. The integration of novel tools, model systems and methods for target identification is driving significant interest in drug development, targeting various aspects of UPS function and advancing the understanding of a diverse range of disease processes.

scholarly journals Orphan Macrodomain Protein (Human C6orf130) Is an O-Acyl-ADP-ribose Deacylase

2011 ◽  
Vol 286 (41) ◽  
pp. 35955-35965 ◽  
Author(s):  
Francis C. Peterson ◽  
Dawei Chen ◽  
Betsy L. Lytle ◽  
Marianna N. Rossi ◽  
Ivan Ahel ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
Phylogenic Tree ◽  
Cellular Processes ◽  
Steady State Kinetic ◽  
Lysine Residues ◽  
Binding Cleft ◽  
And Function ◽  
State Kinetic

Post-translational modification of proteins/histones by lysine acylation has profound effects on the physiological function of modified proteins. Deacylation by NAD+-dependent sirtuin reactions yields as a product O-acyl-ADP-ribose, which has been implicated as a signaling molecule in modulating cellular processes. Macrodomain-containing proteins are reported to bind NAD+-derived metabolites. Here, we describe the structure and function of an orphan macrodomain protein, human C6orf130. This unique 17-kDa protein is a stand-alone macrodomain protein that occupies a distinct branch in the phylogenic tree. We demonstrate that C6orf130 catalyzes the efficient deacylation of O-acetyl-ADP-ribose, O-propionyl-ADP-ribose, and O-butyryl-ADP-ribose to produce ADP-ribose (ADPr) and acetate, propionate, and butyrate, respectively. Using NMR spectroscopy, we solved the structure of C6orf130 in the presence and absence of ADPr. The structures showed a canonical fold with a deep ligand (ADPr)-binding cleft. Structural comparisons of apo-C6orf130 and the ADPr-C6orf130 complex revealed fluctuations of the β5-α4 loop that covers the bound ADPr, suggesting that the β5-α4 loop functions as a gate to sequester substrate and offer flexibility to accommodate alternative substrates. The ADPr-C6orf130 complex identified amino acid residues involved in substrate binding and suggested residues that function in catalysis. Site-specific mutagenesis and steady-state kinetic analyses revealed two critical catalytic residues, Ser-35 and Asp-125. We propose a catalytic mechanism for deacylation of O-acyl-ADP-ribose by C6orf130 and discuss the biological implications in the context of reversible protein acylation at lysine residues.

scholarly journals Molecular basis for specificity of the Met1-linked polyubiquitin signal

2016 ◽  
Vol 44 (6) ◽  
pp. 1581-1602 ◽  
Author(s):  
Paul R. Elliott
Keyword(s):  
Molecular Mechanisms ◽  
Cellular Responses ◽  
Signalling Pathways ◽  
Post Translational Modification ◽  
Polyubiquitin Chains ◽  
Cellular Processes ◽  
Protein Ubiquitination ◽  
Ubiquitin Binding ◽  
Inflammatory Signalling ◽  
Unique Ability

The post-translational modification of proteins provides a rapid and versatile system for regulating all signalling pathways. Protein ubiquitination is one such type of post-translational modification involved in controlling numerous cellular processes. The unique ability of ubiquitin to form polyubiquitin chains creates a highly complex code responsible for different subsequent signalling outcomes. Specialised enzymes (‘writers’) generate the ubiquitin code, whereas other enzymes (‘erasers’) disassemble it. Importantly, the ubiquitin code is deciphered by different ubiquitin-binding proteins (‘readers’) functioning to elicit particular cellular responses. Ten years ago, the methionine1 (Met1)-linked (linear) polyubiquitin code was first identified and the intervening years have witnessed a seismic shift in our understanding of Met1-linked polyubiquitin in cellular processes, particularly inflammatory signalling. This review will discuss the molecular mechanisms of specificity determination within Met1-linked polyubiquitin signalling.

scholarly journals Wrestling and Wrapping: A Perspective on SUMO Proteins in Schwann Cells

Biomolecules ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1055
Author(s):  
Iman F. Fergani ◽  
Luciana R. Frick
Keyword(s):  
Schwann Cells ◽  
Posttranslational Modifications ◽  
Cellular Localization ◽  
Covalent Attachment ◽  
Protein Protein Interaction ◽  
Cellular Processes ◽  
Schwann Cell Development ◽  
Demyelinating Neuropathies ◽  
Underlying Mechanisms ◽  
Substrate Proteins

Schwann cell development and peripheral nerve myelination are finely orchestrated multistep processes; some of the underlying mechanisms are well described and others remain unknown. Many posttranslational modifications (PTMs) like phosphorylation and ubiquitination have been reported to play a role during the normal development of the peripheral nervous system (PNS) and in demyelinating neuropathies. However, a relatively novel PTM, SUMOylation, has not been studied in these contexts. SUMOylation involves the covalent attachment of one or more small ubiquitin-like modifier (SUMO) proteins to a substrate, which affects the function, cellular localization, and further PTMs of the conjugated protein. SUMOylation also regulates other proteins indirectly by facilitating non-covalent protein–protein interaction via SUMO interaction motifs (SIM). This pathway has important consequences on diverse cellular processes, and dysregulation of this pathway has been reported in several diseases including neurological and degenerative conditions. In this article, we revise the scarce literature on SUMOylation in Schwann cells and the PNS, we propose putative substrate proteins, and we speculate on potential mechanisms underlying the possible involvement of this PTM in peripheral myelination and neuropathies.

