Download or read book The Small Ubiquitin related Modifier in the Stress Response and the Use of Mass Spectrometry SUMmOn for Identification of Ubiquitin and Ubiquitin like Protein Conjugation Sites written by Stanley Martin Jeram and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Small Ubiquitin related Mmodifier in the Stress Response and the Use of Mass Spectrometry SUMmOn for Identification of Ubiquitin and Ubiquitin like Protein Conjugation Sites written by Stanley Martin Jeram and published by . This book was released on 2009 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Ubiquitin dependent Protein Degradation written by and published by Academic Press. This book was released on 2019-03-23 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ubiquitination and Protein Stability - Part B, Volume 619, the latest release in the Methods in Enzymology series, highlights new advances in the field, with this updated volume presenting interesting chapters written by an international board of authors. Topics of note include chapters on Assays of SUMO protease function in mammalian cells, In vitro analysis of proteasome-associated USP14 activity for substrate degradation and deubiquitylation, Methods to study proteasome regulatory particle assembly, Native mass spectrometry approaches to study the proteasome, Single-molecule methods to study the ubiquitin-proteasome system, Assays for the function of ubiquitin in the mammalian endocytic pathway, and much more.
Download or read book Regulation of Ubiquitylation and Ubiquitin like Post Translational Modifications written by Ryan Lumpkin and published by . This book was released on 2019 with total page 155 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ubiquitin (Ub) is an 8,500 Da, 76 amino acid protein that is among a family of similar Ubiquitin-like proteins. E3 Ligases facilitate the attachment of Ub onto lysine residues of substrate proteins. Ub can also be attached to another Ub molecule, forming polyubiquitin chains which signal for proteasomal degradation and the immune response. Small ubiquitin-like modifier (SUMO) is involved in cell cycle control and the DNA damage response. Another Ubiquitin-like protein, Neural precursor cell expressed developmentally down-regulated protein 8 (NEDD8), can modify some E3 Ligases to regulate their activation. Chapter II presents a novel method for the side-by-side identification and quantification of Ubiquitin and SUMO modifications. Trypsin digestion of a Ubiquitin-modified protein leaves a diglycyl-lysine at the site of modification, which can be detected by mass spectrometry. Unlike Ubiquitin, detection of SUMOylated proteins is limited by the lack of naturally occurring protease sites in the C-terminal tail of SUMO proteins. This chapter describes detection of endogenous SUMOylation using [alpha]-lytic protease, WaLP. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) probes the solvent accessibility and conformational dynamics of proteins by measuring deuterium uptake on backbone amides over time. Chapter III describes an open-source software package designed to automate the correction, analysis and visualization of HDX-MS data. Chapter IV investigates the structure, dynamics and regulation of an ASB9-CUL-RING E3 Ubiquitin Ligase. The structure of the substrate-receptor complex was determined for the first time by Cryo-EM, identifying changes in both the receptor and the substrate that were not predicted by previous models. Chapter V further investigates the dynamics, regulation and activity of the ASB9-CUL-RING E3 Ubiquitin Ligase. In vitro assays, western blots and mass spectrometry data describe the locations and intensity of ubiquitin modifications. These data show that ARIH2, another E3 ligase, is necessary for initial substrate modification, and that the addition of other E2 enzymes can modulate the poly-ubiquitin chains formed. HDX-MS studies show that modification of the ASB9-CUL-RING ligase causes conformational restructuring that facilitates the binding and activation of ARIH2.
Download or read book SUMOylation and Ubiquitination written by Van G. Wilson and published by . This book was released on 2019-09 with total page 512 pages. Available in PDF, EPUB and Kindle. Book excerpt: Most proteins undergo post-translational modifications altering physical and chemical properties, folding, conformation distribution, stability, activity and function. Ubiquitin and SUMOs are related small proteins that are members of the large ubiquitin superfamily of post-translational modifiers. Written by highly respected leaders in their fields under the expert guidance of the editor, this volume covers the principles of ubiquitination and SUMOylation, presents detailed reviews of current and emerging concepts and highlights new advances in all areas of SUMOylation and ubiquitination. Topics of note include: the ubiquitin superfamily, the ubiquitin toolbox, onco viral exploitation of the SUMO system, small molecule modulators of desumoylation, mass spectrometry, global proteomic profiling of SUMO and ubiquitin, biotin-based approaches, genetic screening, SUMOylation networks in humans, targets for ubiquitin ligases, regulation of p53, protein homeostasis, miRNAs, DNA replication, DNA damage response, telomere biology, intracellular trafficking, regulation of angiogenesis, brain ischemia, autophagy, assembly and activity, antiviral defense, HIV infection, amyloid and amyloid-like proteins, plant immunity. This comprehensive and up-to-date book is the definitive reference volume on all aspects of SUMOylation and ubiquitination and is an essential acquisition for anyone involved in this area of biology.