scholarly journals Emerging roles of the HECT-type E3 ubiquitin ligases in hematological malignancies

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Vincenza Simona Delvecchio ◽  
Claudia Fierro ◽  
Sara Giovannini ◽  
Gerry Melino ◽  
Francesca Bernassola
Keyword(s):  
Hematological Malignancies ◽  
Apoptotic Cell ◽  
Ubiquitin Ligases ◽  
Covalent Attachment ◽  
E3 Ubiquitin Ligases ◽  
Comprehensive Overview ◽  
Altered Expression ◽  
Hect Domain ◽  
Cellular Processes ◽  
Substrate Proteins

AbstractUbiquitination-mediated proteolysis or regulation of proteins, ultimately executed by E3 ubiquitin ligases, control a wide array of cellular processes, including transcription, cell cycle, autophagy and apoptotic cell death. HECT-type E3 ubiquitin ligases can be distinguished from other subfamilies of E3 ubiquitin ligases because they have a C-terminal HECT domain that directly catalyzes the covalent attachment of ubiquitin to their substrate proteins. Deregulation of HECT-type E3-mediated ubiquitination plays a prominent role in cancer development and chemoresistance. Several members of this subfamily are indeed frequently deregulated in human cancers as a result of genetic mutations and altered expression or activity. HECT-type E3s contribute to tumorigenesis by regulating the ubiquitination rate of substrates that function as either tumour suppressors or oncogenes. While the pathological roles of the HECT family members in solid tumors are quite well established, their contribution to the pathogenesis of hematological malignancies has only recently emerged. This review aims to provide a comprehensive overview of the involvement of the HECT-type E3s in leukemogenesis.

scholarly journals Protein Acetylation Induced by Dichloroacetate (DCA) Treatment is Associated with Decreased Respiration in Cultured Hepatocytes: Preliminary Results

2019 ◽  
Author(s):  
Jesse G. Meyer
Keyword(s):  
Pyruvate Dehydrogenase ◽  
Physiological Role ◽  
Pyruvate Dehydrogenase Kinase ◽  
Protein Acetylation ◽  
Post Translational Modification ◽  
Cellular Processes ◽  
Excess Production ◽  
Lysine Residues ◽  
Genetic Perturbations

AbstractProtein post-translational modification (PTM) by acetylation at the ε-amine on lysine residues in proteins regulates various cellular processes including transcription and metabolism. Several metabolic and genetic perturbations are known to increase acetylation of various proteins. Hyper-acetylation can also be induced using deacetylase inhibitors. While there is much interest in discovering drugs that can reverse protein acetylation, pharmacological tools that increase non-enzymatic protein acetylation are needed in order to understand the physiological role of excess protein acetylation. In this study, I assessed whether inhibition of pyruvate dehydrogenase kinase (PDHK) could cause protein hyper-acetylation due to excess production of acetyl-CoA by pyruvate dehydrogenase (PDH). Western blot of total protein from dichloroacetate (DCA) treated hepatocytes with anti-acetyl-lysine antibody showed increased protein acetylation, and seahorse respirometry of DCA pretreated hepatocytes indicated a subtle decrease in basal and maximal respiratory capacity.

scholarly journals Ubiquitomics: An Overview and Future

Biomolecules ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1453 ◽  
Author(s):  
George Vere ◽  
Rachel Kealy ◽  
Benedikt M. Kessler ◽  
Adan Pinto-Fernandez
Keyword(s):  
Chemical Biology ◽  
Biological Diversity ◽  
Analytical Techniques ◽  
Cellular Proteins ◽  
Covalent Attachment ◽  
Post Translational Modification ◽  
Polyubiquitin Chains ◽  
Protein Substrates ◽  
Protein Ubiquitination ◽  
Amino Acid Side Chains

Covalent attachment of ubiquitin, a small globular polypeptide, to protein substrates is a key post-translational modification that determines the fate, function, and turnover of most cellular proteins. Ubiquitin modification exists as mono- or polyubiquitin chains involving multiple ways how ubiquitin C-termini are connected to lysine, perhaps other amino acid side chains, and N-termini of proteins, often including branching of the ubiquitin chains. Understanding this enormous complexity in protein ubiquitination, the so-called ‘ubiquitin code’, in combination with the ∼1000 enzymes involved in controlling ubiquitin recognition, conjugation, and deconjugation, calls for novel developments in analytical techniques. Here, we review different headways in the field mainly driven by mass spectrometry and chemical biology, referred to as “ubiquitomics”, aiming to understand this system’s biological diversity.

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