Download or read book Methods in Yeast Genetics written by Fred Sherman and published by . This book was released on 1987-04-01 with total page 180 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Macromolecular Protein Complexes III Structure and Function written by J. Robin Harris and published by Springer Nature. This book was released on 2020-11-30 with total page 580 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers important topics such as the dynamic structure and function of the 26S proteasome, the DNA replication machine: structure and dynamic function and the structural organization and protein–protein interactions in the human adenovirus capsid, to mention but a few. The 18 chapters included here, written by experts in their specific field, are at the forefront of scientific knowledge. The impressive integration of structural data from X-ray crystallography with that from cryo-electron microscopy is apparent throughout the book. In addition, functional aspects are also given a high priority. Chapter 1 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Download or read book Ubiquitin and Ubiquitin Relative SUMO in DNA Damage Response written by Kristijan Ramadan and published by Frontiers Media SA. This book was released on 2018-02-09 with total page 183 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA damage response (DDR) is a term that includes a variety of highly sophisticated mechanisms that cells have evolved in safeguarding the genome from the deleterious consequences of DNA damage. It is estimated that every single cell receives tens of thousands of DNA lesions per day. Failure of DDR to properly respond to DNA damage leads to stem cell dysfunction, accelerated ageing, various degenerative diseases or cancer. The sole function of DDR is to recognize diverse DNA lesions, signal their presence, activate cell cycle arrest and finally recruit specific DNA repair proteins to fix the DNA damage and thus prevent genomic instability. DDR is composed of hundreds of spatiotemporally regulated and interconnected proteins, which are able to promptly respond to various DNA lesions. So it is not surprising that mutations in genes encoding various DDR proteins cause embryonic lethality, malignancies, neurodegenerative diseases and premature ageing. The importance of DDR for cell survival and genome stability is unquestionable, but how the sophisticated network of hundreds of different DDR proteins is spatiotemporally coordinated is far from being understood. In the last ten years ubiquitin (ubiquitination) and the ubiquitin-relative SUMO (sumoylation) have emerged as essential posttranslational modifications that regulate DDR. Beside a plethora of ubiqutin and sumo E1-activating enzymes, E2-conjugating enzymes, E3-ligases and ubiquitin/sumo proteases involved in ubiquitination and sumoylation, the complexity of ubiqutin and sumo systems is additionally increased by the fact that both ubiquitin and sumo can form a variety of different chains on substrates which govern the substrate fate, such as its interaction with other proteins, changing its enzymatic activity or promoting substrate degradation. The importance of ubiquitin/SUMO systems in the orchestration of DDR is best illustrated in patients with mutations in E3-ubiquitin ligases BRCA1 or RNF168. BRCA1 is essential for proper function of DDR and its mutations lead to triple-negative breast and ovarian cancers. RNF168 is an E3 ubiquitin ligase, which creates the ubiquitin docking platform for recruitment of different DNA damage signalling and repair proteins at sites of DNA lesion, and its mutations cause RIDDLE syndrome characterized by radiosensitivity, immunodeficiency and learning disability. In addition, recently discovered the ubiquitin receptor protein SPRTN is part of the DNA replication machinery and its mutations cause early-onset hepatocellular carcinoma and premature ageing in humans. Despite more than 700 different enzymes directly involved in ubiquitination and sumoylation processes only few of them are known to play a role in DDR. Therefore, we feel that the role of ubiquitin and the ubiquitin-related SUMO in DDR is far from being understood, and that this is the emerging field that will hugely expand in the next decade due to the rapid development of a new generation of technologies, which will allow us a more robust and precise analyses of human genome, transcriptome and proteome. In this Research Topic we provide a comprehensive overview of our current understanding of ubiquitin and SUMO pathways in all aspects of DDR, from DNA replication to different DNA repair pathways, and demonstrate how alterations in these pathways cause genomic instability that is linked to degenerative diseases, cancer and pathological ageing.
Download or read book Ubiquitin Family Modifiers and the Proteasome written by R. Jürgen Dohmen and published by Humana Press. This book was released on 2016-08-23 with total page 666 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ubiquitin-proteasome system (UPS) and ubiquitin-related modifiers are not only involved in cellular protein quality control but also in the regulation of many fundamental cellular processes/pathways as well as in their disease-relevant aberrations. Ubiquitin Family Modifiers and Proteasome: Reviews and Protocols presents both novel developments in UPS research and important methods related to the main recent advances in the field of ubiquitin family modifiers. Divided into five convenient sections, this volume focuses on the enzymology and substrate identification of ubiquitin family modifiers, the recognition and chain formation of these modifiers, the analysis of proteasome biogenesis and function, protein quality control, and finally the use of small molecules and strategies to study or manipulate the function of the UPS and of ubiquitin family modifiers, respectively. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Ubiquitin Family Modifiers and Proteasome: Reviews and Protocols will be of great use to investigators and students engaged in both basic and applied research in life sciences.
Download or read book Abiotic Stress Response in Plants written by Arun Shanker and published by BoD – Books on Demand. This book was released on 2011-08-29 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plants, unlike animals, are sessile. This demands that adverse changes in their environment are quickly recognized, distinguished and responded to with suitable reactions. Drought, heat, cold and salinity are among the major abiotic stresses that adversely affect plant growth and productivity. In general, abiotic stress often causes a series of morphological, physiological, biochemical and molecular changes that unfavorably affect plant growth, development and productivity. Drought, salinity, extreme temperatures (cold and heat) and oxidative stress are often interrelated; these conditions singularly or in combination induce cellular damage. To cope with abiotic stresses, of paramount significance is to understand plant responses to abiotic stresses that disturb the homeostatic equilibrium at cellular and molecular level in order to identify a common mechanism for multiple stress tolerance. This multi authored edited compilation attempts to put forth an all-inclusive biochemical and molecular picture in a systems approach wherein mechanism and adaptation aspects of abiotic stress are dealt with. The chief objective of the book hence is to deliver state of the art information for comprehending the effects of abiotic stress in plants at the cellular level.
Download or read book SUMO Regulation of Cellular Processes written by Van G. Wilson and published by Springer. This book was released on 2017-02-13 with total page 413 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the second edition of a very well received book that details how the sumoylation system functions and how it modulates numerous cellular activities. SUMO is a post-translational modifier in the ubiquitin super-family that has gained recognition over the last twenty years as an essential and prevalent regulatory molecule. Individual chapters explore the biochemistry, molecular biology, and cell biology of the sumoylation system and its substrate proteins. The book is divided into three themed parts: Molecular Functions (I), Cell Growth Regulation (II), and Diseases (III). Parts I and II focus on the contribution of sumoylation to cellular activities in both the nuclear and cytoplasmic compartments. The nuclear activities covered include nucleic acid metabolism (both RNA and DNA), chromosome structure and replication, and nucleocytoplasmic transport. Cytoplasmic processes presented include regulation of membrane ion channels, general metabolism, and apoptotic signalling. Topics in Part III include the role of sumoylation in developmental abnormalities (craniofacial and cardiovascular), diabetes, neurodegenerative diseases, cancer, and infections with viruses and bacteria. Each of the corresponding chapter authors is an active researcher who has made significant contributions to understanding sumoylation. This second edition provides updates and revisions to most of the original chapters plus adds six new chapters to address important developing areas of sumoylation research. This volume is intended for a scientific audience from undergraduates to independent researchers. The content will serve as both a solid introduction for the novice reader and an in depth treatment for the advanced scholar.
Download or read book A Study of the Sumoylation and Ubiquitination of DNA Damage and Replication Checkpoint Proteins in the Fission Yeast Schizosaccharomyces Pombe written by Konstantinos Nestoras and published by . This book was released on 2007 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book An Exploration of Stress Signaling and Ubiquitin like Modifiers written by Michelle Lynn Oeser and published by . This book was released on 2014 with total page 126 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cells face a barrage of internal and external stresses that could inflict severe damage on the molecules essential for life. To cope with environmental challenges, cells have evolved complex stress responses. Posttranslational protein modifications, including ubiquitin-like modifiers, are a major means by through which cells respond to these changing environmental conditions. This thesis explores how the small ubiquitin-like modifier (SUMO) is used to modulate cellular outcomes via transcription, with a particular focus on cellular contexts that require rapid transcriptional changes, such as stress. I present evidence from studies in Saccharomyces cerevisiae that SUMO can be inhibitory to transcription both through direct signaling and non-signaling modes of function. First, I present my findings that SUMO can act as a signal to inhibit the transcription activation potential of a predicted SUMO-targeted ubiquitin ligase that also functions in transcriptional silencing. I discuss potential models for how SUMO might direct switching between transcriptional silencing and activation functions of this protein. Second, discuss independent work demonstrating that SUMO, a highly soluble protein, can promote transcriptional repression in a non-signaling manner by solubilizing transcriptional regulators at risk of misfolding during stress. I show that during hyperosmotic stress, two members of a transcriptional corepressor complex are rapidly and transiently SUMO-modified, and loss of this sumoylation drives accumulation of these proteins into inclusions and correlates with widespread loss of transcriptional repression. Finally, I discuss the broader implications of the signaling and non-signaling functions of SUMO in transcriptional modulation, with a focus on SUMO's potential to drive the adaptive potential of cells in changing environmental contexts.
Download or read book Mineral Nutrition of Higher Plants written by Horst Marschner and published by Gulf Professional Publishing. This book was released on 1995 with total page 920 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text presents the principles of mineral nutrition in the light of current advances. For this second edition more emphasis has been placed on root water relations and functions of micronutrients as well as external and internal factors on root growth and the root-soil interface.
Download or read book Environmental Responses in Plants written by Paula Duque and published by Humana. This book was released on 2016-02-12 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume describes different up-to-date methodological approaches, ranging from physiological assays to imaging and molecular techniques, to study a wide variety of plant responses to environmental cues. Environmental Responses in Plants: Methods and Protocols is divided into four sections: Tropisms, Photoperiodism and Circadian Rhythms, Abiotic Stress Responses, and Plant-Pathogen Interactions. The chapters in these sections include detailed protocols to investigate some of the many key biological processes underlying plant environmental responses, mostly in the model organism Arabidopsis thaliana, but also in Physcomitrella patens and in different crop species such as rice, potato, barley, or tomato. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Environmental Responses in Plants: Methods and Protocols, is a great resource for plant physiologists, biochemists, and cell and molecular scientists interested in this exciting and fast-growing research topic.
Download or read book Characterizing the Human Ubiquitin Conjugating Enzymes written by Deborah Ng and published by . This book was released on 2019 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ubiquitin is a small (76 amino acid) evolutionarily conserved protein that is covalently conjugated to lysine residues (or rarely N-terminal amines) on substrate polypeptides, to alter their half-life, localization or function. Ubiquitin itself also contains seven internal lysine residues, all of which can be modified by additional ubiquitin molecules to form extended ubiquitin "chains". Monoubiquitylation or different types of ubiquitin chain linkages can confer very different biological outcomes to a protein target. The ubiquitin conjugation process is carried out via a three-step enzymatic cascade consisting of an activating enzyme (E1), a conjugating enzyme (E2), and a ligase (E3). More than 600 genes coding for predicted ubiquitin E3 ligases have been identified in the human genome, along with just 35 active E2 genes and two E1s. Importantly, the specific subset of E3s that interacts with each E2, and the specific biological functions of most of the E2 enzymes, have not been elucidated. To better understand E2 functions, I conducted a series of interactome and gene essentiality screens. Proximity-dependent biotinylation (BioID) was performed in Flp-In T-REx 293 cells to identify interacting partners for 31 different E2 proteins. 2296 high confidence protein-protein interactions were identified amongst 964 different polypeptides. To identify E2 genes (and other genes linked to protein homeostasis) essential for cell fitness, CRISPR/Cas9 dropout screens were also performed in HEK293 cells, along with two different lung cancer lines, NCI-H1975 and SW1573. Several different context-specific essential E2 genes (and many other genes linked to protein homeostasis) were identified in this screen, indicating that E2s may represent viable therapeutic targets. Finally, two common methods have been used to identify the types of ubiquitin linkages that can be generated by specific E2-E3 pairs: in vitro autoubiquitylation reactions using recombinant ubiquitin proteins bearing a single lysine-to-arginine mutation, or direct identification using mass spectrometry. We compared these two methods by characterizing the linkage specificity of 12 different E2-E3 combinations, and demonstrated that mass spectrometry-based methods yield far superior results. Together, my work has thus provided important biological context to a poorly understood component of the ubiquitin system, the E2 family.
Download or read book Plant Meiosis written by Wojtek Pawlowski and published by Humana Press. This book was released on 2013-04-05 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Meiosis is one of the most critical processes in eukaryotes, required for continuation of species and generation of new variation. In plants, meiotic recombination is by far the most important source of genetic variation. In Plant Meiosis: Methods and Protocols, expert researchers in the field detail methods for molecular cytogenetics and chromosome analysis in plants. These state-of -the-art protocols allow studying the organization and behavior of the genetic material in a wide range of both model and crop species. Written in the highly successful Methods in Molecular BiologyTMseries format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Plant Meiosis: Methods and Protocols provides and extensive list of protocols developed and used in a number of laboratories at the cutting edge of meiosis and chromosome research.
